Age | Commit message (Collapse) | Author |
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* gnu/packages/bioinformatics.scm (pyicoteo): Delete variable.
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* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable.
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* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable.
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* gnu/packages/bioinformatics.scm (python2-screed): Delete variable.
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* gnu/packages/bioinformatics.scm (miso): Delete variable.
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* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable.
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* gnu/packages/bioinformatics.scm (poretools): Delete variable.
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* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable.
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* gnu/packages/bioinformatics.scm (bamm): Delete variable.
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* gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable.
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* gnu/packages/bioinformatics.scm (python2-htseq): Delete variable.
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* gnu/packages/bioinformatics.scm (pepr): Delete variable.
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* 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.
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* gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable.
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* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
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* gnu/packages/bioinformatics.scm (grit): Delete variable.
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* gnu/packages/bioinformatics.scm (python2-fastalite): Delete variable.
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* gnu/packages/audio.scm (python2-pyaudio): Delete variable.
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* gnu/packages/audio.scm (raul-devel): Delete variable.
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* gnu/packages/audio.scm (raul): Delete variable.
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* gnu/packages/music.scm (ingen): Delete variable.
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* gnu/packages/audio.scm (python2-pyalsaaudio): Delete variable.
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* gnu/packages/admin.scm (graphios): Delete variable.
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* gnu/packages/ada.scm (python2-langkit): Delete variable.
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* gnu/packages/check.scm (python-pytest-runner-2): Delete variable.
(python2-pytest-runner): Likewise.
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* 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).
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* guix/utils.scm (%guix-source-root-directory): New procedure.
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* 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.
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* 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.
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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.
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* guix/packages.scm (package-superseded): Fix typo.
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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.
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* gnu/packages/chromium.scm (%ungoogled-revision): Bump to latest.
(%ungoogled-origin): Update hash.
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* gnu/packages/qt.scm (python-sip-4): Update to 4.19.25.
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* 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.
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* gnu/packages/guile-xyz.scm (guile-ac-d-bus)
[arguments]: Use gexps.
[phases]{build-doc, install-doc}: New phases.
[native-inputs]: Add texinfo.
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* 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.
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* gnu/packages/cran.scm (r-haven)[arguments]: Adjust 'unbundle-readstat phase.
Reported-by: Jonas Freimuth.
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* gnu/packages/python-xyz.scm (python-fsspec): Update to 2022.5.0.
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* 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>
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* 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>
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* gnu/packages/python-xyz.scm (python-click-7): New variable.
* gnu/packages/networking.scm (gandi.cli)[inputs]: Depend on python-click-7.
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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.
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* 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.
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* gnu/packages/graph.scm (python-leidenalg): Update to 0.8.10.
[arguments]: Patch setup.py.
[native-inputs]: Remove python-setuptools; add python-setuptools-scm.
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* gnu/packages/python-xyz.scm (python-dask): Update to 2022.05.2.
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* gnu/packages/python-xyz.scm (python-session-info): New variable.
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* 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.
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* 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.
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* gnu/packages/astronomy.scm (calceph)[properties]: New field.
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