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Author SHA1 Message Date
Marius Bakke 303ef489a1
gnu: rust-bytemuck-derive: Update to 1.3.0. 
* gnu/packages/crates-io.scm (rust-bytemuck-derive-1): Update to 1.3.0.
 2022-12-02 22:44:27 +01:00
Marius Bakke d64e4ad910
gnu: rust-typenum: Update to 1.15.0. 
* gnu/packages/crates-io.scm (rust-typenum-1): Update to 1.15.0.
[arguments]: Add RUST-SCALE-INFO-1 to #:cargo-inputs.
 2022-12-02 22:44:27 +01:00
Marius Bakke 4f427b2e59
gnu: rust-const-oid: Add 0.9.1. 
* gnu/packages/crates-io.scm (rust-const-oid-0.9): New variable.
(rust-const-oid-0.6): Inherit from it.
 2022-12-02 22:44:27 +01:00
Marius Bakke 6187b7de44
gnu: rust-cookie: Move versions closer together. 
* gnu/packages/crates-io.scm (rust-cookie-0.15): Move above other cookies.
(rust-cookie-0.12): Inherit from it.
 2022-12-02 22:44:27 +01:00
Marius Bakke 9202eda3b2
gnu: rust-crypto-common: Update to 0.1.6. 
* gnu/packages/crates-io.scm (rust-crypto-common-0.1): Update to 0.1.6.
[arguments]: Add RUST-TYPENUM to #:cargo-inputs.
 2022-12-02 22:44:06 +01:00
Marius Bakke 92c5f39204
gnu: Add rust-uuid-macro-internal. 
* gnu/packages/crates-io.scm (rust-uuid-macro-internal): New variable.
 2022-12-02 22:44:06 +01:00
Marius Bakke ad1c35b332
gnu: rust-tinyvec: Update to 1.6.0. 
* gnu/packages/crates-io.scm (rust-tinyvec-1): Update to 1.6.0.
[arguments]: Add RUST-ARBITRARY-1 to #:cargo-inputs.
 2022-12-02 22:44:06 +01:00
Marius Bakke 0de1599c98
gnu: rust-arbitrary: Update to 1.2.0. 
* gnu/packages/crates-io.scm (rust-arbitrary-1, rust-derive-arbitrary-1):
Update to 1.2.0.
 2022-12-02 22:44:06 +01:00
Marius Bakke 042ce76caf
gnu: rust-xcb: Add 1.2.0. 
* gnu/packages/crates-io.scm (rust-xcb-1): New variable.
(rust-xcb-0.9): Inherit from it.
 2022-12-02 22:44:05 +01:00
Marius Bakke c3407d52b4
gnu: rust-x11: Update to 2.20.1. 
* gnu/packages/crates-graphics.scm (rust-x11-2): Update to 2.20.1.
[propagated-inputs]: Add MESA.
 2022-12-02 22:44:05 +01:00
Marius Bakke b4f5b54703
gnu: rust-pkg-config: Update to 0.3.26. 
* gnu/packages/crates-io.scm (rust-pkg-config-0.3): Update to 0.3.26.
 2022-12-02 22:44:05 +01:00
Marius Bakke e5455bef85
Merge branch 'master' into staging 2022-12-02 22:42:47 +01:00
Marius Bakke 51d6bd3507
gnu: Add rust-k9. 
* gnu/packages/crates-io.scm (rust-k9-0.11): New variable.
 2022-12-02 22:21:42 +01:00
Marius Bakke 3c5cbd3c9d
gnu: rust-digest: Update to 0.10.6. 
* gnu/packages/crates-io.scm (rust-digest-0.10): Update to 0.10.6.
 2022-12-02 22:21:42 +01:00
Marius Bakke 2066ae53f1
gnu: QtWebEngine: Use more system libraries. 
* gnu/packages/qt.scm (qtwebengine)[source](snippet): Remove more files.
[arguments]: Pass QT_FEATURES_system_foo for all supported libraries.
[inputs]: Replace "harfbuzz" with HARFBUZZ-5.
 2022-12-02 22:21:42 +01:00
Ricardo Wurmus fd44d489b5
gnu: python-biom-format: Update to 2.1.12. 
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.12.
[arguments]: Remove "relax" phase; update "disable-broken-tests" phase.
[propagated-inputs]: Add python-scikit-bio.
 2022-12-02 21:46:36 +01:00
Ricardo Wurmus b93e21a213
gnu: Add python-scikit-bio. 
* gnu/packages/bioinformatics.scm (python-scikit-bio): New variable.
 2022-12-02 21:46:36 +01:00
Ricardo Wurmus b2a9feab92
gnu: Add python-hdmedians. 
* gnu/packages/statistics.scm (python-hdmedians): New variable.
 2022-12-02 21:46:36 +01:00
Ricardo Wurmus 62da3f9837
gnu: python-pairtools: Update to 1.0.2. 
* gnu/packages/bioinformatics.scm (python-pairtools): Update to 1.0.2.
[source]: Update Github URL.
[arguments]: Update patch in "fix-references" phase.
[native-inputs]: Remove python-nose.
[inputs]: Remove.
[propagated-inputs]: Add python-bioframe, python-pandas, python-pysam,
python-pyyaml, and python-scipy.
[home-page]: Update.
 2022-12-02 21:46:36 +01:00
Ricardo Wurmus 089b2e4f65
gnu: python-pairtools: Run tests conditionally. 
* gnu/packages/bioinformatics.scm (python-pairtools)[arguments]: Run tests
conditionally.
 2022-12-02 21:46:36 +01:00
Ricardo Wurmus 631ea9a411
gnu: python-pybedtools: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-pybedtools)[build-system]: Use
pyproject-build-system.
[arguments]: Import (guix build pyproject-build-system).
 2022-12-02 21:46:36 +01:00
Ricardo Wurmus a268b1ba91
gnu: python-htsget: Update to 0.2.6. 
* gnu/packages/bioinformatics.scm (python-htsget): Update to 0.2.6.
[build-system]: Use pyproject-build-system.
 2022-12-02 21:46:35 +01:00
Ricardo Wurmus 16ecce39d2
gnu: python-cellbender: Update to 0.2.2. 
* gnu/packages/bioinformatics.scm (python-cellbender): Update to 0.2.2.
[build-system]: Use pyproject-build-system.
 2022-12-02 21:46:35 +01:00
Marius Bakke f2b6350a50
Merge branch 'master' into staging 2022-12-02 19:13:45 +01:00
Marius Bakke 365b0b5533
gnu: ungoogled-chromium: Use git tag in ungoogled origin. 
* gnu/packages/chromium.scm (%ungoogled-origin)[uri]: Use %UNGOOGLED-REVISION
instead of commit identifier.
 2022-12-02 19:10:51 +01:00
Marius Bakke 11b0670a9d
gnu: kicad: Remove obsolete phases. 
* gnu/packages/engineering.scm (kicad)[arguments]: Remove two phases.
 2022-12-02 19:08:27 +01:00
Marius Bakke ea0e6e5d65
gnu: golly: Update to 4.2. 
* gnu/packages/games.scm (golly): Update to 4.2.
[arguments]: Remove configure phase.
[inputs]: Remove PYTHON-2 and WXWIDGETS-GTK2.  Add PYTHON, SDL2, and
WXWIDGETS.  Remove labels while at it.
 2022-12-02 19:08:27 +01:00
Marius Bakke 6aac95ae2b
gnu: python-wxpython: Update to 4.2.0. 
* gnu/packages/wxwidgets.scm (python-wxpython): Update to 4.2.0.
[propagated-inputs]: Add PYTHON-ATTRDICT.
 2022-12-02 19:08:27 +01:00
Marius Bakke f16358144f
gnu: wxWidgets: Update to 3.2.1. 
* gnu/packages/wxwidgets.scm (wxwidgets): Update to 3.2.1.
[source](modules, snippet): New fields.
[inputs]: Remove SDL.  Add CATCH-FRAMEWORK, EXPAT, GSTREAMER,
GST-PLUGINS-BASE, LIBNOTIFY, LIBPNG, LIBSECRET, PCRE, SDL2,
WEBKITGTK-WITH-LIBSOUP2, and ZLIB
[arguments]: Add "--enable-mediactrl" and "--enable-gui" to #:configure-flags.
Remove aarch64 workaround.  Install catch header in refer-to-inputs phase.
Add phase to adjust WebKitGTK version.
(wxwidgets-3.1, wxwidgets-gtk2-3.1): Remove variables.
(wxwidgets-3.0, (wxwidgets-gtk2-3.0): New variables.
(wxsvg)[inputs]: Change from WXWIDGETS-3.1 to WXWIDGETS.
* gnu/packages/audio.scm (audacity)[inputs]: Likewise.
* gnu/packages/cdrom.scm (dvdstyler)[inputs]: Likewise.
* gnu/packages/astronomy.scm (imppg)[inputs]: Change from WXWIDGETS to
WXWIDGETS-3.0.
* gnu/packages/ftp.scm (filezilla)[inputs]: Likewise.
* gnu/packages/games.scm (megaglest)[inputs]: Likewise.
* gnu/packages/geo.scm (opencpn)[inputs]: Likewise.
* gnu/packages/music.scm (sooperlooper)[inputs]: Likewise.
* gnu/packages/engineering.scm (kicad)[arguments]: Enable EGL support.
 2022-12-02 19:08:27 +01:00
Marius Bakke 8737ee0479
gnu: wxWidgets: Remove input labels. 
* gnu/packages/wxwidgets.scm (wxwidgets)[inputs]: Remove labels.
[arguments]: Use SEARCH-INPUT-FILE.
(wxwidgets-gtk2)[inputs]: Use MODIFY-INPUTS.
 2022-12-02 19:08:27 +01:00
Marius Bakke 2cf835ae28
gnu: jucipp: Update to 1.7.2. 
* gnu/packages/text-editors.scm (jucipp): Update to 1.7.2.
[arguments]: Skip one more test.
 2022-12-02 19:08:26 +01:00
Marius Bakke fa3dac025a
gnu: universal-ctags: Update to 5.9.20221127.0. 
* gnu/packages/code.scm (universal-ctags): Update to 5.9.20221127.0.
 2022-12-02 19:08:26 +01:00
Ricardo Wurmus 62ddd3bc80
gnu: Add python-fanc. 
* gnu/packages/bioinformatics.scm (python-fanc): New variable.

Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
 2022-12-02 17:43:20 +01:00
Ricardo Wurmus ee069ec651
gnu: Add python-genomic-regions. 
* gnu/packages/bioinformatics.scm (python-genomic-regions): New variable.

Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
 2022-12-02 17:20:54 +01:00
Navid Afkhami 9ddc4e5b03
gnu: python-msgpack-numpy: Update to 0.4.8. 
* gnu/packages/python-science.scm (python-msgpack-numpy): Update to 0.4.8.
 2022-12-02 15:04:15 +01:00
Ricardo Wurmus 0c2dad9951
gnu: Add python-pybloom-live. 
* gnu/packages/python-xyz.scm (python-pybloom-live): New variable.
 2022-12-02 15:03:00 +01:00
Ricardo Wurmus 840d543939
gnu: python-xxhash: Update to 3.1.0. 
* gnu/packages/digest.scm (python-xxhash): Update to 3.1.0.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-setuptools-scm.
 2022-12-02 15:03:00 +01:00
Maxim Cournoyer 4781f0458d
Revert "gnu: linux-libre: Move info manual to doc output." 
This reverts commit 748ec62882.  It broke the
linux-libre-module-builder like so:

   builder for
   `/gnu/store/293jxydym9z7ck7afmrjqhiw3xpfs4i1-linux-libre-module-builder-6.0.10.drv'
   failed to produce output path
   `/gnu/store/ghmp1q5w6r1s9364rz53jd42152wgz2v-linux-libre-module-builder-6.0.10-doc'

for reasons difficult to understand.
 2022-12-01 21:37:12 -05:00
Marius Bakke 2775bb95c7
gnu: ungoogled-chromium: Update to 108.0.5359.71-1. 
* gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for M108.
(%chromium-version): Set to 108.0.5359.71-1.
(%arch-revision): Bump to newer commit.
(%ungoogled-origin): Update hash.
(%gcc-patches): Remove.
(%reverse-patches): Remove one patch.
(%arch-patches): New variable.
(%patches): New variable.
(ungoogled-chromium-snippet): Apply %PATCHES instead of individual variables.
(ungoogled-chromium)[source]: Update hash.
[arguments]: Adjust configure flag.
[inputs]: Change from HARFBUZZ-3 to HARFBUZZ-5.
 2022-12-02 00:21:25 +01:00
Marius Bakke 503fb0dcb4
gnu: ungoogled-chromium: Generalize OpenJPEG substitution. 
* gnu/packages/chromium.scm (ungoogled-chromium)[arguments]: Don't hard code
openjpeg version.
 2022-12-02 00:21:25 +01:00
Marius Bakke 1a8d063a44
gnu: harfbuzz: Add 5.3.1. 
* gnu/packages/gtk.scm (harfbuzz-5): New variable.
 2022-12-02 00:21:25 +01:00
Marius Bakke c091339204
gnu: balsa: Update to 2.6.4. 
* gnu/packages/mail.scm (balsa): Update to 2.6.4.
 2022-12-02 00:21:25 +01:00
Marius Bakke dee7c94b59
gnu: balsa: Add release-monitoring-url. 
* gnu/packages/mail.scm (balsa)[properties]: New field.
 2022-12-02 00:21:25 +01:00
Marius Bakke 168afe2976
gnu: svt-av1: Update to 1.3.0. 
* gnu/packages/video.scm (svt-av1): Update to 1.3.0.
[supported-systems]: Remove.
[description]: Update.
 2022-12-02 00:21:25 +01:00
Marius Bakke 84c577d7a7
gnu: QtWebEngine: Simplify code to remove third-party files. 
* gnu/packages/qt.scm (remove-third-party-files): Simplify some procedures.
 2022-12-02 00:21:25 +01:00
Marius Bakke 9252f14722
gnu: qtwebengine@6: Fix third-party code removal snippet. 
* gnu/packages/qt.scm (qtwebengine-5)[source](snippet): Move code to delete
third-party files out to ...
(remove-third-party-files): ... this new variable.
(qtwebengine)[source](snippet): Use that variable instead of the broken
duplicate implementation.  Adjust PRESERVED-THIRD-PARTY-FILES accordingly.
[native-inputs]: Add PYTHON-BEAUTIFULSOUP4.
 2022-12-02 00:21:25 +01:00
Marius Bakke 6f0a8371fe
gnu: gn: Use G-expression. 
* gnu/packages/build-tools.scm (gn)[arguments]: Convert to G-expression.
 2022-12-02 00:21:24 +01:00
Marius Bakke e069db7e30
gnu: gn: Remove input labels. 
* gnu/packages/build-tools.scm (gn)[native-inputs]: Remove labels.
 2022-12-02 00:21:24 +01:00
Marius Bakke c02a77bdd6
gnu: gn: Update to 0.0-2072.1c4151f. 
* gnu/packages/build-tools.scm (gn): Update to 0.0-2072.1c4151f.
[arguments]: Adjust create-last-commit-position phase to be identical with
upstream code.
 2022-12-02 00:21:24 +01:00
Marius Bakke 34a70b1f86
gnu: balsa: Fix build. 
* gnu/packages/mail.scm (balsa)[arguments]: Add #:phase to build with newer
WebKitGTK.
[inputs]: Change from GTKSOURCEVIEW to GTKSOURCEVIEW-4.
 2022-12-02 00:21:24 +01:00