montage-wrapper-0.9.9/0000755000077000000240000000000013137205364014563 5ustar tomstaff00000000000000montage-wrapper-0.9.9/ah_bootstrap.py0000644000077000000240000010434413137204410017617 0ustar tomstaff00000000000000""" This bootstrap module contains code for ensuring that the astropy_helpers package will be importable by the time the setup.py script runs. It also includes some workarounds to ensure that a recent-enough version of setuptools is being used for the installation. This module should be the first thing imported in the setup.py of distributions that make use of the utilities in astropy_helpers. If the distribution ships with its own copy of astropy_helpers, this module will first attempt to import from the shipped copy. However, it will also check PyPI to see if there are any bug-fix releases on top of the current version that may be useful to get past platform-specific bugs that have been fixed. When running setup.py, use the ``--offline`` command-line option to disable the auto-upgrade checks. When this module is imported or otherwise executed it automatically calls a main function that attempts to read the project's setup.cfg file, which it checks for a configuration section called ``[ah_bootstrap]`` the presences of that section, and options therein, determine the next step taken: If it contains an option called ``auto_use`` with a value of ``True``, it will automatically call the main function of this module called `use_astropy_helpers` (see that function's docstring for full details). Otherwise no further action is taken (however, ``ah_bootstrap.use_astropy_helpers`` may be called manually from within the setup.py script). Additional options in the ``[ah_boostrap]`` section of setup.cfg have the same names as the arguments to `use_astropy_helpers`, and can be used to configure the bootstrap script when ``auto_use = True``. See https://github.com/astropy/astropy-helpers for more details, and for the latest version of this module. """ import contextlib import errno import imp import io import locale import os import re import subprocess as sp import sys try: from ConfigParser import ConfigParser, RawConfigParser except ImportError: from configparser import ConfigParser, RawConfigParser if sys.version_info[0] < 3: _str_types = (str, unicode) _text_type = unicode PY3 = False else: _str_types = (str, bytes) _text_type = str PY3 = True # What follows are several import statements meant to deal with install-time # issues with either missing or misbehaving pacakges (including making sure # setuptools itself is installed): # Some pre-setuptools checks to ensure that either distribute or setuptools >= # 0.7 is used (over pre-distribute setuptools) if it is available on the path; # otherwise the latest setuptools will be downloaded and bootstrapped with # ``ez_setup.py``. This used to be included in a separate file called # setuptools_bootstrap.py; but it was combined into ah_bootstrap.py try: import pkg_resources _setuptools_req = pkg_resources.Requirement.parse('setuptools>=0.7') # This may raise a DistributionNotFound in which case no version of # setuptools or distribute is properly installed _setuptools = pkg_resources.get_distribution('setuptools') if _setuptools not in _setuptools_req: # Older version of setuptools; check if we have distribute; again if # this results in DistributionNotFound we want to give up _distribute = pkg_resources.get_distribution('distribute') if _setuptools != _distribute: # It's possible on some pathological systems to have an old version # of setuptools and distribute on sys.path simultaneously; make # sure distribute is the one that's used sys.path.insert(1, _distribute.location) _distribute.activate() imp.reload(pkg_resources) except: # There are several types of exceptions that can occur here; if all else # fails bootstrap and use the bootstrapped version from ez_setup import use_setuptools use_setuptools() # typing as a dependency for 1.6.1+ Sphinx causes issues when imported after # initializing submodule with ah_boostrap.py # See discussion and references in # https://github.com/astropy/astropy-helpers/issues/302 try: import typing # noqa except ImportError: pass # Note: The following import is required as a workaround to # https://github.com/astropy/astropy-helpers/issues/89; if we don't import this # module now, it will get cleaned up after `run_setup` is called, but that will # later cause the TemporaryDirectory class defined in it to stop working when # used later on by setuptools try: import setuptools.py31compat # noqa except ImportError: pass # matplotlib can cause problems if it is imported from within a call of # run_setup(), because in some circumstances it will try to write to the user's # home directory, resulting in a SandboxViolation. See # https://github.com/matplotlib/matplotlib/pull/4165 # Making sure matplotlib, if it is available, is imported early in the setup # process can mitigate this (note importing matplotlib.pyplot has the same # issue) try: import matplotlib matplotlib.use('Agg') import matplotlib.pyplot except: # Ignore if this fails for *any* reason* pass # End compatibility imports... # In case it didn't successfully import before the ez_setup checks import pkg_resources from setuptools import Distribution from setuptools.package_index import PackageIndex from setuptools.sandbox import run_setup from distutils import log from distutils.debug import DEBUG # TODO: Maybe enable checking for a specific version of astropy_helpers? DIST_NAME = 'astropy-helpers' PACKAGE_NAME = 'astropy_helpers' # Defaults for other options DOWNLOAD_IF_NEEDED = True INDEX_URL = 'https://pypi.python.org/simple' USE_GIT = True OFFLINE = False AUTO_UPGRADE = True # A list of all the configuration options and their required types CFG_OPTIONS = [ ('auto_use', bool), ('path', str), ('download_if_needed', bool), ('index_url', str), ('use_git', bool), ('offline', bool), ('auto_upgrade', bool) ] class _Bootstrapper(object): """ Bootstrapper implementation. See ``use_astropy_helpers`` for parameter documentation. """ def __init__(self, path=None, index_url=None, use_git=None, offline=None, download_if_needed=None, auto_upgrade=None): if path is None: path = PACKAGE_NAME if not (isinstance(path, _str_types) or path is False): raise TypeError('path must be a string or False') if PY3 and not isinstance(path, _text_type): fs_encoding = sys.getfilesystemencoding() path = path.decode(fs_encoding) # path to unicode self.path = path # Set other option attributes, using defaults where necessary self.index_url = index_url if index_url is not None else INDEX_URL self.offline = offline if offline is not None else OFFLINE # If offline=True, override download and auto-upgrade if self.offline: download_if_needed = False auto_upgrade = False self.download = (download_if_needed if download_if_needed is not None else DOWNLOAD_IF_NEEDED) self.auto_upgrade = (auto_upgrade if auto_upgrade is not None else AUTO_UPGRADE) # If this is a release then the .git directory will not exist so we # should not use git. git_dir_exists = os.path.exists(os.path.join(os.path.dirname(__file__), '.git')) if use_git is None and not git_dir_exists: use_git = False self.use_git = use_git if use_git is not None else USE_GIT # Declared as False by default--later we check if astropy-helpers can be # upgraded from PyPI, but only if not using a source distribution (as in # the case of import from a git submodule) self.is_submodule = False @classmethod def main(cls, argv=None): if argv is None: argv = sys.argv config = cls.parse_config() config.update(cls.parse_command_line(argv)) auto_use = config.pop('auto_use', False) bootstrapper = cls(**config) if auto_use: # Run the bootstrapper, otherwise the setup.py is using the old # use_astropy_helpers() interface, in which case it will run the # bootstrapper manually after reconfiguring it. bootstrapper.run() return bootstrapper @classmethod def parse_config(cls): if not os.path.exists('setup.cfg'): return {} cfg = ConfigParser() try: cfg.read('setup.cfg') except Exception as e: if DEBUG: raise log.error( "Error reading setup.cfg: {0!r}\n{1} will not be " "automatically bootstrapped and package installation may fail." "\n{2}".format(e, PACKAGE_NAME, _err_help_msg)) return {} if not cfg.has_section('ah_bootstrap'): return {} config = {} for option, type_ in CFG_OPTIONS: if not cfg.has_option('ah_bootstrap', option): continue if type_ is bool: value = cfg.getboolean('ah_bootstrap', option) else: value = cfg.get('ah_bootstrap', option) config[option] = value return config @classmethod def parse_command_line(cls, argv=None): if argv is None: argv = sys.argv config = {} # For now we just pop recognized ah_bootstrap options out of the # arg list. This is imperfect; in the unlikely case that a setup.py # custom command or even custom Distribution class defines an argument # of the same name then we will break that. However there's a catch22 # here that we can't just do full argument parsing right here, because # we don't yet know *how* to parse all possible command-line arguments. if '--no-git' in argv: config['use_git'] = False argv.remove('--no-git') if '--offline' in argv: config['offline'] = True argv.remove('--offline') return config def run(self): strategies = ['local_directory', 'local_file', 'index'] dist = None # First, remove any previously imported versions of astropy_helpers; # this is necessary for nested installs where one package's installer # is installing another package via setuptools.sandbox.run_setup, as in # the case of setup_requires for key in list(sys.modules): try: if key == PACKAGE_NAME or key.startswith(PACKAGE_NAME + '.'): del sys.modules[key] except AttributeError: # Sometimes mysterious non-string things can turn up in # sys.modules continue # Check to see if the path is a submodule self.is_submodule = self._check_submodule() for strategy in strategies: method = getattr(self, 'get_{0}_dist'.format(strategy)) dist = method() if dist is not None: break else: raise _AHBootstrapSystemExit( "No source found for the {0!r} package; {0} must be " "available and importable as a prerequisite to building " "or installing this package.".format(PACKAGE_NAME)) # This is a bit hacky, but if astropy_helpers was loaded from a # directory/submodule its Distribution object gets a "precedence" of # "DEVELOP_DIST". However, in other cases it gets a precedence of # "EGG_DIST". However, when activing the distribution it will only be # placed early on sys.path if it is treated as an EGG_DIST, so always # do that dist = dist.clone(precedence=pkg_resources.EGG_DIST) # Otherwise we found a version of astropy-helpers, so we're done # Just active the found distribution on sys.path--if we did a # download this usually happens automatically but it doesn't hurt to # do it again # Note: Adding the dist to the global working set also activates it # (makes it importable on sys.path) by default. try: pkg_resources.working_set.add(dist, replace=True) except TypeError: # Some (much) older versions of setuptools do not have the # replace=True option here. These versions are old enough that all # bets may be off anyways, but it's easy enough to work around just # in case... if dist.key in pkg_resources.working_set.by_key: del pkg_resources.working_set.by_key[dist.key] pkg_resources.working_set.add(dist) @property def config(self): """ A `dict` containing the options this `_Bootstrapper` was configured with. """ return dict((optname, getattr(self, optname)) for optname, _ in CFG_OPTIONS if hasattr(self, optname)) def get_local_directory_dist(self): """ Handle importing a vendored package from a subdirectory of the source distribution. """ if not os.path.isdir(self.path): return log.info('Attempting to import astropy_helpers from {0} {1!r}'.format( 'submodule' if self.is_submodule else 'directory', self.path)) dist = self._directory_import() if dist is None: log.warn( 'The requested path {0!r} for importing {1} does not ' 'exist, or does not contain a copy of the {1} ' 'package.'.format(self.path, PACKAGE_NAME)) elif self.auto_upgrade and not self.is_submodule: # A version of astropy-helpers was found on the available path, but # check to see if a bugfix release is available on PyPI upgrade = self._do_upgrade(dist) if upgrade is not None: dist = upgrade return dist def get_local_file_dist(self): """ Handle importing from a source archive; this also uses setup_requires but points easy_install directly to the source archive. """ if not os.path.isfile(self.path): return log.info('Attempting to unpack and import astropy_helpers from ' '{0!r}'.format(self.path)) try: dist = self._do_download(find_links=[self.path]) except Exception as e: if DEBUG: raise log.warn( 'Failed to import {0} from the specified archive {1!r}: ' '{2}'.format(PACKAGE_NAME, self.path, str(e))) dist = None if dist is not None and self.auto_upgrade: # A version of astropy-helpers was found on the available path, but # check to see if a bugfix release is available on PyPI upgrade = self._do_upgrade(dist) if upgrade is not None: dist = upgrade return dist def get_index_dist(self): if not self.download: log.warn('Downloading {0!r} disabled.'.format(DIST_NAME)) return None log.warn( "Downloading {0!r}; run setup.py with the --offline option to " "force offline installation.".format(DIST_NAME)) try: dist = self._do_download() except Exception as e: if DEBUG: raise log.warn( 'Failed to download and/or install {0!r} from {1!r}:\n' '{2}'.format(DIST_NAME, self.index_url, str(e))) dist = None # No need to run auto-upgrade here since we've already presumably # gotten the most up-to-date version from the package index return dist def _directory_import(self): """ Import astropy_helpers from the given path, which will be added to sys.path. Must return True if the import succeeded, and False otherwise. """ # Return True on success, False on failure but download is allowed, and # otherwise raise SystemExit path = os.path.abspath(self.path) # Use an empty WorkingSet rather than the man # pkg_resources.working_set, since on older versions of setuptools this # will invoke a VersionConflict when trying to install an upgrade ws = pkg_resources.WorkingSet([]) ws.add_entry(path) dist = ws.by_key.get(DIST_NAME) if dist is None: # We didn't find an egg-info/dist-info in the given path, but if a # setup.py exists we can generate it setup_py = os.path.join(path, 'setup.py') if os.path.isfile(setup_py): with _silence(): run_setup(os.path.join(path, 'setup.py'), ['egg_info']) for dist in pkg_resources.find_distributions(path, True): # There should be only one... return dist return dist def _do_download(self, version='', find_links=None): if find_links: allow_hosts = '' index_url = None else: allow_hosts = None index_url = self.index_url # Annoyingly, setuptools will not handle other arguments to # Distribution (such as options) before handling setup_requires, so it # is not straightforward to programmatically augment the arguments which # are passed to easy_install class _Distribution(Distribution): def get_option_dict(self, command_name): opts = Distribution.get_option_dict(self, command_name) if command_name == 'easy_install': if find_links is not None: opts['find_links'] = ('setup script', find_links) if index_url is not None: opts['index_url'] = ('setup script', index_url) if allow_hosts is not None: opts['allow_hosts'] = ('setup script', allow_hosts) return opts if version: req = '{0}=={1}'.format(DIST_NAME, version) else: req = DIST_NAME attrs = {'setup_requires': [req]} try: if DEBUG: _Distribution(attrs=attrs) else: with _silence(): _Distribution(attrs=attrs) # If the setup_requires succeeded it will have added the new dist to # the main working_set return pkg_resources.working_set.by_key.get(DIST_NAME) except Exception as e: if DEBUG: raise msg = 'Error retrieving {0} from {1}:\n{2}' if find_links: source = find_links[0] elif index_url != INDEX_URL: source = index_url else: source = 'PyPI' raise Exception(msg.format(DIST_NAME, source, repr(e))) def _do_upgrade(self, dist): # Build up a requirement for a higher bugfix release but a lower minor # release (so API compatibility is guaranteed) next_version = _next_version(dist.parsed_version) req = pkg_resources.Requirement.parse( '{0}>{1},<{2}'.format(DIST_NAME, dist.version, next_version)) package_index = PackageIndex(index_url=self.index_url) upgrade = package_index.obtain(req) if upgrade is not None: return self._do_download(version=upgrade.version) def _check_submodule(self): """ Check if the given path is a git submodule. See the docstrings for ``_check_submodule_using_git`` and ``_check_submodule_no_git`` for further details. """ if (self.path is None or (os.path.exists(self.path) and not os.path.isdir(self.path))): return False if self.use_git: return self._check_submodule_using_git() else: return self._check_submodule_no_git() def _check_submodule_using_git(self): """ Check if the given path is a git submodule. If so, attempt to initialize and/or update the submodule if needed. This function makes calls to the ``git`` command in subprocesses. The ``_check_submodule_no_git`` option uses pure Python to check if the given path looks like a git submodule, but it cannot perform updates. """ cmd = ['git', 'submodule', 'status', '--', self.path] try: log.info('Running `{0}`; use the --no-git option to disable git ' 'commands'.format(' '.join(cmd))) returncode, stdout, stderr = run_cmd(cmd) except _CommandNotFound: # The git command simply wasn't found; this is most likely the # case on user systems that don't have git and are simply # trying to install the package from PyPI or a source # distribution. Silently ignore this case and simply don't try # to use submodules return False stderr = stderr.strip() if returncode != 0 and stderr: # Unfortunately the return code alone cannot be relied on, as # earlier versions of git returned 0 even if the requested submodule # does not exist # This is a warning that occurs in perl (from running git submodule) # which only occurs with a malformatted locale setting which can # happen sometimes on OSX. See again # https://github.com/astropy/astropy/issues/2749 perl_warning = ('perl: warning: Falling back to the standard locale ' '("C").') if not stderr.strip().endswith(perl_warning): # Some other unknown error condition occurred log.warn('git submodule command failed ' 'unexpectedly:\n{0}'.format(stderr)) return False # Output of `git submodule status` is as follows: # # 1: Status indicator: '-' for submodule is uninitialized, '+' if # submodule is initialized but is not at the commit currently indicated # in .gitmodules (and thus needs to be updated), or 'U' if the # submodule is in an unstable state (i.e. has merge conflicts) # # 2. SHA-1 hash of the current commit of the submodule (we don't really # need this information but it's useful for checking that the output is # correct) # # 3. The output of `git describe` for the submodule's current commit # hash (this includes for example what branches the commit is on) but # only if the submodule is initialized. We ignore this information for # now _git_submodule_status_re = re.compile( '^(?P[+-U ])(?P[0-9a-f]{40}) ' '(?P\S+)( .*)?$') # The stdout should only contain one line--the status of the # requested submodule m = _git_submodule_status_re.match(stdout) if m: # Yes, the path *is* a git submodule self._update_submodule(m.group('submodule'), m.group('status')) return True else: log.warn( 'Unexpected output from `git submodule status`:\n{0}\n' 'Will attempt import from {1!r} regardless.'.format( stdout, self.path)) return False def _check_submodule_no_git(self): """ Like ``_check_submodule_using_git``, but simply parses the .gitmodules file to determine if the supplied path is a git submodule, and does not exec any subprocesses. This can only determine if a path is a submodule--it does not perform updates, etc. This function may need to be updated if the format of the .gitmodules file is changed between git versions. """ gitmodules_path = os.path.abspath('.gitmodules') if not os.path.isfile(gitmodules_path): return False # This is a minimal reader for gitconfig-style files. It handles a few of # the quirks that make gitconfig files incompatible with ConfigParser-style # files, but does not support the full gitconfig syntax (just enough # needed to read a .gitmodules file). gitmodules_fileobj = io.StringIO() # Must use io.open for cross-Python-compatible behavior wrt unicode with io.open(gitmodules_path) as f: for line in f: # gitconfig files are more flexible with leading whitespace; just # go ahead and remove it line = line.lstrip() # comments can start with either # or ; if line and line[0] in (':', ';'): continue gitmodules_fileobj.write(line) gitmodules_fileobj.seek(0) cfg = RawConfigParser() try: cfg.readfp(gitmodules_fileobj) except Exception as exc: log.warn('Malformatted .gitmodules file: {0}\n' '{1} cannot be assumed to be a git submodule.'.format( exc, self.path)) return False for section in cfg.sections(): if not cfg.has_option(section, 'path'): continue submodule_path = cfg.get(section, 'path').rstrip(os.sep) if submodule_path == self.path.rstrip(os.sep): return True return False def _update_submodule(self, submodule, status): if status == ' ': # The submodule is up to date; no action necessary return elif status == '-': if self.offline: raise _AHBootstrapSystemExit( "Cannot initialize the {0} submodule in --offline mode; " "this requires being able to clone the submodule from an " "online repository.".format(submodule)) cmd = ['update', '--init'] action = 'Initializing' elif status == '+': cmd = ['update'] action = 'Updating' if self.offline: cmd.append('--no-fetch') elif status == 'U': raise _AHBootstrapSystemExit( 'Error: Submodule {0} contains unresolved merge conflicts. ' 'Please complete or abandon any changes in the submodule so that ' 'it is in a usable state, then try again.'.format(submodule)) else: log.warn('Unknown status {0!r} for git submodule {1!r}. Will ' 'attempt to use the submodule as-is, but try to ensure ' 'that the submodule is in a clean state and contains no ' 'conflicts or errors.\n{2}'.format(status, submodule, _err_help_msg)) return err_msg = None cmd = ['git', 'submodule'] + cmd + ['--', submodule] log.warn('{0} {1} submodule with: `{2}`'.format( action, submodule, ' '.join(cmd))) try: log.info('Running `{0}`; use the --no-git option to disable git ' 'commands'.format(' '.join(cmd))) returncode, stdout, stderr = run_cmd(cmd) except OSError as e: err_msg = str(e) else: if returncode != 0: err_msg = stderr if err_msg is not None: log.warn('An unexpected error occurred updating the git submodule ' '{0!r}:\n{1}\n{2}'.format(submodule, err_msg, _err_help_msg)) class _CommandNotFound(OSError): """ An exception raised when a command run with run_cmd is not found on the system. """ def run_cmd(cmd): """ Run a command in a subprocess, given as a list of command-line arguments. Returns a ``(returncode, stdout, stderr)`` tuple. """ try: p = sp.Popen(cmd, stdout=sp.PIPE, stderr=sp.PIPE) # XXX: May block if either stdout or stderr fill their buffers; # however for the commands this is currently used for that is # unlikely (they should have very brief output) stdout, stderr = p.communicate() except OSError as e: if DEBUG: raise if e.errno == errno.ENOENT: msg = 'Command not found: `{0}`'.format(' '.join(cmd)) raise _CommandNotFound(msg, cmd) else: raise _AHBootstrapSystemExit( 'An unexpected error occurred when running the ' '`{0}` command:\n{1}'.format(' '.join(cmd), str(e))) # Can fail of the default locale is not configured properly. See # https://github.com/astropy/astropy/issues/2749. For the purposes under # consideration 'latin1' is an acceptable fallback. try: stdio_encoding = locale.getdefaultlocale()[1] or 'latin1' except ValueError: # Due to an OSX oddity locale.getdefaultlocale() can also crash # depending on the user's locale/language settings. See: # http://bugs.python.org/issue18378 stdio_encoding = 'latin1' # Unlikely to fail at this point but even then let's be flexible if not isinstance(stdout, _text_type): stdout = stdout.decode(stdio_encoding, 'replace') if not isinstance(stderr, _text_type): stderr = stderr.decode(stdio_encoding, 'replace') return (p.returncode, stdout, stderr) def _next_version(version): """ Given a parsed version from pkg_resources.parse_version, returns a new version string with the next minor version. Examples ======== >>> _next_version(pkg_resources.parse_version('1.2.3')) '1.3.0' """ if hasattr(version, 'base_version'): # New version parsing from setuptools >= 8.0 if version.base_version: parts = version.base_version.split('.') else: parts = [] else: parts = [] for part in version: if part.startswith('*'): break parts.append(part) parts = [int(p) for p in parts] if len(parts) < 3: parts += [0] * (3 - len(parts)) major, minor, micro = parts[:3] return '{0}.{1}.{2}'.format(major, minor + 1, 0) class _DummyFile(object): """A noop writeable object.""" errors = '' # Required for Python 3.x encoding = 'utf-8' def write(self, s): pass def flush(self): pass @contextlib.contextmanager def _silence(): """A context manager that silences sys.stdout and sys.stderr.""" old_stdout = sys.stdout old_stderr = sys.stderr sys.stdout = _DummyFile() sys.stderr = _DummyFile() exception_occurred = False try: yield except: exception_occurred = True # Go ahead and clean up so that exception handling can work normally sys.stdout = old_stdout sys.stderr = old_stderr raise if not exception_occurred: sys.stdout = old_stdout sys.stderr = old_stderr _err_help_msg = """ If the problem persists consider installing astropy_helpers manually using pip (`pip install astropy_helpers`) or by manually downloading the source archive, extracting it, and installing by running `python setup.py install` from the root of the extracted source code. """ class _AHBootstrapSystemExit(SystemExit): def __init__(self, *args): if not args: msg = 'An unknown problem occurred bootstrapping astropy_helpers.' else: msg = args[0] msg += '\n' + _err_help_msg super(_AHBootstrapSystemExit, self).__init__(msg, *args[1:]) BOOTSTRAPPER = _Bootstrapper.main() def use_astropy_helpers(**kwargs): """ Ensure that the `astropy_helpers` module is available and is importable. This supports automatic submodule initialization if astropy_helpers is included in a project as a git submodule, or will download it from PyPI if necessary. Parameters ---------- path : str or None, optional A filesystem path relative to the root of the project's source code that should be added to `sys.path` so that `astropy_helpers` can be imported from that path. If the path is a git submodule it will automatically be initialized and/or updated. The path may also be to a ``.tar.gz`` archive of the astropy_helpers source distribution. In this case the archive is automatically unpacked and made temporarily available on `sys.path` as a ``.egg`` archive. If `None` skip straight to downloading. download_if_needed : bool, optional If the provided filesystem path is not found an attempt will be made to download astropy_helpers from PyPI. It will then be made temporarily available on `sys.path` as a ``.egg`` archive (using the ``setup_requires`` feature of setuptools. If the ``--offline`` option is given at the command line the value of this argument is overridden to `False`. index_url : str, optional If provided, use a different URL for the Python package index than the main PyPI server. use_git : bool, optional If `False` no git commands will be used--this effectively disables support for git submodules. If the ``--no-git`` option is given at the command line the value of this argument is overridden to `False`. auto_upgrade : bool, optional By default, when installing a package from a non-development source distribution ah_boostrap will try to automatically check for patch releases to astropy-helpers on PyPI and use the patched version over any bundled versions. Setting this to `False` will disable that functionality. If the ``--offline`` option is given at the command line the value of this argument is overridden to `False`. offline : bool, optional If `False` disable all actions that require an internet connection, including downloading packages from the package index and fetching updates to any git submodule. Defaults to `True`. """ global BOOTSTRAPPER config = BOOTSTRAPPER.config config.update(**kwargs) # Create a new bootstrapper with the updated configuration and run it BOOTSTRAPPER = _Bootstrapper(**config) BOOTSTRAPPER.run() montage-wrapper-0.9.9/astropy_helpers/0000755000077000000240000000000013137205364020006 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/.travis.yml0000644000077000000240000000473313137204755022131 0ustar tomstaff00000000000000# We set the language to c because python isn't supported on the MacOS X nodes # on Travis. However, the language ends up being irrelevant anyway, since we # install Python ourselves using conda. language: c os: - osx - linux # Setting sudo to false opts in to Travis-CI container-based builds. sudo: false # The apt packages below are needed for sphinx builds, which can no longer # be installed with sudo apt-get. addons: apt: packages: - graphviz env: matrix: - PYTHON_VERSION=2.7 EVENT_TYPE='push pull_request cron' - PYTHON_VERSION=3.4 SETUPTOOLS_VERSION=20 - PYTHON_VERSION=3.5 - PYTHON_VERSION=3.6 SETUPTOOLS_VERSION=dev DEBUG=True CONDA_DEPENDENCIES='sphinx cython numpy packaging six appdirs' EVENT_TYPE='push pull_request cron' global: - CONDA_DEPENDENCIES="setuptools sphinx cython numpy" - PIP_DEPENDENCIES="coveralls pytest-cov" - EVENT_TYPE='push pull_request' matrix: include: - os: linux env: PYTHON_VERSION=3.6 SPHINX_VERSION='>1.6' - os: linux env: PYTHON_VERSION=3.6 PIP_DEPENDENCIES='git+https://github.com/sphinx-doc/sphinx.git#egg=sphinx coveralls pytest-cov' CONDA_DEPENDENCIES="setuptools cython numpy" - os: linux env: PYTHON_VERSION=3.5 SPHINX_VERSION='<1.4' - os: linux env: PYTHON_VERSION=3.5 SPHINX_VERSION='<1.5' - os: linux env: PYTHON_VERSION=3.6 SPHINX_VERSION='<1.6' before_install: - if [[ $TRAVIS_OS_NAME == osx ]]; then brew update; brew install graphviz; fi install: - git clone git://github.com/astropy/ci-helpers.git - source ci-helpers/travis/setup_conda.sh # We cannot install the developer version of setuptools using pip because # pip tries to remove the previous version of setuptools before the # installation is complete, which causes issues. Instead, we just install # setuptools manually. - if [[ $SETUPTOOLS_VERSION == dev ]]; then git clone http://github.com/pypa/setuptools.git; cd setuptools; python bootstrap.py; python setup.py install; cd ..; fi before_script: # Some of the tests use git commands that require a user to be configured - git config --global user.name "A U Thor" - git config --global user.email "author@example.com" script: # Use full path for coveragerc; see issue #193 - py.test --cov astropy_helpers --cov-config $(pwd)/astropy_helpers/tests/coveragerc astropy_helpers after_success: - coveralls --rcfile=astropy_helpers/tests/coveragerc montage-wrapper-0.9.9/astropy_helpers/ah_bootstrap.py0000644000077000000240000010434413137204755023056 0ustar tomstaff00000000000000""" This bootstrap module contains code for ensuring that the astropy_helpers package will be importable by the time the setup.py script runs. It also includes some workarounds to ensure that a recent-enough version of setuptools is being used for the installation. This module should be the first thing imported in the setup.py of distributions that make use of the utilities in astropy_helpers. If the distribution ships with its own copy of astropy_helpers, this module will first attempt to import from the shipped copy. However, it will also check PyPI to see if there are any bug-fix releases on top of the current version that may be useful to get past platform-specific bugs that have been fixed. When running setup.py, use the ``--offline`` command-line option to disable the auto-upgrade checks. When this module is imported or otherwise executed it automatically calls a main function that attempts to read the project's setup.cfg file, which it checks for a configuration section called ``[ah_bootstrap]`` the presences of that section, and options therein, determine the next step taken: If it contains an option called ``auto_use`` with a value of ``True``, it will automatically call the main function of this module called `use_astropy_helpers` (see that function's docstring for full details). Otherwise no further action is taken (however, ``ah_bootstrap.use_astropy_helpers`` may be called manually from within the setup.py script). Additional options in the ``[ah_boostrap]`` section of setup.cfg have the same names as the arguments to `use_astropy_helpers`, and can be used to configure the bootstrap script when ``auto_use = True``. See https://github.com/astropy/astropy-helpers for more details, and for the latest version of this module. """ import contextlib import errno import imp import io import locale import os import re import subprocess as sp import sys try: from ConfigParser import ConfigParser, RawConfigParser except ImportError: from configparser import ConfigParser, RawConfigParser if sys.version_info[0] < 3: _str_types = (str, unicode) _text_type = unicode PY3 = False else: _str_types = (str, bytes) _text_type = str PY3 = True # What follows are several import statements meant to deal with install-time # issues with either missing or misbehaving pacakges (including making sure # setuptools itself is installed): # Some pre-setuptools checks to ensure that either distribute or setuptools >= # 0.7 is used (over pre-distribute setuptools) if it is available on the path; # otherwise the latest setuptools will be downloaded and bootstrapped with # ``ez_setup.py``. This used to be included in a separate file called # setuptools_bootstrap.py; but it was combined into ah_bootstrap.py try: import pkg_resources _setuptools_req = pkg_resources.Requirement.parse('setuptools>=0.7') # This may raise a DistributionNotFound in which case no version of # setuptools or distribute is properly installed _setuptools = pkg_resources.get_distribution('setuptools') if _setuptools not in _setuptools_req: # Older version of setuptools; check if we have distribute; again if # this results in DistributionNotFound we want to give up _distribute = pkg_resources.get_distribution('distribute') if _setuptools != _distribute: # It's possible on some pathological systems to have an old version # of setuptools and distribute on sys.path simultaneously; make # sure distribute is the one that's used sys.path.insert(1, _distribute.location) _distribute.activate() imp.reload(pkg_resources) except: # There are several types of exceptions that can occur here; if all else # fails bootstrap and use the bootstrapped version from ez_setup import use_setuptools use_setuptools() # typing as a dependency for 1.6.1+ Sphinx causes issues when imported after # initializing submodule with ah_boostrap.py # See discussion and references in # https://github.com/astropy/astropy-helpers/issues/302 try: import typing # noqa except ImportError: pass # Note: The following import is required as a workaround to # https://github.com/astropy/astropy-helpers/issues/89; if we don't import this # module now, it will get cleaned up after `run_setup` is called, but that will # later cause the TemporaryDirectory class defined in it to stop working when # used later on by setuptools try: import setuptools.py31compat # noqa except ImportError: pass # matplotlib can cause problems if it is imported from within a call of # run_setup(), because in some circumstances it will try to write to the user's # home directory, resulting in a SandboxViolation. See # https://github.com/matplotlib/matplotlib/pull/4165 # Making sure matplotlib, if it is available, is imported early in the setup # process can mitigate this (note importing matplotlib.pyplot has the same # issue) try: import matplotlib matplotlib.use('Agg') import matplotlib.pyplot except: # Ignore if this fails for *any* reason* pass # End compatibility imports... # In case it didn't successfully import before the ez_setup checks import pkg_resources from setuptools import Distribution from setuptools.package_index import PackageIndex from setuptools.sandbox import run_setup from distutils import log from distutils.debug import DEBUG # TODO: Maybe enable checking for a specific version of astropy_helpers? DIST_NAME = 'astropy-helpers' PACKAGE_NAME = 'astropy_helpers' # Defaults for other options DOWNLOAD_IF_NEEDED = True INDEX_URL = 'https://pypi.python.org/simple' USE_GIT = True OFFLINE = False AUTO_UPGRADE = True # A list of all the configuration options and their required types CFG_OPTIONS = [ ('auto_use', bool), ('path', str), ('download_if_needed', bool), ('index_url', str), ('use_git', bool), ('offline', bool), ('auto_upgrade', bool) ] class _Bootstrapper(object): """ Bootstrapper implementation. See ``use_astropy_helpers`` for parameter documentation. """ def __init__(self, path=None, index_url=None, use_git=None, offline=None, download_if_needed=None, auto_upgrade=None): if path is None: path = PACKAGE_NAME if not (isinstance(path, _str_types) or path is False): raise TypeError('path must be a string or False') if PY3 and not isinstance(path, _text_type): fs_encoding = sys.getfilesystemencoding() path = path.decode(fs_encoding) # path to unicode self.path = path # Set other option attributes, using defaults where necessary self.index_url = index_url if index_url is not None else INDEX_URL self.offline = offline if offline is not None else OFFLINE # If offline=True, override download and auto-upgrade if self.offline: download_if_needed = False auto_upgrade = False self.download = (download_if_needed if download_if_needed is not None else DOWNLOAD_IF_NEEDED) self.auto_upgrade = (auto_upgrade if auto_upgrade is not None else AUTO_UPGRADE) # If this is a release then the .git directory will not exist so we # should not use git. git_dir_exists = os.path.exists(os.path.join(os.path.dirname(__file__), '.git')) if use_git is None and not git_dir_exists: use_git = False self.use_git = use_git if use_git is not None else USE_GIT # Declared as False by default--later we check if astropy-helpers can be # upgraded from PyPI, but only if not using a source distribution (as in # the case of import from a git submodule) self.is_submodule = False @classmethod def main(cls, argv=None): if argv is None: argv = sys.argv config = cls.parse_config() config.update(cls.parse_command_line(argv)) auto_use = config.pop('auto_use', False) bootstrapper = cls(**config) if auto_use: # Run the bootstrapper, otherwise the setup.py is using the old # use_astropy_helpers() interface, in which case it will run the # bootstrapper manually after reconfiguring it. bootstrapper.run() return bootstrapper @classmethod def parse_config(cls): if not os.path.exists('setup.cfg'): return {} cfg = ConfigParser() try: cfg.read('setup.cfg') except Exception as e: if DEBUG: raise log.error( "Error reading setup.cfg: {0!r}\n{1} will not be " "automatically bootstrapped and package installation may fail." "\n{2}".format(e, PACKAGE_NAME, _err_help_msg)) return {} if not cfg.has_section('ah_bootstrap'): return {} config = {} for option, type_ in CFG_OPTIONS: if not cfg.has_option('ah_bootstrap', option): continue if type_ is bool: value = cfg.getboolean('ah_bootstrap', option) else: value = cfg.get('ah_bootstrap', option) config[option] = value return config @classmethod def parse_command_line(cls, argv=None): if argv is None: argv = sys.argv config = {} # For now we just pop recognized ah_bootstrap options out of the # arg list. This is imperfect; in the unlikely case that a setup.py # custom command or even custom Distribution class defines an argument # of the same name then we will break that. However there's a catch22 # here that we can't just do full argument parsing right here, because # we don't yet know *how* to parse all possible command-line arguments. if '--no-git' in argv: config['use_git'] = False argv.remove('--no-git') if '--offline' in argv: config['offline'] = True argv.remove('--offline') return config def run(self): strategies = ['local_directory', 'local_file', 'index'] dist = None # First, remove any previously imported versions of astropy_helpers; # this is necessary for nested installs where one package's installer # is installing another package via setuptools.sandbox.run_setup, as in # the case of setup_requires for key in list(sys.modules): try: if key == PACKAGE_NAME or key.startswith(PACKAGE_NAME + '.'): del sys.modules[key] except AttributeError: # Sometimes mysterious non-string things can turn up in # sys.modules continue # Check to see if the path is a submodule self.is_submodule = self._check_submodule() for strategy in strategies: method = getattr(self, 'get_{0}_dist'.format(strategy)) dist = method() if dist is not None: break else: raise _AHBootstrapSystemExit( "No source found for the {0!r} package; {0} must be " "available and importable as a prerequisite to building " "or installing this package.".format(PACKAGE_NAME)) # This is a bit hacky, but if astropy_helpers was loaded from a # directory/submodule its Distribution object gets a "precedence" of # "DEVELOP_DIST". However, in other cases it gets a precedence of # "EGG_DIST". However, when activing the distribution it will only be # placed early on sys.path if it is treated as an EGG_DIST, so always # do that dist = dist.clone(precedence=pkg_resources.EGG_DIST) # Otherwise we found a version of astropy-helpers, so we're done # Just active the found distribution on sys.path--if we did a # download this usually happens automatically but it doesn't hurt to # do it again # Note: Adding the dist to the global working set also activates it # (makes it importable on sys.path) by default. try: pkg_resources.working_set.add(dist, replace=True) except TypeError: # Some (much) older versions of setuptools do not have the # replace=True option here. These versions are old enough that all # bets may be off anyways, but it's easy enough to work around just # in case... if dist.key in pkg_resources.working_set.by_key: del pkg_resources.working_set.by_key[dist.key] pkg_resources.working_set.add(dist) @property def config(self): """ A `dict` containing the options this `_Bootstrapper` was configured with. """ return dict((optname, getattr(self, optname)) for optname, _ in CFG_OPTIONS if hasattr(self, optname)) def get_local_directory_dist(self): """ Handle importing a vendored package from a subdirectory of the source distribution. """ if not os.path.isdir(self.path): return log.info('Attempting to import astropy_helpers from {0} {1!r}'.format( 'submodule' if self.is_submodule else 'directory', self.path)) dist = self._directory_import() if dist is None: log.warn( 'The requested path {0!r} for importing {1} does not ' 'exist, or does not contain a copy of the {1} ' 'package.'.format(self.path, PACKAGE_NAME)) elif self.auto_upgrade and not self.is_submodule: # A version of astropy-helpers was found on the available path, but # check to see if a bugfix release is available on PyPI upgrade = self._do_upgrade(dist) if upgrade is not None: dist = upgrade return dist def get_local_file_dist(self): """ Handle importing from a source archive; this also uses setup_requires but points easy_install directly to the source archive. """ if not os.path.isfile(self.path): return log.info('Attempting to unpack and import astropy_helpers from ' '{0!r}'.format(self.path)) try: dist = self._do_download(find_links=[self.path]) except Exception as e: if DEBUG: raise log.warn( 'Failed to import {0} from the specified archive {1!r}: ' '{2}'.format(PACKAGE_NAME, self.path, str(e))) dist = None if dist is not None and self.auto_upgrade: # A version of astropy-helpers was found on the available path, but # check to see if a bugfix release is available on PyPI upgrade = self._do_upgrade(dist) if upgrade is not None: dist = upgrade return dist def get_index_dist(self): if not self.download: log.warn('Downloading {0!r} disabled.'.format(DIST_NAME)) return None log.warn( "Downloading {0!r}; run setup.py with the --offline option to " "force offline installation.".format(DIST_NAME)) try: dist = self._do_download() except Exception as e: if DEBUG: raise log.warn( 'Failed to download and/or install {0!r} from {1!r}:\n' '{2}'.format(DIST_NAME, self.index_url, str(e))) dist = None # No need to run auto-upgrade here since we've already presumably # gotten the most up-to-date version from the package index return dist def _directory_import(self): """ Import astropy_helpers from the given path, which will be added to sys.path. Must return True if the import succeeded, and False otherwise. """ # Return True on success, False on failure but download is allowed, and # otherwise raise SystemExit path = os.path.abspath(self.path) # Use an empty WorkingSet rather than the man # pkg_resources.working_set, since on older versions of setuptools this # will invoke a VersionConflict when trying to install an upgrade ws = pkg_resources.WorkingSet([]) ws.add_entry(path) dist = ws.by_key.get(DIST_NAME) if dist is None: # We didn't find an egg-info/dist-info in the given path, but if a # setup.py exists we can generate it setup_py = os.path.join(path, 'setup.py') if os.path.isfile(setup_py): with _silence(): run_setup(os.path.join(path, 'setup.py'), ['egg_info']) for dist in pkg_resources.find_distributions(path, True): # There should be only one... return dist return dist def _do_download(self, version='', find_links=None): if find_links: allow_hosts = '' index_url = None else: allow_hosts = None index_url = self.index_url # Annoyingly, setuptools will not handle other arguments to # Distribution (such as options) before handling setup_requires, so it # is not straightforward to programmatically augment the arguments which # are passed to easy_install class _Distribution(Distribution): def get_option_dict(self, command_name): opts = Distribution.get_option_dict(self, command_name) if command_name == 'easy_install': if find_links is not None: opts['find_links'] = ('setup script', find_links) if index_url is not None: opts['index_url'] = ('setup script', index_url) if allow_hosts is not None: opts['allow_hosts'] = ('setup script', allow_hosts) return opts if version: req = '{0}=={1}'.format(DIST_NAME, version) else: req = DIST_NAME attrs = {'setup_requires': [req]} try: if DEBUG: _Distribution(attrs=attrs) else: with _silence(): _Distribution(attrs=attrs) # If the setup_requires succeeded it will have added the new dist to # the main working_set return pkg_resources.working_set.by_key.get(DIST_NAME) except Exception as e: if DEBUG: raise msg = 'Error retrieving {0} from {1}:\n{2}' if find_links: source = find_links[0] elif index_url != INDEX_URL: source = index_url else: source = 'PyPI' raise Exception(msg.format(DIST_NAME, source, repr(e))) def _do_upgrade(self, dist): # Build up a requirement for a higher bugfix release but a lower minor # release (so API compatibility is guaranteed) next_version = _next_version(dist.parsed_version) req = pkg_resources.Requirement.parse( '{0}>{1},<{2}'.format(DIST_NAME, dist.version, next_version)) package_index = PackageIndex(index_url=self.index_url) upgrade = package_index.obtain(req) if upgrade is not None: return self._do_download(version=upgrade.version) def _check_submodule(self): """ Check if the given path is a git submodule. See the docstrings for ``_check_submodule_using_git`` and ``_check_submodule_no_git`` for further details. """ if (self.path is None or (os.path.exists(self.path) and not os.path.isdir(self.path))): return False if self.use_git: return self._check_submodule_using_git() else: return self._check_submodule_no_git() def _check_submodule_using_git(self): """ Check if the given path is a git submodule. If so, attempt to initialize and/or update the submodule if needed. This function makes calls to the ``git`` command in subprocesses. The ``_check_submodule_no_git`` option uses pure Python to check if the given path looks like a git submodule, but it cannot perform updates. """ cmd = ['git', 'submodule', 'status', '--', self.path] try: log.info('Running `{0}`; use the --no-git option to disable git ' 'commands'.format(' '.join(cmd))) returncode, stdout, stderr = run_cmd(cmd) except _CommandNotFound: # The git command simply wasn't found; this is most likely the # case on user systems that don't have git and are simply # trying to install the package from PyPI or a source # distribution. Silently ignore this case and simply don't try # to use submodules return False stderr = stderr.strip() if returncode != 0 and stderr: # Unfortunately the return code alone cannot be relied on, as # earlier versions of git returned 0 even if the requested submodule # does not exist # This is a warning that occurs in perl (from running git submodule) # which only occurs with a malformatted locale setting which can # happen sometimes on OSX. See again # https://github.com/astropy/astropy/issues/2749 perl_warning = ('perl: warning: Falling back to the standard locale ' '("C").') if not stderr.strip().endswith(perl_warning): # Some other unknown error condition occurred log.warn('git submodule command failed ' 'unexpectedly:\n{0}'.format(stderr)) return False # Output of `git submodule status` is as follows: # # 1: Status indicator: '-' for submodule is uninitialized, '+' if # submodule is initialized but is not at the commit currently indicated # in .gitmodules (and thus needs to be updated), or 'U' if the # submodule is in an unstable state (i.e. has merge conflicts) # # 2. SHA-1 hash of the current commit of the submodule (we don't really # need this information but it's useful for checking that the output is # correct) # # 3. The output of `git describe` for the submodule's current commit # hash (this includes for example what branches the commit is on) but # only if the submodule is initialized. We ignore this information for # now _git_submodule_status_re = re.compile( '^(?P[+-U ])(?P[0-9a-f]{40}) ' '(?P\S+)( .*)?$') # The stdout should only contain one line--the status of the # requested submodule m = _git_submodule_status_re.match(stdout) if m: # Yes, the path *is* a git submodule self._update_submodule(m.group('submodule'), m.group('status')) return True else: log.warn( 'Unexpected output from `git submodule status`:\n{0}\n' 'Will attempt import from {1!r} regardless.'.format( stdout, self.path)) return False def _check_submodule_no_git(self): """ Like ``_check_submodule_using_git``, but simply parses the .gitmodules file to determine if the supplied path is a git submodule, and does not exec any subprocesses. This can only determine if a path is a submodule--it does not perform updates, etc. This function may need to be updated if the format of the .gitmodules file is changed between git versions. """ gitmodules_path = os.path.abspath('.gitmodules') if not os.path.isfile(gitmodules_path): return False # This is a minimal reader for gitconfig-style files. It handles a few of # the quirks that make gitconfig files incompatible with ConfigParser-style # files, but does not support the full gitconfig syntax (just enough # needed to read a .gitmodules file). gitmodules_fileobj = io.StringIO() # Must use io.open for cross-Python-compatible behavior wrt unicode with io.open(gitmodules_path) as f: for line in f: # gitconfig files are more flexible with leading whitespace; just # go ahead and remove it line = line.lstrip() # comments can start with either # or ; if line and line[0] in (':', ';'): continue gitmodules_fileobj.write(line) gitmodules_fileobj.seek(0) cfg = RawConfigParser() try: cfg.readfp(gitmodules_fileobj) except Exception as exc: log.warn('Malformatted .gitmodules file: {0}\n' '{1} cannot be assumed to be a git submodule.'.format( exc, self.path)) return False for section in cfg.sections(): if not cfg.has_option(section, 'path'): continue submodule_path = cfg.get(section, 'path').rstrip(os.sep) if submodule_path == self.path.rstrip(os.sep): return True return False def _update_submodule(self, submodule, status): if status == ' ': # The submodule is up to date; no action necessary return elif status == '-': if self.offline: raise _AHBootstrapSystemExit( "Cannot initialize the {0} submodule in --offline mode; " "this requires being able to clone the submodule from an " "online repository.".format(submodule)) cmd = ['update', '--init'] action = 'Initializing' elif status == '+': cmd = ['update'] action = 'Updating' if self.offline: cmd.append('--no-fetch') elif status == 'U': raise _AHBootstrapSystemExit( 'Error: Submodule {0} contains unresolved merge conflicts. ' 'Please complete or abandon any changes in the submodule so that ' 'it is in a usable state, then try again.'.format(submodule)) else: log.warn('Unknown status {0!r} for git submodule {1!r}. Will ' 'attempt to use the submodule as-is, but try to ensure ' 'that the submodule is in a clean state and contains no ' 'conflicts or errors.\n{2}'.format(status, submodule, _err_help_msg)) return err_msg = None cmd = ['git', 'submodule'] + cmd + ['--', submodule] log.warn('{0} {1} submodule with: `{2}`'.format( action, submodule, ' '.join(cmd))) try: log.info('Running `{0}`; use the --no-git option to disable git ' 'commands'.format(' '.join(cmd))) returncode, stdout, stderr = run_cmd(cmd) except OSError as e: err_msg = str(e) else: if returncode != 0: err_msg = stderr if err_msg is not None: log.warn('An unexpected error occurred updating the git submodule ' '{0!r}:\n{1}\n{2}'.format(submodule, err_msg, _err_help_msg)) class _CommandNotFound(OSError): """ An exception raised when a command run with run_cmd is not found on the system. """ def run_cmd(cmd): """ Run a command in a subprocess, given as a list of command-line arguments. Returns a ``(returncode, stdout, stderr)`` tuple. """ try: p = sp.Popen(cmd, stdout=sp.PIPE, stderr=sp.PIPE) # XXX: May block if either stdout or stderr fill their buffers; # however for the commands this is currently used for that is # unlikely (they should have very brief output) stdout, stderr = p.communicate() except OSError as e: if DEBUG: raise if e.errno == errno.ENOENT: msg = 'Command not found: `{0}`'.format(' '.join(cmd)) raise _CommandNotFound(msg, cmd) else: raise _AHBootstrapSystemExit( 'An unexpected error occurred when running the ' '`{0}` command:\n{1}'.format(' '.join(cmd), str(e))) # Can fail of the default locale is not configured properly. See # https://github.com/astropy/astropy/issues/2749. For the purposes under # consideration 'latin1' is an acceptable fallback. try: stdio_encoding = locale.getdefaultlocale()[1] or 'latin1' except ValueError: # Due to an OSX oddity locale.getdefaultlocale() can also crash # depending on the user's locale/language settings. See: # http://bugs.python.org/issue18378 stdio_encoding = 'latin1' # Unlikely to fail at this point but even then let's be flexible if not isinstance(stdout, _text_type): stdout = stdout.decode(stdio_encoding, 'replace') if not isinstance(stderr, _text_type): stderr = stderr.decode(stdio_encoding, 'replace') return (p.returncode, stdout, stderr) def _next_version(version): """ Given a parsed version from pkg_resources.parse_version, returns a new version string with the next minor version. Examples ======== >>> _next_version(pkg_resources.parse_version('1.2.3')) '1.3.0' """ if hasattr(version, 'base_version'): # New version parsing from setuptools >= 8.0 if version.base_version: parts = version.base_version.split('.') else: parts = [] else: parts = [] for part in version: if part.startswith('*'): break parts.append(part) parts = [int(p) for p in parts] if len(parts) < 3: parts += [0] * (3 - len(parts)) major, minor, micro = parts[:3] return '{0}.{1}.{2}'.format(major, minor + 1, 0) class _DummyFile(object): """A noop writeable object.""" errors = '' # Required for Python 3.x encoding = 'utf-8' def write(self, s): pass def flush(self): pass @contextlib.contextmanager def _silence(): """A context manager that silences sys.stdout and sys.stderr.""" old_stdout = sys.stdout old_stderr = sys.stderr sys.stdout = _DummyFile() sys.stderr = _DummyFile() exception_occurred = False try: yield except: exception_occurred = True # Go ahead and clean up so that exception handling can work normally sys.stdout = old_stdout sys.stderr = old_stderr raise if not exception_occurred: sys.stdout = old_stdout sys.stderr = old_stderr _err_help_msg = """ If the problem persists consider installing astropy_helpers manually using pip (`pip install astropy_helpers`) or by manually downloading the source archive, extracting it, and installing by running `python setup.py install` from the root of the extracted source code. """ class _AHBootstrapSystemExit(SystemExit): def __init__(self, *args): if not args: msg = 'An unknown problem occurred bootstrapping astropy_helpers.' else: msg = args[0] msg += '\n' + _err_help_msg super(_AHBootstrapSystemExit, self).__init__(msg, *args[1:]) BOOTSTRAPPER = _Bootstrapper.main() def use_astropy_helpers(**kwargs): """ Ensure that the `astropy_helpers` module is available and is importable. This supports automatic submodule initialization if astropy_helpers is included in a project as a git submodule, or will download it from PyPI if necessary. Parameters ---------- path : str or None, optional A filesystem path relative to the root of the project's source code that should be added to `sys.path` so that `astropy_helpers` can be imported from that path. If the path is a git submodule it will automatically be initialized and/or updated. The path may also be to a ``.tar.gz`` archive of the astropy_helpers source distribution. In this case the archive is automatically unpacked and made temporarily available on `sys.path` as a ``.egg`` archive. If `None` skip straight to downloading. download_if_needed : bool, optional If the provided filesystem path is not found an attempt will be made to download astropy_helpers from PyPI. It will then be made temporarily available on `sys.path` as a ``.egg`` archive (using the ``setup_requires`` feature of setuptools. If the ``--offline`` option is given at the command line the value of this argument is overridden to `False`. index_url : str, optional If provided, use a different URL for the Python package index than the main PyPI server. use_git : bool, optional If `False` no git commands will be used--this effectively disables support for git submodules. If the ``--no-git`` option is given at the command line the value of this argument is overridden to `False`. auto_upgrade : bool, optional By default, when installing a package from a non-development source distribution ah_boostrap will try to automatically check for patch releases to astropy-helpers on PyPI and use the patched version over any bundled versions. Setting this to `False` will disable that functionality. If the ``--offline`` option is given at the command line the value of this argument is overridden to `False`. offline : bool, optional If `False` disable all actions that require an internet connection, including downloading packages from the package index and fetching updates to any git submodule. Defaults to `True`. """ global BOOTSTRAPPER config = BOOTSTRAPPER.config config.update(**kwargs) # Create a new bootstrapper with the updated configuration and run it BOOTSTRAPPER = _Bootstrapper(**config) BOOTSTRAPPER.run() montage-wrapper-0.9.9/astropy_helpers/appveyor.yml0000644000077000000240000000255513137204755022410 0ustar tomstaff00000000000000# AppVeyor.com is a Continuous Integration service to build and run tests under # Windows environment: global: PYTHON: "C:\\conda" MINICONDA_VERSION: "latest" CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\ci-helpers\\appveyor\\windows_sdk.cmd" PYTHON_ARCH: "64" # needs to be set for CMD_IN_ENV to succeed. If a mix # of 32 bit and 64 bit builds are needed, move this # to the matrix section. # babel 2.0 is known to break on Windows: # https://github.com/python-babel/babel/issues/174 CONDA_DEPENDENCIES: "numpy Cython sphinx pytest babel!=2.0" matrix: - PYTHON_VERSION: "2.7" - PYTHON_VERSION: "3.4" - PYTHON_VERSION: "3.5" - PYTHON_VERSION: "3.6" platform: -x64 install: # Set up ci-helpers - "git clone git://github.com/astropy/ci-helpers.git" - "powershell ci-helpers/appveyor/install-miniconda.ps1" - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%" - "activate test" # Some of the tests use git commands that require a user to be configured - git config --global user.name "A U Thor" - git config --global user.email "author@example.com" # Install graphviz - cinst graphviz.portable # Not a .NET project, we build the package in the install step instead build: false test_script: - "%CMD_IN_ENV% py.test astropy_helpers" montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/0000755000077000000240000000000013137205364023231 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/__init__.py0000644000077000000240000000345413104416125025341 0ustar tomstaff00000000000000try: from .version import version as __version__ from .version import githash as __githash__ except ImportError: __version__ = '' __githash__ = '' # If we've made it as far as importing astropy_helpers, we don't need # ah_bootstrap in sys.modules anymore. Getting rid of it is actually necessary # if the package we're installing has a setup_requires of another package that # uses astropy_helpers (and possibly a different version at that) # See https://github.com/astropy/astropy/issues/3541 import sys if 'ah_bootstrap' in sys.modules: del sys.modules['ah_bootstrap'] # Note, this is repeated from ah_bootstrap.py, but is here too in case this # astropy-helpers was upgraded to from an older version that did not have this # check in its ah_bootstrap. # matplotlib can cause problems if it is imported from within a call of # run_setup(), because in some circumstances it will try to write to the user's # home directory, resulting in a SandboxViolation. See # https://github.com/matplotlib/matplotlib/pull/4165 # Making sure matplotlib, if it is available, is imported early in the setup # process can mitigate this (note importing matplotlib.pyplot has the same # issue) try: import matplotlib matplotlib.use('Agg') import matplotlib.pyplot except: # Ignore if this fails for *any* reason* pass import os # Ensure that all module-level code in astropy or other packages know that # we're in setup mode: if ('__main__' in sys.modules and hasattr(sys.modules['__main__'], '__file__')): filename = os.path.basename(sys.modules['__main__'].__file__) if filename.rstrip('co') == 'setup.py': if sys.version_info[0] >= 3: import builtins else: import __builtin__ as builtins builtins._ASTROPY_SETUP_ = True del filename montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/commands/0000755000077000000240000000000013137205364025032 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/commands/__init__.py0000644000077000000240000000000012531030705027121 0ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/commands/_dummy.py0000644000077000000240000000557413104416125026702 0ustar tomstaff00000000000000""" Provides a base class for a 'dummy' setup.py command that has no functionality (probably due to a missing requirement). This dummy command can raise an exception when it is run, explaining to the user what dependencies must be met to use this command. The reason this is at all tricky is that we want the command to be able to provide this message even when the user passes arguments to the command. If we don't know ahead of time what arguments the command can take, this is difficult, because distutils does not allow unknown arguments to be passed to a setup.py command. This hacks around that restriction to provide a useful error message even when a user passes arguments to the dummy implementation of a command. Use this like: try: from some_dependency import SetupCommand except ImportError: from ._dummy import _DummyCommand class SetupCommand(_DummyCommand): description = \ 'Implementation of SetupCommand from some_dependency; ' 'some_dependency must be installed to run this command' # This is the message that will be raised when a user tries to # run this command--define it as a class attribute. error_msg = \ "The 'setup_command' command requires the some_dependency " "package to be installed and importable." """ import sys from setuptools import Command from distutils.errors import DistutilsArgError from textwrap import dedent class _DummyCommandMeta(type): """ Causes an exception to be raised on accessing attributes of a command class so that if ``./setup.py command_name`` is run with additional command-line options we can provide a useful error message instead of the default that tells users the options are unrecognized. """ def __init__(cls, name, bases, members): if bases == (Command, object): # This is the _DummyCommand base class, presumably return if not hasattr(cls, 'description'): raise TypeError( "_DummyCommand subclass must have a 'description' " "attribute.") if not hasattr(cls, 'error_msg'): raise TypeError( "_DummyCommand subclass must have an 'error_msg' " "attribute.") def __getattribute__(cls, attr): if attr in ('description', 'error_msg'): # Allow cls.description to work so that `./setup.py # --help-commands` still works return super(_DummyCommandMeta, cls).__getattribute__(attr) raise DistutilsArgError(cls.error_msg) if sys.version_info[0] < 3: exec(dedent(""" class _DummyCommand(Command, object): __metaclass__ = _DummyCommandMeta """)) else: exec(dedent(""" class _DummyCommand(Command, object, metaclass=_DummyCommandMeta): pass """)) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/commands/_test_compat.py0000644000077000000240000002671213137204755030100 0ustar tomstaff00000000000000""" Old implementation of ``./setup.py test`` command. This has been moved to astropy.tests as of Astropy v1.1.0, but a copy of the implementation is kept here for backwards compatibility. """ from __future__ import absolute_import, unicode_literals import inspect import os import shutil import subprocess import sys import tempfile from setuptools import Command from ..compat import _fix_user_options PY3 = sys.version_info[0] == 3 class AstropyTest(Command, object): description = 'Run the tests for this package' user_options = [ ('package=', 'P', "The name of a specific package to test, e.g. 'io.fits' or 'utils'. " "If nothing is specified, all default tests are run."), ('test-path=', 't', 'Specify a test location by path. If a relative path to a .py file, ' 'it is relative to the built package, so e.g., a leading "astropy/" ' 'is necessary. If a relative path to a .rst file, it is relative to ' 'the directory *below* the --docs-path directory, so a leading ' '"docs/" is usually necessary. May also be an absolute path.'), ('verbose-results', 'V', 'Turn on verbose output from pytest.'), ('plugins=', 'p', 'Plugins to enable when running pytest.'), ('pastebin=', 'b', "Enable pytest pastebin output. Either 'all' or 'failed'."), ('args=', 'a', 'Additional arguments to be passed to pytest.'), ('remote-data', 'R', 'Run tests that download remote data.'), ('pep8', '8', 'Enable PEP8 checking and disable regular tests. ' 'Requires the pytest-pep8 plugin.'), ('pdb', 'd', 'Start the interactive Python debugger on errors.'), ('coverage', 'c', 'Create a coverage report. Requires the coverage package.'), ('open-files', 'o', 'Fail if any tests leave files open. Requires the ' 'psutil package.'), ('parallel=', 'j', 'Run the tests in parallel on the specified number of ' 'CPUs. If negative, all the cores on the machine will be ' 'used. Requires the pytest-xdist plugin.'), ('docs-path=', None, 'The path to the documentation .rst files. If not provided, and ' 'the current directory contains a directory called "docs", that ' 'will be used.'), ('skip-docs', None, "Don't test the documentation .rst files."), ('repeat=', None, 'How many times to repeat each test (can be used to check for ' 'sporadic failures).'), ('temp-root=', None, 'The root directory in which to create the temporary testing files. ' 'If unspecified the system default is used (e.g. /tmp) as explained ' 'in the documentation for tempfile.mkstemp.') ] user_options = _fix_user_options(user_options) package_name = '' def initialize_options(self): self.package = None self.test_path = None self.verbose_results = False self.plugins = None self.pastebin = None self.args = None self.remote_data = False self.pep8 = False self.pdb = False self.coverage = False self.open_files = False self.parallel = 0 self.docs_path = None self.skip_docs = False self.repeat = None self.temp_root = None def finalize_options(self): # Normally we would validate the options here, but that's handled in # run_tests pass # Most of the test runner arguments have the same name as attributes on # this command class, with one exception (for now) _test_runner_arg_attr_map = { 'verbose': 'verbose_results' } def generate_testing_command(self): """ Build a Python script to run the tests. """ cmd_pre = '' # Commands to run before the test function cmd_post = '' # Commands to run after the test function if self.coverage: pre, post = self._generate_coverage_commands() cmd_pre += pre cmd_post += post def get_attr(arg): attr = self._test_runner_arg_attr_map.get(arg, arg) return getattr(self, attr) test_args = filter(lambda arg: hasattr(self, arg), self._get_test_runner_args()) test_args = ', '.join('{0}={1!r}'.format(arg, get_attr(arg)) for arg in test_args) if PY3: set_flag = "import builtins; builtins._ASTROPY_TEST_ = True" else: set_flag = "import __builtin__; __builtin__._ASTROPY_TEST_ = True" cmd = ('{cmd_pre}{0}; import {1.package_name}, sys; result = ' '{1.package_name}.test({test_args}); {cmd_post}' 'sys.exit(result)') return cmd.format(set_flag, self, cmd_pre=cmd_pre, cmd_post=cmd_post, test_args=test_args) def _validate_required_deps(self): """ This method checks that any required modules are installed before running the tests. """ try: import astropy # noqa except ImportError: raise ImportError( "The 'test' command requires the astropy package to be " "installed and importable.") def run(self): """ Run the tests! """ # Ensure there is a doc path if self.docs_path is None: if os.path.exists('docs'): self.docs_path = os.path.abspath('docs') # Build a testing install of the package self._build_temp_install() # Ensure all required packages are installed self._validate_required_deps() # Run everything in a try: finally: so that the tmp dir gets deleted. try: # Construct this modules testing command cmd = self.generate_testing_command() # Run the tests in a subprocess--this is necessary since # new extension modules may have appeared, and this is the # easiest way to set up a new environment # On Python 3.x prior to 3.3, the creation of .pyc files # is not atomic. py.test jumps through some hoops to make # this work by parsing import statements and carefully # importing files atomically. However, it can't detect # when __import__ is used, so its carefulness still fails. # The solution here (admittedly a bit of a hack), is to # turn off the generation of .pyc files altogether by # passing the `-B` switch to `python`. This does mean # that each core will have to compile .py file to bytecode # itself, rather than getting lucky and borrowing the work # already done by another core. Compilation is an # insignificant fraction of total testing time, though, so # it's probably not worth worrying about. retcode = subprocess.call([sys.executable, '-B', '-c', cmd], cwd=self.testing_path, close_fds=False) finally: # Remove temporary directory shutil.rmtree(self.tmp_dir) raise SystemExit(retcode) def _build_temp_install(self): """ Build the package and copy the build to a temporary directory for the purposes of testing this avoids creating pyc and __pycache__ directories inside the build directory """ self.reinitialize_command('build', inplace=True) self.run_command('build') build_cmd = self.get_finalized_command('build') new_path = os.path.abspath(build_cmd.build_lib) # On OSX the default path for temp files is under /var, but in most # cases on OSX /var is actually a symlink to /private/var; ensure we # dereference that link, because py.test is very sensitive to relative # paths... tmp_dir = tempfile.mkdtemp(prefix=self.package_name + '-test-', dir=self.temp_root) self.tmp_dir = os.path.realpath(tmp_dir) self.testing_path = os.path.join(self.tmp_dir, os.path.basename(new_path)) shutil.copytree(new_path, self.testing_path) new_docs_path = os.path.join(self.tmp_dir, os.path.basename(self.docs_path)) shutil.copytree(self.docs_path, new_docs_path) self.docs_path = new_docs_path shutil.copy('setup.cfg', self.tmp_dir) def _generate_coverage_commands(self): """ This method creates the post and pre commands if coverage is to be generated """ if self.parallel != 0: raise ValueError( "--coverage can not be used with --parallel") try: import coverage # noqa except ImportError: raise ImportError( "--coverage requires that the coverage package is " "installed.") # Don't use get_pkg_data_filename here, because it # requires importing astropy.config and thus screwing # up coverage results for those packages. coveragerc = os.path.join( self.testing_path, self.package_name, 'tests', 'coveragerc') # We create a coveragerc that is specific to the version # of Python we're running, so that we can mark branches # as being specifically for Python 2 or Python 3 with open(coveragerc, 'r') as fd: coveragerc_content = fd.read() if PY3: ignore_python_version = '2' else: ignore_python_version = '3' coveragerc_content = coveragerc_content.replace( "{ignore_python_version}", ignore_python_version).replace( "{packagename}", self.package_name) tmp_coveragerc = os.path.join(self.tmp_dir, 'coveragerc') with open(tmp_coveragerc, 'wb') as tmp: tmp.write(coveragerc_content.encode('utf-8')) cmd_pre = ( 'import coverage; ' 'cov = coverage.coverage(data_file="{0}", config_file="{1}"); ' 'cov.start();'.format( os.path.abspath(".coverage"), tmp_coveragerc)) cmd_post = ( 'cov.stop(); ' 'from astropy.tests.helper import _save_coverage; ' '_save_coverage(cov, result, "{0}", "{1}");'.format( os.path.abspath('.'), self.testing_path)) return cmd_pre, cmd_post def _get_test_runner_args(self): """ A hack to determine what arguments are supported by the package's test() function. In the future there should be a more straightforward API to determine this (really it should be determined by the ``TestRunner`` class for whatever version of Astropy is in use). """ if PY3: import builtins builtins._ASTROPY_TEST_ = True else: import __builtin__ __builtin__._ASTROPY_TEST_ = True try: pkg = __import__(self.package_name) if not hasattr(pkg, 'test'): raise ImportError( 'package {0} does not have a {0}.test() function as ' 'required by the Astropy test runner'.format(self.package_name)) argspec = inspect.getargspec(pkg.test) return argspec.args finally: if PY3: del builtins._ASTROPY_TEST_ else: del __builtin__._ASTROPY_TEST_ montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/commands/build_ext.py0000644000077000000240000004636413137204755027403 0ustar tomstaff00000000000000import errno import os import re import shlex import shutil import subprocess import sys import textwrap from distutils import log, ccompiler, sysconfig from distutils.core import Extension from distutils.ccompiler import get_default_compiler from setuptools.command.build_ext import build_ext as SetuptoolsBuildExt from ..utils import get_numpy_include_path, invalidate_caches, classproperty from ..version_helpers import get_pkg_version_module def should_build_with_cython(package, release=None): """Returns the previously used Cython version (or 'unknown' if not previously built) if Cython should be used to build extension modules from pyx files. If the ``release`` parameter is not specified an attempt is made to determine the release flag from `astropy.version`. """ try: version_module = __import__(package + '.cython_version', fromlist=['release', 'cython_version']) except ImportError: version_module = None if release is None and version_module is not None: try: release = version_module.release except AttributeError: pass try: cython_version = version_module.cython_version except AttributeError: cython_version = 'unknown' # Only build with Cython if, of course, Cython is installed, we're in a # development version (i.e. not release) or the Cython-generated source # files haven't been created yet (cython_version == 'unknown'). The latter # case can happen even when release is True if checking out a release tag # from the repository have_cython = False try: import Cython # noqa have_cython = True except ImportError: pass if have_cython and (not release or cython_version == 'unknown'): return cython_version else: return False _compiler_versions = {} def get_compiler_version(compiler): if compiler in _compiler_versions: return _compiler_versions[compiler] # Different flags to try to get the compiler version # TODO: It might be worth making this configurable to support # arbitrary odd compilers; though all bets may be off in such # cases anyway flags = ['--version', '--Version', '-version', '-Version', '-v', '-V'] def try_get_version(flag): process = subprocess.Popen( shlex.split(compiler, posix=('win' not in sys.platform)) + [flag], stdout=subprocess.PIPE, stderr=subprocess.PIPE) stdout, stderr = process.communicate() if process.returncode != 0: return 'unknown' output = stdout.strip().decode('latin-1') # Safest bet if not output: # Some compilers return their version info on stderr output = stderr.strip().decode('latin-1') if not output: output = 'unknown' return output for flag in flags: version = try_get_version(flag) if version != 'unknown': break # Cache results to speed up future calls _compiler_versions[compiler] = version return version # TODO: I think this can be reworked without having to create the class # programmatically. def generate_build_ext_command(packagename, release): """ Creates a custom 'build_ext' command that allows for manipulating some of the C extension options at build time. We use a function to build the class since the base class for build_ext may be different depending on certain build-time parameters (for example, we may use Cython's build_ext instead of the default version in distutils). Uses the default distutils.command.build_ext by default. """ class build_ext(SetuptoolsBuildExt, object): package_name = packagename is_release = release _user_options = SetuptoolsBuildExt.user_options[:] _boolean_options = SetuptoolsBuildExt.boolean_options[:] _help_options = SetuptoolsBuildExt.help_options[:] force_rebuild = False _broken_compiler_mapping = [ ('i686-apple-darwin[0-9]*-llvm-gcc-4.2', 'clang') ] # Warning: Spaghetti code ahead. # During setup.py, the setup_helpers module needs the ability to add # items to a command's user_options list. At this stage we don't know # whether or not we can build with Cython, and so don't know for sure # what base class will be used for build_ext; nevertheless we want to # be able to provide a list to add options into. # # Later, once setup() has been called we should have all build # dependencies included via setup_requires available. distutils needs # to be able to access the user_options as a *class* attribute before # the class has been initialized, but we do need to be able to # enumerate the options for the correct base class at that point @classproperty def user_options(cls): from distutils import core if core._setup_distribution is None: # We haven't gotten into setup() yet, and the Distribution has # not yet been initialized return cls._user_options return cls._final_class.user_options @classproperty def boolean_options(cls): # Similar to user_options above from distutils import core if core._setup_distribution is None: # We haven't gotten into setup() yet, and the Distribution has # not yet been initialized return cls._boolean_options return cls._final_class.boolean_options @classproperty def help_options(cls): # Similar to user_options above from distutils import core if core._setup_distribution is None: # We haven't gotten into setup() yet, and the Distribution has # not yet been initialized return cls._help_options return cls._final_class.help_options @classproperty(lazy=True) def _final_class(cls): """ Late determination of what the build_ext base class should be, depending on whether or not Cython is available. """ uses_cython = should_build_with_cython(cls.package_name, cls.is_release) if uses_cython: # We need to decide late on whether or not to use Cython's # build_ext (since Cython may not be available earlier in the # setup.py if it was brought in via setup_requires) try: from Cython.Distutils.old_build_ext import old_build_ext as base_cls except ImportError: from Cython.Distutils import build_ext as base_cls else: base_cls = SetuptoolsBuildExt # Create and return an instance of a new class based on this class # using one of the above possible base classes def merge_options(attr): base = getattr(base_cls, attr) ours = getattr(cls, '_' + attr) all_base = set(opt[0] for opt in base) return base + [opt for opt in ours if opt[0] not in all_base] boolean_options = (base_cls.boolean_options + [opt for opt in cls._boolean_options if opt not in base_cls.boolean_options]) members = dict(cls.__dict__) members.update({ 'user_options': merge_options('user_options'), 'help_options': merge_options('help_options'), 'boolean_options': boolean_options, 'uses_cython': uses_cython, }) # Update the base class for the original build_ext command build_ext.__bases__ = (base_cls, object) # Create a new class for the existing class, but now with the # appropriate base class depending on whether or not to use Cython. # Ensure that object is one of the bases to make a new-style class. return type(cls.__name__, (build_ext,), members) def __new__(cls, *args, **kwargs): # By the time the command is actually instantialized, the # Distribution instance for the build has been instantiated, which # means setup_requires has been processed--now we can determine # what base class we can use for the actual build, and return an # instance of a build_ext command that uses that base class (right # now the options being Cython.Distutils.build_ext, or the stock # setuptools build_ext) new_cls = super(build_ext, cls._final_class).__new__( cls._final_class) # Since the new cls is not a subclass of the original cls, we must # manually call its __init__ new_cls.__init__(*args, **kwargs) return new_cls def finalize_options(self): # Add a copy of the _compiler.so module as well, but only if there # are in fact C modules to compile (otherwise there's no reason to # include a record of the compiler used) # Note, self.extensions may not be set yet, but # self.distribution.ext_modules is where any extension modules # passed to setup() can be found self._adjust_compiler() extensions = self.distribution.ext_modules if extensions: build_py = self.get_finalized_command('build_py') package_dir = build_py.get_package_dir(packagename) src_path = os.path.relpath( os.path.join(os.path.dirname(__file__), 'src')) shutil.copy(os.path.join(src_path, 'compiler.c'), os.path.join(package_dir, '_compiler.c')) ext = Extension(self.package_name + '._compiler', [os.path.join(package_dir, '_compiler.c')]) extensions.insert(0, ext) super(build_ext, self).finalize_options() # Generate if self.uses_cython: try: from Cython import __version__ as cython_version except ImportError: # This shouldn't happen if we made it this far cython_version = None if (cython_version is not None and cython_version != self.uses_cython): self.force_rebuild = True # Update the used cython version self.uses_cython = cython_version # Regardless of the value of the '--force' option, force a rebuild # if the debug flag changed from the last build if self.force_rebuild: self.force = True def run(self): # For extensions that require 'numpy' in their include dirs, # replace 'numpy' with the actual paths np_include = get_numpy_include_path() for extension in self.extensions: if 'numpy' in extension.include_dirs: idx = extension.include_dirs.index('numpy') extension.include_dirs.insert(idx, np_include) extension.include_dirs.remove('numpy') self._check_cython_sources(extension) super(build_ext, self).run() # Update cython_version.py if building with Cython try: cython_version = get_pkg_version_module( packagename, fromlist=['cython_version'])[0] except (AttributeError, ImportError): cython_version = 'unknown' if self.uses_cython and self.uses_cython != cython_version: build_py = self.get_finalized_command('build_py') package_dir = build_py.get_package_dir(packagename) cython_py = os.path.join(package_dir, 'cython_version.py') with open(cython_py, 'w') as f: f.write('# Generated file; do not modify\n') f.write('cython_version = {0!r}\n'.format(self.uses_cython)) if os.path.isdir(self.build_lib): # The build/lib directory may not exist if the build_py # command was not previously run, which may sometimes be # the case self.copy_file(cython_py, os.path.join(self.build_lib, cython_py), preserve_mode=False) invalidate_caches() def _adjust_compiler(self): """ This function detects broken compilers and switches to another. If the environment variable CC is explicitly set, or a compiler is specified on the commandline, no override is performed -- the purpose here is to only override a default compiler. The specific compilers with problems are: * The default compiler in XCode-4.2, llvm-gcc-4.2, segfaults when compiling wcslib. The set of broken compilers can be updated by changing the compiler_mapping variable. It is a list of 2-tuples where the first in the pair is a regular expression matching the version of the broken compiler, and the second is the compiler to change to. """ if 'CC' in os.environ: # Check that CC is not set to llvm-gcc-4.2 c_compiler = os.environ['CC'] try: version = get_compiler_version(c_compiler) except OSError: msg = textwrap.dedent( """ The C compiler set by the CC environment variable: {compiler:s} cannot be found or executed. """.format(compiler=c_compiler)) log.warn(msg) sys.exit(1) for broken, fixed in self._broken_compiler_mapping: if re.match(broken, version): msg = textwrap.dedent( """Compiler specified by CC environment variable ({compiler:s}:{version:s}) will fail to compile {pkg:s}. Please set CC={fixed:s} and try again. You can do this, for example, by running: CC={fixed:s} python setup.py where is the command you ran. """.format(compiler=c_compiler, version=version, pkg=self.package_name, fixed=fixed)) log.warn(msg) sys.exit(1) # If C compiler is set via CC, and isn't broken, we are good to go. We # should definitely not try accessing the compiler specified by # ``sysconfig.get_config_var('CC')`` lower down, because this may fail # if the compiler used to compile Python is missing (and maybe this is # why the user is setting CC). For example, the official Python 2.7.3 # MacOS X binary was compiled with gcc-4.2, which is no longer available # in XCode 4. return if self.compiler is not None: # At this point, self.compiler will be set only if a compiler # was specified in the command-line or via setup.cfg, in which # case we don't do anything return compiler_type = ccompiler.get_default_compiler() if compiler_type == 'unix': # We have to get the compiler this way, as this is the one that is # used if os.environ['CC'] is not set. It is actually read in from # the Python Makefile. Note that this is not necessarily the same # compiler as returned by ccompiler.new_compiler() c_compiler = sysconfig.get_config_var('CC') try: version = get_compiler_version(c_compiler) except OSError: msg = textwrap.dedent( """ The C compiler used to compile Python {compiler:s}, and which is normally used to compile C extensions, is not available. You can explicitly specify which compiler to use by setting the CC environment variable, for example: CC=gcc python setup.py or if you are using MacOS X, you can try: CC=clang python setup.py """.format(compiler=c_compiler)) log.warn(msg) sys.exit(1) for broken, fixed in self._broken_compiler_mapping: if re.match(broken, version): os.environ['CC'] = fixed break def _check_cython_sources(self, extension): """ Where relevant, make sure that the .c files associated with .pyx modules are present (if building without Cython installed). """ # Determine the compiler we'll be using if self.compiler is None: compiler = get_default_compiler() else: compiler = self.compiler # Replace .pyx with C-equivalents, unless c files are missing for jdx, src in enumerate(extension.sources): base, ext = os.path.splitext(src) pyxfn = base + '.pyx' cfn = base + '.c' cppfn = base + '.cpp' if not os.path.isfile(pyxfn): continue if self.uses_cython: extension.sources[jdx] = pyxfn else: if os.path.isfile(cfn): extension.sources[jdx] = cfn elif os.path.isfile(cppfn): extension.sources[jdx] = cppfn else: msg = ( 'Could not find C/C++ file {0}.(c/cpp) for Cython ' 'file {1} when building extension {2}. Cython ' 'must be installed to build from a git ' 'checkout.'.format(base, pyxfn, extension.name)) raise IOError(errno.ENOENT, msg, cfn) # Current versions of Cython use deprecated Numpy API features # the use of which produces a few warnings when compiling. # These additional flags should squelch those warnings. # TODO: Feel free to remove this if/when a Cython update # removes use of the deprecated Numpy API if compiler == 'unix': extension.extra_compile_args.extend([ '-Wp,-w', '-Wno-unused-function']) return build_ext montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/commands/build_py.py0000644000077000000240000000265612531030705027214 0ustar tomstaff00000000000000from setuptools.command.build_py import build_py as SetuptoolsBuildPy from ..utils import _get_platlib_dir class AstropyBuildPy(SetuptoolsBuildPy): user_options = SetuptoolsBuildPy.user_options[:] boolean_options = SetuptoolsBuildPy.boolean_options[:] def finalize_options(self): # Update build_lib settings from the build command to always put # build files in platform-specific subdirectories of build/, even # for projects with only pure-Python source (this is desirable # specifically for support of multiple Python version). build_cmd = self.get_finalized_command('build') platlib_dir = _get_platlib_dir(build_cmd) build_cmd.build_purelib = platlib_dir build_cmd.build_lib = platlib_dir self.build_lib = platlib_dir SetuptoolsBuildPy.finalize_options(self) def run_2to3(self, files, doctests=False): # Filter the files to exclude things that shouldn't be 2to3'd skip_2to3 = self.distribution.skip_2to3 filtered_files = [] for filename in files: for package in skip_2to3: if filename[len(self.build_lib) + 1:].startswith(package): break else: filtered_files.append(filename) SetuptoolsBuildPy.run_2to3(self, filtered_files, doctests) def run(self): # first run the normal build_py SetuptoolsBuildPy.run(self) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/commands/build_sphinx.py0000644000077000000240000002427713137204755030113 0ustar tomstaff00000000000000from __future__ import print_function import inspect import os import pkgutil import re import shutil import subprocess import sys import textwrap import warnings from distutils import log from distutils.cmd import DistutilsOptionError import sphinx from sphinx.setup_command import BuildDoc as SphinxBuildDoc from ..utils import minversion, AstropyDeprecationWarning PY3 = sys.version_info[0] >= 3 class AstropyBuildDocs(SphinxBuildDoc): """ A version of the ``build_docs`` command that uses the version of Astropy that is built by the setup ``build`` command, rather than whatever is installed on the system. To build docs against the installed version, run ``make html`` in the ``astropy/docs`` directory. This also automatically creates the docs/_static directories--this is needed because GitHub won't create the _static dir because it has no tracked files. """ description = 'Build Sphinx documentation for Astropy environment' user_options = SphinxBuildDoc.user_options[:] user_options.append( ('warnings-returncode', 'w', 'Parses the sphinx output and sets the return code to 1 if there ' 'are any warnings. Note that this will cause the sphinx log to ' 'only update when it completes, rather than continuously as is ' 'normally the case.')) user_options.append( ('clean-docs', 'l', 'Completely clean previous builds, including ' 'automodapi-generated files before building new ones')) user_options.append( ('no-intersphinx', 'n', 'Skip intersphinx, even if conf.py says to use it')) user_options.append( ('open-docs-in-browser', 'o', 'Open the docs in a browser (using the webbrowser module) if the ' 'build finishes successfully.')) boolean_options = SphinxBuildDoc.boolean_options[:] boolean_options.append('warnings-returncode') boolean_options.append('clean-docs') boolean_options.append('no-intersphinx') boolean_options.append('open-docs-in-browser') _self_iden_rex = re.compile(r"self\.([^\d\W][\w]+)", re.UNICODE) def initialize_options(self): SphinxBuildDoc.initialize_options(self) self.clean_docs = False self.no_intersphinx = False self.open_docs_in_browser = False self.warnings_returncode = False def finalize_options(self): SphinxBuildDoc.finalize_options(self) # Clear out previous sphinx builds, if requested if self.clean_docs: dirstorm = [os.path.join(self.source_dir, 'api'), os.path.join(self.source_dir, 'generated')] if self.build_dir is None: dirstorm.append('docs/_build') else: dirstorm.append(self.build_dir) for d in dirstorm: if os.path.isdir(d): log.info('Cleaning directory ' + d) shutil.rmtree(d) else: log.info('Not cleaning directory ' + d + ' because ' 'not present or not a directory') def run(self): # TODO: Break this method up into a few more subroutines and # document them better import webbrowser if PY3: from urllib.request import pathname2url else: from urllib import pathname2url # This is used at the very end of `run` to decide if sys.exit should # be called. If it's None, it won't be. retcode = None # If possible, create the _static dir if self.build_dir is not None: # the _static dir should be in the same place as the _build dir # for Astropy basedir, subdir = os.path.split(self.build_dir) if subdir == '': # the path has a trailing /... basedir, subdir = os.path.split(basedir) staticdir = os.path.join(basedir, '_static') if os.path.isfile(staticdir): raise DistutilsOptionError( 'Attempted to build_docs in a location where' + staticdir + 'is a file. Must be a directory.') self.mkpath(staticdir) # Now make sure Astropy is built and determine where it was built build_cmd = self.reinitialize_command('build') build_cmd.inplace = 0 self.run_command('build') build_cmd = self.get_finalized_command('build') build_cmd_path = os.path.abspath(build_cmd.build_lib) ah_importer = pkgutil.get_importer('astropy_helpers') ah_path = os.path.abspath(ah_importer.path) # Now generate the source for and spawn a new process that runs the # command. This is needed to get the correct imports for the built # version runlines, runlineno = inspect.getsourcelines(SphinxBuildDoc.run) subproccode = textwrap.dedent(""" from sphinx.setup_command import * os.chdir({srcdir!r}) sys.path.insert(0, {build_cmd_path!r}) sys.path.insert(0, {ah_path!r}) """).format(build_cmd_path=build_cmd_path, ah_path=ah_path, srcdir=self.source_dir) # runlines[1:] removes 'def run(self)' on the first line subproccode += textwrap.dedent(''.join(runlines[1:])) # All "self.foo" in the subprocess code needs to be replaced by the # values taken from the current self in *this* process subproccode = self._self_iden_rex.split(subproccode) for i in range(1, len(subproccode), 2): iden = subproccode[i] val = getattr(self, iden) if iden.endswith('_dir'): # Directories should be absolute, because the `chdir` call # in the new process moves to a different directory subproccode[i] = repr(os.path.abspath(val)) else: subproccode[i] = repr(val) subproccode = ''.join(subproccode) optcode = textwrap.dedent(""" class Namespace(object): pass self = Namespace() self.pdb = {pdb!r} self.verbosity = {verbosity!r} self.traceback = {traceback!r} """).format(pdb=getattr(self, 'pdb', False), verbosity=getattr(self, 'verbosity', 0), traceback=getattr(self, 'traceback', False)) subproccode = optcode + subproccode # This is a quick gross hack, but it ensures that the code grabbed from # SphinxBuildDoc.run will work in Python 2 if it uses the print # function if minversion(sphinx, '1.3'): subproccode = 'from __future__ import print_function' + subproccode if self.no_intersphinx: # the confoverrides variable in sphinx.setup_command.BuildDoc can # be used to override the conf.py ... but this could well break # if future versions of sphinx change the internals of BuildDoc, # so remain vigilant! subproccode = subproccode.replace( 'confoverrides = {}', 'confoverrides = {\'intersphinx_mapping\':{}}') log.debug('Starting subprocess of {0} with python code:\n{1}\n' '[CODE END])'.format(sys.executable, subproccode)) # To return the number of warnings, we need to capture stdout. This # prevents a continuous updating at the terminal, but there's no # apparent way around this. if self.warnings_returncode: proc = subprocess.Popen([sys.executable, '-c', subproccode], stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) retcode = 1 with proc.stdout: for line in iter(proc.stdout.readline, b''): line = line.strip(b'\r\n') print(line.decode('utf-8')) if 'build succeeded.' == line.decode('utf-8'): retcode = 0 # Poll to set proc.retcode proc.wait() if retcode != 0: if os.environ.get('TRAVIS', None) == 'true': # this means we are in the travis build, so customize # the message appropriately. msg = ('The build_docs travis build FAILED ' 'because sphinx issued documentation ' 'warnings (scroll up to see the warnings).') else: # standard failure message msg = ('build_docs returning a non-zero exit ' 'code because sphinx issued documentation ' 'warnings.') log.warn(msg) else: proc = subprocess.Popen([sys.executable], stdin=subprocess.PIPE) proc.communicate(subproccode.encode('utf-8')) if proc.returncode == 0: if self.open_docs_in_browser: if self.builder == 'html': absdir = os.path.abspath(self.builder_target_dir) index_path = os.path.join(absdir, 'index.html') fileurl = 'file://' + pathname2url(index_path) webbrowser.open(fileurl) else: log.warn('open-docs-in-browser option was given, but ' 'the builder is not html! Ignoring.') else: log.warn('Sphinx Documentation subprocess failed with return ' 'code ' + str(proc.returncode)) retcode = proc.returncode if retcode is not None: # this is potentially dangerous in that there might be something # after the call to `setup` in `setup.py`, and exiting here will # prevent that from running. But there's no other apparent way # to signal what the return code should be. sys.exit(retcode) class AstropyBuildSphinx(AstropyBuildDocs): # pragma: no cover description = 'deprecated alias to the build_docs command' def run(self): warnings.warn( 'The "build_sphinx" command is now deprecated. Use' '"build_docs" instead.', AstropyDeprecationWarning) AstropyBuildDocs.run(self) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/commands/install.py0000644000077000000240000000074612531030705027051 0ustar tomstaff00000000000000from setuptools.command.install import install as SetuptoolsInstall from ..utils import _get_platlib_dir class AstropyInstall(SetuptoolsInstall): user_options = SetuptoolsInstall.user_options[:] boolean_options = SetuptoolsInstall.boolean_options[:] def finalize_options(self): build_cmd = self.get_finalized_command('build') platlib_dir = _get_platlib_dir(build_cmd) self.build_lib = platlib_dir SetuptoolsInstall.finalize_options(self) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/commands/install_lib.py0000644000077000000240000000100012531030705027657 0ustar tomstaff00000000000000from setuptools.command.install_lib import install_lib as SetuptoolsInstallLib from ..utils import _get_platlib_dir class AstropyInstallLib(SetuptoolsInstallLib): user_options = SetuptoolsInstallLib.user_options[:] boolean_options = SetuptoolsInstallLib.boolean_options[:] def finalize_options(self): build_cmd = self.get_finalized_command('build') platlib_dir = _get_platlib_dir(build_cmd) self.build_dir = platlib_dir SetuptoolsInstallLib.finalize_options(self) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/commands/register.py0000644000077000000240000000454712531030705027232 0ustar tomstaff00000000000000from setuptools.command.register import register as SetuptoolsRegister class AstropyRegister(SetuptoolsRegister): """Extends the built in 'register' command to support a ``--hidden`` option to make the registered version hidden on PyPI by default. The result of this is that when a version is registered as "hidden" it can still be downloaded from PyPI, but it does not show up in the list of actively supported versions under http://pypi.python.org/pypi/astropy, and is not set as the most recent version. Although this can always be set through the web interface it may be more convenient to be able to specify via the 'register' command. Hidden may also be considered a safer default when running the 'register' command, though this command uses distutils' normal behavior if the ``--hidden`` option is omitted. """ user_options = SetuptoolsRegister.user_options + [ ('hidden', None, 'mark this release as hidden on PyPI by default') ] boolean_options = SetuptoolsRegister.boolean_options + ['hidden'] def initialize_options(self): SetuptoolsRegister.initialize_options(self) self.hidden = False def build_post_data(self, action): data = SetuptoolsRegister.build_post_data(self, action) if action == 'submit' and self.hidden: data['_pypi_hidden'] = '1' return data def _set_config(self): # The original register command is buggy--if you use .pypirc with a # server-login section *at all* the repository you specify with the -r # option will be overwritten with either the repository in .pypirc or # with the default, # If you do not have a .pypirc using the -r option will just crash. # Way to go distutils # If we don't set self.repository back to a default value _set_config # can crash if there was a user-supplied value for this option; don't # worry, we'll get the real value back afterwards self.repository = 'pypi' SetuptoolsRegister._set_config(self) options = self.distribution.get_option_dict('register') if 'repository' in options: source, value = options['repository'] # Really anything that came from setup.cfg or the command line # should override whatever was in .pypirc self.repository = value montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/commands/setup_package.py0000644000077000000240000000017013104416125030206 0ustar tomstaff00000000000000from os.path import join def get_package_data(): return {'astropy_helpers.commands': [join('src', 'compiler.c')]} montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/commands/src/0000755000077000000240000000000013137205364025621 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/commands/src/compiler.c0000644000077000000240000000573112531030705027575 0ustar tomstaff00000000000000#include /*************************************************************************** * Macros for determining the compiler version. * * These are borrowed from boost, and majorly abridged to include only * the compilers we care about. ***************************************************************************/ #ifndef PY3K #if PY_MAJOR_VERSION >= 3 #define PY3K 1 #else #define PY3K 0 #endif #endif #define STRINGIZE(X) DO_STRINGIZE(X) #define DO_STRINGIZE(X) #X #if defined __clang__ /* Clang C++ emulates GCC, so it has to appear early. */ # define COMPILER "Clang version " __clang_version__ #elif defined(__INTEL_COMPILER) || defined(__ICL) || defined(__ICC) || defined(__ECC) /* Intel */ # if defined(__INTEL_COMPILER) # define INTEL_VERSION __INTEL_COMPILER # elif defined(__ICL) # define INTEL_VERSION __ICL # elif defined(__ICC) # define INTEL_VERSION __ICC # elif defined(__ECC) # define INTEL_VERSION __ECC # endif # define COMPILER "Intel C compiler version " STRINGIZE(INTEL_VERSION) #elif defined(__GNUC__) /* gcc */ # define COMPILER "GCC version " __VERSION__ #elif defined(__SUNPRO_CC) /* Sun Workshop Compiler */ # define COMPILER "Sun compiler version " STRINGIZE(__SUNPRO_CC) #elif defined(_MSC_VER) /* Microsoft Visual C/C++ Must be last since other compilers define _MSC_VER for compatibility as well */ # if _MSC_VER < 1200 # define COMPILER_VERSION 5.0 # elif _MSC_VER < 1300 # define COMPILER_VERSION 6.0 # elif _MSC_VER == 1300 # define COMPILER_VERSION 7.0 # elif _MSC_VER == 1310 # define COMPILER_VERSION 7.1 # elif _MSC_VER == 1400 # define COMPILER_VERSION 8.0 # elif _MSC_VER == 1500 # define COMPILER_VERSION 9.0 # elif _MSC_VER == 1600 # define COMPILER_VERSION 10.0 # else # define COMPILER_VERSION _MSC_VER # endif # define COMPILER "Microsoft Visual C++ version " STRINGIZE(COMPILER_VERSION) #else /* Fallback */ # define COMPILER "Unknown compiler" #endif /*************************************************************************** * Module-level ***************************************************************************/ struct module_state { /* The Sun compiler can't handle empty structs */ #if defined(__SUNPRO_C) || defined(_MSC_VER) int _dummy; #endif }; #if PY3K static struct PyModuleDef moduledef = { PyModuleDef_HEAD_INIT, "_compiler", NULL, sizeof(struct module_state), NULL, NULL, NULL, NULL, NULL }; #define INITERROR return NULL PyMODINIT_FUNC PyInit__compiler(void) #else #define INITERROR return PyMODINIT_FUNC init_compiler(void) #endif { PyObject* m; #if PY3K m = PyModule_Create(&moduledef); #else m = Py_InitModule3("_compiler", NULL, NULL); #endif if (m == NULL) INITERROR; PyModule_AddStringConstant(m, "compiler", COMPILER); #if PY3K return m; #endif } montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/commands/test.py0000644000077000000240000000252413137204755026371 0ustar tomstaff00000000000000""" Different implementations of the ``./setup.py test`` command depending on what's locally available. If Astropy v1.1.0.dev or later is available it should be possible to import AstropyTest from ``astropy.tests.command``. If ``astropy`` can be imported but not ``astropy.tests.command`` (i.e. an older version of Astropy), we can use the backwards-compat implementation of the command. If Astropy can't be imported at all then there is a skeleton implementation that allows users to at least discover the ``./setup.py test`` command and learn that they need Astropy to run it. """ # Previously these except statements caught only ImportErrors, but there are # some other obscure exceptional conditions that can occur when importing # astropy.tests (at least on older versions) that can cause these imports to # fail try: import astropy # noqa try: from astropy.tests.command import AstropyTest except Exception: from ._test_compat import AstropyTest except Exception: # No astropy at all--provide the dummy implementation from ._dummy import _DummyCommand class AstropyTest(_DummyCommand): command_name = 'test' description = 'Run the tests for this package' error_msg = ( "The 'test' command requires the astropy package to be " "installed and importable.") montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/compat/0000755000077000000240000000000013137205364024514 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/compat/__init__.py0000644000077000000240000000056012333217235026623 0ustar tomstaff00000000000000def _fix_user_options(options): """ This is for Python 2.x and 3.x compatibility. distutils expects Command options to all be byte strings on Python 2 and Unicode strings on Python 3. """ def to_str_or_none(x): if x is None: return None return str(x) return [tuple(to_str_or_none(x) for x in y) for y in options] montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/distutils_helpers.py0000644000077000000240000001736213137204755027365 0ustar tomstaff00000000000000""" This module contains various utilities for introspecting the distutils module and the setup process. Some of these utilities require the `astropy_helpers.setup_helpers.register_commands` function to be called first, as it will affect introspection of setuptools command-line arguments. Other utilities in this module do not have that restriction. """ import os import sys from distutils import ccompiler, log from distutils.dist import Distribution from distutils.errors import DistutilsError from .utils import silence # This function, and any functions that call it, require the setup in # `astropy_helpers.setup_helpers.register_commands` to be run first. def get_dummy_distribution(): """ Returns a distutils Distribution object used to instrument the setup environment before calling the actual setup() function. """ from .setup_helpers import _module_state if _module_state['registered_commands'] is None: raise RuntimeError( 'astropy_helpers.setup_helpers.register_commands() must be ' 'called before using ' 'astropy_helpers.setup_helpers.get_dummy_distribution()') # Pre-parse the Distutils command-line options and config files to if # the option is set. dist = Distribution({'script_name': os.path.basename(sys.argv[0]), 'script_args': sys.argv[1:]}) dist.cmdclass.update(_module_state['registered_commands']) with silence(): try: dist.parse_config_files() dist.parse_command_line() except (DistutilsError, AttributeError, SystemExit): # Let distutils handle DistutilsErrors itself AttributeErrors can # get raise for ./setup.py --help SystemExit can be raised if a # display option was used, for example pass return dist def get_distutils_option(option, commands): """ Returns the value of the given distutils option. Parameters ---------- option : str The name of the option commands : list of str The list of commands on which this option is available Returns ------- val : str or None the value of the given distutils option. If the option is not set, returns None. """ dist = get_dummy_distribution() for cmd in commands: cmd_opts = dist.command_options.get(cmd) if cmd_opts is not None and option in cmd_opts: return cmd_opts[option][1] else: return None def get_distutils_build_option(option): """ Returns the value of the given distutils build option. Parameters ---------- option : str The name of the option Returns ------- val : str or None The value of the given distutils build option. If the option is not set, returns None. """ return get_distutils_option(option, ['build', 'build_ext', 'build_clib']) def get_distutils_install_option(option): """ Returns the value of the given distutils install option. Parameters ---------- option : str The name of the option Returns ------- val : str or None The value of the given distutils build option. If the option is not set, returns None. """ return get_distutils_option(option, ['install']) def get_distutils_build_or_install_option(option): """ Returns the value of the given distutils build or install option. Parameters ---------- option : str The name of the option Returns ------- val : str or None The value of the given distutils build or install option. If the option is not set, returns None. """ return get_distutils_option(option, ['build', 'build_ext', 'build_clib', 'install']) def get_compiler_option(): """ Determines the compiler that will be used to build extension modules. Returns ------- compiler : str The compiler option specified for the build, build_ext, or build_clib command; or the default compiler for the platform if none was specified. """ compiler = get_distutils_build_option('compiler') if compiler is None: return ccompiler.get_default_compiler() return compiler def add_command_option(command, name, doc, is_bool=False): """ Add a custom option to a setup command. Issues a warning if the option already exists on that command. Parameters ---------- command : str The name of the command as given on the command line name : str The name of the build option doc : str A short description of the option, for the `--help` message is_bool : bool, optional When `True`, the option is a boolean option and doesn't require an associated value. """ dist = get_dummy_distribution() cmdcls = dist.get_command_class(command) if (hasattr(cmdcls, '_astropy_helpers_options') and name in cmdcls._astropy_helpers_options): return attr = name.replace('-', '_') if hasattr(cmdcls, attr): raise RuntimeError( '{0!r} already has a {1!r} class attribute, barring {2!r} from ' 'being usable as a custom option name.'.format(cmdcls, attr, name)) for idx, cmd in enumerate(cmdcls.user_options): if cmd[0] == name: log.warn('Overriding existing {0!r} option ' '{1!r}'.format(command, name)) del cmdcls.user_options[idx] if name in cmdcls.boolean_options: cmdcls.boolean_options.remove(name) break cmdcls.user_options.append((name, None, doc)) if is_bool: cmdcls.boolean_options.append(name) # Distutils' command parsing requires that a command object have an # attribute with the same name as the option (with '-' replaced with '_') # in order for that option to be recognized as valid setattr(cmdcls, attr, None) # This caches the options added through add_command_option so that if it is # run multiple times in the same interpreter repeated adds are ignored # (this way we can still raise a RuntimeError if a custom option overrides # a built-in option) if not hasattr(cmdcls, '_astropy_helpers_options'): cmdcls._astropy_helpers_options = set([name]) else: cmdcls._astropy_helpers_options.add(name) def get_distutils_display_options(): """ Returns a set of all the distutils display options in their long and short forms. These are the setup.py arguments such as --name or --version which print the project's metadata and then exit. Returns ------- opts : set The long and short form display option arguments, including the - or -- """ short_display_opts = set('-' + o[1] for o in Distribution.display_options if o[1]) long_display_opts = set('--' + o[0] for o in Distribution.display_options) # Include -h and --help which are not explicitly listed in # Distribution.display_options (as they are handled by optparse) short_display_opts.add('-h') long_display_opts.add('--help') # This isn't the greatest approach to hardcode these commands. # However, there doesn't seem to be a good way to determine # whether build *will be* run as part of the command at this # phase. display_commands = set([ 'clean', 'register', 'setopt', 'saveopts', 'egg_info', 'alias']) return short_display_opts.union(long_display_opts.union(display_commands)) def is_distutils_display_option(): """ Returns True if sys.argv contains any of the distutils display options such as --version or --name. """ display_options = get_distutils_display_options() return bool(set(sys.argv[1:]).intersection(display_options)) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/0000755000077000000240000000000013137205364024536 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/__init__.py0000644000077000000240000000111513137204755026650 0ustar tomstaff00000000000000# The ``astropy_helpers.extern`` sub-module includes modules developed elsewhere # that are bundled here for convenience. At the moment, this consists of the # following two sphinx extensions: # # * `numpydoc `_, a Sphinx extension # developed as part of the Numpy project. This is used to parse docstrings # in Numpy format # # * `sphinx-automodapi `_, a Sphinx # developed as part of the Astropy project. This used to be developed directly # in ``astropy-helpers`` but is now a standalone package. montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/automodapi/0000755000077000000240000000000013137205364026700 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/automodapi/__init__.py0000644000077000000240000000002413137204755031010 0ustar tomstaff00000000000000__version__ = '0.6' montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/automodapi/autodoc_enhancements.py0000644000077000000240000001230413137204755033443 0ustar tomstaff00000000000000""" Miscellaneous enhancements to help autodoc along. """ import inspect import sys import types import sphinx from distutils.version import LooseVersion from sphinx.ext.autodoc import AttributeDocumenter, ModuleDocumenter from sphinx.util.inspect import isdescriptor if sys.version_info[0] == 3: class_types = (type,) else: class_types = (type, types.ClassType) SPHINX_LT_15 = (LooseVersion(sphinx.__version__) < LooseVersion('1.5')) MethodDescriptorType = type(type.__subclasses__) # See # https://github.com/astropy/astropy-helpers/issues/116#issuecomment-71254836 # for further background on this. def type_object_attrgetter(obj, attr, *defargs): """ This implements an improved attrgetter for type objects (i.e. classes) that can handle class attributes that are implemented as properties on a metaclass. Normally `getattr` on a class with a `property` (say, "foo"), would return the `property` object itself. However, if the class has a metaclass which *also* defines a `property` named "foo", ``getattr(cls, 'foo')`` will find the "foo" property on the metaclass and resolve it. For the purposes of autodoc we just want to document the "foo" property defined on the class, not on the metaclass. For example:: >>> class Meta(type): ... @property ... def foo(cls): ... return 'foo' ... >>> class MyClass(metaclass=Meta): ... @property ... def foo(self): ... \"\"\"Docstring for MyClass.foo property.\"\"\" ... return 'myfoo' ... >>> getattr(MyClass, 'foo') 'foo' >>> type_object_attrgetter(MyClass, 'foo') >>> type_object_attrgetter(MyClass, 'foo').__doc__ 'Docstring for MyClass.foo property.' The last line of the example shows the desired behavior for the purposes of autodoc. """ for base in obj.__mro__: if attr in base.__dict__: if isinstance(base.__dict__[attr], property): # Note, this should only be used for properties--for any other # type of descriptor (classmethod, for example) this can mess # up existing expectations of what getattr(cls, ...) returns return base.__dict__[attr] break return getattr(obj, attr, *defargs) if SPHINX_LT_15: # Provided to work around a bug in Sphinx # See https://github.com/sphinx-doc/sphinx/pull/1843 class AttributeDocumenter(AttributeDocumenter): @classmethod def can_document_member(cls, member, membername, isattr, parent): non_attr_types = cls.method_types + class_types + \ (MethodDescriptorType,) isdatadesc = isdescriptor(member) and not \ isinstance(member, non_attr_types) and not \ type(member).__name__ == "instancemethod" # That last condition addresses an obscure case of C-defined # methods using a deprecated type in Python 3, that is not # otherwise exported anywhere by Python return isdatadesc or (not isinstance(parent, ModuleDocumenter) and not inspect.isroutine(member) and not isinstance(member, class_types)) def setup(app): # Must have the autodoc extension set up first so we can override it app.setup_extension('sphinx.ext.autodoc') # Need to import this too since it re-registers all the documenter types # =_= import sphinx.ext.autosummary.generate app.add_autodoc_attrgetter(type, type_object_attrgetter) if sphinx.version_info < (1, 4, 2): # this is a really ugly hack to supress a warning that sphinx 1.4 # generates when overriding an existing directive (which is *desired* # behavior here). As of sphinx v1.4.2, this has been fixed: # https://github.com/sphinx-doc/sphinx/issues/2451 # But we leave it in for 1.4.0/1.4.1 . But if the "needs_sphinx" is # eventually updated to >= 1.4.2, this should be removed entirely (in # favor of the line in the "else" clause) _oldwarn = app._warning _oldwarncount = app._warncount try: try: # *this* is in a try/finally because we don't want to force six as # a real dependency. In sphinx 1.4, six is a prerequisite, so # there's no issue. But in older sphinxes this may not be true... # but the inderlying warning is absent anyway so we let it slide. from six import StringIO app._warning = StringIO() except ImportError: pass app.add_autodocumenter(AttributeDocumenter) finally: app._warning = _oldwarn app._warncount = _oldwarncount else: suppress_warnigns_orig = app.config.suppress_warnings[:] if 'app.add_directive' not in app.config.suppress_warnings: app.config.suppress_warnings.append('app.add_directive') try: app.add_autodocumenter(AttributeDocumenter) finally: app.config.suppress_warnings = suppress_warnigns_orig montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/automodapi/automodapi.py0000644000077000000240000003665113137204755031432 0ustar tomstaff00000000000000# Licensed under a 3-clause BSD style license - see LICENSE.rst """ This directive takes a single argument that must be a module or package. It will produce a block of documentation that includes the docstring for the package, an :ref:`automodsumm` directive, and an :ref:`automod-diagram` if there are any classes in the module. If only the main docstring of the module/package is desired in the documentation, use `automodule`_ instead of `automodapi`_. It accepts the following options: * ``:include-all-objects:`` If present, include not just functions and classes, but all objects. This includes variables, for which a possible docstring after the variable definition will be shown. * ``:no-inheritance-diagram:`` If present, the inheritance diagram will not be shown even if the module/package has classes. * ``:skip: str`` This option results in the specified object being skipped, that is the object will *not* be included in the generated documentation. This option may appear any number of times to skip multiple objects. * ``:no-main-docstr:`` If present, the docstring for the module/package will not be generated. The function and class tables will still be used, however. * ``:headings: str`` Specifies the characters (in one string) used as the heading levels used for the generated section. This must have at least 2 characters (any after 2 will be ignored). This also *must* match the rest of the documentation on this page for sphinx to be happy. Defaults to "-^", which matches the convention used for Python's documentation, assuming the automodapi call is inside a top-level section (which usually uses '='). * ``:no-heading:`` If specified do not create a top level heading for the section. That is, do not create a title heading with text like "packagename Package". The actual docstring for the package/module will still be shown, though, unless ``:no-main-docstr:`` is given. * ``:allowed-package-names: str`` Specifies the packages that functions/classes documented here are allowed to be from, as comma-separated list of package names. If not given, only objects that are actually in a subpackage of the package currently being documented are included. * ``:inherited-members:`` / ``:no-inherited-members:`` The global sphinx configuration option ``automodsumm_inherited_members`` decides if members that a class inherits from a base class are included in the generated documentation. The option ``:inherited-members:`` or ``:no-inherited-members:`` allows the user to overrride the global setting. This extension also adds three sphinx configuration options: * ``automodapi_toctreedirnm`` This must be a string that specifies the name of the directory the automodsumm generated documentation ends up in. This directory path should be relative to the documentation root (e.g., same place as ``index.rst``). Defaults to ``'api'``. * ``automodapi_writereprocessed`` Should be a bool, and if `True`, will cause `automodapi`_ to write files with any `automodapi`_ sections replaced with the content Sphinx processes after `automodapi`_ has run. The output files are not actually used by sphinx, so this option is only for figuring out the cause of sphinx warnings or other debugging. Defaults to `False`. * ``automodsumm_inherited_members`` Should be a bool and if ``True`` members that a class inherits from a base class are included in the generated documentation. Defaults to ``False``. .. _automodule: http://sphinx-doc.org/latest/ext/autodoc.html?highlight=automodule#directive-automodule """ # Implementation note: # The 'automodapi' directive is not actually implemented as a docutils # directive. Instead, this extension searches for the 'automodapi' text in # all sphinx documents, and replaces it where necessary from a template built # into this extension. This is necessary because automodsumm (and autosummary) # use the "builder-inited" event, which comes before the directives are # actually built. import inspect import io import os import re import sys from .utils import find_mod_objs if sys.version_info[0] == 3: text_type = str else: text_type = unicode automod_templ_modheader = """ {modname} {pkgormod} {modhds}{pkgormodhds} {automoduleline} """ automod_templ_classes = """ Classes {clshds} .. automodsumm:: {modname} :classes-only: {clsfuncoptions} """ automod_templ_funcs = """ Functions {funchds} .. automodsumm:: {modname} :functions-only: {clsfuncoptions} """ automod_templ_vars = """ Variables {otherhds} .. automodsumm:: {modname} :variables-only: {clsfuncoptions} """ automod_templ_inh = """ Class Inheritance Diagram {clsinhsechds} .. automod-diagram:: {modname} :private-bases: :parts: 1 {allowedpkgnms} {skip} """ _automodapirex = re.compile(r'^(?:\.\.\s+automodapi::\s*)([A-Za-z0-9_.]+)' r'\s*$((?:\n\s+:[a-zA-Z_\-]+:.*$)*)', flags=re.MULTILINE) # the last group of the above regex is intended to go into finall with the below _automodapiargsrex = re.compile(r':([a-zA-Z_\-]+):(.*)$', flags=re.MULTILINE) def automodapi_replace(sourcestr, app, dotoctree=True, docname=None, warnings=True): """ Replaces `sourcestr`'s entries of ".. automdapi::" with the automodapi template form based on provided options. This is used with the sphinx event 'source-read' to replace `automodapi`_ entries before sphinx actually processes them, as automodsumm needs the code to be present to generate stub documentation. Parameters ---------- sourcestr : str The string with sphinx source to be checked for automodapi replacement. app : `sphinx.application.Application` The sphinx application. dotoctree : bool If `True`, a ":toctree:" option will be added in the ".. automodsumm::" sections of the template, pointing to the appropriate "generated" directory based on the Astropy convention (e.g. in ``docs/api``) docname : str The name of the file for this `sourcestr` (if known - if not, it can be `None`). If not provided and `dotoctree` is `True`, the generated files may end up in the wrong place. warnings : bool If `False`, all warnings that would normally be issued are silenced. Returns ------- newstr :str The string with automodapi entries replaced with the correct sphinx markup. """ spl = _automodapirex.split(sourcestr) if len(spl) > 1: # automodsumm is in this document # Use app.srcdir because api folder should be inside source folder not # at folder where sphinx is run. if dotoctree: toctreestr = ':toctree: ' api_dir = os.path.join(app.srcdir, app.config.automodapi_toctreedirnm) if docname is None: doc_path = '.' else: doc_path = os.path.join(app.srcdir, docname) toctreestr += os.path.relpath(api_dir, os.path.dirname(doc_path)) else: toctreestr = '' newstrs = [spl[0]] for grp in range(len(spl) // 3): modnm = spl[grp * 3 + 1] # find where this is in the document for warnings if docname is None: location = None else: location = (docname, spl[0].count('\n')) # initialize default options toskip = [] inhdiag = maindocstr = top_head = True hds = '-^' allowedpkgnms = [] allowothers = False # look for actual options unknownops = [] inherited_members = None for opname, args in _automodapiargsrex.findall(spl[grp * 3 + 2]): if opname == 'skip': toskip.append(args.strip()) elif opname == 'no-inheritance-diagram': inhdiag = False elif opname == 'no-main-docstr': maindocstr = False elif opname == 'headings': hds = args elif opname == 'no-heading': top_head = False elif opname == 'allowed-package-names': allowedpkgnms.append(args.strip()) elif opname == 'inherited-members': inherited_members = True elif opname == 'no-inherited-members': inherited_members = False elif opname == 'include-all-objects': allowothers = True else: unknownops.append(opname) # join all the allowedpkgnms if len(allowedpkgnms) == 0: allowedpkgnms = '' onlylocals = True else: allowedpkgnms = ':allowed-package-names: ' + ','.join(allowedpkgnms) onlylocals = allowedpkgnms # get the two heading chars if len(hds) < 2: msg = 'Not enough headings (got {0}, need 2), using default -^' if warnings: app.warn(msg.format(len(hds)), location) hds = '-^' h1, h2 = hds.lstrip()[:2] # tell sphinx that the remaining args are invalid. if len(unknownops) > 0 and app is not None: opsstrs = ','.join(unknownops) msg = 'Found additional options ' + opsstrs + ' in automodapi.' if warnings: app.warn(msg, location) ispkg, hascls, hasfuncs, hasother = _mod_info( modnm, toskip, onlylocals=onlylocals) # add automodule directive only if no-main-docstr isn't present if maindocstr: automodline = '.. automodule:: {modname}'.format(modname=modnm) else: automodline = '' if top_head: newstrs.append(automod_templ_modheader.format( modname=modnm, modhds=h1 * len(modnm), pkgormod='Package' if ispkg else 'Module', pkgormodhds=h1 * (8 if ispkg else 7), automoduleline=automodline)) # noqa else: newstrs.append(automod_templ_modheader.format( modname='', modhds='', pkgormod='', pkgormodhds='', automoduleline=automodline)) # construct the options for the class/function sections # start out indented at 4 spaces, but need to keep the indentation. clsfuncoptions = [] if toctreestr: clsfuncoptions.append(toctreestr) if toskip: clsfuncoptions.append(':skip: ' + ','.join(toskip)) if allowedpkgnms: clsfuncoptions.append(allowedpkgnms) if hascls: # This makes no sense unless there are classes. if inherited_members is True: clsfuncoptions.append(':inherited-members:') if inherited_members is False: clsfuncoptions.append(':no-inherited-members:') clsfuncoptionstr = '\n '.join(clsfuncoptions) if hasfuncs: newstrs.append(automod_templ_funcs.format( modname=modnm, funchds=h2 * 9, clsfuncoptions=clsfuncoptionstr)) if hascls: newstrs.append(automod_templ_classes.format( modname=modnm, clshds=h2 * 7, clsfuncoptions=clsfuncoptionstr)) if allowothers and hasother: newstrs.append(automod_templ_vars.format( modname=modnm, otherhds=h2 * 9, clsfuncoptions=clsfuncoptionstr)) if inhdiag and hascls: # add inheritance diagram if any classes are in the module if toskip: clsskip = ':skip: ' + ','.join(toskip) else: clsskip = '' diagram_entry = automod_templ_inh.format( modname=modnm, clsinhsechds=h2 * 25, allowedpkgnms=allowedpkgnms, skip=clsskip) diagram_entry = diagram_entry.replace(' \n', '') newstrs.append(diagram_entry) newstrs.append(spl[grp * 3 + 3]) newsourcestr = ''.join(newstrs) if app.config.automodapi_writereprocessed: # sometimes they are unicode, sometimes not, depending on how # sphinx has processed things if isinstance(newsourcestr, text_type): ustr = newsourcestr else: ustr = newsourcestr.decode(app.config.source_encoding) if docname is None: with io.open(os.path.join(app.srcdir, 'unknown.automodapi'), 'a', encoding='utf8') as f: f.write(u'\n**NEW DOC**\n\n') f.write(ustr) else: env = app.builder.env # Determine the filename associated with this doc (specifically # the extension) filename = docname + os.path.splitext(env.doc2path(docname))[1] filename += '.automodapi' with io.open(os.path.join(app.srcdir, filename), 'w', encoding='utf8') as f: f.write(ustr) return newsourcestr else: return sourcestr def _mod_info(modname, toskip=[], onlylocals=True): """ Determines if a module is a module or a package and whether or not it has classes or functions. """ hascls = hasfunc = hasother = False for localnm, fqnm, obj in zip(*find_mod_objs(modname, onlylocals=onlylocals)): if localnm not in toskip: hascls = hascls or inspect.isclass(obj) hasfunc = hasfunc or inspect.isroutine(obj) hasother = hasother or (not inspect.isclass(obj) and not inspect.isroutine(obj)) if hascls and hasfunc and hasother: break # find_mod_objs has already imported modname # TODO: There is probably a cleaner way to do this, though this is pretty # reliable for all Python versions for most cases that we care about. pkg = sys.modules[modname] ispkg = (hasattr(pkg, '__file__') and isinstance(pkg.__file__, str) and os.path.split(pkg.__file__)[1].startswith('__init__.py')) return ispkg, hascls, hasfunc, hasother def process_automodapi(app, docname, source): source[0] = automodapi_replace(source[0], app, True, docname) def setup(app): app.setup_extension('sphinx.ext.autosummary') # Note: we use __name__ here instead of just writing the module name in # case this extension is bundled into another package from . import automodsumm app.setup_extension(automodsumm.__name__) app.connect('source-read', process_automodapi) app.add_config_value('automodapi_toctreedirnm', 'api', True) app.add_config_value('automodapi_writereprocessed', False, True) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/automodapi/automodsumm.py0000644000077000000240000006265213137204755031642 0ustar tomstaff00000000000000# Licensed under a 3-clause BSD style license - see LICENSE.rst """ This directive will produce an "autosummary"-style table for public attributes of a specified module. See the `sphinx.ext.autosummary`_ extension for details on this process. The main difference from the `autosummary`_ directive is that `autosummary`_ requires manually inputting all attributes that appear in the table, while this captures the entries automatically. This directive requires a single argument that must be a module or package. It also accepts any options supported by the `autosummary`_ directive- see `sphinx.ext.autosummary`_ for details. It also accepts some additional options: * ``:classes-only:`` If present, the autosummary table will only contain entries for classes. This cannot be used at the same time with ``:functions-only:`` or ``:variables-only:``. * ``:functions-only:`` If present, the autosummary table will only contain entries for functions. This cannot be used at the same time with ``:classes-only:`` or ``:variables-only:``. * ``:variables-only:`` If present, the autosummary table will only contain entries for variables (everything except functions and classes). This cannot be used at the same time with ``:classes-only:`` or ``:functions-only:``. * ``:skip: obj1, [obj2, obj3, ...]`` If present, specifies that the listed objects should be skipped and not have their documentation generated, nor be included in the summary table. * ``:allowed-package-names: pkgormod1, [pkgormod2, pkgormod3, ...]`` Specifies the packages that functions/classes documented here are allowed to be from, as comma-separated list of package names. If not given, only objects that are actually in a subpackage of the package currently being documented are included. * ``:inherited-members:`` or ``:no-inherited-members:`` The global sphinx configuration option ``automodsumm_inherited_members`` decides if members that a class inherits from a base class are included in the generated documentation. The flags ``:inherited-members:`` or ``:no-inherited-members:`` allows overrriding this global setting. This extension also adds two sphinx configuration options: * ``automodsumm_writereprocessed`` Should be a bool, and if ``True``, will cause `automodsumm`_ to write files with any ``automodsumm`` sections replaced with the content Sphinx processes after ``automodsumm`` has run. The output files are not actually used by sphinx, so this option is only for figuring out the cause of sphinx warnings or other debugging. Defaults to ``False``. * ``automodsumm_inherited_members`` Should be a bool and if ``True``, will cause `automodsumm`_ to document class members that are inherited from a base class. This value can be overriden for any particular automodsumm directive by including the ``:inherited-members:`` or ``:no-inherited-members:`` options. Defaults to ``False``. .. _sphinx.ext.autosummary: http://sphinx-doc.org/latest/ext/autosummary.html .. _autosummary: http://sphinx-doc.org/latest/ext/autosummary.html#directive-autosummary .. _automod-diagram: automod-diagram directive ========================= This directive will produce an inheritance diagram like that of the `sphinx.ext.inheritance_diagram`_ extension. This directive requires a single argument that must be a module or package. It accepts no options. .. note:: Like 'inheritance-diagram', 'automod-diagram' requires `graphviz `_ to generate the inheritance diagram. .. _sphinx.ext.inheritance_diagram: http://sphinx-doc.org/latest/ext/inheritance.html """ import inspect import os import re import io from sphinx.ext.autosummary import Autosummary from sphinx.ext.inheritance_diagram import InheritanceDiagram from docutils.parsers.rst.directives import flag from .utils import find_mod_objs, cleanup_whitespace def _str_list_converter(argument): """ A directive option conversion function that converts the option into a list of strings. Used for 'skip' option. """ if argument is None: return [] else: return [s.strip() for s in argument.split(',')] class Automodsumm(Autosummary): required_arguments = 1 optional_arguments = 0 final_argument_whitespace = False has_content = False option_spec = dict(Autosummary.option_spec) option_spec['functions-only'] = flag option_spec['classes-only'] = flag option_spec['variables-only'] = flag option_spec['skip'] = _str_list_converter option_spec['allowed-package-names'] = _str_list_converter option_spec['inherited-members'] = flag option_spec['no-inherited-members'] = flag def run(self): env = self.state.document.settings.env modname = self.arguments[0] self.warnings = [] nodelist = [] try: localnames, fqns, objs = find_mod_objs(modname) except ImportError: self.warnings = [] self.warn("Couldn't import module " + modname) return self.warnings try: # set self.content to trick the autosummary internals. # Be sure to respect functions-only and classes-only. funconly = 'functions-only' in self.options clsonly = 'classes-only' in self.options varonly = 'variables-only' in self.options if [clsonly, funconly, varonly].count(True) > 1: self.warning('more than one of functions-only, classes-only, ' 'or variables-only defined. Ignoring.') clsonly = funconly = varonly = False skipnames = [] if 'skip' in self.options: option_skipnames = set(self.options['skip']) for lnm in localnames: if lnm in option_skipnames: option_skipnames.remove(lnm) skipnames.append(lnm) if len(option_skipnames) > 0: self.warn('Tried to skip objects {objs} in module {mod}, ' 'but they were not present. Ignoring.' .format(objs=option_skipnames, mod=modname)) if funconly: cont = [] for nm, obj in zip(localnames, objs): if nm not in skipnames and inspect.isroutine(obj): cont.append(nm) elif clsonly: cont = [] for nm, obj in zip(localnames, objs): if nm not in skipnames and inspect.isclass(obj): cont.append(nm) elif varonly: cont = [] for nm, obj in zip(localnames, objs): if nm not in skipnames and not (inspect.isclass(obj) or inspect.isroutine(obj)): cont.append(nm) else: cont = [nm for nm in localnames if nm not in skipnames] self.content = cont # for some reason, even though ``currentmodule`` is substituted in, # sphinx doesn't necessarily recognize this fact. So we just force # it internally, and that seems to fix things env.temp_data['py:module'] = modname env.ref_context['py:module'] = modname # can't use super because Sphinx/docutils has trouble return # super(Autosummary,self).run() nodelist.extend(Autosummary.run(self)) return self.warnings + nodelist finally: # has_content = False for the Automodsumm self.content = [] def get_items(self, names): self.genopt['imported-members'] = True return Autosummary.get_items(self, names) # <-------------------automod-diagram stuff-----------------------------------> class Automoddiagram(InheritanceDiagram): option_spec = dict(InheritanceDiagram.option_spec) option_spec['allowed-package-names'] = _str_list_converter option_spec['skip'] = _str_list_converter def run(self): try: ols = self.options.get('allowed-package-names', []) ols = True if len(ols) == 0 else ols # if none are given, assume only local nms, objs = find_mod_objs(self.arguments[0], onlylocals=ols)[1:] except ImportError: self.warnings = [] self.warn("Couldn't import module " + self.arguments[0]) return self.warnings # Check if some classes should be skipped skip = self.options.get('skip', []) clsnms = [] for n, o in zip(nms, objs): if n.split('.')[-1] in skip: continue if inspect.isclass(o): clsnms.append(n) oldargs = self.arguments try: if len(clsnms) > 0: self.arguments = [' '.join(clsnms)] return InheritanceDiagram.run(self) finally: self.arguments = oldargs # <---------------------automodsumm generation stuff--------------------------> def process_automodsumm_generation(app): env = app.builder.env filestosearch = [] for docname in env.found_docs: filename = env.doc2path(docname) if os.path.isfile(filename): filestosearch.append(docname + os.path.splitext(filename)[1]) liness = [] for sfn in filestosearch: lines = automodsumm_to_autosummary_lines(sfn, app) liness.append(lines) if app.config.automodsumm_writereprocessed: if lines: # empty list means no automodsumm entry is in the file outfn = os.path.join(app.srcdir, sfn) + '.automodsumm' with open(outfn, 'w') as f: for l in lines: f.write(l) f.write('\n') for sfn, lines in zip(filestosearch, liness): suffix = os.path.splitext(sfn)[1] if len(lines) > 0: generate_automodsumm_docs( lines, sfn, builder=app.builder, warn=app.warn, info=app.info, suffix=suffix, base_path=app.srcdir, inherited_members=app.config.automodsumm_inherited_members) # _automodsummrex = re.compile(r'^(\s*)\.\. automodsumm::\s*([A-Za-z0-9_.]+)\s*' # r'\n\1(\s*)(\S|$)', re.MULTILINE) _lineendrex = r'(?:\n|$)' _hdrex = r'^\n?(\s*)\.\. automodsumm::\s*(\S+)\s*' + _lineendrex _oprex1 = r'(?:\1(\s+)\S.*' + _lineendrex + ')' _oprex2 = r'(?:\1\4\S.*' + _lineendrex + ')' _automodsummrex = re.compile(_hdrex + '(' + _oprex1 + '?' + _oprex2 + '*)', re.MULTILINE) def automodsumm_to_autosummary_lines(fn, app): """ Generates lines from a file with an "automodsumm" entry suitable for feeding into "autosummary". Searches the provided file for `automodsumm` directives and returns a list of lines specifying the `autosummary` commands for the modules requested. This does *not* return the whole file contents - just an autosummary section in place of any :automodsumm: entries. Note that any options given for `automodsumm` are also included in the generated `autosummary` section. Parameters ---------- fn : str The name of the file to search for `automodsumm` entries. app : sphinx.application.Application The sphinx Application object Return ------ lines : list of str Lines for all `automodsumm` entries with the entries replaced by `autosummary` and the module's members added. """ fullfn = os.path.join(app.builder.env.srcdir, fn) with io.open(fullfn, encoding='utf8') as fr: # Note: we use __name__ here instead of just writing the module name in # case this extension is bundled into another package from . import automodapi try: extensions = app.extensions except AttributeError: # Sphinx <1.6 extensions = app._extensions if automodapi.__name__ in extensions: # Must do the automodapi on the source to get the automodsumm # that might be in there docname = os.path.splitext(fn)[0] filestr = automodapi.automodapi_replace(fr.read(), app, True, docname, False) else: filestr = fr.read() spl = _automodsummrex.split(filestr) # 0th entry is the stuff before the first automodsumm line indent1s = spl[1::5] mods = spl[2::5] opssecs = spl[3::5] indent2s = spl[4::5] remainders = spl[5::5] # only grab automodsumm sections and convert them to autosummary with the # entries for all the public objects newlines = [] # loop over all automodsumms in this document for i, (i1, i2, modnm, ops, rem) in enumerate(zip(indent1s, indent2s, mods, opssecs, remainders)): allindent = i1 + (' ' if i2 is None else i2) # filter out functions-only, classes-only, and ariables-only # options if present. oplines = ops.split('\n') toskip = [] allowedpkgnms = [] funcsonly = clssonly = varsonly = False for i, ln in reversed(list(enumerate(oplines))): if ':functions-only:' in ln: funcsonly = True del oplines[i] if ':classes-only:' in ln: clssonly = True del oplines[i] if ':variables-only:' in ln: varsonly = True del oplines[i] if ':skip:' in ln: toskip.extend(_str_list_converter(ln.replace(':skip:', ''))) del oplines[i] if ':allowed-package-names:' in ln: allowedpkgnms.extend(_str_list_converter(ln.replace(':allowed-package-names:', ''))) del oplines[i] if [funcsonly, clssonly, varsonly].count(True) > 1: msg = ('Defined more than one of functions-only, classes-only, ' 'and variables-only. Skipping this directive.') lnnum = sum([spl[j].count('\n') for j in range(i * 5 + 1)]) app.warn('[automodsumm]' + msg, (fn, lnnum)) continue # Use the currentmodule directive so we can just put the local names # in the autosummary table. Note that this doesn't always seem to # actually "take" in Sphinx's eyes, so in `Automodsumm.run`, we have to # force it internally, as well. newlines.extend([i1 + '.. currentmodule:: ' + modnm, '', '.. autosummary::']) newlines.extend(oplines) ols = True if len(allowedpkgnms) == 0 else allowedpkgnms for nm, fqn, obj in zip(*find_mod_objs(modnm, onlylocals=ols)): if nm in toskip: continue if funcsonly and not inspect.isroutine(obj): continue if clssonly and not inspect.isclass(obj): continue if varsonly and (inspect.isclass(obj) or inspect.isroutine(obj)): continue newlines.append(allindent + nm) # add one newline at the end of the autosummary block newlines.append('') return newlines def generate_automodsumm_docs(lines, srcfn, suffix='.rst', warn=None, info=None, base_path=None, builder=None, template_dir=None, inherited_members=False): """ This function is adapted from `sphinx.ext.autosummary.generate.generate_autosummmary_docs` to generate source for the automodsumm directives that should be autosummarized. Unlike generate_autosummary_docs, this function is called one file at a time. """ from sphinx.jinja2glue import BuiltinTemplateLoader from sphinx.ext.autosummary import import_by_name, get_documenter from sphinx.ext.autosummary.generate import (_simple_info, _simple_warn) from sphinx.util.osutil import ensuredir from sphinx.util.inspect import safe_getattr from jinja2 import FileSystemLoader, TemplateNotFound from jinja2.sandbox import SandboxedEnvironment from .utils import find_autosummary_in_lines_for_automodsumm as find_autosummary_in_lines if info is None: info = _simple_info if warn is None: warn = _simple_warn # info('[automodsumm] generating automodsumm for: ' + srcfn) # Create our own templating environment - here we use Astropy's # templates rather than the default autosummary templates, in order to # allow docstrings to be shown for methods. template_dirs = [os.path.join(os.path.dirname(__file__), 'templates'), os.path.join(base_path, '_templates')] if builder is not None: # allow the user to override the templates template_loader = BuiltinTemplateLoader() template_loader.init(builder, dirs=template_dirs) else: if template_dir: template_dirs.insert(0, template_dir) template_loader = FileSystemLoader(template_dirs) template_env = SandboxedEnvironment(loader=template_loader) # read # items = find_autosummary_in_files(sources) items = find_autosummary_in_lines(lines, filename=srcfn) if len(items) > 0: msg = '[automodsumm] {1}: found {0} automodsumm entries to generate' info(msg.format(len(items), srcfn)) # gennms = [item[0] for item in items] # if len(gennms) > 20: # gennms = gennms[:10] + ['...'] + gennms[-10:] # info('[automodsumm] generating autosummary for: ' + ', '.join(gennms)) # remove possible duplicates items = list(set(items)) # keep track of new files new_files = [] # write for name, path, template_name, inherited_mem in sorted(items): if path is None: # The corresponding autosummary:: directive did not have # a :toctree: option continue path = os.path.abspath(os.path.join(base_path, path)) ensuredir(path) try: import_by_name_values = import_by_name(name) except ImportError as e: warn('[automodsumm] failed to import %r: %s' % (name, e)) continue # if block to accommodate Sphinx's v1.2.2 and v1.2.3 respectively if len(import_by_name_values) == 3: name, obj, parent = import_by_name_values elif len(import_by_name_values) == 4: name, obj, parent, module_name = import_by_name_values fn = os.path.join(path, name + suffix) # skip it if it exists if os.path.isfile(fn): continue new_files.append(fn) f = open(fn, 'w') try: doc = get_documenter(obj, parent) if template_name is not None: template = template_env.get_template(template_name) else: tmplstr = 'autosummary_core/%s.rst' try: template = template_env.get_template(tmplstr % doc.objtype) except TemplateNotFound: template = template_env.get_template(tmplstr % 'base') def get_members_mod(obj, typ, include_public=[]): """ typ = None -> all """ items = [] for name in dir(obj): try: documenter = get_documenter(safe_getattr(obj, name), obj) except AttributeError: continue if typ is None or documenter.objtype == typ: items.append(name) public = [x for x in items if x in include_public or not x.startswith('_')] return public, items def get_members_class(obj, typ, include_public=[], include_base=False): """ typ = None -> all include_base -> include attrs that are from a base class """ items = [] # using dir gets all of the attributes, including the elements # from the base class, otherwise use __slots__ or __dict__ if include_base: names = dir(obj) else: if hasattr(obj, '__slots__'): names = tuple(getattr(obj, '__slots__')) else: names = getattr(obj, '__dict__').keys() for name in names: try: documenter = get_documenter(safe_getattr(obj, name), obj) except AttributeError: continue if typ is None or documenter.objtype == typ: items.append(name) public = [x for x in items if x in include_public or not x.startswith('_')] return public, items ns = {} if doc.objtype == 'module': ns['members'] = get_members_mod(obj, None) ns['functions'], ns['all_functions'] = \ get_members_mod(obj, 'function') ns['classes'], ns['all_classes'] = \ get_members_mod(obj, 'class') ns['exceptions'], ns['all_exceptions'] = \ get_members_mod(obj, 'exception') elif doc.objtype == 'class': if inherited_mem is not None: # option set in this specifc directive include_base = inherited_mem else: # use default value include_base = inherited_members api_class_methods = ['__init__', '__call__'] ns['members'] = get_members_class(obj, None, include_base=include_base) ns['methods'], ns['all_methods'] = \ get_members_class(obj, 'method', api_class_methods, include_base=include_base) ns['attributes'], ns['all_attributes'] = \ get_members_class(obj, 'attribute', include_base=include_base) ns['methods'].sort() ns['attributes'].sort() parts = name.split('.') if doc.objtype in ('method', 'attribute'): mod_name = '.'.join(parts[:-2]) cls_name = parts[-2] obj_name = '.'.join(parts[-2:]) ns['class'] = cls_name else: mod_name, obj_name = '.'.join(parts[:-1]), parts[-1] ns['fullname'] = name ns['module'] = mod_name ns['objname'] = obj_name ns['name'] = parts[-1] ns['objtype'] = doc.objtype ns['underline'] = len(obj_name) * '=' # We now check whether a file for reference footnotes exists for # the module being documented. We first check if the # current module is a file or a directory, as this will give a # different path for the reference file. For example, if # documenting astropy.wcs then the reference file is at # ../wcs/references.txt, while if we are documenting # astropy.config.logging_helper (which is at # astropy/config/logging_helper.py) then the reference file is set # to ../config/references.txt if '.' in mod_name: mod_name_dir = mod_name.replace('.', '/').split('/', 1)[1] else: mod_name_dir = mod_name if not os.path.isdir(os.path.join(base_path, mod_name_dir)) \ and os.path.isdir(os.path.join(base_path, mod_name_dir.rsplit('/', 1)[0])): mod_name_dir = mod_name_dir.rsplit('/', 1)[0] # We then have to check whether it exists, and if so, we pass it # to the template. if os.path.exists(os.path.join(base_path, mod_name_dir, 'references.txt')): # An important subtlety here is that the path we pass in has # to be relative to the file being generated, so we have to # figure out the right number of '..'s ndirsback = path.replace(base_path, '').count('/') ref_file_rel_segments = ['..'] * ndirsback ref_file_rel_segments.append(mod_name_dir) ref_file_rel_segments.append('references.txt') ns['referencefile'] = os.path.join(*ref_file_rel_segments) rendered = template.render(**ns) f.write(cleanup_whitespace(rendered)) finally: f.close() def setup(app): # need autodoc fixes # Note: we use __name__ here instead of just writing the module name in # case this extension is bundled into another package from . import autodoc_enhancements app.setup_extension(autodoc_enhancements.__name__) # need inheritance-diagram for automod-diagram app.setup_extension('sphinx.ext.inheritance_diagram') app.add_directive('automod-diagram', Automoddiagram) app.add_directive('automodsumm', Automodsumm) app.connect('builder-inited', process_automodsumm_generation) app.add_config_value('automodsumm_writereprocessed', False, True) app.add_config_value('automodsumm_inherited_members', False, 'env') montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/automodapi/smart_resolver.py0000644000077000000240000000717713137204755032340 0ustar tomstaff00000000000000# Licensed under a 3-clause BSD style license - see LICENSE.rst """ The classes in the astropy docs are documented by their API location, which is not necessarily where they are defined in the source. This causes a problem when certain automated features of the doc build, such as the inheritance diagrams or the `Bases` list of a class reference a class by its canonical location rather than its "user" location. In the `autodoc-process-docstring` event, a mapping from the actual name to the API name is maintained. Later, in the `missing-reference` event, unresolved references are looked up in this dictionary and corrected if possible. """ from docutils.nodes import literal, reference def process_docstring(app, what, name, obj, options, lines): if isinstance(obj, type): env = app.env if not hasattr(env, 'class_name_mapping'): env.class_name_mapping = {} mapping = env.class_name_mapping mapping[obj.__module__ + '.' + obj.__name__] = name def missing_reference_handler(app, env, node, contnode): if not hasattr(env, 'class_name_mapping'): env.class_name_mapping = {} mapping = env.class_name_mapping reftype = node['reftype'] reftarget = node['reftarget'] if reftype in ('obj', 'class', 'exc', 'meth'): reftarget = node['reftarget'] suffix = '' if reftarget not in mapping: if '.' in reftarget: front, suffix = reftarget.rsplit('.', 1) else: suffix = reftarget if suffix.startswith('_') and not suffix.startswith('__'): # If this is a reference to a hidden class or method, # we can't link to it, but we don't want to have a # nitpick warning. return node[0].deepcopy() if reftype in ('obj', 'meth') and '.' in reftarget: if front in mapping: reftarget = front suffix = '.' + suffix if (reftype in ('class', ) and '.' in reftarget and reftarget not in mapping): if '.' in front: reftarget, _ = front.rsplit('.', 1) suffix = '.' + suffix reftarget = reftarget + suffix prefix = reftarget.rsplit('.')[0] inventory = env.intersphinx_named_inventory if (reftarget not in mapping and prefix in inventory): if reftarget in inventory[prefix]['py:class']: newtarget = inventory[prefix]['py:class'][reftarget][2] if not node['refexplicit'] and \ '~' not in node.rawsource: contnode = literal(text=reftarget) newnode = reference('', '', internal=True) newnode['reftitle'] = reftarget newnode['refuri'] = newtarget newnode.append(contnode) return newnode if reftarget in mapping: newtarget = mapping[reftarget] + suffix if not node['refexplicit'] and '~' not in node.rawsource: contnode = literal(text=newtarget) newnode = env.domains['py'].resolve_xref( env, node['refdoc'], app.builder, 'class', newtarget, node, contnode) if newnode is not None: newnode['reftitle'] = reftarget return newnode def setup(app): app.connect('autodoc-process-docstring', process_docstring) app.connect('missing-reference', missing_reference_handler) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/automodapi/templates/0000755000077000000240000000000013137205364030676 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/automodapi/templates/autosummary_core/0000755000077000000240000000000013137205364034274 5ustar tomstaff00000000000000././@LongLink0000000000000000000000000000015400000000000011215 Lustar 00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/automodapi/templates/autosummary_core/base.rstmontage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/automodapi/templates/autosummary_core/b0000644000077000000240000000025213137204755034442 0ustar tomstaff00000000000000{% if referencefile %} .. include:: {{ referencefile }} {% endif %} {{ objname }} {{ underline }} .. currentmodule:: {{ module }} .. auto{{ objtype }}:: {{ objname }} ././@LongLink0000000000000000000000000000015500000000000011216 Lustar 00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/automodapi/templates/autosummary_core/class.rstmontage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/automodapi/templates/autosummary_core/c0000644000077000000240000000221113137204755034440 0ustar tomstaff00000000000000{% if referencefile %} .. include:: {{ referencefile }} {% endif %} {{ objname }} {{ underline }} .. currentmodule:: {{ module }} .. autoclass:: {{ objname }} :show-inheritance: {% if '__init__' in methods %} {% set caught_result = methods.remove('__init__') %} {% endif %} {% block attributes_summary %} {% if attributes %} .. rubric:: Attributes Summary .. autosummary:: {% for item in attributes %} ~{{ name }}.{{ item }} {%- endfor %} {% endif %} {% endblock %} {% block methods_summary %} {% if methods %} .. rubric:: Methods Summary .. autosummary:: {% for item in methods %} ~{{ name }}.{{ item }} {%- endfor %} {% endif %} {% endblock %} {% block attributes_documentation %} {% if attributes %} .. rubric:: Attributes Documentation {% for item in attributes %} .. autoattribute:: {{ item }} {%- endfor %} {% endif %} {% endblock %} {% block methods_documentation %} {% if methods %} .. rubric:: Methods Documentation {% for item in methods %} .. automethod:: {{ item }} {%- endfor %} {% endif %} {% endblock %} ././@LongLink0000000000000000000000000000015600000000000011217 Lustar 00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/automodapi/templates/autosummary_core/module.rstmontage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/automodapi/templates/autosummary_core/m0000644000077000000240000000127713137204755034465 0ustar tomstaff00000000000000{% if referencefile %} .. include:: {{ referencefile }} {% endif %} {{ objname }} {{ underline }} .. automodule:: {{ fullname }} {% block functions %} {% if functions %} .. rubric:: Functions .. autosummary:: {% for item in functions %} {{ item }} {%- endfor %} {% endif %} {% endblock %} {% block classes %} {% if classes %} .. rubric:: Classes .. autosummary:: {% for item in classes %} {{ item }} {%- endfor %} {% endif %} {% endblock %} {% block exceptions %} {% if exceptions %} .. rubric:: Exceptions .. autosummary:: {% for item in exceptions %} {{ item }} {%- endfor %} {% endif %} {% endblock %} montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/automodapi/utils.py0000644000077000000240000001574413137204755030430 0ustar tomstaff00000000000000import inspect import sys import re import os from warnings import warn from sphinx.ext.autosummary.generate import find_autosummary_in_docstring if sys.version_info[0] >= 3: def iteritems(dictionary): return dictionary.items() else: def iteritems(dictionary): return dictionary.iteritems() # We use \n instead of os.linesep because even on Windows, the generated files # use \n as the newline character. SPACE_NEWLINE = ' \n' SINGLE_NEWLINE = '\n' DOUBLE_NEWLINE = '\n\n' TRIPLE_NEWLINE = '\n\n\n' def cleanup_whitespace(text): """ Make sure there are never more than two consecutive newlines, and that there are no trailing whitespaces. """ # Get rid of overall leading/trailing whitespace text = text.strip() + '\n' # Get rid of trailing whitespace on each line while SPACE_NEWLINE in text: text = text.replace(SPACE_NEWLINE, SINGLE_NEWLINE) # Avoid too many consecutive newlines while TRIPLE_NEWLINE in text: text = text.replace(TRIPLE_NEWLINE, DOUBLE_NEWLINE) return text def find_mod_objs(modname, onlylocals=False): """ Returns all the public attributes of a module referenced by name. .. note:: The returned list *not* include subpackages or modules of `modname`,nor does it include private attributes (those that beginwith '_' or are not in `__all__`). Parameters ---------- modname : str The name of the module to search. onlylocals : bool If True, only attributes that are either members of `modname` OR one of its modules or subpackages will be included. Returns ------- localnames : list of str A list of the names of the attributes as they are named in the module `modname` . fqnames : list of str A list of the full qualified names of the attributes (e.g., ``astropy.utils.misc.find_mod_objs``). For attributes that are simple variables, this is based on the local name, but for functions or classes it can be different if they are actually defined elsewhere and just referenced in `modname`. objs : list of objects A list of the actual attributes themselves (in the same order as the other arguments) """ __import__(modname) mod = sys.modules[modname] if hasattr(mod, '__all__'): pkgitems = [(k, mod.__dict__[k]) for k in mod.__all__] else: pkgitems = [(k, mod.__dict__[k]) for k in dir(mod) if k[0] != '_'] # filter out modules and pull the names and objs out ismodule = inspect.ismodule localnames = [k for k, v in pkgitems if not ismodule(v)] objs = [v for k, v in pkgitems if not ismodule(v)] # fully qualified names can be determined from the object's module fqnames = [] for obj, lnm in zip(objs, localnames): if hasattr(obj, '__module__') and hasattr(obj, '__name__'): fqnames.append(obj.__module__ + '.' + obj.__name__) else: fqnames.append(modname + '.' + lnm) if onlylocals: valids = [fqn.startswith(modname) for fqn in fqnames] localnames = [e for i, e in enumerate(localnames) if valids[i]] fqnames = [e for i, e in enumerate(fqnames) if valids[i]] objs = [e for i, e in enumerate(objs) if valids[i]] return localnames, fqnames, objs def find_autosummary_in_lines_for_automodsumm(lines, module=None, filename=None): """Find out what items appear in autosummary:: directives in the given lines. Returns a list of (name, toctree, template, inherited_members) where *name* is a name of an object and *toctree* the :toctree: path of the corresponding autosummary directive (relative to the root of the file name), *template* the value of the :template: option, and *inherited_members* is the value of the :inherited-members: option. *toctree*, *template*, and *inherited_members* are ``None`` if the directive does not have the corresponding options set. .. note:: This is a slightly modified version of ``sphinx.ext.autosummary.generate.find_autosummary_in_lines`` which recognizes the ``inherited-members`` option. """ autosummary_re = re.compile(r'^(\s*)\.\.\s+autosummary::\s*') automodule_re = re.compile( r'^\s*\.\.\s+automodule::\s*([A-Za-z0-9_.]+)\s*$') module_re = re.compile( r'^\s*\.\.\s+(current)?module::\s*([a-zA-Z0-9_.]+)\s*$') autosummary_item_re = re.compile(r'^\s+(~?[_a-zA-Z][a-zA-Z0-9_.]*)\s*.*?') toctree_arg_re = re.compile(r'^\s+:toctree:\s*(.*?)\s*$') template_arg_re = re.compile(r'^\s+:template:\s*(.*?)\s*$') inherited_members_arg_re = re.compile(r'^\s+:inherited-members:\s*$') no_inherited_members_arg_re = re.compile(r'^\s+:no-inherited-members:\s*$') documented = [] toctree = None template = None inherited_members = None current_module = module in_autosummary = False base_indent = "" for line in lines: if in_autosummary: m = toctree_arg_re.match(line) if m: toctree = m.group(1) if filename: toctree = os.path.join(os.path.dirname(filename), toctree) continue m = template_arg_re.match(line) if m: template = m.group(1).strip() continue m = inherited_members_arg_re.match(line) if m: inherited_members = True continue m = no_inherited_members_arg_re.match(line) if m: inherited_members = False continue if line.strip().startswith(':'): warn(line) continue # skip options m = autosummary_item_re.match(line) if m: name = m.group(1).strip() if name.startswith('~'): name = name[1:] if current_module and \ not name.startswith(current_module + '.'): name = "%s.%s" % (current_module, name) documented.append((name, toctree, template, inherited_members)) continue if not line.strip() or line.startswith(base_indent + " "): continue in_autosummary = False m = autosummary_re.match(line) if m: in_autosummary = True base_indent = m.group(1) toctree = None template = None inherited_members = None continue m = automodule_re.search(line) if m: current_module = m.group(1).strip() # recurse into the automodule docstring documented.extend(find_autosummary_in_docstring( current_module, filename=filename)) continue m = module_re.match(line) if m: current_module = m.group(2) continue return documented montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/numpydoc/0000755000077000000240000000000013137205364026374 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/numpydoc/__init__.py0000644000077000000240000000013613137204755030510 0ustar tomstaff00000000000000from __future__ import division, absolute_import, print_function from .numpydoc import setup montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/numpydoc/docscrape.py0000644000077000000240000004323213137204755030720 0ustar tomstaff00000000000000"""Extract reference documentation from the NumPy source tree. """ from __future__ import division, absolute_import, print_function import inspect import textwrap import re import pydoc from warnings import warn import collections import sys class Reader(object): """A line-based string reader. """ def __init__(self, data): """ Parameters ---------- data : str String with lines separated by '\n'. """ if isinstance(data, list): self._str = data else: self._str = data.split('\n') # store string as list of lines self.reset() def __getitem__(self, n): return self._str[n] def reset(self): self._l = 0 # current line nr def read(self): if not self.eof(): out = self[self._l] self._l += 1 return out else: return '' def seek_next_non_empty_line(self): for l in self[self._l:]: if l.strip(): break else: self._l += 1 def eof(self): return self._l >= len(self._str) def read_to_condition(self, condition_func): start = self._l for line in self[start:]: if condition_func(line): return self[start:self._l] self._l += 1 if self.eof(): return self[start:self._l+1] return [] def read_to_next_empty_line(self): self.seek_next_non_empty_line() def is_empty(line): return not line.strip() return self.read_to_condition(is_empty) def read_to_next_unindented_line(self): def is_unindented(line): return (line.strip() and (len(line.lstrip()) == len(line))) return self.read_to_condition(is_unindented) def peek(self, n=0): if self._l + n < len(self._str): return self[self._l + n] else: return '' def is_empty(self): return not ''.join(self._str).strip() class ParseError(Exception): def __str__(self): message = self.message if hasattr(self, 'docstring'): message = "%s in %r" % (message, self.docstring) return message class NumpyDocString(collections.Mapping): def __init__(self, docstring, config={}): orig_docstring = docstring docstring = textwrap.dedent(docstring).split('\n') self._doc = Reader(docstring) self._parsed_data = { 'Signature': '', 'Summary': [''], 'Extended Summary': [], 'Parameters': [], 'Returns': [], 'Yields': [], 'Raises': [], 'Warns': [], 'Other Parameters': [], 'Attributes': [], 'Methods': [], 'See Also': [], 'Notes': [], 'Warnings': [], 'References': '', 'Examples': '', 'index': {} } try: self._parse() except ParseError as e: e.docstring = orig_docstring raise def __getitem__(self, key): return self._parsed_data[key] def __setitem__(self, key, val): if key not in self._parsed_data: warn("Unknown section %s" % key) else: self._parsed_data[key] = val def __iter__(self): return iter(self._parsed_data) def __len__(self): return len(self._parsed_data) def _is_at_section(self): self._doc.seek_next_non_empty_line() if self._doc.eof(): return False l1 = self._doc.peek().strip() # e.g. Parameters if l1.startswith('.. index::'): return True l2 = self._doc.peek(1).strip() # ---------- or ========== return l2.startswith('-'*len(l1)) or l2.startswith('='*len(l1)) def _strip(self, doc): i = 0 j = 0 for i, line in enumerate(doc): if line.strip(): break for j, line in enumerate(doc[::-1]): if line.strip(): break return doc[i:len(doc)-j] def _read_to_next_section(self): section = self._doc.read_to_next_empty_line() while not self._is_at_section() and not self._doc.eof(): if not self._doc.peek(-1).strip(): # previous line was empty section += [''] section += self._doc.read_to_next_empty_line() return section def _read_sections(self): while not self._doc.eof(): data = self._read_to_next_section() name = data[0].strip() if name.startswith('..'): # index section yield name, data[1:] elif len(data) < 2: yield StopIteration else: yield name, self._strip(data[2:]) def _parse_param_list(self, content): r = Reader(content) params = [] while not r.eof(): header = r.read().strip() if ' : ' in header: arg_name, arg_type = header.split(' : ')[:2] else: arg_name, arg_type = header, '' desc = r.read_to_next_unindented_line() desc = dedent_lines(desc) params.append((arg_name, arg_type, desc)) return params _name_rgx = re.compile(r"^\s*(:(?P\w+):`(?P[a-zA-Z0-9_.-]+)`|" r" (?P[a-zA-Z0-9_.-]+))\s*", re.X) def _parse_see_also(self, content): """ func_name : Descriptive text continued text another_func_name : Descriptive text func_name1, func_name2, :meth:`func_name`, func_name3 """ items = [] def parse_item_name(text): """Match ':role:`name`' or 'name'""" m = self._name_rgx.match(text) if m: g = m.groups() if g[1] is None: return g[3], None else: return g[2], g[1] raise ParseError("%s is not a item name" % text) def push_item(name, rest): if not name: return name, role = parse_item_name(name) items.append((name, list(rest), role)) del rest[:] current_func = None rest = [] for line in content: if not line.strip(): continue m = self._name_rgx.match(line) if m and line[m.end():].strip().startswith(':'): push_item(current_func, rest) current_func, line = line[:m.end()], line[m.end():] rest = [line.split(':', 1)[1].strip()] if not rest[0]: rest = [] elif not line.startswith(' '): push_item(current_func, rest) current_func = None if ',' in line: for func in line.split(','): if func.strip(): push_item(func, []) elif line.strip(): current_func = line elif current_func is not None: rest.append(line.strip()) push_item(current_func, rest) return items def _parse_index(self, section, content): """ .. index: default :refguide: something, else, and more """ def strip_each_in(lst): return [s.strip() for s in lst] out = {} section = section.split('::') if len(section) > 1: out['default'] = strip_each_in(section[1].split(','))[0] for line in content: line = line.split(':') if len(line) > 2: out[line[1]] = strip_each_in(line[2].split(',')) return out def _parse_summary(self): """Grab signature (if given) and summary""" if self._is_at_section(): return # If several signatures present, take the last one while True: summary = self._doc.read_to_next_empty_line() summary_str = " ".join([s.strip() for s in summary]).strip() if re.compile('^([\w., ]+=)?\s*[\w\.]+\(.*\)$').match(summary_str): self['Signature'] = summary_str if not self._is_at_section(): continue break if summary is not None: self['Summary'] = summary if not self._is_at_section(): self['Extended Summary'] = self._read_to_next_section() def _parse(self): self._doc.reset() self._parse_summary() sections = list(self._read_sections()) section_names = set([section for section, content in sections]) has_returns = 'Returns' in section_names has_yields = 'Yields' in section_names # We could do more tests, but we are not. Arbitrarily. if has_returns and has_yields: msg = 'Docstring contains both a Returns and Yields section.' raise ValueError(msg) for (section, content) in sections: if not section.startswith('..'): section = (s.capitalize() for s in section.split(' ')) section = ' '.join(section) if section in ('Parameters', 'Returns', 'Yields', 'Raises', 'Warns', 'Other Parameters', 'Attributes', 'Methods'): self[section] = self._parse_param_list(content) elif section.startswith('.. index::'): self['index'] = self._parse_index(section, content) elif section == 'See Also': self['See Also'] = self._parse_see_also(content) else: self[section] = content # string conversion routines def _str_header(self, name, symbol='-'): return [name, len(name)*symbol] def _str_indent(self, doc, indent=4): out = [] for line in doc: out += [' '*indent + line] return out def _str_signature(self): if self['Signature']: return [self['Signature'].replace('*', '\*')] + [''] else: return [''] def _str_summary(self): if self['Summary']: return self['Summary'] + [''] else: return [] def _str_extended_summary(self): if self['Extended Summary']: return self['Extended Summary'] + [''] else: return [] def _str_param_list(self, name): out = [] if self[name]: out += self._str_header(name) for param, param_type, desc in self[name]: if param_type: out += ['%s : %s' % (param, param_type)] else: out += [param] out += self._str_indent(desc) out += [''] return out def _str_section(self, name): out = [] if self[name]: out += self._str_header(name) out += self[name] out += [''] return out def _str_see_also(self, func_role): if not self['See Also']: return [] out = [] out += self._str_header("See Also") last_had_desc = True for func, desc, role in self['See Also']: if role: link = ':%s:`%s`' % (role, func) elif func_role: link = ':%s:`%s`' % (func_role, func) else: link = "`%s`_" % func if desc or last_had_desc: out += [''] out += [link] else: out[-1] += ", %s" % link if desc: out += self._str_indent([' '.join(desc)]) last_had_desc = True else: last_had_desc = False out += [''] return out def _str_index(self): idx = self['index'] out = [] out += ['.. index:: %s' % idx.get('default', '')] for section, references in idx.items(): if section == 'default': continue out += [' :%s: %s' % (section, ', '.join(references))] return out def __str__(self, func_role=''): out = [] out += self._str_signature() out += self._str_summary() out += self._str_extended_summary() for param_list in ('Parameters', 'Returns', 'Yields', 'Other Parameters', 'Raises', 'Warns'): out += self._str_param_list(param_list) out += self._str_section('Warnings') out += self._str_see_also(func_role) for s in ('Notes', 'References', 'Examples'): out += self._str_section(s) for param_list in ('Attributes', 'Methods'): out += self._str_param_list(param_list) out += self._str_index() return '\n'.join(out) def indent(str, indent=4): indent_str = ' '*indent if str is None: return indent_str lines = str.split('\n') return '\n'.join(indent_str + l for l in lines) def dedent_lines(lines): """Deindent a list of lines maximally""" return textwrap.dedent("\n".join(lines)).split("\n") def header(text, style='-'): return text + '\n' + style*len(text) + '\n' class FunctionDoc(NumpyDocString): def __init__(self, func, role='func', doc=None, config={}): self._f = func self._role = role # e.g. "func" or "meth" if doc is None: if func is None: raise ValueError("No function or docstring given") doc = inspect.getdoc(func) or '' NumpyDocString.__init__(self, doc) if not self['Signature'] and func is not None: func, func_name = self.get_func() try: try: signature = str(inspect.signature(func)) except (AttributeError, ValueError): # try to read signature, backward compat for older Python if sys.version_info[0] >= 3: argspec = inspect.getfullargspec(func) else: argspec = inspect.getargspec(func) signature = inspect.formatargspec(*argspec) signature = '%s%s' % (func_name, signature.replace('*', '\*')) except TypeError: signature = '%s()' % func_name self['Signature'] = signature def get_func(self): func_name = getattr(self._f, '__name__', self.__class__.__name__) if inspect.isclass(self._f): func = getattr(self._f, '__call__', self._f.__init__) else: func = self._f return func, func_name def __str__(self): out = '' func, func_name = self.get_func() signature = self['Signature'].replace('*', '\*') roles = {'func': 'function', 'meth': 'method'} if self._role: if self._role not in roles: print("Warning: invalid role %s" % self._role) out += '.. %s:: %s\n \n\n' % (roles.get(self._role, ''), func_name) out += super(FunctionDoc, self).__str__(func_role=self._role) return out class ClassDoc(NumpyDocString): extra_public_methods = ['__call__'] def __init__(self, cls, doc=None, modulename='', func_doc=FunctionDoc, config={}): if not inspect.isclass(cls) and cls is not None: raise ValueError("Expected a class or None, but got %r" % cls) self._cls = cls self.show_inherited_members = config.get( 'show_inherited_class_members', True) if modulename and not modulename.endswith('.'): modulename += '.' self._mod = modulename if doc is None: if cls is None: raise ValueError("No class or documentation string given") doc = pydoc.getdoc(cls) NumpyDocString.__init__(self, doc) if config.get('show_class_members', True): def splitlines_x(s): if not s: return [] else: return s.splitlines() for field, items in [('Methods', self.methods), ('Attributes', self.properties)]: if not self[field]: doc_list = [] for name in sorted(items): try: doc_item = pydoc.getdoc(getattr(self._cls, name)) doc_list.append((name, '', splitlines_x(doc_item))) except AttributeError: pass # method doesn't exist self[field] = doc_list @property def methods(self): if self._cls is None: return [] return [name for name, func in inspect.getmembers(self._cls) if ((not name.startswith('_') or name in self.extra_public_methods) and isinstance(func, collections.Callable) and self._is_show_member(name))] @property def properties(self): if self._cls is None: return [] return [name for name, func in inspect.getmembers(self._cls) if (not name.startswith('_') and (func is None or isinstance(func, property) or inspect.isgetsetdescriptor(func)) and self._is_show_member(name))] def _is_show_member(self, name): if self.show_inherited_members: return True # show all class members if name not in self._cls.__dict__: return False # class member is inherited, we do not show it return True montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/numpydoc/docscrape_sphinx.py0000644000077000000240000002246713137204755032320 0ustar tomstaff00000000000000from __future__ import division, absolute_import, print_function import sys import re import inspect import textwrap import pydoc import sphinx import collections from .docscrape import NumpyDocString, FunctionDoc, ClassDoc if sys.version_info[0] >= 3: sixu = lambda s: s else: sixu = lambda s: unicode(s, 'unicode_escape') class SphinxDocString(NumpyDocString): def __init__(self, docstring, config={}): NumpyDocString.__init__(self, docstring, config=config) self.load_config(config) def load_config(self, config): self.use_plots = config.get('use_plots', False) self.class_members_toctree = config.get('class_members_toctree', True) # string conversion routines def _str_header(self, name, symbol='`'): return ['.. rubric:: ' + name, ''] def _str_field_list(self, name): return [':' + name + ':'] def _str_indent(self, doc, indent=4): out = [] for line in doc: out += [' '*indent + line] return out def _str_signature(self): return [''] if self['Signature']: return ['``%s``' % self['Signature']] + [''] else: return [''] def _str_summary(self): return self['Summary'] + [''] def _str_extended_summary(self): return self['Extended Summary'] + [''] def _str_returns(self, name='Returns'): out = [] if self[name]: out += self._str_field_list(name) out += [''] for param, param_type, desc in self[name]: if param_type: out += self._str_indent(['**%s** : %s' % (param.strip(), param_type)]) else: out += self._str_indent([param.strip()]) if desc: out += [''] out += self._str_indent(desc, 8) out += [''] return out def _str_param_list(self, name): out = [] if self[name]: out += self._str_field_list(name) out += [''] for param, param_type, desc in self[name]: if param_type: out += self._str_indent(['**%s** : %s' % (param.strip(), param_type)]) else: out += self._str_indent(['**%s**' % param.strip()]) if desc: out += [''] out += self._str_indent(desc, 8) out += [''] return out @property def _obj(self): if hasattr(self, '_cls'): return self._cls elif hasattr(self, '_f'): return self._f return None def _str_member_list(self, name): """ Generate a member listing, autosummary:: table where possible, and a table where not. """ out = [] if self[name]: out += ['.. rubric:: %s' % name, ''] prefix = getattr(self, '_name', '') if prefix: prefix = '~%s.' % prefix autosum = [] others = [] for param, param_type, desc in self[name]: param = param.strip() # Check if the referenced member can have a docstring or not param_obj = getattr(self._obj, param, None) if not (callable(param_obj) or isinstance(param_obj, property) or inspect.isgetsetdescriptor(param_obj)): param_obj = None if param_obj and (pydoc.getdoc(param_obj) or not desc): # Referenced object has a docstring autosum += [" %s%s" % (prefix, param)] else: others.append((param, param_type, desc)) if autosum: out += ['.. autosummary::'] if self.class_members_toctree: out += [' :toctree:'] out += [''] + autosum if others: maxlen_0 = max(3, max([len(x[0]) for x in others])) hdr = sixu("=")*maxlen_0 + sixu(" ") + sixu("=")*10 fmt = sixu('%%%ds %%s ') % (maxlen_0,) out += ['', '', hdr] for param, param_type, desc in others: desc = sixu(" ").join(x.strip() for x in desc).strip() if param_type: desc = "(%s) %s" % (param_type, desc) out += [fmt % (param.strip(), desc)] out += [hdr] out += [''] return out def _str_section(self, name): out = [] if self[name]: out += self._str_header(name) out += [''] content = textwrap.dedent("\n".join(self[name])).split("\n") out += content out += [''] return out def _str_see_also(self, func_role): out = [] if self['See Also']: see_also = super(SphinxDocString, self)._str_see_also(func_role) out = ['.. seealso::', ''] out += self._str_indent(see_also[2:]) return out def _str_warnings(self): out = [] if self['Warnings']: out = ['.. warning::', ''] out += self._str_indent(self['Warnings']) return out def _str_index(self): idx = self['index'] out = [] if len(idx) == 0: return out out += ['.. index:: %s' % idx.get('default', '')] for section, references in idx.items(): if section == 'default': continue elif section == 'refguide': out += [' single: %s' % (', '.join(references))] else: out += [' %s: %s' % (section, ','.join(references))] return out def _str_references(self): out = [] if self['References']: out += self._str_header('References') if isinstance(self['References'], str): self['References'] = [self['References']] out.extend(self['References']) out += [''] # Latex collects all references to a separate bibliography, # so we need to insert links to it if sphinx.__version__ >= "0.6": out += ['.. only:: latex', ''] else: out += ['.. latexonly::', ''] items = [] for line in self['References']: m = re.match(r'.. \[([a-z0-9._-]+)\]', line, re.I) if m: items.append(m.group(1)) out += [' ' + ", ".join(["[%s]_" % item for item in items]), ''] return out def _str_examples(self): examples_str = "\n".join(self['Examples']) if (self.use_plots and 'import matplotlib' in examples_str and 'plot::' not in examples_str): out = [] out += self._str_header('Examples') out += ['.. plot::', ''] out += self._str_indent(self['Examples']) out += [''] return out else: return self._str_section('Examples') def __str__(self, indent=0, func_role="obj"): out = [] out += self._str_signature() out += self._str_index() + [''] out += self._str_summary() out += self._str_extended_summary() out += self._str_param_list('Parameters') out += self._str_returns('Returns') out += self._str_returns('Yields') for param_list in ('Other Parameters', 'Raises', 'Warns'): out += self._str_param_list(param_list) out += self._str_warnings() out += self._str_see_also(func_role) out += self._str_section('Notes') out += self._str_references() out += self._str_examples() for param_list in ('Attributes', 'Methods'): out += self._str_member_list(param_list) out = self._str_indent(out, indent) return '\n'.join(out) class SphinxFunctionDoc(SphinxDocString, FunctionDoc): def __init__(self, obj, doc=None, config={}): self.load_config(config) FunctionDoc.__init__(self, obj, doc=doc, config=config) class SphinxClassDoc(SphinxDocString, ClassDoc): def __init__(self, obj, doc=None, func_doc=None, config={}): self.load_config(config) ClassDoc.__init__(self, obj, doc=doc, func_doc=None, config=config) class SphinxObjDoc(SphinxDocString): def __init__(self, obj, doc=None, config={}): self._f = obj self.load_config(config) SphinxDocString.__init__(self, doc, config=config) def get_doc_object(obj, what=None, doc=None, config={}): if what is None: if inspect.isclass(obj): what = 'class' elif inspect.ismodule(obj): what = 'module' elif isinstance(obj, collections.Callable): what = 'function' else: what = 'object' if what == 'class': return SphinxClassDoc(obj, func_doc=SphinxFunctionDoc, doc=doc, config=config) elif what in ('function', 'method'): return SphinxFunctionDoc(obj, doc=doc, config=config) else: if doc is None: doc = pydoc.getdoc(obj) return SphinxObjDoc(obj, doc, config=config) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/numpydoc/linkcode.py0000644000077000000240000000471313137204755030546 0ustar tomstaff00000000000000# -*- coding: utf-8 -*- """ linkcode ~~~~~~~~ Add external links to module code in Python object descriptions. :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. :license: BSD, see LICENSE for details. """ from __future__ import division, absolute_import, print_function import warnings import collections warnings.warn("This extension has been accepted to Sphinx upstream. " "Use the version from there (Sphinx >= 1.2) " "https://bitbucket.org/birkenfeld/sphinx/pull-request/47/sphinxextlinkcode", FutureWarning, stacklevel=1) from docutils import nodes from sphinx import addnodes from sphinx.locale import _ from sphinx.errors import SphinxError class LinkcodeError(SphinxError): category = "linkcode error" def doctree_read(app, doctree): env = app.builder.env resolve_target = getattr(env.config, 'linkcode_resolve', None) if not isinstance(env.config.linkcode_resolve, collections.Callable): raise LinkcodeError( "Function `linkcode_resolve` is not given in conf.py") domain_keys = dict( py=['module', 'fullname'], c=['names'], cpp=['names'], js=['object', 'fullname'], ) for objnode in doctree.traverse(addnodes.desc): domain = objnode.get('domain') uris = set() for signode in objnode: if not isinstance(signode, addnodes.desc_signature): continue # Convert signode to a specified format info = {} for key in domain_keys.get(domain, []): value = signode.get(key) if not value: value = '' info[key] = value if not info: continue # Call user code to resolve the link uri = resolve_target(domain, info) if not uri: # no source continue if uri in uris or not uri: # only one link per name, please continue uris.add(uri) onlynode = addnodes.only(expr='html') onlynode += nodes.reference('', '', internal=False, refuri=uri) onlynode[0] += nodes.inline('', _('[source]'), classes=['viewcode-link']) signode += onlynode def setup(app): app.connect('doctree-read', doctree_read) app.add_config_value('linkcode_resolve', None, '') montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/numpydoc/numpydoc.py0000644000077000000240000001477013137204755030620 0ustar tomstaff00000000000000""" ======== numpydoc ======== Sphinx extension that handles docstrings in the Numpy standard format. [1] It will: - Convert Parameters etc. sections to field lists. - Convert See Also section to a See also entry. - Renumber references. - Extract the signature from the docstring, if it can't be determined otherwise. .. [1] https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt """ from __future__ import division, absolute_import, print_function import sys import re import pydoc import sphinx import inspect import collections if sphinx.__version__ < '1.0.1': raise RuntimeError("Sphinx 1.0.1 or newer is required") from .docscrape_sphinx import get_doc_object, SphinxDocString if sys.version_info[0] >= 3: sixu = lambda s: s else: sixu = lambda s: unicode(s, 'unicode_escape') def mangle_docstrings(app, what, name, obj, options, lines, reference_offset=[0]): cfg = {'use_plots': app.config.numpydoc_use_plots, 'show_class_members': app.config.numpydoc_show_class_members, 'show_inherited_class_members': app.config.numpydoc_show_inherited_class_members, 'class_members_toctree': app.config.numpydoc_class_members_toctree} u_NL = sixu('\n') if what == 'module': # Strip top title pattern = '^\\s*[#*=]{4,}\\n[a-z0-9 -]+\\n[#*=]{4,}\\s*' title_re = re.compile(sixu(pattern), re.I | re.S) lines[:] = title_re.sub(sixu(''), u_NL.join(lines)).split(u_NL) else: doc = get_doc_object(obj, what, u_NL.join(lines), config=cfg) if sys.version_info[0] >= 3: doc = str(doc) else: doc = unicode(doc) lines[:] = doc.split(u_NL) if (app.config.numpydoc_edit_link and hasattr(obj, '__name__') and obj.__name__): if hasattr(obj, '__module__'): v = dict(full_name=sixu("%s.%s") % (obj.__module__, obj.__name__)) else: v = dict(full_name=obj.__name__) lines += [sixu(''), sixu('.. htmlonly::'), sixu('')] lines += [sixu(' %s') % x for x in (app.config.numpydoc_edit_link % v).split("\n")] # replace reference numbers so that there are no duplicates references = [] for line in lines: line = line.strip() m = re.match(sixu('^.. \\[([a-z0-9_.-])\\]'), line, re.I) if m: references.append(m.group(1)) # start renaming from the longest string, to avoid overwriting parts references.sort(key=lambda x: -len(x)) if references: for i, line in enumerate(lines): for r in references: if re.match(sixu('^\\d+$'), r): new_r = sixu("R%d") % (reference_offset[0] + int(r)) else: new_r = sixu("%s%d") % (r, reference_offset[0]) lines[i] = lines[i].replace(sixu('[%s]_') % r, sixu('[%s]_') % new_r) lines[i] = lines[i].replace(sixu('.. [%s]') % r, sixu('.. [%s]') % new_r) reference_offset[0] += len(references) def mangle_signature(app, what, name, obj, options, sig, retann): # Do not try to inspect classes that don't define `__init__` if (inspect.isclass(obj) and (not hasattr(obj, '__init__') or 'initializes x; see ' in pydoc.getdoc(obj.__init__))): return '', '' if not (isinstance(obj, collections.Callable) or hasattr(obj, '__argspec_is_invalid_')): return if not hasattr(obj, '__doc__'): return doc = SphinxDocString(pydoc.getdoc(obj)) if doc['Signature']: sig = re.sub(sixu("^[^(]*"), sixu(""), doc['Signature']) return sig, sixu('') def setup(app, get_doc_object_=get_doc_object): if not hasattr(app, 'add_config_value'): return # probably called by nose, better bail out global get_doc_object get_doc_object = get_doc_object_ app.connect('autodoc-process-docstring', mangle_docstrings) app.connect('autodoc-process-signature', mangle_signature) app.add_config_value('numpydoc_edit_link', None, False) app.add_config_value('numpydoc_use_plots', None, False) app.add_config_value('numpydoc_show_class_members', True, True) app.add_config_value('numpydoc_show_inherited_class_members', True, True) app.add_config_value('numpydoc_class_members_toctree', True, True) # Extra mangling domains app.add_domain(NumpyPythonDomain) app.add_domain(NumpyCDomain) metadata = {'parallel_read_safe': True} return metadata # ------------------------------------------------------------------------------ # Docstring-mangling domains # ------------------------------------------------------------------------------ from docutils.statemachine import ViewList from sphinx.domains.c import CDomain from sphinx.domains.python import PythonDomain class ManglingDomainBase(object): directive_mangling_map = {} def __init__(self, *a, **kw): super(ManglingDomainBase, self).__init__(*a, **kw) self.wrap_mangling_directives() def wrap_mangling_directives(self): for name, objtype in list(self.directive_mangling_map.items()): self.directives[name] = wrap_mangling_directive( self.directives[name], objtype) class NumpyPythonDomain(ManglingDomainBase, PythonDomain): name = 'np' directive_mangling_map = { 'function': 'function', 'class': 'class', 'exception': 'class', 'method': 'function', 'classmethod': 'function', 'staticmethod': 'function', 'attribute': 'attribute', } indices = [] class NumpyCDomain(ManglingDomainBase, CDomain): name = 'np-c' directive_mangling_map = { 'function': 'function', 'member': 'attribute', 'macro': 'function', 'type': 'class', 'var': 'object', } def wrap_mangling_directive(base_directive, objtype): class directive(base_directive): def run(self): env = self.state.document.settings.env name = None if self.arguments: m = re.match(r'^(.*\s+)?(.*?)(\(.*)?', self.arguments[0]) name = m.group(2).strip() if not name: name = self.arguments[0] lines = list(self.content) mangle_docstrings(env.app, objtype, name, None, None, lines) self.content = ViewList(lines, self.content.parent) return base_directive.run(self) return directive montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/extern/setup_package.py0000644000077000000240000000024113137204755027723 0ustar tomstaff00000000000000# Licensed under a 3-clause BSD style license - see LICENSE.rst def get_package_data(): return {'astropy_helpers.extern': ['automodapi/templates/*/*.rst']} montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/git_helpers.py0000644000077000000240000001373013104416125026105 0ustar tomstaff00000000000000# Licensed under a 3-clause BSD style license - see LICENSE.rst """ Utilities for retrieving revision information from a project's git repository. """ # Do not remove the following comment; it is used by # astropy_helpers.version_helpers to determine the beginning of the code in # this module # BEGIN import locale import os import subprocess import warnings def _decode_stdio(stream): try: stdio_encoding = locale.getdefaultlocale()[1] or 'utf-8' except ValueError: stdio_encoding = 'utf-8' try: text = stream.decode(stdio_encoding) except UnicodeDecodeError: # Final fallback text = stream.decode('latin1') return text def update_git_devstr(version, path=None): """ Updates the git revision string if and only if the path is being imported directly from a git working copy. This ensures that the revision number in the version string is accurate. """ try: # Quick way to determine if we're in git or not - returns '' if not devstr = get_git_devstr(sha=True, show_warning=False, path=path) except OSError: return version if not devstr: # Probably not in git so just pass silently return version if 'dev' in version: # update to the current git revision version_base = version.split('.dev', 1)[0] devstr = get_git_devstr(sha=False, show_warning=False, path=path) return version_base + '.dev' + devstr else: # otherwise it's already the true/release version return version def get_git_devstr(sha=False, show_warning=True, path=None): """ Determines the number of revisions in this repository. Parameters ---------- sha : bool If True, the full SHA1 hash will be returned. Otherwise, the total count of commits in the repository will be used as a "revision number". show_warning : bool If True, issue a warning if git returns an error code, otherwise errors pass silently. path : str or None If a string, specifies the directory to look in to find the git repository. If `None`, the current working directory is used, and must be the root of the git repository. If given a filename it uses the directory containing that file. Returns ------- devversion : str Either a string with the revision number (if `sha` is False), the SHA1 hash of the current commit (if `sha` is True), or an empty string if git version info could not be identified. """ if path is None: path = os.getcwd() if not _get_repo_path(path, levels=0): return '' if not os.path.isdir(path): path = os.path.abspath(os.path.dirname(path)) if sha: # Faster for getting just the hash of HEAD cmd = ['rev-parse', 'HEAD'] else: cmd = ['rev-list', '--count', 'HEAD'] def run_git(cmd): try: p = subprocess.Popen(['git'] + cmd, cwd=path, stdout=subprocess.PIPE, stderr=subprocess.PIPE, stdin=subprocess.PIPE) stdout, stderr = p.communicate() except OSError as e: if show_warning: warnings.warn('Error running git: ' + str(e)) return (None, b'', b'') if p.returncode == 128: if show_warning: warnings.warn('No git repository present at {0!r}! Using ' 'default dev version.'.format(path)) return (p.returncode, b'', b'') if p.returncode == 129: if show_warning: warnings.warn('Your git looks old (does it support {0}?); ' 'consider upgrading to v1.7.2 or ' 'later.'.format(cmd[0])) return (p.returncode, stdout, stderr) elif p.returncode != 0: if show_warning: warnings.warn('Git failed while determining revision ' 'count: {0}'.format(_decode_stdio(stderr))) return (p.returncode, stdout, stderr) return p.returncode, stdout, stderr returncode, stdout, stderr = run_git(cmd) if not sha and returncode == 129: # git returns 129 if a command option failed to parse; in # particular this could happen in git versions older than 1.7.2 # where the --count option is not supported # Also use --abbrev-commit and --abbrev=0 to display the minimum # number of characters needed per-commit (rather than the full hash) cmd = ['rev-list', '--abbrev-commit', '--abbrev=0', 'HEAD'] returncode, stdout, stderr = run_git(cmd) # Fall back on the old method of getting all revisions and counting # the lines if returncode == 0: return str(stdout.count(b'\n')) else: return '' elif sha: return _decode_stdio(stdout)[:40] else: return _decode_stdio(stdout).strip() def _get_repo_path(pathname, levels=None): """ Given a file or directory name, determine the root of the git repository this path is under. If given, this won't look any higher than ``levels`` (that is, if ``levels=0`` then the given path must be the root of the git repository and is returned if so. Returns `None` if the given path could not be determined to belong to a git repo. """ if os.path.isfile(pathname): current_dir = os.path.abspath(os.path.dirname(pathname)) elif os.path.isdir(pathname): current_dir = os.path.abspath(pathname) else: return None current_level = 0 while levels is None or current_level <= levels: if os.path.exists(os.path.join(current_dir, '.git')): return current_dir current_level += 1 if current_dir == os.path.dirname(current_dir): break current_dir = os.path.dirname(current_dir) return None montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/setup_helpers.py0000644000077000000240000006406613137204755026504 0ustar tomstaff00000000000000# Licensed under a 3-clause BSD style license - see LICENSE.rst """ This module contains a number of utilities for use during setup/build/packaging that are useful to astropy as a whole. """ from __future__ import absolute_import, print_function import collections import os import re import subprocess import sys import traceback import warnings from distutils import log from distutils.dist import Distribution from distutils.errors import DistutilsOptionError, DistutilsModuleError from distutils.core import Extension from distutils.core import Command from distutils.command.sdist import sdist as DistutilsSdist from setuptools import find_packages as _find_packages from .distutils_helpers import (add_command_option, get_compiler_option, get_dummy_distribution, get_distutils_build_option, get_distutils_build_or_install_option) from .version_helpers import get_pkg_version_module from .utils import (walk_skip_hidden, import_file, extends_doc, resolve_name, AstropyDeprecationWarning) from .commands.build_ext import generate_build_ext_command from .commands.build_py import AstropyBuildPy from .commands.install import AstropyInstall from .commands.install_lib import AstropyInstallLib from .commands.register import AstropyRegister from .commands.test import AstropyTest # These imports are not used in this module, but are included for backwards # compat with older versions of this module from .utils import get_numpy_include_path, write_if_different # noqa from .commands.build_ext import should_build_with_cython, get_compiler_version # noqa _module_state = {'registered_commands': None, 'have_sphinx': False, 'package_cache': None} try: import sphinx # noqa _module_state['have_sphinx'] = True except ValueError as e: # This can occur deep in the bowels of Sphinx's imports by way of docutils # and an occurrence of this bug: http://bugs.python.org/issue18378 # In this case sphinx is effectively unusable if 'unknown locale' in e.args[0]: log.warn( "Possible misconfiguration of one of the environment variables " "LC_ALL, LC_CTYPES, LANG, or LANGUAGE. For an example of how to " "configure your system's language environment on OSX see " "http://blog.remibergsma.com/2012/07/10/" "setting-locales-correctly-on-mac-osx-terminal-application/") except ImportError: pass except SyntaxError: # occurs if markupsafe is recent version, which doesn't support Python 3.2 pass PY3 = sys.version_info[0] >= 3 # This adds a new keyword to the setup() function Distribution.skip_2to3 = [] def adjust_compiler(package): """ This function detects broken compilers and switches to another. If the environment variable CC is explicitly set, or a compiler is specified on the commandline, no override is performed -- the purpose here is to only override a default compiler. The specific compilers with problems are: * The default compiler in XCode-4.2, llvm-gcc-4.2, segfaults when compiling wcslib. The set of broken compilers can be updated by changing the compiler_mapping variable. It is a list of 2-tuples where the first in the pair is a regular expression matching the version of the broken compiler, and the second is the compiler to change to. """ warnings.warn( 'Direct use of the adjust_compiler function in setup.py is ' 'deprecated and can be removed from your setup.py. This ' 'functionality is now incorporated directly into the build_ext ' 'command.', AstropyDeprecationWarning) def get_debug_option(packagename): """ Determines if the build is in debug mode. Returns ------- debug : bool True if the current build was started with the debug option, False otherwise. """ try: current_debug = get_pkg_version_module(packagename, fromlist=['debug'])[0] except (ImportError, AttributeError): current_debug = None # Only modify the debug flag if one of the build commands was explicitly # run (i.e. not as a sub-command of something else) dist = get_dummy_distribution() if any(cmd in dist.commands for cmd in ['build', 'build_ext']): debug = bool(get_distutils_build_option('debug')) else: debug = bool(current_debug) if current_debug is not None and current_debug != debug: build_ext_cmd = dist.get_command_class('build_ext') build_ext_cmd.force_rebuild = True return debug def register_commands(package, version, release, srcdir='.'): if _module_state['registered_commands'] is not None: return _module_state['registered_commands'] if _module_state['have_sphinx']: try: from .commands.build_sphinx import (AstropyBuildSphinx, AstropyBuildDocs) except ImportError: AstropyBuildSphinx = AstropyBuildDocs = FakeBuildSphinx else: AstropyBuildSphinx = AstropyBuildDocs = FakeBuildSphinx _module_state['registered_commands'] = registered_commands = { 'test': generate_test_command(package), # Use distutils' sdist because it respects package_data. # setuptools/distributes sdist requires duplication of information in # MANIFEST.in 'sdist': DistutilsSdist, # The exact form of the build_ext command depends on whether or not # we're building a release version 'build_ext': generate_build_ext_command(package, release), # We have a custom build_py to generate the default configuration file 'build_py': AstropyBuildPy, # Since install can (in some circumstances) be run without # first building, we also need to override install and # install_lib. See #2223 'install': AstropyInstall, 'install_lib': AstropyInstallLib, 'register': AstropyRegister, 'build_sphinx': AstropyBuildSphinx, 'build_docs': AstropyBuildDocs } # Need to override the __name__ here so that the commandline options are # presented as being related to the "build" command, for example; normally # this wouldn't be necessary since commands also have a command_name # attribute, but there is a bug in distutils' help display code that it # uses __name__ instead of command_name. Yay distutils! for name, cls in registered_commands.items(): cls.__name__ = name # Add a few custom options; more of these can be added by specific packages # later for option in [ ('use-system-libraries', "Use system libraries whenever possible", True)]: add_command_option('build', *option) add_command_option('install', *option) add_command_hooks(registered_commands, srcdir=srcdir) return registered_commands def add_command_hooks(commands, srcdir='.'): """ Look through setup_package.py modules for functions with names like ``pre__hook`` and ``post__hook`` where ```` is the name of a ``setup.py`` command (e.g. build_ext). If either hook is present this adds a wrapped version of that command to the passed in ``commands`` `dict`. ``commands`` may be pre-populated with other custom distutils command classes that should be wrapped if there are hooks for them (e.g. `AstropyBuildPy`). """ hook_re = re.compile(r'^(pre|post)_(.+)_hook$') # Distutils commands have a method of the same name, but it is not a # *classmethod* (which probably didn't exist when distutils was first # written) def get_command_name(cmdcls): if hasattr(cmdcls, 'command_name'): return cmdcls.command_name else: return cmdcls.__name__ packages = filter_packages(find_packages(srcdir)) dist = get_dummy_distribution() hooks = collections.defaultdict(dict) for setuppkg in iter_setup_packages(srcdir, packages): for name, obj in vars(setuppkg).items(): match = hook_re.match(name) if not match: continue hook_type = match.group(1) cmd_name = match.group(2) if hook_type not in hooks[cmd_name]: hooks[cmd_name][hook_type] = [] hooks[cmd_name][hook_type].append((setuppkg.__name__, obj)) for cmd_name, cmd_hooks in hooks.items(): commands[cmd_name] = generate_hooked_command( cmd_name, dist.get_command_class(cmd_name), cmd_hooks) def generate_hooked_command(cmd_name, cmd_cls, hooks): """ Returns a generated subclass of ``cmd_cls`` that runs the pre- and post-command hooks for that command before and after the ``cmd_cls.run`` method. """ def run(self, orig_run=cmd_cls.run): self.run_command_hooks('pre_hooks') orig_run(self) self.run_command_hooks('post_hooks') return type(cmd_name, (cmd_cls, object), {'run': run, 'run_command_hooks': run_command_hooks, 'pre_hooks': hooks.get('pre', []), 'post_hooks': hooks.get('post', [])}) def run_command_hooks(cmd_obj, hook_kind): """Run hooks registered for that command and phase. *cmd_obj* is a finalized command object; *hook_kind* is either 'pre_hook' or 'post_hook'. """ hooks = getattr(cmd_obj, hook_kind, None) if not hooks: return for modname, hook in hooks: if isinstance(hook, str): try: hook_obj = resolve_name(hook) except ImportError as exc: raise DistutilsModuleError( 'cannot find hook {0}: {1}'.format(hook, exc)) else: hook_obj = hook if not callable(hook_obj): raise DistutilsOptionError('hook {0!r} is not callable' % hook) log.info('running {0} from {1} for {2} command'.format( hook_kind.rstrip('s'), modname, cmd_obj.get_command_name())) try: hook_obj(cmd_obj) except Exception: log.error('{0} command hook {1} raised an exception: %s\n'.format( hook_obj.__name__, cmd_obj.get_command_name())) log.error(traceback.format_exc()) sys.exit(1) def generate_test_command(package_name): """ Creates a custom 'test' command for the given package which sets the command's ``package_name`` class attribute to the name of the package being tested. """ return type(package_name.title() + 'Test', (AstropyTest,), {'package_name': package_name}) def update_package_files(srcdir, extensions, package_data, packagenames, package_dirs): """ This function is deprecated and maintained for backward compatibility with affiliated packages. Affiliated packages should update their setup.py to use `get_package_info` instead. """ info = get_package_info(srcdir) extensions.extend(info['ext_modules']) package_data.update(info['package_data']) packagenames = list(set(packagenames + info['packages'])) package_dirs.update(info['package_dir']) def get_package_info(srcdir='.', exclude=()): """ Collates all of the information for building all subpackages and returns a dictionary of keyword arguments that can be passed directly to `distutils.setup`. The purpose of this function is to allow subpackages to update the arguments to the package's ``setup()`` function in its setup.py script, rather than having to specify all extensions/package data directly in the ``setup.py``. See Astropy's own ``setup.py`` for example usage and the Astropy development docs for more details. This function obtains that information by iterating through all packages in ``srcdir`` and locating a ``setup_package.py`` module. This module can contain the following functions: ``get_extensions()``, ``get_package_data()``, ``get_build_options()``, ``get_external_libraries()``, and ``requires_2to3()``. Each of those functions take no arguments. - ``get_extensions`` returns a list of `distutils.extension.Extension` objects. - ``get_package_data()`` returns a dict formatted as required by the ``package_data`` argument to ``setup()``. - ``get_build_options()`` returns a list of tuples describing the extra build options to add. - ``get_external_libraries()`` returns a list of libraries that can optionally be built using external dependencies. - ``get_entry_points()`` returns a dict formatted as required by the ``entry_points`` argument to ``setup()``. - ``requires_2to3()`` should return `True` when the source code requires `2to3` processing to run on Python 3.x. If ``requires_2to3()`` is missing, it is assumed to return `True`. """ ext_modules = [] packages = [] package_data = {} package_dir = {} skip_2to3 = [] # Use the find_packages tool to locate all packages and modules packages = filter_packages(find_packages(srcdir, exclude=exclude)) # Update package_dir if the package lies in a subdirectory if srcdir != '.': package_dir[''] = srcdir # For each of the setup_package.py modules, extract any # information that is needed to install them. The build options # are extracted first, so that their values will be available in # subsequent calls to `get_extensions`, etc. for setuppkg in iter_setup_packages(srcdir, packages): if hasattr(setuppkg, 'get_build_options'): options = setuppkg.get_build_options() for option in options: add_command_option('build', *option) if hasattr(setuppkg, 'get_external_libraries'): libraries = setuppkg.get_external_libraries() for library in libraries: add_external_library(library) if hasattr(setuppkg, 'requires_2to3'): requires_2to3 = setuppkg.requires_2to3() else: requires_2to3 = True if not requires_2to3: skip_2to3.append( os.path.dirname(setuppkg.__file__)) for setuppkg in iter_setup_packages(srcdir, packages): # get_extensions must include any Cython extensions by their .pyx # filename. if hasattr(setuppkg, 'get_extensions'): ext_modules.extend(setuppkg.get_extensions()) if hasattr(setuppkg, 'get_package_data'): package_data.update(setuppkg.get_package_data()) # Locate any .pyx files not already specified, and add their extensions in. # The default include dirs include numpy to facilitate numerical work. ext_modules.extend(get_cython_extensions(srcdir, packages, ext_modules, ['numpy'])) # Now remove extensions that have the special name 'skip_cython', as they # exist Only to indicate that the cython extensions shouldn't be built for i, ext in reversed(list(enumerate(ext_modules))): if ext.name == 'skip_cython': del ext_modules[i] # On Microsoft compilers, we need to pass the '/MANIFEST' # commandline argument. This was the default on MSVC 9.0, but is # now required on MSVC 10.0, but it doesn't seem to hurt to add # it unconditionally. if get_compiler_option() == 'msvc': for ext in ext_modules: ext.extra_link_args.append('/MANIFEST') return { 'ext_modules': ext_modules, 'packages': packages, 'package_dir': package_dir, 'package_data': package_data, 'skip_2to3': skip_2to3 } def iter_setup_packages(srcdir, packages): """ A generator that finds and imports all of the ``setup_package.py`` modules in the source packages. Returns ------- modgen : generator A generator that yields (modname, mod), where `mod` is the module and `modname` is the module name for the ``setup_package.py`` modules. """ for packagename in packages: package_parts = packagename.split('.') package_path = os.path.join(srcdir, *package_parts) setup_package = os.path.relpath( os.path.join(package_path, 'setup_package.py')) if os.path.isfile(setup_package): module = import_file(setup_package, name=packagename + '.setup_package') yield module def iter_pyx_files(package_dir, package_name): """ A generator that yields Cython source files (ending in '.pyx') in the source packages. Returns ------- pyxgen : generator A generator that yields (extmod, fullfn) where `extmod` is the full name of the module that the .pyx file would live in based on the source directory structure, and `fullfn` is the path to the .pyx file. """ for dirpath, dirnames, filenames in walk_skip_hidden(package_dir): for fn in filenames: if fn.endswith('.pyx'): fullfn = os.path.relpath(os.path.join(dirpath, fn)) # Package must match file name extmod = '.'.join([package_name, fn[:-4]]) yield (extmod, fullfn) break # Don't recurse into subdirectories def get_cython_extensions(srcdir, packages, prevextensions=tuple(), extincludedirs=None): """ Looks for Cython files and generates Extensions if needed. Parameters ---------- srcdir : str Path to the root of the source directory to search. prevextensions : list of `~distutils.core.Extension` objects The extensions that are already defined. Any .pyx files already here will be ignored. extincludedirs : list of str or None Directories to include as the `include_dirs` argument to the generated `~distutils.core.Extension` objects. Returns ------- exts : list of `~distutils.core.Extension` objects The new extensions that are needed to compile all .pyx files (does not include any already in `prevextensions`). """ # Vanilla setuptools and old versions of distribute include Cython files # as .c files in the sources, not .pyx, so we cannot simply look for # existing .pyx sources in the previous sources, but we should also check # for .c files with the same remaining filename. So we look for .pyx and # .c files, and we strip the extension. prevsourcepaths = [] ext_modules = [] for ext in prevextensions: for s in ext.sources: if s.endswith(('.pyx', '.c', '.cpp')): sourcepath = os.path.realpath(os.path.splitext(s)[0]) prevsourcepaths.append(sourcepath) for package_name in packages: package_parts = package_name.split('.') package_path = os.path.join(srcdir, *package_parts) for extmod, pyxfn in iter_pyx_files(package_path, package_name): sourcepath = os.path.realpath(os.path.splitext(pyxfn)[0]) if sourcepath not in prevsourcepaths: ext_modules.append(Extension(extmod, [pyxfn], include_dirs=extincludedirs)) return ext_modules class DistutilsExtensionArgs(collections.defaultdict): """ A special dictionary whose default values are the empty list. This is useful for building up a set of arguments for `distutils.Extension` without worrying whether the entry is already present. """ def __init__(self, *args, **kwargs): def default_factory(): return [] super(DistutilsExtensionArgs, self).__init__( default_factory, *args, **kwargs) def update(self, other): for key, val in other.items(): self[key].extend(val) def pkg_config(packages, default_libraries, executable='pkg-config'): """ Uses pkg-config to update a set of distutils Extension arguments to include the flags necessary to link against the given packages. If the pkg-config lookup fails, default_libraries is applied to libraries. Parameters ---------- packages : list of str A list of pkg-config packages to look up. default_libraries : list of str A list of library names to use if the pkg-config lookup fails. Returns ------- config : dict A dictionary containing keyword arguments to `distutils.Extension`. These entries include: - ``include_dirs``: A list of include directories - ``library_dirs``: A list of library directories - ``libraries``: A list of libraries - ``define_macros``: A list of macro defines - ``undef_macros``: A list of macros to undefine - ``extra_compile_args``: A list of extra arguments to pass to the compiler """ flag_map = {'-I': 'include_dirs', '-L': 'library_dirs', '-l': 'libraries', '-D': 'define_macros', '-U': 'undef_macros'} command = "{0} --libs --cflags {1}".format(executable, ' '.join(packages)), result = DistutilsExtensionArgs() try: pipe = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE) output = pipe.communicate()[0].strip() except subprocess.CalledProcessError as e: lines = [ ("{0} failed. This may cause the build to fail below." .format(executable)), " command: {0}".format(e.cmd), " returncode: {0}".format(e.returncode), " output: {0}".format(e.output) ] log.warn('\n'.join(lines)) result['libraries'].extend(default_libraries) else: if pipe.returncode != 0: lines = [ "pkg-config could not lookup up package(s) {0}.".format( ", ".join(packages)), "This may cause the build to fail below." ] log.warn('\n'.join(lines)) result['libraries'].extend(default_libraries) else: for token in output.split(): # It's not clear what encoding the output of # pkg-config will come to us in. It will probably be # some combination of pure ASCII (for the compiler # flags) and the filesystem encoding (for any argument # that includes directories or filenames), but this is # just conjecture, as the pkg-config documentation # doesn't seem to address it. arg = token[:2].decode('ascii') value = token[2:].decode(sys.getfilesystemencoding()) if arg in flag_map: if arg == '-D': value = tuple(value.split('=', 1)) result[flag_map[arg]].append(value) else: result['extra_compile_args'].append(value) return result def add_external_library(library): """ Add a build option for selecting the internal or system copy of a library. Parameters ---------- library : str The name of the library. If the library is `foo`, the build option will be called `--use-system-foo`. """ for command in ['build', 'build_ext', 'install']: add_command_option(command, str('use-system-' + library), 'Use the system {0} library'.format(library), is_bool=True) def use_system_library(library): """ Returns `True` if the build configuration indicates that the given library should use the system copy of the library rather than the internal one. For the given library `foo`, this will be `True` if `--use-system-foo` or `--use-system-libraries` was provided at the commandline or in `setup.cfg`. Parameters ---------- library : str The name of the library Returns ------- use_system : bool `True` if the build should use the system copy of the library. """ return ( get_distutils_build_or_install_option('use_system_{0}'.format(library)) or get_distutils_build_or_install_option('use_system_libraries')) @extends_doc(_find_packages) def find_packages(where='.', exclude=(), invalidate_cache=False): """ This version of ``find_packages`` caches previous results to speed up subsequent calls. Use ``invalide_cache=True`` to ignore cached results from previous ``find_packages`` calls, and repeat the package search. """ if not invalidate_cache and _module_state['package_cache'] is not None: return _module_state['package_cache'] packages = _find_packages(where=where, exclude=exclude) _module_state['package_cache'] = packages return packages def filter_packages(packagenames): """ Removes some packages from the package list that shouldn't be installed on the current version of Python. """ if PY3: exclude = '_py2' else: exclude = '_py3' return [x for x in packagenames if not x.endswith(exclude)] class FakeBuildSphinx(Command): """ A dummy build_sphinx command that is called if Sphinx is not installed and displays a relevant error message """ # user options inherited from sphinx.setup_command.BuildDoc user_options = [ ('fresh-env', 'E', ''), ('all-files', 'a', ''), ('source-dir=', 's', ''), ('build-dir=', None, ''), ('config-dir=', 'c', ''), ('builder=', 'b', ''), ('project=', None, ''), ('version=', None, ''), ('release=', None, ''), ('today=', None, ''), ('link-index', 'i', '')] # user options appended in astropy.setup_helpers.AstropyBuildSphinx user_options.append(('warnings-returncode', 'w', '')) user_options.append(('clean-docs', 'l', '')) user_options.append(('no-intersphinx', 'n', '')) user_options.append(('open-docs-in-browser', 'o', '')) def initialize_options(self): try: raise RuntimeError("Sphinx and its dependencies must be installed " "for build_docs.") except: log.error('error: Sphinx and its dependencies must be installed ' 'for build_docs.') sys.exit(1) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/0000755000077000000240000000000013137205364024542 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/__init__.py0000644000077000000240000000066513137204755026665 0ustar tomstaff00000000000000""" This package contains utilities and extensions for the Astropy sphinx documentation. In particular, the `astropy.sphinx.conf` should be imported by the sphinx ``conf.py`` file for affiliated packages that wish to make use of the Astropy documentation format. Note that some sphinx extensions which are bundled as-is (numpydoc and sphinx-automodapi) are included in astropy_helpers.extern rather than astropy_helpers.sphinx.ext. """ montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/conf.py0000644000077000000240000002770413137204755026056 0ustar tomstaff00000000000000# -*- coding: utf-8 -*- # Licensed under a 3-clause BSD style license - see LICENSE.rst # # Astropy shared Sphinx settings. These settings are shared between # astropy itself and affiliated packages. # # Note that not all possible configuration values are present in this file. # # All configuration values have a default; values that are commented out # serve to show the default. import os import sys import warnings from os import path import sphinx from distutils.version import LooseVersion # -- General configuration ---------------------------------------------------- # The version check in Sphinx itself can only compare the major and # minor parts of the version number, not the micro. To do a more # specific version check, call check_sphinx_version("x.y.z.") from # your project's conf.py needs_sphinx = '1.3' on_rtd = os.environ.get('READTHEDOCS', None) == 'True' def check_sphinx_version(expected_version): sphinx_version = LooseVersion(sphinx.__version__) expected_version = LooseVersion(expected_version) if sphinx_version < expected_version: raise RuntimeError( "At least Sphinx version {0} is required to build this " "documentation. Found {1}.".format( expected_version, sphinx_version)) # Configuration for intersphinx: refer to the Python standard library. intersphinx_mapping = { 'python': ('https://docs.python.org/3/', (None, 'http://data.astropy.org/intersphinx/python3.inv')), 'pythonloc': ('http://docs.python.org/', path.abspath(path.join(path.dirname(__file__), 'local/python3_local_links.inv'))), 'numpy': ('https://docs.scipy.org/doc/numpy/', (None, 'http://data.astropy.org/intersphinx/numpy.inv')), 'scipy': ('https://docs.scipy.org/doc/scipy/reference/', (None, 'http://data.astropy.org/intersphinx/scipy.inv')), 'matplotlib': ('http://matplotlib.org/', (None, 'http://data.astropy.org/intersphinx/matplotlib.inv')), 'astropy': ('http://docs.astropy.org/en/stable/', None), 'h5py': ('http://docs.h5py.org/en/latest/', None)} if sys.version_info[0] == 2: intersphinx_mapping['python'] = ( 'https://docs.python.org/2/', (None, 'http://data.astropy.org/intersphinx/python2.inv')) intersphinx_mapping['pythonloc'] = ( 'http://docs.python.org/', path.abspath(path.join(path.dirname(__file__), 'local/python2_local_links.inv'))) # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. exclude_patterns = ['_build'] # Add any paths that contain templates here, relative to this directory. # templates_path = ['_templates'] # The suffix of source filenames. source_suffix = '.rst' # The encoding of source files. #source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # The reST default role (used for this markup: `text`) to use for all # documents. Set to the "smart" one. default_role = 'obj' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None # This is added to the end of RST files - a good place to put substitutions to # be used globally. rst_epilog = """ .. _Astropy: http://astropy.org """ # A list of warning types to suppress arbitrary warning messages. We mean to # override directives in astropy_helpers.sphinx.ext.autodoc_enhancements, # thus need to ignore those warning. This can be removed once the patch gets # released in upstream Sphinx (https://github.com/sphinx-doc/sphinx/pull/1843). # Suppress the warnings requires Sphinx v1.4.2 suppress_warnings = ['app.add_directive', ] # -- Project information ------------------------------------------------------ # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #today_fmt = '%B %d, %Y' # If true, '()' will be appended to :func: etc. cross-reference text. #add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). #add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. #show_authors = False # The name of the Pygments (syntax highlighting) style to use. #pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. #modindex_common_prefix = [] # -- Settings for extensions and extension options ---------------------------- # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.inheritance_diagram', 'sphinx.ext.viewcode', 'astropy_helpers.extern.numpydoc', 'astropy_helpers.extern.automodapi.automodapi', 'astropy_helpers.extern.automodapi.smart_resolver', 'astropy_helpers.sphinx.ext.tocdepthfix', 'astropy_helpers.sphinx.ext.doctest', 'astropy_helpers.sphinx.ext.changelog_links'] if on_rtd: extensions.append('sphinx.ext.mathjax') elif LooseVersion(sphinx.__version__) < LooseVersion('1.4'): extensions.append('sphinx.ext.pngmath') else: extensions.append('sphinx.ext.imgmath') # Above, we use a patched version of viewcode rather than 'sphinx.ext.viewcode' # This can be changed to the sphinx version once the following issue is fixed # in sphinx: # https://bitbucket.org/birkenfeld/sphinx/issue/623/ # extension-viewcode-fails-with-function try: import matplotlib.sphinxext.plot_directive extensions += [matplotlib.sphinxext.plot_directive.__name__] # AttributeError is checked here in case matplotlib is installed but # Sphinx isn't. Note that this module is imported by the config file # generator, even if we're not building the docs. except (ImportError, AttributeError): warnings.warn( "matplotlib's plot_directive could not be imported. " + "Inline plots will not be included in the output") # Don't show summaries of the members in each class along with the # class' docstring numpydoc_show_class_members = False autosummary_generate = True automodapi_toctreedirnm = 'api' # Class documentation should contain *both* the class docstring and # the __init__ docstring autoclass_content = "both" # Render inheritance diagrams in SVG graphviz_output_format = "svg" graphviz_dot_args = [ '-Nfontsize=10', '-Nfontname=Helvetica Neue, Helvetica, Arial, sans-serif', '-Efontsize=10', '-Efontname=Helvetica Neue, Helvetica, Arial, sans-serif', '-Gfontsize=10', '-Gfontname=Helvetica Neue, Helvetica, Arial, sans-serif' ] # -- Options for HTML output ------------------------------------------------- # Add any paths that contain custom themes here, relative to this directory. html_theme_path = [path.abspath(path.join(path.dirname(__file__), 'themes'))] # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. html_theme = 'bootstrap-astropy' # Custom sidebar templates, maps document names to template names. html_sidebars = { '**': ['localtoc.html'], 'search': [], 'genindex': [], 'py-modindex': [], } # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # included in the bootstrap-astropy theme html_favicon = path.join(html_theme_path[0], html_theme, 'static', 'astropy_logo.ico') # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. html_last_updated_fmt = '%d %b %Y' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. #html_theme_options = {} # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". #html_title = None # A shorter title for the navigation bar. Default is the same as html_title. #html_short_title = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. #html_use_smartypants = True # Additional templates that should be rendered to pages, maps page names to # template names. #html_additional_pages = {} # If false, no module index is generated. #html_domain_indices = True # If false, no index is generated. #html_use_index = True # If true, the index is split into individual pages for each letter. #html_split_index = False # If true, links to the reST sources are added to the pages. #html_show_sourcelink = True # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. #html_show_sphinx = True # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. #html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. #html_use_opensearch = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). #html_file_suffix = None # -- Options for LaTeX output ------------------------------------------------ # The paper size ('letter' or 'a4'). #latex_paper_size = 'letter' # The font size ('10pt', '11pt' or '12pt'). #latex_font_size = '10pt' # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. latex_toplevel_sectioning = 'part' # If true, show page references after internal links. #latex_show_pagerefs = False # If true, show URL addresses after external links. #latex_show_urls = False latex_elements = {} # Additional stuff for the LaTeX preamble. latex_elements['preamble'] = r""" % Use a more modern-looking monospace font \usepackage{inconsolata} % The enumitem package provides unlimited nesting of lists and enums. % Sphinx may use this in the future, in which case this can be removed. % See https://bitbucket.org/birkenfeld/sphinx/issue/777/latex-output-too-deeply-nested \usepackage{enumitem} \setlistdepth{15} % In the parameters section, place a newline after the Parameters % header. (This is stolen directly from Numpy's conf.py, since it % affects Numpy-style docstrings). \usepackage{expdlist} \let\latexdescription=\description \def\description{\latexdescription{}{} \breaklabel} % Support the superscript Unicode numbers used by the "unicode" units % formatter \DeclareUnicodeCharacter{2070}{\ensuremath{^0}} \DeclareUnicodeCharacter{00B9}{\ensuremath{^1}} \DeclareUnicodeCharacter{00B2}{\ensuremath{^2}} \DeclareUnicodeCharacter{00B3}{\ensuremath{^3}} \DeclareUnicodeCharacter{2074}{\ensuremath{^4}} \DeclareUnicodeCharacter{2075}{\ensuremath{^5}} \DeclareUnicodeCharacter{2076}{\ensuremath{^6}} \DeclareUnicodeCharacter{2077}{\ensuremath{^7}} \DeclareUnicodeCharacter{2078}{\ensuremath{^8}} \DeclareUnicodeCharacter{2079}{\ensuremath{^9}} \DeclareUnicodeCharacter{207B}{\ensuremath{^-}} \DeclareUnicodeCharacter{00B0}{\ensuremath{^{\circ}}} \DeclareUnicodeCharacter{2032}{\ensuremath{^{\prime}}} \DeclareUnicodeCharacter{2033}{\ensuremath{^{\prime\prime}}} % Make the "warning" and "notes" sections use a sans-serif font to % make them stand out more. \renewenvironment{notice}[2]{ \def\py@noticetype{#1} \csname py@noticestart@#1\endcsname \textsf{\textbf{#2}} }{\csname py@noticeend@\py@noticetype\endcsname} """ # Documents to append as an appendix to all manuals. #latex_appendices = [] # If false, no module index is generated. #latex_domain_indices = True # The name of an image file (relative to this directory) to place at the top of # the title page. #latex_logo = None # -- Options for the linkcheck builder ---------------------------------------- # A timeout value, in seconds, for the linkcheck builder linkcheck_timeout = 60 montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/ext/0000755000077000000240000000000013137205364025342 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/ext/__init__.py0000644000077000000240000000010213137204755027447 0ustar tomstaff00000000000000from __future__ import division, absolute_import, print_function montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/ext/changelog_links.py0000644000077000000240000000542012405252770031044 0ustar tomstaff00000000000000# Licensed under a 3-clause BSD style license - see LICENSE.rst """ This sphinx extension makes the issue numbers in the changelog into links to GitHub issues. """ from __future__ import print_function import re from docutils.nodes import Text, reference BLOCK_PATTERN = re.compile('\[#.+\]', flags=re.DOTALL) ISSUE_PATTERN = re.compile('#[0-9]+') def process_changelog_links(app, doctree, docname): for rex in app.changelog_links_rexes: if rex.match(docname): break else: # if the doc doesn't match any of the changelog regexes, don't process return app.info('[changelog_links] Adding changelog links to "{0}"'.format(docname)) for item in doctree.traverse(): if not isinstance(item, Text): continue # We build a new list of items to replace the current item. If # a link is found, we need to use a 'reference' item. children = [] # First cycle through blocks of issues (delimited by []) then # iterate inside each one to find the individual issues. prev_block_end = 0 for block in BLOCK_PATTERN.finditer(item): block_start, block_end = block.start(), block.end() children.append(Text(item[prev_block_end:block_start])) block = item[block_start:block_end] prev_end = 0 for m in ISSUE_PATTERN.finditer(block): start, end = m.start(), m.end() children.append(Text(block[prev_end:start])) issue_number = block[start:end] refuri = app.config.github_issues_url + issue_number[1:] children.append(reference(text=issue_number, name=issue_number, refuri=refuri)) prev_end = end prev_block_end = block_end # If no issues were found, this adds the whole item, # otherwise it adds the remaining text. children.append(Text(block[prev_end:block_end])) # If no blocks were found, this adds the whole item, otherwise # it adds the remaining text. children.append(Text(item[prev_block_end:])) # Replace item by the new list of items we have generated, # which may contain links. item.parent.replace(item, children) def setup_patterns_rexes(app): app.changelog_links_rexes = [re.compile(pat) for pat in app.config.changelog_links_docpattern] def setup(app): app.connect('doctree-resolved', process_changelog_links) app.connect('builder-inited', setup_patterns_rexes) app.add_config_value('github_issues_url', None, True) app.add_config_value('changelog_links_docpattern', ['.*changelog.*', 'whatsnew/.*'], True) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/ext/doctest.py0000644000077000000240000000244013137204755027364 0ustar tomstaff00000000000000# Licensed under a 3-clause BSD style license - see LICENSE.rst """ This is a set of three directives that allow us to insert metadata about doctests into the .rst files so the testing framework knows which tests to skip. This is quite different from the doctest extension in Sphinx itself, which actually does something. For astropy, all of the testing is centrally managed from py.test and Sphinx is not used for running tests. """ import re from docutils.nodes import literal_block from docutils.parsers.rst import Directive class DoctestSkipDirective(Directive): has_content = True def run(self): # Check if there is any valid argument, and skip it. Currently only # 'win32' is supported in astropy.tests.pytest_plugins. if re.match('win32', self.content[0]): self.content = self.content[2:] code = '\n'.join(self.content) return [literal_block(code, code)] class DoctestRequiresDirective(DoctestSkipDirective): # This is silly, but we really support an unbounded number of # optional arguments optional_arguments = 64 def setup(app): app.add_directive('doctest-requires', DoctestRequiresDirective) app.add_directive('doctest-skip', DoctestSkipDirective) app.add_directive('doctest-skip-all', DoctestSkipDirective) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/ext/edit_on_github.py0000644000077000000240000001334113137204755030704 0ustar tomstaff00000000000000# Licensed under a 3-clause BSD style license - see LICENSE.rst """ This extension makes it easy to edit documentation on github. It adds links associated with each docstring that go to the corresponding view source page on Github. From there, the user can push the "Edit" button, edit the docstring, and submit a pull request. It has the following configuration options (to be set in the project's ``conf.py``): * ``edit_on_github_project`` The name of the github project, in the form "username/projectname". * ``edit_on_github_branch`` The name of the branch to edit. If this is a released version, this should be a git tag referring to that version. For a dev version, it often makes sense for it to be "master". It may also be a git hash. * ``edit_on_github_source_root`` The location within the source tree of the root of the Python package. Defaults to "lib". * ``edit_on_github_doc_root`` The location within the source tree of the root of the documentation source. Defaults to "doc", but it may make sense to set it to "doc/source" if the project uses a separate source directory. * ``edit_on_github_docstring_message`` The phrase displayed in the links to edit a docstring. Defaults to "[edit on github]". * ``edit_on_github_page_message`` The phrase displayed in the links to edit a RST page. Defaults to "[edit this page on github]". * ``edit_on_github_help_message`` The phrase displayed as a tooltip on the edit links. Defaults to "Push the Edit button on the next page" * ``edit_on_github_skip_regex`` When the path to the .rst file matches this regular expression, no "edit this page on github" link will be added. Defaults to ``"_.*"``. """ import inspect import os import re import sys from docutils import nodes from sphinx import addnodes def import_object(modname, name): """ Import the object given by *modname* and *name* and return it. If not found, or the import fails, returns None. """ try: __import__(modname) mod = sys.modules[modname] obj = mod for part in name.split('.'): obj = getattr(obj, part) return obj except: return None def get_url_base(app): return 'http://github.com/%s/tree/%s/' % ( app.config.edit_on_github_project, app.config.edit_on_github_branch) def doctree_read(app, doctree): # Get the configuration parameters if app.config.edit_on_github_project == 'REQUIRED': raise ValueError( "The edit_on_github_project configuration variable must be " "provided in the conf.py") source_root = app.config.edit_on_github_source_root url = get_url_base(app) docstring_message = app.config.edit_on_github_docstring_message # Handle the docstring-editing links for objnode in doctree.traverse(addnodes.desc): if objnode.get('domain') != 'py': continue names = set() for signode in objnode: if not isinstance(signode, addnodes.desc_signature): continue modname = signode.get('module') if not modname: continue fullname = signode.get('fullname') if fullname in names: # only one link per name, please continue names.add(fullname) obj = import_object(modname, fullname) anchor = None if obj is not None: try: lines, lineno = inspect.getsourcelines(obj) except: pass else: anchor = '#L%d' % lineno if anchor: real_modname = inspect.getmodule(obj).__name__ path = '%s%s%s.py%s' % ( url, source_root, real_modname.replace('.', '/'), anchor) onlynode = addnodes.only(expr='html') onlynode += nodes.reference( reftitle=app.config.edit_on_github_help_message, refuri=path) onlynode[0] += nodes.inline( '', '', nodes.raw('', ' ', format='html'), nodes.Text(docstring_message), classes=['edit-on-github', 'viewcode-link']) signode += onlynode def html_page_context(app, pagename, templatename, context, doctree): if (templatename == 'page.html' and not re.match(app.config.edit_on_github_skip_regex, pagename)): doc_root = app.config.edit_on_github_doc_root if doc_root != '' and not doc_root.endswith('/'): doc_root += '/' doc_path = os.path.relpath(doctree.get('source'), app.builder.srcdir) url = get_url_base(app) page_message = app.config.edit_on_github_page_message context['edit_on_github'] = url + doc_root + doc_path context['edit_on_github_page_message'] = page_message def setup(app): app.add_config_value('edit_on_github_project', 'REQUIRED', True) app.add_config_value('edit_on_github_branch', 'master', True) app.add_config_value('edit_on_github_source_root', 'lib', True) app.add_config_value('edit_on_github_doc_root', 'doc', True) app.add_config_value('edit_on_github_docstring_message', '[edit on github]', True) app.add_config_value('edit_on_github_page_message', 'Edit This Page on Github', True) app.add_config_value('edit_on_github_help_message', 'Push the Edit button on the next page', True) app.add_config_value('edit_on_github_skip_regex', '_.*', True) app.connect('doctree-read', doctree_read) app.connect('html-page-context', html_page_context) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/ext/tests/0000755000077000000240000000000013137205364026504 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/ext/tests/__init__.py0000644000077000000240000000000013137204755030606 0ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/ext/tocdepthfix.py0000644000077000000240000000124512333217235030234 0ustar tomstaff00000000000000from sphinx import addnodes def fix_toc_entries(app, doctree): # Get the docname; I don't know why this isn't just passed in to the # callback # This seems a bit unreliable as it's undocumented, but it's not "private" # either: docname = app.builder.env.temp_data['docname'] if app.builder.env.metadata[docname].get('tocdepth', 0) != 0: # We need to reprocess any TOC nodes in the doctree and make sure all # the files listed in any TOCs are noted for treenode in doctree.traverse(addnodes.toctree): app.builder.env.note_toctree(docname, treenode) def setup(app): app.connect('doctree-read', fix_toc_entries) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/local/0000755000077000000240000000000013137205364025634 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/local/python2_local_links.inv0000644000077000000240000000106213104416125032317 0ustar tomstaff00000000000000# Sphinx inventory version 2 # Project: Python # Version: 2.7 and 3.5 # The remainder of this file should be compressed using zlib. xœ¥”=OÃ0@wÿŠ“ºÀà Z!¤n€U µbwœ+1ríp¶KïÇIi›”QeIä˽wþ8g³"Wf ʬÐxK%¬œ²†lS²ï(ý¦¥Ï­‰‘×Í×1 “k&ƒQrÃóp)”ÉÀ.ÀçÊÁBi—Û 3H¤]„ÎaÁ)ó_Z¥I¤‹Ú>d“H¯ï‰,ÅÐ× _M…_Âð"æ’ òbvIî—zЀ8›<ŸŒ?oÙ',O…wg¯B<•o@œÍËâdÁžá»}5ºdsµDüqã¨ÛØÄ8KK®ÂÁÈßô6úo²9 ¤«£%üè|‡¶@Ó­9ȯ]Τ52ÅvMÁ‡ØQÉCý®üR çÚò#ùunÏÑóœPdSkõýeð›]íW³¸Þ€ÉKõ쨰ɨ¥ÍdÎ RÆŸÿû¼êü_­/ªÖø“'RÉšãG4Hâ¯Õ·ØíÒÛÁ½„·ä·±fžªC{ÃÒÖß| åEª»;åö½¤-¿³ï2½ä{ÉÁÌ]iäÄÇMë;û–¨«HÏãm‹8û‹´RKmontage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/local/python2_local_links.txt0000644000077000000240000000314613104416125032347 0ustar tomstaff00000000000000# Sphinx inventory version 2 # Project: Python # Version: 2.7 and 3.5 # The remainder of this file should be compressed using zlib. # python2 IndexError py:exception -1 2/library/exceptions.html#IndexError - IOError py:exception -1 2/library/exceptions.html#IOError - KeyError py:exception -1 2/library/exceptions.html#KeyError - ValueError py:exception -1 2/library/exceptions.html#ValueError - TypeError py:exception -1 2/library/exceptions.html#TypeError - # python3 only TimeoutError py:exception -1 3/library/exceptions.html#TimeoutError - bytes py:function -1 3/library/functions.html#bytes - urllib.request.urlopen py:function -1 3/library/urllib.request.html#urllib.request.urlopen - concurrent.futures.Future py:class -1 3/library/concurrent.futures.html#concurrent.futures.Future - concurrent.futures.ThreadPoolExecutor py:class -1 3/library/concurrent.futures.html#concurrent.futures.ThreadPoolExecutor - queue.Queue py:class -1 3/library/queue.html#queue.Queue - print() py:function -1 3/library/functions.html#print - # python3 only collections.abc collections.Generator py:class -1 3/library/collections.abc.html#collections.abc.Generator - collections.ByteString py:class -1 3/library/collections.abc.html#collections.abc.ByteString - collections.Awaitable py:class -1 3/library/collections.abc.html#collections.abc.Awaitable - collections.Coroutine py:class -1 3/library/collections.abc.html#collections.abc.Coroutine - collections.AsyncIterable py:class -1 3/library/collections.abc.html#collections.abc.AsyncIterable - collections.AsyncIterator py:class -1 3/library/collections.abc.html#collections.abc.AsyncIterator - montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/local/python3_local_links.inv0000644000077000000240000000122213104416125032316 0ustar tomstaff00000000000000# Sphinx inventory version 2 # Project: Python # Version: 3.5 # The remainder of this file should be compressed using zlib. xœ­ÕÁŽÚ0Ð{¾b$.í!YTUâÖîa·ª*!Qq­{h\;µ¶Ù¯ïgÉšlÏÇvÆ ØV…ÔAê#jolG´N Ëdk~#÷kØ4¾0šZv]ï–Ù'`ZÀ*ûHÍ? ‹%“Z ³_H{©\aj% Gব,:‡j'õ/xU2Ï(ºjõ%­PR\Â7’(ºjÖ¥5ýJ?Àò,³ÍCÕöf…/Õ¢ëOûˆ4©µäF´±ûZszš ºouÐO“Ü ‘Ïål;ƒ”Ýð4’û¬`îç›6éyDí¼ðM…ç”AÄ-}Jwq‰!dÞj´!#âÈT·"ç Ú«hè2£oS¡žßˆ~`· “¨t8«¤²Rûwï§ÒjnKÛñcŸRxÂržŒÿ?íéèÒÉ%Ÿ+æ\ˆOb»ÓÆ ’ø3sË»£ü¿ö`„ôV¾Ò»áv@ˆ>2¥bç;!ý•I,=Whª_ÑôÉé'Ôñö™l!þ©Qó¨%Œþ^ûÓBÝ#Ô }inuüÜÂD¹#e³ªŠ\‹ž¸:ï{ø¡tuþ;‰/wx†–yó®–.–¿ !þn²X{0Bz×Þo±øH ùÏ/LúØòxA&UÝXS{ºžâ®¸™ÌÜ5šß£¸‡Ð\’ÈRBiòJFü?montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/local/python3_local_links.txt0000644000077000000240000000540413104416125032347 0ustar tomstaff00000000000000# Sphinx inventory version 2 # Project: Python # Version: 2.7 and 3.5 # The remainder of this file should be compressed using zlib. # python2 only links cPickle py:module -1 2/library/pickle.html#module-cPickle - unicode py:function -1 2/library/functions.html#unicode - bsddb py:module -1 2/library/bsddb.html#module-bsddb - dict.has_key py:method -1 2/library/stdtypes.html#dict.has_key - dict.iteritems py:method -1 2/library/stdtypes.html#dict.iteritems - dict.iterkeys py:method -1 2/library/stdtypes.html#dict.iterkeys - dict.itervalues py:method -1 2/library/stdtypes.html#dict.itervalues - urllib2.urlopen py:function -1 2/library/urllib2.html#urllib2.urlopen - # python3 print() py:function -1 3/library/functions.html#print - # python3 collections.abc collections.Container py:class -1 3/library/collections.abc.html#collections.abc.Container - collections.Hashable py:class -1 3/library/collections.abc.html#collections.abc.Hashable - collections.Sized py:class -1 3/library/collections.abc.html#collections.abc.Sized - collections.Callable py:class -1 3/library/collections.abc.html#collections.abc.Callable - collections.Iterable py:class -1 3/library/collections.abc.html#collections.abc.Iterable - collections.Iterator py:class -1 3/library/collections.abc.html#collections.abc.Iterator - collections.Generator py:class -1 3/library/collections.abc.html#collections.abc.Generator - collections.Sequence py:class -1 3/library/collections.abc.html#collections.abc.Sequence - collections.MutableSequence py:class -1 3/library/collections.abc.html#collections.abc.MutableSequence - collections.ByteString py:class -1 3/library/collections.abc.html#collections.abc.ByteString - collections.Set py:class -1 3/library/collections.abc.html#collections.abc.Set - collections.MutableSet py:class -1 3/library/collections.abc.html#collections.abc.MutableSet - collections.Mapping py:class -1 3/library/collections.abc.html#collections.abc.Mapping - collections.MutableMapping py:class -1 3/library/collections.abc.html#collections.abc.MutableMapping - collections.MappingView py:class -1 3/library/collections.abc.html#collections.abc.MappingView - collections.ItemsView py:class -1 3/library/collections.abc.html#collections.abc.ItemsView - collections.KeysView py:class -1 3/library/collections.abc.html#collections.abc.KeysView - collections.ValuesView py:class -1 3/library/collections.abc.html#collections.abc.ValuesView - collections.Awaitable py:class -1 3/library/collections.abc.html#collections.abc.Awaitable - collections.Coroutine py:class -1 3/library/collections.abc.html#collections.abc.Coroutine - collections.AsyncIterable py:class -1 3/library/collections.abc.html#collections.abc.AsyncIterable - collections.AsyncIterator py:class -1 3/library/collections.abc.html#collections.abc.AsyncIterator - montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/setup_package.py0000644000077000000240000000044413137204755027734 0ustar tomstaff00000000000000# Licensed under a 3-clause BSD style license - see LICENSE.rst def get_package_data(): # Install the theme files return { 'astropy_helpers.sphinx': [ 'local/*.inv', 'themes/bootstrap-astropy/*.*', 'themes/bootstrap-astropy/static/*.*']} montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/themes/0000755000077000000240000000000013137205364026027 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/themes/bootstrap-astropy/0000755000077000000240000000000013137205364031543 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/themes/bootstrap-astropy/globaltoc.html0000644000077000000240000000011112333217235034365 0ustar tomstaff00000000000000

Table of Contents

{{ toctree(maxdepth=-1, titles_only=true) }} montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/themes/bootstrap-astropy/layout.html0000644000077000000240000000655113104416125033746 0ustar tomstaff00000000000000{% extends "basic/layout.html" %} {# Collapsible sidebar script from default/layout.html in Sphinx #} {% set script_files = script_files + ['_static/sidebar.js'] %} {# Add the google webfonts needed for the logo #} {% block extrahead %} {% if not embedded %}{% endif %} {% endblock %} {% block header %}
{{ theme_logotext1 }}{{ theme_logotext2 }}{{ theme_logotext3 }}
  • Index
  • Modules
  • {% block sidebarsearch %} {% include "searchbox.html" %} {% endblock %}
{% endblock %} {% block relbar1 %}

{{ _('Navigation') }}

    {%- if next %}
  • next {{ "»"|safe }}
    • {%- endif %} {%- if prev %}
  • {{ "«"|safe }} previous {% if next %}{{ reldelim2 }}{% endif %}
    • {%- endif %} {%- block rootrellink %}
  • {{ shorttitle|e }} {{ reldelim1 }}
    • {%- endblock %} {%- for parent in parents %}
  • {{ parent.title }}{{ reldelim1 }}
    • {%- endfor %} {# Don't put the title in the relbar for the first (index) page. #} {% if prev %}
  • {{ title }}
    • {% endif %} {%- block relbaritems %} {% endblock %}
{% endblock %} {# Silence the bottom relbar. #} {% block relbar2 %}{% endblock %} {%- block footer %}

{%- if edit_on_github %} {{ edit_on_github_page_message }}   {%- endif %} {%- if show_source and has_source and sourcename %} {{ _('Page Source') }} {%- endif %}   Back to Top

{%- if show_copyright %} {%- if hasdoc('copyright') %} {% trans path=pathto('copyright'), copyright=copyright|e %}© Copyright {{ copyright }}.{% endtrans %}
{%- else %} {% trans copyright=copyright|e %}© Copyright {{ copyright }}.{% endtrans %}
{%- endif %} {%- endif %} {%- if show_sphinx %} {% trans sphinx_version=sphinx_version|e %}Created using Sphinx {{ sphinx_version }}.{% endtrans %}   {%- endif %} {%- if last_updated %} {% trans last_updated=last_updated|e %}Last built {{ last_updated }}.{% endtrans %}
{%- endif %}

{%- endblock %} montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/themes/bootstrap-astropy/localtoc.html0000644000077000000240000000004212333217235034222 0ustar tomstaff00000000000000

Page Contents

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white-space: nowrap; background-color: rgb(238, 238, 238); border-radius: 0 3px 3px 0; -webkit-border-radius: 0 3px 3px 0; } ././@LongLink0000000000000000000000000000015300000000000011214 Lustar 00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/themes/bootstrap-astropy/static/copybutton.jsmontage-wrapper-0.9.9/astropy_helpers/astropy_helpers/sphinx/themes/bootstrap-astropy/static/copybut0000644000077000000240000000532113104416125034434 0ustar tomstaff00000000000000$(document).ready(function() { /* Add a [>>>] button on the top-right corner of code samples to hide * the >>> and ... prompts and the output and thus make the code * copyable. */ var div = $('.highlight-python .highlight,' + '.highlight-python3 .highlight,' + '.highlight-default .highlight') var pre = div.find('pre'); // get the styles from the current theme pre.parent().parent().css('position', 'relative'); var hide_text = 'Hide the prompts and output'; var show_text = 'Show the prompts and output'; var border_width = pre.css('border-top-width'); var border_style = pre.css('border-top-style'); var border_color = pre.css('border-top-color'); var button_styles = { 'cursor':'pointer', 'position': 'absolute', 'top': '0', 'right': '0', 'border-color': border_color, 'border-style': border_style, 'border-width': border_width, 'color': border_color, 'text-size': '75%', 'font-family': 'monospace', 'padding-left': '0.2em', 'padding-right': '0.2em', 'border-radius': '0 3px 0 0' } // create and add the button to all the code blocks that contain >>> div.each(function(index) { var jthis = $(this); if (jthis.find('.gp').length > 0) { var button = $('>>>'); button.css(button_styles) button.attr('title', hide_text); button.data('hidden', 'false'); jthis.prepend(button); } // tracebacks (.gt) contain bare text elements that need to be // wrapped in a span to work with .nextUntil() (see later) jthis.find('pre:has(.gt)').contents().filter(function() { return ((this.nodeType == 3) && (this.data.trim().length > 0)); 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This script adds * in .sphixsidebar, after .sphinxsidebarwrapper, the #sidebarbutton * used to collapse and expand the sidebar. * * When the sidebar is collapsed the .sphinxsidebarwrapper is hidden * and the width of the sidebar and the margin-left of the document * are decreased. When the sidebar is expanded the opposite happens. * This script saves a per-browser/per-session cookie used to * remember the position of the sidebar among the pages. * Once the browser is closed the cookie is deleted and the position * reset to the default (expanded). * * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ $(function() { // global elements used by the functions. // the 'sidebarbutton' element is defined as global after its // creation, in the add_sidebar_button function var bodywrapper = $('.bodywrapper'); var sidebar = $('.sphinxsidebar'); var sidebarwrapper = $('.sphinxsidebarwrapper'); // for some reason, the document has no sidebar; do not run into errors if (!sidebar.length) return; // original margin-left of the bodywrapper and width of the sidebar // with the sidebar expanded var bw_margin_expanded = bodywrapper.css('margin-left'); var ssb_width_expanded = sidebar.width(); // margin-left of the bodywrapper and width of the sidebar // with the sidebar collapsed var bw_margin_collapsed = 12; var ssb_width_collapsed = 12; // custom colors var dark_color = '#404040'; var light_color = '#505050'; function sidebar_is_collapsed() { return sidebarwrapper.is(':not(:visible)'); } function toggle_sidebar() { if (sidebar_is_collapsed()) expand_sidebar(); else collapse_sidebar(); } function collapse_sidebar() { sidebarwrapper.hide(); sidebar.css('width', ssb_width_collapsed); bodywrapper.css('margin-left', bw_margin_collapsed); sidebarbutton.css({ 'margin-left': '-1px', 'height': bodywrapper.height(), 'border-radius': '3px' }); sidebarbutton.find('span').text('»'); sidebarbutton.attr('title', _('Expand sidebar')); document.cookie = 'sidebar=collapsed'; } function expand_sidebar() { bodywrapper.css('margin-left', bw_margin_expanded); sidebar.css('width', ssb_width_expanded); sidebarwrapper.show(); sidebarbutton.css({ 'margin-left': ssb_width_expanded - 12, 'height': bodywrapper.height(), 'border-radius': '0px 3px 3px 0px' }); sidebarbutton.find('span').text('«'); sidebarbutton.attr('title', _('Collapse sidebar')); document.cookie = 'sidebar=expanded'; } function add_sidebar_button() { sidebarwrapper.css({ 'float': 'left', 'margin-right': '0', 'width': ssb_width_expanded - 18 }); // create the button sidebar.append('
«
'); var sidebarbutton = $('#sidebarbutton'); // find the height of the viewport to center the '<<' in the page var viewport_height; if (window.innerHeight) viewport_height = window.innerHeight; else viewport_height = $(window).height(); var sidebar_offset = sidebar.offset().top; var sidebar_height = Math.max(bodywrapper.height(), sidebar.height()); sidebarbutton.find('span').css({ 'font-family': '"Lucida Grande",Arial,sans-serif', 'display': 'block', 'top': Math.min(viewport_height/2, sidebar_height/2 + sidebar_offset) - 10, 'width': 12, 'position': 'fixed', 'text-align': 'center' }); sidebarbutton.click(toggle_sidebar); sidebarbutton.attr('title', _('Collapse sidebar')); sidebarbutton.css({ 'color': '#FFFFFF', 'background-color': light_color, 'border': '1px solid ' + light_color, 'border-radius': '0px 3px 3px 0px', 'font-size': '1.2em', 'cursor': 'pointer', 'height': sidebar_height, 'padding-top': '1px', 'margin': '-1px', 'margin-left': ssb_width_expanded - 12 }); sidebarbutton.hover( function () { $(this).css('background-color', dark_color); }, function () { $(this).css('background-color', light_color); } ); } function set_position_from_cookie() { if (!document.cookie) return; var items = document.cookie.split(';'); for(var k=0; k= (3, 3): import importlib importlib.invalidate_caches() @pytest.fixture(scope='function', autouse=True) def reset_setup_helpers(request): """ Saves and restores the global state of the astropy_helpers.setup_helpers module between tests. """ mod = __import__('astropy_helpers.setup_helpers', fromlist=['']) old_state = mod._module_state.copy() def finalizer(old_state=old_state): mod = sys.modules.get('astropy_helpers.setup_helpers') if mod is not None: mod._module_state.update(old_state) request.addfinalizer(finalizer) @pytest.fixture(scope='function', autouse=True) def reset_distutils_log(): """ This is a setup/teardown fixture that ensures the log-level of the distutils log is always set to a default of WARN, since different settings could affect tests that check the contents of stdout. """ from distutils import log log.set_threshold(log.WARN) @pytest.fixture(scope='module', autouse=True) def fix_hide_setuptools(): """ Workaround for https://github.com/astropy/astropy-helpers/issues/124 In setuptools 10.0 run_setup was changed in such a way that it sweeps away the existing setuptools import before running the setup script. In principle this is nice, but in the practice of testing astropy_helpers this is problematic since we're trying to test code that has already been imported during the testing process, and which relies on the setuptools module that was already in use. """ if hasattr(sandbox, 'hide_setuptools'): sandbox.hide_setuptools = lambda: None TEST_PACKAGE_SETUP_PY = """\ #!/usr/bin/env python from setuptools import setup NAME = 'astropy-helpers-test' VERSION = {version!r} setup(name=NAME, version=VERSION, packages=['_astropy_helpers_test_'], zip_safe=False) """ @pytest.fixture def testpackage(tmpdir, version='0.1'): """ This fixture creates a simplified package called _astropy_helpers_test_ used primarily for testing ah_boostrap, but without using the astropy_helpers package directly and getting it confused with the astropy_helpers package already under test. """ source = tmpdir.mkdir('testpkg') with source.as_cwd(): source.mkdir('_astropy_helpers_test_') init = source.join('_astropy_helpers_test_', '__init__.py') init.write('__version__ = {0!r}'.format(version)) setup_py = TEST_PACKAGE_SETUP_PY.format(version=version) source.join('setup.py').write(setup_py) # Make the new test package into a git repo run_cmd('git', ['init']) run_cmd('git', ['add', '--all']) run_cmd('git', ['commit', '-m', 'test package']) return source def cleanup_import(package_name): """Remove all references to package_name from sys.modules""" for k in list(sys.modules): if not isinstance(k, str): # Some things will actually do this =_= continue elif k.startswith('astropy_helpers.tests'): # Don't delete imported test modules or else the tests will break, # badly continue if k == package_name or k.startswith(package_name + '.'): del sys.modules[k] montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/tests/coveragerc0000644000077000000240000000125113137204755026440 0ustar tomstaff00000000000000[run] source = astropy_helpers omit = astropy_helpers/commands/_test_compat.py astropy_helpers/compat/* astropy_helpers/*/setup_package.py astropy_helpers/extern/* astropy_helpers/extern/*/* astropy_helpers/tests/* */test_pkg/* [report] exclude_lines = # Have to re-enable the standard pragma pragma: no cover # Don't complain about packages we have installed except ImportError # Don't complain if tests don't hit assertions raise AssertionError raise NotImplementedError # Don't complain about script hooks def main\(.*\): # Ignore branches that don't pertain to this version of Python pragma: py{ignore_python_version} montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/tests/test_ah_bootstrap.py0000644000077000000240000003511113137204755030475 0ustar tomstaff00000000000000# -*- coding: utf-8 -*- import glob import os import textwrap from distutils.version import LooseVersion import setuptools from setuptools.package_index import PackageIndex import pytest from . import reset_setup_helpers, reset_distutils_log, fix_hide_setuptools # noqa from . import run_cmd, run_setup, testpackage from ..utils import silence TEST_SETUP_PY = """\ #!/usr/bin/env python from __future__ import print_function import os import sys import ah_bootstrap # reset the name of the package installed by ah_boostrap to # _astropy_helpers_test_--this will prevent any confusion by pkg_resources with # any already installed packages named astropy_helpers # We also disable auto-upgrade by default ah_bootstrap.DIST_NAME = 'astropy-helpers-test' ah_bootstrap.PACKAGE_NAME = '_astropy_helpers_test_' ah_bootstrap.AUTO_UPGRADE = False ah_bootstrap.DOWNLOAD_IF_NEEDED = False try: ah_bootstrap.BOOTSTRAPPER = ah_bootstrap._Bootstrapper.main() ah_bootstrap.use_astropy_helpers({args}) finally: ah_bootstrap.DIST_NAME = 'astropy-helpers' ah_bootstrap.PACKAGE_NAME = 'astropy_helpers' ah_bootstrap.AUTO_UPGRADE = True ah_bootstrap.DOWNLOAD_IF_NEEDED = True # Kind of a hacky way to do this, but this assertion is specifically # for test_check_submodule_no_git # TODO: Rework the tests in this module so that it's easier to test specific # behaviors of ah_bootstrap for each test assert '--no-git' not in sys.argv import _astropy_helpers_test_ filename = os.path.abspath(_astropy_helpers_test_.__file__) filename = filename.replace('.pyc', '.py') # More consistent this way print(filename) """ # The behavior checked in some of the tests depends on the version of # setuptools try: # We need to use LooseVersion here instead of StrictVersion since developer # versions of setuptools ('35.0.2.post20170530') don't satisfy the # StrictVersion criteria even though they satisfy PEP440 SETUPTOOLS_VERSION = LooseVersion(setuptools.__version__).version except: # Broken setuptools? ¯\_(ツ)_/¯ SETUPTOOLS_VERSION = (0, 0, 0) def test_bootstrap_from_submodule(tmpdir, testpackage, capsys): """ Tests importing _astropy_helpers_test_ from a submodule in a git repository. This tests actually performing a fresh clone of the repository without the submodule initialized, and that importing astropy_helpers in that context works transparently after calling `ah_boostrap.use_astropy_helpers`. """ orig_repo = tmpdir.mkdir('orig') # Ensure ah_bootstrap is imported from the local directory import ah_bootstrap # noqa with orig_repo.as_cwd(): run_cmd('git', ['init']) # Write a test setup.py that uses ah_bootstrap; it also ensures that # any previous reference to astropy_helpers is first wiped from # sys.modules orig_repo.join('setup.py').write(TEST_SETUP_PY.format(args='')) run_cmd('git', ['add', 'setup.py']) # Add our own clone of the astropy_helpers repo as a submodule named # astropy_helpers run_cmd('git', ['submodule', 'add', str(testpackage), '_astropy_helpers_test_']) run_cmd('git', ['commit', '-m', 'test repository']) os.chdir(str(tmpdir)) # Creates a clone of our test repo in the directory 'clone' run_cmd('git', ['clone', 'orig', 'clone']) os.chdir('clone') run_setup('setup.py', []) stdout, stderr = capsys.readouterr() path = stdout.strip() # Ensure that the astropy_helpers used by the setup.py is the one that # was imported from git submodule a = os.path.normcase(path) b = os.path.normcase(str(tmpdir.join('clone', '_astropy_helpers_test_', '_astropy_helpers_test_', '__init__.py'))) assert a == b def test_bootstrap_from_submodule_no_locale(tmpdir, testpackage, capsys, monkeypatch): """ Regression test for https://github.com/astropy/astropy/issues/2749 Runs test_bootstrap_from_submodule but with missing locale/language settings. """ for varname in ('LC_ALL', 'LC_CTYPE', 'LANG', 'LANGUAGE'): monkeypatch.delenv(varname, raising=False) test_bootstrap_from_submodule(tmpdir, testpackage, capsys) def test_bootstrap_from_submodule_bad_locale(tmpdir, testpackage, capsys, monkeypatch): """ Additional regression test for https://github.com/astropy/astropy/issues/2749 """ for varname in ('LC_ALL', 'LC_CTYPE', 'LANG', 'LANGUAGE'): monkeypatch.delenv(varname, raising=False) # Test also with bad LC_CTYPE a la http://bugs.python.org/issue18378 monkeypatch.setenv('LC_CTYPE', 'UTF-8') test_bootstrap_from_submodule(tmpdir, testpackage, capsys) def test_check_submodule_no_git(tmpdir, testpackage): """ Tests that when importing astropy_helpers from a submodule, it is still recognized as a submodule even when using the --no-git option. In particular this ensures that the auto-upgrade feature is not activated. """ orig_repo = tmpdir.mkdir('orig') # Ensure ah_bootstrap is imported from the local directory import ah_bootstrap # noqa with orig_repo.as_cwd(): run_cmd('git', ['init']) # Write a test setup.py that uses ah_bootstrap; it also ensures that # any previous reference to astropy_helpers is first wiped from # sys.modules args = 'auto_upgrade=True' orig_repo.join('setup.py').write(TEST_SETUP_PY.format(args=args)) run_cmd('git', ['add', 'setup.py']) # Add our own clone of the astropy_helpers repo as a submodule named # astropy_helpers run_cmd('git', ['submodule', 'add', str(testpackage), '_astropy_helpers_test_']) run_cmd('git', ['commit', '-m', 'test repository']) # Temporarily patch _do_upgrade to fail if called class UpgradeError(Exception): pass def _do_upgrade(*args, **kwargs): raise UpgradeError() orig_do_upgrade = ah_bootstrap._Bootstrapper._do_upgrade ah_bootstrap._Bootstrapper._do_upgrade = _do_upgrade try: run_setup('setup.py', ['--no-git']) except UpgradeError: pytest.fail('Attempted to run auto-upgrade despite importing ' '_astropy_helpers_test_ from a git submodule') finally: ah_bootstrap._Bootstrapper._do_upgrade = orig_do_upgrade # Ensure that the no-git option was in fact set assert not ah_bootstrap.BOOTSTRAPPER.use_git def test_bootstrap_from_directory(tmpdir, testpackage, capsys): """ Tests simply bundling a copy of the astropy_helpers source code in its entirety bundled directly in the source package and not in an archive. """ import ah_bootstrap # noqa source = tmpdir.mkdir('source') testpackage.copy(source.join('_astropy_helpers_test_')) with source.as_cwd(): source.join('setup.py').write(TEST_SETUP_PY.format(args='')) run_setup('setup.py', []) stdout, stderr = capsys.readouterr() stdout = stdout.splitlines() if stdout: path = stdout[-1].strip() else: path = '' # Ensure that the astropy_helpers used by the setup.py is the one that # was imported from git submodule a = os.path.normcase(path) b = os.path.normcase(str(source.join('_astropy_helpers_test_', '_astropy_helpers_test_', '__init__.py'))) assert a == b def test_bootstrap_from_archive(tmpdir, testpackage, capsys): """ Tests importing _astropy_helpers_test_ from a .tar.gz source archive shipped alongside the package that uses it. """ orig_repo = tmpdir.mkdir('orig') # Ensure ah_bootstrap is imported from the local directory import ah_bootstrap # noqa # Make a source distribution of the test package with silence(): run_setup(str(testpackage.join('setup.py')), ['sdist', '--dist-dir=dist', '--formats=gztar']) dist_dir = testpackage.join('dist') for dist_file in dist_dir.visit('*.tar.gz'): dist_file.copy(orig_repo) with orig_repo.as_cwd(): # Write a test setup.py that uses ah_bootstrap; it also ensures that # any previous reference to astropy_helpers is first wiped from # sys.modules args = 'path={0!r}'.format(os.path.basename(str(dist_file))) orig_repo.join('setup.py').write(TEST_SETUP_PY.format(args=args)) run_setup('setup.py', []) stdout, stderr = capsys.readouterr() path = stdout.splitlines()[-1].strip() # Installation from the .tar.gz should have resulted in a .egg # directory that the _astropy_helpers_test_ package was imported from eggs = _get_local_eggs() assert eggs egg = orig_repo.join(eggs[0]) assert os.path.isdir(str(egg)) a = os.path.normcase(path) b = os.path.normcase(str(egg.join('_astropy_helpers_test_', '__init__.py'))) assert a == b def test_download_if_needed(tmpdir, testpackage, capsys): """ Tests the case where astropy_helpers was not actually included in a package, or is otherwise missing, and we need to "download" it. This does not test actually downloading from the internet--this is normally done through setuptools' easy_install command which can also install from a source archive. From the point of view of ah_boostrap the two actions are equivalent, so we can just as easily simulate this by providing a setup.cfg giving the path to a source archive to "download" (as though it were a URL). """ source = tmpdir.mkdir('source') # Ensure ah_bootstrap is imported from the local directory import ah_bootstrap # noqa # Make a source distribution of the test package with silence(): run_setup(str(testpackage.join('setup.py')), ['sdist', '--dist-dir=dist', '--formats=gztar']) dist_dir = testpackage.join('dist') with source.as_cwd(): source.join('setup.py').write(TEST_SETUP_PY.format( args='download_if_needed=True')) source.join('setup.cfg').write(textwrap.dedent("""\ [easy_install] find_links = {find_links} """.format(find_links=str(dist_dir)))) run_setup('setup.py', []) stdout, stderr = capsys.readouterr() # Just take the last line--on Python 2.6 distutils logs warning # messages to stdout instead of stderr, causing them to be mixed up # with our expected output path = stdout.splitlines()[-1].strip() # easy_install should have worked by 'installing' astropy_helpers as a # .egg in the current directory eggs = _get_local_eggs() assert eggs egg = source.join(eggs[0]) assert os.path.isdir(str(egg)) a = os.path.normcase(path) b = os.path.normcase(str(egg.join('_astropy_helpers_test_', '__init__.py'))) assert a == b def test_upgrade(tmpdir, capsys): # Run the testpackage fixture manually, since we use it multiple times in # this test to make different versions of _astropy_helpers_test_ orig_dir = testpackage(tmpdir.mkdir('orig')) # Make a test package that uses _astropy_helpers_test_ source = tmpdir.mkdir('source') dist_dir = source.mkdir('dists') orig_dir.copy(source.join('_astropy_helpers_test_')) with source.as_cwd(): setup_py = TEST_SETUP_PY.format(args='auto_upgrade=True') source.join('setup.py').write(setup_py) # This will be used to later to fake downloading the upgrade package source.join('setup.cfg').write(textwrap.dedent("""\ [easy_install] find_links = {find_links} """.format(find_links=str(dist_dir)))) # Make additional "upgrade" versions of the _astropy_helpers_test_ # package--one of them is version 0.2 and the other is version 0.1.1. The # auto-upgrade should ignore version 0.2 but use version 0.1.1. upgrade_dir_1 = testpackage(tmpdir.mkdir('upgrade_1'), version='0.2') upgrade_dir_2 = testpackage(tmpdir.mkdir('upgrade_2'), version='0.1.1') dists = [] # For each upgrade package go ahead and build a source distribution of it # and copy that source distribution to a dist directory we'll use later to # simulate a 'download' for upgrade_dir in [upgrade_dir_1, upgrade_dir_2]: with silence(): run_setup(str(upgrade_dir.join('setup.py')), ['sdist', '--dist-dir=dist', '--formats=gztar']) dists.append(str(upgrade_dir.join('dist'))) for dist_file in upgrade_dir.visit('*.tar.gz'): dist_file.copy(source.join('dists')) # Monkey with the PackageIndex in ah_bootstrap so that it is initialized # with the test upgrade packages, and so that it does not actually go out # to the internet to look for anything import ah_bootstrap # noqa class FakePackageIndex(PackageIndex): def __init__(self, *args, **kwargs): PackageIndex.__init__(self, *args, **kwargs) self.to_scan = dists def find_packages(self, requirement): # no-op pass ah_bootstrap.PackageIndex = FakePackageIndex try: with source.as_cwd(): # Now run the source setup.py; this test is similar to # test_download_if_needed, but we explicitly check that the correct # *version* of _astropy_helpers_test_ was used run_setup('setup.py', []) stdout, stderr = capsys.readouterr() path = stdout.splitlines()[-1].strip() eggs = _get_local_eggs() assert eggs egg = source.join(eggs[0]) assert os.path.isdir(str(egg)) a = os.path.normcase(path) b = os.path.normcase(str(egg.join('_astropy_helpers_test_', '__init__.py'))) assert a == b assert 'astropy_helpers_test-0.1.1-' in str(egg) finally: ah_bootstrap.PackageIndex = PackageIndex def _get_local_eggs(path='.'): """ Helper utility used by some tests to get the list of egg archive files in a local directory. """ if SETUPTOOLS_VERSION[0] >= 7: eggs = glob.glob(os.path.join(path, '.eggs', '*.egg')) else: eggs = glob.glob('*.egg') return eggs montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/tests/test_git_helpers.py0000644000077000000240000001644213137204755030323 0ustar tomstaff00000000000000import glob import imp import os import pkgutil import re import sys import tarfile import pytest from . import reset_setup_helpers, reset_distutils_log, fix_hide_setuptools # noqa from . import run_cmd, run_setup, cleanup_import PY3 = sys.version_info[0] == 3 if PY3: _text_type = str else: _text_type = unicode # noqa _DEV_VERSION_RE = re.compile(r'\d+\.\d+(?:\.\d+)?\.dev(\d+)') TEST_VERSION_SETUP_PY = """\ #!/usr/bin/env python from setuptools import setup NAME = 'apyhtest_eva' VERSION = {version!r} RELEASE = 'dev' not in VERSION from astropy_helpers.git_helpers import get_git_devstr from astropy_helpers.version_helpers import generate_version_py if not RELEASE: VERSION += get_git_devstr(False) generate_version_py(NAME, VERSION, RELEASE, False, uses_git=not RELEASE) setup(name=NAME, version=VERSION, packages=['apyhtest_eva']) """ TEST_VERSION_INIT = """\ try: from .version import version as __version__ from .version import githash as __githash__ except ImportError: __version__ = __githash__ = '' """ @pytest.fixture def version_test_package(tmpdir, request): def make_test_package(version='42.42.dev'): test_package = tmpdir.mkdir('test_package') test_package.join('setup.py').write( TEST_VERSION_SETUP_PY.format(version=version)) test_package.mkdir('apyhtest_eva').join('__init__.py').write(TEST_VERSION_INIT) with test_package.as_cwd(): run_cmd('git', ['init']) run_cmd('git', ['add', '--all']) run_cmd('git', ['commit', '-m', 'test package']) if '' in sys.path: sys.path.remove('') sys.path.insert(0, '') def finalize(): cleanup_import('apyhtest_eva') request.addfinalizer(finalize) return test_package return make_test_package def test_update_git_devstr(version_test_package, capsys): """Tests that the commit number in the package's version string updates after git commits even without re-running setup.py. """ # We have to call version_test_package to actually create the package test_pkg = version_test_package() with test_pkg.as_cwd(): run_setup('setup.py', ['--version']) stdout, stderr = capsys.readouterr() version = stdout.strip() m = _DEV_VERSION_RE.match(version) assert m, ( "Stdout did not match the version string pattern:" "\n\n{0}\n\nStderr:\n\n{1}".format(stdout, stderr)) revcount = int(m.group(1)) import apyhtest_eva assert apyhtest_eva.__version__ == version # Make a silly git commit with open('.test', 'w'): pass run_cmd('git', ['add', '.test']) run_cmd('git', ['commit', '-m', 'test']) import apyhtest_eva.version imp.reload(apyhtest_eva.version) # Previously this checked packagename.__version__, but in order for that to # be updated we also have to re-import _astropy_init which could be tricky. # Checking directly that the packagename.version module was updated is # sufficient: m = _DEV_VERSION_RE.match(apyhtest_eva.version.version) assert m assert int(m.group(1)) == revcount + 1 # This doesn't test astropy_helpers.get_helpers.update_git_devstr directly # since a copy of that function is made in packagename.version (so that it # can work without astropy_helpers installed). In order to get test # coverage on the actual astropy_helpers copy of that function just call it # directly and compare to the value in packagename from astropy_helpers.git_helpers import update_git_devstr newversion = update_git_devstr(version, path=str(test_pkg)) assert newversion == apyhtest_eva.version.version def test_version_update_in_other_repos(version_test_package, tmpdir): """ Regression test for https://github.com/astropy/astropy-helpers/issues/114 and for https://github.com/astropy/astropy-helpers/issues/107 """ test_pkg = version_test_package() with test_pkg.as_cwd(): run_setup('setup.py', ['build']) # Add the path to the test package to sys.path for now sys.path.insert(0, str(test_pkg)) try: import apyhtest_eva m = _DEV_VERSION_RE.match(apyhtest_eva.__version__) assert m correct_revcount = int(m.group(1)) with tmpdir.as_cwd(): testrepo = tmpdir.mkdir('testrepo') testrepo.chdir() # Create an empty git repo run_cmd('git', ['init']) import apyhtest_eva.version imp.reload(apyhtest_eva.version) m = _DEV_VERSION_RE.match(apyhtest_eva.version.version) assert m assert int(m.group(1)) == correct_revcount correct_revcount = int(m.group(1)) # Add several commits--more than the revcount for the apyhtest_eva package for idx in range(correct_revcount + 5): test_filename = '.test' + str(idx) testrepo.ensure(test_filename) run_cmd('git', ['add', test_filename]) run_cmd('git', ['commit', '-m', 'A message']) import apyhtest_eva.version imp.reload(apyhtest_eva.version) m = _DEV_VERSION_RE.match(apyhtest_eva.version.version) assert m assert int(m.group(1)) == correct_revcount correct_revcount = int(m.group(1)) finally: sys.path.remove(str(test_pkg)) @pytest.mark.parametrize('version', ['1.0.dev', '1.0']) def test_installed_git_version(version_test_package, version, tmpdir, capsys): """ Test for https://github.com/astropy/astropy-helpers/issues/87 Ensures that packages installed with astropy_helpers have a correct copy of the git hash of the installed commit. """ # To test this, it should suffice to build a source dist, unpack it # somewhere outside the git repository, and then do a build and import # from the build directory--no need to "install" as such test_pkg = version_test_package(version) with test_pkg.as_cwd(): run_setup('setup.py', ['build']) try: import apyhtest_eva githash = apyhtest_eva.__githash__ assert githash and isinstance(githash, _text_type) # Ensure that it does in fact look like a git hash and not some # other arbitrary string assert re.match(r'[0-9a-f]{40}', githash) finally: cleanup_import('apyhtest_eva') run_setup('setup.py', ['sdist', '--dist-dir=dist', '--formats=gztar']) tgzs = glob.glob(os.path.join('dist', '*.tar.gz')) assert len(tgzs) == 1 tgz = test_pkg.join(tgzs[0]) build_dir = tmpdir.mkdir('build_dir') tf = tarfile.open(str(tgz), mode='r:gz') tf.extractall(str(build_dir)) with build_dir.as_cwd(): pkg_dir = glob.glob('apyhtest_eva-*')[0] os.chdir(pkg_dir) run_setup('setup.py', ['build']) try: import apyhtest_eva loader = pkgutil.get_loader('apyhtest_eva') # Ensure we are importing the 'packagename' that was just unpacked # into the build_dir assert loader.get_filename().startswith(str(build_dir)) assert apyhtest_eva.__githash__ == githash finally: cleanup_import('apyhtest_eva') montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/tests/test_setup_helpers.py0000644000077000000240000003744113137204755030702 0ustar tomstaff00000000000000import os import sys import stat import shutil import contextlib import pytest from textwrap import dedent from setuptools import Distribution from ..setup_helpers import get_package_info, register_commands from ..commands import build_ext from . import reset_setup_helpers, reset_distutils_log, fix_hide_setuptools # noqa from . import run_setup, cleanup_import def _extension_test_package(tmpdir, request, extension_type='c'): """Creates a simple test package with an extension module.""" test_pkg = tmpdir.mkdir('test_pkg') test_pkg.mkdir('apyhtest_eva').ensure('__init__.py') # TODO: It might be later worth making this particular test package into a # reusable fixture for other build_ext tests if extension_type in ('c', 'both'): # A minimal C extension for testing test_pkg.join('apyhtest_eva', 'unit01.c').write(dedent("""\ #include #ifndef PY3K #if PY_MAJOR_VERSION >= 3 #define PY3K 1 #else #define PY3K 0 #endif #endif #if PY3K static struct PyModuleDef moduledef = { PyModuleDef_HEAD_INIT, "unit01", NULL, -1, NULL }; PyMODINIT_FUNC PyInit_unit01(void) { return PyModule_Create(&moduledef); } #else PyMODINIT_FUNC initunit01(void) { Py_InitModule3("unit01", NULL, NULL); } #endif """)) if extension_type in ('pyx', 'both'): # A minimal Cython extension for testing test_pkg.join('apyhtest_eva', 'unit02.pyx').write(dedent("""\ print("Hello cruel angel.") """)) if extension_type == 'c': extensions = ['unit01.c'] elif extension_type == 'pyx': extensions = ['unit02.pyx'] elif extension_type == 'both': extensions = ['unit01.c', 'unit02.pyx'] extensions_list = [ "Extension('apyhtest_eva.{0}', [join('apyhtest_eva', '{1}')])".format( os.path.splitext(extension)[0], extension) for extension in extensions] test_pkg.join('apyhtest_eva', 'setup_package.py').write(dedent("""\ from setuptools import Extension from os.path import join def get_extensions(): return [{0}] """.format(', '.join(extensions_list)))) test_pkg.join('setup.py').write(dedent("""\ from os.path import join from setuptools import setup from astropy_helpers.setup_helpers import register_commands from astropy_helpers.setup_helpers import get_package_info from astropy_helpers.version_helpers import generate_version_py NAME = 'apyhtest_eva' VERSION = '0.1' RELEASE = True cmdclassd = register_commands(NAME, VERSION, RELEASE) generate_version_py(NAME, VERSION, RELEASE, False, False) package_info = get_package_info() setup( name=NAME, version=VERSION, cmdclass=cmdclassd, **package_info ) """)) if '' in sys.path: sys.path.remove('') sys.path.insert(0, '') def finalize(): cleanup_import('apyhtest_eva') request.addfinalizer(finalize) return test_pkg @pytest.fixture def extension_test_package(tmpdir, request): return _extension_test_package(tmpdir, request, extension_type='both') @pytest.fixture def c_extension_test_package(tmpdir, request): return _extension_test_package(tmpdir, request, extension_type='c') @pytest.fixture def pyx_extension_test_package(tmpdir, request): return _extension_test_package(tmpdir, request, extension_type='pyx') def test_cython_autoextensions(tmpdir): """ Regression test for https://github.com/astropy/astropy-helpers/pull/19 Ensures that Cython extensions in sub-packages are discovered and built only once. """ # Make a simple test package test_pkg = tmpdir.mkdir('test_pkg') test_pkg.mkdir('yoda').mkdir('luke') test_pkg.ensure('yoda', '__init__.py') test_pkg.ensure('yoda', 'luke', '__init__.py') test_pkg.join('yoda', 'luke', 'dagobah.pyx').write( """def testfunc(): pass""") # Required, currently, for get_package_info to work register_commands('yoda', '0.0', False, srcdir=str(test_pkg)) package_info = get_package_info(str(test_pkg)) assert len(package_info['ext_modules']) == 1 assert package_info['ext_modules'][0].name == 'yoda.luke.dagobah' def test_compiler_module(c_extension_test_package): """ Test ensuring that the compiler module is built and installed for packages that have extension modules. """ test_pkg = c_extension_test_package install_temp = test_pkg.mkdir('install_temp') with test_pkg.as_cwd(): # This is one of the simplest ways to install just a package into a # test directory run_setup('setup.py', ['install', '--single-version-externally-managed', '--install-lib={0}'.format(install_temp), '--record={0}'.format(install_temp.join('record.txt'))]) with install_temp.as_cwd(): import apyhtest_eva # Make sure we imported the apyhtest_eva package from the correct place dirname = os.path.abspath(os.path.dirname(apyhtest_eva.__file__)) assert dirname == str(install_temp.join('apyhtest_eva')) import apyhtest_eva._compiler import apyhtest_eva.version assert apyhtest_eva.version.compiler == apyhtest_eva._compiler.compiler assert apyhtest_eva.version.compiler != 'unknown' def test_no_cython_buildext(c_extension_test_package, monkeypatch): """ Regression test for https://github.com/astropy/astropy-helpers/pull/35 This tests the custom build_ext command installed by astropy_helpers when used with a project that has no Cython extensions (but does have one or more normal C extensions). """ test_pkg = c_extension_test_package # In order for this test to test the correct code path we need to fool # build_ext into thinking we don't have Cython installed monkeypatch.setattr(build_ext, 'should_build_with_cython', lambda *args: False) with test_pkg.as_cwd(): run_setup('setup.py', ['build_ext', '--inplace']) sys.path.insert(0, str(test_pkg)) try: import apyhtest_eva.unit01 dirname = os.path.abspath(os.path.dirname(apyhtest_eva.unit01.__file__)) assert dirname == str(test_pkg.join('apyhtest_eva')) finally: sys.path.remove(str(test_pkg)) def test_missing_cython_c_files(pyx_extension_test_package, monkeypatch): """ Regression test for https://github.com/astropy/astropy-helpers/pull/181 Test failure mode when building a package that has Cython modules, but where Cython is not installed and the generated C files are missing. """ test_pkg = pyx_extension_test_package # In order for this test to test the correct code path we need to fool # build_ext into thinking we don't have Cython installed monkeypatch.setattr(build_ext, 'should_build_with_cython', lambda *args: False) with test_pkg.as_cwd(): with pytest.raises(SystemExit) as exc_info: run_setup('setup.py', ['build_ext', '--inplace']) msg = ('Could not find C/C++ file ' '{0}.(c/cpp)'.format('apyhtest_eva/unit02'.replace('/', os.sep))) assert msg in str(exc_info.value) @pytest.mark.parametrize('mode', ['cli', 'cli-w', 'direct', 'deprecated', 'cli-l', 'cli-error']) def test_build_docs(tmpdir, mode): """ Test for build_docs """ import astropy_helpers ah_path = os.path.dirname(astropy_helpers.__file__) test_pkg = tmpdir.mkdir('test_pkg') test_pkg.mkdir('mypackage') test_pkg.join('mypackage').join('__init__.py').write(dedent("""\ def test_function(): pass class A(): pass class B(A): pass """)) docs = test_pkg.mkdir('docs') autosummary = docs.mkdir('_templates').mkdir('autosummary') autosummary.join('base.rst').write('{% extends "autosummary_core/base.rst" %}') autosummary.join('class.rst').write('{% extends "autosummary_core/class.rst" %}') autosummary.join('module.rst').write('{% extends "autosummary_core/module.rst" %}') docs_dir = test_pkg.join('docs') docs_dir.join('conf.py').write(dedent("""\ import sys sys.path.append("../") import warnings with warnings.catch_warnings(): # ignore matplotlib warning warnings.simplefilter("ignore") from astropy_helpers.sphinx.conf import * exclude_patterns.append('_templates') """)) if mode == 'cli-error': docs_dir.join('conf.py').write(dedent(""" raise ValueError("TestException") """)) docs_dir.join('index.rst').write(dedent("""\ .. automodapi:: mypackage """)) test_pkg.join('setup.py').write(dedent("""\ from os.path import join from setuptools import setup, Extension from astropy_helpers.setup_helpers import register_commands, get_package_info NAME = 'mypackage' VERSION = 0.1 RELEASE = True cmdclassd = register_commands(NAME, VERSION, RELEASE) setup( name=NAME, version=VERSION, cmdclass=cmdclassd, **get_package_info() ) """)) with test_pkg.as_cwd(): shutil.copytree(ah_path, 'astropy_helpers') if mode == 'cli': run_setup('setup.py', ['build_docs']) elif mode == 'cli-w': run_setup('setup.py', ['build_docs', '-w']) elif mode == 'cli-l': run_setup('setup.py', ['build_docs', '-l']) elif mode == 'deprecated': run_setup('setup.py', ['build_sphinx']) elif mode == 'direct': # to check coverage with docs_dir.as_cwd(): from sphinx import main try: main(['-b html', '-d _build/doctrees', '.', '_build/html']) except SystemExit as exc: assert exc.code == 0 def test_command_hooks(tmpdir, capsys): """A basic test for pre- and post-command hooks.""" test_pkg = tmpdir.mkdir('test_pkg') test_pkg.mkdir('_welltall_') test_pkg.join('_welltall_', '__init__.py').ensure() # Create a setup_package module with a couple of command hooks in it test_pkg.join('_welltall_', 'setup_package.py').write(dedent("""\ def pre_build_hook(cmd_obj): print('Hello build!') def post_build_hook(cmd_obj): print('Goodbye build!') """)) # A simple setup.py for the test package--running register_commands should # discover and enable the command hooks test_pkg.join('setup.py').write(dedent("""\ from os.path import join from setuptools import setup, Extension from astropy_helpers.setup_helpers import register_commands, get_package_info NAME = '_welltall_' VERSION = 0.1 RELEASE = True cmdclassd = register_commands(NAME, VERSION, RELEASE) setup( name=NAME, version=VERSION, cmdclass=cmdclassd ) """)) with test_pkg.as_cwd(): try: run_setup('setup.py', ['build']) finally: cleanup_import('_welltall_') stdout, stderr = capsys.readouterr() want = dedent("""\ running build running pre_hook from _welltall_.setup_package for build command Hello build! running post_hook from _welltall_.setup_package for build command Goodbye build! """).strip() assert want in stdout def test_adjust_compiler(monkeypatch, tmpdir): """ Regression test for https://github.com/astropy/astropy-helpers/issues/182 """ from distutils import ccompiler, sysconfig class MockLog(object): def __init__(self): self.messages = [] def warn(self, message): self.messages.append(message) good = tmpdir.join('gcc-good') good.write(dedent("""\ #!{python} import sys print('gcc 4.10') sys.exit(0) """.format(python=sys.executable))) good.chmod(stat.S_IRUSR | stat.S_IEXEC) # A "compiler" that reports itself to be a version of Apple's llvm-gcc # which is broken bad = tmpdir.join('gcc-bad') bad.write(dedent("""\ #!{python} import sys print('i686-apple-darwin-llvm-gcc-4.2') sys.exit(0) """.format(python=sys.executable))) bad.chmod(stat.S_IRUSR | stat.S_IEXEC) # A "compiler" that doesn't even know its identity (this reproduces the bug # in #182) ugly = tmpdir.join('gcc-ugly') ugly.write(dedent("""\ #!{python} import sys sys.exit(1) """.format(python=sys.executable))) ugly.chmod(stat.S_IRUSR | stat.S_IEXEC) # Scripts with shebang lines don't work implicitly in Windows when passed # to subprocess.Popen, so... if 'win' in sys.platform: good = ' '.join((sys.executable, str(good))) bad = ' '.join((sys.executable, str(bad))) ugly = ' '.join((sys.executable, str(ugly))) dist = Distribution({}) cmd_cls = build_ext.generate_build_ext_command('astropy', False) cmd = cmd_cls(dist) adjust_compiler = cmd._adjust_compiler @contextlib.contextmanager def test_setup(): log = MockLog() monkeypatch.setattr(build_ext, 'log', log) yield log monkeypatch.undo() @contextlib.contextmanager def compiler_setter_with_environ(compiler): monkeypatch.setenv('CC', compiler) with test_setup() as log: yield log monkeypatch.undo() @contextlib.contextmanager def compiler_setter_with_sysconfig(compiler): monkeypatch.setattr(ccompiler, 'get_default_compiler', lambda: 'unix') monkeypatch.setattr(sysconfig, 'get_config_var', lambda v: compiler) old_cc = os.environ.get('CC') if old_cc is not None: del os.environ['CC'] with test_setup() as log: yield log monkeypatch.undo() monkeypatch.undo() monkeypatch.undo() if old_cc is not None: os.environ['CC'] = old_cc compiler_setters = (compiler_setter_with_environ, compiler_setter_with_sysconfig) for compiler_setter in compiler_setters: with compiler_setter(str(good)): # Should have no side-effects adjust_compiler() with compiler_setter(str(ugly)): # Should just pass without complaint, since we can't determine # anything about the compiler anyways adjust_compiler() # In the following tests we check the log messages just to ensure that the # failures occur on the correct code paths for these cases with compiler_setter_with_environ(str(bad)) as log: with pytest.raises(SystemExit): adjust_compiler() assert len(log.messages) == 1 assert 'will fail to compile' in log.messages[0] with compiler_setter_with_sysconfig(str(bad)): adjust_compiler() assert 'CC' in os.environ and os.environ['CC'] == 'clang' with compiler_setter_with_environ('bogus') as log: with pytest.raises(SystemExit): # Missing compiler? adjust_compiler() assert len(log.messages) == 1 assert 'cannot be found or executed' in log.messages[0] with compiler_setter_with_sysconfig('bogus') as log: with pytest.raises(SystemExit): # Missing compiler? adjust_compiler() assert len(log.messages) == 1 assert 'The C compiler used to compile Python' in log.messages[0] montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/tests/test_utils.py0000644000077000000240000000135713104416125027143 0ustar tomstaff00000000000000import os from ..utils import find_data_files def test_find_data_files(tmpdir): data = tmpdir.mkdir('data') sub1 = data.mkdir('sub1') sub2 = data.mkdir('sub2') sub3 = sub1.mkdir('sub3') for directory in (data, sub1, sub2, sub3): filename = directory.join('data.dat').strpath with open(filename, 'w') as f: f.write('test') filenames = find_data_files(data.strpath, '**/*.dat') filenames = sorted(os.path.relpath(x, data.strpath) for x in filenames) assert filenames[0] == os.path.join('data.dat') assert filenames[1] == os.path.join('sub1', 'data.dat') assert filenames[2] == os.path.join('sub1', 'sub3', 'data.dat') assert filenames[3] == os.path.join('sub2', 'data.dat') montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/utils.py0000644000077000000240000006476513137204755024770 0ustar tomstaff00000000000000# Licensed under a 3-clause BSD style license - see LICENSE.rst from __future__ import absolute_import, unicode_literals import contextlib import functools import imp import inspect import os import sys import glob import textwrap import types import warnings try: from importlib import machinery as import_machinery # Python 3.2 does not have SourceLoader if not hasattr(import_machinery, 'SourceLoader'): import_machinery = None except ImportError: import_machinery = None # Python 3.3's importlib caches filesystem reads for faster imports in the # general case. But sometimes it's necessary to manually invalidate those # caches so that the import system can pick up new generated files. See # https://github.com/astropy/astropy/issues/820 if sys.version_info[:2] >= (3, 3): from importlib import invalidate_caches else: def invalidate_caches(): return None # Python 2/3 compatibility if sys.version_info[0] < 3: string_types = (str, unicode) # noqa else: string_types = (str,) # Note: The following Warning subclasses are simply copies of the Warnings in # Astropy of the same names. class AstropyWarning(Warning): """ The base warning class from which all Astropy warnings should inherit. Any warning inheriting from this class is handled by the Astropy logger. """ class AstropyDeprecationWarning(AstropyWarning): """ A warning class to indicate a deprecated feature. """ class AstropyPendingDeprecationWarning(PendingDeprecationWarning, AstropyWarning): """ A warning class to indicate a soon-to-be deprecated feature. """ def _get_platlib_dir(cmd): """ Given a build command, return the name of the appropriate platform-specific build subdirectory directory (e.g. build/lib.linux-x86_64-2.7) """ plat_specifier = '.{0}-{1}'.format(cmd.plat_name, sys.version[0:3]) return os.path.join(cmd.build_base, 'lib' + plat_specifier) def get_numpy_include_path(): """ Gets the path to the numpy headers. """ # We need to go through this nonsense in case setuptools # downloaded and installed Numpy for us as part of the build or # install, since Numpy may still think it's in "setup mode", when # in fact we're ready to use it to build astropy now. if sys.version_info[0] >= 3: import builtins if hasattr(builtins, '__NUMPY_SETUP__'): del builtins.__NUMPY_SETUP__ import imp import numpy imp.reload(numpy) else: import __builtin__ if hasattr(__builtin__, '__NUMPY_SETUP__'): del __builtin__.__NUMPY_SETUP__ import numpy reload(numpy) try: numpy_include = numpy.get_include() except AttributeError: numpy_include = numpy.get_numpy_include() return numpy_include class _DummyFile(object): """A noop writeable object.""" errors = '' # Required for Python 3.x def write(self, s): pass def flush(self): pass @contextlib.contextmanager def silence(): """A context manager that silences sys.stdout and sys.stderr.""" old_stdout = sys.stdout old_stderr = sys.stderr sys.stdout = _DummyFile() sys.stderr = _DummyFile() exception_occurred = False try: yield except: exception_occurred = True # Go ahead and clean up so that exception handling can work normally sys.stdout = old_stdout sys.stderr = old_stderr raise if not exception_occurred: sys.stdout = old_stdout sys.stderr = old_stderr if sys.platform == 'win32': import ctypes def _has_hidden_attribute(filepath): """ Returns True if the given filepath has the hidden attribute on MS-Windows. Based on a post here: http://stackoverflow.com/questions/284115/cross-platform-hidden-file-detection """ if isinstance(filepath, bytes): filepath = filepath.decode(sys.getfilesystemencoding()) try: attrs = ctypes.windll.kernel32.GetFileAttributesW(filepath) assert attrs != -1 result = bool(attrs & 2) except (AttributeError, AssertionError): result = False return result else: def _has_hidden_attribute(filepath): return False def is_path_hidden(filepath): """ Determines if a given file or directory is hidden. Parameters ---------- filepath : str The path to a file or directory Returns ------- hidden : bool Returns `True` if the file is hidden """ name = os.path.basename(os.path.abspath(filepath)) if isinstance(name, bytes): is_dotted = name.startswith(b'.') else: is_dotted = name.startswith('.') return is_dotted or _has_hidden_attribute(filepath) def walk_skip_hidden(top, onerror=None, followlinks=False): """ A wrapper for `os.walk` that skips hidden files and directories. This function does not have the parameter `topdown` from `os.walk`: the directories must always be recursed top-down when using this function. See also -------- os.walk : For a description of the parameters """ for root, dirs, files in os.walk( top, topdown=True, onerror=onerror, followlinks=followlinks): # These lists must be updated in-place so os.walk will skip # hidden directories dirs[:] = [d for d in dirs if not is_path_hidden(d)] files[:] = [f for f in files if not is_path_hidden(f)] yield root, dirs, files def write_if_different(filename, data): """Write `data` to `filename`, if the content of the file is different. Parameters ---------- filename : str The file name to be written to. data : bytes The data to be written to `filename`. """ assert isinstance(data, bytes) if os.path.exists(filename): with open(filename, 'rb') as fd: original_data = fd.read() else: original_data = None if original_data != data: with open(filename, 'wb') as fd: fd.write(data) def import_file(filename, name=None): """ Imports a module from a single file as if it doesn't belong to a particular package. The returned module will have the optional ``name`` if given, or else a name generated from the filename. """ # Specifying a traditional dot-separated fully qualified name here # results in a number of "Parent module 'astropy' not found while # handling absolute import" warnings. Using the same name, the # namespaces of the modules get merged together. So, this # generates an underscore-separated name which is more likely to # be unique, and it doesn't really matter because the name isn't # used directly here anyway. mode = 'U' if sys.version_info[0] < 3 else 'r' if name is None: basename = os.path.splitext(filename)[0] name = '_'.join(os.path.relpath(basename).split(os.sep)[1:]) if import_machinery: loader = import_machinery.SourceFileLoader(name, filename) mod = loader.load_module() else: with open(filename, mode) as fd: mod = imp.load_module(name, fd, filename, ('.py', mode, 1)) return mod def resolve_name(name): """Resolve a name like ``module.object`` to an object and return it. Raise `ImportError` if the module or name is not found. """ parts = name.split('.') cursor = len(parts) - 1 module_name = parts[:cursor] attr_name = parts[-1] while cursor > 0: try: ret = __import__('.'.join(module_name), fromlist=[attr_name]) break except ImportError: if cursor == 0: raise cursor -= 1 module_name = parts[:cursor] attr_name = parts[cursor] ret = '' for part in parts[cursor:]: try: ret = getattr(ret, part) except AttributeError: raise ImportError(name) return ret if sys.version_info[0] >= 3: def iteritems(dictionary): return dictionary.items() else: def iteritems(dictionary): return dictionary.iteritems() def extends_doc(extended_func): """ A function decorator for use when wrapping an existing function but adding additional functionality. This copies the docstring from the original function, and appends to it (along with a newline) the docstring of the wrapper function. Example ------- >>> def foo(): ... '''Hello.''' ... >>> @extends_doc(foo) ... def bar(): ... '''Goodbye.''' ... >>> print(bar.__doc__) Hello. Goodbye. """ def decorator(func): if not (extended_func.__doc__ is None or func.__doc__ is None): func.__doc__ = '\n\n'.join([extended_func.__doc__.rstrip('\n'), func.__doc__.lstrip('\n')]) return func return decorator # Duplicated from astropy.utils.decorators.deprecated # When fixing issues in this function fix them in astropy first, then # port the fixes over to astropy-helpers def deprecated(since, message='', name='', alternative='', pending=False, obj_type=None): """ Used to mark a function or class as deprecated. To mark an attribute as deprecated, use `deprecated_attribute`. Parameters ------------ since : str The release at which this API became deprecated. This is required. message : str, optional Override the default deprecation message. The format specifier ``func`` may be used for the name of the function, and ``alternative`` may be used in the deprecation message to insert the name of an alternative to the deprecated function. ``obj_type`` may be used to insert a friendly name for the type of object being deprecated. name : str, optional The name of the deprecated function or class; if not provided the name is automatically determined from the passed in function or class, though this is useful in the case of renamed functions, where the new function is just assigned to the name of the deprecated function. For example:: def new_function(): ... oldFunction = new_function alternative : str, optional An alternative function or class name that the user may use in place of the deprecated object. The deprecation warning will tell the user about this alternative if provided. pending : bool, optional If True, uses a AstropyPendingDeprecationWarning instead of a AstropyDeprecationWarning. obj_type : str, optional The type of this object, if the automatically determined one needs to be overridden. """ method_types = (classmethod, staticmethod, types.MethodType) def deprecate_doc(old_doc, message): """ Returns a given docstring with a deprecation message prepended to it. """ if not old_doc: old_doc = '' old_doc = textwrap.dedent(old_doc).strip('\n') new_doc = (('\n.. deprecated:: %(since)s' '\n %(message)s\n\n' % {'since': since, 'message': message.strip()}) + old_doc) if not old_doc: # This is to prevent a spurious 'unexpected unindent' warning from # docutils when the original docstring was blank. new_doc += r'\ ' return new_doc def get_function(func): """ Given a function or classmethod (or other function wrapper type), get the function object. """ if isinstance(func, method_types): func = func.__func__ return func def deprecate_function(func, message): """ Returns a wrapped function that displays an ``AstropyDeprecationWarning`` when it is called. """ if isinstance(func, method_types): func_wrapper = type(func) else: func_wrapper = lambda f: f func = get_function(func) def deprecated_func(*args, **kwargs): if pending: category = AstropyPendingDeprecationWarning else: category = AstropyDeprecationWarning warnings.warn(message, category, stacklevel=2) return func(*args, **kwargs) # If this is an extension function, we can't call # functools.wraps on it, but we normally don't care. # This crazy way to get the type of a wrapper descriptor is # straight out of the Python 3.3 inspect module docs. if type(func) != type(str.__dict__['__add__']): deprecated_func = functools.wraps(func)(deprecated_func) deprecated_func.__doc__ = deprecate_doc( deprecated_func.__doc__, message) return func_wrapper(deprecated_func) def deprecate_class(cls, message): """ Returns a wrapper class with the docstrings updated and an __init__ function that will raise an ``AstropyDeprectationWarning`` warning when called. """ # Creates a new class with the same name and bases as the # original class, but updates the dictionary with a new # docstring and a wrapped __init__ method. __module__ needs # to be manually copied over, since otherwise it will be set # to *this* module (astropy.utils.misc). # This approach seems to make Sphinx happy (the new class # looks enough like the original class), and works with # extension classes (which functools.wraps does not, since # it tries to modify the original class). # We need to add a custom pickler or you'll get # Can't pickle : it's not found as ... # errors. Picklability is required for any class that is # documented by Sphinx. members = cls.__dict__.copy() members.update({ '__doc__': deprecate_doc(cls.__doc__, message), '__init__': deprecate_function(get_function(cls.__init__), message), }) return type(cls.__name__, cls.__bases__, members) def deprecate(obj, message=message, name=name, alternative=alternative, pending=pending): if obj_type is None: if isinstance(obj, type): obj_type_name = 'class' elif inspect.isfunction(obj): obj_type_name = 'function' elif inspect.ismethod(obj) or isinstance(obj, method_types): obj_type_name = 'method' else: obj_type_name = 'object' else: obj_type_name = obj_type if not name: name = get_function(obj).__name__ altmessage = '' if not message or type(message) == type(deprecate): if pending: message = ('The %(func)s %(obj_type)s will be deprecated in a ' 'future version.') else: message = ('The %(func)s %(obj_type)s is deprecated and may ' 'be removed in a future version.') if alternative: altmessage = '\n Use %s instead.' % alternative message = ((message % { 'func': name, 'name': name, 'alternative': alternative, 'obj_type': obj_type_name}) + altmessage) if isinstance(obj, type): return deprecate_class(obj, message) else: return deprecate_function(obj, message) if type(message) == type(deprecate): return deprecate(message) return deprecate def deprecated_attribute(name, since, message=None, alternative=None, pending=False): """ Used to mark a public attribute as deprecated. This creates a property that will warn when the given attribute name is accessed. To prevent the warning (i.e. for internal code), use the private name for the attribute by prepending an underscore (i.e. ``self._name``). Parameters ---------- name : str The name of the deprecated attribute. since : str The release at which this API became deprecated. This is required. message : str, optional Override the default deprecation message. The format specifier ``name`` may be used for the name of the attribute, and ``alternative`` may be used in the deprecation message to insert the name of an alternative to the deprecated function. alternative : str, optional An alternative attribute that the user may use in place of the deprecated attribute. The deprecation warning will tell the user about this alternative if provided. pending : bool, optional If True, uses a AstropyPendingDeprecationWarning instead of a AstropyDeprecationWarning. Examples -------- :: class MyClass: # Mark the old_name as deprecated old_name = misc.deprecated_attribute('old_name', '0.1') def method(self): self._old_name = 42 """ private_name = '_' + name @deprecated(since, name=name, obj_type='attribute') def get(self): return getattr(self, private_name) @deprecated(since, name=name, obj_type='attribute') def set(self, val): setattr(self, private_name, val) @deprecated(since, name=name, obj_type='attribute') def delete(self): delattr(self, private_name) return property(get, set, delete) def minversion(module, version, inclusive=True, version_path='__version__'): """ Returns `True` if the specified Python module satisfies a minimum version requirement, and `False` if not. By default this uses `pkg_resources.parse_version` to do the version comparison if available. Otherwise it falls back on `distutils.version.LooseVersion`. Parameters ---------- module : module or `str` An imported module of which to check the version, or the name of that module (in which case an import of that module is attempted-- if this fails `False` is returned). version : `str` The version as a string that this module must have at a minimum (e.g. ``'0.12'``). inclusive : `bool` The specified version meets the requirement inclusively (i.e. ``>=``) as opposed to strictly greater than (default: `True`). version_path : `str` A dotted attribute path to follow in the module for the version. Defaults to just ``'__version__'``, which should work for most Python modules. Examples -------- >>> import astropy >>> minversion(astropy, '0.4.4') True """ if isinstance(module, types.ModuleType): module_name = module.__name__ elif isinstance(module, string_types): module_name = module try: module = resolve_name(module_name) except ImportError: return False else: raise ValueError('module argument must be an actual imported ' 'module, or the import name of the module; ' 'got {0!r}'.format(module)) if '.' not in version_path: have_version = getattr(module, version_path) else: have_version = resolve_name('.'.join([module.__name__, version_path])) try: from pkg_resources import parse_version except ImportError: from distutils.version import LooseVersion as parse_version if inclusive: return parse_version(have_version) >= parse_version(version) else: return parse_version(have_version) > parse_version(version) # Copy of the classproperty decorator from astropy.utils.decorators class classproperty(property): """ Similar to `property`, but allows class-level properties. That is, a property whose getter is like a `classmethod`. The wrapped method may explicitly use the `classmethod` decorator (which must become before this decorator), or the `classmethod` may be omitted (it is implicit through use of this decorator). .. note:: classproperty only works for *read-only* properties. It does not currently allow writeable/deleteable properties, due to subtleties of how Python descriptors work. In order to implement such properties on a class a metaclass for that class must be implemented. Parameters ---------- fget : callable The function that computes the value of this property (in particular, the function when this is used as a decorator) a la `property`. doc : str, optional The docstring for the property--by default inherited from the getter function. lazy : bool, optional If True, caches the value returned by the first call to the getter function, so that it is only called once (used for lazy evaluation of an attribute). This is analogous to `lazyproperty`. The ``lazy`` argument can also be used when `classproperty` is used as a decorator (see the third example below). When used in the decorator syntax this *must* be passed in as a keyword argument. Examples -------- :: >>> class Foo(object): ... _bar_internal = 1 ... @classproperty ... def bar(cls): ... return cls._bar_internal + 1 ... >>> Foo.bar 2 >>> foo_instance = Foo() >>> foo_instance.bar 2 >>> foo_instance._bar_internal = 2 >>> foo_instance.bar # Ignores instance attributes 2 As previously noted, a `classproperty` is limited to implementing read-only attributes:: >>> class Foo(object): ... _bar_internal = 1 ... @classproperty ... def bar(cls): ... return cls._bar_internal ... @bar.setter ... def bar(cls, value): ... cls._bar_internal = value ... Traceback (most recent call last): ... NotImplementedError: classproperty can only be read-only; use a metaclass to implement modifiable class-level properties When the ``lazy`` option is used, the getter is only called once:: >>> class Foo(object): ... @classproperty(lazy=True) ... def bar(cls): ... print("Performing complicated calculation") ... return 1 ... >>> Foo.bar Performing complicated calculation 1 >>> Foo.bar 1 If a subclass inherits a lazy `classproperty` the property is still re-evaluated for the subclass:: >>> class FooSub(Foo): ... pass ... >>> FooSub.bar Performing complicated calculation 1 >>> FooSub.bar 1 """ def __new__(cls, fget=None, doc=None, lazy=False): if fget is None: # Being used as a decorator--return a wrapper that implements # decorator syntax def wrapper(func): return cls(func, lazy=lazy) return wrapper return super(classproperty, cls).__new__(cls) def __init__(self, fget, doc=None, lazy=False): self._lazy = lazy if lazy: self._cache = {} fget = self._wrap_fget(fget) super(classproperty, self).__init__(fget=fget, doc=doc) # There is a buglet in Python where self.__doc__ doesn't # get set properly on instances of property subclasses if # the doc argument was used rather than taking the docstring # from fget if doc is not None: self.__doc__ = doc def __get__(self, obj, objtype=None): if self._lazy and objtype in self._cache: return self._cache[objtype] if objtype is not None: # The base property.__get__ will just return self here; # instead we pass objtype through to the original wrapped # function (which takes the class as its sole argument) val = self.fget.__wrapped__(objtype) else: val = super(classproperty, self).__get__(obj, objtype=objtype) if self._lazy: if objtype is None: objtype = obj.__class__ self._cache[objtype] = val return val def getter(self, fget): return super(classproperty, self).getter(self._wrap_fget(fget)) def setter(self, fset): raise NotImplementedError( "classproperty can only be read-only; use a metaclass to " "implement modifiable class-level properties") def deleter(self, fdel): raise NotImplementedError( "classproperty can only be read-only; use a metaclass to " "implement modifiable class-level properties") @staticmethod def _wrap_fget(orig_fget): if isinstance(orig_fget, classmethod): orig_fget = orig_fget.__func__ # Using stock functools.wraps instead of the fancier version # found later in this module, which is overkill for this purpose @functools.wraps(orig_fget) def fget(obj): return orig_fget(obj.__class__) # Set the __wrapped__ attribute manually for support on Python 2 fget.__wrapped__ = orig_fget return fget def find_data_files(package, pattern): """ Include files matching ``pattern`` inside ``package``. Parameters ---------- package : str The package inside which to look for data files pattern : str Pattern (glob-style) to match for the data files (e.g. ``*.dat``). This supports the Python 3.5 ``**``recursive syntax. For example, ``**/*.fits`` matches all files ending with ``.fits`` recursively. Only one instance of ``**`` can be included in the pattern. """ if sys.version_info[:2] >= (3, 5): return glob.glob(os.path.join(package, pattern), recursive=True) else: if '**' in pattern: start, end = pattern.split('**') if end.startswith(('/', os.sep)): end = end[1:] matches = glob.glob(os.path.join(package, start, end)) for root, dirs, files in os.walk(os.path.join(package, start)): for dirname in dirs: matches += glob.glob(os.path.join(root, dirname, end)) return matches else: return glob.glob(os.path.join(package, pattern)) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/version.py0000644000077000000240000000670612333217235025276 0ustar tomstaff00000000000000# Autogenerated by Astropy-affiliated package astropy_helpers's setup.py on 2014-05-09 20:29:49.852502 import os import subprocess import warnings def update_git_devstr(version, path=None): """ Updates the git revision string if and only if the path is being imported directly from a git working copy. This ensures that the revision number in the version string is accurate. """ try: # Quick way to determine if we're in git or not - returns '' if not devstr = get_git_devstr(sha=True, show_warning=False, path=path) except OSError: return version if not devstr: # Probably not in git so just pass silently return version if 'dev' in version: # update to the current git revision version_base = version.split('.dev', 1)[0] devstr = get_git_devstr(sha=False, show_warning=False, path=path) return version_base + '.dev' + devstr else: #otherwise it's already the true/release version return version def get_git_devstr(sha=False, show_warning=True, path=None): """ Determines the number of revisions in this repository. Parameters ---------- sha : bool If True, the full SHA1 hash will be returned. Otherwise, the total count of commits in the repository will be used as a "revision number". show_warning : bool If True, issue a warning if git returns an error code, otherwise errors pass silently. path : str or None If a string, specifies the directory to look in to find the git repository. If `None`, the current working directory is used. If given a filename it uses the directory containing that file. Returns ------- devversion : str Either a string with the revsion number (if `sha` is False), the SHA1 hash of the current commit (if `sha` is True), or an empty string if git version info could not be identified. """ if path is None: path = os.getcwd() if not os.path.isdir(path): path = os.path.abspath(os.path.dirname(path)) if sha: cmd = 'rev-parse' # Faster for getting just the hash of HEAD else: cmd = 'rev-list' try: p = subprocess.Popen(['git', cmd, 'HEAD'], cwd=path, stdout=subprocess.PIPE, stderr=subprocess.PIPE, stdin=subprocess.PIPE) stdout, stderr = p.communicate() except OSError as e: if show_warning: warnings.warn('Error running git: ' + str(e)) return '' if p.returncode == 128: if show_warning: warnings.warn('No git repository present! Using default dev ' 'version.') return '' elif p.returncode != 0: if show_warning: warnings.warn('Git failed while determining revision ' 'count: ' + stderr) return '' if sha: return stdout.decode('utf-8')[:40] else: nrev = stdout.decode('utf-8').count('\n') return str(nrev) _last_generated_version = '0.4.dev' version = update_git_devstr(_last_generated_version) githash = get_git_devstr(sha=True, show_warning=False) major = 0 minor = 4 bugfix = 0 release = False debug = False try: from ._compiler import compiler except ImportError: compiler = "unknown" try: from .cython_version import cython_version except ImportError: cython_version = "unknown" montage-wrapper-0.9.9/astropy_helpers/astropy_helpers/version_helpers.py0000644000077000000240000002267313137204755027027 0ustar tomstaff00000000000000# Licensed under a 3-clause BSD style license - see LICENSE.rst """ Utilities for generating the version string for Astropy (or an affiliated package) and the version.py module, which contains version info for the package. Within the generated astropy.version module, the `major`, `minor`, and `bugfix` variables hold the respective parts of the version number (bugfix is '0' if absent). The `release` variable is True if this is a release, and False if this is a development version of astropy. For the actual version string, use:: from astropy.version import version or:: from astropy import __version__ """ from __future__ import division import datetime import imp import os import pkgutil import sys from distutils import log import pkg_resources from . import git_helpers from .distutils_helpers import is_distutils_display_option from .utils import invalidate_caches PY3 = sys.version_info[0] == 3 def _version_split(version): """ Split a version string into major, minor, and bugfix numbers. If any of those numbers are missing the default is zero. Any pre/post release modifiers are ignored. Examples ======== >>> _version_split('1.2.3') (1, 2, 3) >>> _version_split('1.2') (1, 2, 0) >>> _version_split('1.2rc1') (1, 2, 0) >>> _version_split('1') (1, 0, 0) >>> _version_split('') (0, 0, 0) """ parsed_version = pkg_resources.parse_version(version) if hasattr(parsed_version, 'base_version'): # New version parsing for setuptools >= 8.0 if parsed_version.base_version: parts = [int(part) for part in parsed_version.base_version.split('.')] else: parts = [] else: parts = [] for part in parsed_version: if part.startswith('*'): # Ignore any .dev, a, b, rc, etc. break parts.append(int(part)) if len(parts) < 3: parts += [0] * (3 - len(parts)) # In principle a version could have more parts (like 1.2.3.4) but we only # support .. return tuple(parts[:3]) # This is used by setup.py to create a new version.py - see that file for # details. Note that the imports have to be absolute, since this is also used # by affiliated packages. _FROZEN_VERSION_PY_TEMPLATE = """ # Autogenerated by {packagetitle}'s setup.py on {timestamp!s} from __future__ import unicode_literals import datetime {header} major = {major} minor = {minor} bugfix = {bugfix} release = {rel} timestamp = {timestamp!r} debug = {debug} try: from ._compiler import compiler except ImportError: compiler = "unknown" try: from .cython_version import cython_version except ImportError: cython_version = "unknown" """[1:] _FROZEN_VERSION_PY_WITH_GIT_HEADER = """ {git_helpers} _packagename = "{packagename}" _last_generated_version = "{verstr}" _last_githash = "{githash}" # Determine where the source code for this module # lives. If __file__ is not a filesystem path then # it is assumed not to live in a git repo at all. if _get_repo_path(__file__, levels=len(_packagename.split('.'))): version = update_git_devstr(_last_generated_version, path=__file__) githash = get_git_devstr(sha=True, show_warning=False, path=__file__) or _last_githash else: # The file does not appear to live in a git repo so don't bother # invoking git version = _last_generated_version githash = _last_githash """[1:] _FROZEN_VERSION_PY_STATIC_HEADER = """ version = "{verstr}" githash = "{githash}" """[1:] def _get_version_py_str(packagename, version, githash, release, debug, uses_git=True): timestamp = datetime.datetime.now() major, minor, bugfix = _version_split(version) if packagename.lower() == 'astropy': packagetitle = 'Astropy' else: packagetitle = 'Astropy-affiliated package ' + packagename header = '' if uses_git: header = _generate_git_header(packagename, version, githash) elif not githash: # _generate_git_header will already generate a new git has for us, but # for creating a new version.py for a release (even if uses_git=False) # we still need to get the githash to include in the version.py # See https://github.com/astropy/astropy-helpers/issues/141 githash = git_helpers.get_git_devstr(sha=True, show_warning=True) if not header: # If _generate_git_header fails it returns an empty string header = _FROZEN_VERSION_PY_STATIC_HEADER.format(verstr=version, githash=githash) return _FROZEN_VERSION_PY_TEMPLATE.format(packagetitle=packagetitle, timestamp=timestamp, header=header, major=major, minor=minor, bugfix=bugfix, rel=release, debug=debug) def _generate_git_header(packagename, version, githash): """ Generates a header to the version.py module that includes utilities for probing the git repository for updates (to the current git hash, etc.) These utilities should only be available in development versions, and not in release builds. If this fails for any reason an empty string is returned. """ loader = pkgutil.get_loader(git_helpers) source = loader.get_source(git_helpers.__name__) or '' source_lines = source.splitlines() if not source_lines: log.warn('Cannot get source code for astropy_helpers.git_helpers; ' 'git support disabled.') return '' idx = 0 for idx, line in enumerate(source_lines): if line.startswith('# BEGIN'): break git_helpers_py = '\n'.join(source_lines[idx + 1:]) if PY3: verstr = version else: # In Python 2 don't pass in a unicode string; otherwise verstr will # be represented with u'' syntax which breaks on Python 3.x with x # < 3. This is only an issue when developing on multiple Python # versions at once verstr = version.encode('utf8') new_githash = git_helpers.get_git_devstr(sha=True, show_warning=False) if new_githash: githash = new_githash return _FROZEN_VERSION_PY_WITH_GIT_HEADER.format( git_helpers=git_helpers_py, packagename=packagename, verstr=verstr, githash=githash) def generate_version_py(packagename, version, release=None, debug=None, uses_git=True, srcdir='.'): """Regenerate the version.py module if necessary.""" try: version_module = get_pkg_version_module(packagename) try: last_generated_version = version_module._last_generated_version except AttributeError: last_generated_version = version_module.version try: last_githash = version_module._last_githash except AttributeError: last_githash = version_module.githash current_release = version_module.release current_debug = version_module.debug except ImportError: version_module = None last_generated_version = None last_githash = None current_release = None current_debug = None if release is None: # Keep whatever the current value is, if it exists release = bool(current_release) if debug is None: # Likewise, keep whatever the current value is, if it exists debug = bool(current_debug) version_py = os.path.join(srcdir, packagename, 'version.py') if (last_generated_version != version or current_release != release or current_debug != debug): if '-q' not in sys.argv and '--quiet' not in sys.argv: log.set_threshold(log.INFO) if is_distutils_display_option(): # Always silence unnecessary log messages when display options are # being used log.set_threshold(log.WARN) log.info('Freezing version number to {0}'.format(version_py)) with open(version_py, 'w') as f: # This overwrites the actual version.py f.write(_get_version_py_str(packagename, version, last_githash, release, debug, uses_git=uses_git)) invalidate_caches() if version_module: imp.reload(version_module) def get_pkg_version_module(packagename, fromlist=None): """Returns the package's .version module generated by `astropy_helpers.version_helpers.generate_version_py`. Raises an ImportError if the version module is not found. If ``fromlist`` is an iterable, return a tuple of the members of the version module corresponding to the member names given in ``fromlist``. Raises an `AttributeError` if any of these module members are not found. """ if not fromlist: # Due to a historical quirk of Python's import implementation, # __import__ will not return submodules of a package if 'fromlist' is # empty. # TODO: For Python 3.1 and up it may be preferable to use importlib # instead of the __import__ builtin return __import__(packagename + '.version', fromlist=['']) else: mod = __import__(packagename + '.version', fromlist=fromlist) return tuple(getattr(mod, member) for member in fromlist) montage-wrapper-0.9.9/astropy_helpers/astropy_helpers.egg-info/0000755000077000000240000000000013137205364024723 5ustar tomstaff00000000000000montage-wrapper-0.9.9/astropy_helpers/astropy_helpers.egg-info/dependency_links.txt0000644000077000000240000000000112333217235030766 0ustar tomstaff00000000000000 montage-wrapper-0.9.9/astropy_helpers/astropy_helpers.egg-info/not-zip-safe0000644000077000000240000000000112333217235027146 0ustar tomstaff00000000000000 montage-wrapper-0.9.9/astropy_helpers/astropy_helpers.egg-info/PKG-INFO0000644000077000000240000000050612333217235026016 0ustar tomstaff00000000000000Metadata-Version: 1.1 Name: astropy-helpers Version: 0.4.dev59 Summary: UNKNOWN Home-page: http://astropy.org Author: The Astropy Developers Author-email: astropy.team@gmail.com License: BSD Download-URL: http://pypi.python.org/packages/source/a/astropy-helpers/astropy-0.4.dev59.tar.gz Description: UNKNOWN Platform: UNKNOWN montage-wrapper-0.9.9/astropy_helpers/astropy_helpers.egg-info/SOURCES.txt0000644000077000000240000000470212333217236026610 0ustar tomstaff00000000000000LICENSE.rst MANIFEST.in README.rst ah_bootstrap.py ez_setup.py setup.cfg setup.py astropy_helpers/__init__.py astropy_helpers/git_helpers.py astropy_helpers/setup_helpers.py astropy_helpers/test_helpers.py astropy_helpers/utils.py astropy_helpers/version.py astropy_helpers/version_helpers.py astropy_helpers.egg-info/PKG-INFO astropy_helpers.egg-info/SOURCES.txt astropy_helpers.egg-info/dependency_links.txt astropy_helpers.egg-info/not-zip-safe astropy_helpers.egg-info/top_level.txt astropy_helpers/compat/__init__.py astropy_helpers/compat/subprocess.py astropy_helpers/compat/_subprocess_py2/__init__.py astropy_helpers/sphinx/__init__.py astropy_helpers/sphinx/conf.py astropy_helpers/sphinx/setup_package.py astropy_helpers/sphinx/ext/__init__.py astropy_helpers/sphinx/ext/astropyautosummary.py astropy_helpers/sphinx/ext/automodapi.py astropy_helpers/sphinx/ext/automodsumm.py astropy_helpers/sphinx/ext/changelog_links.py astropy_helpers/sphinx/ext/comment_eater.py astropy_helpers/sphinx/ext/compiler_unparse.py astropy_helpers/sphinx/ext/docscrape.py astropy_helpers/sphinx/ext/docscrape_sphinx.py astropy_helpers/sphinx/ext/doctest.py astropy_helpers/sphinx/ext/edit_on_github.py astropy_helpers/sphinx/ext/numpydoc.py astropy_helpers/sphinx/ext/phantom_import.py astropy_helpers/sphinx/ext/tocdepthfix.py astropy_helpers/sphinx/ext/traitsdoc.py astropy_helpers/sphinx/ext/utils.py astropy_helpers/sphinx/ext/viewcode.py astropy_helpers/sphinx/ext/templates/autosummary_core/base.rst astropy_helpers/sphinx/ext/templates/autosummary_core/class.rst astropy_helpers/sphinx/ext/templates/autosummary_core/module.rst astropy_helpers/sphinx/ext/tests/__init__.py astropy_helpers/sphinx/ext/tests/test_automodapi.py astropy_helpers/sphinx/ext/tests/test_automodsumm.py astropy_helpers/sphinx/ext/tests/test_utils.py astropy_helpers/sphinx/themes/bootstrap-astropy/globaltoc.html astropy_helpers/sphinx/themes/bootstrap-astropy/layout.html astropy_helpers/sphinx/themes/bootstrap-astropy/localtoc.html astropy_helpers/sphinx/themes/bootstrap-astropy/searchbox.html astropy_helpers/sphinx/themes/bootstrap-astropy/theme.conf astropy_helpers/sphinx/themes/bootstrap-astropy/static/astropy_linkout_20.png astropy_helpers/sphinx/themes/bootstrap-astropy/static/astropy_logo.ico astropy_helpers/sphinx/themes/bootstrap-astropy/static/astropy_logo_32.png astropy_helpers/sphinx/themes/bootstrap-astropy/static/bootstrap-astropy.css astropy_helpers/sphinx/themes/bootstrap-astropy/static/sidebar.jsmontage-wrapper-0.9.9/astropy_helpers/astropy_helpers.egg-info/top_level.txt0000644000077000000240000000002012333217235027442 0ustar tomstaff00000000000000astropy_helpers montage-wrapper-0.9.9/astropy_helpers/CHANGES.rst0000644000077000000240000003535113137204755021622 0ustar tomstaff00000000000000astropy-helpers Changelog ************************* 2.0.1 (2017-07-28) ------------------ - Fix compatibility with Sphinx <1.5. [#326] 2.0 (2017-07-06) ---------------- - Add support for package that lies in a subdirectory. [#249] - Removing ``compat.subprocess``. [#298] - Python 3.3 is no longer supported. [#300] - The 'automodapi' Sphinx extension (and associated dependencies) has now been moved to a standalone package which can be found at https://github.com/astropy/sphinx-automodapi - this is now bundled in astropy-helpers under astropy_helpers.extern.automodapi for convenience. Version shipped with astropy-helpers is v0.6. [#278, #303, #309, #323] - The ``numpydoc`` Sphinx extension has now been moved to ``astropy_helpers.extern``. [#278] - Fix ``build_docs`` error catching, so it doesn't hide Sphinx errors. [#292] - Fix compatibility with Sphinx 1.6. [#318] - Updating ez_setup.py to the last version before it's removal. [#321] 1.3.1 (2017-03-18) ------------------ - Fixed the missing button to hide output in documentation code blocks. [#287] - Fixed bug when ``build_docs`` when running with the clean (-l) option. [#289] - Add alternative location for various intersphinx inventories to fall back to. [#293] 1.3 (2016-12-16) ---------------- - ``build_sphinx`` has been deprecated in favor of the ``build_docs`` command. [#246] - Force the use of Cython's old ``build_ext`` command. A new ``build_ext`` command was added in Cython 0.25, but it does not work with astropy-helpers currently. [#261] 1.2 (2016-06-18) ---------------- - Added sphinx configuration value ``automodsumm_inherited_members``. If ``True`` this will include members that are inherited from a base class in the generated API docs. Defaults to ``False`` which matches the previous behavior. [#215] - Fixed ``build_sphinx`` to recognize builds that succeeded but have output *after* the "build succeeded." statement. This only applies when ``--warnings-returncode`` is given (which is primarily relevant for Travis documentation builds). [#223] - Fixed ``build_sphinx`` the sphinx extensions to not output a spurious warning for sphinx versions > 1.4. [#229] - Add Python version dependent local sphinx inventories that contain otherwise missing references. [#216] - ``astropy_helpers`` now require Sphinx 1.3 or later. [#226] 1.1.2 (2016-03-9) ----------------- - The CSS for the sphinx documentation was altered to prevent some text overflow problems. [#217] 1.1.1 (2015-12-23) ------------------ - Fixed crash in build with ``AttributeError: cython_create_listing`` with older versions of setuptools. [#209, #210] 1.1 (2015-12-10) ---------------- - The original ``AstropyTest`` class in ``astropy_helpers``, which implements the ``setup.py test`` command, is deprecated in favor of moving the implementation of that command closer to the actual Astropy test runner in ``astropy.tests``. Now a dummy ``test`` command is provided solely for informing users that they need ``astropy`` installed to run the tests (however, the previous, now deprecated implementation is still provided and continues to work with older versions of Astropy). See the related issue for more details. [#184] - Added a useful new utility function to ``astropy_helpers.utils`` called ``find_data_files``. This is similar to the ``find_packages`` function in setuptools in that it can be used to search a package for data files (matching a pattern) that can be passed to the ``package_data`` argument for ``setup()``. See the docstring to ``astropy_helpers.utils.find_data_files`` for more details. [#42] - The ``astropy_helpers`` module now sets the global ``_ASTROPY_SETUP_`` flag upon import (from within a ``setup.py``) script, so it's not necessary to have this in the ``setup.py`` script explicitly. If in doubt though, there's no harm in setting it twice. Putting it in ``astropy_helpers`` just ensures that any other imports that occur during build will have this flag set. [#191] - It is now possible to use Cython as a ``setup_requires`` build requirement, and still build Cython extensions even if Cython wasn't available at the beginning of the build processes (that is, is automatically downloaded via setuptools' processing of ``setup_requires``). [#185] - Moves the ``adjust_compiler`` check into the ``build_ext`` command itself, so it's only used when actually building extension modules. This also deprecates the stand-alone ``adjust_compiler`` function. [#76] - When running the ``build_sphinx`` / ``build_docs`` command with the ``-w`` option, the output from Sphinx is streamed as it runs instead of silently buffering until the doc build is complete. [#197] 1.0.7 (unreleased) ------------------ - Fix missing import in ``astropy_helpers/utils.py``. [#196] 1.0.6 (2015-12-04) ------------------ - Fixed bug where running ``./setup.py build_sphinx`` could return successfully even when the build was not successful (and should have returned a non-zero error code). [#199] 1.0.5 (2015-10-02) ------------------ - Fixed a regression in the ``./setup.py test`` command that was introduced in v1.0.4. 1.0.4 (2015-10-02) ------------------ - Fixed issue with the sphinx documentation css where the line numbers for code blocks were not aligned with the code. [#179, #180] - Fixed crash that could occur when trying to build Cython extension modules when Cython isn't installed. Normally this still results in a failed build, but was supposed to provide a useful error message rather than crash outright (this was a regression introduced in v1.0.3). [#181] - Fixed a crash that could occur on Python 3 when a working C compiler isn't found. [#182] - Quieted warnings about deprecated Numpy API in Cython extensions, when building Cython extensions against Numpy >= 1.7. [#183, #186] - Improved support for py.test >= 2.7--running the ``./setup.py test`` command now copies all doc pages into the temporary test directory as well, so that all test files have a "common root directory". [#189, #190] 1.0.3 (2015-07-22) ------------------ - Added workaround for sphinx-doc/sphinx#1843, a but in Sphinx which prevented descriptor classes with a custom metaclass from being documented correctly. [#158] - Added an alias for the ``./setup.py build_sphinx`` command as ``./setup.py build_docs`` which, to a new contributor, should hopefully be less cryptic. [#161] - The fonts in graphviz diagrams now match the font of the HTML content. [#169] - When the documentation is built on readthedocs.org, MathJax will be used for math rendering. When built elsewhere, the "pngmath" extension is still used for math rendering. [#170] - Fix crash when importing astropy_helpers when running with ``python -OO`` [#171] - The ``build`` and ``build_ext`` stages now correctly recognize the presence of C++ files in Cython extensions (previously only vanilla C worked). [#173] 1.0.2 (2015-04-02) ------------------ - Various fixes enabling the astropy-helpers Sphinx build command and Sphinx extensions to work with Sphinx 1.3. [#148] - More improvement to the ability to handle multiple versions of astropy-helpers being imported in the same Python interpreter session in the (somewhat rare) case of nested installs. [#147] - To better support high resolution displays, use SVG for the astropy logo and linkout image, falling back to PNGs for browsers that support it. [#150, #151] - Improve ``setup_helpers.get_compiler_version`` to work with more compilers, and to return more info. This will help fix builds of Astropy on less common compilers, like Sun C. [#153] 1.0.1 (2015-03-04) ------------------ - Released in concert with v0.4.8 to address the same issues. 0.4.8 (2015-03-04) ------------------ - Improved the ``ah_bootstrap`` script's ability to override existing installations of astropy-helpers with new versions in the context of installing multiple packages simultaneously within the same Python interpreter (e.g. when one package has in its ``setup_requires`` another package that uses a different version of astropy-helpers. [#144] - Added a workaround to an issue in matplotlib that can, in rare cases, lead to a crash when installing packages that import matplotlib at build time. [#144] 1.0 (2015-02-17) ---------------- - Added new pre-/post-command hook points for ``setup.py`` commands. Now any package can define code to run before and/or after any ``setup.py`` command without having to manually subclass that command by adding ``pre__hook`` and ``post__hook`` callables to the package's ``setup_package.py`` module. See the PR for more details. [#112] - The following objects in the ``astropy_helpers.setup_helpers`` module have been relocated: - ``get_dummy_distribution``, ``get_distutils_*``, ``get_compiler_option``, ``add_command_option``, ``is_distutils_display_option`` -> ``astropy_helpers.distutils_helpers`` - ``should_build_with_cython``, ``generate_build_ext_command`` -> ``astropy_helpers.commands.build_ext`` - ``AstropyBuildPy`` -> ``astropy_helpers.commands.build_py`` - ``AstropyBuildSphinx`` -> ``astropy_helpers.commands.build_sphinx`` - ``AstropyInstall`` -> ``astropy_helpers.commands.install`` - ``AstropyInstallLib`` -> ``astropy_helpers.commands.install_lib`` - ``AstropyRegister`` -> ``astropy_helpers.commands.register`` - ``get_pkg_version_module`` -> ``astropy_helpers.version_helpers`` - ``write_if_different``, ``import_file``, ``get_numpy_include_path`` -> ``astropy_helpers.utils`` All of these are "soft" deprecations in the sense that they are still importable from ``astropy_helpers.setup_helpers`` for now, and there is no (easy) way to produce deprecation warnings when importing these objects from ``setup_helpers`` rather than directly from the modules they are defined in. But please consider updating any imports to these objects. [#110] - Use of the ``astropy.sphinx.ext.astropyautosummary`` extension is deprecated for use with Sphinx < 1.2. Instead it should suffice to remove this extension for the ``extensions`` list in your ``conf.py`` and add the stock ``sphinx.ext.autosummary`` instead. [#131] 0.4.7 (2015-02-17) ------------------ - Fixed incorrect/missing git hash being added to the generated ``version.py`` when creating a release. [#141] 0.4.6 (2015-02-16) ------------------ - Fixed problems related to the automatically generated _compiler module not being created properly. [#139] 0.4.5 (2015-02-11) ------------------ - Fixed an issue where ah_bootstrap.py could blow up when astropy_helper's version number is 1.0. - Added a workaround for documentation of properties in the rare case where the class's metaclass has a property of the same name. [#130] - Fixed an issue on Python 3 where importing a package using astropy-helper's generated version.py module would crash when the current working directory is an empty git repository. [#114, #137] - Fixed an issue where the "revision count" appended to .dev versions by the generated version.py did not accurately reflect the revision count for the package it belongs to, and could be invalid if the current working directory is an unrelated git repository. [#107, #137] - Likewise, fixed a confusing warning message that could occur in the same circumstances as the above issue. [#121, #137] 0.4.4 (2014-12-31) ------------------ - More improvements for building the documentation using Python 3.x. [#100] - Additional minor fixes to Python 3 support. [#115] - Updates to support new test features in Astropy [#92, #106] 0.4.3 (2014-10-22) ------------------ - The generated ``version.py`` file now preserves the git hash of installed copies of the package as well as when building a source distribution. That is, the git hash of the changeset that was installed/released is preserved. [#87] - In smart resolver add resolution for class links when they exist in the intersphinx inventory, but not the mapping of the current package (e.g. when an affiliated package uses an astropy core class of which "actual" and "documented" location differs) [#88] - Fixed a bug that could occur when running ``setup.py`` for the first time in a repository that uses astropy-helpers as a submodule: ``AttributeError: 'NoneType' object has no attribute 'mkdtemp'`` [#89] - Fixed a bug where optional arguments to the ``doctest-skip`` Sphinx directive were sometimes being left in the generated documentation output. [#90] - Improved support for building the documentation using Python 3.x. [#96] - Avoid error message if .git directory is not present. [#91] 0.4.2 (2014-08-09) ------------------ - Fixed some CSS issues in generated API docs. [#69] - Fixed the warning message that could be displayed when generating a version number with some older versions of git. [#77] - Fixed automodsumm to work with new versions of Sphinx (>= 1.2.2). [#80] 0.4.1 (2014-08-08) ------------------ - Fixed git revision count on systems with git versions older than v1.7.2. [#70] - Fixed display of warning text when running a git command fails (previously the output of stderr was not being decoded properly). [#70] - The ``--offline`` flag to ``setup.py`` understood by ``ah_bootstrap.py`` now also prevents git from going online to fetch submodule updates. [#67] - The Sphinx extension for converting issue numbers to links in the changelog now supports working on arbitrary pages via a new ``conf.py`` setting: ``changelog_links_docpattern``. By default it affects the ``changelog`` and ``whatsnew`` pages in one's Sphinx docs. [#61] - Fixed crash that could result from users with missing/misconfigured locale settings. [#58] - The font used for code examples in the docs is now the system-defined ``monospace`` font, rather than ``Minaco``, which is not available on all platforms. [#50] 0.4 (2014-07-15) ---------------- - Initial release of astropy-helpers. See `APE4 `_ for details of the motivation and design of this package. - The ``astropy_helpers`` package replaces the following modules in the ``astropy`` package: - ``astropy.setup_helpers`` -> ``astropy_helpers.setup_helpers`` - ``astropy.version_helpers`` -> ``astropy_helpers.version_helpers`` - ``astropy.sphinx`` - > ``astropy_helpers.sphinx`` These modules should be considered deprecated in ``astropy``, and any new, non-critical changes to those modules will be made in ``astropy_helpers`` instead. Affiliated packages wishing to make use those modules (as in the Astropy package-template) should use the versions from ``astropy_helpers`` instead, and include the ``ah_bootstrap.py`` script in their project, for bootstrapping the ``astropy_helpers`` package in their setup.py script. montage-wrapper-0.9.9/astropy_helpers/CONTRIBUTING.md0000644000077000000240000000216512405252770022243 0ustar tomstaff00000000000000Contributing to astropy-helpers =============================== The guidelines for contributing to ``astropy-helpers`` are generally the same as the [contributing guidelines for the astropy core package](http://github.com/astropy/astropy/blob/master/CONTRIBUTING.md). Basically, report relevant issues in the ``astropy-helpers`` issue tracker, and we welcome pull requests that broadly follow the [Astropy coding guidelines](http://docs.astropy.org/en/latest/development/codeguide.html). The key subtlety lies in understanding the relationship between ``astropy`` and ``astropy-helpers``. This package contains the build, installation, and documentation tools used by astropy. It also includes support for the ``setup.py test`` command, though Astropy is still required for this to function (it does not currently include the full Astropy test runner). So issues or improvements to that functionality should be addressed in this package. Any other aspect of the [astropy core package](http://github.com/astropy/astropy) (or any other package that uses ``astropy-helpers``) should be addressed in the github repository for that package. montage-wrapper-0.9.9/astropy_helpers/ez_setup.py0000644000077000000240000003037113137204755022225 0ustar tomstaff00000000000000#!/usr/bin/env python """ Setuptools bootstrapping installer. Maintained at https://github.com/pypa/setuptools/tree/bootstrap. Run this script to install or upgrade setuptools. This method is DEPRECATED. Check https://github.com/pypa/setuptools/issues/581 for more details. """ import os import shutil import sys import tempfile import zipfile import optparse import subprocess import platform import textwrap import contextlib from distutils import log try: from urllib.request import urlopen except ImportError: from urllib2 import urlopen try: from site import USER_SITE except ImportError: USER_SITE = None # 33.1.1 is the last version that supports setuptools self upgrade/installation. DEFAULT_VERSION = "33.1.1" DEFAULT_URL = "https://pypi.io/packages/source/s/setuptools/" DEFAULT_SAVE_DIR = os.curdir DEFAULT_DEPRECATION_MESSAGE = "ez_setup.py is deprecated and when using it setuptools will be pinned to {0} since it's the last version that supports setuptools self upgrade/installation, check https://github.com/pypa/setuptools/issues/581 for more info; use pip to install setuptools" MEANINGFUL_INVALID_ZIP_ERR_MSG = 'Maybe {0} is corrupted, delete it and try again.' log.warn(DEFAULT_DEPRECATION_MESSAGE.format(DEFAULT_VERSION)) def _python_cmd(*args): """ Execute a command. Return True if the command succeeded. """ args = (sys.executable,) + args return subprocess.call(args) == 0 def _install(archive_filename, install_args=()): """Install Setuptools.""" with archive_context(archive_filename): # installing log.warn('Installing Setuptools') if not _python_cmd('setup.py', 'install', *install_args): log.warn('Something went wrong during the installation.') log.warn('See the error message above.') # exitcode will be 2 return 2 def _build_egg(egg, archive_filename, to_dir): """Build Setuptools egg.""" with archive_context(archive_filename): # building an egg log.warn('Building a Setuptools egg in %s', to_dir) _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir) # returning the result log.warn(egg) if not os.path.exists(egg): raise IOError('Could not build the egg.') class ContextualZipFile(zipfile.ZipFile): """Supplement ZipFile class to support context manager for Python 2.6.""" def __enter__(self): return self def __exit__(self, type, value, traceback): self.close() def __new__(cls, *args, **kwargs): """Construct a ZipFile or ContextualZipFile as appropriate.""" if hasattr(zipfile.ZipFile, '__exit__'): return zipfile.ZipFile(*args, **kwargs) return super(ContextualZipFile, cls).__new__(cls) @contextlib.contextmanager def archive_context(filename): """ Unzip filename to a temporary directory, set to the cwd. The unzipped target is cleaned up after. """ tmpdir = tempfile.mkdtemp() log.warn('Extracting in %s', tmpdir) old_wd = os.getcwd() try: os.chdir(tmpdir) try: with ContextualZipFile(filename) as archive: archive.extractall() except zipfile.BadZipfile as err: if not err.args: err.args = ('', ) err.args = err.args + ( MEANINGFUL_INVALID_ZIP_ERR_MSG.format(filename), ) raise # going in the directory subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0]) os.chdir(subdir) log.warn('Now working in %s', subdir) yield finally: os.chdir(old_wd) shutil.rmtree(tmpdir) def _do_download(version, download_base, to_dir, download_delay): """Download Setuptools.""" py_desig = 'py{sys.version_info[0]}.{sys.version_info[1]}'.format(sys=sys) tp = 'setuptools-{version}-{py_desig}.egg' egg = os.path.join(to_dir, tp.format(**locals())) if not os.path.exists(egg): archive = download_setuptools(version, download_base, to_dir, download_delay) _build_egg(egg, archive, to_dir) sys.path.insert(0, egg) # Remove previously-imported pkg_resources if present (see # https://bitbucket.org/pypa/setuptools/pull-request/7/ for details). if 'pkg_resources' in sys.modules: _unload_pkg_resources() import setuptools setuptools.bootstrap_install_from = egg def use_setuptools( version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=DEFAULT_SAVE_DIR, download_delay=15): """ Ensure that a setuptools version is installed. Return None. Raise SystemExit if the requested version or later cannot be installed. """ to_dir = os.path.abspath(to_dir) # prior to importing, capture the module state for # representative modules. rep_modules = 'pkg_resources', 'setuptools' imported = set(sys.modules).intersection(rep_modules) try: import pkg_resources pkg_resources.require("setuptools>=" + version) # a suitable version is already installed return except ImportError: # pkg_resources not available; setuptools is not installed; download pass except pkg_resources.DistributionNotFound: # no version of setuptools was found; allow download pass except pkg_resources.VersionConflict as VC_err: if imported: _conflict_bail(VC_err, version) # otherwise, unload pkg_resources to allow the downloaded version to # take precedence. del pkg_resources _unload_pkg_resources() return _do_download(version, download_base, to_dir, download_delay) def _conflict_bail(VC_err, version): """ Setuptools was imported prior to invocation, so it is unsafe to unload it. Bail out. """ conflict_tmpl = textwrap.dedent(""" The required version of setuptools (>={version}) is not available, and can't be installed while this script is running. Please install a more recent version first, using 'easy_install -U setuptools'. (Currently using {VC_err.args[0]!r}) """) msg = conflict_tmpl.format(**locals()) sys.stderr.write(msg) sys.exit(2) def _unload_pkg_resources(): sys.meta_path = [ importer for importer in sys.meta_path if importer.__class__.__module__ != 'pkg_resources.extern' ] del_modules = [ name for name in sys.modules if name.startswith('pkg_resources') ] for mod_name in del_modules: del sys.modules[mod_name] def _clean_check(cmd, target): """ Run the command to download target. If the command fails, clean up before re-raising the error. """ try: subprocess.check_call(cmd) except subprocess.CalledProcessError: if os.access(target, os.F_OK): os.unlink(target) raise def download_file_powershell(url, target): """ Download the file at url to target using Powershell. Powershell will validate trust. Raise an exception if the command cannot complete. """ target = os.path.abspath(target) ps_cmd = ( "[System.Net.WebRequest]::DefaultWebProxy.Credentials = " "[System.Net.CredentialCache]::DefaultCredentials; " '(new-object System.Net.WebClient).DownloadFile("%(url)s", "%(target)s")' % locals() ) cmd = [ 'powershell', '-Command', ps_cmd, ] _clean_check(cmd, target) def has_powershell(): """Determine if Powershell is available.""" if platform.system() != 'Windows': return False cmd = ['powershell', '-Command', 'echo test'] with open(os.path.devnull, 'wb') as devnull: try: subprocess.check_call(cmd, stdout=devnull, stderr=devnull) except Exception: return False return True download_file_powershell.viable = has_powershell def download_file_curl(url, target): cmd = ['curl', url, '--location', '--silent', '--output', target] _clean_check(cmd, target) def has_curl(): cmd = ['curl', '--version'] with open(os.path.devnull, 'wb') as devnull: try: subprocess.check_call(cmd, stdout=devnull, stderr=devnull) except Exception: return False return True download_file_curl.viable = has_curl def download_file_wget(url, target): cmd = ['wget', url, '--quiet', '--output-document', target] _clean_check(cmd, target) def has_wget(): cmd = ['wget', '--version'] with open(os.path.devnull, 'wb') as devnull: try: subprocess.check_call(cmd, stdout=devnull, stderr=devnull) except Exception: return False return True download_file_wget.viable = has_wget def download_file_insecure(url, target): """Use Python to download the file, without connection authentication.""" src = urlopen(url) try: # Read all the data in one block. data = src.read() finally: src.close() # Write all the data in one block to avoid creating a partial file. with open(target, "wb") as dst: dst.write(data) download_file_insecure.viable = lambda: True def get_best_downloader(): downloaders = ( download_file_powershell, download_file_curl, download_file_wget, download_file_insecure, ) viable_downloaders = (dl for dl in downloaders if dl.viable()) return next(viable_downloaders, None) def download_setuptools( version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=DEFAULT_SAVE_DIR, delay=15, downloader_factory=get_best_downloader): """ Download setuptools from a specified location and return its filename. `version` should be a valid setuptools version number that is available as an sdist for download under the `download_base` URL (which should end with a '/'). `to_dir` is the directory where the egg will be downloaded. `delay` is the number of seconds to pause before an actual download attempt. ``downloader_factory`` should be a function taking no arguments and returning a function for downloading a URL to a target. """ # making sure we use the absolute path to_dir = os.path.abspath(to_dir) zip_name = "setuptools-%s.zip" % version url = download_base + zip_name saveto = os.path.join(to_dir, zip_name) if not os.path.exists(saveto): # Avoid repeated downloads log.warn("Downloading %s", url) downloader = downloader_factory() downloader(url, saveto) return os.path.realpath(saveto) def _build_install_args(options): """ Build the arguments to 'python setup.py install' on the setuptools package. Returns list of command line arguments. """ return ['--user'] if options.user_install else [] def _parse_args(): """Parse the command line for options.""" parser = optparse.OptionParser() parser.add_option( '--user', dest='user_install', action='store_true', default=False, help='install in user site package') parser.add_option( '--download-base', dest='download_base', metavar="URL", default=DEFAULT_URL, help='alternative URL from where to download the setuptools package') parser.add_option( '--insecure', dest='downloader_factory', action='store_const', const=lambda: download_file_insecure, default=get_best_downloader, help='Use internal, non-validating downloader' ) parser.add_option( '--version', help="Specify which version to download", default=DEFAULT_VERSION, ) parser.add_option( '--to-dir', help="Directory to save (and re-use) package", default=DEFAULT_SAVE_DIR, ) options, args = parser.parse_args() # positional arguments are ignored return options def _download_args(options): """Return args for download_setuptools function from cmdline args.""" return dict( version=options.version, download_base=options.download_base, downloader_factory=options.downloader_factory, to_dir=options.to_dir, ) def main(): """Install or upgrade setuptools and EasyInstall.""" options = _parse_args() archive = download_setuptools(**_download_args(options)) return _install(archive, _build_install_args(options)) if __name__ == '__main__': sys.exit(main()) montage-wrapper-0.9.9/astropy_helpers/LICENSE.rst0000644000077000000240000000272312405252770021626 0ustar tomstaff00000000000000Copyright (c) 2014, Astropy Developers All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the Astropy Team nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 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By copying, installing or otherwise using matplotlib 0.98.3, Licensee agrees to be bound by the terms and conditions of this License Agreement. montage-wrapper-0.9.9/astropy_helpers/MANIFEST.in0000644000077000000240000000030013104416125021526 0ustar tomstaff00000000000000include README.rst include CHANGES.rst include LICENSE.rst recursive-include licenses * include ez_setup.py include ah_bootstrap.py exclude *.pyc *.o prune build prune astropy_helpers/tests montage-wrapper-0.9.9/astropy_helpers/README.rst0000644000077000000240000000502113137204755021476 0ustar tomstaff00000000000000astropy-helpers =============== * Stable versions: https://pypi.org/project/astropy-helpers/ * Development version, issue tracker: https://github.com/astropy/astropy-helpers This project provides a Python package, ``astropy_helpers``, which includes many build, installation, and documentation-related tools used by the Astropy project, but packaged separately for use by other projects that wish to leverage this work. The motivation behind this package and details of its implementation are in the accepted `Astropy Proposal for Enhancement (APE) 4 `_. The ``astropy_helpers.extern`` sub-module includes modules developed elsewhere that are bundled here for convenience. At the moment, this consists of the following two sphinx extensions: * `numpydoc `_, a Sphinx extension developed as part of the Numpy project. This is used to parse docstrings in Numpy format * `sphinx-automodapi `_, a Sphinx developed as part of the Astropy project. This used to be developed directly in ``astropy-helpers`` but is now a standalone package. Issues with these sub-modules should be reported in their respective repositories, and we will regularly update the bundled versions to reflect the latest released versions. ``astropy_helpers`` includes a special "bootstrap" module called ``ah_bootstrap.py`` which is intended to be used by a project's setup.py in order to ensure that the ``astropy_helpers`` package is available for build/installation. This is similar to the ``ez_setup.py`` module that is shipped with some projects to bootstrap `setuptools `_. As described in APE4, the version numbers for ``astropy_helpers`` follow the corresponding major/minor version of the `astropy core package `_, but with an independent sequence of micro (bugfix) version numbers. Hence, the initial release is 0.4, in parallel with Astropy v0.4, which will be the first version of Astropy to use ``astropy-helpers``. For examples of how to implement ``astropy-helpers`` in a project, see the ``setup.py`` and ``setup.cfg`` files of the `Affiliated package template `_. .. image:: https://travis-ci.org/astropy/astropy-helpers.svg :target: https://travis-ci.org/astropy/astropy-helpers .. image:: https://coveralls.io/repos/astropy/astropy-helpers/badge.svg :target: https://coveralls.io/r/astropy/astropy-helpers montage-wrapper-0.9.9/astropy_helpers/setup.cfg0000644000077000000240000000015313104416125021617 0ustar tomstaff00000000000000[tool:pytest] norecursedirs = .tox astropy_helpers/tests/package_template python_functions = test_ montage-wrapper-0.9.9/astropy_helpers/setup.py0000755000077000000240000000351613137204755021533 0ustar tomstaff00000000000000#!/usr/bin/env python # Licensed under a 3-clause BSD style license - see LICENSE.rst import ah_bootstrap import pkg_resources from setuptools import setup from astropy_helpers.setup_helpers import register_commands, get_package_info from astropy_helpers.version_helpers import generate_version_py NAME = 'astropy_helpers' VERSION = '2.0.1' RELEASE = 'dev' not in VERSION generate_version_py(NAME, VERSION, RELEASE, False, uses_git=not RELEASE) # Use the updated version including the git rev count from astropy_helpers.version import version as VERSION cmdclass = register_commands(NAME, VERSION, RELEASE) # This package actually doesn't use the Astropy test command del cmdclass['test'] setup( name=pkg_resources.safe_name(NAME), # astropy_helpers -> astropy-helpers version=VERSION, description='Utilities for building and installing Astropy, Astropy ' 'affiliated packages, and their respective documentation.', author='The Astropy Developers', author_email='astropy.team@gmail.com', license='BSD', url=' https://github.com/astropy/astropy-helpers', long_description=open('README.rst').read(), classifiers=[ 'Development Status :: 5 - Production/Stable', 'Intended Audience :: Developers', 'Framework :: Setuptools Plugin', 'Framework :: Sphinx :: Extension', 'Framework :: Sphinx :: Theme', 'License :: OSI Approved :: BSD License', 'Operating System :: OS Independent', 'Programming Language :: Python', 'Programming Language :: Python :: 3', 'Topic :: Software Development :: Build Tools', 'Topic :: Software Development :: Libraries :: Python Modules', 'Topic :: System :: Archiving :: Packaging' ], cmdclass=cmdclass, zip_safe=False, **get_package_info(exclude=['astropy_helpers.tests']) ) montage-wrapper-0.9.9/astropy_helpers/tox.ini0000644000077000000240000000045012531030705021310 0ustar tomstaff00000000000000[tox] envlist = py26,py27,py32,py33,py34 [testenv] deps = pytest numpy Cython Sphinx==1.2.3 # Note: Sphinx is required to run the sphinx.ext tests commands = py.test {posargs} sitepackages = False [testenv:py32] deps = pygments<=1.9 Jinja2<2.7 {[testenv]deps} montage-wrapper-0.9.9/CHANGES.rst0000644000077000000240000000360313137204670016366 0ustar tomstaff000000000000000.9.9 (2017-07-29) ------------------ - Fix bug that caused drizzle factor to be ignored in reproject, reproject_hdu, and reproject_cube. - Fix checking of Montage PATH on Windows. [#33] 0.9.8 (2014-09-14) ------------------ - Added wrapper for mTileImage command. [#14] - Fix typo in name of mFixNaN command. [#16] - Ensure that reproject_hdu cleans up any temporary directories. [#17] - Make sure that temporary directories created by mosaic() are always removed. [#19] - The code base is now fully Python 2 and 3 compatible, and 2to3 is no longer used. [#20] - Use the astropy-helpers package. [#21] 0.9.7 (2013-11-02) ------------------ - Disabled configuration file since it is not used. This gets rid of the warning at import time. - No longer check if Montage is in the PATH on install, but instead just on import. 0.9.6 (2013-10-31) ------------------ - Added missing files required for installation - Added a unit test for `mosaic` 0.9.5 (2013-03-18) ------------------ - removed unused files - added documentation about setting custom MPI command 0.9.4 (2013-03-18) ------------------ - python-montage is now an Astropy affiliated package, and has been renamed to montage_wrapper. - improved performance of mosaic() by ignoring frames that don't overlap with the requested header. Also improved exceptions in mosaic(). - new function ``reproject_cube`` to reproject a FITS cube slice by slice (thanks to Adam Ginsburg). - various bug fixes reported by users, and improved documentation. 0.9.3 ----- - Fixed bug with user-specified work directory - Allow user to specify whether to only adjust levels when carrying out the background matching 0.9.2 ----- - Migrated to GitHub - Improved handing to check whether Montage commands are present - Improved handling of temporary work directory 0.9.1 ----- - Minor bug fixes and improvements 0.9.0 ----- - Initial release montage-wrapper-0.9.9/docs/0000755000077000000240000000000013137205364015513 5ustar tomstaff00000000000000montage-wrapper-0.9.9/docs/_templates/0000755000077000000240000000000013137205364017650 5ustar tomstaff00000000000000montage-wrapper-0.9.9/docs/_templates/autosummary/0000755000077000000240000000000013137205364022236 5ustar tomstaff00000000000000montage-wrapper-0.9.9/docs/_templates/autosummary/base.rst0000644000077000000240000000037212235217076023705 0ustar tomstaff00000000000000{% extends "autosummary_core/base.rst" %} {# The template this is inherited from is in astropy/sphinx/ext/templates/autosummary_core. If you want to modify this template, it is strongly recommended that you still inherit from the astropy template. #}montage-wrapper-0.9.9/docs/_templates/autosummary/class.rst0000644000077000000240000000037312235217076024101 0ustar tomstaff00000000000000{% extends "autosummary_core/class.rst" %} {# The template this is inherited from is in astropy/sphinx/ext/templates/autosummary_core. If you want to modify this template, it is strongly recommended that you still inherit from the astropy template. #}montage-wrapper-0.9.9/docs/_templates/autosummary/module.rst0000644000077000000240000000037412235217076024262 0ustar tomstaff00000000000000{% extends "autosummary_core/module.rst" %} {# The template this is inherited from is in astropy/sphinx/ext/templates/autosummary_core. If you want to modify this template, it is strongly recommended that you still inherit from the astropy template. #}montage-wrapper-0.9.9/docs/conf.py0000644000077000000240000001420013015134404016776 0ustar tomstaff00000000000000# -*- coding: utf-8 -*- # Licensed under a 3-clause BSD style license - see LICENSE.rst # # Astropy documentation build configuration file. # # This file is execfile()d with the current directory set to its containing dir. # # Note that not all possible configuration values are present in this file. # # All configuration values have a default. Some values are defined in # the global Astropy configuration which is loaded here before anything else. # See astropy.sphinx.conf for which values are set there. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # sys.path.insert(0, os.path.abspath('..')) # IMPORTANT: the above commented section was generated by sphinx-quickstart, but # is *NOT* appropriate for astropy or Astropy affiliated packages. It is left # commented out with this explanation to make it clear why this should not be # done. If the sys.path entry above is added, when the astropy.sphinx.conf # import occurs, it will import the *source* version of astropy instead of the # version installed (if invoked as "make html" or directly with sphinx), or the # version in the build directory (if "python setup.py build_sphinx" is used). # Thus, any C-extensions that are needed to build the documentation will *not* # be accessible, and the documentation will not build correctly. import datetime import os import sys try: import astropy_helpers except ImportError: # Building from inside the docs/ directory? if os.path.basename(os.getcwd()) == 'docs': a_h_path = os.path.abspath(os.path.join('..', 'astropy_helpers')) if os.path.isdir(a_h_path): sys.path.insert(1, a_h_path) # Load all of the global Astropy configuration from astropy_helpers.sphinx.conf import * # Get configuration information from setup.cfg try: from ConfigParser import ConfigParser except ImportError: from configparser import ConfigParser conf = ConfigParser() conf.read([os.path.join(os.path.dirname(__file__), '..', 'setup.cfg')]) setup_cfg = dict(conf.items('metadata')) # -- General configuration ---------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. #needs_sphinx = '1.2' # To perform a Sphinx version check that needs to be more specific than # major.minor, call `check_sphinx_version("x.y.z")` here. # check_sphinx_version("1.2.1") # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. exclude_patterns.append('_templates') # This is added to the end of RST files - a good place to put substitutions to # be used globally. rst_epilog += """ """ # -- Project information ------------------------------------------------------ # This does not *have* to match the package name, but typically does project = setup_cfg['package_name'] author = setup_cfg['author'] copyright = '{0}, {1}'.format( datetime.datetime.now().year, setup_cfg['author']) # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. __import__(setup_cfg['package_name']) package = sys.modules[setup_cfg['package_name']] # The short X.Y version. version = package.__version__.split('-', 1)[0] # The full version, including alpha/beta/rc tags. release = package.__version__ # -- Options for HTML output --------------------------------------------------- # A NOTE ON HTML THEMES # The global astropy configuration uses a custom theme, 'bootstrap-astropy', # which is installed along with astropy. A different theme can be used or # the options for this theme can be modified by overriding some of the # variables set in the global configuration. The variables set in the # global configuration are listed below, commented out. # Add any paths that contain custom themes here, relative to this directory. # To use a different custom theme, add the directory containing the theme. #html_theme_path = [] # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. To override the custom theme, set this to the # name of a builtin theme or the name of a custom theme in html_theme_path. #html_theme = None # Custom sidebar templates, maps document names to template names. #html_sidebars = {} # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. #html_favicon = '' # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. #html_last_updated_fmt = '' # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". html_title = '{0} v{1}'.format(project, release) # Output file base name for HTML help builder. htmlhelp_basename = project + 'doc' # -- Options for LaTeX output -------------------------------------------------- # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [('index', project + '.tex', project + u' Documentation', author, 'manual')] # -- Options for manual page output -------------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [('index', project.lower(), project + u' Documentation', [author], 1)] ## -- Options for the edit_on_github extension ---------------------------------------- if eval(setup_cfg.get('edit_on_github')): extensions += ['astropy_helpers.sphinx.ext.edit_on_github'] versionmod = __import__(setup_cfg['package_name'] + '.version') edit_on_github_project = setup_cfg['github_project'] if versionmod.version.release: edit_on_github_branch = "v" + versionmod.version.version else: edit_on_github_branch = "master" edit_on_github_source_root = "" edit_on_github_doc_root = "docs" montage-wrapper-0.9.9/docs/index.rst0000644000077000000240000001264713015134404017355 0ustar tomstaff00000000000000******************************************** Python Montage wrapper (``montage_wrapper``) ******************************************** .. _numpy: http://www.numoy.org Introduction ============ This Astropy-affiliated package provides a python wrapper to the Montage Astronomical Image Mosaic Engine, including both functions to access individual Montage commands, and high-level functions to facilitate mosaicking and re-projecting. Download ======== The latest stable release can be downloaded from `here `_. Installation ============ This package is a wrapper, not a replacement, for the IPAC Montage mosaicking software. Therefore, Montage will need to be downloaded from `http://montage.ipac.caltech.edu `_. Once you have downloaded the latest release on Montage from that website, the installation should look like:: tar xvzf Montage_v3.3.tar.gz cd Montage_v3.3 make then move the ``Montage_v3.3`` directory to wherever you would like to keep the installation, and add ``/Montage_v3.3/bin`` to your ``$PATH``, where ```` is the directory inside which you put ``Montage_v3.3`` (Montage does not support ``make install``). To check that Montage is correctly installed, you can type:: mAdd If you see something like:: [struct stat="ERROR", msg="Usage: mAdd [-p imgdir] [-n(o-areas)] [-a mean|median|count] [-e(xact-size)] [-d level] [-s statusfile] images.tbl template.hdr out.fits"] then the installation succeeded. Otherwise, if you see:: mAdd: command not found then you will need to make sure that the ``Montage_v3.3/bin`` contains commands like ``mAdd``, and that the directory is correctly in your ``$PATH``. Once the IPAC Montage package is installed, you can install the Python wrapper with:: tar xvzf montage-wrapper-x.x.x.tar.gz cd montage-wrapper-x.x.x python setup.py install (replacing ``x.x.x`` with the actual version number). The only dependencies are numpy_ and astropy_. Using `montage_wrapper` ======================= Montage commands ---------------- The Montage wrapper is imported using:: >>> import montage_wrapper or, for clarity:: >>> import montage_wrapper as montage All Montage commands (except ``mJPEG``, ``mMakeImg``, and ``mTileImage``) are accessible via Python functions. For example, to access ``mProject``, use:: >>> montage.mProject(...) # doctest: +SKIP and see :func:`~montage_wrapper.commands.mProject` for available options. Each Montage command returns a :class:`~montage_wrapper.status.Struct` object that contains information/diagnostics. The following example shows how to use the Montage command wrappers, and how to access the diagnostics:: >>> montage.mArchiveList('2MASS', 'K', 'm31', 0.5, 0.5, 'm31_list.tbl') # doctest: +SKIP count : 18 stat : OK >>> montage.mMakeHdr('m31_list.tbl', 'header.hdr', north_aligned=True) # doctest: +SKIP count : 18 lat4 : 41.744136 stat : OK lat1 : 40.912238 lat3 : 41.744136 latsize : 0.831951 clon : 10.717965 lonsize : 0.830562 posang : 0.0 lon4 : 11.274528 lat2 : 40.912238 lon1 : 11.267467 clat : 41.32951 lon2 : 10.168464 lon3 : 10.161403 >>> s = montage.mMakeHdr('m31_list.tbl', 'header.hdr', north_aligned=True) # doctest: +SKIP >>> s.stat # doctest: +SKIP 'OK' >>> s.lon1 # doctest: +SKIP 11.267467 See `Reference/API`_ for a full list of available commands and documentation. High-level functions -------------------- In addition to wrappers to the individual Montage commands, the following high-level functions are available: * `~montage_wrapper.wrappers.reproject`: reproject a FITS file * `~montage_wrapper.wrappers.reproject_hdu`: reproject an FITS HDU object * `~montage_wrapper.wrappers.mosaic`: mosaic all FITS files in a directory For example, to mosaic all FITS files in a directory called `raw` using background matching, use: >>> montage.mosaic('raw', 'mosaic', background_match=True) # doctest: +SKIP In this specific example, a mosaic header will automatically be constructed from the input files. For more details on how to use these, see the `Reference/API`_ section. MPI --- A few Montage commands can be run using MPI for parallelization (see here). For MPI-enabled commands (such as `~montage_wrapper.commands.mProjExec`), the use of MPI is controlled via the mpi= argument. For example, to call ``mProjExec`` using MPI, call ``montage.mProjExec(..., mpi=True)`` (rather than ``montage.mProjExecMPI``, which does not exist). Note however that this requires the MPI versions of the Montage commands to be installed (which is not the case by default). Different MPI installations require different commands (e.g. ``mpirun`` vs ``mpiexec``) as well as different options, so it is possible to customize the MPI command:: >>> import montage_wrapper as montage >>> montage.set_mpi_command('mpiexec -n {n_proc} {executable}') The command string should include ``{n_proc}``, which will be replaced by the number of proceses, and ``{executable}``, which will be replaced by the appropriate Montage executable. The current MPI command can be accessed with:: >>> from montage_wrapper.mpi import MPI_COMMAND >>> MPI_COMMAND 'mpiexec -n {n_proc} {executable}' Reference/API ============= .. automodapi:: montage_wrapper.wrappers .. automodapi:: montage_wrapper.commands .. automodapi:: montage_wrapper.status montage-wrapper-0.9.9/docs/make.bat0000644000077000000240000001064112235217076017123 0ustar tomstaff00000000000000@ECHO OFF REM Command file for Sphinx documentation if "%SPHINXBUILD%" == "" ( set SPHINXBUILD=sphinx-build ) set BUILDDIR=_build set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . if NOT "%PAPER%" == "" ( set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% ) if "%1" == "" goto help if "%1" == "help" ( :help echo.Please use `make ^` where ^ is one of echo. html to make standalone HTML files echo. dirhtml to make HTML files named index.html in directories echo. singlehtml to make a single large HTML file echo. pickle to make pickle files echo. json to make JSON files echo. htmlhelp to make HTML files and a HTML help project echo. qthelp to make HTML files and a qthelp project echo. devhelp to make HTML files and a Devhelp project echo. epub to make an epub echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter echo. text to make text files echo. man to make manual pages echo. changes to make an overview over all changed/added/deprecated items echo. linkcheck to check all external links for integrity echo. doctest to run all doctests embedded in the documentation if enabled goto end ) if "%1" == "clean" ( for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i del /q /s %BUILDDIR%\* goto end ) if "%1" == "html" ( %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html if errorlevel 1 exit /b 1 echo. echo.Build finished. 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The manual pages are in %BUILDDIR%/man. goto end ) if "%1" == "changes" ( %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes if errorlevel 1 exit /b 1 echo. echo.The overview file is in %BUILDDIR%/changes. goto end ) if "%1" == "linkcheck" ( %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck if errorlevel 1 exit /b 1 echo. echo.Link check complete; look for any errors in the above output ^ or in %BUILDDIR%/linkcheck/output.txt. goto end ) if "%1" == "doctest" ( %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest if errorlevel 1 exit /b 1 echo. echo.Testing of doctests in the sources finished, look at the ^ results in %BUILDDIR%/doctest/output.txt. goto end ) :end montage-wrapper-0.9.9/docs/Makefile0000644000077000000240000001117312405246432017154 0ustar tomstaff00000000000000# Makefile for Sphinx documentation # # You can set these variables from the command line. SPHINXOPTS = SPHINXBUILD = sphinx-build PAPER = BUILDDIR = _build # Internal variables. PAPEROPT_a4 = -D latex_paper_size=a4 PAPEROPT_letter = -D latex_paper_size=letter ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest #This is needed with git because git doesn't create a dir if it's empty $(shell [ -d "_static" ] || mkdir -p _static) help: @echo "Please use \`make ' where is one of" @echo " html to make standalone HTML files" @echo " dirhtml to make HTML files named index.html in directories" @echo " singlehtml to make a single large HTML file" @echo " pickle to make pickle files" @echo " json to make JSON files" @echo " htmlhelp to make HTML files and a HTML help project" @echo " qthelp to make HTML files and a qthelp project" @echo " devhelp to make HTML files and a Devhelp project" @echo " epub to make an epub" @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" @echo " latexpdf to make LaTeX files and run them through pdflatex" @echo " text to make text files" @echo " man to make manual pages" @echo " changes to make an overview of all changed/added/deprecated items" @echo " linkcheck to check all external links for integrity" @echo " doctest to run all doctests embedded in the documentation (if enabled)" clean: -rm -rf $(BUILDDIR) -rm -rf _generated html: $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html @echo @echo "Build finished. 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The epub file is in $(BUILDDIR)/epub." latex: $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex @echo @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." @echo "Run \`make' in that directory to run these through (pdf)latex" \ "(use \`make latexpdf' here to do that automatically)." latexpdf: $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex @echo "Running LaTeX files through pdflatex..." make -C $(BUILDDIR)/latex all-pdf @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." text: $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text @echo @echo "Build finished. The text files are in $(BUILDDIR)/text." man: $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man @echo @echo "Build finished. The manual pages are in $(BUILDDIR)/man." changes: $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes @echo @echo "The overview file is in $(BUILDDIR)/changes." linkcheck: $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck @echo @echo "Link check complete; look for any errors in the above output " \ "or in $(BUILDDIR)/linkcheck/output.txt." doctest: $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest @echo "Testing of doctests in the sources finished, look at the " \ "results in $(BUILDDIR)/doctest/output.txt." montage-wrapper-0.9.9/docs/rtd-pip-requirements0000644000077000000240000000010312235217076021531 0ustar tomstaff00000000000000numpy Cython git+http://github.com/astropy/astropy.git#egg=astropy montage-wrapper-0.9.9/ez_setup.py0000644000077000000240000003037113137204410016766 0ustar tomstaff00000000000000#!/usr/bin/env python """ Setuptools bootstrapping installer. Maintained at https://github.com/pypa/setuptools/tree/bootstrap. Run this script to install or upgrade setuptools. This method is DEPRECATED. Check https://github.com/pypa/setuptools/issues/581 for more details. """ import os import shutil import sys import tempfile import zipfile import optparse import subprocess import platform import textwrap import contextlib from distutils import log try: from urllib.request import urlopen except ImportError: from urllib2 import urlopen try: from site import USER_SITE except ImportError: USER_SITE = None # 33.1.1 is the last version that supports setuptools self upgrade/installation. DEFAULT_VERSION = "33.1.1" DEFAULT_URL = "https://pypi.io/packages/source/s/setuptools/" DEFAULT_SAVE_DIR = os.curdir DEFAULT_DEPRECATION_MESSAGE = "ez_setup.py is deprecated and when using it setuptools will be pinned to {0} since it's the last version that supports setuptools self upgrade/installation, check https://github.com/pypa/setuptools/issues/581 for more info; use pip to install setuptools" MEANINGFUL_INVALID_ZIP_ERR_MSG = 'Maybe {0} is corrupted, delete it and try again.' log.warn(DEFAULT_DEPRECATION_MESSAGE.format(DEFAULT_VERSION)) def _python_cmd(*args): """ Execute a command. Return True if the command succeeded. """ args = (sys.executable,) + args return subprocess.call(args) == 0 def _install(archive_filename, install_args=()): """Install Setuptools.""" with archive_context(archive_filename): # installing log.warn('Installing Setuptools') if not _python_cmd('setup.py', 'install', *install_args): log.warn('Something went wrong during the installation.') log.warn('See the error message above.') # exitcode will be 2 return 2 def _build_egg(egg, archive_filename, to_dir): """Build Setuptools egg.""" with archive_context(archive_filename): # building an egg log.warn('Building a Setuptools egg in %s', to_dir) _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir) # returning the result log.warn(egg) if not os.path.exists(egg): raise IOError('Could not build the egg.') class ContextualZipFile(zipfile.ZipFile): """Supplement ZipFile class to support context manager for Python 2.6.""" def __enter__(self): return self def __exit__(self, type, value, traceback): self.close() def __new__(cls, *args, **kwargs): """Construct a ZipFile or ContextualZipFile as appropriate.""" if hasattr(zipfile.ZipFile, '__exit__'): return zipfile.ZipFile(*args, **kwargs) return super(ContextualZipFile, cls).__new__(cls) @contextlib.contextmanager def archive_context(filename): """ Unzip filename to a temporary directory, set to the cwd. The unzipped target is cleaned up after. """ tmpdir = tempfile.mkdtemp() log.warn('Extracting in %s', tmpdir) old_wd = os.getcwd() try: os.chdir(tmpdir) try: with ContextualZipFile(filename) as archive: archive.extractall() except zipfile.BadZipfile as err: if not err.args: err.args = ('', ) err.args = err.args + ( MEANINGFUL_INVALID_ZIP_ERR_MSG.format(filename), ) raise # going in the directory subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0]) os.chdir(subdir) log.warn('Now working in %s', subdir) yield finally: os.chdir(old_wd) shutil.rmtree(tmpdir) def _do_download(version, download_base, to_dir, download_delay): """Download Setuptools.""" py_desig = 'py{sys.version_info[0]}.{sys.version_info[1]}'.format(sys=sys) tp = 'setuptools-{version}-{py_desig}.egg' egg = os.path.join(to_dir, tp.format(**locals())) if not os.path.exists(egg): archive = download_setuptools(version, download_base, to_dir, download_delay) _build_egg(egg, archive, to_dir) sys.path.insert(0, egg) # Remove previously-imported pkg_resources if present (see # https://bitbucket.org/pypa/setuptools/pull-request/7/ for details). if 'pkg_resources' in sys.modules: _unload_pkg_resources() import setuptools setuptools.bootstrap_install_from = egg def use_setuptools( version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=DEFAULT_SAVE_DIR, download_delay=15): """ Ensure that a setuptools version is installed. Return None. Raise SystemExit if the requested version or later cannot be installed. """ to_dir = os.path.abspath(to_dir) # prior to importing, capture the module state for # representative modules. rep_modules = 'pkg_resources', 'setuptools' imported = set(sys.modules).intersection(rep_modules) try: import pkg_resources pkg_resources.require("setuptools>=" + version) # a suitable version is already installed return except ImportError: # pkg_resources not available; setuptools is not installed; download pass except pkg_resources.DistributionNotFound: # no version of setuptools was found; allow download pass except pkg_resources.VersionConflict as VC_err: if imported: _conflict_bail(VC_err, version) # otherwise, unload pkg_resources to allow the downloaded version to # take precedence. del pkg_resources _unload_pkg_resources() return _do_download(version, download_base, to_dir, download_delay) def _conflict_bail(VC_err, version): """ Setuptools was imported prior to invocation, so it is unsafe to unload it. Bail out. """ conflict_tmpl = textwrap.dedent(""" The required version of setuptools (>={version}) is not available, and can't be installed while this script is running. Please install a more recent version first, using 'easy_install -U setuptools'. (Currently using {VC_err.args[0]!r}) """) msg = conflict_tmpl.format(**locals()) sys.stderr.write(msg) sys.exit(2) def _unload_pkg_resources(): sys.meta_path = [ importer for importer in sys.meta_path if importer.__class__.__module__ != 'pkg_resources.extern' ] del_modules = [ name for name in sys.modules if name.startswith('pkg_resources') ] for mod_name in del_modules: del sys.modules[mod_name] def _clean_check(cmd, target): """ Run the command to download target. If the command fails, clean up before re-raising the error. """ try: subprocess.check_call(cmd) except subprocess.CalledProcessError: if os.access(target, os.F_OK): os.unlink(target) raise def download_file_powershell(url, target): """ Download the file at url to target using Powershell. Powershell will validate trust. Raise an exception if the command cannot complete. """ target = os.path.abspath(target) ps_cmd = ( "[System.Net.WebRequest]::DefaultWebProxy.Credentials = " "[System.Net.CredentialCache]::DefaultCredentials; " '(new-object System.Net.WebClient).DownloadFile("%(url)s", "%(target)s")' % locals() ) cmd = [ 'powershell', '-Command', ps_cmd, ] _clean_check(cmd, target) def has_powershell(): """Determine if Powershell is available.""" if platform.system() != 'Windows': return False cmd = ['powershell', '-Command', 'echo test'] with open(os.path.devnull, 'wb') as devnull: try: subprocess.check_call(cmd, stdout=devnull, stderr=devnull) except Exception: return False return True download_file_powershell.viable = has_powershell def download_file_curl(url, target): cmd = ['curl', url, '--location', '--silent', '--output', target] _clean_check(cmd, target) def has_curl(): cmd = ['curl', '--version'] with open(os.path.devnull, 'wb') as devnull: try: subprocess.check_call(cmd, stdout=devnull, stderr=devnull) except Exception: return False return True download_file_curl.viable = has_curl def download_file_wget(url, target): cmd = ['wget', url, '--quiet', '--output-document', target] _clean_check(cmd, target) def has_wget(): cmd = ['wget', '--version'] with open(os.path.devnull, 'wb') as devnull: try: subprocess.check_call(cmd, stdout=devnull, stderr=devnull) except Exception: return False return True download_file_wget.viable = has_wget def download_file_insecure(url, target): """Use Python to download the file, without connection authentication.""" src = urlopen(url) try: # Read all the data in one block. data = src.read() finally: src.close() # Write all the data in one block to avoid creating a partial file. with open(target, "wb") as dst: dst.write(data) download_file_insecure.viable = lambda: True def get_best_downloader(): downloaders = ( download_file_powershell, download_file_curl, download_file_wget, download_file_insecure, ) viable_downloaders = (dl for dl in downloaders if dl.viable()) return next(viable_downloaders, None) def download_setuptools( version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=DEFAULT_SAVE_DIR, delay=15, downloader_factory=get_best_downloader): """ Download setuptools from a specified location and return its filename. `version` should be a valid setuptools version number that is available as an sdist for download under the `download_base` URL (which should end with a '/'). `to_dir` is the directory where the egg will be downloaded. `delay` is the number of seconds to pause before an actual download attempt. ``downloader_factory`` should be a function taking no arguments and returning a function for downloading a URL to a target. """ # making sure we use the absolute path to_dir = os.path.abspath(to_dir) zip_name = "setuptools-%s.zip" % version url = download_base + zip_name saveto = os.path.join(to_dir, zip_name) if not os.path.exists(saveto): # Avoid repeated downloads log.warn("Downloading %s", url) downloader = downloader_factory() downloader(url, saveto) return os.path.realpath(saveto) def _build_install_args(options): """ Build the arguments to 'python setup.py install' on the setuptools package. Returns list of command line arguments. """ return ['--user'] if options.user_install else [] def _parse_args(): """Parse the command line for options.""" parser = optparse.OptionParser() parser.add_option( '--user', dest='user_install', action='store_true', default=False, help='install in user site package') parser.add_option( '--download-base', dest='download_base', metavar="URL", default=DEFAULT_URL, help='alternative URL from where to download the setuptools package') parser.add_option( '--insecure', dest='downloader_factory', action='store_const', const=lambda: download_file_insecure, default=get_best_downloader, help='Use internal, non-validating downloader' ) parser.add_option( '--version', help="Specify which version to download", default=DEFAULT_VERSION, ) parser.add_option( '--to-dir', help="Directory to save (and re-use) package", default=DEFAULT_SAVE_DIR, ) options, args = parser.parse_args() # positional arguments are ignored return options def _download_args(options): """Return args for download_setuptools function from cmdline args.""" return dict( version=options.version, download_base=options.download_base, downloader_factory=options.downloader_factory, to_dir=options.to_dir, ) def main(): """Install or upgrade setuptools and EasyInstall.""" options = _parse_args() archive = download_setuptools(**_download_args(options)) return _install(archive, _build_install_args(options)) if __name__ == '__main__': sys.exit(main()) montage-wrapper-0.9.9/LICENSE.rst0000644000077000000240000000273012405246432016377 0ustar tomstaff00000000000000Copyright (c) 2010-2012, Thomas Robitaille All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the Astropy Team nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. montage-wrapper-0.9.9/montage_wrapper/0000755000077000000240000000000013137205364017755 5ustar tomstaff00000000000000montage-wrapper-0.9.9/montage_wrapper/__init__.py0000644000077000000240000000376113015134404022064 0ustar tomstaff00000000000000# Licensed under a 3-clause BSD style license - see LICENSE.rst """ This is an Astropy affiliated package. """ # Affiliated packages may add whatever they like to this file, but # should keep this content at the top. # ---------------------------------------------------------------------------- from ._astropy_init import * # ---------------------------------------------------------------------------- # For egg_info test builds to pass, put package imports here. if not _ASTROPY_SETUP_: from .commands import * from .wrappers import * from .mpi import set_mpi_command # Check whether Montage is installed installed = False for dir in os.environ['PATH'].split(':'): if os.path.exists(dir + '/mProject'): installed = True break # Check for Windows installation of Montage if not installed: for dir in os.environ['PATH'].split(';'): if os.path.exists(dir + '/mProject.exe'): installed = True break import textwrap error_wrap = textwrap.TextWrapper(initial_indent=" " * 11, subsequent_indent=" " * 11, width=72) MONTAGE_MISSING = """ ERROR: Montage commands could not be found. In order to use the montage_wrapper module, you will first need to install the IPAC Montage software from: http://montage.ipac.caltech.edu and ensure that the Montage commands (e.g. mAdd, mProject, etc.) are in your $PATH. Your current $PATH variable contains the following paths, but none of them contain the Montage commands: PATH = {path} If the Montage commands are in one of these directories, then please report this as an issue with montage-wrapper. """.format(path=error_wrap.fill(os.environ['PATH']).strip()) ON_RTD = os.environ.get('READTHEDOCS', None) == 'True' if not ON_RTD and not installed: print(MONTAGE_MISSING) import sys sys.exit(1) montage-wrapper-0.9.9/montage_wrapper/_astropy_init.py0000644000077000000240000001223113015134404023200 0ustar tomstaff00000000000000# Licensed under a 3-clause BSD style license - see LICENSE.rst __all__ = ['__version__', '__githash__', 'test'] # this indicates whether or not we are in the package's setup.py try: _ASTROPY_SETUP_ except NameError: from sys import version_info if version_info[0] >= 3: import builtins else: import __builtin__ as builtins builtins._ASTROPY_SETUP_ = False try: from .version import version as __version__ except ImportError: __version__ = '' try: from .version import githash as __githash__ except ImportError: __githash__ = '' # set up the test command def _get_test_runner(): import os from astropy.tests.helper import TestRunner return TestRunner(os.path.dirname(__file__)) def test(package=None, test_path=None, args=None, plugins=None, verbose=False, pastebin=None, remote_data=False, pep8=False, pdb=False, coverage=False, open_files=False, **kwargs): """ Run the tests using `py.test `__. A proper set of arguments is constructed and passed to `pytest.main`_. .. _py.test: http://pytest.org/latest/ .. _pytest.main: http://pytest.org/latest/builtin.html#pytest.main Parameters ---------- package : str, optional The name of a specific package to test, e.g. 'io.fits' or 'utils'. If nothing is specified all default tests are run. test_path : str, optional Specify location to test by path. May be a single file or directory. Must be specified absolutely or relative to the calling directory. args : str, optional Additional arguments to be passed to pytest.main_ in the ``args`` keyword argument. plugins : list, optional Plugins to be passed to pytest.main_ in the ``plugins`` keyword argument. verbose : bool, optional Convenience option to turn on verbose output from py.test_. Passing True is the same as specifying ``'-v'`` in ``args``. pastebin : {'failed','all',None}, optional Convenience option for turning on py.test_ pastebin output. Set to ``'failed'`` to upload info for failed tests, or ``'all'`` to upload info for all tests. remote_data : bool, optional Controls whether to run tests marked with @remote_data. These tests use online data and are not run by default. Set to True to run these tests. pep8 : bool, optional Turn on PEP8 checking via the `pytest-pep8 plugin `_ and disable normal tests. Same as specifying ``'--pep8 -k pep8'`` in ``args``. pdb : bool, optional Turn on PDB post-mortem analysis for failing tests. Same as specifying ``'--pdb'`` in ``args``. coverage : bool, optional Generate a test coverage report. The result will be placed in the directory htmlcov. open_files : bool, optional Fail when any tests leave files open. Off by default, because this adds extra run time to the test suite. Requires the `psutil `_ package. parallel : int, optional When provided, run the tests in parallel on the specified number of CPUs. If parallel is negative, it will use the all the cores on the machine. Requires the `pytest-xdist `_ plugin installed. Only available when using Astropy 0.3 or later. kwargs Any additional keywords passed into this function will be passed on to the astropy test runner. This allows use of test-related functionality implemented in later versions of astropy without explicitly updating the package template. """ test_runner = _get_test_runner() return test_runner.run_tests( package=package, test_path=test_path, args=args, plugins=plugins, verbose=verbose, pastebin=pastebin, remote_data=remote_data, pep8=pep8, pdb=pdb, coverage=coverage, open_files=open_files, **kwargs) if not _ASTROPY_SETUP_: import os from warnings import warn from astropy import config # add these here so we only need to cleanup the namespace at the end config_dir = None if not os.environ.get('ASTROPY_SKIP_CONFIG_UPDATE', False): config_dir = os.path.dirname(__file__) config_template = os.path.join(config_dir, __package__ + ".cfg") if os.path.isfile(config_template): try: config.configuration.update_default_config( __package__, config_dir, version=__version__) except TypeError as orig_error: try: config.configuration.update_default_config( __package__, config_dir) except config.configuration.ConfigurationDefaultMissingError as e: wmsg = (e.args[0] + " Cannot install default profile. If you are " "importing from source, this is expected.") warn(config.configuration.ConfigurationDefaultMissingWarning(wmsg)) del e except: raise orig_error montage-wrapper-0.9.9/montage_wrapper/commands.py0000644000077000000240000022453013137204410022125 0ustar tomstaff00000000000000import subprocess import shlex from . import status from .commands_extra import * from .mpi import _get_mpi_command def mAdd(images_table, template_header, out_image, img_dir=None, no_area=False, type=None, exact=False, debug_level=None, status_file=None, mpi=False, n_proc=8): ''' Coadd the reprojected images in an input list to form an output mosaic with FITS header keywords specified in a header file. Creates two output files, one containing the coadded pixel values, and the other containing coadded pixel area values. The pixel area values can be used as a weighting function if the output pixel values are themselves to be coadded with other projected images, and may also be used in validating the fidelity of the output pixel values. Parameters ---------- images_table : str ASCII table (generated by mImgtbl) containing metadata for all images to be coadded. template_header : str FITS header template to be used in generation of output FITS out_image : str Name of output FITS image. img_dir : str, optional Specifies path to directory containing reprojected images. If the img_dir option is not included, mAdd will look for the input images in the current working directory. no_area : bool, optional Co-addition ignores weighting by pixel areas and performs coaddition based only on pixel postions. Will not output an area image for the output image. type : str, optional Select type of averaging to be done on accumulated pixel values (either mean or median). To generate a map showing counts of how many times each pixel was overlapped by the input images, use count. exact : bool, optional Enables exact size mode. The output image will match the header template exactly, instead of shrinking the output to fit the data. debug_level : int, optional Turns on debugging to the specified level (1-3). status_file : str, optional mAdd output and errors will be written to status_file instead of stdout. mpi : bool, optional If set to True, will use the MPI-enabled versions of the Montage executable. n_proc : int, optional If mpi is set to True, n_proc is the number of processes to run simultaneously (default is 8) ''' if mpi: command = _get_mpi_command(executable="mAddMPI", n_proc=n_proc) else: command = "mAdd" if img_dir: command += " -p %s" % str(img_dir) if no_area: command += " -n" if type: command += " -a %s" % str(type) if exact: command += " -e" if debug_level: command += " -d %s" % str(debug_level) if status_file: command += " -s %s" % str(status_file) command += " " + str(images_table) command += " " + str(template_header) command += " " + str(out_image) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mAdd", p.stdout.read().strip()) def mAddExec(images_table, template_header, tile_dir, out_image, img_dir=None, no_area=False, type=None, exact=False, debug_level=None, status_file=None, mpi=False, n_proc=8): ''' Builds a series of outputs (which together make up a tiled output) through multiple executions of the mAdd modules. Parameters ---------- images_table : str ASCII table (generated by mImgtbl) containing metadata for all images to be coadded. template_header : str FITS header template to be used in generation of output FITS tile_dir : str Directory to contain output tile images and header templates out_image : str Prefix for output tile images img_dir : str, optional Specifies path to directory containing reprojected images. If the img_dir option is not included, mAdd will look for the input images in the current working directory. no_area : bool, optional Co-addition ignores weighting by pixel areas and performs coaddition based only on pixel postions. Will not output an area image for the output image. type : str, optional Select type of averaging to be done on accumulated pixel values (either mean or median). exact : bool, optional Enables exact size mode. The output image will match the header template exactly, instead of shrinking the output to fit the data. debug_level : int, optional Turns on debugging to the specified level (1-3). status_file : str, optional mAdd output and errors will be written to status_file instead of stdout. mpi : bool, optional If set to True, will use the MPI-enabled versions of the Montage executable. n_proc : int, optional If mpi is set to True, n_proc is the number of processes to run simultaneously (default is 8) ''' if mpi: command = _get_mpi_command(executable="mAddExecMPI", n_proc=n_proc) else: command = "mAddExec" if img_dir: command += " -p %s" % str(img_dir) if no_area: command += " -n" if type: command += " -a %s" % str(type) if exact: command += " -e" if debug_level: command += " -d %s" % str(debug_level) if status_file: command += " -s %s" % str(status_file) command += " " + str(images_table) command += " " + str(template_header) command += " " + str(tile_dir) command += " " + str(out_image) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mAddExec", p.stdout.read().strip()) def mArchiveExec(region_table, debug_level=None): ''' Given a table of archive images (generated by mArchiveList), calls mArchiveGet on each one in sequence to retrieve all the files into the current directory. Parameters ---------- region_table : str Table of archive images, generated by mArchiveList. debug_level : int, optional Prints out additional debugging information; in this version, the only supported level is 1. ''' command = "mArchiveExec" if debug_level: command += " -d %s" % str(debug_level) command += " " + str(region_table) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mArchiveExec", p.stdout.read().strip()) def mArchiveGet(remote_ref, local_file, debug=False, raw=False): ''' Retrieve a single FITS image from a remote archive, using a basic URL GET but with a structured output. Parameters ---------- remote_ref : str URL of remote FITS file to retrieve (should be in quotes). See mArchiveList for more information. local_file : str Full path/filename of the retrieved file. debug : bool, optional Print additional debugging information. raw : bool, optional "Raw" mode - use a raw HTTP GET (no "HTTP/1.1" etc in the header); necessary for communication with some servers. ''' command = "mArchiveGet" if debug: command += " -d" if raw: command += " -r" command += ' "' + str(remote_ref) + '"' command += " " + str(local_file) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mArchiveGet", p.stdout.read().strip()) def mArchiveList(survey, band, object_or_location, width, height, out_file): ''' Given a location on the sky, archive name, and size in degrees, contact the IRSA server to retrieve a list of archive images. The list contains enough information to support mArchiveGet downloads. Parameters ---------- survey : str Can be one of: 2MASS DSS SDSS DPOSS band : str Case insensitive - can be one of: (2MASS) j, h, k (SDSS) u, g, r, i, z (DPOSS) f, j, n (DSS) DSS1, DSS1R, DSS1B, DSS2, DSS2B, DSS2R, DSS2IR object_or_location : str Object name or coordinate string to be resolved by NED (if string includes spaces, must be surrounded by double quotes) width : float Width of area of interest, in degrees height : float Height of area of interest, in degrees out_file : str Path to output table ''' command = "mArchiveList" command += " " + str(survey) command += " " + str(band) command += ' "' + str(object_or_location) + '"' command += " " + str(width) command += " " + str(height) command += " " + str(out_file) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mArchiveList", p.stdout.read().strip()) def mBackground(in_image, out_image, A, B, C, debug_level=None, no_area=False, status_file=None): ''' Remove a background plane from a FITS image. The background correction applied to the image is specified as Ax+By+C, where (x,y) is the pixel coordinate using the image center as the origin, and (A,B,C) are the background plane parameters specified as linear coefficients. To run in 'table' mode, see mBackground_tab. Parameters ---------- in_image : str Input FITS file out_image : str Output FITS file A, B, C : str Corrections (as given by mFitplane or mFitExec) debug_level : int, optional Turns on debugging to the specified level. no_area : bool, optional Indicates that no area images are present (assumes equal weighting for each data pixel) status_file : str, optional mBackground output and errors will be written to status_file instead of stdout. ''' command = "mBackground" if debug_level: command += " -d %s" % str(debug_level) if no_area: command += " -n" if status_file: command += " -s %s" % str(status_file) command += " " + str(in_image) command += " " + str(out_image) command += " " + str(A) command += " " + str(B) command += " " + str(C) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mBackground", p.stdout.read().strip()) def mBackground_tab(in_image, out_image, images_table, corrections_table, debug_level=None, no_area=False, status_file=None): ''' Remove a background plane from a FITS image. The background correction applied to the image is specified as Ax+By+C, where (x,y) is the pixel coordinate using the image center as the origin, and (A,B,C) are the background plane parameters specified as linear coefficients. This method runs mBackground_tab in 'table' mode. Parameters ---------- in_image : str Input FITS file out_image : str Output FITS file images_table : str Image metadata table to retrieve the filenames of images. corrections_table : str Table of corrections (from mFitplane and mFitExec) to apply to the corresponding image (from images_table). debug_level : int, optional Turns on debugging to the specified level. no_area : bool, optional Indicates that no area images are present (assumes equal weighting for each data pixel) status_file : str, optional mBackground_tab output and errors will be written to status_file instead of stdout. ''' command = "mBackground_tab" if debug_level: command += " -d %s" % str(debug_level) if no_area: command += " -n" if status_file: command += " -s %s" % str(status_file) command += " " + str(in_image) command += " " + str(out_image) command += " " + str(images_table) command += " " + str(corrections_table) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mBackground_tab", p.stdout.read().strip()) def mBestImage(images_table, ra, dec, debug=False): ''' Given a list of images and a position on the sky, determine which image covers the location "best" (i.e., the one where the position is farthest from the nearest edge). Parameters ---------- images_table : str Input table of image metadata (as generated by mImgtbl). ra : float RA of location of interest (in degrees) dec : float Declination of location of interest (in degrees) debug_level : int, optional Turn on debugging to the specified level (1 or 2) ''' command = "mBestImage" if debug: command += " -d" command += " " + str(images_table) command += " " + str(ra) command += " " + str(dec) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mBestImage", p.stdout.read().strip()) def mBgExec(images_table, corrections_table, corr_dir, proj_dir=None, status_file=None, debug=False, no_area=False, mpi=False, n_proc=8): ''' Runs mBackground on all the images in a metadata table, using the corrections generated by mBgModel. Parameters ---------- images_table : str Image metadata table generated by mImgtbl. corrections_table : str Table of corrections generated by mFitExec corr_dir : str Directory where output images should be written proj_dir : str, optional Specifies the path to the directory containing the projected images. status_file : str, optional Writes output message to status_file instead of to stdout debug : bool, optional Turns on debugging no_area : bool, optional Indicates that no area images are present (assumes equal weighting for each pixel) mpi : bool, optional If set to True, will use the MPI-enabled versions of the Montage executable. n_proc : int, optional If mpi is set to True, n_proc is the number of processes to run simultaneously (default is 8) ''' if mpi: command = _get_mpi_command(executable="mBgExecMPI", n_proc=n_proc) else: command = "mBgExec" if proj_dir: command += " -p %s" % str(proj_dir) if status_file: command += " -s %s" % str(status_file) if debug: command += " -d" if no_area: command += " -n" command += " " + str(images_table) command += " " + str(corrections_table) command += " " + str(corr_dir) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mBgExec", p.stdout.read().strip()) def mBgModel(images_table, fits_table, corrections_table, n_iter=None, level_only=False, debug_level=None, ref_img=None, status_file=None): ''' mBgModel is a modelling/fitting program. It uses the image-to-image difference parameter table created by mFitExec to interactively determine a set of corrections to apply to each image in order to achieve a "best" global fit. Parameters ---------- images_table : str Image metadata table generated by mImgtbl. fits_table : str Plane fitting table generated by mFitExec. corrections_table : str Output table of background corrections n_iter : int, optional Number of iterations (without option, defaults to 5000). Can be between 1 and 32767. level_only : bool, optional Calculate level adjustments only (ie, don't attempt to match the slopes) debug_level : int, optional Turns on debugging to the specified level (1-3). ref_img : str, optional Turns on additional debugging for the nth image in images_table. status_file : str, optional mBgModel output and errors are written to status_file instead of to stdout. ''' command = "mBgModel" if n_iter: command += " -i %s" % str(n_iter) if level_only: command += " -l" if debug_level: command += " -d %s" % str(debug_level) if ref_img: command += " -r %s" % str(ref_img) if status_file: command += " -s %s" % str(status_file) command += " " + str(images_table) command += " " + str(fits_table) command += " " + str(corrections_table) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mBgModel", p.stdout.read().strip()) def mCatMap(in_table, out_image, template_header, column=None, ref_mag=None, debug_level=None, size=None): ''' mCatMap is a point-source imaging program. The user defines a general output FITS image, and its pixels are populated from a table of point sources. The source fluxes (or just source counts) from the table are added into the appropriate pixel to create an output image. Parameters ---------- in_table : str Input table of source metadata. out_image : str Path of output FITS file. template_header : str ASCII header template defining output FITS file. column : str, optional Name of the table column that contains flux levels. If not specified, pixels will be populated with source counts rather than summed flux values. ref_mag : float, optional Set a reference magnitude to use when calculating fluxes. debug_level : int, optional Turn on debugging to the specified level (1-3) size : int, optional Set a spread size for point sources (default is to use no spread). Allowed values are 3 or 5. ''' command = "mCatMap" if column: command += " -c %s" % str(column) if ref_mag: command += " -m %s" % str(ref_mag) if debug_level: command += " -d %s" % str(debug_level) if size: command += " -w %s" % str(size) command += " " + str(in_table) command += " " + str(out_image) command += " " + str(template_header) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mCatMap", p.stdout.read().strip()) def mConvert(in_image, out_image, debug_level=None, status_file=None, bitpix=None, min_val=None, max_val=None, blank_value=None): ''' mConvert changes the datatype of an image. When converting to floating point, no additional information is needed. However, when converting from higher precision (e.g. 64-bit floating point) to lower (e.g. 16-bit integer), scaling information is necessary. This can be given explicitly by the user or guessed by the program. Parameters ---------- in_image : str Input image filename out_image : str Output image filename. debug_level : int, optional Turns on debugging to the specified level (1-3). status_file : str, optional mBgModel output and errors are written to status_file instead of to stdout. bitpix : int, optional BITPIX value for the ouput FITS file (default is -64). Possible values are: 8 (character or unsigned binary integer), 16 (16-bit integer), 32 (32-bit integer), -32 (single precision floating point), -64 (double precision floating point). min_val : int, optional Pixel data value in the input image which should be treated as a minimum (value of 0) in the output image when converting from floating point to integer (default for BITPIX 8: 0; BITPIX 16: -32767; BITPIX 32: -2147483647 max_val : int, optional Pixel data value in the input image which should be treated as a maximum (value of 255 or 32768) in the output image when converting from floating point to integer (Default for BITPIX 8: 255; BITPIX 16: 32768; BITPIX 32: 2147483648) blank_value : int, optional If converting down to an integer scale: value to be used in the output image to represent blank pixels (NaN) from the input image. Default value is min_val. ''' command = "mConvert" if debug_level: command += " -d %s" % str(debug_level) if status_file: command += " -s %s" % str(status_file) if bitpix: command += " -b %s" % str(bitpix) if min_val: command += " -min %s" % str(min_val) if max_val: command += " -max %s" % str(max_val) if blank_value: command += " -blank %s" % str(blank_value) command += " " + str(in_image) command += " " + str(out_image) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mConvert", p.stdout.read().strip()) def mDiff(in_image_1, in_image_2, out_image, template_header, debug_level=None, no_area=False, status_file=None): ''' mDiff calculates a simple difference between a single pair of overlapping images. This is meant for use on reprojected images where the pixels already line up exactly. mDiff analyzes an image metadata table to determine a list of overlapping images. Each image is compared with every other image to determine all overlapping image pairs. A pair of images are deemed to overlap if any pixel around the perimeter of one image falls within the boundary of the other image. Parameters ---------- in_image_1 : str First input FITS file (Also needs area image in1_area_image, or use the no_area option) in_image_2 : str Second input FITS file.(Also needs area image in2_area_image, or use the no_area option) out_image : str Difference FITS image to be generated. template_header : str FITS header template used to generate output image. debug_level : int, optional Turns on debugging to the specified level (1-4). no_area : bool, optional No-area-images option. Creates difference image without requiring pixel area FITS image status_file : str, optional Output and errors are sent to status_file instead of to stdout ''' command = "mDiff" if debug_level: command += " -d %s" % str(debug_level) if no_area: command += " -n" if status_file: command += " -s %s" % str(status_file) command += " " + str(in_image_1) command += " " + str(in_image_2) command += " " + str(out_image) command += " " + str(template_header) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mDiff", p.stdout.read().strip()) def mDiffExec(diffs_table, template_header, diff_dir, proj_dir=None, debug=False, no_area=False, status_file=None, mpi=False, n_proc=8): ''' Runs mDiff on all the pairs identified by mOverlaps. Parameters ---------- diffs_table : str Table generated by mOverlaps for the images in proj_dir. template_header : str FITS header template for output files. diff_dir : str Path to output files. proj_dir : str, optional Specifies path to the directory containing reprojected input images. debug : bool, optional Turns on debugging. no_area : bool, optional No-area-images option. Creates difference image without requiring _area FITS images status_file : str, optional Output and errors are sent to status_file instead of to stdout mpi : bool, optional If set to True, will use the MPI-enabled versions of the Montage executable. n_proc : int, optional If mpi is set to True, n_proc is the number of processes to run simultaneously (default is 8) ''' if mpi: command = _get_mpi_command(executable="mDiffExecMPI", n_proc=n_proc) else: command = "mDiffExec" if proj_dir: command += " -p %s" % str(proj_dir) if debug: command += " -d" if no_area: command += " -n" if status_file: command += " -s %s" % str(status_file) command += " " + str(diffs_table) command += " " + str(template_header) command += " " + str(diff_dir) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mDiffExec", p.stdout.read().strip()) def mDiffFitExec(diffs_table, fits_table, diff_dir, debug=False, status_file=None): ''' Using the table of overlaps found by mOverlaps, mDiffFitExec runs both mDiff and mFitplane for each record. The fitting parameters are written to a file to be used by mBgModel. Parameters ---------- diffs_table : str Overlap table generated by mOverlaps, the last column of which contains the filenames of the difference images generated by mDiffExec. fits_table : str Output table of difference paramaters. diff_dir : str Directory containing difference images. debug : bool, optional Turns on debugging status_file : str, optional Writes output message to status_file instead of to stdout ''' command = "mDiffFitExec" if debug: command += " -d" if status_file: command += " -s %s" % str(status_file) command += " " + str(diffs_table) command += " " + str(fits_table) command += " " + str(diff_dir) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mDiffFitExec", p.stdout.read().strip()) def mExec(survey, band, raw_dir=None, n_tile_x=None, n_tile_y=None, level_only=False, keep=False, remove=False, output_image=None, debug_level=None, region_header=None, header=None, workspace_dir=None): ''' The mExec module is a mosaicking executive for 2MASS, SDSS, and DSS data. It includes remote data and metadata access. Alternatively, users can mosaic a set of data already on disk. Parameters ---------- survey, band : str If not mosaicking user-provided data (raw_dir option), must select one of the following combinations of survey and band: 2MASS [j, h, k] SDSS [u, g, r, i, z] DSS [DSS1, DSS1R, DSS1B, DSS2, DSS2B, DSS2R, DSS2IR] raw_dir : str, optional Provide path to directory containing original ("raw") data which will be reprojected and mosaicked. Not necessary if using mExec to retrieve remote data from the 2MASS, SDSS or DSS surveys. n_tile_x : int, optional Number of output tiles to create along the X-axis - default is 1 for a single mosaicked image. n_tile_y : int, optional Number of output tiles to create along the Y-axis - default is equal to n_tile_x. level_only : bool, optional "Level-only" option (see mBgModel) keep : bool, optional If retrieving data from a remote archive, the "keep" option will leave the original data products on disk after generating a mosaic. Without this option, raw data will be deleted (unless it was provided by the user with the "-r" option). remove : bool, optional Remove all temporary files and intermediate data products. Note: if not using the '-o' option to specify an output file, this will also remove mosaic_image. output_image : str, optional Provide your own filename for the output mosaic. Default filename is "mosaic_image." debug_level : int, optional Print out additional debugging information (levels 1-4) region_header : str, optional Path to header template used to create mosaic. header : str, optional Provide header template as text input rather than point to a file; see sample shell script that makes use of this option. workspace_dir : str, optional Directory where intermediate files will be created. If no workspace is given, a unique local subdirectory will be created (e.g.; ./MOSAIC_AAAaa17v) ''' command = "mExec" if raw_dir: command += " -r %s" % str(raw_dir) if n_tile_x: command += " -n %s" % str(n_tile_x) if n_tile_y: command += " -m %s" % str(n_tile_y) if level_only: command += " -l" if keep: command += " -k" if remove: command += " -c" if output_image: command += " -o %s" % str(output_image) if debug_level: command += " -d %s" % str(debug_level) if region_header: command += " -f %s" % str(region_header) if header: command += " -h %s" % str(header) command += " " + str(survey) command += " " + str(band) if workspace_dir: command += " %s" % str(workspace_dir) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mExec", p.stdout.read().strip()) def mFitExec(diffs_table, fits_table, diff_dir, debug=False, status_file=None, mpi=False, n_proc=8): ''' Runs mFitplane on all the difference images identified by mOverlaps and generated by mDiff or mDiffExec. mFitExec creates a table of image-to- image difference parameters. Parameters ---------- diffs_table : str Overlap table generated by mOverlaps, the last column of which contains the filenames of the difference images generated by mDiffExec. fits_table : str Output table of difference paramaters. diff_dir : str Directory containing difference images. debug : bool, optional Turns on debugging status_file : str, optional Writes output message to status_file instead of to stdout mpi : bool, optional If set to True, will use the MPI-enabled versions of the Montage executable. n_proc : int, optional If mpi is set to True, n_proc is the number of processes to run simultaneously (default is 8) ''' if mpi: command = _get_mpi_command(executable="mFitExecMPI", n_proc=n_proc) else: command = "mFitExec" if debug: command += " -d" if status_file: command += " -s %s" % str(status_file) command += " " + str(diffs_table) command += " " + str(fits_table) command += " " + str(diff_dir) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mFitExec", p.stdout.read().strip()) def mFitplane(in_image, border=None, debug_level=None, status_file=None): ''' Uses least squares to fit a plane (excluding outlier pixels) to an image. It is used on the difference images generated using mDiff or mDiffExec. Parameters ---------- in_image : str Input FITS file is a difference file between two other FITS files, as can be generated using mDiff. border : int, optional Number of border pixels to ignore at edges of image. debug_level : int, optional Turns on debugging to the specified level (1-3). status_file : str, optional Output and errors are written to status_file instead of stdout. ''' command = "mFitplane" if border: command += " -b %s" % str(border) if debug_level: command += " -d %s" % str(debug_level) if status_file: command += " -s %s" % str(status_file) command += " " + str(in_image) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mFitplane", p.stdout.read().strip()) def mFixNaN(in_image, out_image, debug_level=None, nan_value=None, min_blank=None, max_blank=None): ''' Converts NaNs found in the image to some other value (given by the user), or converts a range of supplied values into NaNs. Parameters ---------- in_image : str Input FITS image file out_image : str Path of output FITS file. To run in "count" mode without creating an output file, use a dash ("-") for this argument. debug_level : int, optional Turn on debugging to the specified level (1-3) nan_value : float, optional Value to use in place of any NaNs min_blank, max_blank : str, optional If the nan_value option is not used, mFixNaN will replace all pixel values between min_blank and max_blank with NaN. ''' command = "mFixNaN" if debug_level: command += " -d %s" % str(debug_level) if nan_value: command += " -v %s" % str(nan_value) command += " " + str(in_image) command += " " + str(out_image) if min_blank and max_blank: command += " %s" % str(min_blank) command += " %s" % str(max_blank) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mFixNaN", p.stdout.read().strip()) def mFlattenExec(images_table, flat_dir, img_dir=None, debug=False, no_area=False, status_file=None): ''' Runs both mFitPlane and mBackground on a set of images. Parameters ---------- images_table : str Metadata table (generated by mImgtbl) describing images to be flattened. flat_dir : str Path to directory where output files should be created. img_dir : str, optional Specifies path to directory containing images to be flattened. debug : bool, optional Turns on debugging. no_area : bool, optional No-area-images option, indicating that mFlattenExec should not require area images for all the input FITS images. status_file : str, optional Output and errors are sent to status_file instead of to stdout ''' command = "mFlattenExec" if img_dir: command += " -p %s" % str(img_dir) if debug: command += " -d" if no_area: command += " -n" if status_file: command += " -s %s" % str(status_file) command += " " + str(images_table) command += " " + str(flat_dir) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mFlattenExec", p.stdout.read().strip()) def mGetHdr(in_image, img_header, debug=False, hdu=None, status_file=None): ''' Reads in the header from a FITS image and prints it out to a text file. Parameters ---------- in_image : str Path to FITS image from which to retrieve the header. img_header : str Path to text file where FITS header should be written. debug : bool, optional Turns on debugging. hdu : int, optional Retrieve the header from the Fits extention given by hdu. "0" indicates the primary FITS extension, and is the default used by mGetHdr. status_file : str, optional Output and errors are sent to status_file instead of to stdout ''' command = "mGetHdr" if debug: command += " -d" if hdu: command += " -h %s" % str(hdu) if status_file: command += " -s %s" % str(status_file) command += " " + str(in_image) command += " " + str(img_header) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mGetHdr", p.stdout.read().strip()) def mHdr(object_or_location, width, out_file, system=None, equinox=None, height=None, pix_size=None, rotation=None): ''' Connects to the IRSA service HdrTemplate to create a header template based on a location, size, resolution and rotation. Parameters ---------- object_or_location : str Object string or coordinate location width : float Width (x-axis) of area out_file : str Path to output header template system : str, optional Specify a coordinate system. Can be one of: "equatorial" or "eq" (default), "ecliptic" or "ec" "galactic", "ga", "supergalactic" or "sgal" equinox : str, optional Specify an equinox. Default is 2000.0 height : float, optional Height (y-axis) of area in degrees. Default is equal to width pix_size : float, optional Size of a pixel (in arcsec); default is 1 rotation : float, optional Rotation of image; default is 0 ''' command = "mHdr" if system: command += " -s %s" % str(system) if equinox: command += " -e %s" % str(equinox) if height: command += " -h %s" % str(height) if pix_size: command += " -p %s" % str(pix_size) if rotation: command += " -r %s" % str(rotation) command += ' "' + str(object_or_location) + '"' command += " " + str(width) command += " " + str(out_file) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mHdr", p.stdout.read().strip()) def mHdrCheck(in_image, status_file=None): ''' mHdrCheck reads in the header from a FITS image (or an ASCII header template file) and checks to see if any header lines are invalid. If it finds one, it will print out a message stating which keyword is invalid and exit before checking the rest of the header. It will not report on multiple invalid values. If all value are correct, mHdrCheck will print out a "Valid FITS/WCS" message. Parameters ---------- in_image : str Path of FITS file to be validated. status_file : str, optional Output and errors are sent to status_file instead of to stdout ''' command = "mHdrCheck" if status_file: command += " -s %s" % str(status_file) command += " " + str(in_image) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mHdrCheck", p.stdout.read().strip()) def mHdrtbl(directory, images_table, recursive=False, corners=False, debug=False, output_invalid=False, status_file=None, img_list=None): ''' mHdrtbl operates in a fashion similar to mImgtbl, but is used on a set of header template files instead of FITS images. Parameters ---------- directory : str Path to directory containing set of input header templates. images_table : str Path of output metadata table. recursive : bool, optional mHdrtbl can also be used as a standalone program to gather image metadata for other purposes (to populate a database, as a basis for spatial coverage searches, etc.) In this case it is often desirable to collect information on all the files in a directory tree recursively. The recursive option instructs mHdrtbl to search the given directory and all its subdirectories recursively. corners : bool, optional The corners option in mHdrtbl will cause eight extra columns to be added to the output metadata table containing the RA, Dec coordinates (ra1, dec1, ... ra4, dec4) of the image corners. The output is always Equatorial J2000, even if the input is some other system. This has been done to make the metadata uniform so that it can easily be used for coverage searches, etc. The corners option is not needed for normal Montage processing. debug : bool, optional Turn on debugging output_invalid : bool, optional When this option is set, mHdrtbl will explicitly output each header file it finds that does not appear to be valid, along with information on the error. status_file : str, optional Output and errors are written to status_file instead of being written to stdout. img_list : str, optional mHdrtbl will only process files with names specified in table img_list, ignoring any other files in the directory. ''' command = "mHdrtbl" if recursive: command += " -r" if corners: command += " -c" if debug: command += " -d" if output_invalid: command += " -b" if status_file: command += " -s %s" % str(status_file) if img_list: command += " -t %s" % str(img_list) command += " " + str(directory) command += " " + str(images_table) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mHdrtbl", p.stdout.read().strip()) def mImgtbl(directory, images_table, recursive=False, corners=False, include_area=False, debug=False, output_invalid=False, status_file=None, fieldlist=None, img_list=None): ''' mImgtbl extracts the FITS header geometry information from a set of files and creates an ASCII image metadata table which is used by several of the other programs. It only collects data from headers that comply with the FITS standard, but reports a count of images that fail that check. Parameters ---------- directory : str Path to directory containing set of input FITS files. images_table : str Path of output metadata table. recursive : bool, optional mImgtbl can also be used as a standalone program to gather image metadata for other purposes (to populate a database, as a basis for spatial coverage searches, etc.) In this case it is often desirable to collect information on all the files in a directory tree recursively. The recursive option instructs mImgtbl to search the given directory and all its subdirectories recursively. corners : bool, optional The corners option in mImgtbl will cause eight extra columns to be added to the output metadata table containing the RA, Dec coordinates (ra1, dec1, ... ra4, dec4) of the image corners. The output is always Equatorial J2000, even if the input is some other system. Though not required for the core processing modules, we recommend using this option, as some of the utilities may require corner locations to function properly. include_area : bool, optional By default, mImgtbl ignores FITS files with names ending in _area (i.e. name_area_image), assuming them to be Montage-created area images. If you want to generate information on these images, or if you have images with _area in the title other than those generated by Montage, you should turn on this option to force mImgtbl to look at all images in the directory. debug : bool, optional Turn on debugging output_invalid : bool, optional When this option is set, mImgtbl will explicitly output each FITS file it finds that does not appear to be valid, along with information on the error. status_file : str, optional Output and errors are written to status_file instead of being written to stdout. fieldlist : str, optional Used to specify a fieldlist, which will list additional keywords to be read from the FITS headers and included in the output table. Fieldlists should specify the keyword name, type (int,char,double), and size. img_list : str, optional mImgtbl will only process files with names specified in table img_list, ignoring any other files in the directory. ''' command = "mImgtbl" if recursive: command += " -r" if corners: command += " -c" if include_area: command += " -a" if debug: command += " -d" if output_invalid: command += " -b" if status_file: command += " -s %s" % str(status_file) if fieldlist: command += " -f %s" % str(fieldlist) if img_list: command += " -t %s" % str(img_list) command += " " + str(directory) command += " " + str(images_table) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mImgtbl", p.stdout.read().strip()) def mMakeHdr(images_table, template_header, debug_level=None, status_file=None, cdelt=None, north_aligned=False, system=None, equinox=None): ''' From a list of images to be mosaicked together, mMakeHdr generates the FITS header that best describes the output image. Parameters ---------- images_table : str Metadata table (generated by mImgtbl) describing the images to be mosaicked. template_header : str Path to header template to be generated. debug_level : int, optional Turns on debugging to the specified level (1-3). status_file : str, optional Output and errors are written to status_file instead of to stdout. cdelt : float, optional Specify a pixel scale for the header, if different from the input images north_aligned : bool, optional "North-aligned" option. By default, the FITS header generated represents the best fit to the images, often resulting in a slight rotation. If you want north to be straight up in your final mosaic, you should use this option. system : str, optional Specifies the system for the header (default is Equatorial). Possible values are: EQUJ EQUB ECLJ ECLB GAL SGAL equinox : str, optional If a coordinate system is specified, the equinox can also be given in the form YYYY. Default is J2000. ''' command = "mMakeHdr" if debug_level: command += " -d %s" % str(debug_level) if status_file: command += " -s %s" % str(status_file) if cdelt: command += " -p %s" % str(cdelt) if north_aligned: command += " -n" command += " " + str(images_table) command += " " + str(template_header) if system: command += " %s" % str(system) if equinox: command += " %s" % str(equinox) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mMakeHdr", p.stdout.read().strip()) def mOverlaps(images_table, diffs_table, exact=False, debug_level=None, status_file=None): ''' Analyze an image metadata table to determine a list of overlapping images. Each image is compared with every other image to determine all overlapping image pairs. A pair of images are deemed to overlap if any pixel around the perimeter of one image falls within the boundary of the other image. Parameters ---------- images_table : str Table of image metadata generated by mImgtbl. diffs_table : str Path of output table to be generated containing overlap information. exact : bool, optional Enables 'exact' overlaps mode, as opposed to the default approximate algorithm. The default mode uses great-circle connecting lines between image corners to determine which images overlap. Exact mode will instead check the edge pixels of every image to determine which pixels are inside the others. Although the default mode will occasionally report some incorrect overlaps, this is not a concern since mDiff will detect and ignore these false positive results when processing the table. debug_level : int, optional Turns on debugging to the specified level (1 or 2) status_file : str, optional Output and errors are sent to status_file instead of to stdout ''' command = "mOverlaps" if exact: command += " -e" if debug_level: command += " -d %s" % str(debug_level) if status_file: command += " -s %s" % str(status_file) command += " " + str(images_table) command += " " + str(diffs_table) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mOverlaps", p.stdout.read().strip()) def mPix2Coord(template_header, ixpix, jypix, debug=False): ''' Takes an image FITS header template and a pixel (x,y) coordinate, and outputs the corresponding sky location. Parameters ---------- template_header : str ASCII header template describing the image (either a FITS image, or a JPEG file created from the FITS file) ixpix : int X coordinate (pixel location) on image jypix : int Y coordinate (pixel location) on image debug : bool, optional Print out additional debugging information ''' command = "mPix2Coord" if debug: command += " -d" command += " " + str(template_header) command += " " + str(ixpix) command += " " + str(jypix) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mPix2Coord", p.stdout.read().strip()) def mProject(in_image, out_image, template_header, factor=None, debug_level=None, status_file=None, hdu=None, scale=None, weight_file=None, threshold=None, whole=False): ''' mProject reprojects a single image to the scale defined in a FITS header template file (read more about header templates here). The program produces a pair of images: the reprojected image and an "area" image consisting of the fraction input pixel sky area that went into each output pixel. The "drizzle" algorithm is implemented. The algorithm proceeds by mapping pixel corners (as adjusted by drizzle, if called) from the input pixel space to the output pixel space, calculating overlap area with each output pixel, and accumulating an appropriate fraction of the input flux into the output image pixels. In addition, the appropriate fraction of the input pixel area is accumulated into the area image pixels. Projection of points from input pixel space to output pixel space is calculated in two steps: first map from input pixel space to sky coordinates; second map from sky coordinates to output pixel space. Parameters ---------- in_image : str Input FITS file to be reprojected. out_image : str Path of output FITS file to be created. template_header : str FITS header template to be used in generation of output image factor : float, optional Processing is done utilizing the drizzle algorithm. factor is a floating point number; recommended drizzle factors are from 0.5 to 1. debug_level : int, optional Causes additional debugging information to be printed to stdout. Valid levels are 1-5 (for higher debugging levels, it is recommended to redirect the output to a file). status_file : str, optional Output and errors are written to status_file instead of being written to stdout. hdu : int, optional Use the specified FITS extension (default is to use the first HDU with image data) scale : float, optional Apply a correction factor of scale to each pixel weight_file : str, optional Path to a weight map to be used when reading values from the input image. threshold : float, optional Pixels with weights below threshold will be treated as blank. whole : bool, optional Makes the output region (originally defined in the header template) big enough to include all of the input images ''' command = "mProject" if factor: command += " -z %s" % str(factor) if debug_level: command += " -d %s" % str(debug_level) if status_file: command += " -s %s" % str(status_file) if hdu: command += " -h %s" % str(hdu) if scale: command += " -x %s" % str(scale) if weight_file: command += " -w %s" % str(weight_file) if threshold: command += " -t %s" % str(threshold) if whole: command += " -X" command += " " + str(in_image) command += " " + str(out_image) command += " " + str(template_header) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mProject", p.stdout.read().strip()) def mProjectPP(in_image, out_image, template_header, factor=None, debug_level=None, border=None, status_file=None, alternate_header=None, hdu=None, scale=None, weight_file=None, threshold=None, whole=False): ''' mProjectPP reprojects a single image to the scale defined in an alternate FITS header template generated (usually) by mTANhdr. The program produces a pair of images: the reprojected image and an "area" image consisting of the fraction input pixel sky area that went into each output pixel. This area image goes through all the subsequent processing that the reprojected image does, allowing it to be properly coadded at the end. Parameters ---------- in_image : str Input FITS file to be reprojected. out_image : str Path to output FITS file to be created. template_header : str FITS header template to be used in generation of output FITS factor : float, optional Processing is done utilizing the drizzle algorithm. factor is a floating point number; recommended drizzle factors are from 0.5 to 1. debug_level : int, optional Causes additional debugging information to be printed to stdout. Valid levels are 1-5; for levels greater than 1, it's recommended to redirect the output into a text file. border : int, optional Ignores border pixels around the image edge when performing calculations. status_file : str, optional Output and errors are written to status_file instead of being written to stdout. alternate_header : str, optional Specifies an alternate FITS header for use in mProjectPP calculations, allows substitution of psuedo-TAN headers created by mTANHdr. hdu : int, optional Specify the FITS extension to re-project if the FITS image is multi- extension. scale : float, optional Multiple the pixel values by scale when reprojecting. For instance, each 2MASS image has a different scale factor (very near 1.0) to correct for varying magnitude-zero points. weight_file : str, optional Path to a weight map to be used when reading values from the input image. threshold : float, optional If using a weight image; only use those pixels where the weight value is above threshold. whole : bool, optional Reproject the whole image even if part of it is outside the region of interest (don't crop while re-projecting). ''' command = "mProjectPP" if factor: command += " -z %s" % str(factor) if debug_level: command += " -d %s" % str(debug_level) if border: command += " -b %s" % str(border) if status_file: command += " -s %s" % str(status_file) if alternate_header: command += " -[i|o] %s" % str(alternate_header) if hdu: command += " -h %s" % str(hdu) if scale: command += " -x %s" % str(scale) if weight_file: command += " -w %s" % str(weight_file) if threshold: command += " -t %s" % str(threshold) if whole: command += " -X" command += " " + str(in_image) command += " " + str(out_image) command += " " + str(template_header) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mProjectPP", p.stdout.read().strip()) def mProjExec(images_table, template_header, proj_dir, stats_table, raw_dir=None, debug=False, exact=False, whole=False, border=None, restart_rec=None, status_file=None, scale_column=None, mpi=False, n_proc=8): ''' An executive which runs mProject (or, if possible for the input/output projections, mProjectPP) for each image in an image metadata table. Parameters ---------- images_table : str ASCII table (generated by mImgtbl) containing metadata for all images to be reprojected. template_header : str FITS header template to be used in generation of output FITS. proj_dir : str Directory in which to create reprojected images. stats_table : str Name of table for output statistics (time of each reprojection, or error messages). raw_dir : str, optional Specifies the path to the directory containing the images to be reprojected. If the -p option is not included, mProjExec looks for the images in the current working directory. debug : bool, optional Turns on debugging exact : bool, optional Flag indicating output image should exactly match the FITS header template, and not crop off blank pixels whole : bool, optional Force reprojection of whole images, even if they exceed the area of the FITS header template border : int, optional Ignore border width of pixels around edge of images restart_rec : str, optional Allows restart at record number restart_rec, if mProjExec exits upon an error status_file : str, optional Output and errors are written to status_file instead of being written to stdout. scale_column : str, optional Turn on flux rescaling (e.g. magnitude zero point correction): scale_column is the name of a column in images_table which contains scale information. mpi : bool, optional If set to True, will use the MPI-enabled versions of the Montage executable. n_proc : int, optional If mpi is set to True, n_proc is the number of processes to run simultaneously (default is 8) ''' if mpi: command = _get_mpi_command(executable="mProjExecMPI", n_proc=n_proc) else: command = "mProjExec" if raw_dir: command += " -p %s" % str(raw_dir) if debug: command += " -d" if exact: command += " -e" if whole: command += " -X" if border: command += " -b %s" % str(border) if restart_rec: command += " -r %s" % str(restart_rec) if status_file: command += " -s %s" % str(status_file) if scale_column: command += " -x %s" % str(scale_column) command += " " + str(images_table) command += " " + str(template_header) command += " " + str(proj_dir) command += " " + str(stats_table) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mProjExec", p.stdout.read().strip()) def mPutHdr(in_image, out_image, template_header, debug=False, status_file=None, hdu=None): ''' Replaces the header of the input file with one supplied by the user. Parameters ---------- in_image : str Input FITS file. out_image : str Path to output FITS file (with new header) template_header : str ASCII header template to write into out_image. debug : bool, optional Turns on debugging to the specified level (this version only supports level "1"). status_file : str, optional Output and errors are sent to status_file instead of to stdout hdu : int, optional Write to the specified FITS extnension (HDU). ''' command = "mPutHdr" if debug: command += " -d" if status_file: command += " -s %s" % str(status_file) if hdu: command += " -h %s" % str(hdu) command += " " + str(in_image) command += " " + str(out_image) command += " " + str(template_header) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mPutHdr", p.stdout.read().strip()) def mRotate(in_image, out_image, debug_level=None, status_file=None, rotation_angle=None, ra=None, dec=None, xsize=None, ysize=None): ''' Rotates a FITS image by an arbitrary angle. This module is meant for quick-look only; it is not flux conserving. Parameters ---------- in_image : str Input FITS image. out_image : str Path to output (rotated) FITS image. debug_level : int, optional Print out additional debugging information (level can be 1-3) status_file : str, optional Output and errors are written to status_file instead of stdout. rotation_angle : float, optional Provide an angle (in degrees) to rotate the image. ra, dec, xsize : str, optional Center location and width (in degrees) of output image - optional. By default, entire input image area will be included in output image. ysize : float, optional Height (in degrees) of output image, if a new center location and width are provided. Only used if ra, dec, and xsize are specified. Defaults to xsize. ''' command = "mRotate" if debug_level: command += " -d %s" % str(debug_level) if status_file: command += " -s %s" % str(status_file) if rotation_angle: command += " -r %s" % str(rotation_angle) command += " " + str(in_image) command += " " + str(out_image) if ra and dec and xsize: command += " %s" % str(ra) command += " %s" % str(dec) command += " %s" % str(xsize) if ysize: command += " %s" % str(ysize) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mRotate", p.stdout.read().strip()) def mShrink(in_image, out_image, factor, fixed_size=False, debug_level=None, status_file=None): ''' A utility for reducing the size of a FITS file, by averaging blocks of pixels. Parameters ---------- in_image : str Input FITS file out_image : str Path to output FITS file. factor : float Size of blocks, in pixels, to average. File size will be reduced by 1/factor squared. If the fixed_size option is used, factor is the desired width of the output image. fixed_size : bool, optional Fixed-size option - specify output size of image, instead of the size of blocks of pixels to be averaged debug_level : int, optional Turns on debugging to the specified level (1-4). status_file : str, optional Output and errors are sent to status_file instead of to stdout ''' command = "mShrink" if fixed_size: command += " -f" if debug_level: command += " -d %s" % str(debug_level) if status_file: command += " -s %s" % str(status_file) command += " " + str(in_image) command += " " + str(out_image) command += " " + str(factor) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mShrink", p.stdout.read().strip()) def mSubimage(in_image, out_image, ra, dec, xsize, debug=False, all_pixels=False, hdu=None, status_file=None, ysize=None): ''' Creates a subimage (or "cutout") of a FITS file. To use mSubimage in 'pixel' mode, see mSubimage_pix Parameters ---------- in_image : str Input FITS file. out_image : str Path to output FITS file. ra : float RA of center of output image. dec : float Declination of center of output image. xsize : float Width of output image in degrees. debug : bool, optional Turns on debugging. all_pixels : bool, optional All pixels - Force retrieval of whole image (useful to extract an entire HDU) hdu : int, optional Operate on the specified FITS header extension (HDU) status_file : str, optional Output and errors are sent to status_file instead of to stdout ysize : float, optional Height of output image in degrees (default is equal to xsize. ''' command = "mSubimage" if debug: command += " -d" if all_pixels: command += " -a" if hdu: command += " -h %s" % str(hdu) if status_file: command += " -s %s" % str(status_file) command += " " + str(in_image) command += " " + str(out_image) command += " " + str(ra) command += " " + str(dec) command += " " + str(xsize) if ysize: command += " %s" % str(ysize) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mSubimage", p.stdout.read().strip()) def mSubimage_pix(in_image, out_image, xstartpix, ystartpix, xpixsize, debug=False, hdu=None, status_file=None, ypixsize=None): ''' Creates a subimage (or "cutout") of a FITS file ('pixel' mode) Parameters ---------- in_image : str Input FITS file. out_image : str Path to output FITS file. xstartpix : int Pixel along the x-axis where the cutout image will begin ystartpix : int Pixel along the y-axis where the cutout image will begin xpixsize : int Width of output image in pixels debug : bool, optional Turns on debugging. hdu : int, optional Operate on the specified FITS header extension (HDU) status_file : str, optional Output and errors are sent to status_file instead of to stdout ypixsize : int, optional Height of output image in pixels (default is equal to xpix_size ''' command = "mSubimage -p" if debug: command += " -d" if hdu: command += " -h %s" % str(hdu) if status_file: command += " -s %s" % str(status_file) command += " " + str(in_image) command += " " + str(out_image) command += " " + str(xstartpix) command += " " + str(ystartpix) command += " " + str(xpixsize) if ypixsize: command += " %s" % str(ypixsize) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mSubimage_pix", p.stdout.read().strip()) def mSubset(images_table, template_header, subset_table, debug_level=None, fast_mode=False, status_file=None): ''' Generates a table of images that is a subset of the input table, containing only those images that cover the area defined by a given FITS header. Parameters ---------- images_table : str ASCII table (generated by mImgtbl) containing metadata for image collection. template_header : str FITS header template defining the area of interest. subset_table : str Path to output table, which will contain only those FITS images covering the area defined by template_header. debug_level : int, optional Turns on debugging to the specified level (1-3). fast_mode : bool, optional Fast mode - input file must include corners (corners option in mImgtbl) to utilize this mode. status_file : str, optional Output and errors are sent to status_file instead of to stdout ''' command = "mSubset" if debug_level: command += " -d %s" % str(debug_level) if fast_mode: command += " -f" if status_file: command += " -s %s" % str(status_file) command += " " + str(images_table) command += " " + str(template_header) command += " " + str(subset_table) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mSubset", p.stdout.read().strip()) def mTANHdr(orig_header, new_header, debug=False, order=None, max_iter=None, tolerance=None, status_file=None): ''' Analyzes a template file and determines if there would be an adequate equivalent distorted TAN projection, within a specified tolerance, and outputs the alternate header. This header can be used in conjunction with mProjectPP to produce a TAN plane image. This process is considerably faster than projecting with the general purpose tool mProject. Parameters ---------- orig_header : str Input FITS header new_header : str Path to output header to be created debug : bool, optional Print additional debugging information to stdout. order : str, optional Order of output header polynomial focal plane distortions (default = 4) max_iter : int, optional Maximum number of iteration attempts to produce header (default = 50) tolerance : float, optional Distortion tolerance value for acceptable output (default = 0.01) status_file : str, optional Output and errors are written to status_file instead of stdout. ''' command = "mTANHdr" if debug: command += " -d" if order: command += " -o %s" % str(order) if max_iter: command += " -i %s" % str(max_iter) if tolerance: command += " -t %s" % str(tolerance) if status_file: command += " -s %s" % str(status_file) command += " " + str(orig_header) command += " " + str(new_header) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mTANHdr", p.stdout.read().strip()) def mTblSort(in_table, column_name, out_table, debug=False): ''' Sorts a table on numeric values. Parameters ---------- in_table : str Path to input table column_name : str Name of column to sort on (column must contain numeric values) out_table : str Path to output table debug : bool, optional Turns on debugging ''' command = "mTblSort" if debug: command += " -d" command += " " + str(in_table) command += " " + str(column_name) command += " " + str(out_table) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mTblSort", p.stdout.read().strip()) def mTileHdr(orig_header, new_header, n_x, n_y, ix, iy, debug=False, status_file=None, xpad=None, ypad=None): ''' Takes a header template file and creates another which represents one of a regular set of tiles covering the original. The user specifies the tile gridding and which tile is desired. Parameters ---------- orig_header : str ASCII header template from which to derive tiled headers new_header : str Path to output header n_x : int Number of tiles in the x-direction n_y : int Number of tiles in the y-direction ix : int Integer identifying the x location of the output tile on the grid (counting from 0) iy : int Integer identifying the y location of the output tile on the grid (counting from 0) debug : bool, optional Turns on debugging. status_file : str, optional Output and errors are sent to status_file instead of to stdout xpad : int, optional Number of pixels to overlap tiles in the x direction (default is 0) ypad : int, optional Number of pixels to overlap tiles in the y direction (default is 0). Only used if xpad is present. ''' command = "mTileHdr" if debug: command += " -d" if status_file: command += " -s %s" % str(status_file) command += " " + str(orig_header) command += " " + str(new_header) command += " " + str(n_x) command += " " + str(n_y) command += " " + str(ix) command += " " + str(iy) if xpad: command += " %s" % str(xpad) if ypad: command += " %s" % str(ypad) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mTileHdr", p.stdout.read().strip()) montage-wrapper-0.9.9/montage_wrapper/commands_extra.py0000644000077000000240000001246013015134404023325 0ustar tomstaff00000000000000# This file contains commands for which wrappers could not be # auto-generated from the HTML docs import subprocess import shlex from . import status def mCoverageCheck(in_table, out_table, mode, polygon=None, ra=None, dec=None, width=None, height=None, rotation=None, radius=None, header=None, status_file=None): ''' mCoverageCheck can be used to subset an image metadata table (containing FITS/WCS information or image corners) by determining which records in the table represent images that overlap with a region definition (box or circle in the sky) given on the command line. Parameters ---------- in_table : str Input metadata table. out_table : str Output metadata table, to contain subset of in_table. mode : str How to check for coverage: - 'points': use a polygon with points specified by polygon= - 'box': use a rectangular box with center given by ra= and dec=, and the width given by width=. Optionally, the height and rotation can be given by height= and rotation= - 'circle': use a circle with center given by ra= and dec= and radius given by radius= - 'point': use a point given by ra= and dec= - 'header': use a header file given by header= polygon : list A polygon which should be given as [(ra1, dec1), (ra2, dec2), ..., (raN, decN)]. ra : float, optional The right ascension of the box, circle, or point dec : float, optional The declination of the box, circle, or point width : float, optional The width of the box height : float, optional The height of the box rotation : float, optional The rotation of the box radius : float, optional The radius of the circle header : str, optional A header file status_file : str, optional Output and errors are sent to status_file instead of to stdout ''' command = "mCoverageCheck" if status_file: command += " -s %s" % str(status_file) command += " " + str(in_table) command += " " + str(out_table) command += " -" + mode if mode == 'points': if polygon is None: raise Exception("polygon= needs to be specified for mode='points'") for point in polygon: command += " " + str(point[0]) command += " " + str(point[1]) elif mode == 'box': if ra is None: raise Exception("ra= needs to be specified for mode='box'") if dec is None: raise Exception("dec= needs to be specified for mode='box'") if width is None: raise Exception("width= needs to be specified for mode='box'") command += " " + str(ra) command += " " + str(dec) command += " " + str(width) if height is not None: command += " " + str(height) if rotation is not None: command += " " + str(rotation) else: if rotation is not None: raise Exception("Cannot specify rotation without height") elif mode == 'circle': if ra is None: raise Exception("ra= needs to be specified for mode='circle'") if dec is None: raise Exception("dec= needs to be specified for mode='circle'") if radius is None: raise Exception("radius= needs to be specified for mode='circle'") command += " " + str(ra) command += " " + str(dec) command += " " + str(radius) elif mode == 'point': if ra is None: raise Exception("ra= needs to be specified for mode='point'") if dec is None: raise Exception("dec= needs to be specified for mode='point'") command += " " + str(ra) command += " " + str(dec) elif mode == 'header': if header is None: raise Exception("header= needs to be specified for mode='header'") command += " " + header else: raise Exception("Unknown mode: %s" % mode) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mCoverageCheck", p.stdout.read().strip()) def mTileImage(in_image, tiles_x, tiles_y, overlap_x=None, overlap_y=None): ''' mTileImage splits up an image into a given number of tiles. An overlap between each tile can optionally be specified. Parameters ---------- in_image : str Input FITS file tiles_x : int Number of tiles along x axes. tiles_y : int Number of tiles along y axes. overlap_x : int, optional Pixel overlap in x direction. overlap_y : int, optional Pixel overlap in y direction. ''' command = "mTileImage" if overlap_x or overlap_y: command += " -o %s,%s" % (overlap_x, overlap_y) command += " -n %s,%s" % (tiles_x, tiles_y) command += " " + str(in_image) p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read() if stderr: raise Exception(stderr) return status.parse_struct("mTileImage", p.stdout.read().strip()) montage-wrapper-0.9.9/montage_wrapper/conftest.py0000644000077000000240000000154113015134404022144 0ustar tomstaff00000000000000import os # this contains imports plugins that configure py.test for astropy tests. # by importing them here in conftest.py they are discoverable by py.test # no matter how it is invoked within the source tree. from astropy.tests.pytest_plugins import * ## Uncomment the following line to treat all DeprecationWarnings as ## exceptions # enable_deprecations_as_exceptions() try: PYTEST_HEADER_MODULES['Astropy'] = 'astropy' del PYTEST_HEADER_MODULES['h5py'] del PYTEST_HEADER_MODULES['Scipy'] except NameError: # needed to support Astropy < 1.0 pass # This is to figure out the affiliated package version, rather than # using Astropy's from . import version try: packagename = os.path.basename(os.path.dirname(__file__)) TESTED_VERSIONS[packagename] = version.version except NameError: # Needed to support Astropy <= 1.0.0 pass montage-wrapper-0.9.9/montage_wrapper/mpi.py0000644000077000000240000000173012235217076021116 0ustar tomstaff00000000000000MPI_COMMAND = 'mpirun -n {n_proc} {executable}' def set_mpi_command(command): """ Set the MPI Command to use. This should contain {n_proc} to indicate the number of processes, and {executable} to indicate the name of the executable. Parameters ---------- command: str The MPI command for running executables Examples -------- Use ``mpirun``: >>> set_mpi_command('mpirun -n {n_proc} {executable}') Use ``mpiexec`` with host list: >>> set_mpi_command('mpiexec -f mpd.hosts -np {n_proc} {executable}') """ global MPI_COMMAND if "{n_proc}" not in command: raise ValueError("MPI command does not include {n_proc}") if "{executable}" not in command: raise ValueError("MPI command does not include {executable}") MPI_COMMAND = command def _get_mpi_command(executable=None, n_proc=None): return MPI_COMMAND.format(executable=executable, n_proc=n_proc)montage-wrapper-0.9.9/montage_wrapper/status.py0000644000077000000240000000350312235217076021654 0ustar tomstaff00000000000000from __future__ import print_function import hashlib from astropy import log def simplify(value): try: return int(value) except: return float(value) class MontageError(Exception): pass def parse_struct(command, string): # Convert bytes to string string = string.decode('ascii') if "\n" in string: result = [] for substring in string.splitlines(): if 'struct' in substring: result.append(Struct(command, substring)) else: print(substring) else: if 'struct' in string: result = Struct(command, string) else: print(string) result = None if result: return result else: return class Struct(object): def __init__(self, command, string): string = string[8:-1] strings = {} while True: try: p1 = string.index('"') p2 = string.index('"', p1 + 1) substring = string[p1 + 1:p2] key = hashlib.md5(substring.encode('ascii')).hexdigest() strings[key] = substring string = string[:p1] + key + string[p2 + 1:] except: break for pair in string.split(', '): key, value = pair.split('=') if value in strings: self.__dict__[key] = strings[value] else: self.__dict__[key] = simplify(value) if self.stat == "ERROR": raise MontageError("%s: %s" % (command, self.msg)) elif self.stat == "WARNING": log.warn(self.msg) def __repr__(self): string = "" for item in self.__dict__: string += item + " : " + str(self.__dict__[item]) + "\n" return string[:-1] montage-wrapper-0.9.9/montage_wrapper/tests/0000755000077000000240000000000013137205364021117 5ustar tomstaff00000000000000montage-wrapper-0.9.9/montage_wrapper/tests/__init__.py0000644000077000000240000000017112235217076023230 0ustar tomstaff00000000000000# Licensed under a 3-clause BSD style license - see LICENSE.rst """ This packages contains affiliated package tests. """ montage-wrapper-0.9.9/montage_wrapper/tests/coveragerc0000644000077000000240000000140013015134404023144 0ustar tomstaff00000000000000[run] source = {packagename} omit = {packagename}/_astropy_init* {packagename}/conftest* {packagename}/cython_version* {packagename}/setup_package* {packagename}/*/setup_package* {packagename}/*/*/setup_package* {packagename}/tests/* {packagename}/*/tests/* {packagename}/*/*/tests/* {packagename}/version* [report] exclude_lines = # Have to re-enable the standard pragma pragma: no cover # Don't complain about packages we have installed except ImportError # Don't complain if tests don't hit assertions raise AssertionError raise NotImplementedError # Don't complain about script hooks def main\(.*\): # Ignore branches that don't pertain to this version of Python pragma: py{ignore_python_version}montage-wrapper-0.9.9/montage_wrapper/tests/setup_package.py0000644000077000000240000000014013015134404024266 0ustar tomstaff00000000000000def get_package_data(): return { _ASTROPY_PACKAGE_NAME_ + '.tests': ['coveragerc']} montage-wrapper-0.9.9/montage_wrapper/tests/test_commands.py0000644000077000000240000000627313137204410024330 0ustar tomstaff00000000000000import numpy as np from astropy.table import Table from ..commands import * def test_all(): stat = mArchiveList('2MASS', 'k', 'M31', 0.2, 0.2, 'm31_2mass_k.tbl') assert stat.stat == 'OK' t = Table.read('m31_2mass_k.tbl', format='ascii.ipac') stat = mArchiveGet(t[0]['URL'], 'test.fits') assert stat.stat == 'OK' stat = mArchiveExec('m31_2mass_k.tbl') assert stat.stat == 'OK' stat = mBestImage('m31_2mass_k.tbl', 10.717773, 41.064461) assert stat.stat == 'OK' assert stat.file == "2mass-atlas-971024n-k0080044.fits.gz" stat = mGetHdr('2mass-atlas-971024n-k0080044.fits.gz', 'header.hdr') assert stat.stat == 'OK' t = Table() t['ra'] = np.random.uniform(10.70, 10.72, 100) t['dec'] = np.random.uniform(41.05, 41.07, 100) t['flux'] = np.random.random(100) t.write('sources.tbl', format='ascii.ipac') stat = mCatMap('sources.tbl', 'test_with_sources.fits', 'header.hdr', column='flux') assert stat.stat == 'OK' stat = mMakeHdr('m31_2mass_k.tbl', 'full_header.hdr') assert stat.stat == 'OK' stat = mExec('2MASS', 'k', n_tile_x=1, n_tile_y=1, level_only=True, keep=False, remove=True, output_image='test_mosaic.fits', region_header='full_header.hdr') assert stat.stat == 'OK' # Currently fails due to a bug in Montage # stat = mFixNaN('2mass-atlas-971024n-k0080044.fits.gz', 'test_nan.fits', # nan_value=3) # assert stat.stat == 'OK' # stat = mFixNaN('2mass-atlas-971024n-k0080044.fits.gz', 'test_blank.fits', # nan_value=3, min_blank=1, max_blank=3) # assert stat.stat == 'OK' stat = mHdr('M31', 0.3, 'test.hdr', system='eq', height=0.2, pix_size=10, rotation=22) assert stat.stat == 'OK' stat = mHdrCheck('2mass-atlas-971024n-k0080044.fits.gz') assert stat.stat == 'OK' stat = mHdrtbl('.', 'header_table.tbl') assert stat.stat == 'OK' stat = mPix2Coord('test.hdr', 10, 10) assert stat.stat == 'OK' stat = mProject('2mass-atlas-971024n-k0080044.fits.gz', 'test.fits', 'test.hdr', factor=0.7, scale=1.2) assert stat.stat == 'OK' stat = mProjectPP('2mass-atlas-971024n-k0080044.fits.gz', 'test.fits', 'test.hdr', factor=0.7, scale=1.2) assert stat.stat == 'OK' stat = mPutHdr('2mass-atlas-971024n-k0080044.fits.gz', 'new.fits', 'header.hdr') assert stat.stat == 'OK' stat = mRotate('2mass-atlas-971024n-k0080044.fits.gz', 'rotated.fits', rotation_angle=10) assert stat.stat == 'OK' stat = mShrink('2mass-atlas-971024n-k0080044.fits.gz', 'shrunk.fits', 3) assert stat.stat == 'OK' stat = mSubimage('2mass-atlas-971024n-k0080044.fits.gz', 'sub.fits', 10.717773, 41.064461, 0.1) assert stat.stat == 'OK' stat = mSubimage_pix('2mass-atlas-971024n-k0080044.fits.gz', 'subpix.fits', 10, 20, 30) assert stat.stat == 'OK' stat = mSubset('m31_2mass_k.tbl', 'test.hdr', 'subset.tbl') assert stat.stat == 'OK' stat = mTANHdr('test.hdr', 'new.hdr') assert stat.stat == 'OK' stat = mTblSort('m31_2mass_k.tbl', 'crval1', 'sorted.tbl') assert stat.stat == 'OK' stat = mTileHdr('test.hdr', 'new.hdr', 10, 10, 0, 0) assert stat.stat == 'OK' montage-wrapper-0.9.9/montage_wrapper/tests/test_wrappers.py0000644000077000000240000000473413104313456024377 0ustar tomstaff00000000000000import os import shutil import tempfile from hashlib import md5 import numpy as np from numpy.testing import assert_allclose from astropy.wcs import WCS from astropy.io import fits from astropy.tests.helper import pytest from .. import mosaic class TestMosaic(object): def setup_class(self): np.random.seed(12345) w = WCS(naxis=2) lon = np.linspace(10., 11., 5) lat = np.linspace(20., 21., 5) self.tmpdir = tempfile.mkdtemp() os.mkdir(os.path.join(self.tmpdir, 'raw')) for i in range(len(lon)): for j in range(len(lat)): w.wcs.crpix = [50.5, 50.5] w.wcs.cdelt = np.array([-0.0066667, 0.0066667]) w.wcs.crval = [lon[i], lat[j]] w.wcs.ctype = [b"RA---TAN", b"DEC--TAN"] w.wcs.crota = [0, np.random.uniform(0., 360.)] header = w.to_header() hdu = fits.PrimaryHDU(header=header) hdu.data = np.random.random((100,100)) hdu.writeto(os.path.join(self.tmpdir, 'raw', 'test_{0:02d}_{1:02d}.fits'.format(i, j)), clobber=True) def teardown_class(self): shutil.rmtree(self.tmpdir) def test_mosaic(self): mosaic(os.path.join(self.tmpdir, 'raw'),os.path.join(self.tmpdir, 'mosaic'), hdu=0) with fits.open(os.path.join(self.tmpdir, 'mosaic', 'mosaic.fits')) as hdulist: hdu = hdulist[0] assert hdu.data.shape == (288, 282) valid = hdu.data[~np.isnan(hdu.data)] assert len(valid) == 65029 assert_allclose(np.std(valid), 0.12658458001333581, rtol=5e-6) assert_allclose(np.mean(valid), 0.4995945318627074, rtol=5e-6) assert_allclose(np.median(valid), 0.5003376603126526, rtol=5e-6) def test_mosaic_background_match(self): mosaic(os.path.join(self.tmpdir, 'raw'),os.path.join(self.tmpdir, 'mosaic_bkgmatch'), background_match=True) # results are not consistent on different machines so can't compare # with fits.open(os.path.join(self.tmpdir, 'mosaic_bkgmatch', 'mosaic.fits'))[0] as hdulist: # hdu = hdulist[0] # assert hdu.data.shape == (288, 282) # valid = hdu.data[~np.isnan(hdu.data)] # assert len(valid) == 65029 # assert_allclose(np.std(valid), 0.12661606622654725) # assert_allclose(np.mean(valid), 0.4994805202294361) # assert_allclose(np.median(valid), 0.5002447366714478) montage-wrapper-0.9.9/montage_wrapper/version.py0000644000077000000240000001547613137205364022031 0ustar tomstaff00000000000000# Autogenerated by Astropy-affiliated package montage_wrapper's setup.py on 2017-07-29 23:23:48.281399 from __future__ import unicode_literals import datetime import locale import os import subprocess import warnings def _decode_stdio(stream): try: stdio_encoding = locale.getdefaultlocale()[1] or 'utf-8' except ValueError: stdio_encoding = 'utf-8' try: text = stream.decode(stdio_encoding) except UnicodeDecodeError: # Final fallback text = stream.decode('latin1') return text def update_git_devstr(version, path=None): """ Updates the git revision string if and only if the path is being imported directly from a git working copy. This ensures that the revision number in the version string is accurate. """ try: # Quick way to determine if we're in git or not - returns '' if not devstr = get_git_devstr(sha=True, show_warning=False, path=path) except OSError: return version if not devstr: # Probably not in git so just pass silently return version if 'dev' in version: # update to the current git revision version_base = version.split('.dev', 1)[0] devstr = get_git_devstr(sha=False, show_warning=False, path=path) return version_base + '.dev' + devstr else: # otherwise it's already the true/release version return version def get_git_devstr(sha=False, show_warning=True, path=None): """ Determines the number of revisions in this repository. Parameters ---------- sha : bool If True, the full SHA1 hash will be returned. Otherwise, the total count of commits in the repository will be used as a "revision number". show_warning : bool If True, issue a warning if git returns an error code, otherwise errors pass silently. path : str or None If a string, specifies the directory to look in to find the git repository. If `None`, the current working directory is used, and must be the root of the git repository. If given a filename it uses the directory containing that file. Returns ------- devversion : str Either a string with the revision number (if `sha` is False), the SHA1 hash of the current commit (if `sha` is True), or an empty string if git version info could not be identified. """ if path is None: path = os.getcwd() if not _get_repo_path(path, levels=0): return '' if not os.path.isdir(path): path = os.path.abspath(os.path.dirname(path)) if sha: # Faster for getting just the hash of HEAD cmd = ['rev-parse', 'HEAD'] else: cmd = ['rev-list', '--count', 'HEAD'] def run_git(cmd): try: p = subprocess.Popen(['git'] + cmd, cwd=path, stdout=subprocess.PIPE, stderr=subprocess.PIPE, stdin=subprocess.PIPE) stdout, stderr = p.communicate() except OSError as e: if show_warning: warnings.warn('Error running git: ' + str(e)) return (None, b'', b'') if p.returncode == 128: if show_warning: warnings.warn('No git repository present at {0!r}! Using ' 'default dev version.'.format(path)) return (p.returncode, b'', b'') if p.returncode == 129: if show_warning: warnings.warn('Your git looks old (does it support {0}?); ' 'consider upgrading to v1.7.2 or ' 'later.'.format(cmd[0])) return (p.returncode, stdout, stderr) elif p.returncode != 0: if show_warning: warnings.warn('Git failed while determining revision ' 'count: {0}'.format(_decode_stdio(stderr))) return (p.returncode, stdout, stderr) return p.returncode, stdout, stderr returncode, stdout, stderr = run_git(cmd) if not sha and returncode == 129: # git returns 129 if a command option failed to parse; in # particular this could happen in git versions older than 1.7.2 # where the --count option is not supported # Also use --abbrev-commit and --abbrev=0 to display the minimum # number of characters needed per-commit (rather than the full hash) cmd = ['rev-list', '--abbrev-commit', '--abbrev=0', 'HEAD'] returncode, stdout, stderr = run_git(cmd) # Fall back on the old method of getting all revisions and counting # the lines if returncode == 0: return str(stdout.count(b'\n')) else: return '' elif sha: return _decode_stdio(stdout)[:40] else: return _decode_stdio(stdout).strip() def _get_repo_path(pathname, levels=None): """ Given a file or directory name, determine the root of the git repository this path is under. If given, this won't look any higher than ``levels`` (that is, if ``levels=0`` then the given path must be the root of the git repository and is returned if so. Returns `None` if the given path could not be determined to belong to a git repo. """ if os.path.isfile(pathname): current_dir = os.path.abspath(os.path.dirname(pathname)) elif os.path.isdir(pathname): current_dir = os.path.abspath(pathname) else: return None current_level = 0 while levels is None or current_level <= levels: if os.path.exists(os.path.join(current_dir, '.git')): return current_dir current_level += 1 if current_dir == os.path.dirname(current_dir): break current_dir = os.path.dirname(current_dir) return None _packagename = "montage_wrapper" _last_generated_version = "0.9.9" _last_githash = "a09c8b3241f2ca0ac912567d0c7f6754d3db2910" # Determine where the source code for this module # lives. If __file__ is not a filesystem path then # it is assumed not to live in a git repo at all. if _get_repo_path(__file__, levels=len(_packagename.split('.'))): version = update_git_devstr(_last_generated_version, path=__file__) githash = get_git_devstr(sha=True, show_warning=False, path=__file__) or _last_githash else: # The file does not appear to live in a git repo so don't bother # invoking git version = _last_generated_version githash = _last_githash major = 0 minor = 9 bugfix = 9 release = True timestamp = datetime.datetime(2017, 7, 29, 23, 23, 48, 281399) debug = False try: from ._compiler import compiler except ImportError: compiler = "unknown" try: from .cython_version import cython_version except ImportError: cython_version = "unknown" montage-wrapper-0.9.9/montage_wrapper/wrappers.py0000644000077000000240000005162713015134404022174 0ustar tomstaff00000000000000import atexit import os import glob import shutil as sh import warnings import tempfile import numpy from astropy.io import fits from astropy import log from . import commands as m from .status import MontageError def _finalize(cleanup, work_dir, silence=False): if cleanup: # Deleting work directory if not silence: log.info("Deleting work directory %s" % work_dir) sh.rmtree(work_dir) else: # Leave work directory as it is if not silence: log.info("Leaving work directory %s" % work_dir) def reproject_hdu(in_hdu, **kwargs): ''' Reproject an image (HDU version) Parameters ---------- in_hdu : :class:`~astropy.io.fits.PrimaryHDU` or :class:`~astropy.io.fits.ImageHDU` Input FITS HDU to be reprojected. Notes ----- Additional keyword arguments are passed to :func:`~montage_wrapper.wrappers.reproject` ''' cleanup = kwargs.get('cleanup', True) silent_cleanup = kwargs.get('silent_cleanup', True) # Make work directory work_dir = tempfile.mkdtemp() try: in_image = os.path.join(work_dir, 'in.fits') out_image = os.path.join(work_dir, 'out.fits') fits.writeto(in_image, in_hdu.data, in_hdu.header) reproject(in_image, out_image, **kwargs) out_hdu = fits.open(out_image)[0] return out_hdu finally: _finalize(cleanup, work_dir, silent_cleanup) def reproject_cube(in_image, out_image, header=None, bitpix=None, north_aligned=False, system=None, equinox=None, factor=None, common=False, cleanup=True, clobber=False, silent_cleanup=True, hdu=0): ''' Cube reprojection routine. If one input/output image is specified, and the header argument is set, the routine is equivalent to using mProject or mProjectPP. If header= is not set, a new header is computed by taking into account the north_aligned, system, and equinox arguments (if set). Parameters ---------- in_image : str Path of input FITS file to be reprojected. out_image : str Path of output FITS file to be created. header : str, optional Path to the header file to use for re-projection. bitpix : int, optional BITPIX value for the ouput FITS file (default is -64). Possible values are: 8 (character or unsigned binary integer), 16 (16-bit integer), 32 (32-bit integer), -32 (single precision floating point), -64 (double precision floating point). north_aligned : bool, optional Align the pixel y-axis with North system : str, optional Specifies the coordinate system Possible values are: 'EQUJ', 'EQUB', 'ECLJ', 'ECLB', 'GAL', 'SGAL' equinox : str, optional If a coordinate system is specified, the equinox can also be given in the form 'YYYY'. Default is 'J2000'. factor : float, optional Drizzle factor (see `~montage_wrapper.commands.mProject`) clobber : bool, optional Overwrite the data cube if it already exists? silent_cleanup : bool, optional Hide messages related to tmp directory removal (there will be one for each plane of the cube if set to False) hdu: int Defaults to zero. Selects which HDU to use from the FITS file. ''' if header: if north_aligned or system or equinox: warnings.warn("header= is set, so north_aligned=, system=, and equinox= will be ignored") # Find path to input and output file in_image = os.path.abspath(in_image) out_image = os.path.abspath(out_image) if os.path.exists(out_image) and not clobber: raise IOError("File '%s' already exists and clobber=False." % out_image) # Make work directory work_dir = tempfile.mkdtemp() # Set paths raw_dir = os.path.join(work_dir, 'raw') final_dir = os.path.join(work_dir, 'final') if header: header_hdr = os.path.abspath(header) else: header_hdr = os.path.join(work_dir, 'header.hdr') images_raw_tbl = os.path.join(work_dir, 'images_raw.tbl') images_tmp_tbl = os.path.join(work_dir, 'images_tmp.tbl') # Create raw directory os.mkdir(raw_dir) os.mkdir(final_dir) # Make new header if not header: m.mMakeHdr(images_raw_tbl, header_hdr, north_aligned=north_aligned, system=system, equinox=equinox) cubefile = fits.open(in_image) if len(cubefile[hdu].data.shape) != 3 or cubefile[hdu].header.get('NAXIS') != 3: raise Exception("Cube file must have 3 dimensions") # a temporary HDU that will be used to hold different data each time # and reproject each plane separately planefile = fits.PrimaryHDU(data=cubefile[hdu].data[0, :, :], header=cubefile[hdu].header) # generate a blank HDU to store the eventual projected cube # first must remove END card from .hdr file header_temp = header_hdr.replace(".hdr", "_tmp.hdr") headerlines = open(header_hdr, 'r').readlines()[:-1] w = open(header_temp, 'w') w.writelines([line for line in headerlines]) w.close() # when creating the new header, allow the 3rd axis to be # set by the input data cube newheader = fits.Header() newheader.fromTxtFile(header_temp) blank_data = numpy.zeros( [cubefile[hdu].header.get('NAXIS3'), newheader.get('NAXIS2'), newheader.get('NAXIS1')] ) newcube = fits.PrimaryHDU(data=blank_data, header=newheader) for ii, plane in enumerate(cubefile[hdu].data): os.mkdir(os.path.join(final_dir, '%i' % ii)) # reset the data plane within the temporary HDU planefile.data = plane # reproject the individual plane - exact size MUST be specified so that the # data can be put into the specified cube reprojected = reproject_hdu(planefile, header=header_hdr, exact_size=True, factor=factor, bitpix=bitpix, silent_cleanup=silent_cleanup) newcube.data[ii, :, :] = reprojected.data newcube.writeto(out_image, clobber=clobber) _finalize(cleanup, work_dir) return def mProject_auto(*args, **kwargs): ''' Run mProject, automatically selecting whether to run mProject or mProjectPP if possible (fast plane-to-plane projection). For details on required and optional arguments, see help(mProject). ''' try: m.mProjectPP(*args, **kwargs) except MontageError: m.mProject(*args, **kwargs) def reproject(in_images, out_images, header=None, bitpix=None, north_aligned=False, system=None, equinox=None, factor=None, common=False, exact_size=False, hdu=None, cleanup=True, silent_cleanup=False): ''' General-purpose reprojection routine. If one input/output image is specified, and the header argument is set, the routine is equivalent to using mProject or mProjectPP. If header= is not set, a new header is computed by taking into account the north_aligned, system, and equinox arguments (if set). If tuples of input/output images are specified, the tuples need to have the same number of elements. If header= is specified, all images are projected to this common projection. If header= is not specified, then a new header is computed a new header is computed by taking into account the north_aligned, system, and equinox arguments (if set). If common=False, then a header is computed for each individual image, whereas if common=True, an optimal header is computed for all images. Parameters ---------- in_images : str or list Path(s) of input FITS file(s) to be reprojected. out_images : str or list Path(s) of output FITS file(s) to be created. header : str, optional Path to the header file to use for re-projection. bitpix : int, optional BITPIX value for the ouput FITS file (default is -64). Possible values are: 8 (character or unsigned binary integer), 16 (16-bit integer), 32 (32-bit integer), -32 (single precision floating point), -64 (double precision floating point). north_aligned : bool, optional Align the pixel y-axis with North system : str, optional Specifies the coordinate system Possible values are: 'EQUJ', 'EQUB', 'ECLJ', 'ECLB', 'GAL', 'SGAL' equinox : str, optional If a coordinate system is specified, the equinox can also be given in the form 'YYYY'. Default is 'J2000'. factor : float, optional Drizzle factor (see `~montage_wrapper.commands.mProject`) exact_size : bool, optional Whether to reproject the image(s) to the exact header specified (i.e. whether cropping is unacceptable). hdu : int, optional The HDU to use in the file(s) silent_cleanup : bool, optional Hide messages related to tmp directory removal common : str, optional Compute a common optimal header for all images (only used if header=None and if multiple files are being reprojected) ''' if type(in_images) == str and type(out_images) == str: in_images = (in_images, ) out_images = (out_images, ) elif type(in_images) in [tuple, list] and type(out_images) in [tuple, list]: pass else: raise Exception("Inconsistent type for in_images (%s) and out_images (%s)" % (type(in_images), type(out_images))) if header: if north_aligned or system or equinox: warnings.warn("header= is set, so north_aligned=, system=, and equinox= will be ignored") if common and len(in_images) == 1: warnings.warn("only one image is being reprojected, so common= will be ignored") # Find path to input and output file in_images = [os.path.abspath(in_image) for in_image in in_images] out_images = [os.path.abspath(out_image) for out_image in out_images] if len(in_images) > 1 and not header and not common: for i, in_image in enumerate(in_images): reproject(in_images[i], out_images[i], bitpix=bitpix, north_aligned=north_aligned, system=system, equinox=equinox, factor=factor, exact_size=exact_size, cleanup=cleanup, silent_cleanup=silent_cleanup) return # Make work directory work_dir = tempfile.mkdtemp() # Set paths raw_dir = os.path.join(work_dir, 'raw') final_dir = os.path.join(work_dir, 'final') if header: header_hdr = os.path.abspath(header) else: header_hdr = os.path.join(work_dir, 'header.hdr') images_raw_tbl = os.path.join(work_dir, 'images_raw.tbl') images_tmp_tbl = os.path.join(work_dir, 'images_tmp.tbl') # Create raw directory os.mkdir(raw_dir) os.mkdir(final_dir) # Link to images for i, in_image in enumerate(in_images): os.mkdir(os.path.join(raw_dir, '%i' % i)) os.symlink(in_image, os.path.join(raw_dir, '%i' % i, 'image.fits')) # Make image table m.mImgtbl(raw_dir, images_raw_tbl, corners=True, recursive=True) # Make new header if not header: m.mMakeHdr(images_raw_tbl, header_hdr, north_aligned=north_aligned, system=system, equinox=equinox) for i, in_image in enumerate(in_images): os.mkdir(os.path.join(final_dir, '%i' % i)) mProject_auto(in_images[i], os.path.join(final_dir, '%i' % i, 'image_tmp.fits'), header_hdr, hdu=hdu, factor=factor) if exact_size: m.mImgtbl(os.path.join(final_dir, '%i' % i), images_tmp_tbl, corners=True) m.mAdd(images_tmp_tbl, header_hdr, os.path.join(final_dir, '%i' % i, 'image.fits'), img_dir=os.path.join(final_dir, '%i' % i), exact=True) else: os.symlink(os.path.join(final_dir, '%i' % i, 'image_tmp.fits'), os.path.join(final_dir, '%i' % i, 'image.fits')) m.mConvert(os.path.join(final_dir, '%i' % i, 'image.fits'), out_images[i], bitpix=bitpix) _finalize(cleanup, work_dir, silence=silent_cleanup) return def mosaic(input_dir, output_dir, header=None, image_table=None, mpi=False, n_proc=8, background_match=False, imglist=None, combine="mean", exact_size=False, cleanup=True, bitpix=-32, level_only=True, work_dir=None, background_n_iter=None, subset_fast=False, hdu=None): """ Combine FITS files into a mosaic Parameters ---------- input_dir : str The directory containing the input FITS files output_dir : str The output directory to create header : str, optional The header to project to. If this is not specified, then an optimal header is chosen. image_table : str, optional The table file containing the list of input images. This can be specified to avoid recomputing it every time a mosaic is made from the same set of input files. mpi : bool, optional Whether to use MPI whenever possible (requires the MPI-enabled Montage binaries to be installed). n_proc : int, optional The number of processes to use if `mpi` is set to `True` background_match : bool, optional Whether to include a background-matching step imglist : str, optional A list of images to use (useful if not all the files inside `input_dir` should be combined). combine : str, optional How to combine the images - this should be one of ``'mean'``, ``'median'``, or ``'count'``. exact_size : bool, optional Whether the output mosaic should match the input header exactly, or whether the mosaic should be trimmed if possible. cleanup : bool, optional Whether to remove any temporary directories used for mosaicking bitpix : int, optional BITPIX value for the ouput FITS file (default is -32). Possible values are: 8 (character or unsigned binary integer), 16 (16-bit integer), 32 (32-bit integer), -32 (single precision floating point), -64 (double precision floating point). level_only : bool, optional When doing background matching, whether to only allow changes in the level of frames, not the slope. work_dir : str, optional The temporary directory to use for the mosaicking. By default, this is a temporary directory in a system-defined location, but it can be useful to specify this manually for debugging purposes. background_n_iter : int, optional Number of iterations for the background matching (defaults to 5000). Can be between 1 and 32767. subset_fast : bool, optional Whether to use the fast mode for mSubset hdu: int, optional Which HDU to use when mosaicing """ if not combine in ['mean', 'median', 'count']: raise Exception("combine should be one of mean/median/count") # Check that there are files in the input directory if len(glob.glob(os.path.join(input_dir, '*'))) == 0: raise Exception("No files in input directory") # Find path to input and output directory input_dir = os.path.abspath(input_dir) output_dir = os.path.abspath(output_dir) # Make work directory if work_dir: work_dir = os.path.abspath(work_dir) if os.path.exists(work_dir): raise Exception("Work directory already exists") os.mkdir(work_dir) else: # Use a temporary directory such as 'montage_mosaic_ngc2264_EdJyrj', # where 'ngc2264' would be here determined by the input directory. basename = os.path.basename(os.path.normpath(input_dir)) prefix = "montage_mosaic_{0}_".format(basename) work_dir = tempfile.mkdtemp(prefix=prefix) # Make sure the working directory is cleaned up even when something goes # wrong (or Ctrl-C is pressed, raising the KeyboardInterrupt exception) @atexit.register def cleanup_workdir(): """ Run _finalize() if necessary """ if os.path.exists(work_dir): _finalize(cleanup, work_dir) images_raw_all_tbl = os.path.join(work_dir, 'images_raw_all.tbl') images_raw_tbl = os.path.join(work_dir, 'images_raw.tbl') images_projected_tbl = os.path.join(work_dir, 'images_projected.tbl') images_corrected_tbl = os.path.join(work_dir, 'images_corrected.tbl') corrections_tbl = os.path.join(work_dir, 'corrections.tbl') diffs_tbl = os.path.join(work_dir, 'diffs.tbl') stats_tbl = os.path.join(work_dir, 'stats.tbl') fits_tbl = os.path.join(work_dir, 'fits.tbl') raw_dir = os.path.join(work_dir, 'raw') projected_dir = os.path.join(work_dir, 'projected') corrected_dir = os.path.join(work_dir, 'corrected') diffs_dir = os.path.join(work_dir, 'diffs') header_hdr = os.path.join(work_dir, 'header.hdr') # Find path to header file if specified if header is not None: header = os.path.abspath(header) # Find path to image table if specified if image_table is not None: image_table = os.path.abspath(image_table) # Find path to image list if specified if imglist: imglist = os.path.abspath(imglist) # Create output dir if os.path.exists(output_dir): raise IOError("Output directory already exists") else: os.mkdir(output_dir) # Create symbolic links os.symlink(input_dir, raw_dir) if header: os.symlink(header, header_hdr) # Create temporary directories for Montage os.mkdir(projected_dir) if background_match: os.mkdir(diffs_dir) os.mkdir(corrected_dir) # List frames to mosaic if image_table is None: log.info("Listing raw frames") m.mImgtbl(raw_dir, images_raw_all_tbl, img_list=imglist, corners=True) else: sh.copy2(image_table, images_raw_all_tbl) # Compute header if needed if not header: log.info("Computing optimal header") m.mMakeHdr(images_raw_all_tbl, header_hdr) images_raw_tbl = images_raw_all_tbl else: log.info("Checking for coverage") s = m.mSubset(images_raw_all_tbl, header_hdr, images_raw_tbl, fast_mode=subset_fast) if s.nmatches == 0: raise MontageError("No images overlap with the requested header") # Projecting raw frames log.info("Projecting raw frames") if hdu is not None: from astropy.table import Table table = Table.read(images_raw_tbl, format='ascii.ipac') table_filtered = table[table['hdu'] == hdu] table_filtered.write(images_raw_tbl, format='ascii.ipac') m.mProjExec(images_raw_tbl, header_hdr, projected_dir, stats_tbl, raw_dir=raw_dir, mpi=mpi, n_proc=n_proc, exact=exact_size) # List projected frames s = m.mImgtbl(projected_dir, images_projected_tbl) if s.count == 0: raise MontageError("No images were successfully projected") if background_match: log.info("Determining overlaps") s = m.mOverlaps(images_projected_tbl, diffs_tbl) if s.count == 0: log.info("No overlapping frames, backgrounds will not be adjusted") background_match = False if background_match: # Modeling background log.info("Modeling background") m.mDiffExec(diffs_tbl, header_hdr, diffs_dir, proj_dir=projected_dir, mpi=mpi, n_proc=n_proc) m.mFitExec(diffs_tbl, fits_tbl, diffs_dir, mpi=mpi, n_proc=n_proc) m.mBgModel(images_projected_tbl, fits_tbl, corrections_tbl, n_iter=background_n_iter, level_only=level_only) # Matching background log.info("Matching background") m.mBgExec(images_projected_tbl, corrections_tbl, corrected_dir, proj_dir=projected_dir, mpi=mpi, n_proc=n_proc) sh.copy(corrections_tbl, output_dir) # Mosaicking frames log.info("Mosaicking frames") m.mImgtbl(corrected_dir, images_corrected_tbl) m.mAdd(images_corrected_tbl, header_hdr, os.path.join(output_dir, 'mosaic64.fits'), img_dir=corrected_dir, type=combine, exact=exact_size) sh.copy(images_projected_tbl, output_dir) sh.copy(images_corrected_tbl, output_dir) else: # Mosaicking frames log.info("Mosaicking frames") m.mAdd(images_projected_tbl, header_hdr, os.path.join(output_dir, 'mosaic64.fits'), img_dir=projected_dir, type=combine, exact=exact_size) sh.copy(images_projected_tbl, output_dir) m.mConvert(os.path.join(output_dir, 'mosaic64.fits'), os.path.join(output_dir, 'mosaic.fits'), bitpix=bitpix) m.mConvert(os.path.join(output_dir, 'mosaic64_area.fits'), os.path.join(output_dir, 'mosaic_area.fits'), bitpix=bitpix) os.remove(os.path.join(output_dir, "mosaic64.fits")) os.remove(os.path.join(output_dir, "mosaic64_area.fits")) _finalize(cleanup, work_dir) montage-wrapper-0.9.9/PKG-INFO0000644000077000000240000000051613137205364015662 0ustar tomstaff00000000000000Metadata-Version: 1.0 Name: montage-wrapper Version: 0.9.9 Summary: Python wrapper for the Montage mosaicking toolkit Home-page: http://astropy.org/montage-wrapper/ Author: Thomas Robitaille Author-email: thomas.robitaille@gmail.com License: BSD Description: This is an Astropy affiliated package. Platform: UNKNOWN montage-wrapper-0.9.9/README.rst0000644000077000000240000000135213015155217016247 0ustar tomstaff00000000000000About ===== This package provides a python wrapper to the Montage Astronomical Image Mosaic Engine, including both functions to access individual Montage commands, and high-level functions to facilitate mosaicking and re-projecting. Installation and usage instructions are available at http://www.astropy.org/montage-wrapper/ .. image:: http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat :target: http://www.astropy.org :alt: Powered by Astropy Badge .. image:: https://travis-ci.org/astropy/montage-wrapper.svg?branch=master :target: https://travis-ci.org/astropy/montage-wrapper .. image:: https://coveralls.io/repos/astropy/montage-wrapper/badge.svg :target: https://coveralls.io/r/astropy/montage-wrapper montage-wrapper-0.9.9/setup.cfg0000644000077000000240000000106513015134404016375 0ustar tomstaff00000000000000[build_sphinx] source-dir = docs build-dir = docs/_build all_files = 1 [upload_docs] upload-dir = docs/_build/html show-response = 1 [pytest] minversion = 2.2 norecursedirs = build docs/_build doctest_plus = enabled [ah_bootstrap] auto_use = True [metadata] package_name = montage_wrapper description = Python wrapper for the Montage mosaicking toolkit long_description = author = Thomas Robitaille author_email = thomas.robitaille@gmail.com license = BSD url = http://astropy.org/montage-wrapper/ edit_on_github = True github_project = astropy/montage-wrapper montage-wrapper-0.9.9/setup.py0000755000077000000240000000676113137204705016310 0ustar tomstaff00000000000000#!/usr/bin/env python # Licensed under a 3-clause BSD style license - see LICENSE.rst import glob import os import sys import ah_bootstrap from setuptools import setup #A dirty hack to get around some early import/configurations ambiguities if sys.version_info[0] >= 3: import builtins else: import __builtin__ as builtins builtins._ASTROPY_SETUP_ = True from astropy_helpers.setup_helpers import ( register_commands, adjust_compiler, get_debug_option, get_package_info) from astropy_helpers.git_helpers import get_git_devstr from astropy_helpers.version_helpers import generate_version_py # Get some values from the setup.cfg try: from ConfigParser import ConfigParser except ImportError: from configparser import ConfigParser conf = ConfigParser() conf.read(['setup.cfg']) metadata = dict(conf.items('metadata')) PACKAGENAME = metadata.get('package_name', 'packagename') DESCRIPTION = metadata.get('description', 'Astropy affiliated package') AUTHOR = metadata.get('author', '') AUTHOR_EMAIL = metadata.get('author_email', '') LICENSE = metadata.get('license', 'unknown') URL = metadata.get('url', 'http://astropy.org') # Get the long description from the package's docstring __import__(PACKAGENAME) package = sys.modules[PACKAGENAME] LONG_DESCRIPTION = package.__doc__ # Store the package name in a built-in variable so it's easy # to get from other parts of the setup infrastructure builtins._ASTROPY_PACKAGE_NAME_ = PACKAGENAME # VERSION should be PEP386 compatible (http://www.python.org/dev/peps/pep-0386) VERSION = '0.9.9' # Indicates if this version is a release version RELEASE = 'dev' not in VERSION if not RELEASE: VERSION += get_git_devstr(False) # Populate the dict of setup command overrides; this should be done before # invoking any other functionality from distutils since it can potentially # modify distutils' behavior. cmdclassd = register_commands(PACKAGENAME, VERSION, RELEASE) # Adjust the compiler in case the default on this platform is to use a # broken one. adjust_compiler(PACKAGENAME) # Freeze build information in version.py generate_version_py(PACKAGENAME, VERSION, RELEASE, get_debug_option(PACKAGENAME)) # Treat everything in scripts except README.rst as a script to be installed scripts = [fname for fname in glob.glob(os.path.join('scripts', '*')) if os.path.basename(fname) != 'README.rst'] # Get configuration information from all of the various subpackages. # See the docstring for setup_helpers.update_package_files for more # details. package_info = get_package_info() # Add the project-global data package_info['package_data'].setdefault(PACKAGENAME, []) package_info['package_data'][PACKAGENAME].append('data/*') # Include all .c files, recursively, including those generated by # Cython, since we can not do this in MANIFEST.in with a "dynamic" # directory name. c_files = [] for root, dirs, files in os.walk(PACKAGENAME): for filename in files: if filename.endswith('.c'): c_files.append( os.path.join( os.path.relpath(root, PACKAGENAME), filename)) package_info['package_data'][PACKAGENAME].extend(c_files) setup(name=PACKAGENAME.replace('_', '-'), version=VERSION, description=DESCRIPTION, scripts=scripts, install_requires=['astropy'], author=AUTHOR, author_email=AUTHOR_EMAIL, license=LICENSE, url=URL, long_description=LONG_DESCRIPTION, cmdclass=cmdclassd, zip_safe=False, use_2to3=False, **package_info )