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148473 commits

Author SHA1 Message Date
Sharlatan Hellseher
c56505e399
gnu: packages/astronomy: Sort alphabetically.
* gnu/packages/astronomy.scm (python-astral, python-drizzle, splash):
Sort variables alphabetically.

Change-Id: I9876e8e2ad2f83448b65beb9d72aa1220f464581
2024-12-06 22:36:26 +00:00
Sharlatan Hellseher
18da502785
gnu: packages/astronomy: Sort alphabetically.
* gnu/packages/astronomy.scm (python-ccdproc, python-gwcs,
python-jplephem, python-jwst, python-jwst-reffiles): Sort variables
alphabetically.

Change-Id: I8a0b77fe456927a158080570c52cb4c48d58257f
2024-12-06 22:01:54 +00:00
Danny Milosavljevic
4127992ff7
gnu: Add perl-extutils-f77.
* gnu/packages/perl.scm (perl-extutils-f77): New variable.

Change-Id: I50b6e15e30d9b1dd2cfe5c1aae3398085069e303
2024-12-06 22:12:14 +01:00
Danny Milosavljevic
61e91cf90b
gnu: Add perl-sort-versions.
* gnu/packages/perl.scm (perl-sort-versions): New variable.
2024-12-06 22:12:14 +01:00
Danny Milosavljevic
42bf19830d
gnu: Add perl-mojo-dom58.
* gnu/packages/perl-web (perl-mojo-dom58): New variable.
2024-12-06 22:12:14 +01:00
Danny Milosavljevic
041cb5351e
gnu: Add perl-file-map.
* gnu/packages/perl.scm (perl-file-map): New variable.
2024-12-06 22:12:14 +01:00
Danny Milosavljevic
6e6b1c2ceb
gnu: Add perl-sys-sigaction.
* gnu/packages/perl.scm (perl-sys-sigaction): New variable.
2024-12-06 22:12:14 +01:00
Danny Milosavljevic
9f5ee16844
gnu: Add perl-termreadkey.
* gnu/packages/perl.scm (perl-termreadkey): New variable.
2024-12-06 22:12:11 +01:00
Richard Sent
0972a27572
services: wireguard: Support lists of gexps for most fields.
In order to support more flexibility in Wireguard configuration, ungexp the
configuration fields directly instead of ungexp-splicing a sexp
calculator. This allows for the fields to take arbitrary gexps instead of only
strings which is particularly helpful for the Pre/Post Up/Down commands.

* gnu/services/vpn.scm (wireguard-configuration-file): Ungexp configuration
lists instead of ungexp-splicing the code surrounding them.
* doc/guix.texi (VPN Services)[wireguard]: Document it.

Change-Id: If074cbb78473b6fd34e0e4e990d2ed268001d6c7
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2024-12-06 20:09:28 +01:00
Richard Sent
1a17a0f90d
services: wireguard: Add the bootstrap-private-key? field.
The syntax from using the private-key field is more convenient than writing a
custom PreUp command (more formatting and preshared keys). Instead of trying
to guess if private-key is/is not a file path, add an option to disable
bootstrapping while still using private-key.

* gnu/services/vpn.scm (<wireguard-configuration>): Add
bootstrap-private-key?.
(wireguard-activation): Check bootstrap-private-key? before bootstrapping.
* doc/guix.texi (VPN Services)[wireguard]: Document it.

Change-Id: I6ba71ad58b26743057a221a54a246369022f83a5
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2024-12-06 20:09:28 +01:00
Richard Sent
aa12068c91
services: wireguard: Make the private-key field optional.
Users who retrieve the private-key via a PreUp field need to be able to
disable the default retrieval mechanism.

* gnu/services/vpn.scm (<wireguard-configuration>)[private-key]: Change
comment.
(wireguard-configuration-file): Conditionally serialize private-key.
* gnu/services/vpn.scm (wireguard-activation): Do not create private-key if
the field is #f.
* doc/guix.texi (VPN Services)[wireguard-configuration]: Document it.

Change-Id: Iac419809ae94eb76e97ff1f1749e2f4b3e65bb04
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2024-12-06 20:09:28 +01:00
Danny Milosavljevic
d101a6275a
gnu: Add emacs-dired-launch.
* gnu/packages/emacs-xyz.scm (emacs-dired-launch): New variable.
2024-12-06 19:45:54 +01:00
Danny Milosavljevic
3490452fc9
gnu: emacs-jedi: Fix jedi:server-command default.
* gnu/packages/emacs-xyz.scm (emacs-jedi)[arguments]<#:phases>
[patch-jedi:server-command]: Make it a list.
2024-12-06 19:41:31 +01:00
Danny Milosavljevic
5d284ebc8d
gnu: xdg-desktop-portal-gtk: Make possible to use with xdg-desktop-portal-wlr.
* gnu/packages/freedesktop.scm (xdg-desktop-portal-gtk)[propagated-inputs]:
Replace xdg-desktop-portal with xdg-desktop-portal-next.
2024-12-06 19:20:59 +01:00
Danny Milosavljevic
84fa76db42
gnu: python-debugpy: Update to 1.8.9.
* gnu/packages/python-xyz.scm (python-debugpy): Update to 1.8.9.

Change-Id: I323570fc007af04fa8c9c59571cc3cc79833da04
2024-12-06 19:19:19 +01:00
Danny Milosavljevic
331600e55d
gnu: python-pydevd: Update to 3.2.3.
* gnu/packages/python-xyz.scm (python-pydevd): Update to 3.2.3.

Change-Id: Ibb1bb9880b2c456f27bf373259a0e604a62b9515
2024-12-06 19:19:14 +01:00
Ekaitz Zarraga
0c5d7b8480
gnu: Update otpclient to 4.0.2
Requires updating `libcotp` to 3.1.0, that introduced a new way for
testing that requires `criterium`, a package we don't have and that has
dependencies that we don't have either.

As the tests in `libcotp` are not an exhaustive testsuite and
`otpclient` is its only dependent package, tests are disabled for the
moment.

* gnu/packages/authentication.scm (libcotp): Update to 3.1.0
[arguments] Disable tests.
* gnu/packages/password-utils.scm (otpclient): Update to 4.0.2

Change-Id: Ie6d37b5efe59397d4979c7490b94f1c871c27d6d
2024-12-06 14:27:55 +01:00
Hartmut Goebel
d75d1fe6ac
gnu: Fix java-jaxen.
java-jaxen was missing the dom4j and xom sub-packages. This was caused by
java-jaxen-bootstrap deleting the respective directories (which is okay) and
java-javen not removing the phase that does this.

Solve this by removing the #:phases argument for java-jaxen and thus make guix
use the default phases.

* gnu/packages/java-xml.scm (java-jaxen)[arguments]: Remove #:phases.
, making
2024-12-05 22:24:55 +01:00
Simen Endsjø
32ad7173d6
gnu: go-github-com-cyphar-filepath-securejoin: Fix url.
Fix url incorrectly changed in 9399db35c2.

* gnu/packages/golang-xyz.scm (go-github-com-cyphar-filepath-securejoin)
[origin]: Fix url.

Change-Id: Ibac24d11efdd6414bdeb8be2cd2184e21d7f8676
Signed-off-by: Ekaitz Zarraga <ekaitz@elenq.tech>
2024-12-05 22:10:22 +01:00
Guillaume Le Vaillant
704128d4ed
gnu: eisl: Update to 5.38.
* gnu/packages/lisp.scm (eisl): Update to 5.38.

Change-Id: I115706d2b06bed71a24cf2c1ab1f5c1bf2e88284
2024-12-05 19:18:12 +01:00
Guillaume Le Vaillant
3764e8c4bd
gnu: gqrx: Update to 2.17.6.
* gnu/packages/radio.scm (gqrx): Update to 2.17.6.

Change-Id: Ief1ec50d0e64fa325dc2f270612a978105c05f3a
2024-12-05 19:18:12 +01:00
Guillaume Le Vaillant
732fd8e671
gnu: Add cl-simple-matrix.
* gnu/packages/lisp-xyz.scm (cl-simple-matrix, ecl-simple-matrix,
  sbcl-simple-matrix): New variables.

Change-Id: I79499aae2c8c7dc0ba2d1193104f2f3dd1d3621c
2024-12-05 19:18:12 +01:00
Efraim Flashner
46abb5212e
gnu: make-rust-sysroot: Adjust for newer cross-gcc.
* gnu/packages/rust.scm (make-rust-sysroot/implementation)
[native-inputs]: Add gcc-14.

Change-Id: If9bc74bfe2e236accc39dc09e03b28dee62e332d
2024-12-05 14:09:20 +02:00
Efraim Flashner
d3c929a4bd
gnu: make-rust-sysroot: Simplify native-inputs.
* gnu/packages/rust.scm (make-rust-sysroot/implementation)
[native-inputs]: Combine the different modify-input branches into one.

Change-Id: Ia7df5d1566099f9934a76b2660f46a55547c88b9
2024-12-05 14:07:47 +02:00
Efraim Flashner
be53521d4c
gnu: make-rust-sysroot: Accept other mingw targets.
* gnu/packages/rust.scm (make-rust-sysroot/implementation)[arguments]:
Adjust the custom 'patch-for-mingw phase to generate the name of the
mingw input package based on the target architecture.
[inputs, native-inputs]: Use make-mingw-w64 to choose the mingw package
for the target.

Change-Id: I48638095a504675753e65fdb6f0286c31cebde66
2024-12-05 13:20:18 +02:00
Efraim Flashner
76bc375080
gnu: glibc-dynamic-linker: Match all mingw systems.
* gnu/packages/bootstrap.scm (glibc-dynamic-linker): Match any system
which ends in '-mingw'.

Change-Id: I057e3d0abfc37f4b2b8784f444bbaf865c67ce3e
2024-12-05 13:01:18 +02:00
Zheng Junjie
006679d1e6
Partial revert "gnu: bootstrap: %bootstrap-gcc: Also wrap g++ for the 64bit Hurd."
This partially reverts commit 877b925df1.

This part accidentally triggered a world rebuild for non-x86 architectures.

Change-Id: Iabc5422bb0e2bb37816ad437994af94d04830cb0
2024-12-05 01:13:02 +08:00
Zheng Junjie
126a2e8cb4
Partial revert "gnu: bootstrap: %bootstrap-glibc: Also fix libm.so."
This partially reverts commit 204fe1b1f0.

This part accidentally triggered a world rebuild for non-x86 architectures.

Change-Id: I921984ef5eff58792ffc17b64675db6a8e79695c
2024-12-05 01:13:02 +08:00
Zheng Junjie
7b64a96326
Partial revert "gnu: make-bootstrap: Update gcc-static to gcc-14, for the 64bit Hurd."
This partially reverts commit ec8a5ec15f.

This part accidentally triggered a world rebuild for non-x86 architectures.

Change-Id: Id2f9bcbcda8dc86ea407e9a7857a854dc1a742b5
2024-12-05 01:13:02 +08:00
Ricardo Wurmus
e00ca95e08
gnu: Add r-ggupset.
* gnu/packages/cran.scm (r-ggupset): New variable.

Change-Id: I044fff58b66dbb56e6b7fb1ebcb5353e7ab3d1f7
2024-12-04 16:25:20 +01:00
Ricardo Wurmus
3cfd6e11a4
gnu: Add skewer.
* gnu/packages/bioinformatics.scm (skewer): New variable.

Change-Id: Ieeb95ed7449b91ea853d73ecca05e5436121df6a
2024-12-04 16:21:07 +01:00
Sharlatan Hellseher
0c1dddd90f
gnu: packages/python-science: Update copyright header.
* gnu/packages/python-science.scm: Update copyright header for Antero
Mejr <antero@mailbox.org> .

Change-Id: I4153d51d74f7de1629d5a7851346021b77e7352d
2024-12-04 14:38:09 +00:00
Antero Mejr
16c71b7fe3
gnu: Add python-scikit-surprise.
* gnu/packages/python-science.scm (python-scikit-surprise): New variable.

Change-Id: I9b5e13f0c985f34bb0bd759e76ebd27221a340a4
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-12-04 14:28:10 +00:00
Janneke Nieuwenhuizen
1c4a00820a
gnu: ikiwiki: Fix build by disabling a test.
* gnu/packages/web.scm (ikiwiki)[arguments]: In stage "pre-check", disable
failing "t/t.po" test.

Change-Id: I4fc1240512b4d3df3ece837521116aee5746e181
2024-12-04 10:15:24 +01:00
John Kehayias
3e2442de52
Revert "news: Add entry for the Guix survey."
This reverts commit cd26d76fed.  See discussion
at <https://issues.guix.gnu.org/74549>.  Let's keep news.scm to direct user
impact/software (or at least not set a different precedent here).

Change-Id: I1a72474ad3c79bc59100979f35f0216f68f4e88e
2024-12-04 00:49:27 -05:00
Ekaitz Zarraga
9001514e24
doc: contributing: Remove --base=auto
* doc/contributing.texi(Sending a Patch Series): Remove --base=auto from
  examples

Change-Id: Idd421f9d6b592d6a314edfaa66404dee4c1b2241
2024-12-03 22:43:10 +01:00
Ekaitz Zarraga
7b46b8db9a
doc: Explain git format-patch revision format
* doc/contributing.texi(Sending a Patch Series): Add a note about
`git format-patch` revision format and link to git documentation.

Change-Id: Ie08f85dc19e3804165fb184664b74e85a804d7c4
2024-12-03 22:42:54 +01:00
Ricardo Wurmus
595fb0ade7
gnu: r-rcdt: Add missing input.
* gnu/packages/cran.scm (r-rcdt)[native-inputs]: Add r-testthat.

Change-Id: Ic5358aee6d5174052266dc01b81f618edf931cd2
2024-12-03 17:00:01 +01:00
Ricardo Wurmus
8c97926a01
import/cran: Enhance import pattern.
* guix/import/cran.scm (import-pattern): Comment; capture direct namespace
imports as well as silent imports.

Change-Id: Ia54035d6f230d695aa950adb3e691cbce4f2d416
2024-12-03 17:00:01 +01:00
Ricardo Wurmus
1261bf83b8
import/cran: Also add set-HOME phase when R.cache exists.
* guix/import/cran.scm (phases-for-inputs): Add "R.cache" to the list.

Change-Id: Ia65beb7cd535de10b024d108a97db0169045fe1f
2024-12-03 17:00:01 +01:00
Ricardo Wurmus
46badc09bd
gnu: r-msnid: Disable vignettes.
* gnu/packages/bioconductor.scm (r-msnid)[arguments]: Disable vignettes.

Change-Id: I47dc4cf5b6d80699d4f22b2b92382ada7ca3322a
2024-12-03 17:00:01 +01:00
Ricardo Wurmus
2f4814e95c
gnu: r-pcaexplorer: Add missing inputs.
* gnu/packages/bioconductor.scm (r-pcaexplorer)[native-inputs]: Add
r-airway and r-org-hs-eg-db.

Change-Id: Id559bea8cd4308058a06158e74d3e13d7f645572
2024-12-03 17:00:01 +01:00
Ricardo Wurmus
0b64bb6ee5
gnu: Add r-airway.
* gnu/packages/bioconductor.scm (r-airway): New variable.

Change-Id: I521c1bf868566f80997c8ba80609fd5709a95694
2024-12-03 17:00:00 +01:00
Ricardo Wurmus
dedc157d71
gnu: r-reportingtools: Add missing inputs.
* gnu/packages/bioconductor.scm (r-reportingtools)[native-inputs]: Add
r-all, r-genefilter, r-hgu95av2-db, r-org-hs-eg-db, r-org-mm-eg-db,
r-org-sc-sgd-db, r-pasilla, and r-shiny.
[properties]: Tell updater to ignore r-gsealm.

Change-Id: I9512bbc7a96c328ee05e15bc898969494dca4be0
2024-12-03 17:00:00 +01:00
Ricardo Wurmus
f8bbfe1ea9
gnu: Add r-faahko.
* gnu/packages/bioconductor.scm (r-faahko): New variable.

Change-Id: I70cd662bdd202ac78f5f25235fb7b9b9e7d60b37
2024-12-03 17:00:00 +01:00
Ricardo Wurmus
9e72ac0e0c
gnu: r-xcms: Disable tests.
* gnu/packages/bioconductor.scm (r-xcms)[arguments]: Disable tests.
[properties]: Tell updater to ignore r-faahko.
[native-inputs]: Add r-msdata.

Change-Id: I2ee167828534a4046d15d740f6f25d8eff9d589f
2024-12-03 17:00:00 +01:00
Ricardo Wurmus
68c1fab64f
gnu: r-httpgd: Disable tests.
* gnu/packages/statistics.scm (r-httpgd)[arguments]: Disable tests.
[synopsis]: Use lower case and remove extraneous quotes.

Change-Id: I25e69987b6c647d14cc51ba01ba2fcfb1163c568
2024-12-03 17:00:00 +01:00
Ricardo Wurmus
8035314cb1
gnu: r-mcmc: Disable vignettes.
* gnu/packages/cran.scm (r-mcmc)[arguments]: Disable vignettes.

Change-Id: I0453d3a812d8e5fea52ab38d16e82f9c5ea439ac
2024-12-03 17:00:00 +01:00
Ricardo Wurmus
014b08cbc8
gnu: r-biodb: Disable tests.
* gnu/packages/bioconductor.scm (r-biodb)[arguments]: Disable tests.

Change-Id: I40746a3fbfad0801058b7f34182edc358a863fa2
2024-12-03 17:00:00 +01:00
Ricardo Wurmus
b97678925a
gnu: discrover: Add missing input.
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add
texlive-etoolbox.

Change-Id: I42075c05a36a031c40c335a668a8b46a7603b4dd
2024-12-03 17:00:00 +01:00