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2024-01-24gnu: gpredict: Update home-page and description.Sharlatan Hellseher
* gnu/packages/astronomy.scm (gpredict)[home-page]: Update it according to project's README. [description]: Add feature detailed list. Change-Id: If5edc6e50796c7753ac47fac082c267145723361
2024-01-24gnu: indi-2.0: Update to 2.0.5.Sharlatan Hellseher
* gnu/packages/astronomy.scm (indi-2.0): Update to 2.0.5. Change-Id: I9cea7e7d11af5a142066f11a2185eb826570afb5
2024-01-24gnu: stellarium: Update to 23.4.Sharlatan Hellseher
* gnu/packages/astronomy.scm (stellarium): Update to 23.4. [inputs]: Add nlopt. Change-Id: Id205ad84ff75a687f6c1fdababcf3040c0c55abd
2024-01-24gnu: python-pytorch-geometric: Disable one test.Ricardo Wurmus
* gnu/packages/machine-learning.scm (python-pytorch-geometric)[arguments]: Disable test_gdc as it occasionally fails. Change-Id: I9d1dc1b68628801ea1bb5a8bdfa17063990748ea
2024-01-24gnu: libdispatch: Update to 5.9.2.Efraim Flashner
* gnu/packages/c.scm (libdispatch): Update to 5.9.2. Change-Id: I119d1de974673aa2c08eb51a7bcaa7ce24aeb0b2
2024-01-24gnu: range-v3: Update to 0.12.0.Efraim Flashner
* 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
2024-01-24gnu: range-v3: Format with 'guix style'.Efraim Flashner
* gnu/packages/cpp.scm (range-v3): Format with 'guix style'. Change-Id: I249443e5e5d0f7ef49e33de4f140246a862101d2
2024-01-24gnu: range-v3: Build with newer gcc.Efraim Flashner
* gnu/packages/cpp.scm (range-v3)[native-inputs]: Remove gcc-9. Change-Id: I0411d5db3e3df15c6df0a9a010d311fe1c80015c
2024-01-24gnu: python-xgboost: Fix build.Ricardo Wurmus
* 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
2024-01-24gnu: webkitgtk: Update to 2.42.4 [fixes CVE-2023-42883].Andre A. Gomes
* gnu/packages/webkit.scm (webkitgtk): Update to 2.42.4. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2024-01-24gnu: emacs-yasnippet: Update to 0.14.0-0.297546f.Maxim Cournoyer
* 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
2024-01-24gnu: Add python-pytorch-geometric.Ricardo Wurmus
* gnu/packages/machine-learning.scm (python-pytorch-geometric): New variable. Change-Id: I9a016cda7d167159437724a878e6512c37106fea
2024-01-24gnu: singular: Update to 4.3.2p10.Andreas Enge
* gnu/packages/algebra.scm (singular): Update to 4.3.2p10. Change-Id: I196d31e3f5605dd51385146ce091d63a4e9eb340
2024-01-24gnu: Add r-papaja.Ricardo Wurmus
* gnu/packages/cran.scm (r-papaja): New variable. Co-authored-by: Lars-Dominik Braun <lars@6xq.net> Change-Id: Ib5b3a6ff8d52052cf135b2ba36cad3ce295ed6d4
2024-01-24gnu: Add r-tinylabels.Ricardo Wurmus
* gnu/packages/cran.scm (r-tinylabels): New variable. Change-Id: Ie86de4daaf132cd32f896573be747f35e725258e
2024-01-24gnu: Add r-rmdfiltr.Ricardo Wurmus
* gnu/packages/cran.scm (r-rmdfiltr): New variable. Change-Id: I59b92e9364ca4e74a98b80b6cca1a883ab3caec3
2024-01-24gnu: python-chaospy: Ignore deprecation warnings.Ricardo Wurmus
* gnu/packages/statistics.scm (python-chaospy)[arguments]: Add phase 'dont-treat-deprecation-warnings-as-error. Change-Id: Id06404f9e47f7084fefc2e72032882d49e5b546b
2024-01-24gnu: pynac: Update to 0.7.29.Andreas Enge
* gnu/packages/sagemath.scm (pynac): Update to 0.7.29. Change-Id: I3bf2675aea9d8a07fdcfa08471c9d1ca7725e1f7
2024-01-24gnu: python-pyts: Update to 0.13.0.Ricardo Wurmus
* 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
2024-01-24gnu: python-scikit-learn-extra: Update to 0.3.0-1.0f95d8d.Ricardo Wurmus
* 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
2024-01-24gnu: nyxt: Update to 3.11.1.Andre A. Gomes
* 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
2024-01-24gnu: cl-lass: Update to 0.6.0-1.1f2418d.Andre A. Gomes
* 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
2024-01-23gnu: python-pydicom: Update to 2.4.4.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pydicom): Update to 2.4.4. Change-Id: I996115fb3bdf0bd61d2b2dcdb2500b31ce104597
2024-01-23gnu: python-pydicom: Simplify package style.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pydicom)[build-system]: Swap to pyproject-build-system. [description]: Simplify wording, indent. Change-Id: I7ef413ea2da6cbb83eb33424c559f7ac5ed549cb
2024-01-23gnu: python-pynetdicom: Simplify package style.Sharlatan Hellseher
* gnu/package/python-science.scm (python-pynetdicom)[build-system]: Swap to pyproject-build-system. [description]: Simplify wording, indent. Change-Id: If4e80d06edb0080685d0695f30abc2f9db669f45
2024-01-23gnu: Add python-pynetdicom.Antero Mejr
* gnu/packages/python-science.scm (python-pynetdicom): New variable. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-01-23gnu: Add flash.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (flash): New variable. Change-Id: Id657ba7850031ad24b4333b6bc79401511e00a85
2024-01-23gnu: Add isolator.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (isolator): New variable. Change-Id: I950baca5b6898576f358b3364b1fe541b3333298
2024-01-23gnu: Add metal.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (metal): New variable. Change-Id: I70fd30c18303f61a9f6720e70d4b4e57140a7140
2024-01-23gnu: Add randfold.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (randfold): New variable. Change-Id: If2cea9c8d5323296015dc21ea7a3d1b677ae2798
2024-01-23gnu: Add python-pyfasta.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyfasta): New variable. Change-Id: Ib2ab0a6eb250309633d5be33c18409227bce84ba
2024-01-23gnu: Add python-fcsparser.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-fcsparser): New variable. Change-Id: I87ed7f10bbfdf7d689cb6289a5f5ad31872f9de0
2024-01-23gnu: Add lsgkm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (lsgkm): New variable. Change-Id: I0ea35354c7856e7425567cd4ac27ab7fc2ab0d9e
2024-01-23gnu: icecat: Update to 115.7.0-guix0-preview1 [security fixes].Mark H Weaver
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.
2024-01-23Revert "gnu: source-highlight: Wrap scripts."Efraim Flashner
This package causes the rebuild of more than 9000 packages. This reverts commit 367bc2d198f57bc34522441820f761b61fed0ce0.
2024-01-23gnu: kubo: Update to 0.18.0.Artyom V. Poptsov
* 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>
2024-01-23gnu: source-highlight: Wrap scripts.Efraim Flashner
* 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
2024-01-23gnu: trurl: Update to 0.9.Sharlatan Hellseher
* gnu/packages/curl.scm (trurl): Update to 0.9. Change-Id: Ieb0f19e6d48897dceb32e317613a301f521c9b94
2024-01-23gnu: Add eddylab-squid.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (eddylab-squid): New variable. Change-Id: Icb02f42fc95d2001a639e22608a01ef9074158bc
2024-01-23gnu: Add python-magic-impute.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-magic-impute): New variable. Change-Id: Iba5240e9920a1045078c736553cb1d56069963b5
2024-01-23gnu: Add python-graphtools.Ricardo Wurmus
* gnu/packages/graph.scm (python-graphtools): New variable. Change-Id: If08b1460447702f7ec2e64f013a52a7065076b01
2024-01-23gnu: Add python-tasklogger.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-tasklogger): New variable. Change-Id: I53319b70b7788090e8873a912d7c56044c0bb5b2
2024-01-23gnu: python-nose2: Update to 0.14.0.Ricardo Wurmus
* gnu/packages/check.scm (python-nose2): Update to 0.14.0. [native-inputs]: Remove python-coverage. [propagated-inputs]: Remove python-six. Change-Id: I15a30723fe49cca9929524e543d12c9e2f4b02ca
2024-01-23gnu: python-scikit-learn: Disable one test.Ricardo Wurmus
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
2024-01-23gnu: Add python-pygsp.Ricardo Wurmus
* gnu/packages/graph.scm (python-pygsp): New variable. Change-Id: I8dd195216617e5cdb4a7453ecbe23cd9ff9e06a3
2024-01-23gnu: Add r-scenic.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scenic): New variable. Change-Id: Iff1f501a406ba1a12e49093a575e03facc98f303
2024-01-23gnu: python-scipy: Update to 1.12.0.Ricardo Wurmus
* 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
2024-01-23gnu: r-desctools: Update to 0.99.53.Ricardo Wurmus
* gnu/packages/statistics.scm (r-desctools): Update to 0.99.53. Change-Id: I425b37907b51a93fafa193d217bdf68636f608a7
2024-01-23gnu: r-plotly: Update to 4.10.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-plotly): Update to 4.10.4. Change-Id: Idd10685b1ab521056e0468f0c0c188543c11c96a
2024-01-23gnu: r-xml: Update to 3.99-0.16.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-xml): Update to 3.99-0.16.1. Change-Id: I2936eac03ec20b091e45b920f946d92028099973
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