summaryrefslogtreecommitdiff
path: root/gnu/packages/bioinformatics.scm
AgeCommit message (Collapse)Author
2025-01-20gnu: python-celltypist: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-celltypist)[native-inputs]: Add python-wheel. Change-Id: Ife136efe1d6f734951dde25e950148d3d7057d64
2025-01-20gnu: python-metacells: Update to 0.9.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-metacells): Update to 0.9.5. [native-inputs]: Add python-pandas-stubs and python-setuptools. Change-Id: I25d28d0ebbb689c2561e25fec94cf4911c7f5158
2025-01-20gnu: python-scanpy: Patch anndata version check.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Add phase 'patch-version-check. Change-Id: I0d2262197ae05c785fc65bd22e8052764434cab3
2025-01-20gnu: python-metacells: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-metacells)[native-inputs]: Add python-wheel. Change-Id: I5ca117071b43bad1942f499795001fe8bc641546
2025-01-20gnu: python-liana-py: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-liana-py): Update to 1.4.0. [arguments]: Adjust disabled tests. Change-Id: I9245285e2d043b5e7cbce5fb95a30982cd981597
2025-01-20gnu: python-decoupler-py: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-decoupler-py)[native-inputs]: Add python-wheel. Change-Id: I37b8162e0dde4513b3a6f94455315489d7d08499
2025-01-20gnu: python-cell2cell: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cell2cell)[native-inputs]: Add python-wheel. Change-Id: I79015fa48c976489d4c1182cb4506aae139325ad
2025-01-20gnu: python-gseapy: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-gseapy)[native-inputs]: Add python-wheel. Change-Id: I0ce3d3aeb5aa3fb1ab3f2aa524b066738cf9046a
2025-01-20gnu: python-mudata: Update to 0.3.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-mudata): Update to 0.3.1. [arguments]: Add phase 'pretend-version. [native-inputs]: Remove python-flit-core; add python-hatch-vcs and python-hatchling. Change-Id: I87b8dc6ec557e0ca69930d82db7d6e64727228e9
2025-01-20gnu: python-scanpy: Update to 1.10.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.10.4. [arguments]: Update list of disabled tests; rename phase 'discover-anndata to 'add-anndata-source. [native-inputs]: Add python-pytest-mock. Change-Id: I409678c67d15f3d3e4147be68c7a987c0e095d23
2025-01-20gnu: cwltool: Patch tox.ini.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cwltool)[arguments]: Rename 'modify-tests to 'patch-tests; add patch of tox.ini. Change-Id: I2c90a8803e7eb1153cb4c7cc5b683875627c57f1
2025-01-20gnu: cwltool: Use test-flags.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cwltool)[arguments]: Use #:test-flags instead of deleting and patching tests in 'modify-tests phase. Change-Id: I0e4f16d48fba23e4197b69bf1c3923828f178cd0
2025-01-20gnu: python-cwl-utils: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cwl-utils)[native-inputs]: Add python-setuptools and python-wheel. Change-Id: I803a68c04923c96f793d508c23bb08069524bc63
2025-01-20gnu: python-cwl-upgrader: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cwl-upgrader)[native-inputs]: Add python-setuptools and python-wheel. Change-Id: I81531d588e6deb8a01c59f2a824b815e8f95e0f0
2025-01-20gnu: python-schema-salad: Update to 8.8.20241206093842.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to 8.8.20241206093842. [arguments]: Patch tox.ini. [propagated-inputs]: Remove python-importlib-resources, python-setuptools, and python-typing-extensions. [native-inputs]: Add python-cachecontrol, python-mypy, python-setuptools, python-setuptools-scm, python-types-dataclasses, python-types-requests, and python-types-setuptools. Change-Id: I22ca7ad772078192117a1139adca410b53844008
2025-01-20gnu: pyscenic: Update to 0.12.1-1.eaf23eb.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pyscenic): Update to 0.12.1-1.eaf23eb. [arguments]: Update phase 'do-not-reference-deleted-modules. [propagated-inputs]: Add python-numexpr. [native-inputs]: Add python-wheel. Change-Id: Ib1b5a7d36a24b280160befe579057a241d69455d
2025-01-20gnu: macs-3: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (macs-3)[native-inputs]: Add python-wheel. Change-Id: I22b8d8e144434ae537af7c113f4719392933e90c
2025-01-20gnu: python-py2bit: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-py2bit)[build-system]: Use pyproject-build-system. [native-inputs]: Add python-setuptools and python-wheel. Change-Id: I6f66e5f3c0f7612f460e2a6fa931b4c456db6a1b
2025-01-20gnu: python-biom-format: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biom-format)[build-system]: Use pyproject-build-system. [arguments]: Replace phase 'disable-broken-tests with #:test-flags; enable one test; add phase 'build-extensions. [native-inputs]: Remove python-nose. Change-Id: I8399d9b05bdb6da89d8056d536ab7e25dc22f9c2
2025-01-16gnu: Add python-ngesh.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-ngesh): New variable. Change-Id: If51f3075037647e319efa9468331677a845b30cb Signed-off-by: Ricardo Wurmus <[email protected]>
2025-01-15gnu: Add fast5.Ricardo Wurmus
Moved here from guix-science. * gnu/packages/bioinformatics.scm (fast5): New variable. Change-Id: I3373be5d5c80f3600b88fd3f71eadf723443e1c9
2025-01-14gnu: python-cyvcf2: Update to 0.31.1Alexis Simon
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 <[email protected]>
2025-01-06gnu: rust-flate2-1: Move to (gnu packages crates-compression).Efraim Flashner
* gnu/packages/crates-io.scm (rust-flate2-1): Move from here ... * gnu/packages/crates-compression.scm: ... to here. Change-Id: I226c649588baad2b07d93d469b9070b14ee229b1
2025-01-05gnu: Fix whitespace issues in various descriptions.Gabriel Wicki
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 <[email protected]>
2025-01-01gnu: python-scanpy: Ignore plotting tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Also ignore tests from test_plotting.py. Change-Id: I5d2ebb3764e57c5f348be2b3555db99a2ee6ee4f
2025-01-01gnu: python-scanpy: Use more test-flags.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Remove phase 'delete-bad-tests and use #:test-flags instead; add phase 'discover-anndata. Change-Id: Idb5bd59a2bba968fbec820603938802cf9443bad
2025-01-01gnu: python-hicmatrix: Work around defect in python-tables.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicmatrix)[inputs]: Add c-blosc2. [arguments]: Add phase 'find-blosc2. Change-Id: I02ea5e36c24b8da330f763aae07b1616e002ed9a
2025-01-01gnu: python-pybedtools: Update to 0.10.0.Ricardo Wurmus
* 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
2024-12-22gnu: python-cwlformat: Fix build.Zheng Junjie
* gnu/packages/bioinformatics.scm (python-cwlformat): Fix build. [native-inputs]: Add python-setuptools and python-wheel. Change-Id: Id3e4bc116d94f4e432b2b11fc35ad1baf7f6f756
2024-12-21gnu: python-pyahocorasick: Fix build.Danny Milosavljevic
* gnu/packages/bioinformatics.scm (python-pyahocorasick)[native-inputs]: Add python-setuptools. Change-Id: Icbeb9cc8a9a4b08d97e561454ce46a0a234c0852
2024-12-18gnu: python-cwl-utils: Use node-lts instead of node.Jelle Licht
* gnu/packages/bioinformatics.scm (python-cwl-utils)[inputs]: Replace node by node-lts. Change-Id: Ia98601db0a9233a96263051e1520a848dbc40a9c
2024-12-18gnu: cwltool: Use node-lts instead of node.Jelle Licht
* gnu/packages/bioinformatics.scm (cwltool)[inputs]: Replace node by node-lts. Change-Id: Idea8c5cb456080fccd8fff6c6b2c674764ae7bce
2024-12-15gnu: python-deeptools: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Add python-setuptools and python-wheel. Change-Id: I36e563e9fbdaf9c34b9ca8437c3559e04b3f58a6
2024-12-15gnu: python-loompy: Fix build.Ricardo Wurmus
* 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
2024-12-13gnu: Remove python-filelock-3.5.Maxim Cournoyer
* 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
2024-12-13gnu: Remove python-mistune-next.Sharlatan Hellseher
* 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
2024-12-13gnu: build-system/pyproject: Add missing native-inputs.Nicolas Graves
* 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 <[email protected]> Change-Id: Id61cf8cdc47bd4c2871c0a9c8e9a5bfd51157df0
2024-12-13gnu: Add python-setuptools/python-wheel where necessary.Lars-Dominik Braun
Changes to pyproject-build-system require explicit dependency on setuptools/wheel. Change-Id: Icd7699fc1dc56e974ae7568f2ae916dbf876bea5
2024-12-13build-system/pyproject: Use python-sans-pip-wrapper as default-python.Lars-Dominik Braun
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
2024-12-10gnu: Fix synopsis in miscelaneous packages.Gabriel Wicki
* 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 <[email protected]>
2024-12-10gnu: Fix synopsis in various python packages.Gabriel Wicki
* 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 <[email protected]>
2024-12-04gnu: Add skewer.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (skewer): New variable. Change-Id: Ieeb95ed7449b91ea853d73ecca05e5436121df6a
2024-12-03gnu: discrover: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add texlive-etoolbox. Change-Id: I42075c05a36a031c40c335a668a8b46a7603b4dd
2024-12-03gnu: r-btools: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-btools)[arguments]: Disable tests. Change-Id: I0fc83672a3c09908296551b649244ae1993ac01d
2024-12-03gnu: r-cytoexplorer: Add missing inputs.Ricardo Wurmus
* 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
2024-12-03gnu: Add r-cytoexplorerdata.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-cytoexplorerdata): New variable. Change-Id: I5565dff552f033c951bee5bac474cb05c7034066
2024-12-03gnu: r-skitools: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-skitools)[native-inputs]: Add r-bsgenome-hsapiens-ucsc-hg19. Change-Id: I8331e0df21bda001d6e3ec944f02791c0a9301b6
2024-12-03gnu: r-scseqcomm: Remove commented inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scseqcomm): Remove comments. Change-Id: I537f6377da44637674a0413a30ddd6b70a620ad3
2024-12-03gnu: r-chromunity: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-chromunity)[native-inputs]: Add r-testthat. Change-Id: I5d208a5ab0cb63567ab49783d0fbe0733b08161a
2024-12-03gnu: r-liana: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-liana)[native-inputs]: Add r-testthat. Change-Id: I04c9c5f60842e1ed0a0415e51c25b46b64a60104
generated by cgit v1.2.3 (git 2.45.2) at 2025-04-11 07:00:46 +0000