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* 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.
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* gnu/packages/check.scm (behave)[arguments]: Remove the '#:phases' argument.
[propagated-inputs]: Remove python-importlib-metadata and python-six.
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* 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.
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* gnu/packages/web.scm (linkchecker): Remove trailing #t.
[phases]: Do not reorder the check phase after the install phase.
{check}: Do not set PYTHONPATH.
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* gnu/packages/libffi.scm (python-cffi): Remove trailing #t.
[phases]{check}: Do not set PYTHONPATH.
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* gnu/packages/xml.scm (python-xmlschema): Remove trailing #t.
[phases]{check}: Do not set PYTHONPATH.
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* gnu/packages/bioinformatics.scm (python-loompy)
[phases]{check}: Do not set PYTHONPATH.
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* gnu/packages/bioinformatics.scm (python-scanpy)[phases]
{check}: Do not set PYTHONPATH.
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* gnu/packages/bioinformatics.scm (python-screed)[arguments]: Remove field, no
longer necessary.
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* 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.
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* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Remove the
'#:modules' argument.
[phases]: Remove trailing #t.
{check}: Do not manually set PYTHONPATH.
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* gnu/packages/bioinformatics.scm (python-pybedtools): Remove trailing #t.
[phases]{check}: Do not manually set PYTHONPATH.
[arguments]: Remove the '#:modules' argument.
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* gnu/packages/assembly.scm (intel-xed)
[phases]: Delete trailing #t.
{build}: Do not read PYTHONPATH from environment.
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* gnu/packages/admin.scm (solaar)
[phases]{setenv-PATH}: Do not read PYTHONPATH from environment.
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* gnu/packages/python-xyz.scm (python2-virtualenv)[arguments]{phases}: Remove
argument.
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* gnu/packages/python-xyz.scm (python2-packaging-bootstrap)
[propagated-inputs]: Add python2-six-bootstrap.
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* gnu/packages/python-xyz.scm (python-traceback2)[propagated-inputs]:
Add python-six.
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* gnu/packages/python-xyz.scm (python-packaging-bootstrap) [arguments]:
Remove dependency from setup.py, which we do not provide for this
variant.
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* gnu/packages/python-xyz.scm (python-automat) [arguments]: Patch
setup.py.
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* gnu/packages/python-xyz.scm (python-twisted) [arguments]: Patch
setup.py.
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* gnu/packages/python-xyz.scm (python-idna-ssl)[propagated-inputs]: Add
python-idna.
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* gnu/packages/python-xyz.scm (python-traitlets)[propagated-inputs]:
Add python-six.
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* gnu/packages/python-xyz.scm (python-black) [arguments]: Add new phase
to prevent installation of blackd.
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* gnu/packages/python-web.scm (python-websockets) [arguments]: Add new
phase to fix package name.
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* gnu/packages/python-web.scm (python-slugify) [propagated-inputs]: Add
python-text-unidecode.
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* gnu/packages/check.scm (python-pyfakefs) [arguments]: Add new phase to
skip single test.
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* gnu/packages/check.scm (python-pytest-pep8)[arguments]: Remove
dependency on pytest-cache and add proper 'check phase.
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* gnu/packages/check.scm (python-fixtures-bootstrap)
[phases]{sanity-check}: Delete.
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* gnu/packages/check.scm: (python-pytest-xdist)
[arguments]: Relax pytest version requirements.
[propagated-inputs]: Add python-pytest-forked.
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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.
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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.
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* 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>
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* gnu/packages/xdisorg.scm (pixman) [arguments] Pass --enable-timers and
--enable-gnuplot to #:configure-flags.
Signed-off-by: Leo Famulari <leo@famulari.name>
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* 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>
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* 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.
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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.
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* 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.
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* 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.
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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.
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* gnu/packages/libsigsegv.scm (libsigsegv): Update to 2.13.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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* 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>
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* gnu/packages/databases.scm (postgresql)[arguments]: Add 'set-socket-dir
phase.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
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* gnu/packages/certs.scm (certdata2pem)[arguments]: Use cc-for-target.
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* gnu/packages/certs.scm (certdata2pem)[source]: Download just the source.
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* gnu/packages/certs.scm: Use (gnu packages perl).
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* 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).
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* 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.
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* 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>
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* 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.
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* gnu/packages/python-xyz.scm (python-setuptools-scm): Update to 5.0.1.
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