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2022-12-13gnu: python-flask-restful: Update to 0.3.9.Ricardo Wurmus
* gnu/packages/python-web.scm (python-flask-restful): Update to 0.3.9. [source]: Remove patch. [build-system]: Use pyproject-build-system. [arguments]: Disable "test_redirect" test; remove 'fix-imports phase. [native-inputs]: Replace python-nose with python-pytest. * gnu/local.mk (dist_patch_DATA): Remove patch. * gnu/packages/patches/python-flask-restful-werkzeug-compat.patch: Remove file.
2022-12-13gnu: python-cgatcore: Update to 0.6.14.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.14. [build-system]: Use pyproject-build-system. [arguments]: Disable broken tests with #:test-flags; do not replace 'check phase; add phase 'sqlite-compatibility. [native-inputs]: Drop input labels.
2022-12-13gnu: python-apsw: Update to 3.40.0.0.Ricardo Wurmus
* gnu/packages/databases.scm (python-apsw): Update to 3.40.0.0. [source]: Remove obsolete patch. [build-system]: Use pyproject-build-system. [native-inputs]: Add python-cython. [arguments]: Move build-extensions phase before build phase. * gnu/local.mk (dist_patch_DATA): Remove patch. * gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch: Remove file.
2022-12-13gnu: python-bokeh: Skip failing PIL test.Ricardo Wurmus
The test compares base64-encoded gifs; the gifs look identical but the base64-encoded data differs. Since the result seems fine, disabling this PIL test is probably okay. * gnu/packages/python-xyz.scm (python-bokeh)[arguments]: Ignore failing test_transform_PIL test.
2022-12-13gnu: python-dna-features-viewer: Update to 3.1.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dna-features-viewer): Update to 3.1.1. [build-system]: Use pyproject-build-system. [arguments]: Add build phase to fix a compatibility problem with biopython. [propagated-inputs]: Add python-packaging.
2022-12-13gnu: python-hicexplorer: Update to 3.7.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.2. [build-system]: Use pyproject-build-system. [arguments]: Use gexp; remove phase "loosen-up-requirements"; add test-flags to skip some tests; add phase "remove-dependency-on-krbalancing" to remove a dependency on an unlicensed package; add phase "fix-references"; add phase "run-only-low-mem-tests". [propagated-inputs]: Remove python-configparser and python-six; add python-biopython, python-cleanlab-1, python-fit-nbinom, python-graphviz, python-hic2cool, python-hicmatrix, python-hyperopt, python-imbalanced-learn, python-ipykernel, python-psutil, python-pybedtools, python-pygenometracks, python-scikit-learn, and python-tqdm. [native-inputs]: Add graphviz.
2022-12-13gnu: python-pygenometracks: Update to 3.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.5. [build-system]: Use pyproject-build-system. [arguments]: Quote phases instead of full list of arguments; remove trailing #T from build phase.
2022-12-13gnu: python-hicmatrix: Update to 16.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 16. [build-system]: Use pyproject-build-system. [arguments]: Shuffle the quote.
2022-12-13gnu: python-biopython: Update to 1.80.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.80. [build-system]: Use pyproject-build-system. [arguments]: Remove trailing #T from build phase.
2022-12-13gnu: python-hyperopt: Update to 0.2.7.Ricardo Wurmus
* gnu/packages/machine-learning.scm (python-hyperopt): Update to 0.2.7. [arguments]: Adjust check phase; disable test_distribution_rvs test. [build-system]: Use pyproject-build-system. [propagated-inputs]: Add python-py4j. [native-inputs]: Remove python-ipython and python-ipyparallel.
2022-12-13gnu: python-graphviz: Update to 0.20.1.Ricardo Wurmus
* gnu/packages/graphviz.scm (python-graphviz): Update to 0.20.1. [build-system]: Use pyproject-build-system. [arguments]: Remove custom "check" phase; add "prepare-check" phase. [native-inputs]: Remove python-mock.
2022-12-12gnu: python-anndata: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-anndata)[build-system]: Use pyproject-build-system. [arguments]: Replace custom 'build phase with 'set-version phase; remove custom 'install phase; disable doctest via build phase 'disable-doctests and the #:test-flags property. [propagated-inputs]: Add python-scikit-learn. [native-inputs]: Add python-boltons.
2022-12-12gnu: python-zarr: Update to 2.13.3.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-zarr): Update to 2.13.3.
2022-12-12gnu: python-numcodecs: Update to 0.10.2.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-numcodecs): Update to 0.10.2. [build-system]: Use pyproject-build-system. [arguments]: Enable tests; add phase 'build-extensions; remove custom 'check phase. [propagated-inputs]: Add python-entrypoints and python-typing-extensions-next.
2022-12-12gnu: python-typer: Simplify by using pyproject-build-system.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-typer)[build-system]: Use pyproject-build-system. [arguments]: Remove extra quoting; remove custom 'build phase; remove custom 'install phase; remove custom 'check phase; add 'pre-check phase. [synopsis]: Pull onto the same line. [description]: Reformat.
2022-12-12gnu: Add erlang-yamerl.jgart
* gnu/packages/erlang.scm (erlang-yamerl): New variable. Signed-off-by: Christopher Baines <mail@cbaines.net>
2022-12-12gnu: Add erlang-jsx.jgart
* gnu/packages/erlang.scm (erlang-jsx): New variable. Signed-off-by: Christopher Baines <mail@cbaines.net>
2022-12-12services: guix-build-coordinator: Fix service startup.Christopher Baines
Previously the service would keep starting more and more processes. * gnu/services/guix.scm (guix-build-coordinator-shepherd-services): Fix how make-forkexec-constructor is called.
2022-12-12gnu: re2: Update to 2022-12-01.Marius Bakke
* gnu/packages/regex.scm (re2): Update to 2022-12-01.
2022-12-12tests: Add system tests for each supported kernel version.Marius Bakke
* gnu/tests/base.scm (%test-basic-os): Rename to ... (test-basic-os): ... this, and turn into procedure that takes optional KERNEL argument. (%test-basic-os): Use that procedure. (%test-linux-libre-5.15, %test-linux-libre-5.10, %test-linux-libre-5.4, %test-linux-libre-4.19, %test-linux-libre-4.14, %test-linux-libre-4.9): New tests.
2022-12-12gnu: f2fs-tools: Remove obsolete phase.Marius Bakke
* gnu/packages/linux.scm (f2fs-tools)[arguments]: Remove. (f2fs-tools-1.7)[arguments]: Add #:phases.
2022-12-12gnu: f2fs-tools: Update to 1.15.0.Marius Bakke
* gnu/packages/linux.scm (f2fs-tools): Update to 1.15.0. (f2fs-tools/static)[arguments]: Add #:make-flags. Remove make-static phase.
2022-12-12gnu: f2fs-tools@1.7: Don't fetch autogenerated git snapshot.Marius Bakke
* gnu/packages/linux.scm (f2fs-tools-1.7)[source]: Switch to GIT-FETCH.
2022-12-12gnu: f2fs-tools: Don't fetch autogenerated git snapshot.Marius Bakke
* gnu/packages/linux.scm (f2fs-tools)[source]: Switch to GIT-FETCH.
2022-12-12gnu: f2fs-tools: Reverse inheritance relationship.Marius Bakke
* gnu/packages/linux.scm (f2fs-tools): Update to 1.14.0. [arguments]: Remove obsolete #:configure-flags and trailing #t in phase. [inputs]: Remove labels. (f2fs-tools-1.7): Inherit from above; add #:configure-flags. [inputs]: Remove labels.
2022-12-12gnu: ungoogled-chromium: Build with ffmpeg@4.Marius Bakke
This is a follow-up to commit 79564bf9977ebba0b31d8dc291eb039142f51f68. * gnu/packages/chromium.scm (ungoogled-chromium)[inputs]: Change from FFMPEG to FFFMPEG-4.
2022-12-12gnu: Add r-golem.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-golem): New variable.
2022-12-12gnu: Add r-attempt.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-attempt): New variable.
2022-12-12gnu: Add r-anytime.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-anytime): New variable.
2022-12-12gnu: Add r-shinycustomloader.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-shinycustomloader): New variable.
2022-12-12gnu: Add r-logging.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-logging): New variable.
2022-12-12gnu: Add r-asics.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-asics): New variable.
2022-12-12gnu: Add r-pepsnmr.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-pepsnmr): New variable.
2022-12-12gnu: Add r-ptw.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-ptw): New variable.
2022-12-12gnu: Add r-rcppde.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-rcppde): New variable.
2022-12-12gnu: Add r-animalcules.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-animalcules): New variable.
2022-12-12gnu: Add r-plotroc.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-plotroc): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2022-12-12gnu: Add r-gridsvg.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-gridsvg): New variable.
2022-12-12gnu: Add r-gunifrac.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-gunifrac): New variable.
2022-12-12gnu: Add r-dirmult.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-dirmult): New variable.
2022-12-12gnu: Add r-modeest.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-modeest): New variable.
2022-12-12gnu: Add r-fbasics.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-fbasics): New variable.
2022-12-12gnu: Add r-timeseries.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-timeseries): New variable.
2022-12-12gnu: Add r-gss.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-gss): New variable.
2022-12-12gnu: Add r-stable.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-stable): New variable.
2022-12-12gnu: Add r-rmutil.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-rmutil): New variable.
2022-12-12gnu: Add r-statip.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-statip): New variable.
2022-12-12gnu: Add r-amplican.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-amplican): New variable.
2022-12-12gnu: Add r-waffle.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-waffle): New variable.
2022-12-12gnu: Add r-clustercrit.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-clustercrit): New variable.
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