Commit graph

136570 commits

Author SHA1 Message Date
Ricardo Wurmus
9f9127e80a
gnu: ensembl-vep: Update to 112.
* gnu/packages/bioinformatics.scm (ensembl-vep): Update to 112.
[propagated-inputs]: Add perl-list-moreutils.
[native-inputs]: Add perl-test-deep and perl-test-warnings.

Change-Id: I8c7de9f3dbc8c6fe4d1383f9dc215aeba018af0d
2024-05-22 17:44:49 +02:00
guix@mawumag.com
d658f8c9af
gnu: Add r-chameleon.
* gnu/packages/cran.scm (r-chameleon): New variable.

Change-Id: I9e0f3c27e434bb802c86ef9e2877f4d810397158
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-05-22 17:44:49 +02:00
Christopher Baines
4955589f2f
doc: Make changes to the handling of branches.
Require that you create a "Request to merge" issue when you create a branch,
rather than when you wish to merge it.  This should help avoid this step being
missed.

Also, add information on how to manage these branches:

 1. Suggest creating the branch from patches, rather than having a stateful
 branch, since this should help to reduce complexity and avoid merges.

 2. Require that branches don't have unnecessary changes, since this increases
 the risks of conflicts with other branches.

 3. Suggest that the branch not be stateful, and it's just a combination of
 patches.

 4. Suggest avoiding merges since these create a more complicated Git history.

 5. Suggest that the branch be up to date before merging, as this helps avoid
 the combination of master plus the branch differing significantly from the
 branch alone.

 6. Document how to manage branches without commit access.

Finally, require that the branch be deleted once they're merged.  This
prepares for the branch being created again.

* doc/contributing.texi (Managing Patches and Branches): Make changes to the
handling of branches.

Change-Id: Ib9419c6df94f485475bd6f147e82ea254e76cec2
2024-05-22 14:31:01 +01:00
Sharlatan Hellseher
b462cff5ee
gnu: python-pandera: Update to 0.18.0, fix build.
* gnu/packages/python-science.scm (python-pandera): Update to 0.18.0.
[arguments] <#:test-flags>: Disable one more failing test.

Change-Id: I4d3f59dae8d90ea0afbe9cc932fc6163def282c9
2024-05-22 14:23:16 +01:00
Sharlatan Hellseher
b06a460bf5
gnu: python-pymysql: Propagate python-cryptography.
* gnu/packages/databases.scm (python-pymysql)
[inputs]: Swap to [propagated-inputs].
[propagated-inputs]: Add python-pynacl
(mycli, sqlcrush): Remove propagated python-cryptography.

Change-Id: I40ee51087cd14cb98bd2390095fa9f6f0d144b47
2024-05-22 10:13:01 +01:00
Sharlatan Hellseher
5000c417c0
gnu: python-pymysql: Update to 1.1.1 [fixes CVE-2024-36039].
* gnu/packages/databases.scm (python-pymysql): Update to 1.1.1.
[source]: Refresh archive name as seen on
<https://pypi.org/project/PyMySQL/#files>.
[build-system]: Swap to pyproject-build-system.

Change-Id: I20d06f6d1d252f501df001120ee44520e6e5d785
2024-05-22 10:12:05 +01:00
Andy Tai
50bbe668d4
gnu: schmutz: update to commit f8043e.
* gnu/packages/guile-xyz.scm (schmutz): Update to commit f8043e.
  [inputs]: Switch guile-2.2 to guile-3.0.

Change-Id: Ibd3e5a5074119e3d2a9affcd7c98f47cb9f1f677
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-05-22 15:46:32 +08:00
Artyom V. Poptsov
284a8cd681
gnu: axel: Update to 2.17.14.
* gnu/packages/networking.scm (axel): Update to 2.17.14.

Change-Id: I62ce6e62d7f50662e13e89baff8658ae49224f56
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-05-22 15:46:32 +08:00
Michael Ford
750148ce1e
gnu: gcc-13: Update to 13.3.0.
* gnu/packages/gcc.scm (gcc-13): Update to 13.3.0.

Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
Change-Id: Ia2dc3185acbb6671b2719e2d88d55b7d2b8fb92e
2024-05-22 15:46:26 +08:00
Nicolas Graves via Guix-patches via
6bcecb6898
import/elpa: Add proper file-name to origin.
This avoids the lint "the source file name should contain the package
name" with generated packages.

Change-Id: I61c81203d9f3cdd035e2b64a4c7a8d86d1f3dd50
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-05-22 15:21:09 +08:00
David Wilson
d7a65f1e91
gnu: emacs-denote: Update to 2.3.0.
* gnu/packages/emacs-xyz.scm (emacs-denote): Update source location and bump
version to 2.3.0.

Change-Id: I573db7f285832bf27659b33274e1d592d1c5aa45
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2024-05-22 08:51:35 +02:00
Wilko Meyer
f1a573067c
gnu: wlsunset: Update to 0.4.0.
* gnu/packages/xdisorg.scm (wlsunset): Update to 0.4.0.

Change-Id: I4638d89c29fd4da2ae9850955bb43875fb00d416
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-05-22 13:14:04 +08:00
Sören Tempel
bf6602beaf
gnu: wlsunset: Install man pages.
* gnu/packages/xdisorg.scm (wlsunset)[native-inputs]: Add scdoc.

Reviewed-by: Dale Mellor <guix-devel-0brg6a@rdmp.org>
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
Change-Id: Iffeb9427a1fd625f9dac4098107336cba639f5e9
2024-05-22 13:13:39 +08:00
Artyom V. Poptsov
036c0b5843
gnu: btop: Update to 1.3.2.
* gnu/packages/admin.scm (btop): Update to 1.3.2.

Change-Id: I503bc5730dd498640cff76e252825c7b47cd5d11
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-05-22 12:58:47 +08:00
Michael Ford
1fa1325c0b
gnu: LLVM, Clang, libomp, lld: Update to 18.1.6.
* gnu/packages/llvm.scm (llvm-18, clang-18, libomp-18, lld-18):
Update to 18.1.6.

Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
Change-Id: Ifd5ab99f4195c93e9b8d67aa26caead26c8dd5bc
2024-05-22 11:37:42 +08:00
dan
b1db320473
gnu: yambar-wayland: Update to 1.11.0.
* gnu/packages/wm.scm (yambar-wayland): Update to 1.11.0.

Change-Id: I8ee9726a665a97e9dccaead32f1272ab98289c8f
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-05-22 11:37:42 +08:00
dan
9523b968d5
gnu: fnott: Update to 1.6.0.
* gnu/packages/wm.scm (fnott): Update to 1.6.0.
[arguments]<#:phases>: Patch dbus service file install directory.

Change-Id: I0a64c93b0e1ed43f101cb5a77ecfce5025a2b4b0
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-05-22 11:37:38 +08:00
Zheng Junjie
327a1f0779
system: images: Add visionfive2 module.
* gnu/system/images/visionfive2.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.

Change-Id: I8831f1148bcddb0d604e1174034fca85cd2887a1
2024-05-22 11:15:30 +08:00
Zheng Junjie
c7aec90a91
bootloader: Add u-boot-starfive-visionfive2-bootloader.
* gnu/bootloader/u-boot.scm (u-boot-starfive-visionfive2-bootloader): New variable.

Change-Id: I4b73906fe18d481644102c271f5e0883167b3a50
2024-05-22 11:15:30 +08:00
Zheng Junjie
08474ff6ec
gnu: Add u-boot-starfive-visionfive2.
* gnu/packages/bootloaders.scm (u-boot-starfive-visionfive2): New variable.

Change-Id: I2a7d2275b1a0f4253ffc3152c892687aae11a471
2024-05-22 11:15:30 +08:00
Zheng Junjie
800b33786c
gnu: Add opensbi-for-visionfive2.
* gnu/packages/firmware.scm (opensbi-for-visionfive2): New variable.

Change-Id: I27963937410a3900a63193ce2a1033ac20a79919
2024-05-22 11:15:30 +08:00
Zheng Junjie
eaa99648ff
gnu: shepherd-0.10: When target riscv64, use guile-fibers-1.1.
* gnu/packages/admin.scm (shepherd-0.10)[native-inputs]: When target-riscv64?
is true, use guile-fibers-1.1.

Change-Id: I89d2e1a7bd6cbc69d19230d9b1c45ce6e339a13d
2024-05-22 11:15:30 +08:00
Zheng Junjie
e5078ff321
image: Raise error when use both grub-efi* bootloader and not gpt image.
* gnu/system/image.scm: Switch Inversion logic, it allow we use customize
bootloader with gpt image.

Change-Id: I801327f6e826a37588b8f0f5246ca820e742f721
2024-05-22 11:15:29 +08:00
Zheng Junjie
04aa2aab70
gnu: linux-libre-6.8: Add riscv config.
* gnu/packages/aux-files/linux-libre/6.8-riscv.conf: New files.
* Makefile.am (AUX_FILES): Add it.

Change-Id: I293912d4f7fe09e281432b0f973999d9d8db582a
2024-05-22 11:15:29 +08:00
Tomas Volf
413ef75f89
gnu: buildah: Switch to gnu-build-system.
Buildah is fundamentally similar to podman and provides its own Makefile.
This commit switches from go-build-system to gnu-build-system so that the
build can be done using `make' instead of reinvention some parts (like
documentation) in the guile.  The package pretty much follows how podman
package looks like.

* gnu/packages/containers.scm (buildah)[source]: Reformat.
[build-system]: Use gnu-build-system.
[arguments]<#:import-path, #:unpack-path, #:go, #:install-source?>: Delete.
<#:make-flags>: Set make flags.
<#:test-target>: Set, even though the tests are disabled.
<#:imported-modules>: Also import (guix build go-build-system) for the
remove-go-references phase.
<#:phases>{'prepare-install-docs, 'build-docs, 'install-docs}: Delete.
{'configure}: Delete.
{'set-env, 'check, 'symlink-helpers, 'wrap-buildah, 'remove-go-references}
{'install-completions}: New phases.
[inputs]: Remove no longer used cni-plugins, conmon, runc.  Add bash-minimal.
[native-inputs]: Remove gnu-make, add go-1.21 and bats.

Change-Id: I0ddd5febb0116a71a857e2a98a9951dbe8bd40d9
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-05-21 22:46:59 +01:00
Tomas Volf
b55997d9df
gnu: podman: Revamp the package.
Substantial rework of the podman package.  The source is no longer patched (at
all) and all necessary modifications were moved into wrap-program and phases.

Not everything is supported out of the box, but description mentions what
packages to install to get additional functionality working.

* gnu/packages/containers.scm (podman)[source]: Remove snippet and patches.
[arguments]<#:make-flags>: Add HELPER_BINARIES_DIR.  Add GOMD2MAN to actually
use go-github-com-go-md2man package instead of the bundled version.
<#:imported-modules>: Add (guix build go-build-system).
<#:phases>{'set-env}: Set `CC' as an environment variable due to bug in make
before 4.4.
{'fix-hardcoded-paths}: Remove everything except patching `libexec' and `lib'
locations.
{'symlink-helpers}: New phase symlinking tools not discoverable via $PATH into
one directory (`HELPER_BINARIES_DIR').
{'wrap-podman}: New phase wrapping `podman' to set correct $PATH.
{'remove-go-references}: New phase stripping references to the golang
toolchain from the binaries.
[inputs]: Remove no longer needed cni-plugins, slirp4netns.  Remove referenced
in 'wrap-podman conmon, crun, iptables, passt.  Move go-github-com-go-md2man
into native-inputs.  Add bash-minimal.
[native-inputs]: Add custom grep with supported -P.  Use newer go.  Add
mandoc.
[description]: Explain how to get `podman compose' and `podman machine'
working.
* gnu/packages/patches/podman-program-lookup.patch: Delete file.

Change-Id: Ifc28971a68751831d781517b041eec951a617087
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-05-21 22:46:59 +01:00
Tomas Volf
4f02e0b7f8
gnu: buildah: Update to 1.35.3.
* gnu/packages/containers.scm (buildah): Update to 1.35.3.

Change-Id: I0a00d6a73079ddaa38a454856781adfc2d7f158f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-05-21 22:46:59 +01:00
Tomas Volf
19c1c385c7
gnu: gvisor-tap-vsock: Remove references to go.
This is handled automatically by go-build-system, but (obviously) not by the
gnu-build-system, so add the phase manually.

* gnu/packages/containers.scm (gvisor-tap-vsock)[arguments]<#:phases>: Add
'remove-go-references phase.

Change-Id: I5cef0bc03dfa7f219bdfec4226d0e7772401a5a5
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-05-21 22:44:05 +01:00
Tomas Volf
e89bfb919e
gnu: Add podman-compose.
* gnu/packages/containers.scm (podman-compose): New variable.

Change-Id: Ieb5ee4b6e82464599a17ec950be8a7dbb2efa842
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-05-21 22:44:05 +01:00
Wilke Schwiedop
2bfdc768d7
gnu: Add catatonit.
* gnu/packages/containers.scm (catatonit): New variable.

Change-Id: Ib6948bde8204426a8cb008982cb7cc9302f9e6d6
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-05-21 22:33:57 +01:00
Tomas Volf
5bea6482e6
gnu: passt: Update to 2024_03_20.71dd405.
* gnu/packages/containers.scm (passt): Update to 2024_03_20.71dd405.

Change-Id: I089b7e9364058e59139bdb7cb942fad693254c1f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-05-21 22:16:36 +01:00
Tomas Volf
d9e5c0f8d3
gnu: conmon: Update to 2.1.11.
* gnu/packages/containers.scm (conmon): Update to 2.1.11.

Change-Id: I2a46b2dcd344909da34199145fef4ad3fa4418de
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-05-21 22:16:36 +01:00
Tomas Volf
0d6815ae82
gnu: podman: Update to 5.0.2.
* gnu/packages/containers.scm (podman): Update to 5.0.2.

Change-Id: Id12c017e68f30db4ea99547beca54dbd01e3b029
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-05-21 22:16:36 +01:00
Tomas Volf
abc62671e0
gnu: podman: Drop obsolete comment.
cgroup2 is now the default type.

* gnu/packages/containers.scm (podman): Drop the comment.

Change-Id: I197ed7e4901b26ad820295ed7adcaffd7bf533f5
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-05-21 22:16:35 +01:00
Tomas Volf
5c5e2a7491
gnu: crun: Update to 1.15.
* gnu/packages/containers.scm (crun): Update to 1.15.

Change-Id: I769c15663bf668a967cf32243dd8139b6c949953
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-05-21 22:16:35 +01:00
Guillaume Le Vaillant
3fd9f25bb3
gnu: Add cl-in-memory-streams.
* gnu/packages/lisp-xyz.scm (cl-in-memory-streams, ecl-in-memory-streams,
  sbcl-in-memory-streams): New variables.

Change-Id: I5f55f1185dfc396d7287b1a402541ad68f355b56
2024-05-21 15:15:03 +02:00
Guillaume Le Vaillant
e9f9740d42
gnu: Add cl-cf.
* gnu/packages/lisp-xyz.scm (cl-cf, ecl-cf, sbcl-cf): New variables.

Change-Id: Ic377597dceaf4f4d0c71319056185a958df06155
2024-05-21 14:54:15 +02:00
Guillaume Le Vaillant
af2791d4e1
gnu: cl-for: Update to 1.2.0-1.a397829.
* gnu/packages/lisp-xyz.scm (sbcl-for): Update to 1.2.0-1.a397829.

Change-Id: I521ed1cf56bf13934996ba35304cb842c394cdac
2024-05-21 14:38:19 +02:00
Efraim Flashner
b3d8d5511f
gnu: julia-fixedpointnumbers: Update to 0.8.5.
* gnu/packages/julia-xyz.scm (julia-fixedpointnumbers): Update to 0.8.5.
(julia-colortypes)[arguments]: Remove 'skip-failing-test phase.

Change-Id: I18cee60a90311af0a052e5d49e4f2b43b54e7e14
2024-05-21 11:49:56 +03:00
Efraim Flashner
c634135ef9
gnu: perl-dbix-class: Update to 0.082843.
* gnu/packages/databases.scm (perl-dbix-class): Update to 0.082843.
[propagated-inputs]: Remove perl-moo, perl-scalar-list-utils, and
perl-text-balanced; add perl-moo-2.
[native-inputs]: Remove perl-file-temp.
[properties]: New field.

Change-Id: I67f00f7e4f5b1bc71d9632bb90213df3c0a20ce5
2024-05-21 11:08:14 +03:00
Efraim Flashner
81d08d7970
gnu: abseil-cpp: Fix build on i686-linux.
* gnu/packages/cpp.scm (abseil-cpp)[source]: Add patch.
(abseil-cpp-20220623.1)[source]: Same.
* gnu/packages/patches/abseil-cpp-20220623.1-no-kepsilon-i686.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Register it.

Change-Id: I27b9abc2c44ff6dc313209f4b0b12542a92d6fcd
2024-05-21 09:25:07 +03:00
Efraim Flashner
e50fc5380e
gnu: abseil-cpp-20200923.3: Fix test suite on some architectures.
* gnu/packages/cpp.scm (abseil-cpp-20200923.3)[source]: Add patches.
* gnu/packages/patches/abseil-cpp-20200923.3-adjust-sysinfo.patch,
gnu/packages/patches/abseil-cpp-20200923.3-duration-test.patch: New
files.
* gnu/local.mk (dist_patch_DATA): Register them.

Change-Id: I3a0a6c3396a7c2854236c68ec77a68bbdd6af1f4
2024-05-21 09:10:33 +03:00
Efraim Flashner
24db97c10d
gnu: labwc: Build with librsvg-for-system.
* gnu/packages/wm.scm (labwc)[inputs]: Replace librsvg with
librsvg-for-system.

Change-Id: I46505b3f041f46b42b403f9b7fbba5737c128f3f
2024-05-21 08:54:08 +03:00
Efraim Flashner
a1f1148dbd
gnu: enblend-enfuse: Build with librsvg-for-system.
* gnu/packages/photo.scm (enblend-enfuse)[native-inputs]: Replace
librsvg with librsvg-for-system.

Change-Id: I04e046191abf1e36cdbb42d50a5c5abab029edf1
2024-05-21 08:54:08 +03:00
Efraim Flashner
1b98688c29
gnu: lablgtk: Build with librsvg-for-system.
* gnu/packages/ocaml.scm (lablgtk)[inputs]: Replace librsvg with
librsvg-for-system.

Change-Id: I208d68d7f019f046c6ae28028d119a0fe5c96365
2024-05-21 08:54:08 +03:00
Efraim Flashner
246a118767
gnu: inklingreader: Build with librsvg-for-system.
* gnu/packages/inklingreader.scm (inklingreader)[inputs]: Replace
librsvg with librsvg-for-system.

Change-Id: I2cf3d3fbed982f199b94f847b75c6c49472d9b4a
2024-05-21 08:54:00 +03:00
Nicolas Goaziou
7881d60851
gnu: emacs-gptel: Update to 0.8.6.
* gnu/packages/emacs-xyz.scm (emacs-gptel): Update to 0.8.6.
[propagated-inputs]: Remove EMACS-MAP.

Change-Id: I1ae555a8b2213dbd96c2e1d251ebca0e87054fe1
2024-05-20 21:01:26 +02:00
Wilko Meyer
630cbcbae1
gnu: linux-libre 4.19: Update to 4.19.314.
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.314.
(linux-libre-4.19-pristine-source): Update hash.

Change-Id: I52815b6b79d6a9f0cfec531ffa9ba90d8189f426
Signed-off-by: Leo Famulari <leo@famulari.name>
2024-05-20 11:29:49 -04:00
Wilko Meyer
a1bb0afc7b
gnu: linux-libre 5.4: Update to 5.4.276.
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.276.
(linux-libre-5.4-pristine-source): Update hash.

Change-Id: Ieea174e5ca46226f739cb9c092f7518bac44396f
Signed-off-by: Leo Famulari <leo@famulari.name>
2024-05-20 11:29:48 -04:00
Wilko Meyer
49aa670554
gnu: linux-libre 5.10: Update to 5.10.217.
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.217.
(linux-libre-5.10-pristine-source): Update hashes.

Change-Id: I3c9b72da4c45e5b4b91b532ad0db7de5a82a6973
Signed-off-by: Leo Famulari <leo@famulari.name>
2024-05-20 11:29:48 -04:00