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130298 Commits (aea3c44027eab1bcd4fe2c881dff0e54d78368f5)

Author SHA1 Message Date
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
Ricardo Wurmus 6e835cd380
gnu: Add r-scenic. 
* gnu/packages/bioinformatics.scm (r-scenic): New variable.

Change-Id: Iff1f501a406ba1a12e49093a575e03facc98f303
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus 994817bfdc
gnu: python-scipy: Update to 1.12.0. 
* gnu/packages/python-science.scm (python-scipy): Update to 1.12.0.
[propagated-inputs]: Add python-jupytext, python-mpmath, python-mypy,
python-numpydoc, python-pydata-sphinx-theme, python-pydevtool,
python-rich-click, python-sphinx, python-threadpoolctl, and
python-typing-extensions; remove python-pyparsing.
[native-inputs]: Add python-hypothesis, python-pycodestyle, python-pytest-cov,
and python-pytest-xdist; remove python-threadpoolctl.

Change-Id: I81a4831e3d94c58416f7d35ec47de90370b88210
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus 2eb061be79
gnu: r-desctools: Update to 0.99.53. 
* gnu/packages/statistics.scm (r-desctools): Update to 0.99.53.

Change-Id: I425b37907b51a93fafa193d217bdf68636f608a7
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus 24d6410125
gnu: r-plotly: Update to 4.10.4. 
* gnu/packages/statistics.scm (r-plotly): Update to 4.10.4.

Change-Id: Idd10685b1ab521056e0468f0c0c188543c11c96a
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus 863ba4b830
gnu: r-xml: Update to 3.99-0.16.1. 
* gnu/packages/statistics.scm (r-xml): Update to 3.99-0.16.1.

Change-Id: I2936eac03ec20b091e45b920f946d92028099973
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus b4a255c2fb
gnu: r-rsqlite: Update to 2.3.5. 
* gnu/packages/statistics.scm (r-rsqlite): Update to 2.3.5.

Change-Id: I43e95bc4ff0b0dc36cf9f3de1705d63bc5681286
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus bf933e4f11
gnu: r-roxygen2: Update to 7.3.1. 
* gnu/packages/statistics.scm (r-roxygen2): Update to 7.3.1.

Change-Id: I5d23ee576beb4dc4dc1e49d13cc38ffef0d33512
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus 4fa0d97e99
gnu: r-maldiquant: Update to 1.22.2. 
* gnu/packages/cran.scm (r-maldiquant): Update to 1.22.2.

Change-Id: Ia483cff36bb3a2cbf4b691bb4832ce98757aabe0
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus 0a733805d8
gnu: r-modeldata: Update to 1.3.0. 
* gnu/packages/cran.scm (r-modeldata): Update to 1.3.0.

Change-Id: Ibaef5366948e9ca45325d279a99f14417ca43e8e
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus 9eb92d55e0
gnu: r-yardstick: Update to 1.3.0. 
* gnu/packages/cran.scm (r-yardstick): Update to 1.3.0.
[propagated-inputs]: Add r-withr.

Change-Id: I00a5d74cca4396e685df32f85d998004a3e94edc
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus a9de282219
gnu: r-lightgbm: Update to 4.3.0. 
* gnu/packages/cran.scm (r-lightgbm): Update to 4.3.0.

Change-Id: I9da6fbcf9558f1ed47b41abd7183f3c53ba1ec67
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus ad552bf927
gnu: r-rstanarm: Update to 2.32.1. 
* gnu/packages/cran.scm (r-rstanarm): Update to 2.32.1.

Change-Id: Ib83276a66add397aeacd830803f94f713f0c22e3
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus fe495a9c64
gnu: r-matrixextra: Update to 0.1.15. 
* gnu/packages/cran.scm (r-matrixextra): Update to 0.1.15.

Change-Id: I72c274e3075cc40d0f6aafb8199a4594c1a518c6
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus 3995f40cd7
gnu: r-graphlayouts: Update to 1.1.0. 
* gnu/packages/cran.scm (r-graphlayouts): Update to 1.1.0.

Change-Id: I5056c2158af15aeed9d5b53a52149e67d6d50b56
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus 306fa840ed
gnu: r-mcmcpack: Update to 1.7-0. 
* gnu/packages/cran.scm (r-mcmcpack): Update to 1.7-0.

Change-Id: I2e480dee05c23158b9ab58de5f9a90e623a7f6b2
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus 899ee468d3
gnu: r-ggfun: Update to 0.1.4. 
* gnu/packages/cran.scm (r-ggfun): Update to 0.1.4.

Change-Id: I08cf695cd03bf28aaa2f2b7b4a35c6632a7027c4
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus 495372ea1f
gnu: r-rmpfr: Update to 0.9-5. 
* gnu/packages/cran.scm (r-rmpfr): Update to 0.9-5.

Change-Id: I32ba06d98406989aca7129f9f647e836e06663f8
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus da3bd82788
gnu: r-bigrquery: Update to 1.5.0. 
* gnu/packages/cran.scm (r-bigrquery): Update to 1.5.0.
[propagated-inputs]: Remove r-assertthat, r-glue, r-progress, r-rcpp, and r-withr; add
r-clock and r-cpp11.

Change-Id: I3f1eb2e32ce901231303a2eb905e8fd7aa0f995a
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus ef3b092587
gnu: r-fmsb: Update to 0.7.6. 
* gnu/packages/cran.scm (r-fmsb): Update to 0.7.6.

Change-Id: I9acec8e49ba036f263223a37c53cf9d4a82ba59f
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus 617c41f418
gnu: r-quickjsr: Update to 1.1.0. 
* gnu/packages/cran.scm (r-quickjsr): Update to 1.1.0.

Change-Id: Ic2fb19a11c781c25b63cc2ed1bf185201aca0fe8
 2024-01-23 13:36:47 +01:00
Ricardo Wurmus e2284fa77d
gnu: r-cmplot: Update to 4.5.1. 
* gnu/packages/cran.scm (r-cmplot): Update to 4.5.1.

Change-Id: I34faf9e7c4b786aaae660ba18c65b429304db601
 2024-01-23 13:36:47 +01:00