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2021-07-23gnu: java-xmlpull2: Use mirrored source and archived home page.Tobias Geerinckx-Rice
* gnu/packages/xml.scm (java-xmlpull2)[source]: Download from a Gentoo distfiles mirror. [home-page]: Point to an archive.org snapshot.
2021-07-23gnu: graphviz: Use HTTPS home page.Marius Bakke
* gnu/packages/graphviz.scm (graphviz)[home-page]: Use HTTPS.
2021-07-23gnu: php: Update to 7.4.21.Marius Bakke
* gnu/packages/php.scm (php): Update to 7.4.21. [arguments]: Remove trailing #t's. [native-inputs]: Remove INTLTOOL. Add GETTEXT-MINIMAL.
2021-07-23gnu: tmux-themepack: Tweak description.Ludovic Courtès
* gnu/packages/tmux.scm (tmux-themepack)[description]: Tweak.
2021-07-23gnu: tmux-themepack: Update to 1.1.0.Matthew James Kraai
* gnu/packages/tmux.scm (tmux-themepack): Update to 1.1.0. [arguments]: Install only selected files. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-07-23gnu: modules: Avoid FHS file names in 'add.modules'.Ludovic Courtès
* gnu/packages/package-management.scm (modules)[arguments]: Add 'patch-add-modules' phase.
2021-07-23gnu: Add modules.Ivan Gankevich
* gnu/packages/package-management.scm (modules): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-07-23gnu: hpcguix-web: Update to 0.1.0.Ludovic Courtès
* gnu/packages/web.scm (hpcguix-web): Update to 0.1.0. [arguments]: In 'wrap-program' phase, change "/bin/run" to "/bin/hpcguix-web". [inputs]: Add BASH-MINIMAL. * gnu/services/web.scm (hpcguix-web-shepherd-service): Run "/bin/hpcguix-web".
2021-07-23gnu: pari-gp: Update to 2.13.2.Andreas Enge
* gnu/packages/algebra.scm (pari-gp): Update to 2.13.2.
2021-07-23gnu: gnome-maps: Update to 3.38.5.Leo Prikler
* gnu/packages/geo.scm (gnome-maps): Update to 3.38.5.
2021-07-23gnu: Add radvd.Guillaume Le Vaillant
* gnu/packages/admin.scm (radvd): New variable.
2021-07-22gnu: Add drawterm.宋文武
* gnu/packages/plan9.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
2021-07-22gnu: Add cl-libxml2.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (cl-libxml2, ecl-cl-libxml2, sbcl-cl-libxml2): New variables.
2021-07-22gnu: r-opencpu: Update to 2.2.4.Ricardo Wurmus
* gnu/packages/cran.scm (r-opencpu): Update to 2.2.4.
2021-07-22gnu: Add r-opencpuSharlatan Hellseher
* gnu/packages/cran.scm: (r-opencpu): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-07-22gnu: Add r-protoliteSharlatan Hellseher
* gnu/packages/cran.scm: (r-protolite): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2021-07-22gnu: Add r-webutilsSharlatan Hellseher
* gnu/packages/cran.scm (r-webutils): New variable.
2021-07-22gnu: Add python-dolfin-adjoint.Paul Garlick
* gnu/packages/simulation.scm (python-dolfin-adjoint): New variable.
2021-07-22gnu: Add abjad-ext-ipython.jgart
* gnu/packages/music.scm (abjad-ext-ipython): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-22gnu: Add abjad-ext-nauert.jgart
* gnu/packages/music.scm (abjad-ext-nauert): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-22gnu: Add abjad-ext-rmakers.jgart
* gnu/packages/music.scm (abjad-ext-rmakers): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-22gnu: abjad: Remove obsolete phase.Efraim Flashner
* gnu/packages/music.scm (abjad)[arguments]: Remove custom 'patch-source phase.
2021-07-22gnu: abjad: Move lilypond to inputs.Efraim Flashner
* gnu/packages/music.scm (abjad)[native-inputs]: Move lilypond ... [inputs]: ... to here.
2021-07-22gnu: abjad: Improve description.jgart
* gnu/packages/music.scm (abjad)[description]: Improve abjad's description. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-22gnu: abjad: Move python-ply to propagated-inputs.jgart
* gnu/packages/music.scm (abjad)[ntaive-inputs]: Move python-ply ... [propagated-inputs]: ... to here. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-22gnu: python-abjad: Rename to abjad.jgart
* gnu/packages/music.scm (abjad): Rename from python-abjad. (python-abjad): Keep as deprecated package. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-22gnu: python-pysam: Make the check phase honor the tests? argument.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust custom 'check phase to skip tests when #:tests is #f.
2021-07-22gnu: python-pysam: Update to 0.16.0.1.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.16.0.1. [arguments]: Update custom 'check phase. [propagated-inputs]: Replace htslib-1.9 with 1.10. [native-inputs]: Add python-pytest. Replace samtools-1.9 with 1.10, bcftools-1.9 with 1.10. (bcftools-1.9): Replace with bcftools-1.10. [native-inputs]: Replace htslib-1.9 with 1.10. (samtools-1.9): Replace with samtools-1.10. [inputs]: Replace htslib-1.9 with 1.10.
2021-07-22gnu: Add htslib-1.10.Efraim Flashner
* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
2021-07-22gnu: python-biopython: Update to 1.73.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
2021-07-21gnu: onionshare: Update to 2.3.2.Eric Bavier
* gnu/packages/tor.scm (onionshare-cli, onionshare): Update to 2.3.2. (onionshare)[inputs]: Add python-colorama. [arguments]: Insert "import pytest" for later "pytest.mark.skip".
2021-07-22gnu: Add emacs-seeing-is-believing.Joseph LaFreniere
* gnu/packages/emacs-xyz.scm (emacs-seeing-is-believing): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-07-22gnu: guile-git: Update to 0.5.2.Ludovic Courtès
Fixes <https://issues.guix.gnu.org/48855>. Reported by Maxim Cournoyer <maxim.cournoyer@gmail.com>. * gnu/packages/guile.scm (guile-git): Update to 0.5.2.
2021-07-21utils: Do not request block buffering in pretty-print-table.Maxim Cournoyer
Re-testing 'guix package -A' using the default line buffering set in (guix ui), there doesn't seem to be a performance gain to use block buffering, so remove this extraneous side effect. * guix/utils.scm (pretty-print-table): Do not set buffering mode to block. Reported-by: Ludovic Courtès <ludo@gnu.org>
2021-07-21gnu: extempore: Update to 0.8.9.Giacomo Leidi
* gnu/packages/music.scm (extempore): Update to 0.8.6. [source]: Portaudio is no more in-tree. [arguments]: Load external libraries through patched CMakeLists.txt. [phases]: Symlink assets. * gnu/packages/patches/extempore-unbundle-external-dependencies.patch: Update accordingly. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-07-21gnu: Add python-sparqlkernel.Lars-Dominik Braun
* gnu/packages/jupyter.scm (python-sparqlkernel): New variable.
2021-07-21gnu: Add python-sparqlwrapper.Lars-Dominik Braun
* gnu/packages/rdf.scm (python-sparqlwrapper): New variable.
2021-07-21gnu: Add python-bash-kernel.Lars-Dominik Braun
* gnu/packages/jupyter.scm (python-bash-kernel): New variable.
2021-07-21gnu: Add r-battenberg.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
2021-07-21gnu: Add r-ascat.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (r-ascat): New variable.
2021-07-21gnu: Add nanosv.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (nanosv): New variable.
2021-07-21gnu: Add python-pyvcf.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
2021-07-21gnu: checkm: Rename and update to 1.1.3.Lars-Dominik Braun
Renamed from python2-checkm-genome to checkm to better reflect its status as standalone-application and support for Python 3. * gnu/packages/bioinformatics.scm (python2-checkm-genome): Redirect to… (checkm): …here and update to 1.1.3. [propagated-inputs]: Move to inputs. [inputs]: Use Python 3 dependencies. [home-page]: Point to real home-page.
2021-07-21gnu: Add tombo.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (tombo): New variable.
2021-07-21gnu: Add r-rmisc.Lars-Dominik Braun
* gnu/packages/cran.scm (r-rmisc): New variable.
2021-07-21gnu: Add r-glinternet.Lars-Dominik Braun
* gnu/packages/statistics.scm (r-glinternet): New variable.
2021-07-21gnu: Add r-naniar.Lars-Dominik Braun
* gnu/packages/statistics.scm (r-naniar): New variable.
2021-07-21gnu: Add r-norm.Lars-Dominik Braun
* gnu/packages/statistics.scm (r-norm): New variable.
2021-07-21gnu: txr: Reduce closure size.Guillaume Le Vaillant
* gnu/packages/lisp.scm (txr)[inputs]: Replace bash by bash-minimal.
2021-07-21gnu: catfish: Update to 4.16.1.Michael Rohleder
* gnu/packages/xfce.scm (catfish): Update to 4.16.1. [inputs]: Add xfconf. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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