* 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.
* gnu/packages/web.scm (linkchecker): Remove trailing #t.
[phases]: Do not reorder the check phase after the install phase.
{check}: Do not set PYTHONPATH.
* 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/packages/bioinformatics.scm (python-pysam)[arguments]: Remove the
'#:modules' argument.
[phases]: Remove trailing #t.
{check}: Do not manually set PYTHONPATH.
* gnu/packages/bioinformatics.scm (python-pybedtools): Remove trailing #t.
[phases]{check}: Do not manually set PYTHONPATH.
[arguments]: Remove the '#:modules' argument.
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.
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.
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.
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/packages/xdisorg.scm (pixman) [arguments] Pass --enable-timers and
--enable-gnuplot to #:configure-flags.
Signed-off-by: Leo Famulari <leo@famulari.name>
* 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>
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/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.
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/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).
Before this change, only plain directories, tar or zip archives were supported
as the source of a package for the GNU build system; anything else would cause
the unpack phase to fail. Origins relying on snippets would suffer from the
same problem.
This change adds the support to use files of the following extensions: .gz,
.Z, .bz2, .lz, and .xz, even when they are not tarballs. Files of unknown
extensions are treated as uncompressed files and supported as well.
* guix/packages.scm (patch-and-repack): Only add the compressor utility to the
PATH when the file is compressed. Bind more inputs in the mlet, and use them
for decompressing single files. Adjust the decompression and compression
routines.
[decompression-type]: Remove nested variable.
* guix/build/utils.scm (compressor, tarball?): New procedures. Move
%xz-parallel-args to the new 'compression helpers' section.
* tests/packages.scm: Add tests. Add missing copyright year for Jan.
* guix/build/gnu-build-system.scm (first-subdirectory): Return #f when no
sub-directory was found.
(unpack): Support more file types, including uncompressed plain files.
