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2022-05-31gnu: Remove pyicoteo.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (pyicoteo): Delete variable.
2022-05-31gnu: Remove python2-pbcore.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable.
2022-05-31gnu: Remove python2-pyfaidx.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable.
2022-05-31gnu: Remove python2-screed.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-screed): Delete variable.
2022-05-31gnu: Remove miso.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (miso): Delete variable.
2022-05-31gnu: Remove python2-warpedlmm.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable.
2022-05-31gnu: Remove poretools.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (poretools): Delete variable.
2022-05-31gnu: Remove python2-dendropy.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable.
2022-05-31gnu: Remove bamm.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (bamm): Delete variable.
2022-05-31gnu: Remove python2-pybedtools.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable.
2022-05-31gnu: Remove python2-htseq.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-htseq): Delete variable.
2022-05-31gnu: Remove pepr.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (pepr): Delete variable.
2022-05-31gnu: tetoolkit: Update to 2.2.1b.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (tetoolkit): Update to 2.2.1b. [python]: Delete argument. [phases]: Delete trailing #t. {make-writable}: Delete phase. {adjust-requirements}: New phase. {patch-invocations}: Use search-input-file. {wrap-program}: Use search-input-file. [inputs]: Remove python2-argparse. Replace python2-pysam with python-pysam. [home-page]: Update URL.
2022-05-31gnu: Remove python2-pybigwig.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable.
2022-05-31gnu: Remove ribodiff.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
2022-05-31gnu: Remove grit.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (grit): Delete variable.
2022-05-31gnu: Remove python2-fastalite.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-fastalite): Delete variable.
2022-05-31gnu: Remove python2-pyaudio.Maxim Cournoyer
* gnu/packages/audio.scm (python2-pyaudio): Delete variable.
2022-05-31gnu: Remove raul-devel.Maxim Cournoyer
* gnu/packages/audio.scm (raul-devel): Delete variable.
2022-05-31gnu: Remove raul.Maxim Cournoyer
* gnu/packages/audio.scm (raul): Delete variable.
2022-05-31gnu: Remove ingen.Maxim Cournoyer
* gnu/packages/music.scm (ingen): Delete variable.
2022-05-31gnu: Remove python2-pyalsaaudio.Maxim Cournoyer
* gnu/packages/audio.scm (python2-pyalsaaudio): Delete variable.
2022-05-31gnu: Remove graphios.Maxim Cournoyer
* gnu/packages/admin.scm (graphios): Delete variable.
2022-05-31gnu: Remove python2-langkit.Maxim Cournoyer
* gnu/packages/ada.scm (python2-langkit): Delete variable.
2022-05-31gnu: Remove python-pytest-runner-2.Maxim Cournoyer
* gnu/packages/check.scm (python-pytest-runner-2): Delete variable. (python2-pytest-runner): Likewise.
2022-05-31diagnostics: Fix typo about 0-indexed COL in location.Maxim Cournoyer
* guix/diagnostics.scm (source-properties->location): The location column is 0-indexed, not 1-indexed (the same as in source-properties, so the code is accurate).
2022-05-31utils: Add a %guix-source-root-directory procedure.Maxim Cournoyer
* guix/utils.scm (%guix-source-root-directory): New procedure.
2022-05-31utils: Add a 'delete-expression' procedure.Maxim Cournoyer
* guix/utils.scm: Fix copyright lines and order imports. (edit-expression): Fix typo in doc. Add a new 'include-trailing-newline?' keyword argument. Update doc. (delete-expression): New procedure.
2022-05-31etc/committer: Teach it how to commit package removal.Maxim Cournoyer
* etc/committer.scm.in (hunk-types): New variable. (<hunk>): Rename hunk-definition? getter to 'hunk-type'. (diff-info): Mute a git warning by separating file names from arguments with '--'. Rename the 'definitions?' variable to 'type'. Use the 'addition type when a new package addition is detected, 'removal when removed else #f. (add-commit-message): Re-indent. (remove-commit-message): New procedure. (main)[definitions]: Make commit message conditional depending on whether it is an addition or removal. [changes]: Adjust indentation.
2022-05-31etc/committer: Prefix (sxml xpath) symbols to avoid name conflict.Maxim Cournoyer
This avoids a naming conflict for 'filter', provided by both (srfi srfi-1) and (sxml xpath). * etc/committer.scm.in: Use 'use-modules' instead of 'import', and use a prefix for the (sxml xpath) module. (new-sexp): Adjust accordingly. (change-commit-message): Likewise.
2022-05-31packages: Fix typo in package-superseded doc.Maxim Cournoyer
* guix/packages.scm (package-superseded): Fix typo.
2022-05-31gnu: icecat: Update to 91.10.0-guix0-preview1 [security fixes].Mark H Weaver
Includes fixes for CVE-2022-31736, CVE-2022-31737, CVE-2022-31738, CVE-2022-31739, CVE-2022-31740, CVE-2022-31741, CVE-2022-31742, and CVE-2022-31747. * gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update. (icecat-source): Update gnuzilla commit, base version, and hashes.
2022-05-31gnu: ungoogled-chromium: Update to 102.0.5005.61-3.Marius Bakke
* gnu/packages/chromium.scm (%ungoogled-revision): Bump to latest. (%ungoogled-origin): Update hash.
2022-05-31gnu: python-sip-4: Update to 4.19.25.Efraim Flashner
* gnu/packages/qt.scm (python-sip-4): Update to 4.19.25.
2022-05-31gnu: guile-ac-d-bus: Run test suite.Maxim Cournoyer
* gnu/packages/patches/guile-ac-d-bus-fix-tests.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/guile-xyz.scm (guile-ac-d-bus) [source]: Apply patch. [phases]{check}: New phase. [native-inputs]: Add bash-minimal.
2022-05-31gnu: guile-ac-d-bus: Build and install info manual.Maxim Cournoyer
* gnu/packages/guile-xyz.scm (guile-ac-d-bus) [arguments]: Use gexps. [phases]{build-doc, install-doc}: New phases. [native-inputs]: Add texinfo.
2022-05-31gnu: python-distributed: Update to 2022.05.2.Ricardo Wurmus
* gnu/packages/python-science.scm (python-distributed): Update to 2022.05.2. [arguments]: Remove 'sanity-check phase; adjust 'check phase. [propagated-inputs]: Add python-urllib3. [native-inputs]: Add python-pytest-timeout and python-flaky.
2022-05-31gnu: r-haven: Fix build.Ricardo Wurmus
* gnu/packages/cran.scm (r-haven)[arguments]: Adjust 'unbundle-readstat phase. Reported-by: Jonas Freimuth.
2022-05-31gnu: python-fsspec: Update to 2022.5.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-fsspec): Update to 2022.5.0.
2022-05-31image: Add fat32 support.Pavel Shlyak
* gnu/build/image.scm (make-vfat-image): Pass fs-bits as an argument and force 1kb logical sector size only if "ESP" flag is set. (make-partition-image): Add "fat32" partition type, support explicit "fat16" type with vfat alias. * gnu/system/image.scm (partition->dos-type partition): Return file system IDs for "fat16" and "fat32" partitions. (partition->gpt-type partition): Ditto. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2022-05-31gnu: emacs-helpful: Update to 0.19yarl baudig
* gnu/packages/patches/emacs-helpful-docstring-test.patch: New file. * gnu/packages/emacs-xyz.scm (emacs-helpful): Update to 0.19. [source]: Use the patch. * gnu/local.mk (dist_patch_DATA): Register the patch. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2022-05-30gnu: gandi.cli: Fix by downgrading python-click.Pierre Langlois
* gnu/packages/python-xyz.scm (python-click-7): New variable. * gnu/packages/networking.scm (gandi.cli)[inputs]: Depend on python-click-7.
2022-05-30gnu: python-click@8: Remove redundant package.Pierre Langlois
The python-click package is already version 8. * gnu/packages/python-xyz.scm (python-click-8): Remove variable. (python-proselint)[propagated-inputs]: Depend on python-click.
2022-05-30gnu: python-scanpy: Update to 1.9.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.1. [arguments]: Add phase 'set-numba-cache-dir; disable more broken tests. [propagated-inputs]: Add python-dask and python-session-info; replace python-louvain-0.7 with python-louvain.
2022-05-30gnu: python-leidenalg: Update to 0.8.10.Ricardo Wurmus
* gnu/packages/graph.scm (python-leidenalg): Update to 0.8.10. [arguments]: Patch setup.py. [native-inputs]: Remove python-setuptools; add python-setuptools-scm.
2022-05-30gnu: python-dask: Update to 2022.05.2.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask): Update to 2022.05.2.
2022-05-30gnu: Add python-session-info.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-session-info): New variable.
2022-05-30gnu: non-sequencer: Update to 1.9.5-5.257ec59.Ricardo Wurmus
* gnu/packages/music.scm (non-sequencer): Update to 1.9.5-5.257ec59. [source]: Use fork as old repository is defunct; use git-file-name and git-version. [arguments]: Remove python-2; add phase to replace bundled waf. [native-inputs]: Add python-waf. (non-session-manager)[native-inputs]: Add python-waf. (non-mixer)[inputs]: Add lv2 and lilv. [native-inputs]: Add python-waf. (non-timeline)[native-inputs]: Add python-waf.
2022-05-30gnu: quodlibet: Correct wrappers.Liliana Marie Prikler
* gnu/packages/music.scm (quodlibet)[#:phases]: Rename ‘wrap-gi-typelib’ to ‘wrap-extra-paths’. Use ‘=’ for GI_TYPELIB_PATH. Add ‘GST_PLUGIN_SYSTEM_PATH’ with suffix binding.
2022-05-30gnu: calceph: Add 'release-monitoring-url' property.Ludovic Courtès
* gnu/packages/astronomy.scm (calceph)[properties]: New field.
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