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127351 commits

Author SHA1 Message Date
Sharlatan Hellseher
0420667cbe
gnu: python-astropy: Update to 5.3.4.
* gnu/packages/astronomy.scm (python-astropy): Update to 5.3.4.
[arguments]{phases}: Disable one failing test, reported upstream.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 18:09:36 +00:00
Sharlatan Hellseher
20e7aa2732
gnu: libxisf: Update to 0.2.10.
* gnu/packages/astronomy.scm (libxisf): Update to 0.2.10.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 18:09:35 +00:00
Sharlatan Hellseher
966ffbf8c6
gnu: python-pyerfa: Update to 2.0.1.1.
* gnu/packages/astronomy.scm (python-pyerfa): Update to 2.0.1.1.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 18:09:35 +00:00
Sharlatan Hellseher
95a1688229
gnu: erfa: Update to 2.0.1.
* gnu/packages/astronomy.scm (erfa): Update to 2.0.1.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 18:09:35 +00:00
Sharlatan Hellseher
d9b6426cbb
gnu: python-astroalign: Update to 2.5.0.
* gnu/packages/astronomy.scm (python-astroalign): Update to 2.5.0.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 18:09:35 +00:00
Sharlatan Hellseher
10917afe67
gnu: python-cdflib: Update to 1.2.2.
* gnu/packages/astronomy.scm (python-cdflib): Update to 1.2.2.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 18:09:35 +00:00
Sharlatan Hellseher
4d4e9b84ee
gnu: python-pynbody: Update to 1.4.1.
* gnu/packages/astronomy.scm (python-pynbody): Update to 1.4.1.
[source]: Switch to git-fetch.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 18:09:35 +00:00
Sharlatan Hellseher
0d7e51d8ee
gnu: python-spherical-geometry: Enable tests.
* gnu/packages/astronomy.scm (python-spherical-geometry): Enable tests.
[build-system]: Switch to pyproject-build-system.
[arguments]{phases}: Add 'build-extensions phase.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 18:09:35 +00:00
Sharlatan Hellseher
a8c1c98690
gnu: python-spherical-geometry: Simplify package.
* gnu/packages/astronomy.scm (python-spherical-geometry):
[arguments]{phases}<preparations>: Switch to
SETUPTOOLS_SCM_PRETEND_VERSION evnar instead modifying setup.py.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 18:09:35 +00:00
Sharlatan Hellseher
e7b315216a
gnu: imppg: Use standard configure phase.
* gnu/packages/astronomy.scm (imppg): Use G-expressions.
[arguments]{phases}: Use 'configure standard phase instead of
replacement.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 18:09:35 +00:00
Sharlatan Hellseher
b4be620009
gnu: glnemo2: Fix home-page.
* gnu/packages/astronomy.scm (glnemo2): Fix home-page to point to actual
project's one.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 18:09:35 +00:00
Bruno Victal
913d52952b
gnu: font-google-noto: Update to 23.11.1.
[1] indicates that [2] is the new _distribution_ upstream for Noto fonts.

[1]: <https://github.com/notofonts/noto-fonts>
[2]: <https://github.com/notofonts/notofonts.github.io>

* gnu/packages/fonts.scm (font-google-noto): Update to 23.11.1.
[source]<method>: Switch to git-fetch.

Change-Id: I242710336ec81489f9800b68416f45c57d28b2bd
Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 18:08:20 +00:00
Artyom Bologov
04cb25ab9e
gnu: sbcl-cl-webkit: Update to 3.5.10.
gnu/packages/lisp-xyz.scm (sbcl-cl-webkit): Update to 3.5.10.

Signed-off-by: Christopher Baines <mail@cbaines.net>
Change-Id: Ibd54d701a28267fe4fbb979112155839de9d89e5
2023-11-05 18:03:13 +00:00
Jaeme Sifat
0826cc8a07
doc: contributing: Replace reference to dunst.scm.
The contributing documentation makes a reference to dunst.scm as an example of
the build process failing after an update. This patch replaces that reference
with a much more permanent linux.scm.

* doc/contributing.texi: Replace reference to dunst.scm.

Change-Id: I89a4157eb253e25979bc35d6d3b12201a0d19951
Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 17:57:57 +00:00
Jaeme Sifat
bf6fdf76b0
gnu: Remove dunst.scm.
The dunst package is much beter suited to be in wm.scm. This patch deletes
dunst.scm, moves dunst to wm.scm, and removes dunst.scm from the build
process.

* gnu/local.mk (GNU_SYSTEM_MODULES): Remove dunst.scm.
* gnu/packages/dunst.scm: Delete file.
* gnu/packages/wm.scm (dunst): New variable.

Change-Id: I3b074f12f34e14ef1101069ed45ddb33f8d3ea51
Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 17:57:56 +00:00
Jaeme Sifat
a482d3d9ba
gnu: dunst: Update to 1.9.2.
* gnu/packages/dunst.scm (dunst): Update to 1.9.2.
[arguments]: Use gexps.

Change-Id: Ic13f1679074462918991a1ceba8571a46e721224
Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 17:57:49 +00:00
Christopher Baines
aa98a97607
lint: Speed up the formatting linter.
By using go-to-location which caches the number of bytes to seek by to get to
specific lines in a file.

* guix/lint.scm (report-formatting-issues): Use go-to-location.

Change-Id: I34e4d3acfbb1e14e026d2e7f712ba8d22b56c147
Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-05 17:51:38 +00:00
Simon Tournier
1eb3133355
scripts: edit: Fix relative file-name with 'load-path' option.
* guix/scripts/edit.scm (search-path*): Return 'file' if exists when
'search-path' fails.

Change-Id: I891d63d0d28577a7d1732fc59435828ecc0a5c5a
2023-11-05 16:11:17 +01:00
Jelle Licht
ab94e80601
gnu: node-lts: Update to 18.18.2.
* gnu/packages/node.scm (node-lts): Update to 18.18.2.
[arguments]<phases>: Add 'install-node-gyp-wrapper phase.

Change-Id: I6b17de33313505558a8fa9560126adef486fd0e3
2023-11-05 12:37:18 +01:00
VÖRÖSKŐI András
175532b749
gnu: Add rust-blake2-0.10.
* gnu/packages/crates-io.scm (rust-blake2-0.10): New variable.

Change-Id: I8cb30f21a62c563c9c7c559765d9672aed6680ad
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-11-05 12:22:39 +02:00
Janneke Nieuwenhuizen
7684214b3d
gnu: m2-planet: Update to 1.11.0.
* gnu/packages/mes.scm (m2-planet): Update to 1.11.0.

Change-Id: I65ebb434a090e0a57dac50764f16523946a6fa3f
2023-11-05 11:00:16 +01:00
Janneke Nieuwenhuizen
09feb16a0c
gnu: mescc-tools: Update to 1.5.0.
* gnu/packages/mes.scm (mescc-tools): Update to 1.5.0.

Change-Id: I53f6923b8378b5205356e068aa1f1481a9bf7b42
2023-11-05 10:59:40 +01:00
Efraim Flashner
4826856977
gnu: icedtea-7: Fix building on powerpc-linux.
* gnu/packages/java.scm (icedtea-7)[arguments]: Adjust custom
'install-libjvm phase to add support for powerpc-linux.

Change-Id: Ie77a2b53fdef1e0ddc0351e6c2d0241d08b80508
2023-11-05 08:42:48 +02:00
Mădălin Ionel Patrașcu
adf716c171
gnu: Add r-screpertoire.
* gnu/packages/bioconductor.scm (r-screpertoire): New variable.

Change-Id: Iaa876f787d5e39ca2888bf2082da3d7839224e15
2023-11-04 23:13:51 +01:00
Mădălin Ionel Patrașcu
01b7d917a2
gnu: Add r-powertcr.
* gnu/packages/bioconductor.scm (r-powertcr): New variable.

Change-Id: I75fc30a7021d6199b768318da3afcfeaaafcf027
2023-11-04 23:13:51 +01:00
Mădălin Ionel Patrașcu
1678be98f2
gnu: Add r-evmix.
* gnu/packages/cran.scm (r-evmix): New variable.

Change-Id: I93152dee218e9cef85dd66e17231f1728f0ffb52
2023-11-04 23:13:51 +01:00
Mădălin Ionel Patrașcu
ab64815f6a
gnu: Add r-truncdist.
* gnu/packages/cran.scm (r-truncdist): New variable.

Change-Id: Icb9f06a36e5ee5a58828dc2f496b71a850a911b9
2023-11-04 23:13:51 +01:00
Mădălin Ionel Patrașcu
3f991b817d
gnu: Add r-evd.
* gnu/packages/cran.scm (r-evd): New variable.

Change-Id: I1f3b2ee5829807f6f76cf87b4df43ae8005688bc
2023-11-04 23:13:51 +01:00
Wilko Meyer
e3f318f048
gnu: linux-libre 5.10: Fix the hash of the deblob-scripts.
This is a followup to commit e672066097.

* gnu/packages/linux.scm (deblob-scripts 5.10): Update hash.

Signed-off-by: Leo Famulari <leo@famulari.name>
Change-Id: I0fe56dd2694185b6c77468ecc844aaf25ec7564a
2023-07-23 22:26:01 -04:00
Wilko Meyer
3bb6938ffc
gnu: linux-libre 5.15: Fix the hash of the deblob-scripts.
This is a followup to commit b26526ea05.

* gnu/packages/linux.scm (deblob-scripts 5.15): Update hash.

Signed-off-by: Leo Famulari <leo@famulari.name>
Change-Id: Ia59003f2ccfe98e2390593d1ca0b7077f0b7bd5d
2023-07-23 22:26:00 -04:00
Wilko Meyer
1d4813f275
gnu: linux-libre 6.1: Fix the hash of the deblob-scripts.
This is a followup to commit 26709726a8.

* gnu/packages/linux.scm (deblob-scripts 6.1): Update hash.

Signed-off-by: Leo Famulari <leo@famulari.name>
Change-Id: I0035078f4c229763e56cf70ccae730804b123640
2023-07-23 22:26:00 -04:00
Mădălin Ionel Patrașcu
58786c82df
gnu: Add r-rnbeads.
* gnu/packages/bioconductor.scm (r-rnbeads): New variable.

Change-Id: I78b248a449473fc37ac414295faa6e61269b8625
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-04 17:09:53 +01:00
Mădălin Ionel Patrașcu
4c17016019
gnu: Add r-ewastools.
* gnu/packages/bioinformatics.scm (r-ewastools): New variable.

Change-Id: I4117dbee188c7d9547fe63b2b89ec9258bbda60b
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-04 17:03:24 +01:00
Mădălin Ionel Patrașcu
a04800b811
gnu: Add r-mblm.
* gnu/packages/cran.scm (r-mblm): New variable.

Change-Id: Iddfa9bc03a4e5782623253cb70d1ae888545e2ec
2023-11-04 17:03:24 +01:00
Mădălin Ionel Patrașcu
e16d152463
gnu: Add r-dnamcrosshyb.
* gnu/packages/bioinformatics.scm (r-dnamcrosshyb): New variable.

Change-Id: I19e332e6adf0ce9cc721d89bb74a1aa709778873
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-04 16:30:11 +01:00
Mădălin Ionel Patrașcu
cb0e60cccf
gnu: Add r-bsgenome-hsapiens-ucsc-hg38-masked.
* gnu/packages/bioconductor.scm
  (r-bsgenome-hsapiens-ucsc-hg38-masked): New variable.

Change-Id: Ic1b646a3bd3b7262dd82f0972961c2e89628e90b
2023-11-04 16:30:11 +01:00
Jack Hill
9dcd8802f5
gnu: python-pikepdf: Fix embedded version string.
* gnu/packages/python-xyz.scm (python-pikepdf)[native-inputs]: Add
python-setuptools-scm to correct embedded version form 0.0.0 to 1.17.0.

Change-Id: I659ed3e725fff6afe17abe6f55449567ba84cdfc
2023-11-04 19:05:28 +08:00
Nicolas Graves
33644303a1
gnu: emacs-org-ql-dynamic-agenda: Rename to emacs-org-dynamic-agenda-ql.
* /gnu/packages/emacs-xyz.scm (emacs-org-ql-dynamic-agenda): Rename to…
(emacs-org-dynamic-agenda-ql): …this.
[arguments]<#:include>: Adjust according to source change.

Change-Id: I4b09933a17d301e3017f1628414eade1ee174538
2023-11-04 19:03:39 +08:00
Mădălin Ionel Patrașcu
7eeab6417f
gnu: Add r-methylaid.
* gnu/packages/bioconductor.scm (r-methylaid): New variable.

Change-Id: I7839035e5316bdbe5f1386b7b41ed2fc440fb432
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-04 11:37:15 +01:00
Clément Lassieur
f54f36b363
gnu: passff-host: Add explicit references to inputs and remove some.
This removes ‘coreutils’, ‘grep’, ‘sed’, ‘which’, ‘bash-minimal’ and
‘gnu-make’ inputs, which were only used by the Makefile and
install_host_app.sh.  Instead of running install_host_app.sh (through
‘make’) which does a few text substitutions, do the text substitutions with
Scheme code.  This simplifies things and avoids unnecessary native inputs.

* gnu/packages/browser-extensions.scm (passff-host)[build-system]: Change to
copy-build-system.
[arguments]: Copy passff.json and passff.py.  Do text substitutions on
them rather than running make.  Refer to ‘password-store’ and ‘python’ through
inputs rather than directly.
[inputs]: Add PASSWORD-STORE and PYTHON.

Change-Id: I8fdb757516a7c30eae36b15f2a8d91e1445b19a5
2023-11-04 00:52:39 +01:00
Clément Lassieur
625cfb4c4c
gnu: password-store: Add missing ‘tail’ input.
* gnu/packages/password-utils.scm (password-store)[arguments]: Add “tail” to
the list of requisites.
[inputs]: Add COREUTILS.

Change-Id: I7f59e6c0abfb5396b9548edaec08d3b0a7c0eb23
2023-11-04 00:52:38 +01:00
Afkhami, Navid
10d728139d
gnu: Add r-ggbreak.
* gnu/packages/cran.scm (r-ggbreak): New variable.

Change-Id: I27d62d0110fb56e77dc8cf82581adb6259317c2d
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-03 23:39:57 +01:00
Vinicius Monego
479fdc8451
gnu: python-pymc: Update to 5.9.1.
* gnu/packages/statistics.scm (python-pymc): Update to 5.9.1.

Change-Id: I3d7927e7173f36ba4edeab06bd930c285432c29f
2023-11-03 19:25:36 -03:00
Vinicius Monego
43d9fa0802
gnu: python-pytensor: Update to 2.17.3.
* gnu/packages/python-science.scm (python-pytensor): Update to 2.17.3.

Change-Id: I2843aca1df4d43883bf643e6e363bd3700202c45
2023-11-03 19:25:36 -03:00
Vinicius Monego
1879bfd88f
gnu: python-deepxde: Update to 1.10.0.
* gnu/packages/machine-learning.scm (python-deepxde): Update to 1.10.0.

Change-Id: Ibc37f9e7df45c49f590beb1dda87236e853b88c1
2023-11-03 19:25:36 -03:00
Vinicius Monego
96e8502faa
gnu: Add python-emcee.
* gnu/packages/statistics.scm (python-emcee): New variable.
2023-11-03 19:25:35 -03:00
Vinicius Monego
a7d56852e3
gnu: Add python-salib.
* gnu/packages/python-science.scm (python-salib): New variable.
2023-11-03 19:25:35 -03:00
Vinicius Monego
9642b1c7af
gnu: python-openturns: Update to 1.21.1.
* gnu/packages/statistics.scm (python-openturns): Update to 1.21.1.
2023-11-03 19:25:35 -03:00
Vinicius Monego
a55c3110be
gnu: python-opentsne: Update to 1.0.0.
* gnu/packages/machine-learning.scm (python-opentsne): Update to 1.0.0.
2023-11-03 19:25:35 -03:00
Vinicius Monego
ef473d3422
gnu: symengine: Update to 0.11.1.
* gnu/packages/algebra.scm (symengine): Update to 0.11.1.
2023-11-03 19:25:31 -03:00