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Author SHA1 Message Date
Nicolas Graves via Guix-patches via
229674573c
cve: Add cpe-vendor and lint-hidden-cpe-vendors properties. 
* guix/cve.scm: Exploit cpe vendors information.
(cpe->package-name): Rename to...
(cpe->package-identifier): Renamed from cpe->package-name. Use
cpe_vendor:cpe_name in place or cpe_name.
(vulnerabily-matches?): Add helper function.
(vulnerabilities->lookup-proc): Extract cpe_name for table
hashes. Add vendor and hidden-vendor arguments. Adapt condition to
pass vulnerabilities to result in the fold.
(write-cache, fetch-vulnerabilities): Update the format version.

* guix/lint.scm (package-vulnerabilities): Use additional arguments
from vulnerabilities->lookup-proc.

* tests/cve.scm (%expected-vulnerabilities): Adapt variable to changes
in guix/cve.scm.

Signed-off-by: Zheng Junjie <z572@z572.online>
 2025-06-23 12:31:09 +08:00
jgart
f511be7bcc
gnu: trealla: Update to 2.74.23. 
* gnu/packages/prolog.scm (trealla): Update to 2.74.23.

Change-Id: Iaee68925dc45e05e8309d80332c1ee1c020aef1f
 2025-06-22 21:24:19 -04:00
jgart
fa75614243
gnu: dex: Enable verbose flag for tests. 
* gnu/packages/xdisorg.scm (dex)[arguments]: Enable verbose flag for tests.

Change-Id: I05742e954c704833c032db1add9673a18e6b3e80
 2025-06-22 21:20:57 -04:00
Andrew Wong
72902b4199
gnu: dex: Update to 0.10.1. 
* gnu/packages/xdisorg.scm (dex): Update to 0.10.1.
[arguments]: Switch to G-expressions and implement tests.
[description]: Mention autostart functionality.

Change-Id: I8462ce6de80bdf46594b39caee36488fcd2cd810
Signed-off-by: jgart <jgart@dismail.de>
 2025-06-22 21:20:57 -04:00
Vinicius Monego
1cbe0d7db6
gnu: python-textual: Update to 3.5.0. 
* gnu/packages/python-xyz.scm (python-textual): Update to 3.5.0.
[arguments]<#:test-flags>: Update failing tests.
[propagated-inputs]: Remove python-mdit-py-plugins. Add
python-platformdirs.
[native-inputs]: Add python-pytest-xdist.

Change-Id: I7ff7d663e223da8b7ff924a863a419be11bd478e
 2025-06-22 22:04:18 -03:00
Vinicius Monego
f4f6d9ac7e
gnu: python-ueberzug: Update to 18.3.1. 
* gnu/packages/python-xyz.scm (python-ueberzug): Update to 18.3.1.
[build-system]: Use pyproject-build-system.
[arguments]: Skip the 'check' phase.
[native-inputs]: Add meson-python, pkg-config.
[inputs]: Add libxres.
[propagated-inputs]: Remove python-xlib.
[home-page]: Switch to maintained repository.

Change-Id: Ia93f8d98767e0887b3f18335a5e4bfc8d925abf7
 2025-06-22 22:04:17 -03:00
Vinicius Monego
73b7e4686a
gnu: python-logbook: Update to 1.8.2. 
* gnu/packages/python-xyz.scm (python-logbook): Update to 1.8.2.
[source]: Update URI.
[build-system]: Use pyproject-build-system.
[arguments]<#:phases>: Delete unnecessary phase 'cythonize-sources'. Do
not override the 'check' phase.
[native-inputs]: Remove python-cython, python-mock,
python-pytest-cov. Add python-cython-3, python-setuptools, python-wheel.

Change-Id: I4b4c8ea60bc0ad7fdcb4d5320e5337f3ca38ed6f
 2025-06-22 22:04:17 -03:00
Ludovic Courtès
99f85246e1
git authenticate: Do nothing when invoked from the keyring branch. 
Fixes <https://issues.guix.gnu.org/78283>.

* guix/scripts/git/authenticate.scm (guix-git-authenticate): Call
‘current-branch’ and do nothing if it returns the keyring branch.

Reported-by: Vagrant Cascadian <vagrant@debian.org>
Change-Id: I66c2a3f4babf68ac1df0913db6bc708ac0c7968e
 2025-06-22 23:45:36 +02:00
Ludovic Courtès
0ec5cab132
git authenticate: Gracefully handle passing an annotated tag to ‘--end’. 
Partly fixes <https://issues.guix.gnu.org/74583>.

Previously, passing an annotated tag to ‘--end’, as can happen when
‘guix git authenticate’ is invoked by the pre-push hook when pushing
tags, would lead to an error:

  guix git: error: Git error: the requested type does not match the type in the ODB

* guix/scripts/git/authenticate.scm (ensure-commit-id): New procedure.
(guix-git-authenticate): Use it.
* tests/guix-git-authenticate.sh: Test with $v1_2_0_annotated_tag.

Change-Id: I22e8eb665609522c80c1f0dcb9e77a46c23c0c3c
 2025-06-22 23:45:36 +02:00
Ludovic Courtès
56eb949f3b
git authenticate: Upgrade pre-push hook with a fixed version. 
Partly fixes <https://issues.guix.gnu.org/74583>.

* guix/scripts/git/authenticate.scm (%pre-push-hook): New variable.
(install-hooks): Use it.
(broken-pre-push-hook?, maybe-upgrade-hooks): New procedures.
(guix-git-authenticate): Call ‘maybe-upgrade-hooks’ when ‘configured?’
returns true.

Change-Id: I39d34ab66ffe0f34170c0f562e9f97f2f69c9fdc
 2025-06-22 23:45:36 +02:00
Ludovic Courtès
55b38ddefc
git authenticate: Remove support for Guile-Git < 0.7.0. 
Guile-Git 0.7.0 was released in May 2024.

* guix/scripts/git/authenticate.scm (record-configuration): Remove
‘module-defined?’ condition for Guile-Git < 0.7.0.
(install-hooks): Likewise.

Change-Id: I27af82068b989d6a18ff1a66453e0a8d397ed380
 2025-06-22 23:45:32 +02:00
Brice Waegeneire
a9548c198c
gnu: qgis: Fix build. 
Fixing #723.

* gnu/packages/geo.scm (python-sip-6.8-instead-of-python-sip): New procedure.
(python-pyqt+qscintilla-with-python-sip-6.8, python-sip-6.8): New variables.
(qgis)[inputs]: Add python-lxml. Replace python-pyqt+qscintilla with
python-pyqt+qscintilla-with-python-sip-6.8 and python-sip with
python-sip-6.8.

Change-Id: I0f845400012d381cb4d78aadc3b1e2a47f6c3090
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 22:27:29 +01:00
wrobell
437809ffe2
gnu: python-charset-normalizer-3: Update to 3.4.2. 
* gnu/packages/python-xyz.scm (python-charset-normalizer-3): Update to
  3.4.2.
  [build-system]: Use pyproject-build-system.
  [arguments] <phases>: Add 'fix-scripts.
  [native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I32c89a63c3fd1aaf3c323d4986808b7860c2d999
Co-authored-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 22:02:02 +01:00
Liam Hupfer
36dc401bbd
gnu: fzf: Use bashrc.d for Bash integration. 
fzf comes with two Bash integration files.

The first, completion.bash, enables fzf-powered completion of various
types (files, variable names, processes, etc) for various commands (cat,
export, kill, etc).  This is in contrast with the Bash completions most
packages ship, which are based on the bash-completion package and only
include completions for the package binaries.  The bash-completion
package lazily loads completions from bash_completion.d directories when
the user invokes completion for a given command.  fzf’s completion.bash
shouldn’t be installed to etc/bash_completion.d/fzf, since it doesn’t
depend on bash-completion and it supplies completions for more than just
the fzf binary.  Instead, install it to the more general bashrc.d, where
users can source it so fzf-powered completions are immediately available
for common commands.

The second, key-bindings.bash, provides fzf-based history search for C-r
as well as a couple other convenient bindings. Install it to bashrc.d as
well so users can source it.

* gnu/packages/terminals.scm (fzf): [phases]{install-completions}: Use
bashrc.d for Bash integration files.

Change-Id: Ied0ec1187a04bcc74d39ee22957fc9b4573b5992
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 21:38:04 +01:00
Sharlatan Hellseher
a706e205cf
gnu: gopls: Move to golang-apps. 
* gnu/packages/golang-xyz.scm (gopls): Move from here ...
* gnu/packages/golang-apps.scm: ... to here.

Change-Id: I4132af631198bffe36f6defb1e5390ab1326242f
 2025-06-22 21:36:44 +01:00
Sharlatan Hellseher
a599ff7a48
gnu: packages/golang-apps: Add module commentary. 
* gnu/packages/golang-apps.scm: Comment on the purpose of this module.

Change-Id: Ia1353db23b23f2ac992f72c64dd9a139252d0107
 2025-06-22 21:36:44 +01:00
Sharlatan Hellseher
cdac3642fd
gnu: Rename go-apps to golang-apps. 
It's to follow the same naming style as other golang.scm and
golang-*.scm modules.

* gnu/packages/go-apps.scm: Rename file to golang-apps.scm
* gnu/local.mk (GNU_SYSTEM_MODULES): Rename go-apps to golang-apps.
* gnu/packages/emacs-xyz.scm: Replace used module go-apps with golang-apps.

Change-Id: I72642f2f6ea1cb3382e17b637cab52aa79d910c9
 2025-06-22 21:36:44 +01:00
Maxim Cournoyer
fa1eababe3
gnu: Add gomacro. 
* gnu/packages/go-apps.scm (gomacro): New variable.

Change-Id: Ie3575a72baacb2ea3010d727d27f2d50749f93ea
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 21:36:44 +01:00
jgart
8f97502396
gnu: python-diskcache: Update to 5.6.3. 
* gnu/packages/python-xyz.scm (python-diskcache): Update to 5.6.3.
[source]: Use GitHub origin since PyPI missing docs which are needed for
tests.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add required native-inputs.

Change-Id: I169c24c02356407902a69cc4937a4761be47b6e6
 2025-06-22 15:54:19 -04:00
Cayetano Santos
60c6133a98
gnu: emacs-guix: Update to 0.5.2-8.66b9350. 
* gnu/packages/emacs-xyz.scm (emacs-guix): Update to 0.5.2-8.66b9350.
[source]: Update URL.

Change-Id: Ie6ebba6ff4e070ca03de91f4e316f6e48707e37d
Signed-off-by: Ian Eure <ian@retrospec.tv>
 2025-06-22 12:42:40 -07:00
Giacomo Leidi
1aca7d3be8
gnu: prometheus-postgres-exporter. 
* gnu/packages/monitoring.scm (prometheus-postgres-exporter): New variable.

Change-Id: I32c922244dbd485d0b882e7b150fc8c7d5624875
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 18:09:25 +01:00
Vinicius Monego
8696eca5c0
gnu: python-pyjanitor: Update to 0.31.0. 
* gnu/packages/python-science.scm (python-pyjanitor): Update to 0.31.0.
[arguments]<#:test-flags>: Skip tests depending on Polars. Enable
previously failing test.
<#:phases>: Delete unnecessary phase 'pandas-compat'.

Change-Id: I2991e06fafea2928bb6ea45c42624bf372da2eba
 2025-06-22 12:41:00 -03:00
Vinicius Monego
e660638d0d
gnu: python-pingouin: Update to 0.5.5. 
* gnu/packages/python-science.scm (python-pingouin): Update to 0.5.5.
[arguments]<#:test-flags>: Enable previously failing test. Skip two more
failing tests.
<#:phases>: Delete unnecessary phases 'loosen-requirements',
'remove-outdated-check', 'sklearn-compatibility'.

Change-Id: Iac44747d65c9be52831ae792a24b9cc5604c54dc
 2025-06-22 12:41:00 -03:00
Vinicius Monego
d32e619d47
gnu: python-simple-pid: Update to 2.0.1. 
* gnu/packages/python-science.scm (python-simple-pid): Update to 2.0.1.
[source]: Update URI.
[build-system]: Use pyproject-build-system.
[arguments]<#:phases>: Do not override the 'check' phase.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.

Change-Id: I26c7b3097d30ac067a370c8a3a0600779d13efb6
 2025-06-22 12:41:00 -03:00
Vinicius Monego
4a38059258
gnu: python-pandas-flavor: Update to 0.7.0. 
* gnu/packages/python-science.scm (python-pandas-flavor): Update to
0.7.0.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-pytest.

Change-Id: Ie582c778d84b342eab41f8bc88f2c4bb410bbbb6
 2025-06-22 12:40:59 -03:00
Vinicius Monego
5b983cd239
gnu: python-baycomp: Update to 1.0.3. 
* gnu/packages/python-science.scm (python-baycomp): Update to 1.0.3.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.

Change-Id: I2249fc981a91ebc175a5e0ff221bb6243126fb6f
 2025-06-22 12:40:59 -03:00
Cayetano Santos
d437b9cb46
gnu: emacs-org-roam-bibtex: Update to 0.6.2-0.b065198. 
* gnu/packages/emacs-xyz.scm (emacs-org-roam-bibtex): Update to 0.6.2-0.b065198.

Change-Id: I6db838df4a9b120c0bfda964cf5fe1d903a1e571
Signed-off-by: jgart <jgart@dismail.de>
 2025-06-22 11:29:05 -04:00
Vinicius Monego
272fc9c223
gnu: pelican: Enable tests. 
* gnu/packages/python-xyz.scm (pelican)[arguments]: Remove '#:tests?'.
<#:test-flags>: Skip three failing tests.
[native-inputs]: Add python-anyio, python-beautifulsoup4, python-lxml,
python-pytest, python-smartypants, python-typogrify.

Change-Id: Ibcbfa1a405753bfcf68028be86a90c1c318cb1b7
 2025-06-22 11:21:48 -03:00
Vinicius Monego
a4892265fa
gnu: pelican: Update to 4.11.0. 
* gnu/packages/python-xyz.scm (pelican): Update to 4.11.0.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-pdm-backend.
[inputs]: Remove python-markdown, python-pytz. Add python-ordered-set,
python-tzdata, python-watchfiles.

Change-Id: I586668a17b7b646227a5bd78703fda2c9bc6fb63
 2025-06-22 11:21:48 -03:00
Vinicius Monego
a44710fc63
gnu: python-feedgenerator: Update to 2.1.0. 
* gnu/packages/python-xyz.scm (python-feedgenerator): Update to 2.1.0.
[source]: Remove unnecessary snippet.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-pytest, python-pytest-cov,
python-setuptools, python-wheel.
[propagated-inputs]: Remove python-six.

Change-Id: I2451794d21c0c473183f9f90f14ad8b198883455
 2025-06-22 11:21:48 -03:00
Vinicius Monego
97b3b63fcd
gnu: python-scapy: Update to 2.6.1. 
* gnu/packages/python-xyz.scm (python-scapy): Update to 2.6.1.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-setuptools, python-wheel.

Change-Id: I56f0f87e0eb1a49bd79cad6f36451dfdd6eb78e0
 2025-06-22 11:21:44 -03:00
Kjartan Oli Agustsson
f731d71846
gnu: tetoolkit: Run guix style 
* gnu/packages/bioinformatics.scm (tetoolkit): Run guix style.

Change-Id: I5f4c6a647a41a9d60e5bc1d2b4fbee045626dc12
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:11 +01:00
Kjartan Oli Agustsson
09a3e09fa8
gnu: tetoolkit: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (tetoolkit): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I4fce644bee87c5d6c64a9a3cdf3581a1bae12909
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:11 +01:00
Kjartan Oli Agustsson
825ceadb5f
gnu: tbsp: Run guix style 
* gnu/packages/bioinformatics.scm (tbsp): Run guix style.

Change-Id: I3301f95963aac1f47b28e86a40374df2171732f8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:11 +01:00
Kjartan Oli Agustsson
8ed2fcd5aa
gnu: tbsp: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (tbsp): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I6d454d95050862378b7f06c09a42994efd9875a6
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:11 +01:00
Kjartan Oli Agustsson
abeb7cd9fa
gnu: stpipeline: Run guix style 
* gnu/packages/bioinformatics.scm (stpipeline): Run guix style.

Change-Id: I341e0b7adce82c079b1dcff94a2128d3e1773a4a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
3bb992a357
gnu: stpipeline: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (stpipeline): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Ibfeea2feb08878d14becf15be5408689ba4c7c3f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
18d5c62c6a
gnu: python-vireosnp: Run guix style 
* gnu/packages/bioinformatics.scm (python-vireosnp): Run guix style.

Change-Id: I301322fbfa45b3ef7cb1c82eadc60aa1de33d442
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
b7ec773e5a
gnu: python-vireosnp: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-vireosnp): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Id49911001b3672402a17f0902a7e5a565168ab61
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
002d6e4109
gnu: python-velocyto: Run guix style 
* gnu/packages/bioinformatics.scm (python-velocyto): Run guix style.

Change-Id: Ieda2b56cf13ae519e539ecef286ef63595532a7a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
5853163fbf
gnu: python-velocyto: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-velocyto): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Ie5e605136a7eb7a1acd3850313f2796bf7c83c31
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
5eebea1b76
gnu: python-slamdunk: Run guix style 
* gnu/packages/bioinformatics.scm (python-slamdunk): Run guix style.

Change-Id: I5235a49f7c2d128df6c903f35908fefe022fd50a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
9aff205c4f
gnu: python-slamdunk: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-slamdunk): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I935dd9a0a7c08985dfb7ca989346783ebf024d50
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
15c4134067
gnu: python-scanorama: Run guix style 
* gnu/packages/bioinformatics.scm (python-scanorama): Run guix style.

Change-Id: I43bfbe845f6e54dab94c6e0055ee811f70026ab4
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
492035dfa8
gnu: python-scanorama: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-scanorama): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Ie437414bff54c361ab61ee2e9baea670762c9ce5
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
673a485a6b
gnu: python-pyliftover: Run guix style 
* gnu/packages/bioinformatics.scm (python-pyliftover): Run guix style.

Change-Id: I45bf0066db834fd99a2bbc1e64d4bc3e20e92cde
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
66ab4c5bc1
gnu: python-pyliftover: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-pyliftover): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Ifcdbfba497527edd82625a20e4baf6b2504f3f92
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
0809db9016
gnu: python-pyfit-sne: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-pyfit-sne): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I8f62f2dc30d2bd182a791830bb835adf778d2ecf
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
247afd63f2
gnu: python-ikarus: Run guix style 
* gnu/packages/bioinformatics.scm (python-ikarus): Run guix style.

Change-Id: I493beb55986808a8ba27eadcc48d8a2a20b1678e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
1ff6229402
gnu: python-ont-fast5-api: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-ont-fast5-api): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Idb3b5a65767998e232fcc31534cb923ea6f5fed8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:09 +01:00