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Author SHA1 Message Date
Sharlatan Hellseher e5923f4f3c
gnu: python-crds: Update to 11.17.14. 
* gnu/packages/astronomy.scm (python-crds): Update to 11.17.14.
[description]: Indent it and apply TexInfo style on URLs.

Change-Id: Icd298578cf685cfbc454d5b16b9f89c6d050b93a
 2024-01-24 22:24:37 +00:00
Sharlatan Hellseher 25b69fcac8
gnu: libxisf: Update to 0.2.11. 
* gnu/packages/astronomy.scm (libxisf): Update to 0.2.11.

Change-Id: I79242d42af3db660c46be0baf05e11ea7ac680f7
 2024-01-24 22:24:37 +00:00
Sharlatan Hellseher eb4cee3a9c
gnu: gpredict: Update home-page and description. 
* gnu/packages/astronomy.scm (gpredict)[home-page]: Update it according
to project's README.
[description]: Add feature detailed list.

Change-Id: If5edc6e50796c7753ac47fac082c267145723361
 2024-01-24 22:24:37 +00:00
Sharlatan Hellseher b4f638879d
gnu: indi-2.0: Update to 2.0.5. 
* gnu/packages/astronomy.scm (indi-2.0): Update to 2.0.5.

Change-Id: I9cea7e7d11af5a142066f11a2185eb826570afb5
 2024-01-24 22:24:37 +00:00
Sharlatan Hellseher 800b09aeef
gnu: stellarium: Update to 23.4. 
* gnu/packages/astronomy.scm (stellarium): Update to 23.4.
[inputs]: Add nlopt.

Change-Id: Id205ad84ff75a687f6c1fdababcf3040c0c55abd
 2024-01-24 22:24:37 +00:00
Ricardo Wurmus 2266754382
gnu: python-pytorch-geometric: Disable one test. 
* gnu/packages/machine-learning.scm (python-pytorch-geometric)[arguments]:
Disable test_gdc as it occasionally fails.

Change-Id: I9d1dc1b68628801ea1bb5a8bdfa17063990748ea
 2024-01-24 22:37:14 +01:00
Efraim Flashner 362ab8bf18
gnu: libdispatch: Update to 5.9.2. 
* gnu/packages/c.scm (libdispatch): Update to 5.9.2.

Change-Id: I119d1de974673aa2c08eb51a7bcaa7ce24aeb0b2
 2024-01-24 22:25:00 +02:00
Efraim Flashner da3e6aea0a
gnu: range-v3: Update to 0.12.0. 
* gnu/packages/cpp.scm (range-v3): Update to 0.12.0.
[source]: Remove patch.
* gnu/packages/patches/range-v3-build-with-gcc10.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Change-Id: I078937f9aff0da31ede8d472d8739e48bb775c55
 2024-01-24 19:15:30 +02:00
Efraim Flashner c0f3c0cfd9
gnu: range-v3: Format with 'guix style'. 
* gnu/packages/cpp.scm (range-v3): Format with 'guix style'.

Change-Id: I249443e5e5d0f7ef49e33de4f140246a862101d2
 2024-01-24 19:15:30 +02:00
Efraim Flashner 3643389ba7
gnu: range-v3: Build with newer gcc. 
* gnu/packages/cpp.scm (range-v3)[native-inputs]: Remove gcc-9.

Change-Id: I0411d5db3e3df15c6df0a9a010d311fe1c80015c
 2024-01-24 19:15:25 +02:00
Ricardo Wurmus c3353791a4
gnu: python-xgboost: Fix build. 
* gnu/packages/machine-learning.scm (python-xgboost)[build-system]: Use
pyproject-build-system.
[arguments]: Move test flags to #:test-flags; disable a few more tests, mostly
to account for a removed dataset; use G-expression; remove custom 'check phase.

Change-Id: I6841a8c159919df85acaa8558248a8775ec5be80
 2024-01-24 17:37:37 +01:00
Andre A. Gomes 2c5faa9ab8
gnu: webkitgtk: Update to 2.42.4 [fixes CVE-2023-42883]. 
* gnu/packages/webkit.scm (webkitgtk): Update to 2.42.4.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2024-01-24 10:47:05 -05:00
Maxim Cournoyer e479920cfd
gnu: emacs-yasnippet: Update to 0.14.0-0.297546f. 
* gnu/packages/emacs-xyz.scm (emacs-yasnippet): Update to 0.14.0-0.297546f.
Remove fix-tests patch.
* gnu/packages/patches/emacs-yasnippet-fix-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): De-register it.

Change-Id: I3fda2bb3d879d88f06f9d814b6c8d835d9eafc9f
 2024-01-24 10:42:42 -05:00
Maxim Cournoyer 1348be9115
gitconfig: b4: Automatically add 'Signed-off-by' when applying patches. 
Also use --3way to ease conflict resolutions.

* etc/git/gitconfig [b4]: Add shazam-am-flags option.

Change-Id: I6a92909a5b23a8680c16251aafa084b9a48944ea
 2024-01-24 10:42:41 -05:00
Ricardo Wurmus c797abdd29
gnu: Add python-pytorch-geometric. 
* gnu/packages/machine-learning.scm (python-pytorch-geometric): New variable.

Change-Id: I9a016cda7d167159437724a878e6512c37106fea
 2024-01-24 16:36:37 +01:00
Andreas Enge e54124ca4d
gnu: singular: Update to 4.3.2p10. 
* gnu/packages/algebra.scm (singular): Update to 4.3.2p10.

Change-Id: I196d31e3f5605dd51385146ce091d63a4e9eb340
 2024-01-24 14:31:16 +01:00
Ricardo Wurmus db96cc0ba2
gnu: Add r-papaja. 
* gnu/packages/cran.scm (r-papaja): New variable.

Co-authored-by: Lars-Dominik Braun <lars@6xq.net>
Change-Id: Ib5b3a6ff8d52052cf135b2ba36cad3ce295ed6d4
 2024-01-24 13:02:01 +01:00
Ricardo Wurmus d5e7ad7188
gnu: Add r-tinylabels. 
* gnu/packages/cran.scm (r-tinylabels): New variable.

Change-Id: Ie86de4daaf132cd32f896573be747f35e725258e
 2024-01-24 13:01:52 +01:00
Ricardo Wurmus 90b9cb1298
gnu: Add r-rmdfiltr. 
* gnu/packages/cran.scm (r-rmdfiltr): New variable.

Change-Id: I59b92e9364ca4e74a98b80b6cca1a883ab3caec3
 2024-01-24 13:01:41 +01:00
Ricardo Wurmus 420692482f
gnu: python-chaospy: Ignore deprecation warnings. 
* gnu/packages/statistics.scm (python-chaospy)[arguments]: Add phase
'dont-treat-deprecation-warnings-as-error.

Change-Id: Id06404f9e47f7084fefc2e72032882d49e5b546b
 2024-01-24 12:49:29 +01:00
Andreas Enge 43a82ad545
gnu: pynac: Update to 0.7.29. 
* gnu/packages/sagemath.scm (pynac): Update to 0.7.29.

Change-Id: I3bf2675aea9d8a07fdcfa08471c9d1ca7725e1f7
 2024-01-24 12:31:21 +01:00
Efraim Flashner 4939425918
teams: Remove Efraim Flashner from the science team. 
* etc/teams.scm (Efraim Flashner): Remove science team.

Change-Id: I790fe329cde11fcb4b706b01b9aa59ad29d8c874
 2024-01-24 12:49:43 +02:00
Ricardo Wurmus afd0fe50b0
gnu: python-pyts: Update to 0.13.0. 
* gnu/packages/python-science.scm (python-pyts): Update to 0.13.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; enable all tests.
[propagated-inputs]: Remove python-matplotlib.

Change-Id: Iafcc047d8bb14e1eef514fd92aa53f8fda38eab0
 2024-01-24 11:34:35 +01:00
Ricardo Wurmus 6a22f65d66
gnu: python-scikit-learn-extra: Update to 0.3.0-1.0f95d8d. 
* gnu/packages/machine-learning.scm (python-scikit-learn-extra): Update to
0.3.0-1.0f95d8d.
[arguments]: Move test flags out of 'check phase and to #:test-flags.
[propagated-inputs]: Add python-packaging.

Change-Id: I4081a9364a0646d0c6960a3d155315e8eff8af59
 2024-01-24 11:34:35 +01:00
Andre A. Gomes 90f9528748
gnu: nyxt: Update to 3.11.1. 
* gnu/packages/web-browsers.scm (nyxt): Update to 3.11.1.
  [inputs]: Remove sbcl-fset and sbcl-mk-string-metrics. Add gst-libav,
  gst-plugins-bad, gst-plugins-base, gst-plugins-good, gst-plugins-ugly.
  [arguments]: Update 'configure-tests' phase.
  [home-page]: Update URL.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
Change-Id: If35d6f0153339b311057bea05562fefb215c3f0d
 2024-01-24 11:18:02 +01:00
Andre A. Gomes 8aa3ae15dd
gnu: cl-lass: Update to 0.6.0-1.1f2418d. 
* gnu/packages/lisp-xyz.scm (sbcl-lass): Update to 0.6.0-1.1f2418d.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
Change-Id: I51dfe84b9194b4d94d76502ffd47f88cbc1583fb
 2024-01-24 11:18:02 +01:00
Sharlatan Hellseher 3419c216b4
gnu: python-pydicom: Update to 2.4.4. 
* gnu/packages/python-science.scm (python-pydicom): Update to 2.4.4.

Change-Id: I996115fb3bdf0bd61d2b2dcdb2500b31ce104597
 2024-01-23 23:57:32 +00:00
Sharlatan Hellseher b537437af7
gnu: python-pydicom: Simplify package style. 
* gnu/packages/python-science.scm (python-pydicom)[build-system]: Swap
to pyproject-build-system.
[description]: Simplify wording, indent.

Change-Id: I7ef413ea2da6cbb83eb33424c559f7ac5ed549cb
 2024-01-23 23:54:44 +00:00
Sharlatan Hellseher 5a616cc14b
gnu: python-pynetdicom: Simplify package style. 
* gnu/package/python-science.scm (python-pynetdicom)[build-system]: Swap
to pyproject-build-system.
[description]: Simplify wording, indent.

Change-Id: If4e80d06edb0080685d0695f30abc2f9db669f45
 2024-01-23 23:51:48 +00:00
Antero Mejr e71abbc643
gnu: Add python-pynetdicom. 
* gnu/packages/python-science.scm (python-pynetdicom): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-23 23:38:02 +00:00
Ricardo Wurmus c376298c7c
gnu: Add flash. 
* gnu/packages/bioinformatics.scm (flash): New variable.

Change-Id: Id657ba7850031ad24b4333b6bc79401511e00a85
 2024-01-23 23:47:31 +01:00
Ricardo Wurmus 825b3ca763
gnu: Add isolator. 
* gnu/packages/bioinformatics.scm (isolator): New variable.

Change-Id: I950baca5b6898576f358b3364b1fe541b3333298
 2024-01-23 23:43:19 +01:00
Mathieu Othacehe 3aa60e4096
ci: Don't cross compile to or1k-elf. 
* gnu/ci.scm (cross-jobs)[pointless?]: Don't build any packages for or1k-elf.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
Change-Id: I294429d5318b94fb8e7780a37f3608b5321cf6ca
 2024-01-23 21:45:36 +01:00
Ricardo Wurmus b9a5c50d8c
gnu: Add metal. 
* gnu/packages/bioinformatics.scm (metal): New variable.

Change-Id: I70fd30c18303f61a9f6720e70d4b4e57140a7140
 2024-01-23 21:41:58 +01:00
Ricardo Wurmus 25f0964c3e
gnu: Add randfold. 
* gnu/packages/bioinformatics.scm (randfold): New variable.

Change-Id: If2cea9c8d5323296015dc21ea7a3d1b677ae2798
 2024-01-23 21:31:51 +01:00
Ricardo Wurmus ebad9d6c0e
gnu: Add python-pyfasta. 
* gnu/packages/bioinformatics.scm (python-pyfasta): New variable.

Change-Id: Ib2ab0a6eb250309633d5be33c18409227bce84ba
 2024-01-23 21:26:50 +01:00
Ricardo Wurmus f7373261e9
gnu: Add python-fcsparser. 
* gnu/packages/bioinformatics.scm (python-fcsparser): New variable.

Change-Id: I87ed7f10bbfdf7d689cb6289a5f5ad31872f9de0
 2024-01-23 21:22:45 +01:00
Ricardo Wurmus 469405375c
gnu: Add lsgkm. 
* gnu/packages/bioinformatics.scm (lsgkm): New variable.

Change-Id: I0ea35354c7856e7425567cd4ac27ab7fc2ab0d9e
 2024-01-23 21:18:07 +01:00
Mark H Weaver 648085dab6
gnu: icecat: Update to 115.7.0-guix0-preview1 [security fixes]. 
Includes fixes for CVE-2024-0741, CVE-2024-0742, CVE-2024-0746,
CVE-2024-0747, CVE-2024-0749, CVE-2024-0750, CVE-2024-0751,
CVE-2024-0753, and CVE-2024-0755.

* gnu/packages/gnuzilla.scm (%icecat-base-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.
 2024-01-23 11:09:02 -05:00
Efraim Flashner 40fb160a5e
Revert "gnu: source-highlight: Wrap scripts." 
This package causes the rebuild of more than 9000 packages.

This reverts commit 367bc2d198.
 2024-01-23 17:33:54 +02:00
Artyom V. Poptsov e3f4ab49b1
gnu: kubo: Update to 0.18.0. 
* gnu/packages/ipfs.scm (kubo): Update to 0.18.0.
  [inputs]: Add go-github-com-gorilla-mux.

Change-Id: I4eccdfcf9eadbdf25728fcca766c5238efb0d57f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-23 14:07:01 +00:00
Efraim Flashner 367bc2d198
gnu: source-highlight: Wrap scripts. 
* gnu/packages/pretty-print.scm (source-highlight)[arguments]: Add a
phase to wrap shell scripts so they can find the source-hightlight
binary.
[inputs]: Add guile-3.0.

Change-Id: Ia8d006d969385210d5c82b4a0dd1f78178306ac2
 2024-01-23 16:04:42 +02:00
Sharlatan Hellseher fbeae77ae6
gnu: trurl: Update to 0.9. 
* gnu/packages/curl.scm (trurl): Update to 0.9.

Change-Id: Ieb0f19e6d48897dceb32e317613a301f521c9b94
 2024-01-23 14:01:51 +00:00
Ricardo Wurmus d3129b3f1e
gnu: Add eddylab-squid. 
* gnu/packages/bioinformatics.scm (eddylab-squid): New variable.

Change-Id: Icb02f42fc95d2001a639e22608a01ef9074158bc
 2024-01-23 13:52:36 +01:00
Ricardo Wurmus 6a82745746
gnu: Add python-magic-impute. 
* gnu/packages/bioinformatics.scm (python-magic-impute): New variable.

Change-Id: Iba5240e9920a1045078c736553cb1d56069963b5
 2024-01-23 13:42:55 +01:00
Ricardo Wurmus 1bdc4eeb46
gnu: Add python-graphtools. 
* gnu/packages/graph.scm (python-graphtools): New variable.

Change-Id: If08b1460447702f7ec2e64f013a52a7065076b01
 2024-01-23 13:42:55 +01:00
Ricardo Wurmus a313875476
gnu: Add python-tasklogger. 
* gnu/packages/python-xyz.scm (python-tasklogger): New variable.

Change-Id: I53319b70b7788090e8873a912d7c56044c0bb5b2
 2024-01-23 13:36:48 +01:00
Ricardo Wurmus 561d429aa4
gnu: python-nose2: Update to 0.14.0. 
* gnu/packages/check.scm (python-nose2): Update to 0.14.0.
[native-inputs]: Remove python-coverage.
[propagated-inputs]: Remove python-six.

Change-Id: I15a30723fe49cca9929524e543d12c9e2f4b02ca
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus a6b6d1bd6a
gnu: python-scikit-learn: Disable one test. 
This test fails with the upgrade of scipy.

* gnu/packages/machine-learning.scm (python-scikit-learn)[arguments]: Disable
test_singular_matrix test.

Change-Id: I47627403826bb5c52f4d578399c7cabaa3f8838d
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus 123c880fe9
gnu: Add python-pygsp. 
* gnu/packages/graph.scm (python-pygsp): New variable.

Change-Id: I8dd195216617e5cdb4a7453ecbe23cd9ff9e06a3
 2024-01-23 13:36:47 +01:00