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136599 Commits (a67218efeea1ed9c5f793a061f0c6602bb11d674)

Author SHA1 Message Date
Sharlatan Hellseher a67218efee
gnu: kubo: Remove propagated package. 
* gnu/packages/ipfs.scm (kubo)
[inputs]: Remove go-golang-org-x-text. Add annotation for indirect
inputs where they are needed for.

Change-Id: I90eb26ab5d386a70f3581030ef4b3f9b35e05e88
 2024-05-23 15:39:40 +01:00
Efraim Flashner aeba4849b4
gnu: abseil-cpp: Fix linking on riscv64-linux. 
* gnu/packages/cpp.scm (abseil-cpp)[arguments]: When building for
riscv64-linux adjust the configure-flags to link with latomic.

Change-Id: I12099d1a99b54f20f7ddbba2fbd495379a05476b
 2024-05-23 08:56:41 +03:00
Timotej Lazar 28b336d02e
gnu: wireshark: Update to 4.2.5 [security fixes]. 
Fixes CVE-2024-4853, CVE-2024-4854, CVE-2024-4855.

* gnu/packages/networking.scm (wireshark): Update to 4.2.5.

Change-Id: I1f60714bbea05a44d78f420404af5044d344fd12
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
 2024-05-23 13:28:19 +08:00
Nicolas Graves via Guix-patches via 63ee61a56d
gnu: dcmtk: Update to 3.6.8. [security-fixes] 
This fixes CVE-2022-43272.

* gnu/packages/image-processing.scm (dcmtk): Update to 3.6.8.

Change-Id: I4e0203219280a2571267f566cdfc8c2a9ea3fd18
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
 2024-05-23 13:24:50 +08:00
Tomas Volf 2d49d727b3
gnu: podman: Update to 5.0.3 [security fixes]. 
This fixes CVE-2024-3727.

* gnu/packages/containers.scm (podman): Update to 5.0.3.

Change-Id: Iefe98746c993830ef12c49733b8407b10305d065
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
 2024-05-23 13:18:31 +08:00
Tomas Volf 792155da11
gnu: buildah: Update to 1.35.4 [security fixes]. 
This fixes CVE-2024-3727 and CVE-2024-28180.

* gnu/packages/containers.scm (buildah): Update to 1.35.4.

Change-Id: I5ee2b4591b39ee85d7236aedda7a2508df8e0e48
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
 2024-05-23 13:09:18 +08:00
Tomas Volf 4fbce61aa9
gnu: skopeo: Update to 1.15.1 [security fixes]. 
This fixes CVE-2024-3727.

* gnu/packages/virtualization.scm (skopeo): Update to 1.15.1.

Change-Id: Icebb6f50e7317bce9ff106d71ad30dcfa6665666
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
 2024-05-23 13:01:23 +08:00
Artyom V. Poptsov 90514e3c1d
gnu: bvi: Update to 1.4.2. 
* gnu/packages/hexedit.scm (bvi): Update to 1.4.2.

Change-Id: I9ac29adb8707f6daf61f397778a1f94b94f808ae
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
 2024-05-23 11:52:12 +08:00
Tomas Volf 940fbce604
gnu: passt: Update to 2024_05_10.7288448. 
* gnu/packages/containers.scm (passt): Update to 2024_05_10.7288448.

Change-Id: Ic7b1e3423ad18c0ce0f06ce111f3dfdab04e860f
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
 2024-05-23 11:45:53 +08:00
Andy Tai d4118a34e3
gnu: Add pkcs11-helper. 
* gnu/packages/security-token.scm (pkcs11-helper): New variable.

Change-Id: Ib17e0cf209a6fe797d0c797829ba91091b719028
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
 2024-05-23 11:39:50 +08:00
Sharlatan Hellseher c3fe248e69
gnu: kubo: Unbundle go-github-com-quic-go-quic-go. 
* gnu/packages/ipfs.scm (kubo): Unbundle go-github-com-quic-go-quic-go.
[inputs]: Remove go-github-com-francoispqt-gojay and
go-github-com-gogo-protobuf; add go-github-com-quic-go-quic-go.

Change-Id: I4838bfed195b5e094f68ef73333ce9c7c7c7566e
 2024-05-23 00:45:44 +01:00
Sharlatan Hellseher 2234a1f282
gnu: Remove go-github-com-lucas-clemente-quic-go. 
* gnu/packages/golang-web.scm (go-github-com-lucas-clemente-quic-go): Delete variable.

Change-Id: Iac5dfdf15badb1de74323040267f814cdf7cd0f9
 2024-05-23 00:45:43 +01:00
Sharlatan Hellseher 120ad702e0
gnu: go-github-com-quic-go-quic-go: Enable tests. 
* gnu/packages/golang-web.scm (go-github-com-quic-go-quic-go): Enable tests.
[arguments] <#:phases>: Add 'remove-failing-tests. Use custom 'check
phase.
[propagated-inputs]: Remove go-github-com-cheekybits-genny,
go-github-com-golang-protobuf-proto,
go-github-com-marten-seemann-chacha20, and
go-github-com-quic-go-qtls-go1-20; add
go-github-com-francoispqt-gojay.
[native-inputs]: Add go-ginkgo, go-github-com-onsi-ginkgo-v2,
go-go-uber-org-mock, and go-golang-org-x-time.

Change-Id: I8bc03cbe1e9766188157e621f4d7f9e3a7f6adeb
 2024-05-23 00:45:43 +01:00
Sharlatan Hellseher 3ebb39eb42
gnu: go-github-com-syndtr-goleveldb-leveldb: Move to golang-xyz. 
* gnu/packages/golang.scm (go-github-com-syndtr-goleveldb-leveldb): Move
from here ...
* gnu/packages/golang-xyz.scm: ... to here.

Change-Id: Ib457abe33612b371c33985c6b3b0e9372221e37d
 2024-05-23 00:45:43 +01:00
Sharlatan Hellseher a3318b4ede
gnu: go-github-com-syndtr-goleveldb-leveldb: Use go-1.21. 
* gnu/packages/golang.scm (go-github-com-syndtr-goleveldb-leveldb)
[arguments] <#:go>: Swap to go-1.21.

Change-Id: I6ecbfb8d2cbf29dc177536345fb1caa5001f35df
 2024-05-23 00:32:37 +01:00
Sharlatan Hellseher 8c6fb68203
gnu: Add go-ginkgo. 
* gnu/packages/golang-check.scm (go-ginkgo): New variable.

Change-Id: I5c56c87a75c383ec159cee4e7eaa7808bfdcd1f7
 2024-05-22 23:44:02 +01:00
Sharlatan Hellseher fb8ddfc57f
gnu: go-github-com-onsi-gomega: Update to 1.33.1. 
* gnu/packages/golang-check.scm (go-github-com-onsi-gomega): Update to 1.33.1.
[arguments] <#:go>: Swap to go-1.21.
[propagated-inputs]: Remove go-gopkg-in-yaml-v2; add go-gopkg-in-yaml-v3.

Change-Id: I910206fd44198550bdc7da1ebdaff3874d89f1ed
 2024-05-22 23:43:22 +01:00
Sharlatan Hellseher 003a65cafa
gnu: go-github-com-onsi-ginkgo-v2: Update to 2.18.0. 
* gnu/packages/golang-check.scm (go-github-com-onsi-ginkgo-v2): Update to 2.18.0.
[propagated-inputs]: Remove go-github-com-go-task-slim-sprig; add
go-github-com-go-task-slim-sprig-v3 and go-github-com-google-pprof.

Change-Id: I3af9d36e1428745557173135fcaa1e4623d4f57f
 2024-05-22 23:16:16 +01:00
Sharlatan Hellseher 265452e122
gnu: Add go-github-com-go-task-slim-sprig-v3. 
* gnu/packages/golang-xyz.scm (go-github-com-go-task-slim-sprig-v3): New
variable.

Change-Id: I46ef3728993556dfc2d6c9349da6962d747e2664
 2024-05-22 23:12:35 +01:00
Sharlatan Hellseher 33a2644963
gnu: go-github-com-go-task-slim-sprig: Enable tests. 
* gnu/packages/golang-xyz.scm (go-github-com-go-task-slim-sprig)
[arguments] <#:tests>: Enable it.
<#:phases>: Add 'remove-failing-tests phase.

Change-Id: I32424925a96defd69e2871dee079db8bef2861b2
 2024-05-22 22:59:00 +01:00
Sharlatan Hellseher 697252da1c
gnu: go-github-com-go-task-slim-sprig: Move to golang-xyz. 
* gnu/packages/golang.scm (go-github-com-go-task-slim-sprig): Move from
here ...
* gnu/packages/golang-xyz.scm: ... to here.

Change-Id: I540e4211e7e4006d654c7da40bba35e2bd577c78
 2024-05-22 22:50:07 +01:00
Sharlatan Hellseher 0cc9d66b45
gnu: Add go-go-uber-org-mock. 
* gnu/packages/golang-check.scm (go-go-uber-org-mock): New variable.

Change-Id: I9028edc15f1acd3301fde3a49eae8cc28568c6a5
 2024-05-22 22:22:24 +01:00
Artyom V. Poptsov 8f0b5e35f3
gnu: Add python-augeas. 
* gnu/packages/python-xyz.scm (python-augeas): New variable.

Change-Id: I46d409debfbc358f0ff27c505fba089ceab4e195
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-22 21:31:52 +01:00
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