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2021-02-01gnu: fifengine: Do not alter PYTHONPATH....* gnu/packages/games.scm (fifengine): Import the (guix build python-build-system) module. [phases]{check}: Simplify by using the 'add-installed-pythonpath' procedure. Remove trailing #t. Maxim Cournoyer
2021-02-01gnu: intel-xed: Update to 12.0.1....This fixes the build on Python 3.9. * gnu/packages/assembly.scm (intel-xed): Update to 12.0.1. Maxim Cournoyer
2021-02-01gnu: python-hyperkitty: Do not set PYTHONPATH....* gnu/packages/mail.scm (python-hyperkitty) [phases]{check}: Do not set PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: graphite2: Do not alter PYTHONPATH....* gnu/packages/fontutils.scm (graphite2)[arguments]: Remove field. Maxim Cournoyer
2021-02-01gnu: python-django-url-filter: Do not alter PYTHONPATH....* gnu/packages/django.scm (python-django-url-filter) [phases]: Delete trailing #t. {check}: Do not alter PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-django-statici18n: Do not read PYTHONPATH....* gnu/packages/django.scm (python-django-statici18n) [phases]{check}: Do not read PYTHONPATH from environment. Do not set build/lib explicitly (the install site path is already in the Guix PYTHONPATH). Maxim Cournoyer
2021-02-01gnu: python-django-appconf: Do not alter PYTHONPATH....* gnu/packages/django.scm (python-django-appconf) [phases]{check}: Do not alter PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-django-sortedm2m: Do not alter PYTHONPATH....* gnu/packages/django.scm (python-django-sortedm2m) [phases]{check}: Do not alter PYTHONPATH. Remove trailing #t. Maxim Cournoyer
2021-02-01gnu: python-django-pipeline: Do not alter PYTHONPATH....* gnu/packages/django.scm (python-django-pipeline): Remove trailing #t. [phases]{check}: Do not alter PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-django-contact-form: Do not alter PYTHONPATH....* gnu/packages/django.scm (python-django-contact-form): [phases]{check}: Do not alter PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-pytest-django: Do not alter PYTHONPATH....* gnu/packages/django.scm (python-django): Remove trailing #t. [phases]{check}: Do not alter PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-django: Do not alter PYTHONPATH....* gnu/packages/django.scm (python-django): Remove trailing #t. [phases]{pre-check,check}: Do not alter PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-rpy2: Do not set PYTHONPATH....* gnu/packages/statistics.scm (python-rpy2)[arguments]: Remove the '#:modules' argument. [phases]{check}: Do not set PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: ghmm: Do not set PYTHONPATH....* gnu/packages/machine-learning.scm (ghmm): Remove trailing #t. [phases]: Do not reorder the check phase after the install phase. {fix-PYTHONPATH}: Remove phase. Maxim Cournoyer
2021-02-01gnu: tensorflow: Do not alter PYTHONPATH....* gnu/packages/machine-learning.scm (tensorflow)[phases]: Delete trailing #t. {fix-python-build}: Do not alter PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-libtmux: Do not set PYTHONPATH....* gnu/packages/tmux.scm (python-libtmux)[phases]{check}: Do not set PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-pyhamcrest: Update to 2.0.2....* gnu/packages/check.scm (python-pyhamcrest): Update to 2.0.2. [propagated-inputs]: Remove python-six. [phases]{check}: Do not set PYTHONPATH. (python2-pyhamcrest): Remove variable. Maxim Cournoyer
2021-02-01gnu: behave: Do not set PYTHONPATH....* gnu/packages/check.scm (behave)[arguments]: Remove the '#:phases' argument. [propagated-inputs]: Remove python-importlib-metadata and python-six. Maxim Cournoyer
2021-02-01gnu: ganeti: Do not set PYTHONPATH....* gnu/packages/virtualization.scm (ganeti): Remove trailing #t. [phases]{build-bash-completions}: Do not set PYTHONPATH. {pre-check}: Do patch PYTHONPATH from script. {wrap}: Use the new GUIX_PYTHONPATH environment variable. Maxim Cournoyer
2021-02-01gnu: linkchecker: Do not set PYTHONPATH....* gnu/packages/web.scm (linkchecker): Remove trailing #t. [phases]: Do not reorder the check phase after the install phase. {check}: Do not set PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-cffi: Do not set PYTHONPATH....* gnu/packages/libffi.scm (python-cffi): Remove trailing #t. [phases]{check}: Do not set PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-xmlschema: Do not set PYTHONPATH....* gnu/packages/xml.scm (python-xmlschema): Remove trailing #t. [phases]{check}: Do not set PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-loompy: Do not set PYTHONPATH....* gnu/packages/bioinformatics.scm (python-loompy) [phases]{check}: Do not set PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-scanpy: Do not set PYTHONPATH....* gnu/packages/bioinformatics.scm (python-scanpy)[phases] {check}: Do not set PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-screed: Adjust following Python build system changes....* gnu/packages/bioinformatics.scm (python-screed)[arguments]: Remove field, no longer necessary. Maxim Cournoyer
2021-02-01gnu: bamm: Update following changes to the Python build system....* gnu/packages/bioinformatics.scm (bamm): Delete trailing #t. [phases]{check}: Override rather than delete phase. Remove trailing #t. {post-install-check}: Delete phase. {wrap-executable}: Also wrap with the new GUIX_PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-pysam: Adjust following Python build system changes....* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Remove the '#:modules' argument. [phases]: Remove trailing #t. {check}: Do not manually set PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-pybedtools: Streamline following Python build system changes....* gnu/packages/bioinformatics.scm (python-pybedtools): Remove trailing #t. [phases]{check}: Do not manually set PYTHONPATH. [arguments]: Remove the '#:modules' argument. Maxim Cournoyer
2021-02-01gnu: intel-xed: Adjust build phase....* gnu/packages/assembly.scm (intel-xed) [phases]: Delete trailing #t. {build}: Do not read PYTHONPATH from environment. Maxim Cournoyer
2021-02-01gnu: solaar: Do not read PYTHONPATH from environment....* gnu/packages/admin.scm (solaar) [phases]{setenv-PATH}: Do not read PYTHONPATH from environment. Maxim Cournoyer
2021-02-01gnu: python2-virtualenv: Fix build....* gnu/packages/python-xyz.scm (python2-virtualenv)[arguments]{phases}: Remove argument. Maxim Cournoyer
2021-02-01gnu: python2-packaging-bootstrap: Add missing dependency...* gnu/packages/python-xyz.scm (python2-packaging-bootstrap) [propagated-inputs]: Add python2-six-bootstrap. Lars-Dominik Braun
2021-02-01gnu: python-traceback2: Add missing dependency....* gnu/packages/python-xyz.scm (python-traceback2)[propagated-inputs]: Add python-six. Lars-Dominik Braun
2021-02-01gnu: python-packaging-bootstrap: Remove dependency....* gnu/packages/python-xyz.scm (python-packaging-bootstrap) [arguments]: Remove dependency from setup.py, which we do not provide for this variant. Lars-Dominik Braun
2021-02-01gnu: python-automat: Remove broken console script....* gnu/packages/python-xyz.scm (python-automat) [arguments]: Patch setup.py. Lars-Dominik Braun
2021-02-01gnu: python-twisted: Remove broken console scripts....* gnu/packages/python-xyz.scm (python-twisted) [arguments]: Patch setup.py. Lars-Dominik Braun
2021-02-01gnu: python-idna-ssl: Add missing input....* gnu/packages/python-xyz.scm (python-idna-ssl)[propagated-inputs]: Add python-idna. Lars-Dominik Braun
2021-02-01gnu: python-traitlets: Add missing input....* gnu/packages/python-xyz.scm (python-traitlets)[propagated-inputs]: Add python-six. Lars-Dominik Braun
2021-02-01gnu: python-black: Remove blackd....* gnu/packages/python-xyz.scm (python-black) [arguments]: Add new phase to prevent installation of blackd. Lars-Dominik Braun
2021-02-01gnu: python-websockets: Fix Python package name....* gnu/packages/python-web.scm (python-websockets) [arguments]: Add new phase to fix package name. Lars-Dominik Braun
2021-02-01gnu: python-slugify: Add missing input....* gnu/packages/python-web.scm (python-slugify) [propagated-inputs]: Add python-text-unidecode. Lars-Dominik Braun
2021-02-01gnu: python-pyfakefs: Disable unreliable test...* gnu/packages/check.scm (python-pyfakefs) [arguments]: Add new phase to skip single test. Lars-Dominik Braun
2021-02-01gnu: python-pytest-pep8: Fix package....* gnu/packages/check.scm (python-pytest-pep8)[arguments]: Remove dependency on pytest-cache and add proper 'check phase. Lars-Dominik Braun
2021-02-01gnu: python-fixtures-bootstrap: Do not sanity check....* gnu/packages/check.scm (python-fixtures-bootstrap) [phases]{sanity-check}: Delete. Lars-Dominik Braun
2021-02-01gnu: python-pytest-xdist: Add missing input, relax pytest requirement....* gnu/packages/check.scm: (python-pytest-xdist) [arguments]: Relax pytest version requirements. [propagated-inputs]: Add python-pytest-forked. Lars-Dominik Braun
2021-02-01build/python: Add a sanity check phase....Add a new phase validating the usability of installed Python packages. * gnu/packages/aux-files/python/sanity-check.py: New file. * Makefile.am (AUX_FILES): Register it. * guix/build-system/python.scm (sanity-check.py): New variable. (lower): Add the script as an implicit input. * guix/build/python-build-system.scm: Remove trailing #t. (sanity-check): New phase. (%standard-phases): Use it. * tests/builders.scm: (make-python-dummy) (dummy-ok, dummy-dummy-nosetuptools, dummy-fail-requirements) (dummy-fail-import, dummy-fail-console-script): New variables. ("python-build-system: dummy-ok") ("python-build-system: dummy-dummy-nosetuptools") ("python-build-system: dummy-fail-requirements") ("python-build-system: dummy-fail-import") ("python-build-system: dummy-fail-console-script"): Add tests. Lars-Dominik Braun
2021-02-01gnu: python: Replace PYTHONPATH by GUIX_PYTHONPATH....Using PYTHONPATH as a mean to discover the Python packages had the following issues: 1. It is not versioned, so different versions of Python would clash if installed in a shared profile. 2. It would interfere with the host Python site on foreign distributions, sometimes preventing a a user to login their GDM session (!). 3. It would take precedence over user installed Python packages installed through pip. 4. It would leak into Python virtualenvs, which are supposed to create isolated Python environments. This changes fixes the above issues by making use of a sitecustomize.py module. The newly introduced GUIX_PYTHONPATH environment variable is read from the environment, filtered for the current Python version of the interpreter, and spliced in 'sys.path' just before Python's own site location, which provides the expected behavior. * gnu/packages/aux-files/python/sitecustomize.py: New file. * Makefile.am: Register it. * gnu/packages/python.scm (customize-site) (guix-pythonpath-search-path): New procedures. (python-2.7)[phases]{install-sitecustomize.py}: New phase. [native-inputs]{sitecustomize.py}: New input. [native-search-paths]: Replace PYTHONPATH with GUIX_PYTHONPATH. (python-3.9)[native-search-paths]: Likewise. [phases]{install-sitecustomize}: Override with correct version. [native-search-paths]: Replace PYTHONPATH with GUIX_PYTHONPATH. * gnu/packages/commencement.scm (python-boot0): [phases]{install-sitecustomize}: Likewise. [native-inputs]{sitecustomize.py}: New input. [native-search-paths]: Replace PYTHONPATH with GUIX_PYTHONPATH. * guix/build/python-build-system.scm (site-packages): Do not add a trailing '/'. squash! gnu: python: Replace PYTHONPATH by GUIX_PYTHONPATH. Maxim Cournoyer
2021-01-31gnu: pixman: Update to 0.40.0....* gnu/packages/xdisorg.scm (pixman) [version]: Update to 0.40.0. [license]: Change from X11 to expat. Signed-off-by: Leo Famulari <leo@famulari.name> Raghav Gururajan
2021-01-31gnu: pixman: Enable some features....* gnu/packages/xdisorg.scm (pixman) [arguments] Pass --enable-timers and --enable-gnuplot to #:configure-flags. Signed-off-by: Leo Famulari <leo@famulari.name> Raghav Gururajan
2021-01-31gnu: openjpeg: Enable tests....* gnu/packages/image.scm (openjpeg)[arguments]: Enable the test suite. Pass -DBUILD_UNIT_TESTS, -DBUILD_TESTING, and -DOPJ_DATA_ROOT to #:configure-flags. Add a new 'disable-failing-tests' phase. [native-inputs]: Add openjpeg-data. Signed-off-by: Leo Famulari <leo@famulari.name> Raghav Gururajan