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2026-03-07gnu: r-singlet: Update to 0.99.8-1.ef4a374.Ricardo Wurmus
Yes, this is an update, even though the patch level used to be .26 and now is .8. That's post-semantic versioning. * gnu/packages/bioinformatics.scm (r-singlet): Update to 0.99.8-1.ef4a374. [propagated-inputs]: Add r-statmod. Change-Id: I95d1d60966c68cb8f66d79b6af6cab82bcf16a62
2026-03-07gnu: r-voltron: Replace custom phase with #:skipped-tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-voltron)[arguments]: Remove phase 'skip-bad-tests; provide #:skipped-tests argument. Change-Id: I00ddc80185972d5bf7e01856b8ab0c47ffcf3fd2
2026-03-06gnu: bwa: Update to 0.7.19.Spencer King
* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.19. Merges: https://codeberg.org/guix/guix/pulls/6925 Change-Id: I066277d3746e291426156ae36a70c8a51a59f23f Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-03-05gnu: Pin old pybind11 version.Gabriel Wicki
* gnu/packages/python-xyz.scm (pybind11): Move definition to (pybind11-2). (python-awkward-cpp, python-contourpy, python-hnswlib, python-dm-tree, python-matplotlib, python-pikepdf, python-optree, python-fusepy): Change reference to pybind11-2. * gnu/packages/astronomy.scm (aoflagger, python-galsim, python-pyclp), gnu/packages/bioinformatics.scm (python-metacells, python-strawc, python-coolbox, python-pyspoa, python-scvelo), gnu/packages/chemistry.scm (avogadrolibs), gnu/packages/computer-architecture.scm (gem5), gnu/packages/duckdb.scm (python-duckdb), gnu/packages/electronics.scm (nextpnr, prjtrellis), gnu/packages/engineering.scm (python-orocos-kinematics-dynamics), gnu/packages/geo.scm (ogs-serial), gnu/packages/graphics.scm (openshadinglanguage, openimageio), gnu/packages/image-processing.scm (opencolorio), gnu/packages/machine-learning.scm (python-fasttext, python-ml-dtypes, onnx, onnx-optimizer, onnxruntime, dlib, tensorflow-lite, tensorpipe, python-pytorch, python-torchvision, python-ctranslate2, python-hmmlearn, python-dlib), gnu/packages/maths.scm (python-accupy, python-ducc0), gnu/packages/networking.scm (libcamera), gnu/packages/opencl.scm (python-pyopencl), gnu/packages/package-management.scm (python-libmambapy), gnu/packages/physics.scm (python-brille, python-gofit), gnu/packages/python-check.scm (python-xdoctest), gnu/packages/python-science.scm (pyre, python-boost-histogram, python-cvxpy, python-iminuit, python-osqp, python-pyamg, python-qdldl, python-scikit-build-core, python-scipy, python-vaex-core, python-pyfma), gnu/packages/radio.scm (gnuradio, gr-osmosdr, gr-dsd, gr-iqbal, gr-satellites, limesuite-ng), gnu/packages/simulation.scm (fenics, python-dolfin-adjoint), gnu/packages/statistics.scm (python-diptest, python-george), gnu/packages/syndication.scm (syndication-domination): Change reference to pybind11-2. Change-Id: Ib6abc8580fc2b4c35172f251ff6ba7d80ced4b7b Signed-off-by: Gabriel Wicki <gabriel@erlikon.ch>
2026-02-27gnu: Deprecate swig and swig-next in vafor of swig-4.0 and swig-4.4.Sharlatan Hellseher
This is a following up change after discussion in <https://codeberg.org/guix/guix/pulls/3701#issuecomment-11048648>. * gnu/packages/swig.scm (swig-4.0, swig-4.4): New variables. (swig, swig-next): Deprecate swig and swig-next in vafor of swig-4.0 and swig-4.4. * gnu/packages/accessibility.scm (libbraille) * gnu/packages/apparmor.scm (libapparmor) * gnu/packages/bioinformatics.scm (htseq, imp, libsbml) * gnu/packages/bootloaders.scm (dtc, u-boot) * gnu/packages/disk.scm (volume-key) * gnu/packages/dns.scm (ldns, unbound) * gnu/packages/electronics.scm (opensta, trilinos-serial-xyce, uhdm) * gnu/packages/embedded.scm (python-libmpsse) * gnu/packages/engineering.scm (freecad, kicad, meep, mpb) * gnu/packages/fabric-management.scm (ibutils) * gnu/packages/game-development.scm (python-pybox2d) * gnu/packages/games.scm (kiki) * gnu/packages/geo.scm (saga) * gnu/packages/gnome.scm (libratbag) * gnu/packages/gnucash.scm (gnucash) * gnu/packages/gnupg.scm (python-gpg) * gnu/packages/graphviz.scm (graphviz) * gnu/packages/guile-xyz.scm (guile-xapian) * gnu/packages/image.scm (mypaint) * gnu/packages/instrumentation.scm (babeltrace, lttng-tools) * gnu/packages/kodi.scm (kodi) * gnu/packages/libftdi.scm (libftdi) * gnu/packages/linux.scm (libnl) * gnu/packages/llvm.scm (lldb) * gnu/packages/machine-learning.scm (openmm, tensorflow-lite) * gnu/packages/maths.scm (nlopt) * gnu/packages/ncurses.scm (stfl) * gnu/packages/oneapi.scm (python-onetbb) * gnu/packages/pretty-print.scm (highlight) * gnu/packages/python-crypto.scm (python-m2crypto) * gnu/packages/python-graphics.scm (python-pivy) * gnu/packages/radio.scm (hamlib, soapysdr) * gnu/packages/security-token.scm (python-pyscard, python-yubikey-manager) * gnu/packages/selinux.scm (libselinux, libsemanage, python-setools) * gnu/packages/speech.scm (pocketsphinx) * gnu/packages/statistics.scm (python-openturns, r-spams) * gnu/packages/tbb.scm (python-tbb) * gnu/packages/version-control.scm (subversion) * gnu/packages/video.scm (libopenshot, mlt, obs) [native-inputs]: Remove swig; add swig-4.0. * gnu/packages/geo.scm (gdal) * gnu/packages/graph.scm (python-faiss) [inputs]: Remove swig; add swig-4.0. * gnu/packages/games.scm (fifengine): Update to 0.4.2. [inputs]: Remove swig; add swig-4.0. [native-inputs]: Likewise. * gnu/packages/image-processing.scm (insight-toolkit, simpleitk) * gnu/packages/pdf.scm (mupdf, python-pymupdf) [native-inputs]: Remove swig-next; add swig-4.4. Change-Id: I544bef0a0b1a81004596fad9f116610ef5cb52ae
2026-02-25gnu: wfmash: Install split_approx_mappings_in_chunks script.Arun Isaac
* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Add install-scripts phase. [inputs]: Add python-wrapper. Change-Id: I1a68399d1b14e9783a2a2c2fe8d65fc777de18b6
2026-02-24gnu: lammps-serial: Finalize update to 250722.3.Leo Orveillon
* gnu/packages/bioinformatics.scm (lammps-serial): Adapt to updated lammps. [configure-flags]: Same as lammps, but remove MPI and openMP related ones. [phases]{link-lammps-so}: Change binary names due to LAMMPS_MACHINE flag removal. [inputs]: Remove pnetcdf. Replace hdf5-parallel-openmpi with hdf5. Change-Id: I585e75fc7894c3e38f7b144f400193c9a767741a Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-02-24gnu: lammps: Update to 250722.3 and refacto.Leo Orveillon
* gnu/packages/bioinformatics.scm (lammps): Update to 250722.3. [build-system]: Switch from gnu to cmake. [configure-flags]: Add more packages. [phases]{link-lammps-so}: Link lammps libraries to the main binary. [inputs]: Add fftw, n2p2, gsl, hdf5-parallel-openmpi, openblas, libomp, eigen, netcdf, pnetcdf, python-numpy. Remove gfortran. [native-inputs]: Add pkg-config, python-cython, patchelf, gfortran. Change-Id: I65f0739c1df11981691aa54868e5dbf69ac29496 Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-02-23gnu: Remove wfa2-lib.Andreas Enge
* gnu/packages/bioinformatics.scm (wfa2-lib): Delete variable. Fixes: guix/guix#3705 Change-Id: Ib19e25a84c982ab7a6403a9578adf2ecbaa46b9b
2026-02-23gnu: Remove vcflib.Andreas Enge
* gnu/packages/bioinformatics.scm (vcflib): Delete variable. Change-Id: I3ffdcfdbd8a3bb9d573fc0d5dc03da59acdd482e
2026-02-23gnu: Remove freebayes.Andreas Enge
* gnu/packages/bioinformatics.scm (freebayes): Delete variable. Change-Id: I19fadd85a384cb4520160cfab04b114e5ca47cec
2026-02-20gnu: r-voltron: Skip bad tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-voltron)[arguments]: Add phase 'skip-bad-tests. Change-Id: I51b33fd613f9eb744b4fd51400cad55e5b2c65ef
2026-02-20gnu: r-giotto: Update to 4.2.2-1.7988300.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-giotto): Update to 4.2.2-1.7988300. [source]: Fetch from true upstream. [arguments]: Disable tests. [propagated-inputs]: Add r-arrow, r-biocparallel, r-biocsingular, r-bluster, r-checkmate, r-future-apply, r-giottoclass, r-giottoutils, r-giottovisuals, r-limma, r-matrixgenerics, r-sparsematrixstats, r-terra, and r-uwot; remove r-cowplot, r-deldir, r-farver, r-ggrepel, r-irlba, r-lfa, r-magick, r-magrittr, r-matrixstats, r-qvalue, r-rcolorbrewer, r-rcpp, r-reshape2, and r-rtsne. [native-inputs]: Add r-testthat. [home-page]: Update to true upstream. Change-Id: I938e0c19fcc68fe4b100646fe051ff1a42411092
2026-02-20gnu: Add r-giottovisuals.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-giottovisuals): New variable. Change-Id: I403d712ac4ce99cd5c08215ea83d5bf3cf2dd50a
2026-02-20gnu: Add r-giottodata.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-giottodata): New variable. Change-Id: Icaed4b19a20e866523703e2241025943096954ba
2026-02-20gnu: Add r-giottoutils.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-giottoutils): New variable. Change-Id: Ia7acb1fc364f7076cf73f08d9335cd05a23b5f43
2026-02-20gnu: Add r-giottoclass.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-giottoclass): New variable. Change-Id: Icf95b3fd1f6dd4f14a13bc71d52a6febf6713b3e
2026-02-20gnu: r-anndatar: Update to 1.0.1.Ricardo Wurmus
anndataR is now on Bioconductor. * gnu/packages/bioinformatics.scm (r-anndatar): Move from here... * gnu/packages/bioconductor.scm (r-anndatar): ...to here; update to 1.0.1. [properties]: Remove updater-extra-native-inputs. [inputs]: Add python-wrapper and python-anndata. [native-inputs]: Add r-processx, r-s4vectors, r-seurat, r-spelling, and r-withr; remove r-vctrs. [propagated-inputs]: Add r-cli, r-lifecycle, r-purrr, r-reticulate, and r-rlang. Change-Id: I2410f00b33451c60d8b1657ac30a6c1b014e260d
2026-02-20gnu: r-voltron: Update to 0.2.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.3. [inputs]: Replace python with python-wrapper. Change-Id: I180622af927e2386d45a4dadad4ebdad6e7ab6ac
2026-02-20gnu: r-imagearray: Update to 0.99.6-1.2f90694.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-imagearray): Update to 0.99.6-1.2f90694. [propagated-inputs]: Add r-ebimage, r-rarr, r-rhdf5, and r-s4vectors; remove r-zarrarray. [native-inputs]: Add r-knitr and r-testthat. [synopsis]: Update. [description]: Update. Change-Id: Ife5670dacaad9c5b737ab282e7fc939126e845d8
2026-02-20gnu: r-hdf5dataframe: Update to 0.99.3-1.61c52cb.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5dataframe): Update to 0.99.3-1.61c52cb. [propagated-inputs]: Add r-h5mread. [synopsis]: Update to what upstream provides. Change-Id: Ie46ac432d6635a4aa824f17b46bfd0b6b002a1c0
2026-02-19gnu: blast+: Add 'sqlite' dependency.Simon Tournier
Follow up of 80e27d57bf64311ea7b510889871811156ee63a4. * gnu/packages/bioinformatics.scm (blast+)[inputs]: Add sqlite. Fixes: guix/guix#3731 Change-Id: Ifdb7b20bd800f4eaab83c9cbb5b756489b230f6b Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-02-18gnu: bandage: Support Wayland.Danny Milosavljevic
* gnu/packages/bioinformatics.scm (bandage)[inputs]: Add qtwayland-5. Change-Id: Ib4836ddef55236547bc6710d94090a3f8d163786
2026-02-17gnu: Remove tophat.Andreas Enge
* gnu/packages/bioinformatics.scm (tophat): Delete variable. Fixes: guix/guix#5660 Change-Id: I57eb5355b1eb3da2acbd539e5f795c66f3e1fae6
2026-02-15gnu: Remove pin on go-1.23 by setting -vet=off in tests.Ethan Blanton
This is a follow up commit 87661cea77be67d7fdfcc607ee3a621d005e909c: "Pin some golang packages to use go-1.23" wich adds "-vet=off" to test args so that make check works with go 1.24+. * gnu/packages/authentication.scm: (oauth2l) * gnu/packages/bioinformatics.scm: (go-github-com-biogo-store) * gnu/packages/containers.scm: (dive) * gnu/packages/databases.scm: (go-github-com-cockroachdb-pebble) * gnu/packages/education.scm: (exercism) * gnu/packages/file-systems.scm: (fscrypt, gocryptfs) * gnu/packages/golang-check.scm: (go-github-com-cheekybits-is, go-github-com-coder-quartz, go-github-com-data-dog-go-sqlmock, go-github-com-google-gofuzz, go-github-com-matryer-is, go-github-com-onsi-ginkgo, go-github-com-onsi-ginkgo-v2, go-github-com-onsi-gomega, go-github-com-otiai10-mint, go-github-com-smarty-assertions, go-github-com-smarty-gunit, go-github-com-warpfork-go-testmark, go-sigs-k8s-io-randfill) * gnu/packages/golang-crypto.scm: (go-github-com-99designs-keyring, go-github-com-blanu-dust, go-github-com-chmduquesne-rollinghash) * gnu/packages/golang-maths.scm: (go-github-com-montanaflynn-stats, go-gonum-org-v1-gonum) * gnu/packages/golang-vcs.scm: (go-github-com-jiangxin-goconfig) * gnu/packages/golang-web.scm: (go-git-sr-ht-emersion-gqlclient, go-git-sr-ht-rockorager-go-jmap, go-github-com-apex-log, go-github-com-apex-log-bootstrap, go-github-com-cenkalti-backoff-v4, go-github-com-digitalocean-godo, go-github-com-donovanhide-eventsource, go-github-com-emersion-go-smtp, go-github-com-flosch-pongo2-v6, go-github-com-go-chi-chi-v5, go-github-com-go-jose-go-jose-v3, go-github-com-go-openapi-errors, go-github-com-go-openapi-runtime, go-github-com-go-openapi-validate, go-github-com-gobwas-httphead, go-github-com-goccy-go-json, go-github-com-gogo-protobuf, go-github-com-google-safehtml, go-github-com-jcmturner-gokrb5-v8, go-github-com-jhillyerd-enmime, go-github-com-jlaffaye-ftp, go-github-com-jmespath-go-jmespath, go-github-com-json-iterator-go, go-github-com-labbsr0x-goh, go-github-com-makeworld-the-better-one-go-gemini, go-github-com-ovn-kubernetes-libovsdb, go-github-com-pascaldekloe-goe, go-github-com-perimeterx-marshmallow, go-github-com-pion-stun, go-github-com-pion-stun-v2, go-github-com-pion-stun-v3, go-github-com-rcrowley-go-metrics, go-github-com-swaggo-swag, go-github-com-urfave-negroni, go-github-com-urfave-negroni-v3, go-github-com-xeipuuv-gojsonschema, go-maunium-net-go-mautrix) * gnu/packages/golang-xyz.scm: (go-github-com-d5-tengo-v2, go-github-com-godbus-dbus, go-github-com-hashicorp-hcl-v2, go-github-com-itchyny-go-flags, go-github-com-jedib0t-go-pretty-v6, go-github-com-jessevdk-go-flags, go-github-com-mattn-go-shellwords, go-github-com-moby-sys-mountinfo, go-github-com-nlpodyssey-spago, go-github-com-pingcap-errors, go-github-com-pmezard-go-difflib, go-github-com-russross-blackfriday-v2, go-go-mongodb-org-mongo-driver, go-go4-org, go-k8s-io-klog-v2, go-sigs-k8s-io-kustomize-kyaml, go-zgo-at-zstd) * gnu/packages/irc.scm: (soju) * gnu/packages/password-utils.scm: (aws-vault) * gnu/packages/text-editors.scm: (micro) * gnu/packages/version-control.scm: (hut) * gnu/packages/video.scm: (ytarchive) * gnu/packages/web-browsers.scm: (bombadillo) * gnu/packages/web.scm: (webhook) Change-Id: If7ffae01869404796467f8deed29a03e7a7020d7 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-02-14gnu: r-saige: Update to 1.5.1-1.7172b7f.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-saige): Update to 1.5.1-1.7172b7f. Change-Id: I076cd1247efff7d311beae9b0dabc13ee13ea694
2026-02-11gnu: Add alignoth.Alexis Simon
* gnu/packages/bioinformatics.scm (alignoth): New entry. * gnu/packages/rust-crates.scm (lookup-cargo-inputs)[alignoth]: New entry. Change-Id: I35c0daf9d930f196551de1e5618b0569314a03db Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2026-02-10gnu: Remove PKG_CONFIG_EXECUTABLE configure-flags.Dariqq
* gnu/packages/bioinformatics.scm (vcflib): Remove setting PKG_CONFIG_EXECUTABLE flag. * gnu/packages/cpp.scm (hyprlang): same. * gnu/packages/cpp.scm (hyprutils): same. * gnu/packages/debian.scm (apt-cacher-ng): Same * gnu/packages/linux.scm (rdma-core): Same. * gnu/packages/radio.scm (libiio): Same. * gnu/packages/security-token.scm (libfido2): Same. * gnu/packages/version-control.scm (libgit2-1.9,libgit2-1.7): Same * gnu/packages/vulkan.scm (vulcan-loader): Same. Change-Id: I12cb5fb7f1a93fa01766b37a32777a269d4c089c Signed-off-by: Greg Hogan <code@greghogan.com>
2026-02-09gnu: rcas-web: Update to 0.2.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.2.0. [inputs]: Add r-biocmanager. Change-Id: I8ddf52180700ca917e75e099378c4fe9a7cdd9bb
2026-02-07gnu: Remove python-biofluff.Andreas Enge
* gnu/packages/bioinformatics.scm (python-biofluff): Delete variable. Fixes: guix/guix#5249 Change-Id: I01a3672be5d344aba4e14f280350d27b910c9e61
2026-02-07gnu: scvelo: Relocate phase 'set-numba-cache-dir.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (scvelo): [arguments]<#:phases>: Relocate phase 'set-home. Relates-to: guix/guix#5892 Change-Id: Ia51609df06d64d41b7a272d0e17e96cf973df2f8
2026-02-07gnu: python-ikarus: Update to 0.0.3.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-ikarus): Update to 0.0.3. Use G-Expressions. [arguments] <test-backend, test-flags>: Use custom. <phases>: Remove 'fix-issue-12; reallocate 'set-numba-cache-dir. [native-inputs]: Remove python-wheel. Change-Id: I4bf1b5bbda56373fd632f31aca59d473ab37252a
2026-02-07gnu: python-celltypist: Update to 1.7.1.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-celltypist): Update to 1.7.1. [arguments] <tests?>: Enable simple runtime regression check. <phases>: Remove 'set-home and 'set-numba-cache-dir; add 'set-environment; use custom 'check phase. [native-inputs]: Remove python-wheel; add python-setuptools. Change-Id: I7ec16da8c6d3af8ad0d8eb96d5f9b50d9858eae3
2026-02-07gnu: python-scanpy: Skip one more test.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-scanpy): [arguments]<test-flags>: Skip one more shaky test. Change-Id: I6093f2365fbab05ada6cc8cbdfede5bfdfb6f27d
2026-02-07gnu: python-splicekit: Refresh package style.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-splicekit): Re order inputs and arguments and start description from a new line. Change-Id: I0ae7b2434669cbfee19a39283933fc2af45362a2
2026-02-07gnu: python-pybio: Relocate phase 'set-home.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-pybio)[arguments]<#:phases>: Relocate phase 'set-home. Relates-to: guix/guix#5892 Change-Id: Ifeceb52b20348f2f495217ee371b84be7bbf590b
2026-02-07gnu: pairadise: Disable missing tests.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (pairadise): [arguments] <tests?>: No tests. [native-inputs]: Remove python-wheel. Change-Id: I0545b4ce56562ba9c5f875133cff33fbd1126459
2026-02-07gnu: python-tornado: Update to 6.4.2.Sharlatan Hellseher
* gnu/packages/python-web.scm (python-tornado): Absorb definition of python-tornado-6. (python-tornado-5): New variable, inherit from python-tornado. (python-tornado-6): Deprecate variable. * gnu/packages/jupyter.scm (python-jupyterlite-core) * gnu/packages/jupyter.scm (python-pytest-jupyter) * gnu/packages/jupyter.scm (python-voila) * gnu/packages/python-xyz.scm (python-pypugjs) * gnu/packages/python-xyz.scm (python-tenacity): [native-inputs]: Remove python-tornado-6; add python-tornado. * gnu/packages/machine-learning.scm (kaldi-gstreamer-server): [inputs]: Remove python-tornado-6; add python-tornado. * gnu/packages/bioinformatics.scm (python-bulkvis) * gnu/packages/jupyter.scm (python-ipykernel) * gnu/packages/jupyter.scm (python-jupyter-client) * gnu/packages/jupyter.scm (python-jupyter-client-7) * gnu/packages/jupyter.scm (python-jupyter-server) * gnu/packages/jupyter.scm (python-nbclassic) * gnu/packages/jupyter.scm (python-nbdime) * gnu/packages/jupyter.scm (python-notebook) * gnu/packages/jupyter.scm (python-terminado) * gnu/packages/python-check.scm (python-pytest-tornasync) * gnu/packages/python-science.scm (python-distributed) * gnu/packages/python-xyz.scm (python-bokeh) * gnu/packages/python-xyz.scm (python-ipyparallel-bootstrap) * gnu/packages/python-xyz.scm (python-nbconvert) [propagated-inputs]: Remove python-tornado-6; add python-tornado. Change-Id: I437d73a0711c88e329666b6bc853f6332c277098
2026-02-07gnu: Drop setting SETUPTOOLS_SCM_PRETEND_VERSION in some packages.Nicolas Graves
* gnu/packages/astronomy.scm (python-asdf-compression) (python-asdf-fits-schemas, python-cdflib, python-sunkit-spex): * gnu/packages/bioinformatics.scm (python-whatshap, python-mudata) (python-pyfaidx, python-ctxcore, scvelo): * gnu/packages/bootloaders.scm (dtc): * gnu/packages/check.scm (python-pytest-xdist, python-pytest-forked): * gnu/packages/databases.scm (python-fastparquet): * gnu/packages/disk.scm (greaseweazle-host-tools): * gnu/packages/docker.scm (python-docker): * gnu/packages/finance.scm (python-ledgerblue): * gnu/packages/fontutils.scm (python-compreffor) (python-defcon-bootstrap, nototools): * gnu/packages/games.scm (sc-controller): * gnu/packages/machine-learning.scm (python-botorch): * gnu/packages/music.scm (python-pylast): * gnu/packages/package-management.scm (conda): * gnu/packages/python-build.scm (python-exceptiongroup): * gnu/packages/python-science.scm (python-dask-image) (python-distributed, python-osqp): * gnu/packages/python-web.scm (python-branca, python-smart-open): * gnu/packages/python-xyz.scm (python-conda-content-trust) (python-menuinst, python-isort, python-pyclibrary) (python-pyclipper, python-csb43-0.10, python-orgparse) (python-deepmerge, python-scooby, python-uuid6): * gnu/packages/radio.scm (nanovna-saver): * gnu/packages/sphinx.scm (python-sphinx-autodoc-typehints): [arguments]: Remove phases setting SETUPTOOLS_SCM_PRETEND_VERSION. * gnu/packages/python-xyz.scm (python-bagit) [arguments]: Refactor manual 'check phase into #:test-flags. Change-Id: I0713d6603f982a7f956d02fc3b85a384f4dd6ce4 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-02-07gnu: Remove python-importlib-metadata input from some packages.Nicolas Graves
Remove python-importlib-metadata from [native-inputs, inputs, or propagated-inputs] in the following packages as not required for build/tests/install: * gnu/packages/android.scm (python-miio) * gnu/packages/astronomy.scm (python-jwst, python-stpipe) * gnu/packages/bioinformatics.scm (python-demuxem, python-hotspotsc, python-weblogo, python-metacells) * gnu/packages/calendar.scm (khal) * gnu/packages/django.scm (python-django-q2) * gnu/packages/engineering.scm (python-asyncua) * gnu/packages/jupyter.scm (python-jupyterlab-server, python-jupyterlite-core) * gnu/packages/machine-learning.scm (python-pynndescent, python-gymnasium) * gnu/packages/maths.scm (python-orthopy, python-quadpy) * gnu/packages/package-management.scm (poetry) * gnu/packages/python-compression.scm (python-pybcj) * gnu/packages/python-crypto.scm (python-keyring) * gnu/packages/python-web.scm (python-jsonpickle, python-flask) * gnu/packages/python-xyz.scm (python-jsonschema-3, python-pystitcher, python-lsp-server, python-nbconvert, python-dns-lexicon, python-signedjson, python-verlib2) * gnu/packages/sphinx.scm (python-sphinx-6) * gnu/packages/spreadsheet.scm (visidata) Change-Id: Ifac8350aa60528dc2ccacf2570120dbcf1c74ab8 Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-02-07gnu: Remove python-flake8 native-input from some packages.Nicolas Graves
Remove python-flake8 from [native-inputs] in the following packages as not required for build/tests/install: * gnu/packages/bioinformatics.scm: (python-doubletdetection) * gnu/packages/ebook.scm: (calibre) * gnu/packages/graph.scm: (python-pygsp) * gnu/packages/machine-learning.scm: (python-pymanopt, python-pyro-api) * gnu/packages/python-web.scm: (python-furl) * gnu/packages/python-xyz.scm: (python-jinja2-cli) * gnu/packages/simulation.scm: (python-dolfin-adjoint) * gnu/packages/vpn.scm: (sshuttle) * gnu/packages/music.scm (python-mutagen): [arguments]<#:test-flags>: Ignore flake8 quality tests. [native-inputs]: Remove python-flake8. Change-Id: I2789b8711faf3aa60a4bfa2062f95616e216d6c3 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-02-07gnu: python-doubletdetection: Remove python-black native-input.Nicolas Graves
* gnu/packages/bioinformatics.scm (python-doubletdetection) [native-inputs]: Remove python-black. Change-Id: Iaa12a1b73bb2f97a053c7b6365b3e1bc7c53080d Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-02-07gnu: python-pybedtools: Update to 0.12.0.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.12.0. Use G-Expresions. [source] <snippet>: Move phase {remove-cython-generated-files} here. [argumets] <modules>: Drop all. <build-backend>: Use setuptools.build_meta. <test-flags>: Run test from installed module via "--pyargs". <phases>: Remove 'build-extenstions; add 'remove-local-source. [native-inputs]: Remove python-wheel. Change-Id: I993aaee8a4bae900d4c6b61d5b4804d8afbe1131
2026-02-07build-system/pyproject: Remove uneeded use of pyproject-guile-json.Nicolas Graves
* gnu/packages/bioinformatics.scm (python-bed-reader, python-gseapy) * gnu/packages/chemistry.scm (gemmi, ringdecomposerlib, rdkit) * gnu/packages/cinnamon.scm (libxapp) * gnu/packages/cups.scm (hplip) * gnu/packages/djvu.scm (ocrodjvu) * gnu/packages/finance.scm (electron-cash) * gnu/packages/gnome.scm (terminator) * gnu/packages/image-processing.scm (insight-toolkit) * gnu/packages/machine-learning.scm (onnxruntime, tensorflow-lite, koboldcpp, python-tokenizers) * gnu/packages/maths.scm (gmsh, z3, fp16) * gnu/packages/music.scm (quodlibet) * gnu/packages/photo.scm (lensfun) * gnu/packages/python-science.scm (python-clarabel) * gnu/packages/python-xyz.scm (python-orjson, python-libcst, python-rpds-py, python-streamtracer, python-tiktoken) * gnu/packages/rpm.scm (createrepo-c) * gnu/packages/rust-apps.scm (maturin) * gnu/packages/sugar.scm (sugar, sugar-datastore) * gnu/packages/version-control.scm (mercurial, hg-commitsigs) * gnu/packages/vpn.scm (python-proton-vpn-local-agent) [arguments]<#:phases>: Remove uneeded use of pyproject-guile-json extension. * gnu/packages/python-xyz.scm (python-streamtracer)[arguments] <#:phases>: Also rewrite 'check phase replacement. Change-Id: I779c354120ada3d94f07a127b9ec5011e73254c2 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-02-05gnu: Remove python-multivelo.Simon Tournier
* gnu/packages/bioinformatics.scm (python-multivelo): Delete variable. Fixes: guix/guix#5364 Change-Id: I7636eb262c9a3fcebde3678bad18110301ce8889 Merges: #6131
2026-02-04gnu: scvelo: Deprecate in favor of python-scvelo.Nguyễn Gia Phong
* gnu/packages/bioinformatics.scm (python-scvelo): New variable. (scvelo): Deprecate in favor of python-scvelo. (r-netid)[propagated-inputs], (python-multivelo)[propagated-inputs]: Replace scvelo with python-scvelo. Change-Id: I45160537670785682e7d8a9333952b7105dc8c1f Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-02-02gnu: salmon: Update dependency on tbb.Cayetano Santos
* gnu/packages/bioinformatics.scm (salmon)[inputs]: Remove tbb; add onetbb. Change-Id: I6b18757e62cffafc65fcf7f79590d0c1bada7c83
2026-01-28gnu: bowtie: Update to 2.5.4.Cayetano Santos
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.5.4. [source]: Use G-Expressions in ’snippet. [arguments]: Use G-Expressions. <#:make-flags>: Add CC. <#:phases>: Add ’tests? arguments to ’check phase; add ’fix-prefix. [inputs]: Drop variables, add onetbb, delete tbb-2020 and python-wrapper. [native-inputs]: Add python-wrapper, which and perl-file-which. Merges guix/guix!5491 Change-Id: I12686b06911c11170748b64af722c5311b2e542d
2026-01-25gnu: r-zarrarray: Update to 1.0-2.3cc3e6a.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-zarrarray): Update to 1.0-2.3cc3e6a. [properties]: Record updater-extra-native-inputs. [propagated-inputs]: Remove r-pizzarr; add r-rarr. [native-inputs]: Add r-testthat. [arguments]: Disable tests. Change-Id: Id3a9b564c21ee779e4a46e02cd478d06d9dd5bc9 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: r-pizzarr: Update to 0.1.0-2.5f47057.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-pizzarr): Update to 0.1.0-2.5f47057. Change-Id: Id5f24214e67dcc00093ceaa1d6f2297b6146aa51 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
generated by cgit v1.3 (git 2.53.0) at 2026-05-30 04:41:27 +0000