| Commit message (Expand) | Author | Age | Files | Lines |
|---|
| * | gnu: Add r-sigfit.•••* gnu/packages/bioinformatics.scm (r-sigfit): New variable.
Change-Id: I9d63975d3512cf8583e7ec22f450bb4963c9ff2f
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Alexis Simon | 8 days | 1 | -0/+37 |
| * | gnu: r-voltron: Update to 0.2.0-2.bbd7abb.•••* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.0-2.bbd7abb.
[arguments]: Add phase 'do-not-use-conda.
[propagated-inputs]: Remove r-basilisk; add r-pizzarr and r-rhdf5.
Change-Id: I4c57c154c8bac41d056fadb936a109ca6310d8d6
| Ricardo Wurmus | 9 days | 1 | -8/+24 |
| * | gnu: Add r-pizzarr.•••* gnu/packages/bioinformatics.scm (r-pizzarr): New variable.
Change-Id: Ia922dfb4ef418ecd4317ce6127b88ecf91bd2cc7
| Ricardo Wurmus | 9 days | 1 | -0/+27 |
| * | gnu: python-biom-format: Add missing input.•••* gnu/packages/bioinformatics.scm (python-biom-format)[native-inputs]: Add
python-wheel.
Change-Id: I7d462a05a73335bd1be72ab615d2550ed48a0383
| Ricardo Wurmus | 9 days | 1 | -1/+2 |
| * | gnu: Move python-pysnptools to (gnu packages bioinformatics).•••* gnu/packages/python-xyz.scm (python-pysnptools): Move from here...
* gnu/packages/bioinformatics.scm (python-pysnptools): ...to here.
Change-Id: I4dbd9cbe3f2d9a6dd4906be79b78862b39a57c28
| Ricardo Wurmus | 10 days | 1 | -0/+42 |
| * | gnu: Add python-bed-reader.•••* gnu/packages/bioinformatics.scm (python-bed-reader): New variable.
Change-Id: Iad3f1d1c05abe706d8cd52a4d046247a5a9738e2
| Ricardo Wurmus | 10 days | 1 | -0/+120 |
| * | gnu: python-fanc: Update to 0.9.28.•••* gnu/packages/bioinformatics.scm (python-fanc): Update to 0.9.28.
[arguments]: Remove custom 'check phase; disable tests that seemingly freeze.
[propagated-inputs]: Add python-imageio, python-pywavelets, and
python-tifffile; remove python-pytest.
[native-inputs]: Add python-pytest, python-setuptools, and python-wheel.
Change-Id: Ia83f5fe1d0cbbf56840061feb9561e439380e965
| Ricardo Wurmus | 10 days | 1 | -19/+14 |
| * | gnu: Deprecate fanc.•••fanc is a duplicate of python-fanc.
* gnu/packages/bioinformatics.scm (fanc): Define as deprecated name for
python-fanc.
Change-Id: I28e330d9bfe64fd59b49001ecc56e2c6fd191b55
| Ricardo Wurmus | 10 days | 1 | -58/+3 |
| * | gnu: python-screed: Update to 1.1.3.•••* gnu/packages/bioinformatics.scm (python-screed): Update to 1.1.3.
[native-inputs]: Add python-importlib-resources, python-pycodestyle,
python-pytest, python-setuptools-scm, and python-setuptools-scm-git-archive;
removve python-pytest-runner.
Change-Id: I3ce12acedbbc97d58f2266e042872494556afd3b
| Ricardo Wurmus | 10 days | 1 | -4/+8 |
| * | gnu: python-mofax: Update to 0.3.7-1.e4821fe.•••This looks like a downgrade, but it is in fact a more recent commit.
* gnu/packages/bioinformatics.scm (python-mofax): Update to 0.3.7-1.e4821fe.
[source]: Remove obsolete snippet.
[arguments]: Remove test flags.
[propagated-inputs]: Move python-poetry-core from here...
[native-inputs]: ...to here.
Change-Id: I6093d282887135f6b99d34a853cd9371cffe98f1
| Ricardo Wurmus | 10 days | 1 | -19/+6 |
| * | gnu: python-pybio: Fix build.•••* gnu/packages/bioinformatics.scm (python-pybio)[native-inputs]: Add
python-setuptools and python-wheel.
Change-Id: I1eca46c4a8dc5aa6eb090e20de387129c4590529
| 宋文武 | 10 days | 1 | -1/+1 |
| * | gnu: python-whatshap: Add missing input.•••* gnu/packages/bioinformatics.scm (python-whatshap)[native-inputs]: Add
python-wheel.
Change-Id: I51f9bb3791434befb61ecc6225060d6a4eb92dab
| Ricardo Wurmus | 10 days | 1 | -1/+2 |
| * | gnu: python-pyrodigal: Add missing input.•••* gnu/packages/bioinformatics.scm (python-pyrodigal)[native-inputs]: Add
python-wheel.
Change-Id: Ide41099084a50748f32a9ba11cbbe9dd4514094f
| Ricardo Wurmus | 10 days | 1 | -1/+5 |
| * | gnu: instrain: Update to 1.9.0.•••* gnu/packages/bioinformatics.scm (instrain): Update to 1.9.0.
[source]: Fetch git repository.
[build-system]: Use pyproject-build-system.
[arguments]: Disable tests.
[inputs]: Move all from here...
[propagated-inputs]: ...to here; remove python-boto3, python-numba,
python-scikit-learn, and python-drep.
[native-inputs]: Add python-boto3, python-setuptools, and python-wheel.
Change-Id: Ied1e909a6b22518908b95a43b8db5f35bd6c6ac6
| Ricardo Wurmus | 10 days | 1 | -15/+25 |
| * | gnu: scregseg: Patch for numpy compatibility.•••* gnu/packages/bioinformatics.scm (scregseg)[arguments]: Add phase
'compatibility.
Change-Id: I738d675c10acdbae7d40b3f806703ba8f7936a19
| Ricardo Wurmus | 10 days | 1 | -0/+5 |
| * | gnu: python-episcanpy: Add missing input.•••* gnu/packages/bioinformatics.scm (python-episcanpy)[native-inputs]: Add
python-wheel.
Change-Id: Iba4ac520faf00e3db64df3532752b1de3eec1bc6
| Ricardo Wurmus | 10 days | 1 | -1/+1 |
| * | gnu: python-celltypist: Add missing input.•••* gnu/packages/bioinformatics.scm (python-celltypist)[native-inputs]: Add
python-wheel.
Change-Id: Ife136efe1d6f734951dde25e950148d3d7057d64
| Ricardo Wurmus | 10 days | 1 | -0/+1 |
| * | gnu: python-metacells: Update to 0.9.5.•••* gnu/packages/bioinformatics.scm (python-metacells): Update to 0.9.5.
[native-inputs]: Add python-pandas-stubs and python-setuptools.
Change-Id: I25d28d0ebbb689c2561e25fec94cf4911c7f5158
| Ricardo Wurmus | 10 days | 1 | -3/+5 |
| * | gnu: python-scanpy: Patch anndata version check.•••* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Add phase
'patch-version-check.
Change-Id: I0d2262197ae05c785fc65bd22e8052764434cab3
| Ricardo Wurmus | 10 days | 1 | -0/+10 |
| * | gnu: python-metacells: Add missing input.•••* gnu/packages/bioinformatics.scm (python-metacells)[native-inputs]: Add
python-wheel.
Change-Id: I5ca117071b43bad1942f499795001fe8bc641546
| Ricardo Wurmus | 10 days | 1 | -1/+2 |
| * | gnu: python-liana-py: Update to 1.4.0.•••* gnu/packages/bioinformatics.scm (python-liana-py): Update to 1.4.0.
[arguments]: Adjust disabled tests.
Change-Id: I9245285e2d043b5e7cbce5fb95a30982cd981597
| Ricardo Wurmus | 10 days | 1 | -4/+20 |
| * | gnu: python-decoupler-py: Add missing input.•••* gnu/packages/bioinformatics.scm (python-decoupler-py)[native-inputs]: Add
python-wheel.
Change-Id: I37b8162e0dde4513b3a6f94455315489d7d08499
| Ricardo Wurmus | 10 days | 1 | -1/+1 |
| * | gnu: python-cell2cell: Add missing input.•••* gnu/packages/bioinformatics.scm (python-cell2cell)[native-inputs]: Add
python-wheel.
Change-Id: I79015fa48c976489d4c1182cb4506aae139325ad
| Ricardo Wurmus | 10 days | 1 | -0/+1 |
| * | gnu: python-gseapy: Add missing input.•••* gnu/packages/bioinformatics.scm (python-gseapy)[native-inputs]: Add
python-wheel.
Change-Id: I0ce3d3aeb5aa3fb1ab3f2aa524b066738cf9046a
| Ricardo Wurmus | 10 days | 1 | -1/+1 |
| * | gnu: python-mudata: Update to 0.3.1.•••* 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
| Ricardo Wurmus | 10 days | 1 | -3/+14 |
| * | gnu: python-scanpy: Update to 1.10.4.•••* 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
| Ricardo Wurmus | 10 days | 1 | -33/+33 |
| * | gnu: cwltool: Patch tox.ini.•••* gnu/packages/bioinformatics.scm (cwltool)[arguments]: Rename 'modify-tests
to 'patch-tests; add patch of tox.ini.
Change-Id: I2c90a8803e7eb1153cb4c7cc5b683875627c57f1
| Ricardo Wurmus | 10 days | 1 | -1/+3 |
| * | gnu: cwltool: Use test-flags.•••* gnu/packages/bioinformatics.scm (cwltool)[arguments]: Use #:test-flags
instead of deleting and patching tests in 'modify-tests phase.
Change-Id: I0e4f16d48fba23e4197b69bf1c3923828f178cd0
| Ricardo Wurmus | 10 days | 1 | -17/+11 |
| * | gnu: python-cwl-utils: Add missing inputs.•••* gnu/packages/bioinformatics.scm (python-cwl-utils)[native-inputs]: Add
python-setuptools and python-wheel.
Change-Id: I803a68c04923c96f793d508c23bb08069524bc63
| Ricardo Wurmus | 10 days | 1 | -1/+3 |
| * | gnu: python-cwl-upgrader: Add missing inputs.•••* gnu/packages/bioinformatics.scm (python-cwl-upgrader)[native-inputs]: Add
python-setuptools and python-wheel.
Change-Id: I81531d588e6deb8a01c59f2a824b815e8f95e0f0
| Ricardo Wurmus | 10 days | 1 | -1/+1 |
| * | gnu: python-schema-salad: Update to 8.8.20241206093842.•••* 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
| Ricardo Wurmus | 10 days | 1 | -8/+16 |
| * | gnu: pyscenic: Update to 0.12.1-1.eaf23eb.•••* 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
| Ricardo Wurmus | 10 days | 1 | -27/+31 |
| * | gnu: macs-3: Add missing input.•••* gnu/packages/bioinformatics.scm (macs-3)[native-inputs]: Add python-wheel.
Change-Id: I22b8d8e144434ae537af7c113f4719392933e90c
| Ricardo Wurmus | 10 days | 1 | -1/+5 |
| * | gnu: python-py2bit: Use pyproject-build-system.•••* gnu/packages/bioinformatics.scm (python-py2bit)[build-system]: Use
pyproject-build-system.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: I6f66e5f3c0f7612f460e2a6fa931b4c456db6a1b
| Ricardo Wurmus | 10 days | 1 | -1/+2 |
| * | gnu: python-biom-format: Use pyproject-build-system.•••* 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
| Ricardo Wurmus | 10 days | 1 | -33/+15 |
| * | gnu: Add python-ngesh.•••* gnu/packages/bioinformatics.scm (python-ngesh): New variable.
Change-Id: If51f3075037647e319efa9468331677a845b30cb
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami | 2025-01-16 | 1 | -1/+28 |
| * | gnu: Add fast5.•••Moved here from guix-science.
* gnu/packages/bioinformatics.scm (fast5): New variable.
Change-Id: I3373be5d5c80f3600b88fd3f71eadf723443e1c9
| Ricardo Wurmus | 2025-01-15 | 1 | -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 Simon | 2025-01-14 | 1 | -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 Flashner | 2025-01-06 | 1 | -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 Wicki | 2025-01-05 | 1 | -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 Wurmus | 2025-01-01 | 1 | -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 Wurmus | 2025-01-01 | 1 | -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 Wurmus | 2025-01-01 | 1 | -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 Wurmus | 2025-01-01 | 1 | -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 Junjie | 2024-12-22 | 1 | -0/+1 |
| * | gnu: python-pyahocorasick: Fix build.•••* gnu/packages/bioinformatics.scm (python-pyahocorasick)[native-inputs]: Add
python-setuptools.
Change-Id: Icbeb9cc8a9a4b08d97e561454ce46a0a234c0852
| Danny Milosavljevic | 2024-12-21 | 1 | -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 Licht | 2024-12-18 | 1 | -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 Licht | 2024-12-18 | 1 | -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 Wurmus | 2024-12-15 | 1 | -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 Wurmus | 2024-12-15 | 1 | -9/+10 |
