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2022-12-04gnu: rust-proc-macro2: Update to 1.0.47.Marius Bakke
* gnu/packages/crates-io.scm (rust-proc-macro2-1): Update to 1.0.47.
2022-12-02gnu: rust-ordered-float: Add 3.4.0.Marius Bakke
* gnu/packages/crates-io.scm (rust-ordered-float-3): New variable. (rust-ordered-float-2): Inherit from it.
2022-12-02gnu: Add rust-speedy.Marius Bakke
* gnu/packages/crates-io.scm (rust-speedy-0.8, rust-speedy-derive-0.8): New variables.
2022-12-02gnu: rust-rkyv: Add 0.7.39.Marius Bakke
* gnu/packages/crates-io.scm (rust-rkyv-0.7, rust-rkyv-derive-0.7): New variables. (rust-rkyv-0.6, rust-rkyv-derive-0.6): Inherit accordingly.
2022-12-02gnu: Add rust-rend.Marius Bakke
* gnu/packages/crates-io.scm (rust-rend-0.3): New variable.
2022-12-02gnu: rust-bytecheck: Add 0.6.9.Marius Bakke
* gnu/packages/crates-io.scm (rust-bytecheck-0.6, rust-bytecheck-derive-0.6): New variables. (rust-bytecheck-0.5, rust-bytecheck-derive-0.5): Inherit accordingly.
2022-12-02gnu: rust-uuid: Add 1.2.2.Marius Bakke
* gnu/packages/crates-io.scm (rust-uuid-1): New variable. (rust-uuid-0.8): Inherit from it.
2022-12-02gnu: rust-bytemuck: Update to 1.12.3.Marius Bakke
* gnu/packages/crates-io.scm (rust-bytemuck-1): Update to 1.12.3. (rust-bytemuck-1.5): Remove variable. (rust-glam-0.17, rust-glam-0.16, rust-glam-0.15, rust-glam-0.14, rust-glam-0.13, rust-nalgebra-0.26)[arguments]: Change from RUST-BYTEMUCK-1.15 to RUST-BYTEMUCK-1.
2022-12-02gnu: rust-bytemuck-derive: Update to 1.3.0.Marius Bakke
* gnu/packages/crates-io.scm (rust-bytemuck-derive-1): Update to 1.3.0.
2022-12-02gnu: rust-typenum: Update to 1.15.0.Marius Bakke
* gnu/packages/crates-io.scm (rust-typenum-1): Update to 1.15.0. [arguments]: Add RUST-SCALE-INFO-1 to #:cargo-inputs.
2022-12-02gnu: rust-const-oid: Add 0.9.1.Marius Bakke
* gnu/packages/crates-io.scm (rust-const-oid-0.9): New variable. (rust-const-oid-0.6): Inherit from it.
2022-12-02gnu: rust-cookie: Move versions closer together.Marius Bakke
* gnu/packages/crates-io.scm (rust-cookie-0.15): Move above other cookies. (rust-cookie-0.12): Inherit from it.
2022-12-02gnu: rust-crypto-common: Update to 0.1.6.Marius Bakke
* gnu/packages/crates-io.scm (rust-crypto-common-0.1): Update to 0.1.6. [arguments]: Add RUST-TYPENUM to #:cargo-inputs.
2022-12-02gnu: Add rust-uuid-macro-internal.Marius Bakke
* gnu/packages/crates-io.scm (rust-uuid-macro-internal): New variable.
2022-12-02gnu: rust-tinyvec: Update to 1.6.0.Marius Bakke
* gnu/packages/crates-io.scm (rust-tinyvec-1): Update to 1.6.0. [arguments]: Add RUST-ARBITRARY-1 to #:cargo-inputs.
2022-12-02gnu: rust-arbitrary: Update to 1.2.0.Marius Bakke
* gnu/packages/crates-io.scm (rust-arbitrary-1, rust-derive-arbitrary-1): Update to 1.2.0.
2022-12-02gnu: rust-xcb: Add 1.2.0.Marius Bakke
* gnu/packages/crates-io.scm (rust-xcb-1): New variable. (rust-xcb-0.9): Inherit from it.
2022-12-02gnu: rust-x11: Update to 2.20.1.Marius Bakke
* gnu/packages/crates-graphics.scm (rust-x11-2): Update to 2.20.1. [propagated-inputs]: Add MESA.
2022-12-02gnu: rust-pkg-config: Update to 0.3.26.Marius Bakke
* gnu/packages/crates-io.scm (rust-pkg-config-0.3): Update to 0.3.26.
2022-12-02Merge branch 'master' into stagingMarius Bakke
2022-12-02gnu: Add rust-k9.Marius Bakke
* gnu/packages/crates-io.scm (rust-k9-0.11): New variable.
2022-12-02gnu: rust-digest: Update to 0.10.6.Marius Bakke
* gnu/packages/crates-io.scm (rust-digest-0.10): Update to 0.10.6.
2022-12-02gnu: QtWebEngine: Use more system libraries.Marius Bakke
* 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.
2022-12-02gnu: python-biom-format: Update to 2.1.12.Ricardo Wurmus
* 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.
2022-12-02gnu: Add python-scikit-bio.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scikit-bio): New variable.
2022-12-02gnu: Add python-hdmedians.Ricardo Wurmus
* gnu/packages/statistics.scm (python-hdmedians): New variable.
2022-12-02gnu: python-pairtools: Update to 1.0.2.Ricardo Wurmus
* 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.
2022-12-02gnu: python-pairtools: Run tests conditionally.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pairtools)[arguments]: Run tests conditionally.
2022-12-02gnu: python-pybedtools: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pybedtools)[build-system]: Use pyproject-build-system. [arguments]: Import (guix build pyproject-build-system).
2022-12-02gnu: python-htsget: Update to 0.2.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-htsget): Update to 0.2.6. [build-system]: Use pyproject-build-system.
2022-12-02gnu: python-cellbender: Update to 0.2.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cellbender): Update to 0.2.2. [build-system]: Use pyproject-build-system.
2022-12-02Merge branch 'master' into stagingMarius Bakke
2022-12-02gnu: ungoogled-chromium: Use git tag in ungoogled origin.Marius Bakke
* gnu/packages/chromium.scm (%ungoogled-origin)[uri]: Use %UNGOOGLED-REVISION instead of commit identifier.
2022-12-02gnu: kicad: Remove obsolete phases.Marius Bakke
* gnu/packages/engineering.scm (kicad)[arguments]: Remove two phases.
2022-12-02gnu: golly: Update to 4.2.Marius Bakke
* 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.
2022-12-02gnu: python-wxpython: Update to 4.2.0.Marius Bakke
* gnu/packages/wxwidgets.scm (python-wxpython): Update to 4.2.0. [propagated-inputs]: Add PYTHON-ATTRDICT.
2022-12-02gnu: wxWidgets: Update to 3.2.1.Marius Bakke
* 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.
2022-12-02gnu: wxWidgets: Remove input labels.Marius Bakke
* gnu/packages/wxwidgets.scm (wxwidgets)[inputs]: Remove labels. [arguments]: Use SEARCH-INPUT-FILE. (wxwidgets-gtk2)[inputs]: Use MODIFY-INPUTS.
2022-12-02gnu: jucipp: Update to 1.7.2.Marius Bakke
* gnu/packages/text-editors.scm (jucipp): Update to 1.7.2. [arguments]: Skip one more test.
2022-12-02gnu: universal-ctags: Update to 5.9.20221127.0.Marius Bakke
* gnu/packages/code.scm (universal-ctags): Update to 5.9.20221127.0.
2022-12-02gnu: Add python-fanc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-fanc): New variable. Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2022-12-02gnu: Add python-genomic-regions.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-genomic-regions): New variable. Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2022-12-02gnu: python-msgpack-numpy: Update to 0.4.8.Navid Afkhami
* gnu/packages/python-science.scm (python-msgpack-numpy): Update to 0.4.8.
2022-12-02gnu: Add python-pybloom-live.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-pybloom-live): New variable.
2022-12-02gnu: python-xxhash: Update to 3.1.0.Ricardo Wurmus
* gnu/packages/digest.scm (python-xxhash): Update to 3.1.0. [build-system]: Use pyproject-build-system. [native-inputs]: Add python-setuptools-scm.
2022-12-01Revert "gnu: linux-libre: Move info manual to doc output."Maxim Cournoyer
This reverts commit 748ec628826cea3faa3679074d87fae9bc810080. 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.
2022-12-02gnu: ungoogled-chromium: Update to 108.0.5359.71-1.Marius Bakke
* 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.
2022-12-02gnu: ungoogled-chromium: Generalize OpenJPEG substitution.Marius Bakke
* gnu/packages/chromium.scm (ungoogled-chromium)[arguments]: Don't hard code openjpeg version.
2022-12-02gnu: harfbuzz: Add 5.3.1.Marius Bakke
* gnu/packages/gtk.scm (harfbuzz-5): New variable.
2022-12-02gnu: balsa: Update to 2.6.4.Marius Bakke
* gnu/packages/mail.scm (balsa): Update to 2.6.4.
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