pax_global_header 0000666 0000000 0000000 00000000064 13376012530 0014512 g ustar 00root root 0000000 0000000 52 comment=599a88ae58b88054c0089ee3c4411fb8a1a76379
ruffus-2.8.1/ 0000775 0000000 0000000 00000000000 13376012530 0013034 5 ustar 00root root 0000000 0000000 ruffus-2.8.1/.gitignore 0000664 0000000 0000000 00000000147 13376012530 0015026 0 ustar 00root root 0000000 0000000 *.pyc
*.egg-info
.tox
dist
build
_build
doc/hosted_site.cmd
.ruffus_history.sqlite
ruffus_development.* ruffus-2.8.1/.gitmodules 0000664 0000000 0000000 00000000166 13376012530 0015214 0 ustar 00root root 0000000 0000000 [submodule "doc/sphinx_rtd_theme"]
path = doc/sphinx_rtd_theme
url = https://github.com/bunbun/sphinx_rtd_theme.git
ruffus-2.8.1/.hgignore 0000664 0000000 0000000 00000000143 13376012530 0014635 0 ustar 00root root 0000000 0000000 .*\.pyc$
^nested_dict.egg-info/.+
^dist
_build$
doc/hosted_site.cmd
^.tox
^.ruffus_history.sqlite$
ruffus-2.8.1/.nojekyll 0000664 0000000 0000000 00000000000 13376012530 0014652 0 ustar 00root root 0000000 0000000 ruffus-2.8.1/.travis.yml 0000664 0000000 0000000 00000000626 13376012530 0015151 0 ustar 00root root 0000000 0000000 language: python
# all python versions tested via pip in tox
python:
- "2.7"
- "3.4"
- "3.5"
- "3.6"
# Travis does not properly support this yet.
# https://github.com/travis-ci/travis-ci/issues/9815
matrix:
include:
- python: 3.7
dist: xenial
sudo: true
before_install:
install: python setup.py install
script: cd ruffus/test && /bin/bash run_all_unit_tests.cmd
sudo: false
ruffus-2.8.1/CHANGES.TXT 0000664 0000000 0000000 00000110737 13376012530 0014516 0 ustar 00root root 0000000 0000000 = v. 2.6=
2015-03-12
============================================================================================================================================================
Bug fixes
============================================================================================================================================================
* ``pipeline_printout_graph()`` incompatibility with python3 fixed
* checkpointing did not work correctly with :ref:`@split(...) ` and :ref:`@subdivide(...) `
=====================================================================================================================
`@transform `(..., suffix("xxx"),` :red:`output_dir` `= "/new/output/path")`
=====================================================================================================================
* Thanks to the suggestion of Milan Simonovic.
* :ref:`@transform ` takes an optional ``output_dir`` named parameter with :ref:`suffix() `.
* Output files go to the specified directory.
=====================================================================================================================
Named parameters
=====================================================================================================================
* Decorators can take named parameters.
* These are self documenting, and improve clarity.
=============================================
New object orientated syntax for Ruffus
=============================================
* Ruffus Pipelines can now be created directly using the new ``Pipeline`` and ``Task`` objects instead of via decorators.
* This new syntax is fully compatible and inter-operates with traditional Ruffus syntax using decorators.
* Apart from cosmetic changes, the new syntax allows different instances of modular Ruffus sub-pipelines
to be defined separately, in different python modules and then joined together flexible at runtime.
= v. 2.5=
2014-08-06
============================================================================================================================================================
Python3 compatability
============================================================================================================================================================
At least python 2.6 is now required.
============================================================================================================================================================
Ctrl-C interrupts
============================================================================================================================================================
Ruffus now mostly(!) terminates gracefully when interrupted by Ctrl-C .
============================================================================================================================================================
Customising flowcharts in pipeline_printout_graph() with ``@graphviz``
============================================================================================================================================================
*Contributed by Sean Davis, with improved syntax via Jake Biesinger*
The graphics for each task can have its own attributes (URL, shape, colour) etc. by adding
`graphviz attributes `__
using the ``@graphviz`` decorator.
============================================================================================================================================================
Consistent verbosity levels
============================================================================================================================================================
The verbosity levels are now more fine-grained and consistent between pipeline_printout and pipeline_run.
============================================================================================================================================================
Allow abbreviated paths from ``pipeline_run`` or ``pipeline_printout``
============================================================================================================================================================
Ruffus now allows either
1) Only the nth top level sub-directories to be included
2) The message to be truncated to a specified number of characters (to fit on a line, for example)
============================================================================================================================================================
Bug fixes
============================================================================================================================================================
* BUG FIX: Output producing wild cards was not saved in the checksum files!!!
* BUG FIX: @mkdir bug under Windows. Thanks to Sean Turley. (Aargh! Different exceptions are thrown in Windows vs. Linux for the same condition!)
* Added :ref:`pipeline_get_task_names(...) ` which returns all task name as a list of strings. Thanks to Clare Sloggett
= v. 2.4.1=
2014-04-26
* Breaking changes to drmaa API suggested by Bernie Pope to ensure portability across different drmaa implementations (SGE, SLURM etc.)
= v. 2.4=
2014-04-03
============================================================================================================================================================
Additions to ``ruffus`` namespace
============================================================================================================================================================
* :ref:`formatter() ` (:ref:`syntax `)
* :ref:`originate() ` (:ref:`syntax `)
* :ref:`subdivide() ` (:ref:`syntax `)
============================================================================================================================================================
Installation: use pip
============================================================================================================================================================
::
sudo pip install ruffus --upgrade
============================================================================================================================================================
1) Command Line support
============================================================================================================================================================
The optional ``Ruffus.cmdline`` module provides support for a set of common command
line arguments which make writing *Ruffus* pipelines much more pleasant.
See :ref:`manual `
============================================================================================================================================================
2) Check pointing
============================================================================================================================================================
* Contributed by **Jake Biesinger**
* See :ref:`Manual `
* Uses a fault resistant sqlite database file to log i/o files, and additional checksums
* defaults to checking file timestamps stored in the current directory (``ruffus_utilility.RUFFUS_HISTORY_FILE = '.ruffus_history.sqlite'``)
* :ref:`pipeline_run(..., checksum_level = N, ...) `
* level 0 = CHECKSUM_FILE_TIMESTAMPS : Classic mode. Use only file timestamps (no checksum file will be created)
* level 1 = CHECKSUM_HISTORY_TIMESTAMPS : Also store timestamps in a database after successful job completion
* level 2 = CHECKSUM_FUNCTIONS : As above, plus a checksum of the pipeline function body
* level 3 = CHECKSUM_FUNCTIONS_AND_PARAMS : As above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators
* defaults to level 1
* Can speed up trivial tasks: Previously Ruffus always added an extra 1 second pause between tasks
to guard against file systems (Ext3, FAT, some NFS) with low timestamp granularity.
============================================================================================================================================================
3) :ref:`subdivide() ` (:ref:`syntax `)
============================================================================================================================================================
*
* Take a list of input jobs (like :ref:`@transform `) but further splits each into multiple jobs, i.e. it is a **many->even more** relationship
* synonym for the deprecated ``@split(..., regex(), ...)``
========================================================================================================================================================================================================================================================================================================================
4) :ref:`mkdir() ` (:ref:`syntax `) with :ref:`formatter() `, :ref:`suffix() ` and :ref:`regex() `
========================================================================================================================================================================================================================================================================================================================
* allows directories to be created depending on runtime parameters or the output of previous tasks
* behaves just like :ref:`@transform ` but with its own (internal) function which does the actual work of making a directory
* Previous behavior is retained:``mkdir`` continues to work seamlessly inside :ref:`@follows `
============================================================================================================================================================
5) :ref:`originate() ` (:ref:`syntax `)
============================================================================================================================================================
* Generates output files without dependencies from scratch (*ex nihilo*!)
* For first step in a pipeline
* Task function obviously only takes output and not input parameters. (There *are* no inputs!)
* synonym for :ref:`@split(None,...) `
* See :ref:`Summary ` / :ref:`Manual `
========================================================================================================================================================================================================================================================================================================================
6) New flexible :ref:`formatter() ` (:ref:`syntax `) alternative to :ref:`regex() ` & :ref:`suffix() `
========================================================================================================================================================================================================================================================================================================================
* Easy manipulation of path subcomponents in the style of `os.path.split() `__
* Regular expressions are no longer necessary for path manipulation
* Familiar python syntax
* Optional regular expression matches
* Can refer to any in the list of N input files (not only the first file as for ``regex(...)``)
* Can even refer to individual letters within a match
============================================================================================================================================================
7) Combinatorics (all vs. all decorators)
============================================================================================================================================================
* :ref:`@product ` (See `itertools.product `__)
* :ref:`@permutations ` (See `itertools.permutations `__)
* :ref:`@combinations ` (See `itertools.combinations `__)
* :ref:`@combinations_with_replacement ` (See `itertools.combinations_with_replacement `__)
* in optional :ref:`combinatorics ` module
* Only :ref:`formatter() ` provides the necessary flexibility to construct the output. (:ref:`suffix() ` and :ref:`regex() ` are not supported.)
* See :ref:`Summary ` / :ref:`Manual `
============================================================================================================================================================
8) drmaa support and multithreading:
============================================================================================================================================================
* :ref:`ruffus.drmaa_wrapper.run_job() ` (:ref:`syntax `)
* Optional helper module allows jobs to dispatch work to a computational cluster and wait until it completes.
* Requires ``multithread`` rather than ``multiprocess``
============================================================================================================================================================
9) ``pipeline_run(...)`` and exceptions
============================================================================================================================================================
See :ref:`Manual `
* Optionally terminate pipeline after first exception
* Display exceptions without delay
============================================================================================================================================================
10) Miscellaneous
============================================================================================================================================================
Better error messages for ``formatter()``, ``suffix()`` and ``regex()`` for ``pipeline_printout(..., verbose >= 3, ...)``
* Error messages for showing mismatching regular expression and offending file name
* Wrong capture group names or out of range indices will raise informative Exception
= v. 2.3=
_03/October/2011_
* ``@active_if`` turns off tasks at runtime
The Design and initial implementation were contributed by Jacob Biesinger
Takes one or more parameters which can be either booleans or functions or callable objects which return True / False::
run_if_true_1 = True
run_if_true_2 = False
@active_if(run_if_true, lambda: run_if_true_2)
def this_task_might_be_inactive():
pass
The expressions inside @active_if are evaluated each time
``pipeline_run``, ``pipeline_printout`` or ``pipeline_printout_graph`` is called.
Dormant tasks behave as if they are up to date and have no output.
* Command line parsing
* Supports both argparse (python 2.7) and optparse (python 2.6):
* ``Ruffus.cmdline`` module is optional.
* See :ref:`manual `
* Optionally terminate pipeline after first exception
To have all exceptions interrupt immediately::
pipeline_run(..., exceptions_terminate_immediately = True)
By default ruffus accumulates ``NN`` errors before interrupting the pipeline prematurely. ``NN`` is the specified parallelism for ``pipeline_run(..., multiprocess = NN)``.
Otherwise, a pipeline will only be interrupted immediately if exceptions of type ``ruffus.JobSignalledBreak`` are thrown.
* Display exceptions without delay
By default, Ruffus re-throws exceptions in ensemble after pipeline termination.
To see exceptions as they occur::
pipeline_run(..., log_exceptions = True)
``logger.error(...)`` will be invoked with the string representation of the each exception, and associated stack trace.
The default logger prints to sys.stderr, but this can be changed to any class from the logging module or compatible object via ``pipeline_run(..., logger = ???)``
* Improved ``pipeline_printout()``
* `@split` operations now show the 1->many output in pipeline_printout
This make it clearer that ``@split`` is creating multiple output parameters (rather than a single output parameter consisting of a list)::
Task = split_animals
Job = [None
-> cows
-> horses
-> pigs
, any_extra_parameters]
* File date and time are displayed in human readable form and out of date files are flagged with asterisks.
= v. 2.2=
_21/July/2010_
* Simplifying **@transform** syntax with **suffix(...)**
Regular expressions within ruffus are very powerful, and can allow files to be moved
from one directory to another and renamed at will.
However, using consistent file extensions and
``@transform(..., suffix(...))`` makes the code much simpler and easier to read.
Previously, ``suffix(...)`` did not cooperate well with ``inputs(...)``.
For example, finding the corresponding header file (".h") for the matching input
required a complicated ``regex(...)`` regular expression and ``input(...)``. This simple case,
e.g. matching "something.c" with "something.h", is now much easier in Ruffus.
For example:
::
source_files = ["something.c", "more_code.c"]
@transform(source_files, suffix(".c"), add_inputs(r"\1.h", "common.h"), ".o")
def compile(input_files, output_file):
( source_file,
header_file,
common_header) = input_files
# call compiler to make object file
This is equivalent to calling:
::
compile(["something.c", "something.h", "common.h"], "something.o")
compile(["more_code.c", "more_code.h", "common.h"], "more_code.o")
The ``\1`` matches everything *but* the suffix and will be applied to both ``glob``\ s and file names.
For simplicity and compatibility with previous versions, there is always an implied r"\1" before
the output parameters. I.e. output parameters strings are *always* substituted.
* Tasks and glob in **inputs(...)** and **add_inputs(...)**
``glob``\ s and tasks can be added as the prerequisites / input files using
``inputs(...)`` and ``add_inputs(...)``. ``glob`` expansions will take place when the task
is run.
* Advanced form of **@split** with **regex**:
The standard ``@split`` divided one set of inputs into multiple outputs (the number of which
can be determined at runtime).
This is a ``one->many`` operation.
An advanced form of ``@split`` has been added which can split each of several files further.
In other words, this is a ``many->"many more"`` operation.
For example, given three starting files:
::
original_files = ["original_0.file",
"original_1.file",
"original_2.file"]
We can split each into its own set of sub-sections:
::
@split(original_files,
regex(r"starting_(\d+).fa"), # match starting files
r"files.split.\1.*.fa" # glob pattern
r"\1") # index of original file
def split_files(input_file, output_files, original_index):
"""
Code to split each input_file
"original_0.file" -> "files.split.0.*.fa"
"original_1.file" -> "files.split.1.*.fa"
"original_2.file" -> "files.split.2.*.fa"
"""
This is, conceptually, the reverse of the @collate(...) decorator
* Ruffus will complain about unescaped regular expression special characters:
Ruffus uses "\\1" and "\\2" in regular expression substitutions. Even seasoned python
users may not remember that these have to be 'escaped' in strings. The best option is
to use 'raw' python strings e.g.
::
r"\1_substitutes\2correctly\3four\4times"
Ruffus will throw an exception if it sees an unescaped "\\1" or "\\2" in a file name,
which should catch most of these bugs.
* Prettier output from *pipeline_printout_graph*
Changed to nicer colours, symbols etc. for a more professional look.
@split and @merge tasks now look different from @transform.
Colours, size and resolution are now fully customisable::
pipeline_printout_graph( #...
user_colour_scheme = {
"colour_scheme_index":1,
"Task to run" : {"fillcolor":"blue"},
pipeline_name : "My flowchart",
size : (11,8),
dpi : 120)})
An SVG bug in firefox has been worked around so that font size are displayed correctly.
= v. 2.1.1=
_12/March/2010_
* **@transform(.., add_inputs(...))**
``add_inputs(...)`` allows the addition of extra input dependencies / parameters for each job.
Unlike ``inputs(...)``, the original input parameter is retained:
::
from ruffus import *
@transform(["a.input", "b.input"], suffix(".input"), add_inputs("just.1.more","just.2.more"), ".output")
def task(i, o):
""
Produces:
::
Job = [[a.input, just.1.more, just.2.more] ->a.output]
Job = [[b.input, just.1.more, just.2.more] ->b.output]
Like ``inputs``, ``add_inputs`` accepts strings, tasks and ``glob`` s
This minor syntactic change promises add much clarity to Ruffus code.
``add_inputs()`` is available for ``@transform``, ``@collate`` and ``@split``
= v. 2.1.0=
_2/March/2010_
* **@jobs_limit**
Some tasks are resource intensive and too many jobs should not be run at the
same time. Examples include disk intensive operations such as unzipping, or
downloading from FTP sites.
Adding::
@jobs_limit(4)
@transform(new_data_list, suffix(".big_data.gz"), ".big_data")
def unzip(i, o):
"unzip code goes here"
would limit the unzip operation to 4 jobs at a time, even if the rest of the
pipeline runs highly in parallel.
(Thanks to Rob Young for suggesting this.)
= v. 2.0.10=
_27/February/2010_
* **touch_files_only** option for **pipeline_run**
When the pipeline runs, task functions will not be run. Instead, the output files for
each job (in each task) will be ``touch``\ -ed if necessary.
This can be useful for simulating a pipeline run so that all files look as
if they are up-to-date.
Caveats:
* This may not work correctly where output files are only determined at runtime, e.g. with **@split**
* Only the output from pipelined jobs which are currently out-of-date will be ``touch``\ -ed.
In other words, the pipeline runs *as normal*, the only difference is that the
output files are ``touch``\ -ed instead of being created by the python task functions
which would otherwise have been called.
* Parameter substitution for **inputs(...)**
The **inputs(...)** parameter in **@transform**, **@collate** can now take tasks and ``glob`` s,
and these will be expanded appropriately (after regular expression replacement).
For example::
@transform("dir/a.input", regex(r"(.*)\/(.+).input"),
inputs((r"\1/\2.other", r"\1/*.more")), r"elsewhere/\2.output")
def task1(i, o):
"""
Some pipeline task
"""
Is equivalent to calling::
task1(("dir/a.other", "dir/1.more", "dir/2.more"), "elsewhere/a.output")
\
Here::
r"\1/*.more"
is first converted to::
r"dir/*.more"
which matches::
"dir/1.more"
"dir/2.more"
= v. 2.0.9=
_25/February/2010_
* Better display of logging output
* Advanced form of **@split**
This is an experimental feature.
Hitherto, **@split** only takes 1 set of input (tasks/files/``glob`` s) and split these
into an indeterminate number of output.
This is a one->many operation.
Sometimes it is desirable to take multiple input files, and split each of them further.
This is a many->many (more) operation.
It is possible to hack something together using **@transform** but downstream tasks would not
aware that each job in **@transform** produces multiple outputs (rather than one input,
one output per job).
The syntax looks like::
@split(get_files, regex(r"(.+).original"), r"\1.*.split")
def split_files(i, o):
pass
If ``get_files()`` returned ``A.original``, ``B.original`` and ``C.original``,
``split_files()`` might lead to the following operations::
A.original
-> A.1.original
-> A.2.original
-> A.3.original
B.original
-> B.1.original
-> B.2.original
C.original
-> C.1.original
-> C.2.original
-> C.3.original
-> C.4.original
-> C.5.original
Note that each input (``A/B/C.original``) can produce a number of output, the exact
number of which does not have to be pre-determined.
This is similar to **@split**
Tasks following ``split_files`` will have ten inputs corresponding to each of the
output from ``split_files``.
If **@transform** was used instead of **@split**, then tasks following ``split_files``
would only have 3 inputs.
= v. 2.0.8=
_22/January/2010_
* File names can be in unicode
* File systems with 1 second timestamp granularity no longer cause problems.
* Now accepts unicode file names:
Change `isinstance(x,str)` to `isinstance(x, basestring)`
(Thanks to P.J. Davis for contributing this.)
* inputs(...) now raises an exception when passed multiple arguments.
If the input parameter is being passed a tuple, add an extra set of enclosing
brackets. Documentation updated accordingly.
(Thanks to Z. Harris for spotting this.)
* tasks where regular expressions are incorrectly specified are a great source of frustration
and puzzlement.
Now if no regular expression matches occur, a warning is printed
(Thanks to C. Nellaker for suggesting this)
= v. 2.0.7=
_11/December/2009_
* graph printout blows up because of missing run time data error
(Thanks to A. Heger for reporting this!)
= v. 2.0.6=
_10/December/2009_
* several minor bugs
* better error messages when eoncountering decorator problems when checking if the pipeline is uptodate
* Exception when output specifications in @split were expanded (unnecessarily) in logging.
(Thanks to N. Spies for reporting this!)
= v. 2.0.4=
_22/November/2009_
* Bug Fix
* task.get_job_names() dies for jobs with no parameters
* JobSignalledBreak was not exported
= v. 2.0.3=
_18/November/2009_
* @transform accepts single file names. Thanks Chris N.
= v. 2.0.2=
_18/November/2009_
* pipeline_printout output much prettier
* pipeline_run at high verbose levels
Shows which tasks are being checked
to see if they are up-to-date or not
* New tutorial / manual
* pretty code figures
= v. 2.0.1=
_18/November/2009_
All unit tests passed
* Numerous bugs to do with ordering of glob / job output consistency
= v. 2.0.1 beta4=
_16/November/2009_
* Fixed problems with tasks depending on @split
= v. 2.0 beta=
_30/October/2009_
With the experience and feedback over the past few months, I have reworked **Ruffus**
completely mainly to make the syntax more transparent, with fewer gotchas.
Previous limitations to do with parameters have been removed.
The experience with what *Ruffus* calls "Indicator Objects" has been very positive
and there are more of them.
These are dummy classes with obvious names like "regex" or "suffix" which indicate the
type of optional parameters much like named parameters.
* Revamped documentation:
* Rewritten tutorial
* Comprehensive manual
* New syntax help
* Major redesign. New decorators include
* :ref:`@split `
* :ref:`@transform `
* :ref:`@merge `
* :ref:`@collate `
* Major redesign. Decorator *inputs* can mix
* Output from previous tasks
* |glob|_ patterns e.g. ``*.txt``
* Files names
* Any other data type
* Deprecated Decorators:
* @files_re
Functionality is divided among the new decorators
* New Features
* Files can be chained from task to task, implicit dependencies are inferred automatically
* Limitations on parameters removed. Any degree of nesting is allowed.
* Strings contain glob letters ``[]?*`` automatically inferred as globs and expanded
* input and output parameters containing strings assumed to be filenames, whatever the nested data structures they are found in
* Documentation
* New documentation almost complete
* New Simplified 7 step tutorial
* New manual work in progress
* Bug Fix
* Scheduling errors
= v. 1.1.4=
_15/October/2009_
* New Feature
* Tasks can get their input by automatically chaining to the output from one or more parent tasks using the `@files_re`
* Added example showing how files can be split up into multiple jobs and then recombined
# Run `test/test_filesre_split_and_combine.py` with `-v|--verbose` `-s|--start_again`
# Run with `-D|--debug` to test.
* Documentation to follow
* Bug Fix
* Scheduling race conditions
= v. 1.1.3=
_14/October/2009_
* Bug Fix
* Minor (but show stopping) bug in task.generic_job_descriptor
= v. 1.1.2=
_9/October/2009_
* Bug Fix
* Nasty (long standing) bug for single job tasks only decorated with `@follows(mkdir(...))` to be caught in an infinite loop
* Code Changes
* Add example of combining multiple input files depending on a regular expression pattern.
# Run `test/test_filesre_combine.py` with -v (verbose)
# Run with -D (debug) to test.
= v. 1.1.1=
_8/October/2009_
* New Feature
* _Combine multiple input files using a regular expression_
* Added `combine` syntax to `@files_re` decorators:
* Documentation to follow...
* Example from `src/ruffus/test/test_branching_dependencies.py`:
::
@files_re('*.*', '(.*/)(.*\.[345]$)', combine(r'\1\2'), r'\1final.6')
def test(input_files, output_files):
pass`
* will take all files in the current directory
* will identify files which end in `.3`, `.4` and `.5` as input files
* will use `final.6` as the output file
* `input_files == [a.3, a.4, b.3, b.5]` (for example)
* `output_files == [final.6]`
* Bug Fix
* All (known) bugs for running jobs from independent tasks in parallel
= v. 1.0.9=
_8/October/2009_
* New Feature
_Multitasking independent tasks_
* In a major piece of retooling, jobs from independent tasks which do not depend on each other will be run in parallel.
* This involves major changes to the scheduling code.
* Please contact me asap if anything breaks.
* Code Changes
* Add example of independent tasks running concurrently in
`test/test_branching_dependencies.py`
* Run with -v (verbose) and -j 1 or -j 10 to show the indeterminancy of multiprocessing.
* Run with -D (debug) to test.
= v. 1.0.8=
_12/August/2009_
* Documentation
* Errors fixed. Thanks to Matteo Bertini!
* Code Changes
* Added functions which print out job parameters more prettily.
* `task.shorten_filenames_encoder`
* `task.ignore_unknown_encoder`
* Parameters which look like file paths will only have the file part printed
(i.e. `"/a/b/c" -> 'c'`)
* Test scripts `simpler_with_shared_logging.py` and `test_follows_mkdir.py`
have been changed to test for this.
= v. 1.0.7=
_17/June/2009_
* Code Changes
* Added `proxy_logger` module for accessing a shared log across multiple jobs in
different processes.
= v. 1.0.6=
_12/June/2009_
* Bug Fix
* _Ruffus_ version module (`ruffus_version.py`) links fixed
Soft links in linux do not travel well
* `mkdir` now can take a list of strings
added test case
* Documentation
* Added history of changes
= v. 1.0.5=
_11/June/2009_
* Bug Fix
* Changed "graph_printout" to `pipeline_printout_graph` in documentation.
This function had been renamed in the code but not in the documentation :-(
* Documentation
* Added example for sharing synchronising data between jobs.
This shows how different jobs can write to a common log file while still leaveraging the full power of _ruffus_.
* Code Changes
* The graph and print_dependencies modules are no longer exported by default from task.
Please email me if this breaks anything.
* More informative error message when refer to unadorned (without _Ruffus_ decorators) python functions as pipelined Tasks
* Added Ruffus version module `ruffus_version.py`
= v. 1.0.4=
_05/June/2009_
* Bug fix:
* `task.task_names_to_tasks` did not include tasks specified by function rather than name
* `task.run_all_jobs_in_task` did not work properly without multiprocessing (# of jobs = 1)
* `task.pipeline_run` only uses multiprocessing pools if `multiprocess` (# of jobs) > 1
* Changes to allow python 2.4/2.5 to run
* `setup.py` changed to remove dependency
* `simplejson` can be loaded instead of python 2.6 `json` module
* Changed `NamedTemporaryFile` to `mkstemp` because delete parameter is not available before python 2.6
* Windows programmes
It is necessary to protect the "entry point" of the program under windows.
Otherwise, a new process with be created recursively, like the magicians's apprentice
See: http://docs.python.org/library/multiprocessing.html#multiprocessing-programming
= v. 1.0.3=
_04/June/2009_
* Documentation
Including SGE `qrsh` workaround in FAQ.
= v. 1.0.1=
_22/May/2009_
* Add simple tutorial.
No major bugs so far...!!
= v. 1.0.0 beta =
_28/April/2009_
Initial Release in Oxford
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ruffus/__init__.py
ruffus/adjacent_pairs_iterate.py
ruffus/cmdline.py
ruffus/combinatorics.py
ruffus/dbdict.py
ruffus/drmaa_wrapper.py
ruffus/file_name_parameters.py
ruffus/graph.py
ruffus/parse_old_style_ruffus.py
ruffus/print_dependencies.py
ruffus/proxy_logger.py
ruffus/ruffus_exceptions.py
ruffus/ruffus_utility.py
ruffus/ruffus_version.py
ruffus/task.py
ruffus/test/complicated_example.py
ruffus/test/create_test_script_from_dependency_tree.py
ruffus/test/draw_specified_dependency_tree.py
ruffus/test/five_second.py
ruffus/test/manual_test_ctrl_c_exceptions.py
ruffus/test/manual_test_drmaa.py
ruffus/test/play_with_colours.py
ruffus/test/qrsh_workaround.py
ruffus/test/run_all_unit_tests.cmd
ruffus/test/run_all_unit_tests3.cmd
ruffus/test/simpler_with_shared_logging.py
ruffus/test/slow_process_for_testing.py
ruffus/test/test_N_x_M_and_collate.py
ruffus/test/test_active_if.py
ruffus/test/test_branching_dependencies.py
ruffus/test/test_cmdline.py
ruffus/test/test_collate.py
ruffus/test/test_combinatorics.py
ruffus/test/test_drmaa_wrapper_run_job_locally.py
ruffus/test/test_empty_files_decorator.py
ruffus/test/test_exceptions.py
ruffus/test/test_file_name_parameters.py
ruffus/test/test_files_decorator.py
ruffus/test/test_filesre_combine.py
ruffus/test/test_filesre_split_and_combine.py
ruffus/test/test_follows_mkdir.py
ruffus/test/test_graphviz.py
ruffus/test/test_inputs_with_multiple_args_raising_exception.py
ruffus/test/test_job_completion_checksums.py
ruffus/test/test_job_history_with_exceptions.py
ruffus/test/test_mkdir.py
ruffus/test/test_newstyle_combinatorics.py
ruffus/test/test_newstyle_proxy.py
ruffus/test/test_newstyle_regex_error_messages.py
ruffus/test/test_pausing.py
ruffus/test/test_pipeline_printout_graph.py
ruffus/test/test_posttask_merge.py
ruffus/test/test_proxy_logger.py
ruffus/test/test_regex_error_messages.py
ruffus/test/test_ruffus_utility.py
ruffus/test/test_ruffus_utility_parse_task_arguments.py
ruffus/test/test_runtime_data.py
ruffus/test/test_softlink_uptodate.py
ruffus/test/test_split_and_combine.py
ruffus/test/test_split_regex_and_collate.py
ruffus/test/test_split_subdivide_checkpointing.py
ruffus/test/test_subpipeline.py
ruffus/test/test_subpipeline_cmdline.py
ruffus/test/test_suffix_output_dir.py
ruffus/test/test_task_file_dependencies.py
ruffus/test/test_task_misc.py
ruffus/test/test_transform_add_inputs.py
ruffus/test/test_transform_formatter.py
ruffus/test/test_transform_inputs.py
ruffus/test/test_transform_with_no_re_matches.py
ruffus/test/test_tutorial7.py
ruffus/test/test_unicode_filenames.py
ruffus/test/test_verbosity.py
ruffus/test/test_with_logger.py
ruffus-2.8.1/MANIFEST.in 0000664 0000000 0000000 00000000257 13376012530 0014576 0 ustar 00root root 0000000 0000000 include *.TXT
recursive-include doc *
recursive-include ruffus *.py
include ruffus/test/run_all_unit_tests.cmd
include ruffus/test/run_all_unit_tests3.cmd
include README.rst
ruffus-2.8.1/README.rst 0000664 0000000 0000000 00000007352 13376012530 0014532 0 ustar 00root root 0000000 0000000 ***************************************
Overview
***************************************
The ruffus module is a lightweight way to add support
for running computational pipelines.
Computational pipelines are often conceptually quite simple, especially
if we breakdown the process into simple stages, or separate **tasks**.
Each stage or **task** in a computational pipeline is represented by a python function
Each python function can be called in parallel to run multiple **jobs**.
Ruffus was originally designed for use in bioinformatics to analyse multiple genome
data sets.
***************************************
Documentation
***************************************
Ruffus documentation can be found `here `_ ,
with `installation notes `_ ,
a `short tutorial `_ and
an `in-depth manual `_ .
***************************************
Background
***************************************
The purpose of a pipeline is to determine automatically which parts of a multi-stage
process needs to be run and in what order in order to reach an objective ("targets")
Computational pipelines, especially for analysing large scientific datasets are
in widespread use.
However, even a conceptually simple series of steps can be difficult to set up and
to maintain, perhaps because the right tools are not available.
***************************************
Design
***************************************
The ruffus module has the following design goals:
* Simplicity. Can be picked up in 10 minutes
* Elegance
* Lightweight
* Unintrusive
* Flexible/Powerful
***************************************
Features
***************************************
Automatic support for
* Managing dependencies
* Parallel jobs
* Re-starting from arbitrary points, especially after errors
* Display of the pipeline as a flowchart
* Reporting
***************************************
A Simple example
***************************************
Use the **@transform(...)** python decorator before the function definitions:
.. code-block:: python
from ruffus import *
# make 10 dummy DNA data files
data_files = [(prefix + ".fastq") for prefix in range("abcdefghij")]
for df in data_files:
open(df, "w").close()
@transform(data_files, suffix(".fastq"), ".bam")
def run_bwa(input_file, output_file):
print "Align DNA sequences in %s to a genome -> %s " % (input_file, output_file)
# make dummy output file
open(output_file, "w").close()
@transform(run_bwa, suffix(".bam"), ".sorted.bam")
def sort_bam(input_file, output_file):
print "Sort DNA sequences in %s -> %s " % (input_file, output_file)
# make dummy output file
open(output_file, "w").close()
pipeline_run([sort_bam], multithread = 5)
the ``@transform`` decorator indicate that the data flows from the ``run_bwa`` function to ``sort_bwa`` down
the pipeline.
********
Usage
********
Each stage or **task** in a computational pipeline is represented by a python function
Each python function can be called in parallel to run multiple **jobs**.
1. Import module::
import ruffus
1. Annotate functions with python decorators
2. Print dependency graph if you necessary
- For a graphical flowchart in ``jpg``, ``svg``, ``dot``, ``png``, ``ps``, ``gif`` formats::
pipeline_printout_graph ("flowchart.svg")
This requires ``dot`` to be installed
- For a text printout of all jobs ::
pipeline_printout(sys.stdout)
3. Run the pipeline::
pipeline_run(list_of_target_tasks, verbose = NNN, [multithread | multiprocess = NNN])
ruffus-2.8.1/USAGE.TXT 0000664 0000000 0000000 00000016577 13376012530 0014321 0 ustar 00root root 0000000 0000000 Each stage or task in a computational pipeline is represented by a python function
Each python function can be called in parallel to run multiple jobs.
1. Import module::
from ruffus import *
2. Annotate functions with python decorators
e.g.::
from ruffus import *
import sys
def first_task():
print "First task"
@follows(first_task)
def second_task():
print "Second task"
@follows(second_task)
def final_task():
print "Final task"
Examples of decorators:
+------------------------+-------------------------------------+-----------------------------------------------------------------------------------------------------+
| Decorator | Purpose | Example |
+========================+=====================================+=====================================================================================================+
|**@follows** | - Indicate task dependency | ``@follows(task1, "task2")`` |
| | | |
| | - mkdir prerequisite shorthand | ``@follows(task1, mkdir("my/directory/for/results"))`` |
+------------------------+-------------------------------------+-----------------------------------------------------------------------------------------------------+
|**@files** | - I/O parameters | ``@files(parameter_list)`` |
| | | |
| | - skips up-to-date jobs | ``@files(parameter_generating_function)`` |
| | | |
| | | ``@files(input, output, other_params_for_a_single_job)`` |
+------------------------+-------------------------------------+-----------------------------------------------------------------------------------------------------+
|**@split** | - Splits a single input into | ``@split ( tasks_or_file_names, output_files, [extra_parameters,...] )`` |
| | multiple output | |
| | - Globs in output can specify an | |
| | indeterminate number of files. | |
+------------------------+-------------------------------------+-----------------------------------------------------------------------------------------------------+
|**@transform** | - Applies the task function to | ``@transform ( tasks_or_file_names, suffix(suffix_string), output_pattern, [extra_parameters,..] )``|
| | transform input data to output. | |
| | | ``@transform ( tasks_or_file_names, regex(regex_pattern), output_pattern, [extra_parameters,...] )``|
+------------------------+-------------------------------------+-----------------------------------------------------------------------------------------------------+
|**@merge** | - Merges multiple input | ``@merge (tasks_or_file_names, output, [extra_parameters,...] )`` |
| | into a single output. | |
+------------------------+-------------------------------------+-----------------------------------------------------------------------------------------------------+
|**@collate** | - Groups together sets of input | ``@collate ( tasks_or_file_names, regex(matching_regex), output_pattern, [extra_parameters,...] )`` |
| | into a few outputs | |
+------------------------+-------------------------------------+-----------------------------------------------------------------------------------------------------+
|**@posttask** | - Call function after task | ``@posttask(signal_task_completion_function)`` |
| | | |
| | - touch file shorthand | ``@posttask(touch_file("task1.completed")`` |
+------------------------+-------------------------------------+-----------------------------------------------------------------------------------------------------+
3. Print dependency graph if you necessary
- For a graphical flowchart in ``jpg``, ``svg``, ``dot``, ``png``, ``ps``, ``gif`` formats::
graph_printout ( open("flowchart.svg", "w"),
"svg",
list_of_target_tasks)
This requires ``dot`` to be installed
- For a text printout of all jobs ::
pipeline_printout(sys.stdout, list_of_target_tasks)
4. Run the pipeline::
pipeline_run(list_of_target_tasks, [list_of_tasks_forced_to_rerun, multiprocess = N_PARALLEL_JOBS])
ruffus-2.8.1/doc/ 0000775 0000000 0000000 00000000000 13376012530 0013601 5 ustar 00root root 0000000 0000000 ruffus-2.8.1/doc/Makefile 0000664 0000000 0000000 00000015756 13376012530 0015257 0 ustar 00root root 0000000 0000000 # Makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER = a4
BUILDDIR = _build
# User-friendly check for sphinx-build
ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
endif
# Internal variables.
PAPEROPT_a4 = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
# the i18n builder cannot share the environment and doctrees with the others
I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
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 " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
@echo " text to make text files"
@echo " man to make manual pages"
@echo " texinfo to make Texinfo files"
@echo " info to make Texinfo files and run them through makeinfo"
@echo " gettext to make PO message catalogs"
@echo " changes to make an overview of all changed/added/deprecated items"
@echo " xml to make Docutils-native XML files"
@echo " pseudoxml to make pseudoxml-XML files for display purposes"
@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)/*
html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
htmlsync:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
rsync -t --delete --recursive _build/html/* mus:/home/lg/public_html/oss/ruffus
rsync -t --delete --recursive _build/html/* u36264041@www.llewgoodstadt.org.uk:/kunden/homepages/33/d100248119/htdocs/ruffus
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html and copied to the test web directory."
dirhtml:
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
singlehtml:
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
@echo
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
pickle:
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
@echo
@echo "Build finished; now you can process the pickle files."
json:
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
@echo
@echo "Build finished; now you can process the JSON files."
htmlhelp:
$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
@echo
@echo "Build finished; now you can run HTML Help Workshop with the" \
".hhp project file in $(BUILDDIR)/htmlhelp."
qthelp:
$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
@echo
@echo "Build finished; now you can run "qcollectiongenerator" with the" \
".qhcp project file in $(BUILDDIR)/qthelp, like this:"
@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/ruffus.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/ruffus.qhc"
devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/ruffus"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/ruffus"
@echo "# devhelp"
epub:
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
@echo
@echo "Build finished. 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."
latexpdfja:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through platex and dvipdfmx..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
@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."
texinfo:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo
@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
@echo "Run \`make' in that directory to run these through makeinfo" \
"(use \`make info' here to do that automatically)."
info:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo "Running Texinfo files through makeinfo..."
make -C $(BUILDDIR)/texinfo info
@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
gettext:
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
@echo
@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
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."
xml:
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
@echo
@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
@echo
@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
ruffus-2.8.1/doc/_templates/ 0000775 0000000 0000000 00000000000 13376012530 0015736 5 ustar 00root root 0000000 0000000 ruffus-2.8.1/doc/_templates/index.html 0000664 0000000 0000000 00000013377 13376012530 0017746 0 ustar 00root root 0000000 0000000 {% extends "layout.html" %}
{% set title = 'Ruffus' %}
{% block extrahead %}
{% endblock %}
{% block body %}
Ruffus is a Computation Pipeline library for python. It is open-sourced,
powerful and user-friendly, and widely used in science and bioinformatics.
Citation:
Please cite Ruffus as:
Leo Goodstadt (2010) :
Ruffus: a lightweight Python library for computational pipelines. Bioinformatics 26(21): 2778-2779
Welcome
Ruffus is designed to allow scientific and other analyses to
be automated with the minimum of fuss and the least effort.
These are Ruffus's strengths:
- Lightweight: Suitable for the simplest of tasks
- Scalable: Handles even fiendishly complicated pipelines
which would cause make or scons to go cross-eyed and recursive.
- Standard python: No "clever magic", no pre-processing.
- Unintrusive: Unambitious, lightweight syntax which tries to do this
one small thing well.
Please join me (email: ruffus_lib at llew.org.uk) in setting the direction of
this project if you are interested.
|
|
Documentation
Download
to install Ruffus
Simple Tutorial
Start here for a quick introduction to Ruffus
Manual
(pdf)
for an-depth demonstration of all
Ruffus features
|
Table of contents
for an complete listing of all the documentation
Frequently Answered Questions
for any common problems, clever solutions from the community
Design
to understand the design of Ruffus
Cheat Sheet
for Ruffus syntax
|
Get Ruffus
Ruffus is available as an easy-installable package on the Python Package
Index.
Just run:
sudo pip install ruffus --upgrade
or
The very latest (in development) code can be obtained via git :
git clone https://bunbun68@code.google.com/p/ruffus/
Feedback and Getting Involved:
{% endblock %}
ruffus-2.8.1/doc/_templates/layout.html 0000664 0000000 0000000 00000011466 13376012530 0020151 0 ustar 00root root 0000000 0000000 {% extends "!layout.html" %}
{% block sidebarsearch %}
{{ super() }}
Quick Reference:
{% endblock %}
{% block rootrellink %}
Ruffus v. {{ release }}
Home |
Contents |
Install |
Manual /
(TOC) |
FAQ |
Cheat sheet |
Command Line |
Gallery |
New syntax in v 2.6 |
Latest Changes »
{% endblock %}
ruffus-2.8.1/doc/cheatsheet.rst 0000664 0000000 0000000 00000005276 13376012530 0016462 0 ustar 00root root 0000000 0000000 .. include:: global.inc
.. _cheat_sheet:
#####################
Cheat Sheet
#####################
The ``ruffus`` module is a lightweight way to add support
for running computational pipelines.
| Each stage or **task** in a computational pipeline is represented by a python function
| Each python function can be called in parallel to run multiple **jobs**.
================================================
1. Annotate functions with **Ruffus** decorators
================================================
******
Core
******
.. csv-table::
:header: "Decorator", "Syntax"
:widths: 100, 600,1
"@originate (:ref:`Manual `)
", "
:ref:`@originate ` ( ``output_files``, [``extra_parameters``,...] )
", ""
"@split (:ref:`Manual `)
", "
:ref:`@split ` ( ``tasks_or_file_names``, ``output_files``, [``extra_parameters``,...] )
", ""
"@transform (:ref:`Manual `)
", "
| :ref:`@transform ` ( ``tasks_or_file_names``, :ref:`suffix `\ *(*\ ``suffix_string``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
| :ref:`@transform ` ( ``tasks_or_file_names``, :ref:`regex `\ *(*\ ``regex_pattern``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
", ""
"@merge (:ref:`Manual `)
", "
:ref:`@merge ` (``tasks_or_file_names``, ``output``, [``extra_parameters``,...] )
", ""
"@posttask (:ref:`Manual `)
", "
| :ref:`@posttask ` ( ``signal_task_completion_function`` )
| :ref:`@posttask ` (:ref:`touch_file `\ ( ``'task1.completed'`` ))
", ""
************************************************************************************************
See :ref:`Decorators ` for a complete list of decorators
************************************************************************************************
================================================
2. Print dependency graph if necessary
================================================
- For a graphical flowchart in ``jpg``, ``svg``, ``dot``, ``png``, ``ps``, ``gif`` formats::
pipeline_printout_graph ( "flowchart.svg")
.. comment
This requires the `dot programme `_ to be installed
- For a text printout of all jobs ::
pipeline_printout()
================================================
3. Run the pipeline
================================================
::
pipeline_run(multiprocess = N_PARALLEL_JOBS)
ruffus-2.8.1/doc/complex_dags/ 0000775 0000000 0000000 00000000000 13376012530 0016246 5 ustar 00root root 0000000 0000000 ruffus-2.8.1/doc/complex_dags/dot/ 0000775 0000000 0000000 00000000000 13376012530 0017034 5 ustar 00root root 0000000 0000000 ruffus-2.8.1/doc/complex_dags/dot/all.dot 0000664 0000000 0000000 00000006324 13376012530 0020321 0 ustar 00root root 0000000 0000000 digraph tree
{
size="8,11!";
splines=true;
fontsize=30;
ranksep = 0.3;
subgraph clustertasks
{
label = "Pipeline:";
edge[minlen=2];
node[fontsize=20];
t0[fontcolor=blue, shape=plaintext, label="task1"];
t2[color=olivedrab, fontcolor=blue, shape=tripleoctagon, label="task7"];
t0 -> t2[color=blue];
t3[color=olivedrab, fontcolor=blue, shape=tripleoctagon, label="task8"];
t2 -> t3[color=blue];
t4[fontcolor=blue, shape=plaintext, label="task9"];
t3 -> t4[color=blue];
t5[fontcolor=blue, shape=plaintext, label="task10"];
t4 -> t5[color=blue];
t6[color=olivedrab, fontcolor=blue, shape=tripleoctagon, label="task11"];
t5 -> t6[color=blue];
t1[fontcolor=blue, shape=plaintext, label="task2"];
t0 -> t1[color=blue];
t8[fontcolor=blue, shape=plaintext, label="task3"];
t1 -> t8[color=blue];
t9[fontcolor=blue, shape=plaintext, label="task4"];
t8 -> t9[color=blue];
t10[fontcolor=blue, shape=plaintext, label="task5"];
t9 -> t10[color=blue];
t11[fontcolor=blue, shape=plaintext, label="task6"];
t10 -> t11[color=blue];
t7[fontcolor=blue, shape=plaintext, label="task12"];
t11 -> t7[color=blue];
t6 -> t7[color=blue];
t13[fontcolor=blue, shape=plaintext, label="task18"];
t7 -> t13[color=blue];
t19[fontcolor=blue, shape=plaintext, label="task19"];
t13 -> t19[color=blue];
t20[color=olivedrab, fontcolor=blue, shape=tripleoctagon, label="task20"];
t19 -> t20[color=blue];
t21[fontcolor=blue, shape=plaintext, label="task21"];
t20 -> t21[color=blue];
t8 -> t21[color=blue];
t22[fontcolor=blue, shape=plaintext, label="task22"];
t21 -> t22[color=blue];
t23[fontcolor=blue, shape=plaintext, label="task23"];
t22 -> t23[color=blue];
t12[fontcolor=blue, shape=plaintext, label="task13"];
t7 -> t12[color=blue];
t14[color=olivedrab, fontcolor=blue, shape=tripleoctagon, label="task14"];
t12 -> t14[color=blue];
t15[fontcolor=blue, shape=plaintext, label="task15"];
t14 -> t15[color=blue];
t4 -> t15[color=blue];
t16[fontcolor=blue, shape=plaintext, label="task16"];
t15 -> t16[color=blue];
t6 -> t16[color=blue];
t17[fontcolor=blue, shape=plaintext, label="task17"];
t16 -> t17[color=blue];
t18[fontcolor=blue, shape=plaintext, label="task24"];
t17 -> t18[color=blue];
t24[color=orange, fontcolor=orange, shape=tripleoctagon, label="task25"];
t23 -> t24[color=blue];
t18 -> t24[color=blue];
}
subgraph clusterkey
{
style=filled;
fontsize=30;
color=gray90;
label = "Key:";
node[fontsize=10];
k1[color=orange, fontcolor=orange, shape=tripleoctagon, fontsize=15, label="Final target"];
k2[shape=box, style=filled, fontsize=15, fillcolor=red, label="Vicious cycle"];
k3[fontcolor=blue, shape=plaintext, fontsize=15, label="Task to run"];
k4[color=blue, fontcolor=blue, shape=tripleoctagon, fontsize=15, label="Force pipeline run from this task"];
k5[color=gray, fontcolor=gray, shape=tripleoctagon, fontsize=15, label="Up-to-date Final target"];
k6[color=olivedrab, fontcolor=blue, shape=tripleoctagon, fontsize=15, label="Up-to-date task forced to rerun"];
k7[style=filled, color=olivedrab, label="Up-to-date task", shape=octagon, fontsize=15, fillcolor=olivedrab, fontcolor=black];
k8[style=filled, color=gray, label="Up-to-date dependence", shape=octagon, fontsize=15, fillcolor=white, fontcolor=gray];
k1->k2[color=red];k2->k1 [color=red];k2->k3->k4->k5[color=blue];k5->k6->k7->k8[color=gray];}
}
ruffus-2.8.1/doc/complex_dags/dot/non_dag.dot 0000664 0000000 0000000 00000006425 13376012530 0021160 0 ustar 00root root 0000000 0000000 digraph tree
{
size="8,11!";
splines=true;
fontsize=30;
ranksep = 0.3;
subgraph clustertasks
{
label = "Pipeline:";
edge[minlen=2];
node[fontsize=20];
t2[fontcolor=blue, shape=plaintext, label="task7"];
t0 -> t2[color=blue];
t3[fontcolor=blue, shape=plaintext, label="task8"];
t2 -> t3[color=blue];
t4[fontcolor=blue, shape=plaintext, label="task9"];
t3 -> t4[color=blue];
t4 -> t5[color=blue];
t8[fontcolor=blue, shape=plaintext, label="task3"];
t1 -> t8[color=blue];
t9[fontcolor=blue, shape=plaintext, label="task4"];
t8 -> t9[color=blue];
t9 -> t10[color=blue];
t13[fontcolor=blue, shape=plaintext, label="task18"];
t7 -> t13[color=blue];
t19[fontcolor=blue, shape=plaintext, label="task19"];
t13 -> t19[color=blue];
t20[fontcolor=blue, shape=plaintext, label="task20"];
t19 -> t20[color=blue];
t21[fontcolor=blue, shape=plaintext, label="task21"];
t20 -> t21[color=blue];
t8 -> t21[color=blue];
t22[fontcolor=blue, shape=plaintext, label="task22"];
t21 -> t22[color=blue];
t23[fontcolor=blue, shape=plaintext, label="task23"];
t22 -> t23[color=blue];
t12[fontcolor=blue, shape=plaintext, label="task13"];
t7 -> t12[color=blue];
t14[fontcolor=blue, shape=plaintext, label="task14"];
t12 -> t14[color=blue];
t15[fontcolor=blue, shape=plaintext, label="task15"];
t14 -> t15[color=blue];
t4 -> t15[color=blue];
t16[fontcolor=blue, shape=plaintext, label="task16"];
t15 -> t16[color=blue];
t6 -> t16[color=blue];
t17[fontcolor=blue, shape=plaintext, label="task17"];
t16 -> t17[color=blue];
t18[fontcolor=blue, shape=plaintext, label="task24"];
t17 -> t18[color=blue];
t24[color=orange, fontcolor=orange, shape=tripleoctagon, label="task25"];
t23 -> t24[color=blue];
t18 -> t24[color=blue];
t1[shape=box, style=filled, fillcolor=red, label="task2"];
t0 -> t1[color=red ];
t0[shape=box, style=filled, fillcolor=red, label="task1"];
t1 -> t0[color=red , constraint=false];
t5[shape=box, style=filled, fillcolor=red, label="task10"];
t7 -> t5[color=red , constraint=false];
t6[shape=box, style=filled, fillcolor=red, label="task11"];
t5 -> t6[color=red ];
t10[shape=box, style=filled, fillcolor=red, label="task5"];
t5 -> t10[color=red ];
t11[shape=box, style=filled, fillcolor=red, label="task6"];
t10 -> t11[color=red ];
t7[shape=box, style=filled, fillcolor=red, label="task12"];
t11 -> t7[color=red , constraint=false];
t6 -> t7[color=red ];
}
subgraph clusterkey
{
style=filled;
fontsize=30;
color=gray90;
label = "Key:";
node[fontsize=10];
k1[color=orange, fontcolor=orange, shape=tripleoctagon, fontsize=15, label="Final target"];
k2[shape=box, style=filled, fontsize=15, fillcolor=red, label="Vicious cycle"];
k3[fontcolor=blue, shape=plaintext, fontsize=15, label="Task to run"];
k4[color=blue, fontcolor=blue, shape=tripleoctagon, fontsize=15, label="Force pipeline run from this task"];
k5[color=gray, fontcolor=gray, shape=tripleoctagon, fontsize=15, label="Up-to-date Final target"];
k6[color=olivedrab, fontcolor=blue, shape=tripleoctagon, fontsize=15, label="Up-to-date task forced to rerun"];
k7[style=filled, color=olivedrab, label="Up-to-date task", shape=octagon, fontsize=15, fillcolor=olivedrab, fontcolor=black];
k8[style=filled, color=gray, label="Up-to-date dependence", shape=octagon, fontsize=15, fillcolor=white, fontcolor=gray];
k1->k2[color=red];k2->k1 [color=red];k2->k3->k4->k5[color=blue];k5->k6->k7->k8[color=gray];}
}
ruffus-2.8.1/doc/complex_dags/dot/task17.dot 0000664 0000000 0000000 00000007273 13376012530 0020667 0 ustar 00root root 0000000 0000000 digraph tree
{
size="8,11!";
splines=true;
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ranksep = 0.3;
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