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Author SHA1 Message Date
Tobias Geerinckx-Rice
34242fe5c7
gnu: isc-dhcp: Update to 4.4.3-P1 [fixes CVE-2022-2928, CVE-2022-2929]. 
* gnu/packages/admin.scm (isc-dhcp): Update to 4.4.3-P1.
 2022-12-11 01:00:03 +01:00
Tobias Geerinckx-Rice
b853dbd0e2
gnu: nmrpflash: Rephrase synopsis. 
* gnu/packages/admin.scm (nmrpflash)[synopsis]: Rework awkward wording.
 2022-12-11 01:00:02 +01:00
Tobias Geerinckx-Rice
54e7efd5cf
gnu: nmrpflash: Update to 0.9.19. 
* gnu/packages/admin.scm (nmrpflash): Update to 0.9.19.
 2022-12-11 01:00:02 +01:00
Tobias Geerinckx-Rice
2202fc9003
gnu: nnn: Update to 4.7. 
* gnu/packages/admin.scm (nnn): Update to 4.7.
 2022-12-11 01:00:02 +01:00
Tobias Geerinckx-Rice
bd268c21e5
gnu: inxi-minimal: Reduce reliance on input names. 
* gnu/packages/admin.scm (inxi-minimal)[arguments]:
Use SEARCH-INPUT-FILE.
 2022-12-11 01:00:02 +01:00
Tobias Geerinckx-Rice
932409da9c
gnu: inxi-minimal: Remove input labels. 
* gnu/packages/admin.scm (inxi-minimal)[inputs]:
Remove input labels.
 2022-12-11 01:00:02 +01:00
Tobias Geerinckx-Rice
2dfc21d9ce
gnu: inxi-minimal: Update to 3.3.24-1. 
* gnu/packages/admin.scm (inxi-minimal): Update to 3.3.24-1.
 2022-12-11 01:00:02 +01:00
Tobias Geerinckx-Rice
6c50e416a5
gnu: hyfetch: Update to 1.4.4. 
* gnu/packages/admin.scm (hyfetch): Update to 1.4.4.
 2022-12-11 01:00:02 +01:00
Tobias Geerinckx-Rice
992773d3a2
gnu: dash: Capitalise description sentences. 
* gnu/packages/shells.scm (dash)[description]: Capitalise ‘dash’.
 2022-12-11 01:00:02 +01:00
Tobias Geerinckx-Rice
55e2b9b0a4
gnu: dash: Update to 0.5.12. 
* gnu/packages/shells.scm (dash): Update to 0.5.12.
[arguments]: Don't explicitly return #t from phases.
 2022-12-11 01:00:01 +01:00
Tobias Geerinckx-Rice
885903e2f6
gnu: botan: Update to 2.19.3. 
* gnu/packages/crypto.scm (botan): Update to 2.19.3.
 2022-12-11 01:00:01 +01:00
Tobias Geerinckx-Rice
187880b814
gnu: global: Update to 6.6.9. 
* gnu/packages/code.scm (global): Update to 6.6.9.
 2022-12-11 01:00:01 +01:00
Tobias Geerinckx-Rice
62cb0eae3e
gnu: libhx: Update to 4.8. 
* gnu/packages/c.scm (libhx): Update to 4.8.
 2022-12-11 01:00:01 +01:00
Tobias Geerinckx-Rice
885f18d750
gnu: libdeflate: Update to 1.15. 
* gnu/packages/compression.scm (libdeflate): Update to 1.15.
[build-system]: Use CMake.
[arguments]: Remove #:make-flags and all custom phases.
Add equivalent #:configure-flags and a custom 'check phase.
 2022-12-11 01:00:01 +01:00
Tobias Geerinckx-Rice
2ed751715f
gnu: python-aiounittest: Update to 1.4.2. 
* gnu/packages/check.scm (python-aiounittest): Update to 1.4.2.
 2022-12-11 01:00:01 +01:00
Tobias Geerinckx-Rice
816c7f4e84
gnu: doctest: Update to 2.4.9. 
* gnu/packages/check.scm (doctest): Update to 2.4.9.
 2022-12-11 01:00:01 +01:00
Tobias Geerinckx-Rice
039bef4ac8
gnu: ccache: Update to 4.7.4. 
* gnu/packages/ccache.scm (ccache): Update to 4.7.4.
 2022-12-11 01:00:00 +01:00
Tobias Geerinckx-Rice
aceb4e49d1
gnu: byacc: Update to 20221106. 
* gnu/packages/c.scm (byacc): Update to 20221106.
 2022-12-11 01:00:00 +01:00
Tobias Geerinckx-Rice
2b7b0cac71
gnu: fio: Update to 3.33. 
* gnu/packages/benchmark.scm (fio): Update to 3.33.
 2022-12-11 01:00:00 +01:00
Tobias Geerinckx-Rice
930b94809d
gnu: libltc: Update to 1.3.2. 
* gnu/packages/audio.scm (libltc): Update to 1.3.2.
 2022-12-11 01:00:00 +01:00
Tobias Geerinckx-Rice
b0913931e9
gnu: realmd: Update to 0.17.1. 
* gnu/packages/admin.scm (realmd): Update to 0.17.1.
 2022-12-11 01:00:00 +01:00
Jelle Licht
688028931f
gnu: emacs-pdf-tools: Update home page. 
* gnu/packages/emacs-xyz.scm (emacs-pdf-tools)[home-page]: Update.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2022-12-13 21:31:28 +01:00
Konrad Hinsen
a67461f0e1
gnu: emacs-hyperbole: Add missing files. 
* gnu/packages/emacs-xyz.scm (emacs-hyperbole)[arguments]: Add a new
INSTALL-DOC phase.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2022-12-13 21:24:09 +01:00
Nicolas Goaziou
7d570036f0
gnu: emacs-pg: Update to 0.20. 
* gnu/packages/emacs-xyz.scm (emacs-pg): Update to 0.20.
 2022-12-13 21:24:09 +01:00
Nicolas Goaziou
c922d935c3
gnu: emacs-fountain-mode: Update to 3.6.1. 
* gnu/packages/emacs-xyz.scm (emacs-fountain-mode): Update to 3.6.1.
 2022-12-13 21:24:08 +01:00
Nicolas Goaziou
98f7332aa8
gnu: emacs-debbugs: Update to 0.35. 
* gnu/packages/emacs-xyz.scm (emacs-debbugs): Update to 0.35.
 2022-12-13 21:24:08 +01:00
Nicolas Goaziou
89795dec98
gnu: emacs-project: Update to 0.9.3. 
* gnu/packages/emacs-xyz.scm (emacs-project): Update to 0.9.3.
 2022-12-13 21:24:08 +01:00
dan
e4ab2ccb18
gnu: emacs-beancount: Update to 0.0.0-1.687775d. 
* gnu/packages/finance.scm (emacs-beancount): Update to 0.0.0-1.687775d.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2022-12-13 21:24:02 +01:00
Mark H Weaver
d83eef22b2
gnu: icecat: Update to 102.6.0-guix0-preview1 [security fixes]. 
Includes fixes for CVE-2022-46872, CVE-2022-46874, CVE-2022-46875,
CVE-2022-46878, CVE-2022-46880, CVE-2022-46881, and CVE-2022-46882.

* gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.
 2022-12-13 12:36:39 -05:00
Ricardo Wurmus
3d2b2f12e5
gnu: bedops: Update to 2.4.41. 
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.41.
[arguments]: Remove trailing #T from build phases; do not set BINDIR in
make-flags; set CC; replace 'install phase.
[native-inputs]: Add diffutils, perl, and which.
 2022-12-13 18:22:55 +01:00
Petr Hodina
22acc0b029
services: nix: Add more configuration fields. 
* gnu/services/nix.scm (<nix-configuration>)[build-directory]: New field.
(nix-service-etc, nix-shepherd-service): Take them into account.
* doc/guix.texi (Nix): Update it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-12-13 17:46:39 +01:00
Ludovic Courtès
a2f0297af0
gnu: guile-gnutls: Add properties for the 'generic-git' updater. 
* gnu/packages/tls.scm (guile-gnutls)[properties]: New field.
 2022-12-13 17:46:39 +01:00
Ricardo Wurmus
23322c2de8
gnu: tophat: Remove trailing #T from build phases and snippet. 
* gnu/packages/bioinformatics.scm (tophat)[source]: Remove trailing #T from
snippet.
[arguments]: Remove trailing #T from build phases.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus
b339e181e1
gnu: python-bx-python: Update to 0.9.0. 
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.9.0.
[build-system]: Use pyproject-build-system.
[arguments]: Add phase 'build-extensions and 'disable-cython-doctests.
[native-inputs]: Replace python-nose with python-pytest.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus
de30c74b63
gnu: bioawk: Use gexp. 
* gnu/packages/bioinformatics.scm (bioawk)[arguments]: Use gexp and simplify
'install phase.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus
057579495f
gnu: blasr-libcpp: Remove trailing #T from build phases. 
* gnu/packages/bioinformatics.scm (blasr-libcpp)[arguments]: Remove
trailing #T from build phases.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus
eaf5198a5e
gnu: pbbam: Drop input labels. 
* gnu/packages/bioinformatics.scm (pbbam)[native-inputs]: Drop labels.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus
8b2fdcb2c3
gnu: pbbam: Update to 2.1.0. 
* gnu/packages/bioinformatics.scm (pbbam): Update to 2.1.0.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus
684d046e6c
gnu: pbcopper: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (pbcopper): Update to 2.0.0.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus
53f65f7315
gnu: bedtools: Remove unnecessary quasiquotation. 
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Remove quasiquote.
[native-inputs]: Drop input label.
 2022-12-13 16:31:54 +01:00
Ricardo Wurmus
4f1a36bd7b
gnu: bamutils: Update to 1.0.15. 
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.15.
[arguments]: Remove quasiquoting; remove USER_WARNINGS from make-flags.
[native-inputs]: Update libstatgen.
 2022-12-13 16:31:54 +01:00
Ricardo Wurmus
8cc22866c2
gnu: bamtools: Update to 2.5.2. 
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.2.
[arguments]: Enable tests; remove extra phases.
[inputs]: Add jsoncpp.
[native-inputs]: Add pkg-config.
 2022-12-13 16:31:54 +01:00
Ricardo Wurmus
6d2afaf25b
gnu: aragorn: Update to 1.2.41. 
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.41.
[source]: Fetch C source file from new location.
[arguments]: Drop trailing #T in build phases; use gexp.
[native-inputs]: Add origin for man page.
[home-page]: Update to new home page.
[license]: Update to GPLv3+.
 2022-12-13 16:31:54 +01:00
Maxim Cournoyer
93b0c1e35e
gnu: Add rpi-imager. 
* gnu/packages/raspberry-pi.scm (rpi-imager): New variable.
 2022-12-13 10:11:20 -05:00
jgart
87638cdd48
gnu: mercury: Update to 22.01.4. 
* gnu/packages/mercury.scm (mercury-minimal): Update to 22.01.4.
[arguments]: Remove obsolete and non-existent file from being patched.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:12 +00:00
jgart
1810d67ad4
gnu: mercury-minimal: Update to 22.01.4. 
* gnu/packages/mercury.scm (mercury-minimal): Update to 22.01.4.
[arguments]: Remove obsolete file path, update libatomic-ops, and update
libgc-8.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:12 +00:00
Sharlatan Hellseher
0682e7c2e3
gnu: python-h5netcdf: Update to 1.1.0. 
* gnu/packages/python-xyz.scm (python-h5netcdf): Update to 1.1.0.
[build-system]: Use pyproject-build-system, to simplify package.
[description]: Style content and add links to referenced projects.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:11 +00:00
Sharlatan Hellseher
1a0dcc2112
gnu: python-asdf-astropy: Update to 0.3.0. 
* gnu/packages/astronomy.scm (python-asdf-astropy): Update to 0.3.0.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:11 +00:00
EuAndreh
866eb7fffb
gnu: Add tmux-plugin-resurrect. 
* gnu/packages/tmux.scm (tmux-plugin-resurrect): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:11 +00:00
Paul A. Patience
36bd9121d6
gnu: Add rust-csv-index-0.1. 
* gnu/packages/crates-io.scm (rust-csv-index-0.1): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:11 +00:00
Martin Schmidt
34cf5e06a9
gnu: nheko: Support video calls. 
* gnu/packages/messaging.scm (nheko)[inputs]: Replace GST-PLUGINS-GOOD with
GST-PLUGINS-GOOD-QT to fix video calls.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:11 +00:00
Martin Schmidt
27efd3ed3c
gnu: Add gst-plugins-good-qt. 
* gnu/packages/gstreamer.scm (gst-plugins-good-qt): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:11 +00:00
Christopher Baines
2fb187ed7c
gnu: guix-data-service: Update to 0.0.1-36.7b69611. 
* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-36.7b69611.
 2022-12-13 13:42:11 +00:00
Ricardo Wurmus
81841559f4
gnu: kaldi: Update to 0-1.be22248. 
* gnu/packages/machine-learning.scm (kaldi): Update to 0-1.be22248.
 2022-12-13 14:38:13 +01:00
Ricardo Wurmus
f764947dab
gnu: kaldi: Remove trailing #T from build phases. 
* gnu/packages/machine-learning.scm (kaldi)[arguments]: Remove trailing #T
from build phases.
 2022-12-13 14:38:12 +01:00
Ricardo Wurmus
c978ae3c6b
gnu: kaldi-gstreamer-server: Update to 0-3.f79e204. 
* gnu/packages/machine-learning.scm (kaldi-gstreamer-server): Update to
0-3.f79e204.
 2022-12-13 14:38:12 +01:00
Ricardo Wurmus
8466aceb13
gnu: kaldi-gstreamer-server: Drop input labels. 
* gnu/packages/machine-learning.scm (kaldi-gstreamer-server)[inputs]: Drop
package labels.
 2022-12-13 14:38:12 +01:00
Ricardo Wurmus
79cf84c7ab
gnu: kaldi-gstreamer-server: Remove trailing #T from build phases. 
* gnu/packages/machine-learning.scm (kaldi-gstreamer-server)[arguments]:
Remove trailing #T from build phases.
 2022-12-13 14:38:12 +01:00
Ricardo Wurmus
01f4617b99
gnu: gst-kaldi-nnet2-online: Update to 0-3.7888ae5. 
* gnu/packages/machine-learning.scm (gst-kaldi-nnet2-online): Update to
0-3.7888ae5.
[arguments]: Do to quote list; remove trailing #T from build phases; augment
CPLUS_INCLUDE_PATH instead of replacing it.
[inputs]: Replace openfst with openfst-1.7.3.
 2022-12-13 14:38:03 +01:00
Pierre Neidhardt
417604ec25
gnu: sbcl-alloy: Update to 20221126. 
* gnu/packages/lisp-xyz.scm (sbcl-alloy): Update to 20221126.
 2022-12-13 11:18:59 +01:00
Pierre Neidhardt
706dead679
gnu: sbcl-3b-bmfont: Update to 20220327. 
* gnu/packages/lisp-xyz.scm (sbcl-3b-bmfont): Update to 20220327.
 2022-12-13 11:18:59 +01:00
Pierre Neidhardt
e7eefbf85c
gnu: Add cl-sdf. 
* gnu/packages/lisp-xyz.scm (cl-sdf, ecl-sdf, sbcl-sdf): New variables.
 2022-12-13 11:18:59 +01:00
Pierre Neidhardt
f0ebbe1598
gnu: sbcl-cl-vectors: Build all subsystems. 
* gnu/packages/lisp-xyz.scm (sbcl-cl-vectors)[arguments]: Build cl-paths,
cl-aa and cl-aa-misc as well.
 2022-12-13 11:18:59 +01:00
Pierre Neidhardt
4f64d30b5d
gnu: Add cl-binpack. 
* gnu/packages/lisp-xyz.scm (cl-binpack, ecl-binpack, sbcl-binpack): New variables.
 2022-12-13 11:18:59 +01:00
Pierre Neidhardt
63b508e4fb
gnu: Add cl-uax-14. 
* gnu/packages/lisp-xyz.scm (cl-uax-14, ecl-uax-14, sbcl-uax-14): New variables.
 2022-12-13 11:18:59 +01:00
Pierre Neidhardt
752b65935d
gnu: Add cl-font-discovery. 
* gnu/packages/lisp-xyz.scm (cl-font-discovery, ecl-font-discovery,
sbcl-font-discovery): New variables.
 2022-12-13 11:18:59 +01:00
Pierre Neidhardt
206b97c102
gnu: Add cl-colored. 
* gnu/packages/lisp-xyz.scm (cl-colored, ecl-colored, sbcl-colored): New variables.
 2022-12-13 11:18:59 +01:00
Bruno Victal
ca735decfb
gnu: mympd: Update to 10.1.6. 
* gnu/packages/mpd.scm (mympd): Update to 10.1.6.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2022-12-13 14:17:30 +08:00
Robby Zambito
648b1605dd
gnu: gauche: Update to 0.9.12 
* gnu/packages/scheme.scm (gauche): Update to 0.9.12.
[source]: Project migrated to GitHub.
libatomic-ops is no longer in the Gauche source tree.
[arguments]: Renamed network test file.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2022-12-13 14:10:26 +08:00
Ricardo Wurmus
e84042fdd4
gnu: cnvkit: Update to 0.9.9. 
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.9.
[build-system]: Use pyproject-build-system.
[arguments]: Relax restriction on python-joblib.
[propagated-inputs]: Add python-pomegranate and python-scikit-learn.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
1369b53d49
gnu: seqmagick: Update to 0.8.4. 
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.4.
[build-system]: Use pyproject-build-system.
[inputs]: Add python-pygtrie.
[native-inputs]: Replace python-nose with python-pytest.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
9bf2101049
gnu: python-flasgger: Update to 0.9.5. 
* gnu/packages/python-xyz.scm (python-flasgger): Update to 0.9.5.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add 'prepare-check phase; disable
"test_swag" test via #:test-flags.
[native-inputs]: Add python-apispec-webframeworks and python-flask-jwt.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
8c197f990b
gnu: python-pyjwt: Update to 2.6.0. 
* gnu/packages/python-xyz.scm (python-pyjwt): Update to 2.6.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.
[native-inputs]: Add pytohn-coverage, python-pre-commit, python-sphinx, and
python-sphinx-rtd-theme.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
99a29b4933
gnu: python-apispec: Update to 6.0.2. 
* gnu/packages/python-xyz.scm (python-apispec): Update to 6.0.2.
[build-system]: Use pyproject-build-system.
[arguments]: Disable test through test-flags, not by replacing the 'check
phase.
[propagated-inputs]: Remove python-pyyaml; add python-packaging.
[native-inputs]: Add python-flake8, python-flake8-bugbear, python-mypy,
python-pre-commit, and python-pyyaml.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
0fcba8b01c
gnu: python-marshmallow: Update to 3.19.0. 
* gnu/packages/python-xyz.scm (python-marshmallow): Update to 3.19.0.
[build-system]: Use pyproject-build-system.
[propagated-inputs]: Remove python-dateutil and python-simplejson; add
python-packaging.
[native-inputs]: Add python-flake8, python-flake8-bugbear, python-mypy,
python-pre-commit, and python-simplejson.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
71dc990f22
gnu: python-flask-restful: Update to 0.3.9. 
* gnu/packages/python-web.scm (python-flask-restful): Update to 0.3.9.
[source]: Remove patch.
[build-system]: Use pyproject-build-system.
[arguments]: Disable "test_redirect" test; remove 'fix-imports phase.
[native-inputs]: Replace python-nose with python-pytest.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/python-flask-restful-werkzeug-compat.patch: Remove file.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
461dff2651
gnu: python-cgatcore: Update to 0.6.14. 
* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.14.
[build-system]: Use pyproject-build-system.
[arguments]: Disable broken tests with #:test-flags; do not replace 'check
phase; add phase 'sqlite-compatibility.
[native-inputs]: Drop input labels.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
2f1d8fb129
gnu: python-apsw: Update to 3.40.0.0. 
* gnu/packages/databases.scm (python-apsw): Update to 3.40.0.0.
[source]: Remove obsolete patch.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-cython.
[arguments]: Move build-extensions phase before build phase.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch: Remove file.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
08b9e29d46
gnu: python-bokeh: Skip failing PIL test. 
The test compares base64-encoded gifs; the gifs look identical but the
base64-encoded data differs.  Since the result seems fine, disabling this PIL
test is probably okay.

* gnu/packages/python-xyz.scm (python-bokeh)[arguments]: Ignore failing
test_transform_PIL test.
 2022-12-13 00:08:13 +01:00
Ricardo Wurmus
b72df3bbb3
gnu: python-dna-features-viewer: Update to 3.1.1. 
* gnu/packages/bioinformatics.scm (python-dna-features-viewer):
Update to 3.1.1.
[build-system]: Use pyproject-build-system.
[arguments]: Add build phase to fix a compatibility problem with biopython.
[propagated-inputs]: Add python-packaging.
 2022-12-13 00:07:23 +01:00
Ricardo Wurmus
b66b6bdf70
gnu: python-hicexplorer: Update to 3.7.2. 
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.2.
[build-system]: Use pyproject-build-system.
[arguments]: Use gexp; remove phase "loosen-up-requirements"; add test-flags
to skip some tests; add phase "remove-dependency-on-krbalancing" to remove a
dependency on an unlicensed package; add phase "fix-references"; add phase
"run-only-low-mem-tests".
[propagated-inputs]: Remove python-configparser and python-six; add
python-biopython, python-cleanlab-1, python-fit-nbinom, python-graphviz,
python-hic2cool, python-hicmatrix, python-hyperopt, python-imbalanced-learn,
python-ipykernel, python-psutil, python-pybedtools, python-pygenometracks,
python-scikit-learn, and python-tqdm.
[native-inputs]: Add graphviz.
 2022-12-13 00:07:23 +01:00
Ricardo Wurmus
c3e330cf36
gnu: python-pygenometracks: Update to 3.5. 
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.5.
[build-system]: Use pyproject-build-system.
[arguments]: Quote phases instead of full list of arguments; remove trailing #T
from build phase.
 2022-12-13 00:07:22 +01:00
Ricardo Wurmus
6e9518e201
gnu: python-hicmatrix: Update to 16. 
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 16.
[build-system]: Use pyproject-build-system.
[arguments]: Shuffle the quote.
 2022-12-13 00:07:22 +01:00
Ricardo Wurmus
5167881a60
gnu: python-biopython: Update to 1.80. 
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.80.
[build-system]: Use pyproject-build-system.
[arguments]: Remove trailing #T from build phase.
 2022-12-13 00:07:22 +01:00
Ricardo Wurmus
de70f957b2
gnu: python-hyperopt: Update to 0.2.7. 
* gnu/packages/machine-learning.scm (python-hyperopt): Update to 0.2.7.
[arguments]: Adjust check phase; disable test_distribution_rvs test.
[build-system]: Use pyproject-build-system.
[propagated-inputs]: Add python-py4j.
[native-inputs]: Remove python-ipython and python-ipyparallel.
 2022-12-13 00:07:22 +01:00
Ricardo Wurmus
3d388fe3d0
gnu: python-graphviz: Update to 0.20.1. 
* gnu/packages/graphviz.scm (python-graphviz): Update to 0.20.1.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom "check" phase; add "prepare-check" phase.
[native-inputs]: Remove python-mock.
 2022-12-13 00:07:22 +01:00
Ricardo Wurmus
75331dc6e6
gnu: python-anndata: Use pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-anndata)[build-system]: Use
pyproject-build-system.
[arguments]: Replace custom 'build phase with 'set-version phase; remove
custom 'install phase; disable doctest via build phase 'disable-doctests and
the #:test-flags property.
[propagated-inputs]: Add python-scikit-learn.
[native-inputs]: Add python-boltons.
 2022-12-12 23:59:39 +01:00
Ricardo Wurmus
2c65106cf5
gnu: python-zarr: Update to 2.13.3. 
* gnu/packages/python-xyz.scm (python-zarr): Update to 2.13.3.
 2022-12-12 23:59:39 +01:00
Ricardo Wurmus
8b9c9051ba
gnu: python-numcodecs: Update to 0.10.2. 
* gnu/packages/python-xyz.scm (python-numcodecs): Update to 0.10.2.
[build-system]: Use pyproject-build-system.
[arguments]: Enable tests; add phase 'build-extensions; remove custom 'check
phase.
[propagated-inputs]: Add python-entrypoints and python-typing-extensions-next.
 2022-12-12 23:59:39 +01:00
Ricardo Wurmus
c4bcb5db49
gnu: python-typer: Simplify by using pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-typer)[build-system]: Use
pyproject-build-system.
[arguments]: Remove extra quoting; remove custom 'build phase; remove custom
'install phase; remove custom 'check phase; add 'pre-check phase.
[synopsis]: Pull onto the same line.
[description]: Reformat.
 2022-12-12 23:59:29 +01:00
jgart
1d160f41f5
gnu: Add erlang-yamerl. 
* gnu/packages/erlang.scm (erlang-yamerl): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-12 20:39:41 +00:00
jgart
e4fd04fb92
gnu: Add erlang-jsx. 
* gnu/packages/erlang.scm (erlang-jsx): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-12 20:34:57 +00:00
Christopher Baines
d5ad3dd59a
services: guix-build-coordinator: Fix service startup. 
Previously the service would keep starting more and more processes.

* gnu/services/guix.scm (guix-build-coordinator-shepherd-services): Fix how
make-forkexec-constructor is called.
 2022-12-12 19:58:25 +00:00
Marius Bakke
c1695bcadd
gnu: re2: Update to 2022-12-01. 
* gnu/packages/regex.scm (re2): Update to 2022-12-01.
 2022-12-12 20:23:32 +01:00
Marius Bakke
2c1b488d19
tests: Add system tests for each supported kernel version. 
* gnu/tests/base.scm (%test-basic-os): Rename to ...
(test-basic-os): ... this, and turn into procedure that takes optional KERNEL
argument.
(%test-basic-os): Use that procedure.
(%test-linux-libre-5.15, %test-linux-libre-5.10, %test-linux-libre-5.4,
%test-linux-libre-4.19, %test-linux-libre-4.14, %test-linux-libre-4.9): New
tests.
 2022-12-12 20:23:32 +01:00
Marius Bakke
9fc171b62a
gnu: f2fs-tools: Remove obsolete phase. 
* gnu/packages/linux.scm (f2fs-tools)[arguments]: Remove.
(f2fs-tools-1.7)[arguments]: Add #:phases.
 2022-12-12 20:23:31 +01:00
Marius Bakke
a2c6cc4354
gnu: f2fs-tools: Update to 1.15.0. 
* gnu/packages/linux.scm (f2fs-tools): Update to 1.15.0.
(f2fs-tools/static)[arguments]: Add #:make-flags.  Remove make-static phase.
 2022-12-12 20:23:31 +01:00
Marius Bakke
e1fc45b3ea
gnu: f2fs-tools@1.7: Don't fetch autogenerated git snapshot. 
* gnu/packages/linux.scm (f2fs-tools-1.7)[source]: Switch to GIT-FETCH.
 2022-12-12 20:23:31 +01:00
Marius Bakke
61f67290b9
gnu: f2fs-tools: Don't fetch autogenerated git snapshot. 
* gnu/packages/linux.scm (f2fs-tools)[source]: Switch to GIT-FETCH.
 2022-12-12 20:23:31 +01:00
Marius Bakke
58e33da5f5
gnu: f2fs-tools: Reverse inheritance relationship. 
* gnu/packages/linux.scm (f2fs-tools): Update to 1.14.0.
[arguments]: Remove obsolete #:configure-flags and trailing #t in phase.
[inputs]: Remove labels.
(f2fs-tools-1.7): Inherit from above; add #:configure-flags.
[inputs]: Remove labels.
 2022-12-12 20:23:31 +01:00
Marius Bakke
999783b92d
gnu: ungoogled-chromium: Build with ffmpeg@4. 
This is a follow-up to commit 79564bf997.

* gnu/packages/chromium.scm (ungoogled-chromium)[inputs]: Change from FFMPEG
to FFFMPEG-4.
 2022-12-12 20:23:31 +01:00
Mădălin Ionel Patrașcu
3640310d69
gnu: Add r-golem. 
* gnu/packages/cran.scm (r-golem): New variable.
 2022-12-12 19:01:21 +01:00
Mădălin Ionel Patrașcu
79ecb5f35f
gnu: Add r-attempt. 
* gnu/packages/cran.scm (r-attempt): New variable.
 2022-12-12 19:01:21 +01:00
Mădălin Ionel Patrașcu
75a9ee5b8e
gnu: Add r-anytime. 
* gnu/packages/cran.scm (r-anytime): New variable.
 2022-12-12 18:45:32 +01:00
Mădălin Ionel Patrașcu
61124bc7b0
gnu: Add r-shinycustomloader. 
* gnu/packages/cran.scm (r-shinycustomloader): New variable.
 2022-12-12 18:45:31 +01:00
Mădălin Ionel Patrașcu
ca7141234d
gnu: Add r-logging. 
* gnu/packages/cran.scm (r-logging): New variable.
 2022-12-12 18:45:31 +01:00
Mădălin Ionel Patrașcu
b9014985be
gnu: Add r-asics. 
* gnu/packages/bioconductor.scm (r-asics): New variable.
 2022-12-12 18:41:13 +01:00
Mădălin Ionel Patrașcu
061ce5500a
gnu: Add r-pepsnmr. 
* gnu/packages/bioconductor.scm (r-pepsnmr): New variable.
 2022-12-12 18:40:46 +01:00
Mădălin Ionel Patrașcu
1e5c9bb0d2
gnu: Add r-ptw. 
* gnu/packages/cran.scm (r-ptw): New variable.
 2022-12-12 18:40:11 +01:00
Mădălin Ionel Patrașcu
c2d25c7b5e
gnu: Add r-rcppde. 
* gnu/packages/cran.scm (r-rcppde): New variable.
 2022-12-12 18:39:26 +01:00
Mădălin Ionel Patrașcu
e0746ee4c4
gnu: Add r-animalcules. 
* gnu/packages/bioconductor.scm (r-animalcules): New variable.
 2022-12-12 17:30:05 +01:00
Mădălin Ionel Patrașcu
8f80c99e2b
gnu: Add r-plotroc. 
* gnu/packages/cran.scm (r-plotroc): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2022-12-12 17:24:07 +01:00
Mădălin Ionel Patrașcu
b6873a836c
gnu: Add r-gridsvg. 
* gnu/packages/cran.scm (r-gridsvg): New variable.
 2022-12-12 16:22:28 +01:00
Mădălin Ionel Patrașcu
5154e76a2e
gnu: Add r-gunifrac. 
* gnu/packages/cran.scm (r-gunifrac): New variable.
 2022-12-12 16:21:50 +01:00
Mădălin Ionel Patrașcu
48e6e67990
gnu: Add r-dirmult. 
* gnu/packages/cran.scm (r-dirmult): New variable.
 2022-12-12 16:20:36 +01:00
Mădălin Ionel Patrașcu
e99b3c0d25
gnu: Add r-modeest. 
* gnu/packages/cran.scm (r-modeest): New variable.
 2022-12-12 16:19:49 +01:00
Mădălin Ionel Patrașcu
7ec230fe12
gnu: Add r-fbasics. 
* gnu/packages/cran.scm (r-fbasics): New variable.
 2022-12-12 16:19:49 +01:00
Mădălin Ionel Patrașcu
3e6e0696cc
gnu: Add r-timeseries. 
* gnu/packages/cran.scm (r-timeseries): New variable.
 2022-12-12 16:19:18 +01:00
Mădălin Ionel Patrașcu
9e03e01aae
gnu: Add r-gss. 
* gnu/packages/cran.scm (r-gss): New variable.
 2022-12-12 16:18:43 +01:00
Mădălin Ionel Patrașcu
9c81ab8b39
gnu: Add r-stable. 
* gnu/packages/cran.scm (r-stable): New variable.
 2022-12-12 16:18:17 +01:00
Mădălin Ionel Patrașcu
977a15d8e8
gnu: Add r-rmutil. 
* gnu/packages/cran.scm (r-rmutil): New variable.
 2022-12-12 16:17:39 +01:00
Mădălin Ionel Patrașcu
8d2222fac6
gnu: Add r-statip. 
* gnu/packages/cran.scm (r-statip): New variable.
 2022-12-12 16:17:07 +01:00
Mădălin Ionel Patrașcu
5fb5af5658
gnu: Add r-amplican. 
* gnu/packages/bioconductor.scm (r-amplican): New variable.
 2022-12-12 15:50:28 +01:00
Mădălin Ionel Patrașcu
84392cd024
gnu: Add r-waffle. 
* gnu/packages/cran.scm (r-waffle): New variable.
 2022-12-12 15:48:37 +01:00
Mădălin Ionel Patrașcu
ec2388d6b4
gnu: Add r-clustercrit. 
* gnu/packages/cran.scm (r-clustercrit): New variable.
 2022-12-12 15:48:03 +01:00
Mădălin Ionel Patrașcu
8363719476
gnu: Add r-harshlight. 
* gnu/packages/bioconductor.scm (r-harshlight): New variable.
 2022-12-12 15:37:15 +01:00
Mădălin Ionel Patrașcu
85d5ce4901
gnu: Add r-altcdfenvs. 
* gnu/packages/bioconductor.scm (r-altcdfenvs): New variable.
 2022-12-12 15:37:15 +01:00
Mădălin Ionel Patrașcu
97b36ca4d3
gnu: Add r-makecdfenv. 
* gnu/packages/bioconductor.scm (r-makecdfenv): New variable.
 2022-12-12 15:37:15 +01:00
Tobias Geerinckx-Rice
776632c0be
gnu: yajl: Improve description. 
* gnu/packages/web.scm (yajl)[synopsis, description]: Edit.  Mark up.
Note generator.
 2022-12-11 01:00:00 +01:00
Tobias Geerinckx-Rice
2a779dc9bd
gnu: yajl: Remove trailing #t from phases. 
* gnu/packages/web.scm (yajl)[arguments]: Don't explicitly return #t from phases.
 2022-12-11 01:00:00 +01:00
Tobias Geerinckx-Rice
8fe6d3e844
gnu: yajl: Drop custom ‘lib-’ prefix. 
* gnu/packages/web.scm (yajl): New variable, renamed from…
(libyajl): …this one, which is now a DEPRECATED-PACKAGE alias of yajl.
Adjust all users.
 2022-12-11 01:00:00 +01:00
Marius Bakke
b5f3a1b84e
gnu: Remove unused module import. 
* gnu/packages/version-control.scm: Don't import (guix build python-build-system).
 2022-12-12 15:12:58 +01:00
Marius Bakke
16f87d883b
services: zabbix-server: Increase Shepherd grace period. 
* gnu/services/monitoring.scm (zabbix-server-shepherd-service)[stop]: Add
 #:grace-period.
 2022-12-12 15:12:58 +01:00
Marius Bakke
79564bf997
gnu: ffmpeg: Promote version 5 to the default. 
* gnu/packages/video.scm (ffmpeg): Alias to FFMPEG-5.
(mlt-6)[inpust]: Replace "ffmpeg" with FFMPEG-4.
(transcode, libquicktime, ffmpegthumbnailer, mplayer, obs,
simplescreenrecorder, handbrake, ffms2, libopenshot, wlstream)[inputs]: Change
from FFMPEG to FFMPEG-4.
* gnu/packages/arcan.scm (arcan)[inputs]: Likewise.
* gnu/packages/astronomy.scm (stackistry, libskry)[inputs]: Likewise.
* gnu/packages/audio.scm (aubio, bs1770gain)[inputs]: Likewise.
* gnu/packages/education.scm (openboard)[inputs]: Likewise.
* gnu/packages/emulators.scm (dolphin-emu, retroarch, pcsxr, ppsspp)[inputs]:
Likewise.
* gnu/packages/game-development.scm (warsow-qfusion)[inputs]: Likewise.
* gnu/packages/games.scm (oshu, hedgewars)[inputs]: Likewise.
* gnu/packages/gnunet.scm (libextractor)[inputs]: Likewise.
* gnu/packages/graphics.scm (openscenegraph)[inputs]: Likewise.
* gnu/packages/image-processing.scm (opencv, paraview-5.9)[inputs]: Likewise.
* gnu/packages/julia-jll.scm (julia-ffmpeg-jll)[inputs]: Likewise.
* gnu/packages/kde-multimedia.scm (kid3)[inputs]: Likewise.
* gnu/packages/kodi.scm (kodi)[inputs]: Likewise.
* gnu/packages/linphone.scm (mediastreamer2)[inputs]: Likewise.
* gnu/packages/linux.scm (pipewire)[inputs]: Likewise.
(pipewire-0.3)[inputs]: Replace "ffmpeg" with FFMPEG.
* gnu/packages/mp3.scm (chromaprint)[inputs]: Change from FFMPEG to FFMPEG-4.
* gnu/packages/music.scm (musikcube)[inputs]: Likewise.
* gnu/packages/rdesktop.scm (freerdp)[inputs]: Likewise.
* gnu/packages/qt.scm (qtwebengine-5)[inputs]: Likewise.
 2022-12-12 15:12:58 +01:00
Marius Bakke
bf9d119e32
gnu: Sort module imports in (gnu packages scheme). 
* gnu/packages/scheme.scm: Sort imports.  Remove one duplicate.
 2022-12-12 15:12:58 +01:00
Marius Bakke
240c823ae1
gnu: pianobar: Update to 2022.04.01. 
* gnu/packages/music.scm (pianobar): Update to 2022.04.01.
 2022-12-12 15:12:58 +01:00
Marius Bakke
1572071b68
gnu: motion: Remove input labels. 
* gnu/packages/video.scm (motion)[native-inputs, inputs]: Remove labels.
 2022-12-12 15:12:57 +01:00
Marius Bakke
dce40ccc47
gnu: motion: Update to 4.5.0. 
* gnu/packages/video.scm (motion): Update to 4.5.0.
 2022-12-12 15:12:57 +01:00
Marius Bakke
3dc667b6f8
gnu: vapoursynth: Remove input labels. 
* gnu/packages/video.scm (vapoursynth)[native-inputs]: Remove labels.
 2022-12-12 15:12:57 +01:00
Marius Bakke
85ea2dfc4c
gnu: vapoursynth: Update to 61. 
* gnu/packages/video.scm (vapoursynth): Update to 61.
 2022-12-12 15:12:57 +01:00
Marius Bakke
6bfde85d36
gnu: wxsvg: Update to 1.5.24. 
* gnu/packages/wxwidgets.scm (wxsvg): Update to 1.5.24.
 2022-12-12 15:12:57 +01:00
Marius Bakke
f9fb8460ce
gnu: tracker-miners: Remove obsolete input. 
* gnu/packages/gnome.scm (tracker-miners)[native-inputs]: Remove INTLTOOL.
Add GETTEXT-MINIMAL.
 2022-12-12 15:12:57 +01:00
Marius Bakke
b8b4d63137
gnu: OpenLDAP: Update to 2.6.3. 
* gnu/packages/openldap.scm (openldap-2.6): Update to 2.6.3.
 2022-12-12 15:12:57 +01:00
Ludovic Courtès
302a84a593
Merge branch 'version-1.4.0' 2022-12-12 15:03:35 +01:00
Ricardo Wurmus
94e9651241
gnu: Add python-pomegranate. 
* gnu/packages/python-xyz.scm (python-pomegranate): New variable.
 2022-12-12 14:37:04 +01:00
Ricardo Wurmus
bc47a1bf02
gnu: Add python-pygtrie. 
* gnu/packages/python-xyz.scm (python-pygtrie): New variable.
 2022-12-12 14:37:03 +01:00
Ricardo Wurmus
49ec1fbc8f
gnu: Add python-flask-jwt. 
* gnu/packages/python-web.scm (python-flask-jwt): New variable.
 2022-12-12 14:37:03 +01:00
Ricardo Wurmus
be9e8c3963
gnu: Add python-apispec-webframeworks. 
* gnu/packages/python-xyz.scm (python-apispec-webframeworks): New variable.
 2022-12-12 14:37:03 +01:00
Ricardo Wurmus
a88fa1ced7
gnu: Add python-fit-nbinom. 
* gnu/packages/python-xyz.scm (python-fit-nbinom): New variable.
 2022-12-12 14:37:03 +01:00
Ricardo Wurmus
97cfa1cd78
gnu: Add python-py4j. 
* gnu/packages/python-xyz.scm (python-py4j): New variable.
 2022-12-12 14:37:03 +01:00