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* gnu: python-xmlschema: Do not set PYTHONPATH.Maxim Cournoyer2021-02-01
| | | | | * gnu/packages/xml.scm (python-xmlschema): Remove trailing #t. [phases]{check}: Do not set PYTHONPATH.
* gnu: python-loompy: Do not set PYTHONPATH.Maxim Cournoyer2021-02-01
| | | | | * gnu/packages/bioinformatics.scm (python-loompy) [phases]{check}: Do not set PYTHONPATH.
* gnu: python-scanpy: Do not set PYTHONPATH.Maxim Cournoyer2021-02-01
| | | | | * gnu/packages/bioinformatics.scm (python-scanpy)[phases] {check}: Do not set PYTHONPATH.
* gnu: python-screed: Adjust following Python build system changes.Maxim Cournoyer2021-02-01
| | | | | * gnu/packages/bioinformatics.scm (python-screed)[arguments]: Remove field, no longer necessary.
* gnu: bamm: Update following changes to the Python build system.Maxim Cournoyer2021-02-01
| | | | | | | * 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.
* gnu: python-pysam: Adjust following Python build system changes.Maxim Cournoyer2021-02-01
| | | | | | | * gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Remove the '#:modules' argument. [phases]: Remove trailing #t. {check}: Do not manually set PYTHONPATH.
* gnu: python-pybedtools: Streamline following Python build system changes.Maxim Cournoyer2021-02-01
| | | | | | * gnu/packages/bioinformatics.scm (python-pybedtools): Remove trailing #t. [phases]{check}: Do not manually set PYTHONPATH. [arguments]: Remove the '#:modules' argument.
* gnu: intel-xed: Adjust build phase.Maxim Cournoyer2021-02-01
| | | | | | * gnu/packages/assembly.scm (intel-xed) [phases]: Delete trailing #t. {build}: Do not read PYTHONPATH from environment.
* gnu: solaar: Do not read PYTHONPATH from environment.Maxim Cournoyer2021-02-01
| | | | | * gnu/packages/admin.scm (solaar) [phases]{setenv-PATH}: Do not read PYTHONPATH from environment.
* gnu: python2-virtualenv: Fix build.Maxim Cournoyer2021-02-01
| | | | | * gnu/packages/python-xyz.scm (python2-virtualenv)[arguments]{phases}: Remove argument.
* gnu: python2-packaging-bootstrap: Add missing dependencyLars-Dominik Braun2021-02-01
| | | | | * gnu/packages/python-xyz.scm (python2-packaging-bootstrap) [propagated-inputs]: Add python2-six-bootstrap.
* gnu: python-traceback2: Add missing dependency.Lars-Dominik Braun2021-02-01
| | | | | * gnu/packages/python-xyz.scm (python-traceback2)[propagated-inputs]: Add python-six.
* gnu: python-packaging-bootstrap: Remove dependency.Lars-Dominik Braun2021-02-01
| | | | | | * gnu/packages/python-xyz.scm (python-packaging-bootstrap) [arguments]: Remove dependency from setup.py, which we do not provide for this variant.
* gnu: python-automat: Remove broken console script.Lars-Dominik Braun2021-02-01
| | | | | * gnu/packages/python-xyz.scm (python-automat) [arguments]: Patch setup.py.
* gnu: python-twisted: Remove broken console scripts.Lars-Dominik Braun2021-02-01
| | | | | * gnu/packages/python-xyz.scm (python-twisted) [arguments]: Patch setup.py.
* gnu: python-idna-ssl: Add missing input.Lars-Dominik Braun2021-02-01
| | | | | * gnu/packages/python-xyz.scm (python-idna-ssl)[propagated-inputs]: Add python-idna.
* gnu: python-traitlets: Add missing input.Lars-Dominik Braun2021-02-01
| | | | | * gnu/packages/python-xyz.scm (python-traitlets)[propagated-inputs]: Add python-six.
* gnu: python-black: Remove blackd.Lars-Dominik Braun2021-02-01
| | | | | * gnu/packages/python-xyz.scm (python-black) [arguments]: Add new phase to prevent installation of blackd.
* gnu: python-websockets: Fix Python package name.Lars-Dominik Braun2021-02-01
| | | | | * gnu/packages/python-web.scm (python-websockets) [arguments]: Add new phase to fix package name.
* gnu: python-slugify: Add missing input.Lars-Dominik Braun2021-02-01
| | | | | * gnu/packages/python-web.scm (python-slugify) [propagated-inputs]: Add python-text-unidecode.
* gnu: python-pyfakefs: Disable unreliable testLars-Dominik Braun2021-02-01
| | | | | * gnu/packages/check.scm (python-pyfakefs) [arguments]: Add new phase to skip single test.
* gnu: python-pytest-pep8: Fix package.Lars-Dominik Braun2021-02-01
| | | | | * gnu/packages/check.scm (python-pytest-pep8)[arguments]: Remove dependency on pytest-cache and add proper 'check phase.
* gnu: python-fixtures-bootstrap: Do not sanity check.Lars-Dominik Braun2021-02-01
| | | | | * gnu/packages/check.scm (python-fixtures-bootstrap) [phases]{sanity-check}: Delete.
* gnu: python-pytest-xdist: Add missing input, relax pytest requirement.Lars-Dominik Braun2021-02-01
| | | | | | * gnu/packages/check.scm: (python-pytest-xdist) [arguments]: Relax pytest version requirements. [propagated-inputs]: Add python-pytest-forked.
* build/python: Add a sanity check phase.Lars-Dominik Braun2021-02-01
| | | | | | | | | | | | | | | | | | | | 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.
* gnu: python: Replace PYTHONPATH by GUIX_PYTHONPATH.Maxim Cournoyer2021-02-01
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* gnu: pixman: Update to 0.40.0.Raghav Gururajan2021-01-31
| | | | | | | * 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>
* gnu: pixman: Enable some features.Raghav Gururajan2021-01-31
| | | | | | | * gnu/packages/xdisorg.scm (pixman) [arguments] Pass --enable-timers and --enable-gnuplot to #:configure-flags. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: openjpeg: Enable tests.Raghav Gururajan2021-01-31
| | | | | | | | | * 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>
* gnu: fontconfig: Update to 2.13.93.Maxim Cournoyer2021-01-29
| | | | | | | | | | | | | * gnu/packages/patches/fontconfig-hurd-path-max.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Un-register file. * gnu/packages/fontutils.scm (fontconfig)[source] {uri}: Use the .tar.xz archive. {patches}: Remove field. The patch was merged upstream. [native-inputs]: Add python-minimal. [phases]{skip-problematic-tests}: Add phase. [configure-flags]: Do not set PYTHON to false. * gnu/packages/fontutils.scm (fontconfig-with-documentation) [native-inputs]: Add docbook-utils.
* gnu: fontconfig-with-documentation: New variable.Maxim Cournoyer2021-01-29
| | | | | | | | | | | | | | | In what will become fontconfig 2.14, the complete documentation of fontconfig requires multiple dependencies that would be problematic to add to this core package; instead, keep the 'fontconfig' variable package lean and create a new 'fontconfig-with-documentation' package that will be known as "fontconfig" to the users. * gnu/packages/fontutils.scm (fontconfig): Hide package. [outputs]: Remove doc output. [configure-flags]: Add "--disable-docs" argument. [phases]{remove-pdf-files}: Remove phase. {move-man-sections}: Move to... (fontconfig-with-documentation): ... this new variable with a doc output.
* gnu: Replace all uses of texlive-union by texlive-updmap.cfg.Maxim Cournoyer2021-01-29
| | | | | | | | | | | | | | | | | | | | | | | * doc/build.scm (pdf-manual) Replace texlive-union by texlive-updmap.cfg. * gnu/packages/algebra.scm (pari-gp): Likewise. * gnu/packages/bioinformatics.scm (discrover, velvet): Likewise. * gnu/packages/chez.scm (chez-scheme, chez-web, chez-sockets): Likewise. * gnu/packages/docbook.scm (dblatex): Likewise. * gnu/packages/emacs-xyz.scm (emacs-auctex): Likewise. * gnu/packages/engineering.scm (fastcap): Likewise. * gnu/packages/guile-xyz.scm (emacsy, guile-cv): Likewise. * gnu/packages/lisp.scm (sbcl): Likewise. * gnu/packages/maths.scm (octave, hypre): Likewise. * gnu/packages/music.scm (lilypond): Likewise. * gnu/packages/plotutils.scm (asymptote): Likewise. * gnu/packages/python-xyz.scm (python-numpy-documentation) (python-matplotlib-documentation, python-ipython-documentation) (python-pypandoc): Likewise. * gnu/packages/radio.scm (gnuradio, libosmo-dsp): Likewise. * gnu/packages/scheme.scm (mit-scheme): Likewise. * gnu/packages/statistics.scm (r-with-tests): Likewise. * gnu/packages/tex.scm (simple-texlive-package) (texlive-xmltex, texlive-tiny, texlive-jadetex, teximpatient, lyx): Likewise.
* gnu: texlive-amsfonts: Adjust to build with texlive-updmap.cfg.Maxim Cournoyer2021-01-29
| | | | | | | | | | | * gnu/packages/tex.scm (texlive-amsfonts)[phases] {build-fonts}: Do not set SOURCE_DATE_EPOCH, already done by the build system. Let resources be auto-discovered by TeX Live machinery by simply setting GUIX_TEXMF. Remove references to the texlive-union input. Remove trailing #t. {install-generated-fonts}: Remove trailing #t. [native-inputs]: Replace texlive-union by texlive-updmap.cfg. Remove the texlive-cm and texlive-metafont arguments of texlive-updmap.cfg.
* gnu: texlive-bin: Enable the use of multiple TeX Live trees.Maxim Cournoyer2021-01-29
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Attempting to compose multiple TeX Live trees (such as can happen when using a texlive-union generated package) proved problematic; only the texmf.cnf configuration file from the union would be honored, causing other TeX Live components to be ignored. This change does away with TeX Live unions, instead relying on the default texmf.cnf configuration file provided by the texlive-bin package to honor individual TeX Live trees referred to via the newly introduced GUIX_TEXMF variable, and replacing the texlive-union procedure by texlive-updmap.cfg, to explicit that generating the fonts map configuration is now its sole purpose. * gnu/packages/tex.scm (texlive-bin)[phases]{customize-texmf}: New phase. {postint}: Move the patching of the texmf.cnf file to the new above phase. Patch the updmap.pl script to find its Perl modules. [native-search-paths]: Rename the TEXMF variable to GUIX_TEXMF. Remove the TEXMFCNF variable. * guix/profiles.scm (texlive-configuration): Remove procedure. (%default-profile-hooks)[texlive-configuration]: Unregister hook. (texlive-union): Alias to what has moved to... (texlivke-updmap.cfg): ... here. Update doc. Do not provide a different texmf.cnf configuration. [inherit]: Do not inherit from texlive-base. [build-system]: Switch to the copy-build-system. [arguments]{install-plan}: New argument. [phases]{regenerate-updmap.cfg}: New phase, which keeps only the fonts map generating code from the previous builder code. [inputs]: Remove bash, and move to ... [propagated-inputs]: ... here. [native-inputs]: Remove field, and move the source of the base updmap.cfg file to... [source]: ... here. [synopsis]: Update. [description]: Likewise. [license]: Delete duplicates.
* gnu: libsigsegv: Update to 2.13.Vincent Legoll2021-01-28
| | | | | | * gnu/packages/libsigsegv.scm (libsigsegv): Update to 2.13. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: libsndfile: Add opus support.Alexandros Theodotou2021-01-28
| | | | | | | | * gnu/packages/pulseaudio.scm (libsndfile)[inputs]: Move libvorbis, libogg, flac ... [propagated-inputs]: ... to here. Add opus. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: postgresql: Set default socket directory.Mathieu Othacehe2021-01-28
| | | | | | | * gnu/packages/databases.scm (postgresql)[arguments]: Add 'set-socket-dir phase. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
* gnu: certdata2pem: Fix cross compiling.Efraim Flashner2021-01-27
| | | | * gnu/packages/certs.scm (certdata2pem)[arguments]: Use cc-for-target.
* gnu: certdata2pem: Fix source URI.Efraim Flashner2021-01-27
| | | | * gnu/packages/certs.scm (certdata2pem)[source]: Download just the source.
* gnu: certs.scm: Add missing import.Efraim Flashner2021-01-27
| | | | * gnu/packages/certs.scm: Use (gnu packages perl).
* gnu: nss-certs: Remove Python 2 and Perl build dependencies.Maxim Cournoyer2021-01-27
| | | | | | | | * gnu/packages/certs.scm (certdata2pem): Swap package to a C variant. (nss-certs): Use 'openssl rehash' instead of the Perl 'c_rehash' script. Adjust for the new certdata2pem program. The number of certificates installed compared to when using the previous script remains unchanged (139 at the time of this commit).
* gnu: nss-certs: Sync with the sources used for nss.Maxim Cournoyer2021-01-27
| | | | | | | * gnu/packages/certs.scm (nss-certs)[version]: Reuse nss version. [source]: Reuse nss source. [phases]{install}: Adjust for the new NSS source files hierarchy. Remove trailing #t.
* gnu: boost: Patch transitive linking bug.Greg Hogan2021-01-26
| | | | | | | | * gnu/packages/patches/boost-fix-transitive-linking.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/boost.scm (boost)[source]: Use it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: nss: Update to the latest changeset to resolve test failures.Maxim Cournoyer2021-01-26
| | | | | | | | | | | | | | * gnu/packages/patches/nss-3.56-pkgconfig.patch: Update and ajdust. * gnu/packages/patches/nss-increase-test-timeout.patch: Adjust. * gnu/packages/nss.scm (nss)[version]: Compute with the git-version procedure. [source]: Switch to use the latest changeset. Adjust snippet to match restructuring of the source file hierarchy. [make-flags]: Do not chdir to the "nss" directory. [phases]: Delete trailing #t. {check}: Honor the '#:tests?' argument. Update the date used with faketime and adjust for the new all.sh script location. {install}: Adapt to the location of the 'dist/' directory, which is now at the same level as the 'source' checkout.
* gnu: python-setuptools-scm: Update to 5.0.1.Nicolas Goaziou2021-01-26
| | | | * gnu/packages/python-xyz.scm (python-setuptools-scm): Update to 5.0.1.
* gnu: mercurial: Update to 5.6.1.Maxim Cournoyer2021-01-26
| | | | | | | | | This fixes the build on Python 3.9. * gnu/packages/version-control.scm (mercurial): Update to 5.6.1. Delete trailing #t. [phases]{check}: Remove the "test-transaction-rollback-on-sigpipe.t" test file and add a comment.
* gnu: bison: Update to 3.7.5.Efraim Flashner2021-01-26
| | | | * gnu/packages/bison.scm (bison): Update to 3.7.5.
* gnu: binutils: Update to 2.36.Efraim Flashner2021-01-26
| | | | * gnu/packages/base.scm (binutils): Update to 2.36.
* gnu: %boot-tcc-inputs: Use gash-utils.Efraim Flashner2021-01-24
| | | | | | * gnu/packages/commencement.scm (%boot-tcc-inputs): Remove diffutils-mesboot. Add gash-utils-boot. (diffutils-mesboot): Remove variable.
* gnu: guile: Disable parallel builds.Ludovic Courtès2021-01-23
| | | | | | | This works around <https://bugs.gnu.org/20272>, as discussed in <https://lists.gnu.org/archive/html/guix-devel/2021-01/msg00273.html>. * gnu/packages/guile.scm (guile-2.0)[arguments]: Pass #:parallel-build? #f.
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