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133108 Commits (e1a0562dae8b723cfb6c123c2c22f58b76da6a14)

Author SHA1 Message Date
Troy Figiel e1a0562dae
gnu: Add go-github-com-pkg-sftp. 
* gnu/packages/golang-web.scm (go-github-com-pkg-sftp): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-06 23:28:30 +00:00
Troy Figiel 48b8655667
gnu: sqls: Add missing inputs. 
* gnu/packages/databases (sqls): Add missing inputs.
[native-inputs]: Add go-github-com-google-go-cmp-cmp and
go-github-com-k0kubun-pp.

* gnu/packages/databases: Add (gnu packages golang-xyz) module.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-06 23:28:30 +00:00
Troy Figiel 15b96de852
gnu: Add go-github-com-k0kubun-pp. 
* gnu/packages/golang-xyz.scm (go-github-com-k0kubun-pp): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-06 23:28:30 +00:00
Troy Figiel a28498d83d
gnu: Add go-github-com-ugorji-go-codec. 
* gnu/packages/golang-web.scm (go-github-com-ugorji-go-codec): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-06 23:28:30 +00:00
Troy Figiel dda217f25a
gnu: Add go-github-com-nwaples-rardecode-v2. 
* gnu/packages/golang-compression.scm (go-github-com-nwaples-rardecode-v2): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-06 23:28:30 +00:00
Sharlatan Hellseher b75db99600
gnu: go-github.com-ulikunitz-xz: Adjust name. 
* gnu/packages/golang-compression.scm (go-github.com-ulikunitz-xz):
Rename variable to go-github-com-ulikunitz-xz to follow golang naming
style.

* gnu/packages/admin.scm (fiano) [inputs]: Remove
go-github.com-ulikunitz-xz. Add go-github-com-ulikunitz-xz.

* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-cram)
[propagated-inputs]: Remove go-github.com-ulikunitz-xz. Add
go-github-com-ulikunitz-xz.

Change-Id: Id2f2556666c4f9a08e0203f5ca7eb8352c492051
 2024-03-06 23:28:29 +00:00
Troy Figiel da582bcf50
gnu: Add go-github-com-hhrutter-tiff. 
* gnu/packages/golang-xyz.scm (go-github-com-hhrutter-tiff): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-06 23:28:29 +00:00
Troy Figiel 1583fe7e24
gnu: Add go-github-com-hhrutter-lzw. 
* gnu/packages/golang-compression.scm (go-github-com-hhrutter-lzw): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-06 23:28:29 +00:00
Troy Figiel fbc7a0efa7
gnu: Add go-github-com-dave-jennifer. 
* gnu/packages/golang-xyz.scm (go-github-com-dave-jennifer): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-06 23:28:29 +00:00
Sharlatan Hellseher 9af99245e7
gnu: go-github-com-vividcortex-ewma: Move to golang-xyz. 
* gnu/packages/golang.scm (go-github-com-vividcortex-ewma): Move from
here ...
* gnu/packages/golang-xyz.scm: ... to here.

Change-Id: Iabf8a6ee15240c0817d80584a34e80dcbce1c974
 2024-03-06 23:28:29 +00:00
Sharlatan Hellseher c21f468cf1
gnu: go-github-com-cheggaaa-pb-v3: Move to golang-xyz. 
* gnu/packages/golang.scm (go-github-com-cheggaaa-pb-v3): Move from here ...
* gnu/packages/golang-xyz.scm: ... to here.

* gnu/packages/golang.scm (go-github-com-cheggaaa-pb): Remove variable.

Change-Id: Ieddfddfec841e5b35c14002dbfe8655a7b5dec0f
 2024-03-06 23:28:29 +00:00
Sharlatan Hellseher 532914a389
gnu: go-github-com-vividcortex-ewma: Update description. 
* gnu/packages/golang.scm (go-github-com-vividcortex-ewma)
[description]: Provide link to a wiki page sourced from the project's
README.

Change-Id: I0520b0502f676b8891ddd746774acd483358b95e
 2024-03-06 23:28:29 +00:00
Troy Figiel 036b364138
gnu: go-github-com-cheggaaa-pb-v3: Remove unnecessary inputs. 
* gnu/packages/golang.scm (go-github-com-cheggaaa-pb-v3): Remove unnecessary
inputs.
[propagated-inputs]: Remove go-golang-org-x-sys and go-github-com-rivo-uniseg.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-06 23:28:29 +00:00
Troy Figiel 436cd5a625
gnu: go-github-com-cheggaaa-pb-v3: Enable tests. 
* gnu/packages/golang.scm (go-github-com-cheggaaa-pb-v3): Enable tests.
[arguments] <#:tests?>: Set to true.
<#:unpack-path>: Set unpack-path to the repository root.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: Ic8b64dcf4717ff6a163d8a674e5e7c2c6d162b98
 2024-03-06 23:28:29 +00:00
Troy Figiel 2477aea26d
gnu: go-github-com-vividcortex-ewma: Fix import-path. 
* gnu/packages/golang.scm (go-github-com-vividcortex-ewma): Fix import-path.
[arguments]<#:import-path>: Use proper capitalization.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-06 23:28:29 +00:00
Troy Figiel 7991eedd03
gnu: Add go-github-com-shirou-gopsutil-v3. 
* gnu/packages/golang-xyz.scm (go-github-com-shirou-gopsutil-v3): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: Ibbfe76f0a56daf76fc4a4ecd844b445e9355a7ce
 2024-03-06 23:28:28 +00:00
Troy Figiel 06d6f3debf
gnu: go-github-com-shirou-gopsutil: Reformat with guix style. 
* gnu/packages/golang-xyz.scm (go-github-com-shirou-gopsutil): Reformat with
guix style.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-06 23:28:28 +00:00
Troy Figiel 12b8b129b3
gnu: go-github-com-shirou-gopsutil: Update to 2.21.11. 
* gnu/packages/golang-xyz.scm (go-github-com-shirou-gopsutil): Update to
2.21.11.
[arguments]: Fix tests.
<#:go>: Update to go-1.18.
<#:phases>: Add 'remove-v3 and 'remove-failing-tests phases.
[propagated-inputs]: Add go-golang-org-x-sys.
[native-inputs]: Add go-github-com-stretchr-testify and procps.

* gnu/packages/golang-xyz.scm: Add (gnu packages linux) module.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-06 23:28:28 +00:00
Troy Figiel 8468c55565
gnu: go-github-com-shirou-gopsutil: Move to golang-xyz. 
* gnu/packages/golang.scm (go-github-com-shirou-gopsutil): Move from here ...
* gnu/packages/golang-xyz.scm: ... to here.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-06 23:28:28 +00:00
Sharlatan Hellseher 51a10d3316
gnu: Add go-numcpus. 
* gnu/packages/golang-xyz.scm (go-numcpus): New variable.

Change-Id: I2edb2f355fd14f2f9a470c91519e7fe1581cc243
 2024-03-06 23:28:28 +00:00
Troy Figiel bd4c6bbf0a
gnu: Add go-github-com-tklauser-go-sysconf. 
* gnu/packages/golang-xyz.scm (go-github-com-tklauser-go-sysconf): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-06 23:28:28 +00:00
Troy Figiel 548a4ac51c
gnu: Add go-github-com-tklauser-numcpus. 
* gnu/packages/golang-xyz.scm (go-github-com-tklauser-numcpus): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-06 23:28:28 +00:00
Ricardo Wurmus 201f90f34f
gnu: emacs-ess: Disable two bad tests. 
These tests used to be disabled before and they do still fail.

* gnu/packages/statistics.scm (emacs-ess)[arguments]: Disable two more tests.

Change-Id: I44a18b43d4fa6af2c9244bb8f3697a01c6c8d255
 2024-03-07 00:15:44 +01:00
Ricardo Wurmus 228ee09d35
gnu: r-with-tests: Update to 4.3.3. 
* gnu/packages/statistics.scm (r-with-tests): Update to 4.3.3.

Change-Id: Ida43d1e7f747245b01aa6fc73716b79611f0bbfd
 2024-03-06 23:47:00 +01:00
Zheng Junjie 64d269b983
gnu: libtheora: Fix cross-compiling to riscv64-linux. 
* gnu/packages/xiph.scm (libtheora):
[native-inputs]: When cross compiling to riscv64-linux-gnu, add config.
[arguments]: When target riscv64-linux-gnu, add update-config phase.

Change-Id: Ie055cd4f6cb9d2a4601b93d1f9db227598349c7c
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2024-03-06 23:25:51 +01:00
Zheng Junjie 5980c8a6b1
gnu: libtheora: Use Gexps. 
* gnu/packages/xiph.scm (libtheora): Use Gexps.

Change-Id: Ie055cd4f6cb9d2a4601b93d1f9db227598349c7c
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2024-03-06 23:25:51 +01:00
Giacomo Leidi 01f685d560
gnu: home: dotfiles: Properly support both plain and Stow directory layouts. 
Fixes <https://issues.guix.gnu.org/68848>.

The current implementation of the home-dotfiles-service-type contradicts
the Guix manual.  This patch properly implements both the plain and Stow
dotfiles directory layouts.

It does so by refactoring home-dotfiles-configuration adding a new
packages field to support GNU Stow's users workflow and introducing
a new layout field to switch between the two directory layouts.

* gnu/home/services/dotfiles (home-dotfiles-configuration): Migrate to
(gnu services configuration);
[packages]: new field;
[layout]: new field;
(strip-stow-dotfile): new variable;
(strip-plain-dotfile): new variable;
(home-dotfiles-configuration->files): use the new fields;
[directory-contents]: allow for
selecting a subset of application dotfile directories;
* doc/guix.texi: document the new layouts.

Change-Id: I2e96037608353e360828290f055ec5271cfdfd48
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2024-03-06 23:25:51 +01:00
Ludovic Courtès 9e3061a163
services: virtual-build-machine: Disable substitutes by default. 
These are useless when offloading yet were causing problems on systems
where the default substitute servers are unreachable.

* gnu/services/virtualization.scm (%virtual-build-machine-operating-system):
Add ‘use-substitutes?’ field to ‘guix-configuration’.

Change-Id: I7d5e380a6f2e2d537de43fdb3c550958ed4db255
 2024-03-06 23:25:51 +01:00
Ludovic Courtès 364422d0ac
doc: Fix typo in “Getting Started with the System”. 
* doc/guix.texi (Getting Started with the System): Fix typo.

Change-Id: Idc52b9a4d5f5003899613595b6b275e098f6a3a8
 2024-03-06 23:25:51 +01:00
Ricardo Wurmus 06e61f9cd2
gnu: r-seuratdata: Update to 0.2.2.9001-1.4dc08e0. 
* gnu/packages/cran.scm (r-seuratdata): Update to 0.2.2.9001-1.4dc08e0.
[propagated-inputs]: Add r-seurat and r-seuratobject.

Change-Id: I8bf21d23ec0bdfbc0b8930673ac5750d081ac780
 2024-03-06 15:44:45 +01:00
Ricardo Wurmus f3ea06baca
gnu: r-snprelate: Update to 1.36.1. 
* gnu/packages/bioconductor.scm (r-snprelate): Update to 1.36.1.

Change-Id: I5cf14d463c0f4ca3707a8ac33c7a06baa4337789
 2024-03-06 11:31:32 +01:00
Ricardo Wurmus 82a449419c
gnu: r-s4arrays: Update to 1.2.1. 
* gnu/packages/bioconductor.scm (r-s4arrays): Update to 1.2.1.

Change-Id: I68c0ee03264073e8816fc92fbaa97ebb6c5036ed
 2024-03-06 11:31:32 +01:00
Ricardo Wurmus c202079ef8
gnu: r-ggcyto: Update to 1.30.2. 
* gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.30.2.

Change-Id: I29c123aa60347b491412631f036923c3bbb7d6c9
 2024-03-06 11:31:32 +01:00
Ricardo Wurmus f83fbb9353
gnu: r-ggtree: Update to 3.10.1. 
* gnu/packages/bioconductor.scm (r-ggtree): Update to 3.10.1.

Change-Id: I62eec59a6be3f806261198a1d39eb38ee86a9a79
 2024-03-06 11:31:31 +01:00
Ricardo Wurmus 7ddc66bd36
gnu: r-nebulosa: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-nebulosa): Update to 1.12.1.
[propagated-inputs]: Remove r-seurat; add r-ggrastr and r-seuratobject.

Change-Id: If301102ec02ce618ed1ebeff17a9d7e0845e847c
 2024-03-06 11:31:31 +01:00
Carlo Zancanaro 9d9bb8955a
scripts: import: elpa: Unquote-splice package sexp contents. 
* guix/scripts/import/elpa.scm (guix-import-elpa): Unquote-splice the contents
of the package sexp so the matched package definition is returned unchanged.

Change-Id: Iaaa7e72390c73c6d6671811fe9ac284d599b44c6
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-03-06 11:09:55 +01:00
Ricardo Wurmus 86552708c3
gnu: r-datasaurus: Update to 0.1.8. 
* gnu/packages/statistics.scm (r-datasaurus): Update to 0.1.8.

Change-Id: Ida2de5f36bbb7bbb42f6088bffafaa0059c02ec3
 2024-03-06 09:42:06 +01:00
Ricardo Wurmus 85cdebc014
gnu: r-naniar: Update to 1.1.0. 
* gnu/packages/statistics.scm (r-naniar): Update to 1.1.0.
[propagated-inputs]: Add r-lifecycle.

Change-Id: I01815422981039a0b4c23a2d91fae37300e9d5da
 2024-03-06 09:42:06 +01:00
Ricardo Wurmus 5ec0ff2dc8
gnu: r-rcppeigen: Update to 0.3.4.0.0. 
* gnu/packages/statistics.scm (r-rcppeigen): Update to 0.3.4.0.0.

Change-Id: Ie879a04dcc7c22fac69da0f72a82868f14571f59
 2024-03-06 09:42:06 +01:00
Ricardo Wurmus 839a6ed474
gnu: r-vgam: Update to 1.1-10. 
* gnu/packages/statistics.scm (r-vgam): Update to 1.1-10.

Change-Id: I0f116e19095577e20ac9c6644e00141dcc953d84
 2024-03-06 09:42:06 +01:00
Ricardo Wurmus 91be200249
gnu: r-rcpparmadillo: Update to 0.12.8.1.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.12.8.1.0.

Change-Id: Ic0e678dadd5fcbbea3b0edda60a6bc465bdbe98c
 2024-03-06 09:42:06 +01:00
Ricardo Wurmus 3db9c83498
gnu: r-data-table: Update to 1.15.2. 
* gnu/packages/statistics.scm (r-data-table): Update to 1.15.2.

Change-Id: I1e68949514e1f525bc70218752d3f978b787d4b6
 2024-03-06 09:42:06 +01:00
Ricardo Wurmus 9519b412e7
gnu: r-locfit: Update to 1.5-9.9. 
* gnu/packages/statistics.scm (r-locfit): Update to 1.5-9.9.

Change-Id: I792b37ef9b5f10b95b14ca633d254843a9de9aab
 2024-03-06 09:42:06 +01:00
Ricardo Wurmus 17f602aec2
gnu: r-gdtools: Update to 0.3.7. 
* gnu/packages/statistics.scm (r-gdtools): Update to 0.3.7.

Change-Id: I6f784e10a6856c3b651fca44f658810750a255fc
 2024-03-06 09:42:06 +01:00
Ricardo Wurmus f0ea78f219
gnu: r-gganimate: Update to 1.0.9. 
* gnu/packages/cran.scm (r-gganimate): Update to 1.0.9.
[propagated-inputs]: Add r-cli, r-lifecycle, r-transformr, and r-vctrs.

Change-Id: I6fbee3cf380992caeeedaa738aa21dabad670950
 2024-03-06 09:42:06 +01:00
Ricardo Wurmus 1c13f01037
gnu: r-mlr3tuning: Update to 0.20.0. 
* gnu/packages/cran.scm (r-mlr3tuning): Update to 0.20.0.

Change-Id: I4eff54cf5e5961ea8389e606fcdf8b197c9a0b43
 2024-03-06 09:42:06 +01:00
Ricardo Wurmus 85c9d158f3
gnu: r-bbotk: Update to 0.8.0. 
* gnu/packages/cran.scm (r-bbotk): Update to 0.8.0.

Change-Id: I5ecb9e126b96970db6aee5374ae809cd03eab9f4
 2024-03-06 09:42:05 +01:00
Ricardo Wurmus 74a179bc44
gnu: r-mlr3: Update to 0.18.0. 
* gnu/packages/cran.scm (r-mlr3): Update to 0.18.0.

Change-Id: I4694be8897b834dc107b80aff89ccf2fb43759d1
 2024-03-06 09:42:05 +01:00
Ricardo Wurmus 03c6a20fc1
gnu: r-seurat: Update to 5.0.2. 
* gnu/packages/cran.scm (r-seurat): Update to 5.0.2.

Change-Id: I358d4bcab984b207ab9ee69ebdaeecf440626b70
 2024-03-06 09:42:05 +01:00
Ricardo Wurmus 7b1bdd0ecc
gnu: r-spatstat-random: Update to 3.2-3. 
* gnu/packages/cran.scm (r-spatstat-random): Update to 3.2-3.

Change-Id: Ie8496efc4fbb4ab7ed296353ac746c7f2fb6f5ab
 2024-03-06 09:42:05 +01:00