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Sarah Morgensen 27cc25e1a4
gnu: pre-commit: Remove obsolete phase. 
* gnu/packages/version-control.scm (pre-commit)[arguments]<#:phases>:
Remove 'make-gz-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:51 -05:00
Sarah Morgensen 95cb49b475
gnu: go-github-com-prometheus-common: Remove obsolete phase. 
* gnu/packages/syncthing.scm (go-github-com-prometheus-common)
[arguments]<#:phases>: Remove 'make-gzip-archive-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:51 -05:00
Sarah Morgensen fa7b52ff57
gnu: python-pdfminer-six: Remove obsolete phase. 
* gnu/packages/python-xyz.scm (python-pdfminer-six)[arguments]
<#:phases>: Remove 'make-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:50 -05:00
Sarah Morgensen a97d659e13
gnu: arcanist: Remove obsolete phase. 
* gnu/packages/phabricator.scm (arcanist)[arguments]<#:phases>: Remove
'make-compressed-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:50 -05:00
Sarah Morgensen b623ee2fb6
gnu: helm: Remove obsolete phase. 
* gnu/packages/music.scm (helm)[arguments]<#:phases>: Remove
'make-gz-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:50 -05:00
Sarah Morgensen 9d55296898
gnu: lmms: Remove obsolete phase. 
* gnu/packages/music.scm (lmms)[arguments]<#:phases>: Remove
'make-manpages-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:50 -05:00
Sarah Morgensen f7d4bf6205
gnu: jalv-select: Remove obsolete phase. 
* gnu/packages/music.scm (jalv-select)[arguments]<#:phases>: Remove
'make-manpages-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:50 -05:00
Sarah Morgensen 18e872b805
gnu: python-scikit-learn: Remove obsolete phase. 
* gnu/packages/machine-learning.scm (python-scikit-learn)[arguments]
<#:phases>: Remove 'make-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:49 -05:00
Sarah Morgensen b67d82972e
gnu: go-ipfs: Remove obsolete phase. 
* gnu/packages/ipfs.scm (go-ipfs)[arguments]<#:phases>: Remove
'make-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:49 -05:00
Sarah Morgensen 1ba19f4bf1
gnu: python-plotly: Remove obsolete phase. 
* gnu/packages/graph.scm (python-plotly)[arguments]<#:phases>: Remove
'make-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:49 -05:00
Sarah Morgensen 21566bfd49
gnu: go-github-com-gdamore-tcell: Remove obsolete phase. 
* gnu/packages/golang.scm (go-github-com-gdamore-tcell)[arguments]
<#:phases>: Remove 'make-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:49 -05:00
Sarah Morgensen 8347c49e56
gnu: go-github-com-docker-distribution: Remove obsolete phase. 
* gnu/packages/golang.scm (go-github-com-docker-distribution)[arguments]
<#:phases>: Remove 'make-gzip-archive-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:49 -05:00
Sarah Morgensen 37f6126f9f
gnu: go-golang-org-x-crypto: Remove obsolete phase. 
* gnu/packages/golang.scm (go-golang-org-x-crypto)[arguments]<#:phases>:
Remove 'make-gzip-archive-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:48 -05:00
Sarah Morgensen e0940ed843
gnu: po4a: Remove obsolete phase. 
* gnu/packages/gettext.scm (po4a)[arguments]<#:phases>: Remove 'make-compressed-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:48 -05:00
Sarah Morgensen 6dc8a61bb1
gnu: emacs: Remove obsolete phase. 
* gnu/packages/emacs.scm (emacs)[arguments]<#:phases>: Remove
'make-compressed-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:48 -05:00
Sarah Morgensen 0d04504362
gnu: cups-minimal: Remove obsolete phase. 
* gnu/packages/cups.scm (cups-minimal)[arguments]<#:phases>: Remove
'make-manpages-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:48 -05:00
Sarah Morgensen b9e703da9d
gnu: clipper: Remove obsolete phase. 
* gnu/packages/bioinformatics.scm (clipper)[arguments]<#:phases>: Remove
'make-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:48 -05:00
Sarah Morgensen 85e43978a4
gnu: python-biom-format: Remove obsolete phase. 
* gnu/packages/bioinformatics.scm (python-biom-format)[arguments]
<#:phases>: Remove 'make-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:47 -05:00
Sarah Morgensen 0f71f55a60
build-system/gnu: Make gzip files writable before resetting timestamps. 
guix/build/gnu-build-system.scm (reset-gzip-timestamps): Ensure gzip
files are writable before resetting their timestamps.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:47 -05:00
Maxim Cournoyer c61e742854
gnu: tbb-2020: Use ld.gold to work around segfaults in check phase. 
* gnu/packages/tbb.scm (tbb-2020)
[configure-flags]: Use -fuse-ld=gold in CFLAGS.
[native-inputs]: Add ld-gold-wrapper.
 2022-01-10 11:44:47 -05:00
Maxim Cournoyer 5651e46983
gnu: python-igraph: Update to 0.9.8. 
* gnu/packages/graph.scm (python-igraph): Update to 0.9.8.
[origin]: Fetch from git.
[configure-flags]: Delete argument.
[phases]{build}: No longer override phase.
{check}: Preserve ordering and streamline.
{specify-libigraph-location}: New phase.
[native-inputs]: Remove pkg-config.
[home-page]: Update.
 2022-01-10 11:44:47 -05:00
Maxim Cournoyer 3c50cb75ee
gnu: igraph: Update to 0.9.5. 
* gnu/packages/graph.scm (igraph): Update to 0.9.5.
[source]: Add snippet to fully unbundle.
[build-system]: Use cmake-build-system.
[configure-flags]: Replace all by just '-DBUILD_SHARED_LIBS=ON'.
[native-inputs]: Add pkg-config.
[inputs]{zlib}: Delete input.
{arpack-ng, plfit, suitesparse}: New inputs.
 2022-01-10 11:44:47 -05:00
Maxim Cournoyer 36681885d4
gnu: Add plfit. 
* gnu/packages/graph.scm (plfit): New variable.
 2022-01-10 11:44:46 -05:00
Maxim Cournoyer 64dac22b17
gnu: python-pysam: Update to 0.18.0. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.18.0.
[source]: Add FIXME to clarify bundled libraries in use.
[phases]{check}: Streamline.
[propagated-inputs]: Use latest htslib (1.14).
[native-inputs]: Use latest samtools and bcftools (1.14).  Remove python-nose.
 2022-01-10 11:44:46 -05:00
Maxim Cournoyer 801d0ed622
gnu: bcftools: Update to 1.14. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.14.
(bcftools-1.12): New variable.
(bcftools-1.10): Use package/inherit and delete trailing #t.
[name]: Delete field.
 2022-01-10 11:44:46 -05:00
Maxim Cournoyer 23fdb5a69c
gnu: samtools: Update to 1.14. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.14.
[modules]: Delete argument.
[phases]{install-library, install-headers}: Delete phases.  This version no
longer includes the legacy library (it links to htslib directly).
(samtools-1.12): New variable.
 2022-01-10 11:44:46 -05:00
Maxim Cournoyer 74af2dd148
gnu: htslib: Update to 1.14. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.14.
(htslib-1.12): New variable.
(htslib-1.10, htslib-1.9, htslib-1.3)
(htslib-for-samtools-1.2): Normalize style.
 2022-01-10 11:44:46 -05:00
Maxim Cournoyer 3c9a98bf34
gnu: python-beautifulsoup4: Update to 4.10.0. 
* gnu/packages/python-xyz.scm (python-beautifulsoup4): Update to 4.10.0.
[propagated-inputs]{python-html5lib, python-lxml}: New inputs.
[arguments]: Delete field.
(python2-beautifulsoup4): Peg at version 4.9.3.
 2022-01-10 11:44:45 -05:00
Maxim Cournoyer 01a01c88f8
gnu: poetry: Update to 1.1.12. 
* gnu/packages/python-xyz.scm (poetry): Update to 1.1.12.
[phases]{patch-setup-py}: Relax packaging version requirement.
[propagated-inputs]{python-msgpack-transitional}: Replace with...
{python-msgpack}: ... this.
{python-requests-toolbelt-0.9.1}: Replace with...
{python-requests-toolbelt}: ... this.
{python-msgpack-transitional}: Delete variable.
 2022-01-10 11:44:45 -05:00
Maxim Cournoyer 08769d0bce
gnu: python-requests-toolbelt: Update to 0.9.1 and enable tests. 
* gnu/packages/python-web.scm (pyhton-requests-toolbelt): Update to 0.9.1.
[phases]{delete-problematic-tests}: New phase.
(python-requests-toolbelt-0.9.1): Delete variable.
(python2-requests-toolbelt): Likewise.
(python-cloudscraper): Adjust accordingly.
 2022-01-10 11:44:45 -05:00
Maxim Cournoyer f0be3ddadf
gnu: python-cachecontrol: Update to 0.12.10. 
* gnu/packages/python-web.scm (python-cachecontrol): Update to 0.12.10.
 2022-01-10 11:44:45 -05:00
Maxim Cournoyer 0be48040dc
gnu: python-os-testr: Propagate python-testtools and python-babel. 
Lack of python-testtools was causing the sanity-check phase to fail.

* gnu/packages/openstack.scm (python-os-testr)
[native-inputs]{python-testtools, python-babel}: Move to...
[propagated-inputs]: ... here.
 2022-01-10 11:44:44 -05:00
Maxim Cournoyer 7aa7d85bac
gnu: webkitgtk: Enable GStreamer GL support. 
* gnu/packages/webkit.scm (webkitgtk)[configure-flags]: Remove the
'-DUSE_GSTREAMER_GL=OFF' build option.
 2022-01-10 11:44:44 -05:00
Maxim Cournoyer 00e4bd2500
gnu: webkitgtk: Add a note about plugins in description. 
This is in response to <https://issues.guix.gnu.org/52375>.

* gnu/packages/webkit.scm (webkitgtk): Add a note about GStreamer plugins.

Reported-by: Jack Hill <jackhill@jackhill.us>
 2022-01-10 11:44:44 -05:00
Maxim Cournoyer c704bdd95b
gnu: python2-matplotlib: Update to 2.2.5. 
* gnu/packages/python-xyz.scm (python2-matplotlib): Update to 2.2.5.
[phases]: Use G-exp.
{install-jquery-ui}: Delete phase.  JQuery is bundled in this release.
[native-inputs]: Remove all exception pkg-config.
[propagated-inputs]: Sort and explicitly specify all inputs to ease
maintenance.
 2022-01-10 11:44:44 -05:00
Maxim Cournoyer ea0ed65c59
gnu: python-matplotlib: Update to 3.5.1 and run tests in parallel. 
* gnu/packages/python-xyz.scm (python-matplotlib): Update to 3.5.1.
[propagated-inputs]: Add python-fonttools, python-wxpython
and python-packaging.
[native-inputs]: Remove python-mock, python-wheel, unzip and jquery-ui.
Add python-pytest-timeout, python-pytest-xdist, python-setuptools-scm and
python-setuptools-scm-git-archive.
[phases]: Delete trailing #t.
{pretend-version}: New phase.
{install-jquery-ui}: Delete phase.
{check}: Honor TESTS?.  Do not skip webagg tests anymore.  Invoke using
'-n' argument to run tests in parallel via pytest-xdist.
{configure-environment}: Do not set LD_LIBRARY_PATH nor HOME.  Rename
setup.cfg to mplsetup.cfg.  Set the backend to Agg.
 2022-01-10 11:44:43 -05:00
Maxim Cournoyer e5e533c221
gnu: python-fonttools: Update to 4.28.5. 
* gnu/packages/python-xyz.scm (python-fonttools): Update to 4.28.5 and hide
the package.
[properties]: New field.
(python-fonttools-with-tests): New variable.
 2022-01-10 11:44:43 -05:00
Maxim Cournoyer b4e18112ef
gnu: Add python-zopfli. 
* gnu/packages/python-compression.scm (python-zopfli): New variable.
 2022-01-10 11:44:43 -05:00
Maxim Cournoyer 53d7e92e68
gnu: Add zopfli. 
* gnu/packages/compression.scm (zopfli): New variable.
 2022-01-10 11:44:43 -05:00
Maxim Cournoyer b794dff00a
gnu: Add python-fs. 
* gnu/packages/python-xyz.scm (python-fs): New variable.
 2022-01-10 11:44:42 -05:00
Maxim Cournoyer 32f1ae3616
gnu: Add python-pyftpdlib. 
* gnu/packages/python-xyz.scm (python-pyftpdlib): New variable.
 2022-01-10 11:44:42 -05:00
Maxim Cournoyer d07d0835a9
gnu: Add python-pysendfile. 
* gnu/packages/python-xyz.scm (python-pysendfile): New variable.
 2022-01-10 11:44:42 -05:00
Maxim Cournoyer 2fa2b91d59
gnu: python-pylint: Update to 2.12.2. 
* gnu/packages/check.scm (python-pylint): Update to 2.12.2.
[phases]{check}: Override phase.
[native-inputs]: Remove python-pytest-benchmark, python-pytest-runner.
[propagated-inputs]: Add python-platformdirs, python-typing-extensions.
[synopsis]: Streamline.
 2022-01-10 11:44:42 -05:00
Maxim Cournoyer b9839ee1c5
gnu: python-platformdirs: Update to 2.4.0, run tests and fix metadata. 
* gnu/packages/python-xyz.scm (python-platformdirs): Update to 2.4.0.
[phases]{pretend-version}: New phase.
{check}: Override to run tests.
[native-inputs]{python-setuptools-scm}: New input.
 2022-01-10 11:44:41 -05:00
Maxim Cournoyer 5b218cc14a
gnu: python-flit: Update to 3.5.1, enable tests and apply guix style. 
* gnu/packages/python-xyz.scm (python-flit)[origin]: Fetch from pypi-uri, to
ease updating the package.
[phases]{bootstrap}: Delete phase.
{build, install}: Do a PEP 517 build using pypa-build.
{check}: New phase.
[tests?]: Enable.
[propagated-inputs]{python-pytoml, python-toml}: Remove.
{python-pypa-build, python-tomli-w, python-flit-core, python-requests}: New
inputs.
{python-docutils}: New input, moved from...
[native-inputs]: ... here.  Apply guix style.
{python-testpath}: Use the regular python-testpath package.
[synopsis, description]: Re-indent.
 2022-01-10 11:44:41 -05:00
Maxim Cournoyer 3307224bf9
gnu: python-testpath: Update to 0.5.0 and enable tests. 
* gnu/packages/check.scm (python-testpath): Update to 0.5.0.
[phases]{relax-requirements}: New phase
{build}: Build using pypa-build's 'build' command.
{check}: Override phase.
{install}: Adjust.
[native-inputs]: Remove python-flit.  Add python-pypa-build and python-pytest.
[home-page]: Update.
 2022-01-10 11:44:41 -05:00
Maxim Cournoyer 84558f252e
gnu: Add python-tomli-w. 
* gnu/packages/python-build.scm (python-tomli-w): New variable.
 2022-01-10 11:44:41 -05:00
Maxim Cournoyer ded3b554f9
gnu: python-astroid: Update to 2.9.0. 
* gnu/packages/python-xyz.scm (python-astroid): Update to 2.9.0.
[native-inputs]: Add python-typing-extensions.
[properties]: Delete field.
(python2-astroid): Delete variable.
 2022-01-10 11:44:40 -05:00
Maxim Cournoyer b328a829fb
gnu: python-typing-extensions: Update to 4.0.1. 
* gnu/packages/python-xyz.scm (python-typing-extensions): Update to 4.0.1.
[origin]: Use git-fetch.
[tests?]: Disable.
[phases]{unpack, build, install}: New phases.
[native-inputs]: Add python-pypa-build, python-flit-core.
[home-page]: Shorten URL.
 2022-01-10 11:44:40 -05:00
Maxim Cournoyer 992b66a124
gnu: python-typing: Update to 3.10.0.0. 
* gnu/packages/python-xyz.scm (python-typing): Update to 3.10.0.0.
 2022-01-10 11:44:40 -05:00