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Author SHA1 Message Date
Ricardo Wurmus
e4e43cebba
gnu: r-chromunity: Update to 0.0.2-2.101e30a.
* gnu/packages/bioinformatics.scm (r-chromunity): Update to 0.0.2-2.101e30a.
[arguments]: Disable one test.

Change-Id: I522e993d86cf88914a95c9fb15d933c7af906c41
2025-05-12 08:55:51 +02:00
Ricardo Wurmus
901020cdeb
gnu: pigx-scrnaseq: Use Snakemake 5.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-7
with snakemake-5.
[arguments]: Set HOME.

Change-Id: I45257e138c4cf468d179ff35b0c705bc73046052
2025-05-12 08:55:51 +02:00
Ricardo Wurmus
d6f9f9b585
gnu: pigx-bsseq: Set HOME.
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Add phase 'pre-check.

Change-Id: Ic88976554e6e7c7955ae9ab4f0232330060446c9
2025-05-12 08:55:50 +02:00
Ricardo Wurmus
c80e1e958b
gnu: pigx-chipseq: Set HOME.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Add phase 'pre-check.

Change-Id: Ia95db9209b5ea0cb340f9827197bdcc851266961
2025-05-12 08:55:50 +02:00
Ricardo Wurmus
b0aaf60a38
gnu: pigx-rnaseq: Set HOME.
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'pre-check.

Change-Id: Ibabfa8f14b8eaec6d25ae72a2cd0f33e6a7d2819
2025-05-12 08:55:50 +02:00
Ricardo Wurmus
d05e09fb61
gnu: pigx-sars-cov-2: Use Snakemake 7.
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[inputs]: Replace snakemake
with snakemake-7.

Change-Id: I059ea25c0e4a45e42f8f288cd92f548b9684e624
2025-05-12 08:55:50 +02:00
Ricardo Wurmus
fdc8303a27
gnu: pigx-scrnaseq: Use Snakemake 7.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake
with snakemake-7.

Change-Id: I9b903dba192e862d3b5b6ca4e0018ed88069937d
2025-05-12 08:55:49 +02:00
Ricardo Wurmus
150ecd1579
gnu: pigx-bsseq: Use Snakemake 7.
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake
with snakemake-7.

Change-Id: If82236f94d46c8e1f7f325e6eaf76f68397218d1
2025-05-12 08:55:49 +02:00
Ricardo Wurmus
c43c9f9849
gnu: pigx-chipseq: Use Snakemake 7.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake
with snakemake-7.

Change-Id: Ib4d7d95713be3535b44ad10b655cf1a217048121
2025-05-12 08:55:49 +02:00
Ricardo Wurmus
46ccde1476
gnu: pigx-rnaseq: Use Snakemake 7.
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace snakemake
with snakemake-7.

Change-Id: I2ab8af1438b59c3d36951b5901aeb57039b4aafc
2025-05-12 08:55:49 +02:00
Nicolas Goaziou
1a8b36329f
gnu: texlive-libkpathsea: Tweak "texmf.cnf" variables.
* gnu/packages/tex.scm (texlive-libkpathsea): Use XDG variables instead of
HOME for cache and user configuration.  Re-instate TEXMFLOCAL, which may be
necessary for external TeX installations.
(texlive-luatex): Re-instate TEXFLOCAL.
* gnu/packages/algebra.scm (gap):
* gnu/packages/assembly.scm (asl):
(yaehmop):
* gnu/packages/bioinformatics.scm (discrover):
* gnu/packages/chez.scm (chez-scheme-for-racket):
* gnu/packages/engineering.scm (fastcap):
* gnu/packages/fsf.scm (book-faif):
* gnu/packages/maths.scm (hypre):
(stex-boostrap):
(suitesparse-amd):
(suitesparse-camd):
(suitesparse-cholmod):
(suitesparse-klu):
(suitesparse-ldl):
(suitesparse-mongoose):
(suitesparse-spex):
(suitesparse-spqr):
(suitesparse-umfpack):
* gnu/packages/ocaml.scm (ocaml-bibtex2html):
(unison):
* gnu/packages/python-xyz.scm (python-nbconvert):
* gnu/packages/statistics.scm (r-with-tests)[arguments]: Set TEXMFVAR to
a writable location.

Change-Id: I3d2d069cf41a92214d9d6fb7f4d54fc81fe6db7a
2025-05-06 11:25:07 +02:00
Nicolas Goaziou
b1ef3bce13
gnu: Update TeX Live to 2025.2.
* gnu/packages/tex.scm:  Update TeX Live to 2025.2.
* gnu/packages/bioinformatics.scm (discrover):
* gnu/packages/python-xyz.scm (python-nbconvert): Remove texlive-ms package.

Change-Id: Ia6c6753ddb889413522e3351f38a95dd24912984
2025-05-06 11:25:07 +02:00
Nicolas Goaziou
4df6eda30f
gnu: Rename texlive-updmap.cfg' into texlive-local-tree'.
* doc/build.scm (pdf-manual):
* doc/contributing.texi (Submitting Patches):
* gnu/packages/algebra.scm (pari-gp):
(giac):
* gnu/packages/assembly.scm (asl):
* gnu/packages/audio.scm (chow-tape-model):
* gnu/packages/bioconductor.scm (r-biocstyle):
* gnu/packages/bioinformatics.scm (discrover):
(phyml):
(velvet):
* gnu/packages/chemistry.scm (yaehmop):
* gnu/packages/chez.scm (chez-scheme-for-racket):
(stex-bootstrap):
(chez-web):
(chez-sockets):
* gnu/packages/cran.scm (r-papaja):
(r-prereg):
* gnu/packages/docbook.scm (dblatex):
* gnu/packages/emacs-xyz.scm (emacs-auctex):
* gnu/packages/engineering.scm (fastcap):
* gnu/packages/finance.scm (optionmatrix):
* gnu/packages/fsf.scm (book-faif):
* gnu/packages/gettext.scm (po4a):
(po4a-minimal):
* gnu/packages/graphics.scm (mmg):
* gnu/packages/graphviz.scm (dot2tex):
* gnu/packages/guile-xyz.scm (emacsy):
(guile-cv):
* gnu/packages/lisp.scm (sbcl):
* gnu/packages/maths.scm (cddlib):
(gnuplot):
(itpp):
(octave):
(suitesparse-amd):
(suitesparse-camd):
(suitesparse-cholmod):
(suitesparse-klu):
(suitesparse-ldl):
(suitesparse-mongoose):
(suitesparse-spex):
(suitesparse-spqr):
(suitesparse-umfpack):
(hypre):
* gnu/packages/music.scm (lilypond):
* gnu/packages/ocaml.scm (unison):
(ocaml-bibtex2html):
* gnu/packages/pdf.scm (extractpdfmark):
* gnu/packages/photo.scm (enblend-enfuse):
* gnu/packages/plotutils.scm (asymptote):
* gnu/packages/python-xyz.scm (python-numpy-documentation):
(python-ipython-documentation):
(python-pypandoc):
* gnu/packages/radio.scm (gnuradio):
(libosmo-dsp):
* gnu/packages/scheme.scm (mit-scheme):
* gnu/packages/security-token.scm (yubico-piv-tool):
* gnu/packages/sphinx.scm (python-sphinx):
(python-sphinx-5):
* gnu/packages/statistics.scm (r-with-tests):
(r-spams):
* gnu/packages/tex.scm (texlive-local-tree): Renamed from…
(texlive-updmap.cfg): … this. Deprecate the latter.
(texlive-biblatex-philosophy):
(texlive-bropd):
(texlive-fontsize):
(texlive-poetrytex):
(texlive-reverxii):
(texlive-stix):
(texlive-suftesi):
(texlive-thucoursework):
(texlive-ulqda):
(texlive-yathesis):
(texlive-makecell):
(texlive-robotarm):
(texlive-bbold):
(texlive-babel-romansh):
(texlive-polyglossia):
(texlive-innerscript):
(teximpatient):
(texlive-xkeyval):
(texlive-arabxetex):
(texlive-blox):
(texlive-ecgdraw):
(texlive-gradientframe):
(texlive-everyhook):
(texlive-actuarialangle):
(texlive-actuarialsymbol):
(texlive-autopdf):
(texlive-etaremune):
(texlive-extract):
(texlive-forarray):
(texlive-graphicx-psmin):
(texlive-ha-prosper):
(texlive-namespc):
(texlive-newspaper):
(texlive-powerdot):
(texlive-recipecard):
(texlive-show2e):
(texlive-tablists):
(texlive-ted):
(texlive-xargs):
(texlive-xpeek):
* gnu/packages/xdisorg.scm (xforms):
* gnu/packages/algebra.scm (gap):
* gnu/packages/cpp.scm (jthread):
* guix/lint.scm (check-inputs-should-be-native): Rename `texlive-updmap.cfg' into `texlive-local-tree'.

Change-Id: I129280807c418e57acbcbda399545ab27a9e0a33
2025-05-06 11:25:06 +02:00
Sharlatan Hellseher
668fcb2418
gnu: python-muon: Update to 0.1.7.
* gnu/packages/bioinformatics.scm (python-muon): Update to 0.1.7.
[arguments] <test-flags>: Skip 2 failing tests.

Change-Id: I178efe9e54246130f6b467f0245495b820a6a303
2025-05-04 10:42:48 +01:00
Andreas Enge
3c1191b96e
gnu: r-velocyto: Remove deprecated input.
* gnu/packages/bioinformatics.scm (r-velocyto)[propagated-inputs]: Remove
r-h5.

Change-Id: I3c624833f933d1b1bf8b5fd9d7fa81e3ac4d44c4
2025-04-29 11:48:54 +02:00
Andreas Enge
7431232496
gnu: Remove variant-tools.
The package does not compile any more and has no dependent packages.
The last release dates from 2020; there is an additional commit in 2022;
the git repository has been archived in 2023.

* gnu/packages/bioinformatics.scm (variant-tools): Delete variable.

Change-Id: Idb5df024121c5085f764f179d31ac67cff3fc5c7
2025-04-29 11:34:51 +02:00
Nicolas Graves
bfdf6a85b8
gnu: python-bed-reader: Improve phases' style.
* gnu/packages/bioinformatics.scm (python-bed-reader)
[arguments]{phases}: Improve phases 'install-python-library and
'check-python with site-packages procedure.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-24 04:53:41 +01:00
Sharlatan Hellseher
6c09bf9434
gnu: python-mgatk: Update to 0.7.0.
* gnu/packages/bioinformatics.scm (python-mgatk): Update to 0.7.0.
[arguments] <phases>: Remove 'python3-compatibility as resolved
upstream.

Change-Id: I389dd546f4a112bf52758c216baedfdcf0613bf9
2025-04-19 10:17:34 +01:00
Nicolas Graves
ea99274af3
gnu: cnvkit: Update to 0.9.12.
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.12.
[build-system]: Switch to pyproject.
[native-inputs]: Add python-setuptools, python-wheel.

Change-Id: Ia48f681ac2c45872c92214d685819579a40eae7a
Signed-off-by: Steve George <steve@futurile.net>
2025-04-16 11:46:31 +02:00
Sharlatan Hellseher
6cd3a6595f
gnu: python-decoupler-py: Update to 1.8.0.
* gnu/packages/bioinformatics.scm (python-decoupler-py): Update to 1.8.0.
[arguments] <phases>: Add 'relax-requirements.
[native-inputs]: Remove python-wheel; add python-poetry-core.

Change-Id: I6ef7548dcbe90c87e049fef12402bcc58f807ce4
2025-04-16 11:46:29 +02:00
Nicolas Graves
e58d654373
gnu: python-pysnptools: Fix build and enable tests.
* gnu/packages/bioinformatics.scm (python-pysnptools): Fix build and enable
tests.
[arguments]{test-flags}: Ignore failing tests.
{phases}: Add 'patch-data-path and 'loosen-requirements phases.

(pysnptools-examples-files): Add origin.
(bgen-sample-files): Add origin.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:28 +02:00
Nicolas Graves
db14ce5c4d
gnu: python-bed-reader: Fix build and enable tests.
* gnu/packages/bioinformatics.scm (python-bed-reader): Fix build and enable tests.
[source]{snippet}: Delete bundled website-related javascript.
{patches}: Use the store-cached instead of pooch-cached samples.
[arguments]{tests?}: Enable them.
{cargo-test-flags}: Skip doc tests. Skip failing tests.
{cargo-inputs}: Improve style.
{cargo-development-inputs}: Improve style.
{phases}: Add phases 'set-data-path, 'patch-data-path to use
store-cached samples for library and tests.  Rewrite phase
'prepare-python-module to rely more on the existing info in
pyproject.toml.  Rewrite phase 'check-python entirely, and
marginaly rewrite phase 'install-python-library to match 'check-python
phase style.
{modules}: Adapt accordingly.
{propagated-inputs}: Remove python-pooch. Add python-scipy.

(bed-sample-files): Add origin, used in python-bed-reader.

* gnu/packages/patches/python-bed-reader-use-store-samples.patch: Add
patch.
* gnu/local.mk: Record patch.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:28 +02:00
Nicolas Graves
e01edc1146
gnu: mageck: Add missing native-inputs.
* gnu/packages/bioinformatics.scm (mageck)[native-inputs]: Add
python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:26 +02:00
Nicolas Graves
89a891a7e1
gnu: scregseg: Add missing native-inputs.
* gnu/packages/bioinformatics.scm (scregseg)[native-inputs]: Add
python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:26 +02:00
Nicolas Graves
29661328c7
gnu: umi-tools: Update to 1.1.6.
* gnu/packages/bioinformatics.scm (umi-tools): Update to 1.1.6.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[inputs]: Add python-pybktree, python-scipy.
[native-inputs]: Add python-setuptools, python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:25 +02:00
Nicolas Graves
a5d3be8a89
gnu: taxtastic: Update to 0.11.1.
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.11.1.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Ignore failing test.
{phases}: Improve style with gexp. Update phase
'prepare-directory. Improve phase 'check with test-flags inclusion.
[native-inputs]: Add python-setuptools, python-wheel.
[propagated-inputs]: Sort inputs. Replace python-psycopg2 by both
python-psycopg and python-psycopg2-binary. Add python-sqlparse.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:24 +02:00
Nicolas Graves
5139f5e47f
gnu: Remove python-pyfasta.
This package is archived and deprecated in favor or python-pyfaidx for
7 years.

* gnu/packages/bioinformatics.scm (python-pyfasta): Delete variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:24 +02:00
Nicolas Graves
4d8be83440
gnu: seqmagick: Update to 0.8.6-0.dee6ab9.
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.6-0.dee6ab9.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:24 +02:00
Nicolas Graves
0b875355d5
gnu: rseqc: Switch to pyproject-build-system.
* gnu/packages/bioinformatics.scm (rseqc):
[build-system]: Switch to pyproject-build-system.
[inputs]: Sort inputs. Add python-pyparsing, python-setuptools,
python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:24 +02:00
Nicolas Graves
31a494c658
gnu: python-pyvcf: Use the fork python-pyvcf3.
* gnu/packages/bioinformatics.scm (python-pyvcf): Define in terms of
'deprecated-package'.
(python-pyvcf3): New variable.
(python-nanosv): Replace python-pyvcf by python-pyvcf3.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:24 +02:00
Sharlatan Hellseher
1a3482af80
gnu: python-ont-fast5-api: Update to 4.1.3.
* gnu/packages/bioinformatics.scm (python-ont-fast5-api): Update to 4.1.3.

Change-Id: I8dc6f2a911624b62fbf419b28cfad840200a207c
2025-04-16 11:46:23 +02:00
Sharlatan Hellseher
1e46fbd812
gnu: python-iced: Update to 0.5.13.
* gnu/packages/bioinformatics.scm (python-iced): Update to 0.5.13.
[native-inputs]: Add python-pytest, python-setuptools, and python-wheel.

Change-Id: I2251b0ba37dab29bf82a2db73be1e05fee11c34e
2025-04-16 11:46:23 +02:00
Sharlatan Hellseher
8afbc6f9ac
gnu: python-peaks2utr: Update to 1.4.1 and fix build.
* gnu/packages/bioinformatics.scm (python-peaks2utr): Update to 1.4.1.
[arguments] <test-flags>: Skip 2 more similar failing test.
<phases>: Add 'relax-requirements.

Change-Id: Ia26903116915c4ef031b4a6bdb5dae64d109a1f4
2025-04-16 11:46:22 +02:00
Sharlatan Hellseher
18a2ef9c62
gnu: python-gffutils: Update to 0.13 and fix build.
* gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.13.
[build-system]: Swap to pypproject-build-system.
[arguments] <phases>: Use default 'check, add 'set-HOME.
[propagated-inputs]: Remove python-six.
[native-inputs]: Remove python-nose; add python-pytest,
python-setuptools, and python-wheel.

Change-Id: I77b1ed5be8750bdd2f2cdff3135430207b80f6fc
2025-04-16 11:46:22 +02:00
Sharlatan Hellseher
a7885e4b3d
gnu: python-parabam: Add a maintenance note.
* gnu/packages/bioinformatics.scm (python-parabam): Add a maintenance
note on package build issue, reported upstream.

Change-Id: I447fa2354a2318b19d0eca5acf844a574e49db09
2025-04-16 11:46:22 +02:00
Nicolas Graves
a759a6f342
gnu: python-pegasusio: Update to 0.9.1.
* gnu/packages/bioinformatics.scm (python-pegasusio): Update to 0.9.1.
[propagated-inputs]: Add python-cython, python-setuptools. Remove
python-importlib-metadata.
[native-inputs]: Styling from guix style.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:21 +02:00
Nicolas Graves
0edfbc0475
gnu: python-cell2cell: Update to 0.7.4.
* gnu/packages/bioinformatics.scm (python-cell2cell): Update to 0.7.4.
[source]{origin}: Relax requirements in snippet.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:21 +02:00
Nicolas Graves
7bf4329019
gnu: crossmap: Add missing python-pyparsing native-input.
* gnu/packages/bioinformatics.scm (python-pyparsing)[native-inputs]:
Add python-pyparsing.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:21 +02:00
Nicolas Graves
5b6622c4e9
gnu: python-bx-python: Update to 0.13.0.
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.13.0.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:20 +02:00
Nicolas Graves
591908f804
gnu: pairadise: Add missing native-inputs.
* gnu/packages/bioinformatics.scm (pairadise)[native-inputs]: Add
python-setuptools and python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:20 +02:00
Nicolas Graves
d8b3d0ec8e
gnu: python-biom-format: Update to 2.1.16.
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.16.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:20 +02:00
Ricardo Wurmus
8a0e82f26d
gnu: python-biopython-1.73: Make compatible with Python 3.11.
* gnu/packages/bioinformatics.scm (python-biopython-1.73)[arguments]: Add
phases 'python3.11-compatibility, 'numpy-compatibility, 'set-home,
'build-extensions, and 'patch-tests.

Change-Id: Iac6b0638dd5699a7b11862bff9cce1e7b2fee49b
2025-04-16 11:46:19 +02:00
Ricardo Wurmus
ca3d1683d7
gnu: python-biopython: Update to 1.85.
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.85.
[arguments]: Add phase 'numpy-compatibility; replace 'check phase.

Change-Id: I4e3ef0d9a357155e36ef61052af4d90f4fa95d5e
2025-04-16 11:46:19 +02:00
Ricardo Wurmus
eb70b7c57f
gnu: bedtools: Update to 2.31.1.
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.31.1.

Change-Id: I9f104d68fbdc2040fee41f1565d48a40999bc219
2025-04-16 11:46:17 +02:00
Ricardo Wurmus
6fa27ee0f4
gnu: python-pysam: Update to 0.23.0.
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.23.0.
[arguments]: Use #:test-flags instead of custom 'check phase; add 'pre-check
phase.

Change-Id: I92c715d5dfd5cbdbcf6dd61fc5e472f6c6ca977d
2025-04-16 11:46:17 +02:00
Ricardo Wurmus
80bdd80e52
gnu: htscodecs: Update to 1.6.1.
* gnu/packages/bioinformatics.scm (htscodecs): Update to 1.6.1.

Change-Id: If5b4af407a8b639891d0b444056e81724cebac8c
2025-04-16 11:46:17 +02:00
Ricardo Wurmus
cd8d613e0e
gnu: bcftools: Update to 1.21.
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.21.

Change-Id: I4a2a6c106f804a68c16074a6ce8ae449c299724e
2025-04-16 11:46:17 +02:00
Ricardo Wurmus
89408dc096
gnu: htslib: Update to 1.21.
* gnu/packages/bioinformatics.scm (htslib): Update to 1.21.
(htslib-1.19): New variable.

Change-Id: If2a53871e69c606d3aebe820ee75bcc945d939b0
2025-04-16 11:46:17 +02:00
Ricardo Wurmus
17be2f2af7
gnu: scvelo: Remove custom 'check phase.
* gnu/packages/bioinformatics.scm (scvelo)[arguments]: Remove custom 'check
phase by using pyargs.

Change-Id: I3fb0a7aa9d6dd8ceb623e0372df32fb7f3cc8478
2025-04-16 11:46:11 +02:00
Ricardo Wurmus
c5b627045d
gnu: python-scanpy: Patch broken version check.
* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Patch broken
anndata version check.

Change-Id: I28e72116d1f8520102f3331bf3f45dd87f79eb33
2025-04-16 11:46:11 +02:00