Commit graph

116196 commits

Author SHA1 Message Date
Navid Afkhami
f056d4f168
gnu: Add python-decoupler-py.
* gnu/packages/bioinformatics.scm (python-decoupler-py): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
2023-06-06 21:35:37 +02:00
Mark H Weaver
72243da2fb
gnu: icecat: Update to 102.12.0-guix0-preview1 [security fixes].
Includes fixes for CVE-2023-34414 and CVE-2023-34416.

* gnu/packages/gnuzilla.scm (%icecat-base-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.
2023-06-06 14:41:03 -04:00
Gruruya
2199546a83
gnu: nim: Update to 1.6.12.
Without the attached patch, Nim is broken on Guix as it searches
for its stdlib in /lib while it was placed in /lib/nim.

* gnu/packages/nim.scm (nim): Update to 1.6.12.
[arguments]: In 'patch-installer phase install stdlib source to the
right directory.  In 'patch-more-shebangs phase edit substitute* to
point to the new osproc source.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-06 19:24:47 +03:00
Josselin Poiret
1a2eb26286
services: Check if service is #f before applying clause.
* gnu/services.scm (apply-clauses): Check if service is #f before trying to
apply clause.  Follow up of 1819512073.
2023-06-06 13:38:35 +02:00
Ricardo Wurmus
0ae29db11d
gnu: python-anaconda-client: Fix build with Python 3.10.
* gnu/packages/package-management.scm (python-anaconda-client)[build-system]:
Use pyproject-bulid-system.
[arguments]: Move contents of 'remove-network-tests phase to #:test-flags;
drop trailing #T from 'set-HOME phase; add phase 'python3.10-compatibility;
disable test_conda_root and test_conda_root_outside_root_environment.
2023-06-06 13:04:14 +02:00
Navid Afkhami
f800e7e88b
gnu: Add r-caretensemble.
* gnu/packages/cran.scm (r-caretensemble): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-06-06 12:55:52 +02:00
Ludovic Courtès
1819512073
services: 'modify-services' preserves service ordering.
Fixes <https://issues.guix.gnu.org/63921>.

The regression was introduced in
dbbc7e9461, which changed the order of
services.  As a result, someone using 'modify-services' could find
themselves with incorrect ordering of expressions in the "boot" script,
whereby the cleanup expressions would come after (execl ".../shepherd").
This, in turn, would lead shepherd to error out at boot with EADDRINUSE
on /var/run/shepherd/socket.

* gnu/services.scm (%delete-service, %apply-clauses): Remove.
(clause-alist): New macro.
(apply-clauses): New procedure.
(modify-services): Use it.  Adjust docstring.
* tests/services.scm ("modify-services: do nothing"): Remove 'sort' call.
("modify-services: delete service"): Likewise, and add 't4' service.
("modify-services: change value"): Remove 'sort' call and fix expected value.
2023-06-06 11:54:39 +02:00
Ludovic Courtès
dc0c5d56ee
records: Use SRFI-11 instead of SRFI-71, for Guile 2.0 compatibility.
This fixes a failure of 'tests/packages.scm' introduced in
b88e38d4b5: some of the tests import (guix
records) on the build side, which uses '%bootstrap-guile' (Guile 2.0)
where SRFI-71 is unavailable.

* guix/records.scm (match-record-inner): Use SRFI-11 instead of SRFI-71.
2023-06-06 11:54:39 +02:00
Ludovic Courtès
d62c6170ef
doc: Add missing node to the main menu.
This is a followup to 110462bb2f.

* doc/guix.texi (Top): Add "Mail Home Services" to the menu.
2023-06-06 11:54:39 +02:00
Guillaume Le Vaillant
9ad8b0c2ef
gnu: sbcl-stmx: Update to 2.0.5-2.f71e742.
* gnu/packages/lisp-xyz.scm (sbcl-stmx): Update to 2.0.5-2.f71e742.
  [arguments]: Add 'fix-build' phase.
2023-06-06 10:46:45 +02:00
Guillaume Le Vaillant
b30c60316c
gnu: txr: Update to 287.
* gnu/packages/lisp.scm (txr): Update to 287.
2023-06-06 10:01:10 +02:00
Guillaume Le Vaillant
b019b49c74
gnu: sbcl: Update to 2.3.5.
* gnu/packages/lisp.scm (sbcl): Update to 2.3.5.
2023-06-06 09:54:23 +02:00
Jean-Pierre De Jesus DIAZ
e3cd3f0320
gnu: openocd: Update to 0.12.0.
* gnu/packages/embedded.scm (openocd): Update to 0.12.0.
[inputs]: Remove libusb-compat as openocd dropped support for libusb0.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-06 09:55:52 +03:00
Jean-Pierre De Jesus DIAZ
f351f2aaf2
gnu: jimtcl: Update to 0.82.
* gnu/packages/embedded (jimtcl): Update to 0.82.
[arguments]: Use G-Expressions and update failing test, TTY test doesn't
fail anymore.
[inputs]: Add openssl as an input as now by default jimtcl enables the
SSL configuration option.
* gnu/packages/embedded (openocd): Support jimtcl 0.82.
[arguments]: Link against libssl and libcrypto.
[inputs]: Add openssl.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-06 09:55:35 +03:00
Jean-Pierre De Jesus DIAZ
cdbd87b6f3
gnu: libjaylink: Update to 0.3.1.
* gnu/packages/embedded (libjaylink): Update to 0.3.1.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-06 09:55:32 +03:00
Z572
d6ae80c742
gnu: thc-ipv6: Do not build with "-march=native".
* gnu/packages/networking.scm (thc-ipv6)[origin]: Add 'snippet'.
[properties]: New field.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-06 09:22:46 +03:00
Leo Famulari
8937898af9
gnu: linux-libre 5.4: Update to 5.4.245.
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.245.
(linux-libre-5.4-pristine-source): Update hash.
2023-06-05 19:18:56 -04:00
Leo Famulari
00e2d8d8ae
gnu: linux-libre 5.10: Update to 5.10.182.
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.182.
(linux-libre-5.10-pristine-source): Update hash.
2023-06-05 19:18:55 -04:00
Leo Famulari
f9755ff2ac
gnu: linux-libre 5.15: Update to 5.15.115.
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.115.
(linux-libre-5.15-pristine-source): Update hash.
2023-06-05 19:18:55 -04:00
Leo Famulari
455e88bc84
gnu: linux-libre 6.1: Update to 6.1.32.
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.32.
(linux-libre-6.1-pristine-source): Update hash.
2023-06-05 19:18:55 -04:00
Leo Famulari
b3dfa5b671
gnu: linux-libre: Update to 6.3.6.
* gnu/packages/linux.scm (linux-libre-6.3-version): Update to 6.3.6.
(linux-libre-6.3-pristine-source): Update hash.
2023-06-05 19:18:47 -04:00
Efraim Flashner
f598f5b870
gnu: blurhash: Update to 0.2.0.
* gnu/packages/image.scm (blurhash): Update to 0.2.0.
[native-inputs]: Remove cmake. Add pkg-config.
2023-06-05 22:05:13 +03:00
Efraim Flashner
ff6bb37299
gnu: cpp-httplib: Update to 0.12.5.
* gnu/packages/cpp.scm (cpp-httplib): Update to 0.12.5.
[arguments]: Adjust configure-flags to build the tests.  Add a make-flag
to set CXX.  Adjust custom 'disable-network-tests phase to skip more
network tests. Remove custom 'check phase.
[native-inputs]: Add googletest.
2023-06-05 22:00:56 +03:00
Efraim Flashner
c1b8f1bc7a
doc: Fix some typos in the manual.
* doc/guix.texi (Invoking guix pull): Correct followings to following.
(Using Guix Interactively): Correct expresssion to expression.
(Base Services): Correct overriden to overridden.
(Audio Services): Correct Supress to Suppress.
(Setuid Programs): Correct goup to group.
(Essential Home Services): Correct apropiate to appropriate, similiar to
similar.
(Messaging Home Services): Correct seperately to separately.
(image Reference): Correct instanciated to instantiated.
(Full-Source Bootstrap): Correct udpate to update, Frome to From.
2023-06-05 21:36:09 +03:00
Efraim Flashner
cad86f8dcd
gnu: python-codespell: Update to 2.2.4.
* gnu/packages/python-xyz.scm (python-codespell): Update to 2.2.4.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Remove python-check-manifest; add python-pygments and
python-tomli.
2023-06-05 21:36:09 +03:00
Efraim Flashner
5cf38fb6d6
doc: cookbook: Update example my-libgit2 package.
* doc/guix-cookbook.texi (Packaging Tutorial): Improve the code quality
of the example my-libgit2 package.
2023-06-05 21:36:06 +03:00
Ricardo Wurmus
a025d8fee6
import/cran: Ensure current package is not among inputs.
* guix/import/cran.scm (cran-package-inputs): Remove the current package from
the result.
2023-06-05 18:55:11 +02:00
Ricardo Wurmus
52e0a77a1b
gnu: proj-7: Add upstream patch.
* gnu/packages/patches/proj-7-initialize-memory.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/geo.scm (proj-7)[source]: Add it.
2023-06-05 17:55:38 +02:00
Ricardo Wurmus
4f2ec0f2d1
gnu: python-bulkvis: Reference upstream issue.
* gnu/packages/bioinformatics.scm (python-bulkvis)[arguments]: Add comment
with link to upstream issue for bokeh compatibility patch.
2023-06-05 17:20:52 +02:00
Ricardo Wurmus
77d6d5783b
gnu: python-tenacity: Use pyproject-build-system.
* gnu/packages/python-xyz.scm (python-tenacity)[build-system]: Use
pyproject-build-system.
[arguments]: Remove.
2023-06-05 17:11:15 +02:00
Ricardo Wurmus
46fc4c01a0
gnu: python-tenacity: Use Tornado 6.
* gnu/packages/python-xyz.scm (python-tenacity)[native-inputs]: Replace
python-tornado with python-tornado-6.
2023-06-05 17:11:15 +02:00
Ricardo Wurmus
1671aa25d4
gnu: python-bokeh: Use Tornado 6.
* gnu/packages/python-xyz.scm (python-bokeh)[propagated-inputs]: Replace
python-tornado with python-tornado-6.
2023-06-05 17:11:15 +02:00
Navid Afkhami
6559adea29
gnu: Add python-bulkvis.
* gnu/packages/bioinformatics.scm (python-bulkvis): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-06-05 17:11:15 +02:00
Navid Afkhami
91e75bb35f
gnu: Add python-readpaf.
* gnu/packages/bioinformatics.scm (python-readpaf): New variable.
2023-06-05 17:11:14 +02:00
Efraim Flashner
940665301d
gnu: gcompris-qt: Update to 3.2.
* gnu/packages/education.scm (gcompris-qt): Update to 3.2.
[inputs]: Add qtcharts, qtquickcontrols2-5. Remove qtquickcontrols-5,
qtxml-5.
2023-06-05 11:35:52 +03:00
Timotej Lazar
a95edc3d7b
gnu: mupdf: Update to 1.22.1.
* gnu/packages/pdf.scm (mupdf): Update to 1.22.1.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-05 10:29:01 +03:00
Efraim Flashner
eed55a6544
gnu: lagrange: Update to 1.16.3.
* gnu/packages/web-browsers.scm (lagrange): Update to 1.16.3.
2023-06-04 21:08:30 +03:00
Efraim Flashner
c15470671a
gnu: keepassxc: Update to 2.7.5.
* gnu/packages/password-utils.scm (keepassxc): Update to 2.7.5.
2023-06-04 21:08:30 +03:00
Efraim Flashner
f8b82976d6
gnu: urlscan: Update to 1.0.0.
* gnu/packages/mail.scm (urlscan): Update to 1.0.0.
[arguments]: Skip the test phase.
[build-system]: Switch to the pyproject-build-system.
[native-inputs]: Add python-hatch-vcs, python-hatchling.
2023-06-04 21:06:47 +03:00
Efraim Flashner
9d9e793da5
gnu: tree: Update to 2.1.1.
* gnu/packages/admin.scm (tree): Update to 2.1.1.
[arguments]: Remove unneeded 'fix-manpage-version phase.
2023-06-04 19:02:15 +03:00
Zheng Junjie
ae04b3996b
gnu: jpegoptim: Fix cross-compiling to riscv64.
* gnu/packages/image.scm (jpegoptim)[arguments]: When cross-compiling t
riscv64, add phase to update-config-scripts.
[native-inputs]: When cross-compiling to riscv64, add config.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-04 15:28:53 +03:00
Zheng Junjie
4f3e5548fc
gnu: libicns: Fix cross-compiling to riscv64.
* gnu/packages/image.scm (libicns)[arguments]: When cross-compiling to
riscv64, add phase to update-config-scripts.
[native-inputs]: When cross-compiling to riscv64, add config.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-04 15:28:20 +03:00
Zheng Junjie
713da38002
gnu: gsettings-desktop-schemas: Fix cross-compiling.
* gnu/packages/gnome.scm(gsettings-desktop-schemas)[inputs]: Add
gobject-introspection.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-04 15:02:07 +03:00
Zheng Junjie
3f45c3b12b
gnu: gobject-introspection: Fix cross-compiling.
* gnu/packages/glib.scm(gobject-introspection)[native-inputs]: When
cross-compiling add python.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-04 14:58:28 +03:00
Zheng Junjie
188da31fe5
gnu: mtdev: Fix cross-compiling to riscv64.
* gnu/packages/xdisorg.scm (mtdev)[arguments]: When cross-compiling to
riscv64 add a phase to update config.{guess,sub}.
[native-inputs]: When cross-compiling to riscv64 add config.
2023-06-04 14:56:09 +03:00
Zheng Junjie
0ee6c9ea01
gnu: xcb-util-wm: Fix cross-compiling to riscv64.
* gnu/packages/xorg.scm (xcb-util-wm)[arguments]: Add
update-config-scripts phase when cross-compiling to riscv64.
[native-inputs]: Add config when cross-compiling to riscv64.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-04 14:46:56 +03:00
Zheng Junjie
81515a4029
gnu: libxtst: Fix cross-compiling to riscv64.
* gnu/packages/xorg.scm (libxtst)[arguments]: When cross-compiling to
riscv64, add phase to update config.{guess,sub}.
[native-inputs]: When cross-compiling to riscv64, add config.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-04 14:44:55 +03:00
Efraim Flashner
d845178050
gnu: libdeflate: Use default tests.
* gnu/packages/compression.scm (libdeflate)[arguments]: Adjust
configure-flags to build the test suite. Remove custom 'check phase.
2023-06-04 14:18:23 +03:00
Josselin Poiret
cacc0cb6ab
channels: Raise an error if dependency's introduction is malformed
* guix/channels.scm (sexp->channel-introduction): Do it.
2023-06-04 11:30:18 +02:00
Josselin Poiret
e198fe4e94
gnu: agda-ial: Update to ded30c410d5d40142249686572aa1acd1b2f8cc7.
* gnu/packages/agda.scm (agda-ial): Update to
ded30c410d5d40142249686572aa1acd1b2f8cc7, use agda-build-system, switch to
G-Exps, reorder fields.
2023-06-04 11:04:54 +02:00