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2026-03-05python: tensorflow: Update to 2.18.1.wip-tensorflowRicardo Wurmus1-19/+91
Unlike version 2.20.0, this version lets us use Bazel 6.5, which we have previously packaged. Unlike 2.13.1 this version works with Numpy 2, which has become the default for Python packages in Guix. * guix-science/packages/python.scm (tensorflow-system-libs): Adjust. (tensorflow)[source]: Patch sources to inject a patch for Python toolchain discovery. [arguments]: Use bazel-6.5; update the fetch and build targets; adjust the 'configure phase; override the platforms repository; adjust 'install phase due to script name change. [native-inputs]: Remove python-setuptools and add bazel platforms 0.0.8.
2026-03-05Revert "python: tensorflow: Update to 2.20.0."Ricardo Wurmus1-2/+2
This reverts commit 39a038c54c2047b04cf6c51550554cabb54b935d. See https://codeberg.org/guix-science/guix-science/issues/593
2026-03-05rstudio: rstudio-server: Update to 2023.12.1+402.Ricardo Wurmus2-166/+251
* patches/rstudio-server-install.patch: New file. * guix-science/packages/rstudio.scm (rstudio-server) [source]: Fetch from upstream repository; add patch. [arguments]: Drop unnecessary configure flag; set RSTUDIO_NODE_VERSION; add phase 'create-os-release; update phase 'patch-paths to address node locations; use THIS-PACKAGE-INPUT where possible. [native-inputs]: Drop labels. [inputs]: Drop labels; add node.
2026-03-04neuroscience: elastix: Update to 5.3.0.Jake Forster1-6/+13
* guix-science/packages/neuroscience.scm (elastix): Update to 5.3.0. [arguments]<#:test-exclude>: Exclude failing tests. Signed-off-by: Ghislain Vaillant <ghislain.vaillant@inria.fr>
2026-03-04medical: stir: Fix build.Jake Forster1-1/+1
* guix-science/packages/medical.scm (stir) [native-inputs]: Replace swig-next with swig-4.0. Signed-off-by: Ghislain Vaillant <ghislain.vaillant@inria.fr>
2026-03-02bioinformatics: Add staden-io-lib.Ghislain Vaillant1-0/+63
* guix-science/packages/bioinformatics.scm (staden-io-lib): New variable.
2026-02-26bazel: bazel-6.1: Fix build.Ricardo Wurmus1-0/+10
* guix-science/packages/bazel.scm (bazel-6.1)[arguments]: Ignore implicit function declarations in zlib; link with -labsl_synchronization.
2026-02-25rstudio: Fix build of rstudio-server-multi-version.Ricardo Wurmus9-133/+153
The patches from the upstream fork were outdated and did not actually work for version 2023.06.1+524. * patches/rstudio-server-multi-version: Update patches from upstream. * guix-science/packages/rstudio.scm (rstudio-server-multi-version) [source]: Replace patches. [arguments]: Add phase 'patch-gwt-build. [native-inputs]: Add python-wrapper and python-lxml.
2026-02-25machine-learning: python-datasets: Fix build.Ghislain Vaillant1-9/+12
* guix-science/packages/machine-learning.scm (python-datasets) [arguments]<#:test-flags>: Ignore integration tests, they require many optional dependencies and would increase the closure size for little benefit. [native-inputs]: Add python-backports-zstd.
2026-02-25python-xyz: Add python-deisa.Benoit Martin1-0/+23
Signed-off-by: Romain GARBAGE <romain.garbage@inria.fr>
2026-02-25machine-learning: python-ray/wheel: Update vendored inputs hash.Romain GARBAGE1-1/+1
* guix-science/packages/machine-learning.scm (python-ray/wheel): Update vendored inputs hash.
2026-02-25python-xyz: Add python-deisa-dask.Benoit Martin1-0/+23
Signed-off-by: Romain GARBAGE <romain.garbage@inria.fr>
2026-02-25python-xyz: Add python-deisa-core.Benoit Martin1-0/+22
Signed-off-by: Romain GARBAGE <romain.garbage@inria.fr>
2026-02-25version-control: python-scmrepo: Update to 3.6.1.Ghislain Vaillant1-8/+14
* guix-science/packages/version-control.scm (python-scmrepo) [source]: Update to 3.6.1, update URL. [arguments]<#:test-flags>: Update filters. [propagated-inputs]: Replace python-dulwich-0.24 by python-dulwich. [native-inputs]: Remove python-pytest-test-utils. [description]: Rephrase.
2026-02-25version-control: python-dvc-task: Update metadata.Ghislain Vaillant1-1/+2
* guix-science/packages/version-control.scm (python-dvc-task) [description]: Rephrase.
2026-02-25version-control: python-dvc-studio-client: Update metadata.Ghislain Vaillant1-5/+4
* guix-science/packages/version-control.scm (python-dvc-studio-client) [source]: Update URL. [propagated-inputs]: Replace python-dulwich-0.24 by python-dulwich. [home-page]: Use the same as dvc. [description]: Rephrase.
2026-02-25version-control: python-dvc-ssh: Update metadata.Ghislain Vaillant1-2/+2
* guix-science/packages/version-control.scm (python-dvc-ssh) [source]: Update URL. [description]: Rephrase.
2026-02-25version-control: python-dvc-render: Update metadata.Ghislain Vaillant1-2/+2
* guix-science/packages/version-control.scm (python-dvc-render) [source]: Update URL. [home-page]: Use the same as dvc.
2026-02-25version-control: python-dvc-http: Update metadata.Ghislain Vaillant1-2/+2
* guix-science/packages/version-control.scm (python-dvc-http) [source]: Update URL. [description]: Rephrase.
2026-02-25version-control: dvc: Improve style.Ghislain Vaillant1-10/+9
* guix-science/packages/version-control.scm (dvc) [arguments]<#:phases>: Use full phase names, use serach-input-file instead of which. [inputs]: Move below propagated-inputs.
2026-02-25version-control: Add python-dvc-objects.Ghislain Vaillant1-0/+37
* guix-science/packages/version-control.scm (python-dvc-objects): New variable.
2026-02-25version-control: Add python-dvc-data.Ghislain Vaillant1-0/+43
* guix-science/packages/version-control.scm (python-dvc-data): New variable.
2026-02-25version-control: dvc: Update to 3.66.1.Ghislain Vaillant1-20/+12
* guix-science/packages/version-control.scm (dvc) [source]: Update to 3.66.1, update URL. [arguments]<#:test-flags>: Run unit tests only, update filters. [propagated-inputs]: Replace python-dulwich-0.24 by python-dulwich. [native-inputs]: Add python-breautifulsoup4, remove python-pytest-test-utils.
2026-02-25README: Add a paragraph related to commit formatting.Romain GARBAGE1-0/+34
* README.rst: Add a paragraph related to commit formatting.
2026-02-25README: Refactor Contributing/Hacking this repository sections.Romain GARBAGE1-12/+12
* README.rst: Move guix lint/packaging guideline bits from the Contributing section to the Hacking this repository section.
2026-02-24bioinformatics: Rename cat to cat-pack.Ghislain Vaillant1-2/+5
* guix-science/packages/bioinformatics.scm: Rename cat to cat-pack, declare cat as a deprecated alias.
2026-02-24bioinformatics: cat: Update to 6.0.1.Ghislain Vaillant1-12/+26
* guix-science/packages/bioinformatics.scm (cat) [source]: Update to 6.0.1. [arguments]<#:phases>: Replace CAT with CAT_pack. [inputs]: Add bash-minimal, bwa, mmseqs2 and samtools.
2026-02-23rstudio: rstudio-server: Use Boost@1.83.Simon Tournier1-1/+1
* guix-science/packages/rstudio.scm (rstudio-server)[inputs]: Replace 'boost' by older version 'boost-1.83'.
2026-02-23machine-learning: python-tensorstore: Update to 0.1.80.Romain GARBAGE1-20/+2
* guix-science/packages/machine-learning.scm (python-tensorstore): Update to 0.1.80.
2026-02-23machine-learning: python-tensorstore: Fix after Numpy 2 update.Romain GARBAGE1-1/+1
* guix-science/packages/machine-learning.scm (python-tensorstore): Fix after Numpy 2 update.
2026-02-23machine-learning: python-tensorstore: Fix missing module error.Romain GARBAGE1-37/+44
* guix-science/packages/machine-learning.scm (python-tensorstore): Fix missing module error.
2026-02-22bioinformatics: Add mmseqs2.Ghislain Vaillant1-0/+46
* guix-science/packages/bioinformatics.scm (mmseqs2): New variable.
2026-02-21bioinformatics: cat: Update style.Ghislain Vaillant1-22/+28
* guix-science/packages/bioinformatics.scm (cat): Run guix lint. [description]: Use acronyms where appropriate.
2026-02-21bioinformatics: cat: Update to 5.3 and enable tests.Ghislain Vaillant1-15/+30
* guix-science/packages/bioinformatics.scm (cat) [source]: Update to 5.3. [arguments]<#:tests?>: Enable tests. <#:phases>: Simplify install phase, add separate wrap phase after install, fix wrapping of main executable.
2026-02-21bioinformatics: cat: Switch to git.Ghislain Vaillant1-9/+10
* guix-science/packages/bioinformatics.scm (cat) [source]: Switch to git, update remote. [home-page]: Change to new organisation.
2026-02-21machine-learning: python-datasets: Fix build.Ghislain Vaillant1-1/+1
* guix-science/packages/machine-learning.scm (python-datasets) [arguments]<#:phases>: Fix faulty regex in fix-requirements.
2026-02-21compression: Add bsc.Ghislain Vaillant1-0/+35
* guix-science/packages/compression.scm (bsc): New variable.
2026-02-20cran: r-reactlog: Add missing dependency.Simon Tournier1-1/+1
* guix-science/packages/cran.scm (r-reactlog)[native-inputs]: Add missing dependency and fix the build. Merges: #580
2026-02-20python-xyz: python-mayavi: Fix build.Ghislain Vaillant1-6/+6
* guix-science/packages/python-xyz.scm (python-mayavi) [arguments]<#:phases>: Replace before-check by start-xorg-server (after build) and build-extensions (before check). [propagated-inputs]: Replace vtk by vtk-9.4.
2026-02-20statistics: python-iterative-stats: Fix build.Ghislain Vaillant1-0/+5
* guix-science/packages/statistics.scm (python-iterative-stats) [arguments]<#:phases> Add fix-requirements phase after unpack, which removes upper version limits in dependencies.
2026-02-20machine-learning: python-melissa-core: Fix build.Ghislain Vaillant1-4/+7
* guix-science/packages/machine-learning.scm (python-melissa-core) [arguments]<#:phases>: Enable builds with numpy@2+.
2026-02-20bioinformatics: Add booster.Ghislain Vaillant1-0/+63
* guix-science/packages/bioinformatics.scm (booster): New variable.
2026-02-20bioinformatics: iqtree3: Use packaged cmaple and lsd2.Ghislain Vaillant1-15/+13
* guix-science/packages/bioinformatics.scm (iqtree3) [source]: Disable recursive git fetch. [arguments]<#:phases>: Copy cmaple and lsd2 sources where expected. [native-inputs]: Add (package-source cmaple) and (package-source lsd2).
2026-02-20bioinformatics: iqtree2: Use packaged cmaple and lsd2.Ghislain Vaillant1-15/+13
* guix-science/packages/bioinformatics.scm (iqtree2) [source]: Disable recursive git fetch. [arguments]<#:phases>: Copy cmaple and lsd2 sources where expected. [native-inputs]: Add (package-source cmaple) and (package-source lsd2).
2026-02-20bioinformatics: Add cmaple.Ghislain Vaillant1-0/+53
* guix-science/packages/bioinformatics.scm (cmaple): New variable.
2026-02-20bioinformatics: Add lsd2.Ghislain Vaillant1-0/+45
* guix-science/packages/bioinformatics.scm (lsd2): New variable.
2026-02-19bioinformatics: seqan: Fix build by using GCC@12.Simon Tournier1-1/+3
* guix-science/packages/bioinformatics.scm (seqan-3.0.2)[native-inputs]: Add gcc-toolchain-12. Merges: #570
2026-02-19algebra: chameleon: Exclude tests added in version 1.4.Romain GARBAGE1-1/+7
These tests are not relevant for testing basic MPI related functionality, they test custom distribution of tiles on MPI ranks. * guix-science/packages/algebra.scm (chameleon): Exclude tests added in version 1.4.
2026-02-19algebra: pastix: Run single precision tests only.Romain GARBAGE1-2/+5
Closes #563. * guix-science/packages/algebra.scm (pastix): Run single precision tests only.
2026-02-19python: tensorflow: Update to 2.20.0.Romain GARBAGE1-2/+2
* guix-science/packages/python.scm (tensorflow): Update to 2.20.0.
generated by cgit v1.2.3 (git 2.25.1) at 2026-09-03 05:15:04 +0000