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Author SHA1 Message Date
Maxim Cournoyer
836daaf8f6
gnu: python-pandas: Update to 1.3.5. 
* gnu/packages/python-science.scm (python-pandas): Update to 1.3.5.
[phases]{check}: Add a reference to the network accessing tests issue, now
reported upstream.  Reinstate the excelwriter tests.
[propagated-inputs]: Add python-xlsxwriter.
[native-inputs]: Remove python-nose.
 2022-01-10 11:47:02 -05:00
Maxim Cournoyer
b92d09cda1
gnu: python-xlwt: Add comment about maintainership of the package. 
The package appears to be abandoned.

* gnu/packages/python-xyz.scm (python-xlwt): Add comment.
 2022-01-10 11:47:02 -05:00
Maxim Cournoyer
00bad443ef
gnu: python-openpyxl: Update to 3.0.9. 
* gnu/packages/python-xyz.scm (python-openpyxl): Update to 3.0.9.
 2022-01-10 11:47:01 -05:00
Maxim Cournoyer
0c83eca719
gnu: python-xlrd: Update to 2.0.1. 
* gnu/packages/python-xyz.scm (python-xlrd): Update to 2.0.1.
[source]: Use git-fetch.
[arguments]: Delete field.
[native-inputs]: Add python-pytest.
 2022-01-10 11:47:01 -05:00
Maxim Cournoyer
48baca342d
gnu: mutter: Add python to native inputs. 
* gnu/packages/gnome.scm (mutter)[native-inputs]: Add python.
 2022-01-10 11:47:01 -05:00
Maxim Cournoyer
ac1f60f4fe
gnu: libgweather: Add python to native inputs. 
* gnu/packages/gnome.scm (libgweather)[native-inputs]: Add python.
 2022-01-10 11:47:01 -05:00
Maxim Cournoyer
235a083103
gnu: baobab: Add python to native inputs. 
* gnu/packages/gnome.scm (baobab)[native-inputs]: Add python.
 2022-01-10 11:47:00 -05:00
Maxim Cournoyer
c1482ef315
gnu: python-pytest-timeout: Update to 2.0.2. 
* gnu/packages/check.scm (python-pytest-timeout): Update to 2.0.2.
 2022-01-10 11:47:00 -05:00
Leo Famulari
8636d02955
gnu: binutils: Fix CVE-2021-45078. 
This is for the release branch.

Should we also use a graft for the master branch? It would be even
better if we could add a binutils-next package that users could install,
in my opinion.

* gnu/packages/patches/binutils-CVE-2021-45078.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/base.scm (binutils)[source]: Use it.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:46:57 -05:00
Maxim Cournoyer
db912d77a8
gnu: glib: Update to 2.70.2. 
* gnu/packages/glib.scm (glib): Update to 2.70.2.
 2022-01-10 11:44:52 -05:00
Maxim Cournoyer
ec26595e30
gnu: meson: Update to 0.60.3. 
* gnu/packages/build-tools.scm (gn): Update to 0.60.3.
 2022-01-10 11:44:52 -05:00
Maxim Cournoyer
abb5a92cbc
gnu: glibmm: Update to 2.70.0 and apply guix style. 
* gnu/packages/glib.scm (glibmm): Update to 2.70.0.
[native-inputs]: Use new style.
 2022-01-10 11:44:51 -05:00
Sarah Morgensen
64f7e53a5d
gnu: cpuid: Remove obsolete file permissions change. 
* gnu/packages/linux.scm (cpuid)[arguments]<#:phases>{fix-makefile}:
Remove Makefile gzip permissions patch.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:51 -05:00
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