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136626 Commits (73b3f941d7d911a1b2bb2bf77d37cb3a12ed4291)

Author SHA1 Message Date
Artyom V. Poptsov ee86a504e9
gnu: augeas: Update to 1.14.1.
* gnu/packages/augeas.scm (augeas): Update to 1.14.1.
  [source]: Use tarballs from GitHub.
  [inputs]: Change to "native-inputs".  Add readline.

Change-Id: I9ca46b8a50d11c75ff6d816f2f15e1f005877244
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-05-22 21:31:52 +01:00
Marco Baggio 3597c73658
gnu: Add r-tglkmeans.
* gnu/packages/cran.scm (r-tglkmeans): New variable.

Change-Id: I13aa0e8c4ab062993d84c99811971ebf6e9179bd
2024-05-22 17:44:49 +02:00
Marco Baggio c46f46f2f3
gnu: Add r-slanter.
* gnu/packages/cran.scm (r-slanter): New variable.

Change-Id: I3b6c76431940f5e6be6a86344029552dded54e54
2024-05-22 17:44:49 +02:00
Ricardo Wurmus a4d8a93abc
gnu: Add r-shinydashboardplus.
* gnu/packages/cran.scm (r-shinydashboardplus): New variable.

Change-Id: Ie50bd8a0234af0fb5ea63377aa005655acad01bd
2024-05-22 17:44:49 +02:00
Ricardo Wurmus b1b981a477
gnu: Add r-waiter.
* gnu/packages/cran.scm (r-waiter): New variable.

Change-Id: I98b27630eba86ab700ac30a361baf14a5d58dae8
2024-05-22 17:44:49 +02:00
Ricardo Wurmus 675d31a5df
gnu: Add esbuild-node.
* gnu/packages/web.scm (esbuild-node): New variable.

Change-Id: I5e1a353a13ef7b4018fcf4aef4832af25f3dabe2
2024-05-22 17:44:49 +02:00
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