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* gnu: Add fast5.•••Moved here from guix-science. * gnu/packages/bioinformatics.scm (fast5): New variable. Change-Id: I3373be5d5c80f3600b88fd3f71eadf723443e1c9 Ricardo Wurmus4 days1-0/+39
* gnu: python-cyvcf2: Update to 0.31.1•••This commit also fixes the previous build failure. * gnu/packages/bioinformatics.scm (python-cyvcf2): Update to 0.31.1. [native-inputs]: Add python-setuptools and python-wheel. Change-Id: Icc5057cf9f5e6ba141e6e29e8f4db657cd04c1d2 Signed-off-by: jgart <jgart@dismail.de> Alexis Simon4 days1-3/+7
* gnu: rust-flate2-1: Move to (gnu packages crates-compression).•••* gnu/packages/crates-io.scm (rust-flate2-1): Move from here ... * gnu/packages/crates-compression.scm: ... to here. Change-Id: I226c649588baad2b07d93d469b9070b14ee229b1 Efraim Flashner13 days1-0/+1
* gnu: Fix whitespace issues in various descriptions.•••This mainly addresses `double-space after sentence end period' and `trailing white space' issues. * gnu/packages/audio.scm (ecasound): Fix description. * gnu/packages/axoloti.scm (ksoloti-runtime, ksoloti-patcher): Fix description. * gnu/packages/bioinformatics.scm (trf, ghc-int-interval-map): Fix description. * gnu/packages/chez.scm (chez-scheme, chez-scheme-bootstrap-bootfiles): Fix description. * gnu/packages/code.scm (cscope): Fix description. * gnu/packages/compression.scm (c-blosc): Fix description. * gnu/packages/connman.scm (connman): Fix description. * gnu/packages/crypto.scm (libxcrypt): Fix description. * gnu/packages/display-managers.scm (abstractdark-sddm-theme): Fix description. * gnu/packages/docker.scm (docker-registry): Fix description. * gnu/packages/freedesktop.scm (xdg-user-dirs): Fix description. * gnu/packages/game-development.scm (deutex, grfcodec): Fix description. * gnu/packages/games.scm (chroma): Fix description. * gnu/packages/geo.scm (xygrib): Fix description. * gnu/packages/gnunet.scm (gnunet-scheme): Fix description. * gnu/packages/ipfs.scm (go-github-com-ipfs-go-block-format): Fix description. * gnu/packages/kodi.scm (fstrcmp): Fix description. * gnu/packages/machine-learning.scm (vosk-api): Fix description. * gnu/packages/messaging.scm (biboumi): Fix description. * gnu/packages/music.scm (sooperlooper, samplebrain): Fix description. * gnu/packages/perl.scm (perl-file-readbackwards): Fix description. * gnu/packages/rocm.scm (rocm-bandwidth-test): Fix description. * gnu/packages/scanner.scm (sane-airscan): Fix description. * gnu/packages/security-token.scm (pkcs11-helper): Fix description. * gnu/packages/shellutils.scm (shell-functools): Fix description. * gnu/packages/textutils.scm (catdoc): Fix description. * gnu/packages/tor.scm (tor): Fix description. * gnu/packages/xdisorg.scm (xftwidth, xwallpaper): Fix description. * gnu/packages/xfce.scm (xfce4-volumed-pulse): Fix description. Change-Id: I911836d66eb780c0fa279e3aebf9d7fbd53bf00a Signed-off-by: Vagrant Cascadian <vagrant@debian.org> Gabriel Wicki13 days1-2/+2
* gnu: python-scanpy: Ignore plotting tests.•••* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Also ignore tests from test_plotting.py. Change-Id: I5d2ebb3764e57c5f348be2b3555db99a2ee6ee4f Ricardo Wurmus2025-01-011-0/+1
* gnu: python-scanpy: Use more test-flags.•••* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Remove phase 'delete-bad-tests and use #:test-flags instead; add phase 'discover-anndata. Change-Id: Idb5bd59a2bba968fbec820603938802cf9443bad Ricardo Wurmus2025-01-011-22/+23
* gnu: python-hicmatrix: Work around defect in python-tables.•••* gnu/packages/bioinformatics.scm (python-hicmatrix)[inputs]: Add c-blosc2. [arguments]: Add phase 'find-blosc2. Change-Id: I02ea5e36c24b8da330f763aae07b1616e002ed9a Ricardo Wurmus2025-01-011-0/+11
* gnu: python-pybedtools: Update to 0.10.0.•••* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.10.0. [arguments]: Use #:test-flags to disable one test instead of patching test files in 'disable-broken-tests phase; add new phases 'fix-references and 'build-extensions. [propagated-inputs]: Remove python-matplotlib; add kentutils, python-numpy, python-pandas, and python-psutil. [inputs]: Add zlib. [native-inputs]: Remove python-numpy, python-pandas, python-psutil, python-six, and kentutils. Change-Id: I62948b1f3169f93f752896fdf02d2887740e98cc Ricardo Wurmus2025-01-011-34/+25
* gnu: python-cwlformat: Fix build.•••* gnu/packages/bioinformatics.scm (python-cwlformat): Fix build. [native-inputs]: Add python-setuptools and python-wheel. Change-Id: Id3e4bc116d94f4e432b2b11fc35ad1baf7f6f756 Zheng Junjie2024-12-221-0/+1
* gnu: python-pyahocorasick: Fix build.•••* gnu/packages/bioinformatics.scm (python-pyahocorasick)[native-inputs]: Add python-setuptools. Change-Id: Icbeb9cc8a9a4b08d97e561454ce46a0a234c0852 Danny Milosavljevic2024-12-211-1/+2
* gnu: python-cwl-utils: Use node-lts instead of node.•••* gnu/packages/bioinformatics.scm (python-cwl-utils)[inputs]: Replace node by node-lts. Change-Id: Ia98601db0a9233a96263051e1520a848dbc40a9c Jelle Licht2024-12-181-1/+1
* gnu: cwltool: Use node-lts instead of node.•••* gnu/packages/bioinformatics.scm (cwltool)[inputs]: Replace node by node-lts. Change-Id: Idea8c5cb456080fccd8fff6c6b2c674764ae7bce Jelle Licht2024-12-181-1/+1
* gnu: python-deeptools: Add missing inputs.•••* gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Add python-setuptools and python-wheel. Change-Id: I36e563e9fbdaf9c34b9ca8437c3559e04b3f58a6 Ricardo Wurmus2024-12-151-1/+1
* gnu: python-loompy: Fix build.•••* gnu/packages/bioinformatics.scm (python-loompy)[build-system]: Use pyproject-build-system. [arguments]: Remove custom 'check phase; add phase 'numpy-compatibility. [native-inputs]: Add python-setuptools and python-wheel. Change-Id: I2a3121e042fb7f7980bae14cea3e256fd4c9b115 Ricardo Wurmus2024-12-151-9/+10
* gnu: Remove python-filelock-3.5.•••* gnu/packages/bioinformatics.scm (python-filelock-3.5): Delete variable. (python-genomepy) [propagated-inputs]: Replace python-filelock-3.5 with python-filelock. Change-Id: I74b58c5143dc3f633e44cc9b92307520b160f43f Maxim Cournoyer2024-12-131-3/+1
* gnu: Remove python-mistune-next.•••* gnu/packages/python-xyz.scm (python-mistune-next): Delete variable. * gnu/packages/bioinformatics.scm (python-schema-salad) [propagated-inputs]: Remove python-mistune-next; add python-mistune. * gnu/packages/mail.scm (python-hyperkitty): Likewise. * gnu/packages/syndication.scm (giara): Likewise. Change-Id: Iccf5ffde2b2c5a8c9b8e1c0e6ebd6fa7eab9f144 Sharlatan Hellseher2024-12-131-1/+1
* gnu: build-system/pyproject: Add missing native-inputs.•••* gnu/packages/bioinformatics.scm (python-ega-download-client) [native-inputs]: Add python-setuptools and python-wheel. * gnu/packages/databases.scm (datasette)[native-inputs]: Add python-pip. * gnu/packages/django.scm (python-django-localflavor, python-django-contact-form)[native-inputs]: Add python-setuptools and python-wheel. * gnu/packages/graphviz.scm (python-uqbar)[native-inputs]: Add python-setuptools and python-wheel. * gnu/packages/jupyter.scm (python-jupyterlab-server)[native-inputs]: Add python-wheel. (python-nbstripout)[native-inputs]: Add python-setuptools and python-wheel. * gnu/packages/machine-learning.scm (python-captum, python-linear-operator, python-gpytorch)[native-inputs]: Add python-setuptools. * gnu/packages/music.scm (abjad, abjad-ext-rmarkers, abjed-ext-nauert, python-mutagen)[native-inputs]: Add python-setuptools and python-wheel. * gnu/packages/package-management.scm (python-conda-package-handling)[native-inputs]: Add python-setuptools and python-wheel. (conda)[native-inputs]: Add python-wheel. * gnu/packages/python-check.scm (python-pyinstrument, python-pytest-testmon, python-pytest-trio, python-nbval, python-pytest-toolbox)[native-inputs]: Add python-setuptools and python-wheel. (python-nptyping)[native-inputs]: Add python-setuptools. * gnu/packages/python-check.scm (python-dask-expr)[native-inputs]: Add python-setuptools and python-wheel. * gnu/packages/python-web.scm (parfive, python-aioftp, python-hupper, python-sanic, python-mechanicalsoup, python-tinycss, python-aiostream, python-cbor2, gunicorn)[native-inputs]: Add python-setuptools and python-wheel. * gnu/packages/python-xyz.scm (python-apprise, python-jaraco-classes, python-sparse, python-shtab, python-pyan3)[native-inputs]: Add python-setuptools. (python-jupytext, python-orderedmultidict, python-identify, python-nodeenv, python-cfgv, python-zarr, python-multipart, python-nbconvert, python-cram, python-immutables, python-numpydoc, python-cairosvg, python-unidecode, python-black, python-multidict, python-mpv-jsonipc, python-humanize, python-cmd2)[native-inputs]: Add python-setuptools and python-wheel. (python-partd, python-dask, python-zarr)[native-inputs]: Add python-wheel. (python-nbconvert)[propagated-inputs]: Add texlive-etoolbox. Remove duplicate textlive-jknapltx. (python-isort)[native-inputs]: Add python-pip. * gnu/packages/simulation.scm (python-fenics-dijitso)[native-inputs]: Add python-setuptools and python-wheel. * gnu/packages/sphinx.scm (python-pydata-sphinx-theme, python-sphinx-autodoc-typehints)[native-inputs]: Add python-setuptools. * gnu/packages/syndication.scm (tuir)[native-inputs]: Add python-setuptools and python-wheel. * gnu/packages/terminals.scm (python-halo)[native-inputs]: Add python-setuptools and python-wheel. * gnu/packages/time.scm (python-arrow, python-dateutil) [native-inputs]: Add python-setuptools and python-wheel. * gnu/packages/version-control.scm (pre-commit)[native-inputs]: Add python-setuptools and python-wheel. Remove input labels. * gnu/packages/virtualization.scm (python-qemu-qmp, python-transient)[native-inputs]: Add python-setuptools and python-wheel. * gnu/packages/xorg.scm (python-xcffib)[native-inputs]: Add python-setuptools and python-wheel. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Change-Id: Id61cf8cdc47bd4c2871c0a9c8e9a5bfd51157df0 Nicolas Graves2024-12-131-2/+8
* gnu: Add python-setuptools/python-wheel where necessary.•••Changes to pyproject-build-system require explicit dependency on setuptools/wheel. Change-Id: Icd7699fc1dc56e974ae7568f2ae916dbf876bea5 Lars-Dominik Braun2024-12-131-6/+17
* build-system/pyproject: Use python-sans-pip-wrapper as default-python.•••Also adds python-setuptools and python-wheel to relevant packages, either to native-inputs or to propagated inputs if the pkg_resources Python module is loaded at runtime. * guix/build-system/pyproject.scm (default-python): Default to python-sans-pip-wrapper. Change-Id: I2d986c2225114f54459dd6bb360913106e52cdf4 Lars-Dominik Braun2024-12-131-22/+68
* gnu: Fix synopsis in miscelaneous packages.•••* gnu/packages/astronomy.scm (calcmysky-qt5): Fix synopsis. * gnu/packages/base.scm (hello): Fix synopsis. * gnu/packages/bioinformatics.scm (vembrane): Fix synopsis. * gnu/packages/browser-extensions.scm (passff): Fix synopsis. * gnu/packages/browser-extensions.scm (noscript): Fix synopsis. * gnu/packages/c.scm (orangeduck-mpc): Fix synopsis. * gnu/packages/cran.scm (r-d3r): Fix synopsis. * gnu/packages/docbook.scm (docbook-mathml-1.0): Fix synopsis. * gnu/packages/finance.scm (flowee): Fix synopsis. * gnu/packages/firmware.scm (seabios): Fix synopsis. * gnu/packages/games.scm (pinball): Fix synopsis. (morris): Fix synopsis. * gnu/packages/gawk.scm (cppawk-egawk): Fix synopsis. * gnu/packages/gnome.scm (gssdp): Fix synopsis. * gnu/packages/gstreamer.scm (gst-plugins-espeak): Fix synopsis. * gnu/packages/heads.scm (musl-cross): Fix synopsis. * gnu/packages/irc.scm (epic5): Fix synopsis. * gnu/packages/kde-pim.scm (itinerary): Fix synopsis. * gnu/packages/kde-plasma.scm (mpvqt): Fix synopsis. * gnu/packages/lesstif.scm (motif): Fix synopsis. * gnu/packages/linux.scm (ecryptfs-utils): Fix synopsis. * gnu/packages/linux.scm (falcosecurity-libs): Fix synopsis. * gnu/packages/mail.scm (pan): Fix synopsis. * gnu/packages/messaging.scm (biboumi): Fix synopsis. * gnu/packages/ocaml.scm (ocaml-ppx-import): Fix synopsis. * gnu/packages/pascal.scm (p2c): Fix synopsis. * gnu/packages/pdf.scm (unpaper): Fix synopsis. * gnu/packages/pure.scm (pure): Fix synopsis. * gnu/packages/qt.scm (qxlsx-qt5): Fix synopsis. * gnu/packages/smalltalk.scm (smalltalk): Fix synopsis. * gnu/packages/sugar.scm (sugar): Fix synopsis. * gnu/packages/terminals.scm (roxterm): Fix synopsis. * gnu/packages/virtualization.scm (xen): Fix synopsis. * gnu/packages/vpn.scm (sshoot): Fix synopsis. * gnu/packages/web.scm (buku-run): Fix synopsis. Signed-off-by: Vagrant Cascadian <vagrant@debian.org> Gabriel Wicki2024-12-101-1/+1
* gnu: Fix synopsis in various python packages.•••* gnu/packages/python-compression.scm (python-inflate64): Fix synopsis. * gnu/packages/python-science.scm (python-xarray-dataclasses): Fix synopsis. * gnu/packages/python-web.scm (python-waybackpack): Fix synopsis. * gnu/packages/python-xyz.scm (python-mir-eval): Fix synopsis. (python-restructuredtext-lint): Fix synopsis. (python-pixelmatch): Fix synopsis. (python-google-pasta): Fix synopsis. (python-xmp-toolkit): Fix synopsis. * gnu/packages/bioinformatics.scm (python-mgatk): Fix synopsis. * gnu/packages/rpc.scm (python-grpc-stubs): Fix synopsis. * gnu/packages/simulation.scm (python-commonroad-io): Fix synopsis. Signed-off-by: Vagrant Cascadian <vagrant@debian.org> Gabriel Wicki2024-12-101-1/+1
* gnu: Add skewer.•••* gnu/packages/bioinformatics.scm (skewer): New variable. Change-Id: Ieeb95ed7449b91ea853d73ecca05e5436121df6a Ricardo Wurmus2024-12-041-0/+36
* gnu: discrover: Add missing input.•••* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add texlive-etoolbox. Change-Id: I42075c05a36a031c40c335a668a8b46a7603b4dd Ricardo Wurmus2024-12-031-0/+1
* gnu: r-btools: Disable tests.•••* gnu/packages/bioinformatics.scm (r-btools)[arguments]: Disable tests. Change-Id: I0fc83672a3c09908296551b649244ae1993ac01d Ricardo Wurmus2024-12-031-0/+2
* gnu: r-cytoexplorer: Add missing inputs.•••* gnu/packages/bioinformatics.scm (r-cytoexplorer)[native-inputs]: Drop labels; add r-cytoexplorerdata, r-mockery, and r-testthat. [arguments]: Add phase 'skip-bad-tests. Change-Id: I5060b1ae4ad42ae122a46db018f10910340985d6 Ricardo Wurmus2024-12-031-13/+40
* gnu: Add r-cytoexplorerdata.•••* gnu/packages/bioinformatics.scm (r-cytoexplorerdata): New variable. Change-Id: I5565dff552f033c951bee5bac474cb05c7034066 Ricardo Wurmus2024-12-031-0/+25
* gnu: r-skitools: Add missing input.•••* gnu/packages/bioinformatics.scm (r-skitools)[native-inputs]: Add r-bsgenome-hsapiens-ucsc-hg19. Change-Id: I8331e0df21bda001d6e3ec944f02791c0a9301b6 Ricardo Wurmus2024-12-031-0/+1
* gnu: r-scseqcomm: Remove commented inputs.•••* gnu/packages/bioinformatics.scm (r-scseqcomm): Remove comments. Change-Id: I537f6377da44637674a0413a30ddd6b70a620ad3 Ricardo Wurmus2024-12-031-2/+0
* gnu: r-chromunity: Add missing input.•••* gnu/packages/bioinformatics.scm (r-chromunity)[native-inputs]: Add r-testthat. Change-Id: I5d208a5ab0cb63567ab49783d0fbe0733b08161a Ricardo Wurmus2024-12-031-0/+1
* gnu: r-liana: Add missing input.•••* gnu/packages/bioinformatics.scm (r-liana)[native-inputs]: Add r-testthat. Change-Id: I04c9c5f60842e1ed0a0415e51c25b46b64a60104 Ricardo Wurmus2024-12-031-1/+1
* gnu: r-circus: Add missing input.•••* gnu/packages/bioinformatics.scm (r-circus)[native-inputs]: Add r-testthat. Change-Id: I7178baece0a8134923fd550e2f1cc303f32aaaea Ricardo Wurmus2024-12-031-1/+1
* gnu: Remove r-numbat.•••This is a duplicate of a package in (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-numbat): Delete variable. Change-Id: Ic1f5d9779a594432a0dd8bd0be9059423a2f5b34 Ricardo Wurmus2024-12-031-72/+0
* gnu: r-spectre: Disable tests.•••* gnu/packages/bioinformatics.scm (r-spectre)[arguments]: Disable tests. Change-Id: I7978b05d0c1c2de3ada6b1b490ae36b28171f17c Ricardo Wurmus2024-12-031-0/+3
* gnu: r-gchain: Add missing inputs.•••* gnu/packages/bioinformatics.scm (r-gchain)[native-inputs]: Add r-pwalign and r-testthat. [arguments]: Add phase 'skip-bad-tests. Change-Id: Ia11c6e50e0d2886762ec551df3e5d73ef98547f8 Ricardo Wurmus2024-12-031-0/+21
* gnu: r-seraster: Add missing input.•••* gnu/packages/bioinformatics.scm (r-seraster)[native-inputs]: Add r-testthat. Change-Id: I88fb4a51831aff1b08437ef08adb62e344185a07 Ricardo Wurmus2024-12-031-0/+1
* gnu: r-gtrack: Add missing input.•••* gnu/packages/bioinformatics.scm (r-gtrack)[native-inputs]: Add r-testthat. Change-Id: I7b0cad1b8fd27d88ff766c5a46bd01dae2933422 Ricardo Wurmus2024-12-031-0/+1
* gnu: r-doubletcollection: Add missing input and disable tests.•••* gnu/packages/bioinformatics.scm (r-doubletcollection)[native-inputs]: Add r-testthat. [arguments]: Disable tests. Change-Id: I8802f703ecfd8d69e6e457cffb28e34d3f4f2b06 Ricardo Wurmus2024-12-031-0/+3
* gnu: r-pando: Add missing inputs and disable tests.•••* gnu/packages/bioinformatics.scm (r-pando)[native-inputs]: Add r-bsgenome-hsapiens-ucsc-hg38, r-devtools, r-doparallel, and r-ensdb-hsapiens-v86. [arguments]: Disable tests. Change-Id: Ic66679e2b8c4cdb9835ce08dc4dbb0a42e35e291 Ricardo Wurmus2024-12-031-1/+8
* gnu: r-anpan: Add missing input.•••* gnu/packages/bioinformatics.scm (r-anpan)[native-inputs]: Add r-testthat. Change-Id: I69be3fa82db5f9c4e1302c9a3bd2d4f5253bde13 Ricardo Wurmus2024-12-031-1/+1
* gnu: r-hdwgcna: Add missing inputs.•••* gnu/packages/bioinformatics.scm (r-hdwgcna)[native-inputs]: Add r-devtools and r-testthat. Change-Id: I553d4fc2f1a682e5d552862c5e50a31140528073 Ricardo Wurmus2024-12-031-1/+3
* gnu: r-ewastools: Add missing inputs.•••* gnu/packages/bioinformatics.scm (r-ewastools)[native-inputs]: Add r-enmix, r-illuminahumanmethylationepicanno-ilm10b4-hg19, r-minfi, r-stringi, and r-testthat. Change-Id: I8ba2b1c46a4898b27874a7dc8648bb142f4b5a70 Ricardo Wurmus2024-12-031-1/+7
* gnu: r-bamutils: Add test inputs and disable tests.•••* gnu/packages/bioinformatics.scm (r-bamutils)[arguments]: Disable tests. [native-inputs]: Add r-testthat and samtools. Change-Id: I781c38fb59355a51f2cd27a833d7ed5dbe5277ab Ricardo Wurmus2024-12-031-0/+3
* gnu: r-bamutils: Update to 0.0.0.9000-2.0a7d2d9.•••* gnu/packages/bioinformatics.scm (r-bamutils): Update to 0.0.0.9000-2.0a7d2d9. Change-Id: I04e86c2ff1059f23a34615ac6067926cdd9cb355 Ricardo Wurmus2024-12-031-3/+3
* gnu: r-dropbead: Disable tests.•••* gnu/packages/bioinformatics.scm (r-dropbead)[native-inputs]: Add r-data-table. [arguments]: Disable tests. Change-Id: I48c74a7b4253695ab5c877f6f1cebdca6ed42cb7 Ricardo Wurmus2024-12-031-0/+3
* gnu: r-sleuth: Disable tests.•••* gnu/packages/bioinformatics.scm (r-sleuth)[native-inputs]: Add r-testthat. [arguments]: Disable tests. Change-Id: Ib060eb18f8964212eb38b7025a35c16f0aca97b9 Ricardo Wurmus2024-12-031-1/+3
* gnu: r-ggsankey: Add missing inputs.•••* gnu/packages/bioinformatics.scm (r-ggsankey)[native-inputs]: Add r-testthat. Change-Id: Iaafb75cc47e89a4a25232003d410f98c304ff021 Ricardo Wurmus2024-12-031-0/+1
* gnu: r-streamgraph: Add missing input.•••* gnu/packages/bioinformatics.scm (r-streamgraph)[native-inputs]: Add r-testthat. Change-Id: I1209a467c5a966c916f0d0416c6c1e283ae9226d Ricardo Wurmus2024-12-031-1/+1
* gnu: r-signac: Add missing input.•••* gnu/packages/bioinformatics.scm (r-signac)[native-inputs]: Add r-testthat. Change-Id: I0aacabf77171903cca2bc0f443f77e479b6331b2 Ricardo Wurmus2024-12-031-0/+1
* gnu: r-psupertime: Add missing input.•••* gnu/packages/bioinformatics.scm (r-psupertime)[native-inputs]: Add r-testthat. Change-Id: I9993547e2e757b4218c2229495a7eaa0c8fecbe2 Ricardo Wurmus2024-12-031-1/+1
* gnu: r-demuxmix: Add missing input.•••* gnu/packages/bioinformatics.scm (r-demuxmix)[native-inputs]: Add r-testthat. Change-Id: Ia09b929b4d5bb521d58fb74f17f1ac91a4d44a60 Ricardo Wurmus2024-12-031-1/+1