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2017-03-20gnu: Add python-astroid....* gnu/packages/python.scm (python-astroid, python2-astroid): New variables. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Arun Isaac
2017-03-19Merge branch 'master' into core-updatesMark H Weaver
2017-03-19gnu: python-minimal@2: Add dependencies on libffi and zlib....* gnu/packages/python.scm (python2-minimal)[inputs]: Add LIBFFI and ZLIB. [arguments]: Remove. Ludovic Courtès
2017-03-17gnu: snakemake: Update to 3.11.2....* gnu/packages/python.scm (snakemake): Update to 3.11.2. Ricardo Wurmus
2017-03-17gnu: r: Rename to r-minimal....* gnu/packages/statistics.scm (r): Rename to... (r-minimal): ...this new variable. (r-with-recommended-packages): Rename to... (r): ...this. * guix/build-system/r.scm (default-r): Reference r-minimal. * gnu/packages/emacs.scm (emacs-ess)[inputs], gnu/packages/machine-learning.scm (shogun)[inputs], gnu/packages/python.scm (python-rpy2)[inputs], gnu/packages/bioinformatics.scm (ribotaper)[inputs], (couger)[propagated-inputs], (roary)[inputs], (rsem)[inputs], (rcas-web)[inputs]: Change "r" to "r-minimal". Ricardo Wurmus
2017-03-17gnu: r: Do not build recommended packages....* gnu/packages/statistics.scm (r)[arguments]: Rename phase "build-recommended-packages-reproducibly" to "build-reproducibly"; add configure flag "--without-recommended-packages". * guix/import/cran.scm (default-r-packages): Remove recommended packages. * gnu/packages/python.scm (python-rpy2)[inputs]: Add r-survival. * gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice and r-nlme. (r-vegan)[propagated-inputs]: Add r-mass. (r-genefilter)[propagated-inputs]: Add r-survival. (r-grohmm)[propagated-inputs]: Add r-mass. (r-bioccheck)[propagated-inputs]: Add r-codetools. (r-summarizedexperiment)[propagated-inputs]: Add r-matrix. (r-topgo)[propagated-inputs]: Add r-lattice. (r-sva)[propagated-inputs]: Add r-mgcv. (r-raremetals2)[propagated-inputs]: Add r-mass. (r-vsn)[propagated-inputs]: Add r-lattice. (r-pcamethods)[propagated-inputs]: Add r-mass. * gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass. (r-locfit)[propagated-inputs]: Add r-lattice. (r-coda)[propagated-inputs]: Add r-lattice. (r-irlba)[propagated-inputs]: Add r-matrix. (r-glmnet)[propagated-inputs]: Add r-matrix. (r-e1071)[propagated-inputs]: Add r-class. (r-spams)[propagated-inputs]: Add r-lattice and r-matrix. (r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and r-rpart. (r-zoo)[propagated-inputs]: Add r-lattice. (r-mixtools)[propagated-inputs]: Add r-boot and r-mass. (r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet. (r-prabclus)[propagated-inputs]: Add r-mass. (r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass. (r-rcppeigen)[propagated-inputs]: Add r-matrix. (r-matrixmodels)[propagated-inputs]: Add r-matrix. (r-lme4)[propagated-inputs]: Add r-mass and r-nlme. (r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix. (r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet. (r-tclust)[propagated-inputs]: Add r-cluster. Ricardo Wurmus
2017-03-16Merge remote-tracking branch 'origin/master' into core-updatesEfraim Flashner
2017-03-16gnu: python-publicsuffix2: Update to 2.20160818....* gnu/packages/python.scm (python-publicsuffix2): Update to 2.20160818. Tobias Geerinckx-Rice
2017-03-16gnu: awscli: Update to 1.11.63....* gnu/packages/python.scm (awscli): Update to 1.11.63. Tobias Geerinckx-Rice
2017-03-16gnu: python-botocore: Update to 1.5.26....* gnu/packages/python.scm (python-botocore): Update to 1.5.26. Tobias Geerinckx-Rice
2017-03-16gnu: python-ptyprocess: Update to 0.5.1....* gnu/packages/python.scm (python-ptyprocess): Update to 0.5.1. Tobias Geerinckx-Rice
2017-03-15Merge branch 'master' into core-updatesMarius Bakke
2017-03-15gnu: python-waf: Update to 1.9.8....* gnu/packages/python.scm (python-waf, python2-waf): Update to 1.9.8. [home-page]: Use https. Efraim Flashner
2017-03-14gnu: python-parsedatetime: Update to 2.3....Version 2.1 was apparently time-sensitive and started failing like this: ====================================================================== FAIL: testFloat (tests.TestDelta.test) ---------------------------------------------------------------------- Traceback (most recent call last): File "/tmp/guix-build-python2-parsedatetime-2.1.drv-0/parsedatetime-2.1/tests/TestDelta.py", line 64, in testFloat self.cal.parse('1.4 months ago', self.source), months=-1.4) File "/tmp/guix-build-python2-parsedatetime-2.1.drv-0/parsedatetime-2.1/tests/TestDelta.py", line 37, in assertDelta self.assertTrue(diff < 0.05, '%s is not less than 0.05' % diff) AssertionError: 0.0666666666667 is not less than 0.05 ---------------------------------------------------------------------- * gnu/packages/python.scm (python-parsedatetime): Update to 2.3. [native-inputs]: Add PYTHON-PYTEST and PYTHON-PYTEST-RUNNER. [propagated-inputs]: New field. Ludovic Courtès
2017-03-14gnu: python@2.7: Update to 2.7.13...* gnu/packages/python.scm (python-2.7): Update to 2.7.13. Leo Famulari
2017-03-14gnu: python@2.7: Fix getentropy() calls on kernels < 3.17....* gnu/packages/patches/python-2.7-getentropy-on-old-kernels.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/python.scm (python-2.7)[source]: Use it. Leo Famulari
2017-03-13Merge remote-tracking branch 'origin/master' into core-updatesEfraim Flashner
2017-03-13gnu: Remove python-3.4....* gnu/packages/python.scm (python-3.4): Remove variable. * gnu/packages/patches/python-3.4-fix-tests.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Leo Famulari
2017-03-13gnu: Add python-flask-login....* gnu/packages/python.scm (python-flask-login, python2-flask-login): New variables. Signed-off-by: Marius Bakke <mbakke@fastmail.com> humanitiesNerd
2017-03-13gnu: Add python-flask-htmlmin....* gnu/packages/python.scm (python-flask-htmlmin, python2-flask-htmlmin): New variables. Signed-off-by: Marius Bakke <mbakke@fastmail.com> humanitiesNerd
2017-03-13gnu: Add python-htmlmin....* gnu/packages/python.scm (python-htmlmin, python2-htmlmin): New variables. Signed-off-by: Marius Bakke <mbakke@fastmail.com> humanitiesNerd
2017-03-12gnu: python@3.5: Fix getentropy() calls on kernels < 3.17....* gnu/packages/patches/python-3.5-getentropy-on-old-kernels.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/python.scm (python-3.5, python-minimal, python-minimal-wrapper, python-wrapper)[source]: Use it. Marius Bakke
2017-03-12gnu: python@3.5: Update to 3.5.3....* gnu/packages/python.scm (python-3.5, python-minimal, python-minimal-wrapper, python-wrapper): Update to 3.5.3. * gnu/packages/patches/python-fix-tests.patch: Adjust patch context. * gnu/packages/patches/python-3.5-fix-tests.patch: Likewise. Patch one new test. Marius Bakke
2017-03-09gnu: Add python2-larch....* gnu/packages/python.scm (python2-larch): New variable. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Arun Isaac
2017-03-09gnu: Add python2-tracing....* gnu/packages/python.scm (python2-tracing): New variable. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Arun Isaac
2017-03-09gnu: Add python2-ttystatus....* gnu/packages/python.scm (python2-ttystatus): New variable. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Arun Isaac
2017-03-09gnu: Add python2-cliapp....* gnu/packages/python.scm (python2-cliapp): New variable. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Arun Isaac
2017-03-09gnu: python-numpy-documentation: Use full git commit hash in submodule....* gnu/packages/python.scm (python-numpy-documentation, python2-numpy-documentation)[native-inputs]: Update hash of SCIPY-SPHINX-THEME. Fix indentation of a line. Marius Bakke
2017-03-09gnu: Remove obsolete numpy comment....* gnu/packages/python.scm: Remove comment. Marius Bakke
2017-03-09Merge branch 'master' into core-updatesLudovic Courtès
2017-03-08gnu: python-pandas: Fix build on 32-bit....* gnu/packages/patches/python-pandas-skip-failing-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/python.scm (python-pandas, python2-pandas): Use it. Marius Bakke
2017-03-08gnu: Add python-faker....* gnu/packages/patches/python-fake-factory-fix-build-32bit.patch: Adjust paths. Also rename to ... * gnu/packages/patches/python-faker-fix-build-32bit.patch: ... this. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/python.scm (python-faker, python2-faker): New variables. (python-fake-factory)[properties]: Superseded by PYTHON-FAKER. (python2-fake-factory)[properties]: Superseded by PYTHON2-FAKER. (python-orator, python2-orator)[propagated-inputs]: Replace PYTHON-FAKE-FACTORY with PYTHON-FAKER. Marius Bakke
2017-03-08gnu: python-matplotlib-documentation: Fix build....* gnu/packages/python.scm (python-matplotlib-documentation)[native-inputs]: Add python-mock and graphviz. [arguments]: Use separate build and install phases; correctly set latex paper size. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Thomas Danckaert
2017-03-07gnu: python-rpy2: Propagate python2-singledispatch....* gnu/packages/python.scm (python-rp2)[native-inputs]: Rename to... [propagated-inputs]: ... this. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Pjotr Prins
2017-03-06gnu: python-colorspacious: Run tests....* gnu/packages/python.scm (python-colorspacious, python2-colorspacious)[native-inputs]: Add python-nose. [arguments]: Add custom 'check phase which runs nosetests. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Thomas Danckaert
2017-03-06gnu: Remove python-sphinx-1.2.3....* gnu/packages/python.scm (python-sphinx-1.2.3, python2-sphinx-1.2.3): Remove variables. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Thomas Danckaert
2017-03-06gnu: python-pandas: Update to 0.19.2....* gnu/packages/python.scm (python-pandas, python2-pandas): Update to 0.19.2. [source]: Use 'pypi-uri'. Marius Bakke
2017-03-06gnu: python-matplotlib: Update to 2.0.0....* gnu/packages/python.scm (python-matplotlib, python2-matplotlib): Update to 2.0.0. [source]: Remove Tk backend patch, use Github instead of Sourceforge. [outputs]: Remove "doc" output. [inputs]: Add python-pyqt. [propagated-inputs]: Add python-cycler. [native-inputs]: Remove python-sphinx, python-numpydoc, texlive and texinfo. (python2-matplotlib)[native-inputs]: Add python2-functools32 and python2-subprocess32. (python-matplotlib-documentation, python2-matplotlib-documentation): New variables. * gnu/packages/patches/matplotlib-setupext-tk.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Thomas Danckaert
2017-03-06gnu: Add python2-subprocess32....* gnu/packages/python.scm (python2-subprocess32): New variable. * gnu/packages/patches/python2-subprocess32-disable-input-test.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Marius Bakke
2017-03-06gnu: python-numpy: Update to 1.12.0....* gnu/packages/python.scm (python-numpy): Update to 1.12.0. [source]: Use github instead of sourceforge. [native-inputs]: Add python-cython. To simplify the handling of dependency cycles (numpy documentation depends on matplotlib, which depends on numpy), we split out the documentation into a separate package: (python-numpy-bootstrap, python2-numpy-bootstrap): Remove variables. (python-numpy-documentation, python2-numpy-documentation): New variables. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Thomas Danckaert
2017-03-06gnu: python-setuptools-scm: Update to 1.15.0....* gnu/packages/python.scm (python-setuptools-scm): Update to 1.15.0. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Troy Sankey
2017-03-06gnu: python2-backports-shutil-get-terminal-size: Enable tests....* gnu/packages/python.scm (python2-backports-shutil-get-terminal-size)[arguments]: Replace 'check' phase with custom command. [native-inputs]: Add PYTHON2-PYTEST. Marius Bakke
2017-03-06gnu: python-ipython: Update to 5.2.2....* gnu/packages/python.scm (python-ipython): Update to 5.2.2. [propagated-inputs]: Add pyhon-prompt-toolkit and python-nbformat. (python2-ipython) [arguments]: Enable tests. [propagated-inputs]: Add python2-backports-shutil-get-terminal-size. [native-inputs]: Add graphviz. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org> Thomas Danckaert
2017-03-06gnu: python-scipy: Update to 0.18.1....* gnu/packages/python.scm (python-scipy): Update to 0.18.1. [source]: Use github instead of sourceforge. [native-inputs]: Add python-cython. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org> Thomas Danckaert
2017-03-06gnu: python-testpath: Fix library location for python2 version....* gnu/packages/python.scm (python-testpath)[arguments]: Install module in the proper "lib/pythonx.y" location for all Python versions. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org> Thomas Danckaert
2017-03-06gnu: Add python-colorspacious....* gnu/packages/python.scm (python-colorspacious, python2-colorspacious): New variables. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org> Thomas Danckaert
2017-03-06gnu: Add python2-backports-shutil-get-terminal-size....* gnu/packages/python.scm (python2-backports-shutil-get-terminal-size): New variable. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org> Thomas Danckaert
2017-03-03Merge branch 'python-tests'Marius Bakke
2017-03-03gnu: python-requests: Update to 2.13.0....* gnu/packages/python.scm (python-requests, python2-requests): Update to 2.13.0. Leo Famulari
2017-03-02gnu: Add python-pykka....* gnu/packages/python.scm (python-pykka): New variable. Signed-off-by: Kei Kebreau <kei@openmailbox.org> ng0
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