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2021-02-01gnu: python-django-statici18n: Do not read PYTHONPATH.Maxim Cournoyer
* 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).
2021-02-01gnu: python-django-appconf: Do not alter PYTHONPATH.Maxim Cournoyer
* gnu/packages/django.scm (python-django-appconf) [phases]{check}: Do not alter PYTHONPATH.
2021-02-01gnu: python-django-sortedm2m: Do not alter PYTHONPATH.Maxim Cournoyer
* gnu/packages/django.scm (python-django-sortedm2m) [phases]{check}: Do not alter PYTHONPATH. Remove trailing #t.
2021-02-01gnu: python-django-pipeline: Do not alter PYTHONPATH.Maxim Cournoyer
* gnu/packages/django.scm (python-django-pipeline): Remove trailing #t. [phases]{check}: Do not alter PYTHONPATH.
2021-02-01gnu: python-django-contact-form: Do not alter PYTHONPATH.Maxim Cournoyer
* gnu/packages/django.scm (python-django-contact-form): [phases]{check}: Do not alter PYTHONPATH.
2021-02-01gnu: python-pytest-django: Do not alter PYTHONPATH.Maxim Cournoyer
* gnu/packages/django.scm (python-django): Remove trailing #t. [phases]{check}: Do not alter PYTHONPATH.
2021-02-01gnu: python-django: Do not alter PYTHONPATH.Maxim Cournoyer
* gnu/packages/django.scm (python-django): Remove trailing #t. [phases]{pre-check,check}: Do not alter PYTHONPATH.
2021-02-01gnu: python-rpy2: Do not set PYTHONPATH.Maxim Cournoyer
* gnu/packages/statistics.scm (python-rpy2)[arguments]: Remove the '#:modules' argument. [phases]{check}: Do not set PYTHONPATH.
2021-02-01gnu: ghmm: Do not set PYTHONPATH.Maxim Cournoyer
* gnu/packages/machine-learning.scm (ghmm): Remove trailing #t. [phases]: Do not reorder the check phase after the install phase. {fix-PYTHONPATH}: Remove phase.
2021-02-01gnu: tensorflow: Do not alter PYTHONPATH.Maxim Cournoyer
* gnu/packages/machine-learning.scm (tensorflow)[phases]: Delete trailing #t. {fix-python-build}: Do not alter PYTHONPATH.
2021-02-01gnu: python-libtmux: Do not set PYTHONPATH.Maxim Cournoyer
* gnu/packages/tmux.scm (python-libtmux)[phases]{check}: Do not set PYTHONPATH.
2021-02-01gnu: python-pyhamcrest: Update to 2.0.2.Maxim Cournoyer
* 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.
2021-02-01gnu: behave: Do not set PYTHONPATH.Maxim Cournoyer
* gnu/packages/check.scm (behave)[arguments]: Remove the '#:phases' argument. [propagated-inputs]: Remove python-importlib-metadata and python-six.
2021-02-01gnu: ganeti: Do not set PYTHONPATH.Maxim Cournoyer
* 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.
2021-02-01gnu: linkchecker: Do not set PYTHONPATH.Maxim Cournoyer
* gnu/packages/web.scm (linkchecker): Remove trailing #t. [phases]: Do not reorder the check phase after the install phase. {check}: Do not set PYTHONPATH.
2021-02-01gnu: python-cffi: Do not set PYTHONPATH.Maxim Cournoyer
* gnu/packages/libffi.scm (python-cffi): Remove trailing #t. [phases]{check}: Do not set PYTHONPATH.
2021-02-01gnu: python-xmlschema: Do not set PYTHONPATH.Maxim Cournoyer
* gnu/packages/xml.scm (python-xmlschema): Remove trailing #t. [phases]{check}: Do not set PYTHONPATH.
2021-02-01gnu: python-loompy: Do not set PYTHONPATH.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python-loompy) [phases]{check}: Do not set PYTHONPATH.
2021-02-01gnu: python-scanpy: Do not set PYTHONPATH.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python-scanpy)[phases] {check}: Do not set PYTHONPATH.
2021-02-01gnu: python-screed: Adjust following Python build system changes.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python-screed)[arguments]: Remove field, no longer necessary.
2021-02-01gnu: bamm: Update following changes to the Python build system.Maxim Cournoyer
* 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.
2021-02-01gnu: python-pysam: Adjust following Python build system changes.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Remove the '#:modules' argument. [phases]: Remove trailing #t. {check}: Do not manually set PYTHONPATH.
2021-02-01gnu: python-pybedtools: Streamline following Python build system changes.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python-pybedtools): Remove trailing #t. [phases]{check}: Do not manually set PYTHONPATH. [arguments]: Remove the '#:modules' argument.
2021-02-01gnu: intel-xed: Adjust build phase.Maxim Cournoyer
* gnu/packages/assembly.scm (intel-xed) [phases]: Delete trailing #t. {build}: Do not read PYTHONPATH from environment.
2021-02-01gnu: solaar: Do not read PYTHONPATH from environment.Maxim Cournoyer
* gnu/packages/admin.scm (solaar) [phases]{setenv-PATH}: Do not read PYTHONPATH from environment.
2021-02-01gnu: python2-virtualenv: Fix build.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python2-virtualenv)[arguments]{phases}: Remove argument.
2021-02-01gnu: python2-packaging-bootstrap: Add missing dependencyLars-Dominik Braun
* gnu/packages/python-xyz.scm (python2-packaging-bootstrap) [propagated-inputs]: Add python2-six-bootstrap.
2021-02-01gnu: python-traceback2: Add missing dependency.Lars-Dominik Braun
* gnu/packages/python-xyz.scm (python-traceback2)[propagated-inputs]: Add python-six.
2021-02-01gnu: python-packaging-bootstrap: Remove dependency.Lars-Dominik Braun
* gnu/packages/python-xyz.scm (python-packaging-bootstrap) [arguments]: Remove dependency from setup.py, which we do not provide for this variant.
2021-02-01gnu: python-automat: Remove broken console script.Lars-Dominik Braun
* gnu/packages/python-xyz.scm (python-automat) [arguments]: Patch setup.py.
2021-02-01gnu: python-twisted: Remove broken console scripts.Lars-Dominik Braun
* gnu/packages/python-xyz.scm (python-twisted) [arguments]: Patch setup.py.
2021-02-01gnu: python-idna-ssl: Add missing input.Lars-Dominik Braun
* gnu/packages/python-xyz.scm (python-idna-ssl)[propagated-inputs]: Add python-idna.
2021-02-01gnu: python-traitlets: Add missing input.Lars-Dominik Braun
* gnu/packages/python-xyz.scm (python-traitlets)[propagated-inputs]: Add python-six.
2021-02-01gnu: python-black: Remove blackd.Lars-Dominik Braun
* gnu/packages/python-xyz.scm (python-black) [arguments]: Add new phase to prevent installation of blackd.
2021-02-01gnu: python-websockets: Fix Python package name.Lars-Dominik Braun
* gnu/packages/python-web.scm (python-websockets) [arguments]: Add new phase to fix package name.
2021-02-01gnu: python-slugify: Add missing input.Lars-Dominik Braun
* gnu/packages/python-web.scm (python-slugify) [propagated-inputs]: Add python-text-unidecode.
2021-02-01gnu: python-pyfakefs: Disable unreliable testLars-Dominik Braun
* gnu/packages/check.scm (python-pyfakefs) [arguments]: Add new phase to skip single test.
2021-02-01gnu: python-pytest-pep8: Fix package.Lars-Dominik Braun
* gnu/packages/check.scm (python-pytest-pep8)[arguments]: Remove dependency on pytest-cache and add proper 'check phase.
2021-02-01gnu: python-fixtures-bootstrap: Do not sanity check.Lars-Dominik Braun
* gnu/packages/check.scm (python-fixtures-bootstrap) [phases]{sanity-check}: Delete.
2021-02-01gnu: python-pytest-xdist: Add missing input, relax pytest requirement.Lars-Dominik Braun
* gnu/packages/check.scm: (python-pytest-xdist) [arguments]: Relax pytest version requirements. [propagated-inputs]: Add python-pytest-forked.
2021-02-01build/python: Add a sanity check phase.Lars-Dominik Braun
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.
2021-02-01build/python: Adjust wrap phase to use the new GUIX_PYTHONPATH.Maxim Cournoyer
* guix/build/python-build-system.scm (wrap): Adjust to use the new GUIX_PYTHONPATH. Remove trailing #t.
2021-02-01build/python: Add the installation bin directory to PATH.Maxim Cournoyer
This also to reduce the need for boilerplate code found in check phase overrides. * guix/build/python-build-system.scm (add-install-to-path): New phase. (%standard-phases): Order it before the check phase.
2021-02-01build/python: Always add the install prefix to the Guix PYTHONPATH.Maxim Cournoyer
This is to remove the need for common boilerplate code in check phase overrides. * guix/build/python-build-system.scm (add-installed-pythonpath): Streamline. This phase depends on the presence of a "python" input; thus GUIX_PYTHONPATH is guaranteed to be defined. Update doc. (add-install-to-pythonpath): New phase. (%standard-phases): Order it before the check phase.
2021-02-01build/python: Replace PYTHONPATH by GUIX_PYTHONPATH.Maxim Cournoyer
* guix/build/python-build-system.scm (add-installed-pythonpath): Replace "PYTHONPATH" by "GUIX_PYTHONPATH".
2021-02-01gnu: python: Replace PYTHONPATH by GUIX_PYTHONPATH.Maxim Cournoyer
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.
2021-02-01guix package: Add '--export-channels'.Ludovic Courtès
* guix/channels.scm (sexp->channel): Export. * guix/describe.scm: Use (guix channels). (manifest-entry-provenance): New procedure. * guix/scripts/package.scm (channel=?, export-channels): New procedures. (show-help, %options): Add '--export-channels'. (process-query): Honor it. * build-aux/build-self.scm (build-program)[select?]: Exclude (guix channels) to account for the (guix describe) change above. * doc/guix.texi (Invoking guix package): Document it.
2021-02-01channels: Add 'channel->code'.Ludovic Courtès
* guix/channels.scm (channel->code): New procedure, taken from... * guix/scripts/describe.scm (channel->sexp): ... here. Adjust callers accordingly.
2021-02-01guix describe: Use 'manifest-entry-channel'.Ludovic Courtès
* guix/channels.scm (manifest-entry-channel): Export. * guix/scripts/describe.scm (display-profile-content): Use it.
2021-02-01channels: Add the channel name to channel sexps.Ludovic Courtès
* guix/channels.scm (channel-instance->sexp): Add 'name'. (sexp->channel): Extract the name from SEXP, using the optional argument as a fallback.
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