debian/0000755000000000000000000000000012044236636007174 5ustar debian/source/0000755000000000000000000000000012044235402010462 5ustar debian/source/format0000644000000000000000000000001412044235402011670 0ustar 3.0 (quilt) debian/python-pymc-doc.docs0000644000000000000000000000001312044235402013060 0ustar build/html debian/watch0000644000000000000000000000031012044235402010205 0ustar # Compulsory line, this is a version 3 file version=3 opts="dversionmangle=s/\+ds\d*//,filenamemangle=s/.*\/(.*)/pymc-$1\.tar\.gz/" \ http://github.com/pymc-devs/pymc/tags .*tarball/v(\d[\d\.a-z]+) debian/patches/0000755000000000000000000000000012044235402010611 5ustar debian/patches/series0000644000000000000000000000005412044235402012025 0ustar deb_htmldoc_path deb_no_static_blas_linking debian/patches/deb_no_static_blas_linking0000644000000000000000000000232512044235402016047 0ustar From: Yaroslav Halchenko Subject: Do not staticly link again blas pieces if those will be dynamicly linked anyways due to lapack_info + throw exception if no blas/lapack was found Origin: Debian Last-Update: 2012-10-19 --- a/setup.py +++ b/setup.py @@ -69,6 +69,8 @@ except: if lapack_info: config.add_extension(name='gp.linalg_utils',sources=['pymc/gp/linalg_utils.f','pymc/blas_wrap.f'], extra_info=lapack_info) config.add_extension(name='gp.incomplete_chol',sources=['pymc/gp/incomplete_chol.f'], extra_info=lapack_info) +else: + raise RuntimeError("Debian build requires system-wide presence of blas/lapack") if not lapack_info or dist in ['bdist', 'sdist']: print('No optimized BLAS or Lapack libraries found, building from source. This may take a while...') @@ -86,7 +88,7 @@ if not lapack_info or dist in ['bdist', # Compile covariance functions config.add_extension(name='gp.cov_funs.isotropic_cov_funs',\ -sources=['pymc/gp/cov_funs/isotropic_cov_funs.f','blas/BLAS/dscal.f'],\ +sources=['pymc/gp/cov_funs/isotropic_cov_funs.f'],\ extra_info=lapack_info) config.add_extension(name='gp.cov_funs.distances',sources=['pymc/gp/cov_funs/distances.f'], extra_info=lapack_info) debian/patches/deb_htmldoc_path0000644000000000000000000000042412044235402014014 0ustar --- a/docs/Makefile +++ b/docs/Makefile @@ -6,7 +6,7 @@ SPHINXOPTS = SPHINXBUILD = sphinx-build PAPER = BUILDDIR = _build -HTMLBUILDDIR = ~/Code/pymc-pages +HTMLBUILDDIR = ../build/html # Internal variables. PAPEROPT_a4 = -D latex_paper_size=a4 debian/changelog0000644000000000000000000000024512044235402011035 0ustar pymc (2.2+ds-1) unstable; urgency=low * Initial Debian release (Closes: #690800) -- Yaroslav Halchenko Tue, 30 Oct 2012 19:03:47 -0400 debian/copyright0000644000000000000000000001012612044235402011115 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: pymc Upstream-Contact: Christopher Fonnesbeck Source: https://github.com/pymc-devs/pymc Files: * Copyright: 2006 Christopher J. Fonnesbeck 2007-2008 Christopher J. Fonnesbeck, Anand.Prabhakar Patil, David Huard 2009-2012 PyMC Authors License: Expat Files: cephes Copyright: 1984-2000 Steve Moshier License: This code comes from the CEPHES library. Although the library sources itself contains no proper license statement, the copyright holder previously agreed to release it under the terms of the GPL. This is documented in the Debian packaging of the labplot package. Please see . http://packages.debian.org/changelogs/pool/main/l/labplot/labplot_1.5.1-1/labplot.copyright . for references. . Here is a verbatim copy of the statement: . This email from Steve Moshier, the copyright owner of cephes, to Helen Faulkner (Debian maintainer of labplot), and other interested parties (labplot and grace authors, grace maintainer and labplot sponsor), confirms that we may release labplot with cephes licensed under the GPL. . . -------- Original Message -------- Subject: Re: licensing of cephes Date: Sun, 2 Jan 2005 21:48:02 -0500 (EST) From: Steve Moshier To: Helen Faulkner CC: twerner@debian.org, Ben Burton , evgeny@stambulchik.net, Stefan Gerlach References: <41D14354.4040506@yahoo.co.uk> <41D17BE3.3020708@yahoo.co.uk> <41D1FB8D.6030002@yahoo.co.uk> <41D2D8EF.9010702@yahoo.co.uk> <41D41B2E.80508@yahoo.co.uk> . . . On Thu, 30 Dec 2004, Helen Faulkner wrote: . > http://www.debian.org/social_contract#guidelines . This is fine with me. To acknowedge your terms explicily, how about augmenting the permission to read something like the following -- . This software is derived from the Cephes Math Library. It is incorporated herein, and licensed in accordance with DFSG, by permission of the author. . . If you are trying to get me to suggest a specific form for your license, then from looking at Debian programs such as dpkg it seems to me that you would find the GPL to be appropriate and the permission statement could reference one of the GPL documents instead of DFSG. Alternatively, the packages you have been talking about distributing with Debian presumably come with some sort of licenses and it would make sense to propose those licenses. . On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. Files: pymc/six.py Copyright: 2010-2011 Benjamin Peterson License: Expat Files: debian/* Copyright: 2012, Yaroslav Halchenko License: Expat License: Expat Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. debian/python-pymc-doc.doc-base0000644000000000000000000000041012044235402013606 0ustar Document: pymc Title: PyMC User's Guide Author: PyMC Developers Abstract: This manual describes PyMC Python module Section: Science/Data Analysis Format: HTML Index: /usr/share/doc/python-pymc-doc/html/index.html Files: /usr/share/doc/python-pymc-doc/html/*.html debian/rules0000755000000000000000000000326012044235402010243 0ustar #!/usr/bin/make -f # -*- mode: makefile; coding: utf-8 -*- # override HOME (for weave) and matplotlib config directory # to allow building in chroots with read-only HOME export HOME=$(CURDIR)/build export MPLCONFIGDIR=$(HOME) include /usr/share/python/python.mk ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) export OPT+=-O0 export FOPT+=-O0 endif # one rule to rule them all ... %: # need to enforce distutils, since we also have a makefile dh $@ --buildsystem=python_distutils --builddirectory=build override_dh_auto_build: : # Cython pyx sources for f in */*.pyx; do cython $$f; done dh_auto_build echo "backend : Agg" >| build/matplotlibrc : # and docs PYTHONPATH=$(CURDIR)/$(call py_builddir_sh) \ $(MAKE) -C docs html : # but remove jquery copy (later on link to Debian's version) -rm build/html/_static/jquery.js -rm build/html/_static/underscore.js : # objects inventory is of no use for the package -rm build/html/objects.inv : # also doc source files only consume space -rm -r build/html/_sources override_dh_auto_test: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) for v in $(shell pyversions -vr); do \ echo "I: Running PyMC unittests using python$$v"; \ python$$v /usr/bin/nosetests -v -s --exclude='test_(interactive|gradients|LazyFunction|consistency|random|missing)' \ $(call py_builddir_sh, $$v)/pymc || exit 1 ;\ done endif override_dh_install: dh_install dh_numpy ## immediately useable documentation ## and exemplar data (they are small excerpts anyway) override_dh_compress: dh_compress -X.py -X.html -X.css -X.jpg -X.txt -X.js -X.json -X.rtc -X.par -X.bin override_dh_auto_clean: dh_auto_clean for f in */*.pyx; do rm -f $${f%.pyx}.c; done debian/python-pymc-doc.links0000644000000000000000000000030212044235402013251 0ustar usr/share/javascript/jquery/jquery.js usr/share/doc/python-pymc-doc/html/_static/jquery.js usr/share/javascript/underscore/underscore.js usr/share/doc/python-pymc-doc/html/_static/underscore.js debian/python-pymc.install0000644000000000000000000000002612044235402013037 0ustar debian/tmp/usr/* usr/ debian/gbp.conf0000644000000000000000000000035212044235402010601 0ustar [DEFAULT] # the default branch for upstream sources: upstream-branch = dfsg # the default branch for the debian patch: debian-branch = debian # the default tag formats used: upstream-tag = v%(version)s debian-tag = debian/%(version)s debian/control0000644000000000000000000000370712044235402010574 0ustar Source: pymc Section: python Priority: extra Maintainer: NeuroDebian Team Uploaders: Yaroslav Halchenko , Michael Hanke Build-Depends: debhelper (>= 7.2.18), gfortran, liblapack-dev, python-all-dev (>= 2.5), python-numpy (>= 1.6), python-scipy, python-nose, python-sphinx, cython, python-tables, python-matplotlib, Standards-Version: 3.9.3 Homepage: http://pymc-devs.github.com/pymc/ Vcs-Browser: https://github.com/neurodebian/pymc Vcs-Git: git://github.com/neurodebian/pymc.git XS-Python-Version: >= 2.6 Package: python-pymc Architecture: any Depends: ${misc:Depends}, ${python:Depends}, ${shlibs:Depends}, python-numpy, python-scipy, python-matplotlib, python-nose Recommends: python-tables, Suggests: python-pydot, ipython Description: Bayesian statistical models and fitting algorithms PyMC is a Python module that implements Bayesian statistical models and fitting algorithms, including Markov chain Monte Carlo. Its flexibility and extensibility make it applicable to a large suite of problems. Along with core sampling functionality, PyMC includes methods for summarizing output, plotting, goodness-of-fit and convergence diagnostics. Package: python-pymc-doc Section: doc Architecture: all Depends: ${misc:Depends}, libjs-jquery, libjs-underscore Description: Bayesian statistical models and fitting algorithms PyMC is a Python module that implements Bayesian statistical models and fitting algorithms, including Markov chain Monte Carlo. Its flexibility and extensibility make it applicable to a large suite of problems. Along with core sampling functionality, PyMC includes methods for summarizing output, plotting, goodness-of-fit and convergence diagnostics. . This package provides the documentation in HTML format. debian/README.Debian-source0000644000000000000000000000136012044235402012521 0ustar Packaging is based straight on the upstream's GIT repository, which serves as a canonical source for source distribution tarballs provided e.g. from pypi (and source distribution tarballs do not contain the original .pyx files for Cython). We enabled building of .c files out of original .pyx files to stay up-to-date with Cython version in Debian (so bugfixes in Cython could propagate via binNMUs of dependees) and to ease extended testing of new versions of Cython regarding compatibility with packages depending on it. dfsg branch tracks releases while removing components which might be absent in upstream source distribution (e.g. pymc/gp/Docs) and/or just duplicates of libraries provided system-wide (e.g. atlas/blas) -- Yaroslav Halchenkodebian/compat0000644000000000000000000000000212044235402010360 0ustar 7