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2026-05-19gnu: python-scprep: Skip more tests.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-scprep): [arguments] <test-flags>: Skip 7 more tests. Change-Id: I70ef7eb97d638c37d31ce4ea00cb59bd0a1da440
2026-05-18gnu: pigx-scrnaseq: Fix build on Python@3.12.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): [native-inputs]: Add python-setuptools. Change-Id: I80ed3e99e23e6d04f2e4a670283efce80fc43dfb
2026-05-18gnu: python-baltica: Build with snakemake@8.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-baltica): [propagated-inputs]: Remove snakemake-7; add snakemake. Change-Id: Ic3a755d8218da2f71d411ddd2535af79bbe43f72
2026-05-18gnu: python-bed-reader: Fix build with Python@3.12.Nicolas Graves
* gnu/packages/bioinformatics.scm (python-bed-reader) [native-inputs]: Add python-setuptools. Change-Id: I9fd1e16e2149710a9644a58517876757d799211a Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-18gnu: python-arboreto: Fix tests with Python@3.12.Nicolas Graves
* gnu/packages/bioinformatics.scm (python-arboreto) [arguments]<#:phases>: Add phase 'python-3.12-compatibility. Change-Id: I2f766ea064a9a5dc38543318dd5107d35a0db240 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-18gnu: taxtastic: Fix tests.Nicolas Graves
* gnu/packages/bioinformatics.scm (taxtastic) [arguments]<#:phases>: Drop 'check phase replacement. [native-inputs]: Add python-pytest. Remove python-wheel. Change-Id: Idd4d13019ec3b02d659601d6bfffc9a01e770458 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-18gnu: python-pdbfixer: Update to 1.12.Nicolas Graves
* gnu/packages/bioinformatics.scm (python-pdbfixer): Update to 1.12. [arguments]<#:test-flags>: Refresh them. Change-Id: I982c17921ae458a586f202cde93566938e4c09b5 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-18gnu: python-parabam: Add a fixing patch.Nicolas Graves
* gnu/packages/bioinformatics.scm (python-parabam)[source]: Add a fixing patch. Change-Id: I08073bd18a6b8cb715d844174186239ec8a5f958 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-18gnu: python-cooler: Update to 0.10.4-0.6c2d65b.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-cooler): Update to 6c2d65b1420a636193b7f05100a96410ea252147 commit. [source]: Switch to git-source. [arguments] <test-flags>: Rework skipped tests. Change-Id: Ib7e3f1da0ab9c8ee3e333a9f3307a2f4a721e8d1
2026-05-18gnu: porechop: Update to 0.2.3-2.109e437.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (porechop): Update to 109e437280436d1ec27e5a5b7a34ffb752176390 commit. [arguments] <test-flags>: Skip 6 tests. [native-inputs]: Remove python-wheel. Change-Id: Ia58a3f6785d9f0ff459fe9659634ef5783530529
2026-05-18gnu: instrain: Update to 1.10.0-1.f172367.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (instrain): Update to f172367e599851a6cb90048ae890d1bb6569063f commit. [arguments] <tests?, test-flags>: Enable the most of the tests. [phases]{relax-requirements}: Relax python-biopython lower constrain version. [propagated-inputs]: Remove python-biopython-1.73; add python-biopython. [native-inputs]: Add python-boto3 and python-pytest. Change-Id: I777bba3120d97d51dbeb5c380b6556a784a1f604
2026-05-18gnu: lofreq: Fix build on Python@3.12.Nicolas Graves
* gnu/packages/bioinformatics.scm (lofreq)[native-inputs]: Add python-setuptools. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-18gnu: shorah: Update to 1.99.3.Nicolas Graves
* gnu/packages/bioinformatics.scm (shorah): Update to 1.99.3. [native-inputs]: Add python-setuptools.
2026-05-18gnu: python-peaks2utr: Update to 1.5.0.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-peaks2utr): Update to 1.5.0. Use G-Expressions. [source]: Switch to git-fetch. [arguments] <test-flags>: Run all tests. [phases]{relax-requirements}: Relax upper constrain for NumPy. [propagated-inputs]: Remove macs, and python-numpy-1; add macs-3, and python-numpy. [native-inputs]: Remove python-wheel; add python-pytest. Change-Id: I7466e00eb99c7fa12263ed8aaedde614c2119d4b
2026-05-18gnu: macs-3: Update to 3.0.4.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (macs-3): Update to 3.0.4. [arguments] <test-flags>: Skip one test. Change-Id: I7bb990fbaa25bdb3a1f4047cc65a581ffdcd59f7
2026-05-18gnu: packages: Drop python-pytest-runner native-inputs.Nicolas Graves
This commit was generated using https://codeberg.org/guix/guix/pulls/5862: guix style -S remove-native-inputs --parameter=python-pytest-runner and adding back python-pytest if necessary. * gnu/packages/geo.scm (python-pyshp) * gnu/packages/backup.scm (vorta) [native-inptus]: Remove python-pytest-runner, add python-pytest. * gnu/packages/backup.scm (duplicity) * gnu/packages/linux.scm (python-spython) * gnu/packages/bioinformatics.scm (python-cwl-utils) * gnu/packages/databases.scm (python-pyarrow, datasette) * gnu/packages/fontutils.scm (python-cu2qu) * gnu/packages/gnome.scm (terminator) * gnu/packages/music.scm (stargate) * gnu/packages/python-science.scm (python-upsetplot) * gnu/packages/python-web.scm (python-falcon, python-cssselect2) * gnu/packages/python-xyz.scm (python-docrep, python-cairocffi, python-entrypoint2) * gnu/packages/task-management.scm (todoman) * gnu/packages/video.scm (yle-dl) * gnu/packages/vpn.scm (sshuttle) [native-inptus]: Remove python-pytest-runner. Relates-to: https://codeberg.org/guix/guix/issues/7474 Change-Id: Ia79595309ba8965c4374e7c24a1ef4c3e36fe1ea Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-18guix: build-system: Set pypi-uri in pyproject, drop python module.Nicolas Graves
After this commit, when both modules are imported: - if pyproject is imported before, the warning is 'pypi-uri' is deprecated, use '(@ (guix build-system pyproject) pypi-uri)' instead - if python is imported before, the warning is `pypi-uri' imported from both (guix build-system python) and (guix build-system pyproject) This seems convenient enough to warn for deprecation in the short term, while avoiding any breaking changes. * guix/build-system/pyproject.scm (pypi-uri): Move the procedure from (guix build-system python) here. * guix/build-system/python (pypi-uri): Drop definition, import it from (guix build-system pyproject) and deprecate it. * gnu/packages/openldap.scm: Reorder modules to get the right warning. * gnu/packages/pypy.scm: Likewise. * gnu/packages/*.scm : Drop module (guix build-system python). * tests/import/pypi.scm: Likewise. Merges: https://codeberg.org/guix/guix/pulls/7448 Change-Id: Ib42f53bc545052eb7918a25afe9db6d5fc2cb834 Reviewed-by: Nguyễn Gia Phong <cnx@loang.net> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-18gnu: python-mysql-connector-python: Relocate and rename.Nicolas Graves
* gnu/packages/python-xyz.scm (python-mysql-connector-python): Move from here… * gnu/packages/databases.scm (mysql-connector-python): …to here. (python-mysql-connector-python): Deprecate package. * gnu/packages/bioinformatics.scm (python-genomepy)[propagated-inputs]: Replace python-mysql-connector-python by mysql-connector-python. Change-Id: Ib48e3b998d3bf946d03d2c7aaf246a8251776402 Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-18gnu: python-cooler: Drop phase 'fix-pytest-config.Nicolas Graves
* gnu/packages/bioinformatics.scm (python-cooler)[arguments]<#:phases>: Drop phase 'fix-pytest-config. Change-Id: Iddad5557655691c11ded0f0a20b1f23b7791b896 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-18gnu: gdc-client: Drop phase 'fix-pytest-config.Nicolas Graves
* gnu/packages/bioinformatics.scm (gdc-client)[arguments]<#:phases>: Drop phase 'fix-pytest-config. Change-Id: I12f5dd5306a4c6d562d03b48837bf4bc1ae8ddda Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-18build-system/pyproject: Remove python-pytest-cov native-input.Nicolas Graves
* gnu/packages/astronomy.scm (python-wiimatch) * gnu/packages/audio.scm (python-resampy, python-librosa) * gnu/packages/backup.scm (borgmatic) * gnu/packages/bioinformatics.scm (python-bed-reader, python-pysnptool) (python-pairtools): * gnu/packages/check.scm (python-pytest-nunit, python-pytest-perf) * gnu/packages/dav.scm (vdirsyncer, radicale) * gnu/packages/django.scm (python-django-redis) * gnu/packages/engineering.scm (python-scikit-rf) * gnu/packages/fediverse.scm (python-mastodon-py) * gnu/packages/fontutils.scm (psautohint) * gnu/packages/geo.scm (python-pyogrio) * gnu/packages/graphviz.scm (python-uqbar) * gnu/packages/jupyter.scm (python-jupyterlab-server python-nbclient, python-jupyterlite-core, python-ipydatawidgets) * gnu/packages/machine-learning.scm (python-pymanopt, python-tensorly, python-torchmetrics) * gnu/packages/maths.scm (python-libensemble) * gnu/packages/music.scm (stargate) * gnu/packages/python-check.scm (python-atpublic, python-vcrpy) * gnu/packages/python-compression.scm (python-zipstream-ng) * gnu/packages/python-science.scm (python-plotnine, python-pandaparallel, python-pyts, python-pingouin) * gnu/packages/python-web.scm (python-devpi-process, python-cheroot, python-jsonpickle, python-flask-babel, python-url-normalize, python-elasticsearch, python-hupper, python-simple-websocket, python-apiron, python-huggingface-hub, python-aiosignal, python-ovh, python-cbor2, python-zeep, hypercorn, python-warcio, python-aioftp, python-oauthlib, python-tinycss2, python-cssselect2, python-httpcore, python-wsgiprox, python-venusian, gunicorn) * gnu/packages/python-xyz.scm (python-janus, python-affine, python-contourpy, python-echo, python-rasterio, python-rich-tables, python-babel, python-pymarshal, python-portalocker, python-expandvars, python-mizani, python-cligj, autokey, python-robotframework-pythonlibcore, python-lsp-jsonrpc, python-numpydoc, python-pillow, python-manimpango, python-cairocffi, python-pubmed-parser, python-sentry-sdk, python-prettytable, python-sniffio, python-ipywidgets, python-pyproject-api, python-pymemcache, python-async-lru, python-numcodecs, python-mwclient, python-cmd2, python-pyan3, python-platformdirs, python-multipart, python-shtab, python-scooby) * gnu/packages/rdf.scm (python-rdflib-6) * gnu/packages/simulation.scm (python-fenics-dijitso) * gnu/packages/sphinx.scm (python-sphinx-design) * gnu/packages/statistics.scm (python-patsy, python-rchitect) * gnu/packages/task-management.scm (todoman) * gnu/packages/vpn.scm (sshuttle) * gnu/packages/web.scm (anonip, python-tibanna) [native-inputs]: Remove python-pytest-cov. Change-Id: I32f027794e90333c27fdff5871180779f603846c Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-04gnu: Remove discrover.Andreas Enge
* gnu/packages/bioinformatics.scm (discrover): Delete variable. Fixes: guix/guix#7640 Change-Id: Ic8588831d80485d42e4927a47b2174180a906043
2026-04-28gnu: r-bpcells: Build with SSE2 for on x86 32-bit platforms.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bpcells)[arguments]: Conditionally add phase 'require-sse2. Change-Id: I4927d9701e47dc34cc435d24c64a3043ad984f0d
2026-04-28gnu: r-bpcells: Update to 0.3.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bpcells): Update to 0.3.1. [arguments]: Do not patch r/configure. Change-Id: Ia16297dc02bfecaf353de04452026df98ea5c826
2026-04-20gnu: Remove fsom.Andreas Enge
* gnu/packages/bioinformatics.scm (fsom): Delete variable. Change-Id: I2881a1addec0c9c100141bd181a1f7a84a964c94
2026-04-13gnu: Remove mantis.Andreas Enge
* gnu/packages/bioinformatics.scm (mantis): Delete variable. Fixes: guix/guix#7055 Change-Id: I4655b0dc2b9de2b3cb5924538d562539454d5240
2026-04-10gnu: r-pando: Update to 1.1.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-pando): Update to 1.1.1. [source]: Update repository URL. [arguments]: Delete phase 'loosen-requirements. Change-Id: If3709336de2794da4c16a648137c6538d192c232
2026-04-09gnu: bioparser: Update to 3.1.0.Ghislain Vaillant
* gnu/packages/bioinformatics.scm (bioparser): Update to 3.1.0. [source]: Use version tag as commit. [arguments]<#:phases>: Remove override of check phase. Add phase to enable testing in CMake instead. Change-Id: I641481e49bd98d32cae067dde984985a4ad0c5a9 Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-04-09gnu: biosoup: Update to 0.11.0.Ghislain Vaillant
* gnu/packages/bioinformatics.scm (biosoup): Update to 0.11.0. [source]: Use version tag as commit. [arguments]<#:phases>: Remove override of check phase. Add phase to enable testing in CMake instead. Change-Id: I426d1014cf020bbbf15e47c44e2902f823ddd09c Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-04-09gnu: Remove circtools.Andreas Enge
* gnu/packages/bioinformatics.scm (circtools): Delete variable. * gnu/packages/rust-crates.scm: Remove cargo-inputs for circtools. Fixes: guix/guix#5313 Change-Id: Ic94e9ba7c1500b018fc71e1a10bc25594af16b92
2026-04-09gnu: Remove ciri-long.Andreas Enge
* gnu/packages/bioinformatics.scm (ciri-long): Delete variable. Change-Id: Id1f595a162881e6765cb2fb192ba87740667bd9b
2026-04-08gnu: ravanan: Use git fetch.Cayetano Santos
* gnu/packages/bioinformatics.scm (ravanan)[source]: Switch to get-fetch. Change-Id: Icbd58b742a1d5e145b8b071c1708b3ff01c72972
2026-04-08gnu: ravanan: Build with the same Guile as the ‘guix’ package.Ludovic Courtès
Fixes a regression introduced in c3fefb065c53703e3dc6507c813182101c5c3a38. * gnu/packages/bioinformatics.scm (ravanan)[inputs]: Replace ‘guile-3.0’ by a ‘lookup-package-input’ call. Merges guix/guix!7734 Change-Id: I584bf55ddbf44e3cc13896f2ef48ccc8f305059d Signed-off-by: Cayetano Santos <csantosb@inventati.org>
2026-04-06gnu: delly: Update to 1.7.3.Hugo Buddelmeijer
* gnu/packages/bioinformatics.scm (delly): Update to 1.7.3. Merges: https://codeberg.org/guix/guix/pulls/7710 Change-Id: Ib88fe130f3073bbda7725d00a15cf2045c5d60e6 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-04-02gnu: r-bpcells: Do not build bundled highway library.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bpcells)[source]: Remove bundled highway sources. [arguments]: Fix check. [inputs]: Add google-highway. Change-Id: Ib70e7f9f64053b9e840c8c5f04e966beb4cf2869
2026-03-28gnu: python-pysam: Update to 0.23.3.Nicolas Graves
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.23.3. [native-inputs]: Replace python-cython-0 by python-cython. Remove python-wheel. Change-Id: I4e93e7ab1a9e763d2d84b6b7601a64e918b0eda8 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-03-25gnu: cnvkit: Update to 0.9.13.Andreas Enge
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.13. Change-Id: I69da49fe80b2e350ff351d39182dcf1e8cf97eb4
2026-03-24gnu: cwltool: Update to 3.1.20260315121657.Arun Isaac
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20260315121657. Change-Id: I1c4503aa65a638a905f8b49235578564fa40802f
2026-03-23gnu: bpp-core: Build with default gcc.Efraim Flashner
* gnu/packages/bioinformatics.scm (bpp-core)[native-inputs]: Remove gcc-10. [arguments]: Add a phase to add a missing include statement. Change-Id: I53cd0c86df7cf5476149c22746c1de971d6770e8
2026-03-23gnu: skewer: Relabel as version 0.2.2.Efraim Flashner
This is the tag for the given commit. * gnu/packages/bioinformatics.scm (skewer)[version]: Set to 0.2.2. Change-Id: I7f24b0320b5e20ba36e56c0a0708ea64ec7ba86a
2026-03-23gnu: skewer: Build with default gcc.Efraim Flashner
* gnu/packages/bioinformatics.scm (skewer)[arguments]: Add make-flag to set the C++ standard used. [native-inputs]: Remove gcc-10. Change-Id: I96515ec527cc0e2639def0b9a0b76d2ccb1062b9
2026-03-20gnu: jellyfish: Fix build on python-3.12.Nicolas Graves
* gnu/packages/bioinformatics.scm (jellyfish)[native-inputs]: Add python-setuptools. Change-Id: I742e32681380277151a0d4b4986d81cc6112c380 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-03-20gnu: python-schema-salad: Update to 8.9.20251102115403.Nicolas Graves
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to 8.9.20251102115403. [arguments]<#:test-flags>: Update them. <#:phases>: Drop phase 'skip-failing-tests. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-03-20gnu: Reference the inherited inputs values.Ludovic Courtès
This commit was made by running this command: sed -e's/modify-inputs (package-\([a-z-]*\)inputs [a-zA-Z0-9-]\+)/modify-inputs \1inputs/g' -i gnu/packages/*.scm … and then reverting individual hunks where the change would trigger unbound variable warnings or other issues (such as ‘native-inputs’ is bound in the body of the ‘inputs’ field, but it refers to the ‘native-inputs’ thunk defined just above). Change-Id: I6d94819f2809313fa1fbefc61897502ee7d66fab
2026-03-20gnu: Reference the inherited ‘arguments’ value.Ludovic Courtès
This commit was made by running this command: sed -e's/substitute-keyword-arguments (package-arguments [a-zA-Z0-9-]\+)/substitute-keyword-arguments arguments/g' -i gnu/packages/*.scm … and then: 1. reverting changes from ‘gnu/packages/rust.scm’ and ‘gnu/packages/java.scm’ since they would incur derivation changes and/or breakage; 2. reverting the change for ‘gcc-final’ in ‘gnu/packages/commencement.scm’; 3. reverting the change for ‘onnx-optimizer’, ‘openquest’, and ‘certbot’, which use ‘substitute-keyword-arguments’ for arguments that are not inherited (and thus ‘arguments’ would be unbound); 4. reverting the change for ‘insight-toolkit-legacy’ and ‘wine64-staging’ which make bogus assumptions about inherited arguments. Change-Id: I122a7cf517b6b63cae38944b5d33ade4b1f5a89c
2026-03-19gnu: plink: Build with gcc-7.Efraim Flashner
* gnu/packages/bioinformatics.scm (plink)[native-inputs]: Remove gcc-8, add gcc-7. Change-Id: Idd2182ba90509d6bff4fc733e2b6750a210c9dfb
2026-03-19gnu: plink: Add missing input.Efraim Flashner
* gnu/packages/bioinformatics.scm (plink)[inputs]: Add libxcrypt. Change-Id: I5994c2d02424972f0c1473ea3baf0a496db029bb
2026-03-18gnu: python-metacells: Fix build.Hugo Buddelmeijer
* gnu/packages/bioinformatics.scm (python-metacells): Fix build. [arguments]<#:phases>: Add pre-sanity-check phase. [homepage]: Update with redirect. Change-Id: I9e6c2dfd4d944a589f87716ab8347a161ff630c5 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-03-18gnu: Remove fastx-toolkit.Andreas Enge
* gnu/packages/bioinformatics.scm (fastx-toolkit): Delete variable. Change-Id: Ie710da17d23a04cfaafc1de28b2dc6aae23ccfd4
2026-03-18gnu: deacon: Update to 0.15.0.Spencer King
* gnu/packages/bioinformatics.scm (deacon): Update to 0.15.0. * gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for deacon. Change-Id: I6f1a8812d251228e50eabd9f0105c40ed4261a80 Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
generated by cgit v1.3 (git 2.53.0) at 2026-07-11 01:28:47 +0000