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Author SHA1 Message Date
Ludovic Courtès 1665bb0cec
gnu: hpcguix-web: Update to 0.1.0. 
* 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".
 2021-07-23 17:02:28 +02:00
Andreas Enge b48bc8953d
gnu: pari-gp: Update to 2.13.2. 
* gnu/packages/algebra.scm (pari-gp): Update to 2.13.2.
 2021-07-23 15:28:03 +02:00
Leo Prikler 4e19ad0fde
gnu: gnome-maps: Update to 3.38.5. 
* gnu/packages/geo.scm (gnome-maps): Update to 3.38.5.
 2021-07-23 12:41:01 +02:00
Guillaume Le Vaillant 785c96fbe1
gnu: Add radvd. 
* gnu/packages/admin.scm (radvd): New variable.
 2021-07-23 11:33:36 +02:00
宋文武 89ea0918a4
gnu: Add drawterm. 
* gnu/packages/plan9.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2021-07-22 19:52:53 +08:00
Pierre Neidhardt d98fc80ffb
gnu: Add cl-libxml2. 
* gnu/packages/lisp-xyz.scm (cl-libxml2, ecl-cl-libxml2, sbcl-cl-libxml2): New
variables.
 2021-07-22 13:03:52 +02:00
Ricardo Wurmus aa2686c368
gnu: r-opencpu: Update to 2.2.4. 
* gnu/packages/cran.scm (r-opencpu): Update to 2.2.4.
 2021-07-22 11:37:25 +02:00
Sharlatan Hellseher 9cfa6c3c58
gnu: Add r-opencpu 
* gnu/packages/cran.scm: (r-opencpu): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-07-22 11:37:25 +02:00
Sharlatan Hellseher 2b6dd1bde5
gnu: Add r-protolite 
* gnu/packages/cran.scm: (r-protolite): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2021-07-22 11:37:25 +02:00
Sharlatan Hellseher c5baff1796
gnu: Add r-webutils 
* gnu/packages/cran.scm (r-webutils): New variable.
 2021-07-22 11:37:21 +02:00
Paul Garlick b05a1eb5e3
gnu: Add python-dolfin-adjoint. 
* gnu/packages/simulation.scm (python-dolfin-adjoint): New variable.
 2021-07-22 10:03:53 +01:00
jgart 4c63efa5e3
gnu: Add abjad-ext-ipython. 
* gnu/packages/music.scm (abjad-ext-ipython): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-22 11:50:14 +03:00
jgart ccfcbadd68
gnu: Add abjad-ext-nauert. 
* gnu/packages/music.scm (abjad-ext-nauert): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-22 11:48:45 +03:00
jgart a909460099
gnu: Add abjad-ext-rmakers. 
* gnu/packages/music.scm (abjad-ext-rmakers): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-22 11:48:41 +03:00
Efraim Flashner 454460ca55
gnu: abjad: Remove obsolete phase. 
* gnu/packages/music.scm (abjad)[arguments]: Remove custom 'patch-source
phase.
 2021-07-22 11:14:33 +03:00
Efraim Flashner 91c42e4767
gnu: abjad: Move lilypond to inputs. 
* gnu/packages/music.scm (abjad)[native-inputs]: Move lilypond ...
[inputs]: ... to here.
 2021-07-22 11:13:57 +03:00
jgart 18f9e21b18
gnu: abjad: Improve description. 
* gnu/packages/music.scm (abjad)[description]: Improve abjad's
description.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-22 11:06:58 +03:00
jgart dd7c2d2b1d
gnu: abjad: Move python-ply to propagated-inputs. 
* gnu/packages/music.scm (abjad)[ntaive-inputs]: Move python-ply ...
[propagated-inputs]: ... to here.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-22 11:05:41 +03:00
jgart 5535d5435e
gnu: python-abjad: Rename to abjad. 
* gnu/packages/music.scm (abjad): Rename from python-abjad.
(python-abjad): Keep as deprecated package.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-22 11:04:10 +03:00
Efraim Flashner fd8aea010f
gnu: python-pysam: Make the check phase honor the tests? argument. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust
custom 'check phase to skip tests when #:tests is #f.
 2021-07-22 10:58:22 +03:00
Efraim Flashner 877792a6a7
gnu: python-pysam: Update to 0.16.0.1. 
* 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.
 2021-07-22 10:57:41 +03:00
Efraim Flashner cc4906d13b
gnu: Add htslib-1.10. 
* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
 2021-07-22 10:50:58 +03:00
Efraim Flashner 309b38bed6
gnu: python-biopython: Update to 1.73. 
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
 2021-07-22 09:14:12 +03:00
Eric Bavier 55db762b31
gnu: onionshare: Update to 2.3.2. 
* 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".
 2021-07-21 23:08:14 -05:00
Joseph LaFreniere e9d47ee718
gnu: Add emacs-seeing-is-believing. 
* gnu/packages/emacs-xyz.scm (emacs-seeing-is-believing): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-07-22 00:02:33 +02:00
Ludovic Courtès de1ae96184
gnu: guile-git: Update to 0.5.2. 
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.
 2021-07-22 00:02:30 +02:00
Maxim Cournoyer 4f51a4ac27
utils: Do not request block buffering in pretty-print-table. 
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>
 2021-07-21 17:42:30 -04:00
Giacomo Leidi 1f07d4436c
gnu: extempore: Update to 0.8.9. 
* 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>
 2021-07-21 23:00:51 +02:00
Lars-Dominik Braun 403a689625
gnu: Add python-sparqlkernel. 
* gnu/packages/jupyter.scm (python-sparqlkernel): New variable.
 2021-07-21 13:36:09 +02:00
Lars-Dominik Braun 281808170a
gnu: Add python-sparqlwrapper. 
* gnu/packages/rdf.scm (python-sparqlwrapper): New variable.
 2021-07-21 13:36:09 +02:00
Lars-Dominik Braun d57c34d26b
gnu: Add python-bash-kernel. 
* gnu/packages/jupyter.scm (python-bash-kernel): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun 73830b5da3
gnu: Add r-battenberg. 
* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun ed636babfa
gnu: Add r-ascat. 
* gnu/packages/bioinformatics.scm (r-ascat): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun 690df95d1a
gnu: Add nanosv. 
* gnu/packages/bioinformatics.scm (nanosv): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun 2b665b8a49
gnu: Add python-pyvcf. 
* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun 086c6800cf
gnu: checkm: Rename and update to 1.1.3. 
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.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun 18a02fe7ca
gnu: Add tombo. 
* gnu/packages/bioinformatics.scm (tombo): New variable.
 2021-07-21 13:36:07 +02:00
Lars-Dominik Braun 117988b7ca
gnu: Add r-rmisc. 
* gnu/packages/cran.scm (r-rmisc): New variable.
 2021-07-21 13:36:07 +02:00
Lars-Dominik Braun 2925d84196
gnu: Add r-glinternet. 
* gnu/packages/statistics.scm (r-glinternet): New variable.
 2021-07-21 13:36:07 +02:00
Lars-Dominik Braun f711ba28d2
gnu: Add r-naniar. 
* gnu/packages/statistics.scm (r-naniar): New variable.
 2021-07-21 13:36:07 +02:00
Lars-Dominik Braun f6802a9247
gnu: Add r-norm. 
* gnu/packages/statistics.scm (r-norm): New variable.
 2021-07-21 13:36:07 +02:00
Guillaume Le Vaillant ce27cde262
gnu: txr: Reduce closure size. 
* gnu/packages/lisp.scm (txr)[inputs]: Replace bash by bash-minimal.
 2021-07-21 10:57:27 +02:00
Michael Rohleder 2f41e9540d
gnu: catfish: Update to 4.16.1. 
* gnu/packages/xfce.scm (catfish): Update to 4.16.1.
[inputs]: Add xfconf.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-07-21 01:26:15 +02:00
Ivan Gankevich 9d21c67d7b
gnu: Add libgpiod. 
* gnu/packages/linux.scm (libgpiod): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-07-20 22:36:51 +02:00
Paul A. Patience 4a136a3b7f
gnu: dealii: Update to 9.3.1 and clean up. 
The cleanup notably:

* Builds and installs the documentation into a separate doc output (in
the process moving around some files erroneously installed into the root
directory); and
* Removes unnecessary inputs and moves some inputs into
propagated-inputs (the candidates of which were determined with a search
for "include.*LIBNAME" in include/deal.II).

* gnu/packages/maths.scm (dealii): Reword comments.
[version]: Update to 9.3.1.
[outputs]: New field including doc output.
[native-inputs]: New field.
[inputs]: Sort them. Remove p4est (deal.II interfaces with it only when
MPI is enabled). Move boost, suitesparse and tbb to...
[propagated-inputs]: ...here. New field including hdf5, which is
actually supported in deal.II without MPI.
[arguments]<#:tests?>: New argument. The tests were not being run before
anyway.
<#:configure-flags>[-DDEAL_II_COMPONENT_DOCUMENTATION]: New flag.
[-DDEAL_II_DOCREADME_RELDIR]: New flag. Prevents the LICENSE.md,
README.md, detailed.log and summary.log files from being installed in
the root directory (though note that the logs are removed in the new
remove-build-logs phase).
[-DDEAL_II_DOCHTML_RELDIR]: New flag.
[-DDEAL_II_COMPILE_EXAMPLES]: New flag.
[-DDEAL_II_EXAMPLES_RELDIR]: New flag. Prevents the examples directory
from being installed in the root directory.
[-DCMAKE_POSITION_INDEPENDENT_CODE]: Remove flag. The issue has been
resolved.
<#:phases>{remove-build-logs}: New phase.
[home-page]: Add trailing slash.
(dealii-openmpi): Use package/inherit.
[inputs]: Sort them. Remove mumps-metis-openmpi (deal.II no longer
interfaces with MUMPS). Move hdf5-parallel-openmpi, openmpi,
p4est-openmpi, petsc-openmpi and slepc-openmpi to...
[propagated-inputs]: ...here. New field.
[arguments]<#:configure-flags>: Rename cf variable to flags.
<#:phases>{mpi-setup}: Remove phase which is unused because the tests
are disabled.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-07-20 22:36:51 +02:00
Efraim Flashner 2c1cdbb19b
gnu: xorg.scm: Add missing module import. 
This is a follow-up to 1a4c7ddefe.

* gnu/packages/xorg.scm: Add missing module import.
 2021-07-20 22:19:12 +03:00
Tanguy Le Carrour 526171269d
gnu: Add python-tldr. 
* gnu/packages/python-xyz.scm (python-tldr): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-20 22:10:35 +03:00
Efraim Flashner e2dae72dab
gnu: rust-openssl-sys-extras-0.7: Skip build. 
* gnu/packages/crates-io.scm (rust-openssl-sys-extras-0.7)
[arguments]: Skip build.
[inputs]: Remove openssl-1.0.
 2021-07-20 22:04:40 +03:00
Efraim Flashner 7f43bc6839
gnu: rust-openssl-0.7: Skip build. 
* gnu/packages/crates-io.scm (rust-openssl-0.7)[arguments]: Skip build.
Remove tests keyword.
[inputs]: Remove openssl-1.0.
 2021-07-20 22:02:59 +03:00
Efraim Flashner 3f403bb750
gnu: rust-sha1-0.2: Skip tests. 
* gnu/packages/crates-io.scm (rust-sha1-0.2)[arguments]: Skip tests.
[inputs]: Remove openssl-1.0.
 2021-07-20 21:59:56 +03:00