Commit graph

96827 commits

Author SHA1 Message Date
Maxim Cournoyer
ba09192168
gnu: Remove python2-pbcore.
* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable.
2022-05-31 14:52:19 -04:00
Maxim Cournoyer
8287979669
gnu: Remove python2-pyfaidx.
* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable.
2022-05-31 14:52:18 -04:00
Maxim Cournoyer
850bd0c329
gnu: Remove python2-screed.
* gnu/packages/bioinformatics.scm (python2-screed): Delete variable.
2022-05-31 14:52:18 -04:00
Maxim Cournoyer
a94bc7798a
gnu: Remove miso.
* gnu/packages/bioinformatics.scm (miso): Delete variable.
2022-05-31 14:52:18 -04:00
Maxim Cournoyer
23e133a907
gnu: Remove python2-warpedlmm.
* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable.
2022-05-31 14:52:18 -04:00
Maxim Cournoyer
bb35b50adc
gnu: Remove poretools.
* gnu/packages/bioinformatics.scm (poretools): Delete variable.
2022-05-31 14:52:18 -04:00
Maxim Cournoyer
bcdd45be6f
gnu: Remove python2-dendropy.
* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable.
2022-05-31 14:52:17 -04:00
Maxim Cournoyer
d2c971e67b
gnu: Remove bamm.
* gnu/packages/bioinformatics.scm (bamm): Delete variable.
2022-05-31 14:52:17 -04:00
Maxim Cournoyer
1010c05800
gnu: Remove python2-pybedtools.
* gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable.
2022-05-31 14:52:17 -04:00
Maxim Cournoyer
725b562962
gnu: Remove python2-htseq.
* gnu/packages/bioinformatics.scm (python2-htseq): Delete variable.
2022-05-31 14:52:17 -04:00
Maxim Cournoyer
8bcb07d089
gnu: Remove pepr.
* gnu/packages/bioinformatics.scm (pepr): Delete variable.
2022-05-31 14:52:17 -04:00
Maxim Cournoyer
3d63c5f1ba
gnu: tetoolkit: Update to 2.2.1b.
* gnu/packages/bioinformatics.scm (tetoolkit): Update to 2.2.1b.
[python]: Delete argument.
[phases]: Delete trailing #t.
{make-writable}: Delete phase.
{adjust-requirements}: New phase.
{patch-invocations}: Use search-input-file.
{wrap-program}: Use search-input-file.
[inputs]: Remove python2-argparse.  Replace python2-pysam with python-pysam.
[home-page]: Update URL.
2022-05-31 14:52:16 -04:00
Maxim Cournoyer
d29d50a556
gnu: Remove python2-pybigwig.
* gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable.
2022-05-31 14:52:16 -04:00
Maxim Cournoyer
98c4f97d18
gnu: Remove ribodiff.
* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
2022-05-31 14:52:16 -04:00
Maxim Cournoyer
9f4c958d62
gnu: Remove grit.
* gnu/packages/bioinformatics.scm (grit): Delete variable.
2022-05-31 14:52:16 -04:00
Maxim Cournoyer
7963e12568
gnu: Remove python2-fastalite.
* gnu/packages/bioinformatics.scm (python2-fastalite): Delete variable.
2022-05-31 14:52:16 -04:00
Maxim Cournoyer
fd4668b111
gnu: Remove python2-pyaudio.
* gnu/packages/audio.scm (python2-pyaudio): Delete variable.
2022-05-31 14:52:15 -04:00
Maxim Cournoyer
1a60e11a98
gnu: Remove raul-devel.
* gnu/packages/audio.scm (raul-devel): Delete variable.
2022-05-31 14:52:15 -04:00
Maxim Cournoyer
94e8f2b9b5
gnu: Remove raul.
* gnu/packages/audio.scm (raul): Delete variable.
2022-05-31 14:52:15 -04:00
Maxim Cournoyer
a5a84babb9
gnu: Remove ingen.
* gnu/packages/music.scm (ingen): Delete variable.
2022-05-31 14:52:15 -04:00
Maxim Cournoyer
cfce386aba
gnu: Remove python2-pyalsaaudio.
* gnu/packages/audio.scm (python2-pyalsaaudio): Delete variable.
2022-05-31 14:52:15 -04:00
Maxim Cournoyer
cd46c8c34b
gnu: Remove graphios.
* gnu/packages/admin.scm (graphios): Delete variable.
2022-05-31 14:52:14 -04:00
Maxim Cournoyer
74641c7f66
gnu: Remove python2-langkit.
* gnu/packages/ada.scm (python2-langkit): Delete variable.
2022-05-31 14:52:14 -04:00
Maxim Cournoyer
787a026f00
gnu: Remove python-pytest-runner-2.
* gnu/packages/check.scm (python-pytest-runner-2): Delete variable.
(python2-pytest-runner): Likewise.
2022-05-31 14:52:14 -04:00
Maxim Cournoyer
53cd5923ef
diagnostics: Fix typo about 0-indexed COL in location.
* guix/diagnostics.scm (source-properties->location): The location column is
0-indexed, not 1-indexed (the same as in source-properties, so the code is
accurate).
2022-05-31 14:52:14 -04:00
Maxim Cournoyer
d7c4e7a0c2
utils: Add a %guix-source-root-directory procedure.
* guix/utils.scm (%guix-source-root-directory): New procedure.
2022-05-31 14:52:14 -04:00
Maxim Cournoyer
5bc1ede862
utils: Add a 'delete-expression' procedure.
* guix/utils.scm: Fix copyright lines and order imports.
(edit-expression): Fix typo in doc.  Add a new 'include-trailing-newline?'
keyword argument.  Update doc.
(delete-expression): New procedure.
2022-05-31 14:52:13 -04:00
Maxim Cournoyer
5e6efdfeec
etc/committer: Teach it how to commit package removal.
* etc/committer.scm.in (hunk-types): New variable.
(<hunk>): Rename hunk-definition? getter to 'hunk-type'.
(diff-info): Mute a git warning by separating file names from arguments with
'--'.  Rename the 'definitions?' variable to 'type'.
Use the 'addition type when a new package addition is detected, 'removal when
removed else #f.
(add-commit-message): Re-indent.
(remove-commit-message): New procedure.
(main)[definitions]: Make commit message conditional depending on whether it
is an addition or removal.
[changes]: Adjust indentation.
2022-05-31 14:52:13 -04:00
Maxim Cournoyer
6c956243bc
etc/committer: Prefix (sxml xpath) symbols to avoid name conflict.
This avoids a naming conflict for 'filter', provided by both (srfi srfi-1)
and (sxml xpath).

* etc/committer.scm.in: Use 'use-modules' instead of 'import', and use a
prefix for the (sxml xpath) module.
(new-sexp): Adjust accordingly.
(change-commit-message): Likewise.
2022-05-31 14:52:13 -04:00
Maxim Cournoyer
51b6715960
packages: Fix typo in package-superseded doc.
* guix/packages.scm (package-superseded): Fix typo.
2022-05-31 14:52:13 -04:00
Mark H Weaver
20432b839b
gnu: icecat: Update to 91.10.0-guix0-preview1 [security fixes].
Includes fixes for CVE-2022-31736, CVE-2022-31737, CVE-2022-31738,
CVE-2022-31739, CVE-2022-31740, CVE-2022-31741, CVE-2022-31742, and
CVE-2022-31747.

* gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.
2022-05-31 14:12:31 -04:00
Marius Bakke
be85c4d40f
gnu: ungoogled-chromium: Update to 102.0.5005.61-3.
* gnu/packages/chromium.scm (%ungoogled-revision): Bump to latest.
(%ungoogled-origin): Update hash.
2022-05-31 19:54:04 +02:00
Efraim Flashner
2c4c504272
gnu: python-sip-4: Update to 4.19.25.
* gnu/packages/qt.scm (python-sip-4): Update to 4.19.25.
2022-05-31 20:45:05 +03:00
Maxim Cournoyer
d11d27e2e4
gnu: guile-ac-d-bus: Run test suite.
* gnu/packages/patches/guile-ac-d-bus-fix-tests.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/guile-xyz.scm (guile-ac-d-bus)
[source]: Apply patch.
[phases]{check}: New phase.
[native-inputs]: Add bash-minimal.
2022-05-31 11:20:28 -04:00
Maxim Cournoyer
34c8558af2
gnu: guile-ac-d-bus: Build and install info manual.
* gnu/packages/guile-xyz.scm (guile-ac-d-bus)
[arguments]: Use gexps.
[phases]{build-doc, install-doc}: New phases.
[native-inputs]: Add texinfo.
2022-05-31 11:20:28 -04:00
Ricardo Wurmus
07909eb092
gnu: python-distributed: Update to 2022.05.2.
* gnu/packages/python-science.scm (python-distributed): Update to 2022.05.2.
[arguments]: Remove 'sanity-check phase; adjust 'check phase.
[propagated-inputs]: Add python-urllib3.
[native-inputs]: Add python-pytest-timeout and python-flaky.
2022-05-31 15:18:22 +02:00
Ricardo Wurmus
3d5144db5a
gnu: r-haven: Fix build.
* gnu/packages/cran.scm (r-haven)[arguments]: Adjust 'unbundle-readstat phase.

Reported-by: Jonas Freimuth.
2022-05-31 15:18:22 +02:00
Ricardo Wurmus
098d0012f5
gnu: python-fsspec: Update to 2022.5.0.
* gnu/packages/python-xyz.scm (python-fsspec): Update to 2022.5.0.
2022-05-31 15:18:22 +02:00
Pavel Shlyak
8b680b00d4
image: Add fat32 support.
* gnu/build/image.scm (make-vfat-image): Pass fs-bits as an argument and force
1kb logical sector size only if "ESP" flag is set.
(make-partition-image): Add "fat32" partition type, support explicit "fat16"
type with vfat alias.
* gnu/system/image.scm (partition->dos-type partition): Return file system IDs
for "fat16" and "fat32" partitions.
(partition->gpt-type partition): Ditto.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2022-05-31 14:51:13 +02:00
yarl baudig
6169c582d1
gnu: emacs-helpful: Update to 0.19
* gnu/packages/patches/emacs-helpful-docstring-test.patch: New file.
* gnu/packages/emacs-xyz.scm (emacs-helpful): Update to 0.19.
[source]: Use the patch.
* gnu/local.mk (dist_patch_DATA): Register the patch.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2022-05-31 06:16:18 +02:00
Pierre Langlois
b8fc3403d3
gnu: gandi.cli: Fix by downgrading python-click.
* gnu/packages/python-xyz.scm (python-click-7): New variable.
* gnu/packages/networking.scm (gandi.cli)[inputs]: Depend on python-click-7.
2022-05-30 22:18:21 +01:00
Pierre Langlois
f12d08c6d2
gnu: python-click@8: Remove redundant package.
The python-click package is already version 8.

* gnu/packages/python-xyz.scm (python-click-8): Remove variable.
(python-proselint)[propagated-inputs]: Depend on python-click.
2022-05-30 22:18:12 +01:00
Ricardo Wurmus
0bcd28e58c
gnu: python-scanpy: Update to 1.9.1.
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.1.
[arguments]: Add phase 'set-numba-cache-dir; disable more broken tests.
[propagated-inputs]: Add python-dask and python-session-info; replace
python-louvain-0.7 with python-louvain.
2022-05-30 23:09:46 +02:00
Ricardo Wurmus
ca2516f065
gnu: python-leidenalg: Update to 0.8.10.
* gnu/packages/graph.scm (python-leidenalg): Update to 0.8.10.
[arguments]: Patch setup.py.
[native-inputs]: Remove python-setuptools; add python-setuptools-scm.
2022-05-30 23:09:46 +02:00
Ricardo Wurmus
7c8f3dfa34
gnu: python-dask: Update to 2022.05.2.
* gnu/packages/python-xyz.scm (python-dask): Update to 2022.05.2.
2022-05-30 23:09:46 +02:00
Ricardo Wurmus
1257c4c663
gnu: Add python-session-info.
* gnu/packages/python-xyz.scm (python-session-info): New variable.
2022-05-30 23:09:46 +02:00
Ricardo Wurmus
216fb59b9b
gnu: non-sequencer: Update to 1.9.5-5.257ec59.
* gnu/packages/music.scm (non-sequencer): Update to 1.9.5-5.257ec59.
[source]: Use fork as old repository is defunct; use git-file-name and
git-version.
[arguments]: Remove python-2; add phase to replace bundled waf.
[native-inputs]: Add python-waf.
(non-session-manager)[native-inputs]: Add python-waf.
(non-mixer)[inputs]: Add lv2 and lilv.
[native-inputs]: Add python-waf.
(non-timeline)[native-inputs]: Add python-waf.
2022-05-30 23:09:46 +02:00
Liliana Marie Prikler
df43e8d45c
gnu: quodlibet: Correct wrappers.
* gnu/packages/music.scm (quodlibet)[#:phases]: Rename ‘wrap-gi-typelib’ to
‘wrap-extra-paths’.  Use ‘=’ for GI_TYPELIB_PATH.  Add
‘GST_PLUGIN_SYSTEM_PATH’ with suffix binding.
2022-05-30 21:28:53 +02:00
Ludovic Courtès
fed51b2614
gnu: calceph: Add 'release-monitoring-url' property.
* gnu/packages/astronomy.scm (calceph)[properties]: New field.
2022-05-30 16:34:41 +02:00
Sharlatan Hellseher
d730bbbbb3
gnu: Add calceph.
* gnu/packages/astronomy.scm (calceph): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-30 16:34:40 +02:00