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Author SHA1 Message Date
Sharlatan Hellseher
6eef69608e
gnu: parfive: Renamve variable. 
The most of the time Parfive is used as Python's library which
complicates using Guix import, this change align the name with expected
by importer.

* gnu/packages/python-web.scm (parfive): Rename variable to python-parfive.
* gnu/packages/astronomy.scm (python-sunpy, python-sunpy-minimal)
[propagated-inputs]: Remove parfive; add python-parfive.

Change-Id: I1a6d29f64d9aa49caff2838125f0ee2ca0e65b46
 2025-05-12 20:25:41 +01:00
Sharlatan Hellseher
22a9f2dad1
gnu: parfive: Update to 2.2.0. 
* gnu/packages/python-web.scm (parfive): Update to 2.2.0.
[native-inputs]: Remove python-setuptools-scm; add python-setuptools-scm-next.

Change-Id: I1236f5e4a79e68314ea288eb8361c4f0d2addec6
 2025-05-12 20:25:41 +01:00
Sharlatan Hellseher
269e090f64
gnu: nikola: Adjust inputs. 
As it's the final program and not a future Python library to keep
runtime dependencies in propagated input is not required, this change
swaps to inputs.

* gnu/packages/python-xyz.scm: Swap PROPAGATED-INPUTS to INPUTS.

Change-Id: Ib388f8515b6785348562ede96e88344d3c511b54
 2025-05-12 20:25:41 +01:00
Sharlatan Hellseher
1197093d7c
gnu: limnoria: Update to 2025.5.3. 
* gnu/packages/irc.scm (limnoria): Update to 2025.5.3.
[build-system]: Switch to pyproject.
[arguments] <phases>: Use custom 'check.
[native-inputs]: Remove python-mock; add python-setuptools, and
python-wheel.

Change-Id: I9a9a412e6a1bd199e498c31f7b5c4455dd29bd87
 2025-05-12 20:18:32 +01:00
Christopher Baines
e25cd565bf
gnu: nar-herder: Update source uri. 
* gnu/packages/package-management.scm (nar-herder):[source]: Use Codeberg.

Change-Id: I98819543f753ec2f4a3a6b2d9458cee2a4a8cf5c
 2025-05-12 16:08:22 +01:00
Christopher Baines
751a679b53
gnu: guix-build-coordinator: Update source uri. 
* gnu/packages/package-management.scm (guix-build-coordinator):[source]: Use
Codeberg.

Change-Id: Ibe973bced83d5a485f28fcf0a40be3bf95dbefd8
 2025-05-12 16:00:17 +01:00
Christopher Baines
5e967fbd19
gnu: guix-data-service: Update source uri. 
* gnu/packages/web.scm (guix-data-service):[source]: Use Codeberg repository.

Change-Id: I529a76b9480e6af18f381871776d4f6b959c5005
 2025-05-12 15:58:38 +01:00
Christopher Baines
8a7e623eeb
doc: build.scm: Handle (current-source-directory) being #f. 
Since this seems to be the case when the devel manual is being built on
bayfront.

* doc/build.scm: Use the current working directory as a fallback
if (current-source-directory) is #f, and log the value of root.

Change-Id: Ic43fd05a4a0822d9efb935069850f0a8cadd80aa
 2025-05-12 15:54:52 +01:00
Cayetano Santos
bf11e3327b
gnu: abc-yosyshq: Update to 0.53. 
* gnu/packages/fpga.scm (abc-yosyshq): Update to 0.53.

Change-Id: I32e4973a26e831c558ab13b2cf7e00bea87637a1
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Reviewed-by: Gabriel Wicki <gabriel@erlikon.ch>
 2025-05-12 21:51:27 +09:00
Cayetano Santos
554c227a8f
gnu: python-hdlmake: Update to 3.3-1.9338e3e and enable tests. 
* gnu/packages/fpga.scm (python-hdlmake): Update to 3.3-1.9338e3e.
[source]: Update URL.
[arguments] <#:tests?>: Delete.
[native-inputs]: Add python-pytest.
[home-page]: Update URL.

Change-Id: Ied124a3ceb22be427c5255b5d139f5f63031e260
Co-authored-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Reviewed-by: Gabriel Wicki <gabriel@erlikon.ch>
 2025-05-12 21:51:27 +09:00
Cayetano Santos
3f955bd243
gnu: yosys: Update to 0.53. 
* gnu/packages/fpga.scm (yosys): Update to 0.53.

Change-Id: I7bd53033860ca9bcad367c4360625ac406fbad04
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Reviewed-by: Gabriel Wicki <gabriel@erlikon.ch>
 2025-05-12 21:51:27 +09:00
Andreas Enge
b780e5a38e
gnu: libinfinity: Fix test. 
* gnu/packages/patches/libinfinity-renew-test-certificate.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register patch.
* gnu/packages/gobby.scm (source): Add patch.

Change-Id: I37fe93799e443d3ecdba5e75fc15b2e183dfb4df
 2025-05-12 14:39:56 +02:00
Ashish SHUKLA
e923c73403
gnu: knot-resolver: Update to 5.7.5. [security fixes] 
* gnu/packages/dns.scm (knot-resolver): Update to 5.7.5.

Change-Id: I8e62f61c13a8161fae4fb909fad7b1522d4c3d52
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2025-05-12 10:40:03 +02:00
Ahmad Draidi
65399d697d
gnu: Add ntpsec. 
* gnu/packages/ntp.scm: Add use-modules (gnu packages gps),
(gnu packages m4), (gnu packages python), (gnu packages python-xyz),
(gnu packages time), (guix build-system waf).
(ntpsec): New variable.

Change-Id: I34704665c338475f146fd1b61979b9e3dd8f23f4
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2025-05-12 10:40:02 +02:00
Ahmad Draidi
4d5e16ee29
gnu: Add pps-tools. 
* gnu/packages/time.scm (pps-tools): New variable.

Change-Id: I06a10988acbf4dcd684721e1bee6a2d0c6f2dac6
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2025-05-12 10:40:02 +02:00
Congcong Kuo
5f3518ca83
daemon: Replace ‘random_shuffle’ with ‘shuffle’. 
‘std::random_shuffle’ was removed in C++14.

* nix/libstore/gc.cc (LocalStore::collectGarbage): Use ‘std::random’ and
‘std::shuffle’.

Change-Id: If91ed3ec3596a419ae7c87d7ce677e0970853e9f
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2025-05-12 10:40:02 +02:00
Ludovic Courtès
437bb9ece5
linux-container: Do not attempt to lock mounts for ‘guix system container’. 
Fixes <https://issues.guix.gnu.org/78356>.

* gnu/system/linux-container.scm (container-script): Pass #:lock-mounts? #f
to ‘call-with-container’.

Reported-by: Rutherther <rutherther@ditigal.xyz>
Change-Id: Ie670868147f32baf2c2a94c9c7b1636bc84d0a0a
 2025-05-12 10:40:02 +02:00
Ricardo Wurmus
e4e43cebba
gnu: r-chromunity: Update to 0.0.2-2.101e30a. 
* gnu/packages/bioinformatics.scm (r-chromunity): Update to 0.0.2-2.101e30a.
[arguments]: Disable one test.

Change-Id: I522e993d86cf88914a95c9fb15d933c7af906c41
 2025-05-12 08:55:51 +02:00
Ricardo Wurmus
b927cbe70d
gnu: Remove r-snapcgh. 
This package has been removed with the release of Bioconductor 3.19, and it
now fails to build.

* gnu/packages/bioconductor.scm (r-snapcgh): Remove variable.

Change-Id: Id4408ea2d17d07913fea359292eb3e5d7329b13d
 2025-05-12 08:55:51 +02:00
Ricardo Wurmus
901020cdeb
gnu: pigx-scrnaseq: Use Snakemake 5. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-7
with snakemake-5.
[arguments]: Set HOME.

Change-Id: I45257e138c4cf468d179ff35b0c705bc73046052
 2025-05-12 08:55:51 +02:00
Ricardo Wurmus
d6f9f9b585
gnu: pigx-bsseq: Set HOME. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Add phase 'pre-check.

Change-Id: Ic88976554e6e7c7955ae9ab4f0232330060446c9
 2025-05-12 08:55:50 +02:00
Ricardo Wurmus
c80e1e958b
gnu: pigx-chipseq: Set HOME. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Add phase 'pre-check.

Change-Id: Ia95db9209b5ea0cb340f9827197bdcc851266961
 2025-05-12 08:55:50 +02:00
Ricardo Wurmus
b0aaf60a38
gnu: pigx-rnaseq: Set HOME. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'pre-check.

Change-Id: Ibabfa8f14b8eaec6d25ae72a2cd0f33e6a7d2819
 2025-05-12 08:55:50 +02:00
Ricardo Wurmus
f54467968d
gnu: r-tradeseq: Add missing input. 
* gnu/packages/bioconductor.scm (r-tradeseq)[native-inputs]: Add
r-delayedmatrixstats.
[properties]: Record it in updater-extra-native-inputs.

Change-Id: Icc877a48320083d2e5c4987643d52d60c9b11f05
 2025-05-12 08:55:50 +02:00
Ricardo Wurmus
3f3b2e31a8
gnu: r-screpertoire: Disable one more test. 
* gnu/packages/bioconductor.scm (r-screpertoire)[arguments]: Disable one more test.

Change-Id: I9d44fc50137f6e90f69a2e871a375aff192045ae
 2025-05-12 08:55:50 +02:00
Ricardo Wurmus
73be836f25
gnu: r-duckdb: Disable tests. 
* gnu/packages/cran.scm (r-duckdb)[arguments]: Disable tests.

Change-Id: I046fe9e9fb34f35c9f2fcaa6bbb726fb4bbfd81c
 2025-05-12 08:55:50 +02:00
Ricardo Wurmus
1ae270f125
gnu: r-scdd: Add missing input. 
* gnu/packages/bioconductor.scm (r-scdd)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-testthat.

Change-Id: Ibd0925b94ae82145055a0b2c5d53f38df202b077
 2025-05-12 08:55:50 +02:00
Ricardo Wurmus
d05e09fb61
gnu: pigx-sars-cov-2: Use Snakemake 7. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[inputs]: Replace snakemake
with snakemake-7.

Change-Id: I059ea25c0e4a45e42f8f288cd92f548b9684e624
 2025-05-12 08:55:50 +02:00
Ricardo Wurmus
fdc8303a27
gnu: pigx-scrnaseq: Use Snakemake 7. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake
with snakemake-7.

Change-Id: I9b903dba192e862d3b5b6ca4e0018ed88069937d
 2025-05-12 08:55:49 +02:00
Ricardo Wurmus
150ecd1579
gnu: pigx-bsseq: Use Snakemake 7. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake
with snakemake-7.

Change-Id: If82236f94d46c8e1f7f325e6eaf76f68397218d1
 2025-05-12 08:55:49 +02:00
Ricardo Wurmus
c43c9f9849
gnu: pigx-chipseq: Use Snakemake 7. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake
with snakemake-7.

Change-Id: Ib4d7d95713be3535b44ad10b655cf1a217048121
 2025-05-12 08:55:49 +02:00
Ricardo Wurmus
46ccde1476
gnu: pigx-rnaseq: Use Snakemake 7. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace snakemake
with snakemake-7.

Change-Id: I2ab8af1438b59c3d36951b5901aeb57039b4aafc
 2025-05-12 08:55:49 +02:00
Ricardo Wurmus
d21eb7129e
gnu: r-automap: Update to 1.1-16. 
* gnu/packages/cran.scm (r-automap): Update to 1.1-16.

Change-Id: Id03925a9a292d8761facc8174e4a7baa854209d0
 2025-05-12 08:55:49 +02:00
Ricardo Wurmus
06a85865b0
gnu: r-spacefillr: Update to 0.4.0. 
* gnu/packages/cran.scm (r-spacefillr): Update to 0.4.0.

Change-Id: I313d740322b991ce5aacaa5d7177d49f2b25bc25
 2025-05-12 08:55:49 +02:00
Ricardo Wurmus
dbf27f8254
gnu: r-mathjaxr: Update to 1.8-0. 
* gnu/packages/cran.scm (r-mathjaxr): Update to 1.8-0.

Change-Id: I1c4286b47602493facbbe72a914319df15b05e86
 2025-05-12 08:55:49 +02:00
Ricardo Wurmus
030f024fbf
gnu: r-vgam: Update to 1.1-13. 
* gnu/packages/cran.scm (r-vgam): Update to 1.1-13.

Change-Id: Ief01a8634a55b6387e767166a0e146d2d151dbf8
 2025-05-12 08:55:49 +02:00
Ricardo Wurmus
693476b135
gnu: r-zoltr: Update to 1.0.2. 
* gnu/packages/cran.scm (r-zoltr): Update to 1.0.2.
[native-inputs]: Add r-devtools.

Change-Id: If358691f354a2d32a79002a7833e57483f63a916
 2025-05-12 08:55:49 +02:00
Ricardo Wurmus
2142f563f2
gnu: r-zonebuilder: Update to 0.1.0. 
* gnu/packages/cran.scm (r-zonebuilder): Update to 0.1.0.

Change-Id: If5875def520050b5adfa6fe1c6443979a9646b24
 2025-05-12 08:55:48 +02:00
Ricardo Wurmus
56de997fa1
gnu: r-paws: Update to 0.9.0. 
* gnu/packages/cran.scm (r-paws): Update to 0.9.0.

Change-Id: I4a115b73bfa89ba18c4ee1b4dec4777b383fc35d
 2025-05-12 08:55:48 +02:00
Ricardo Wurmus
8f593ec87c
gnu: r-paws-compute: Update to 0.9.0. 
* gnu/packages/cran.scm (r-paws-compute): Update to 0.9.0.

Change-Id: I41716a54b9fb69fca298d2a516b5461970414caf
 2025-05-12 08:55:48 +02:00
Ricardo Wurmus
cf4ab5e416
gnu: r-paws-storage: Update to 0.9.0. 
* gnu/packages/cran.scm (r-paws-storage): Update to 0.9.0.

Change-Id: Iee12b7a726eb1a09729d307a54a55f57acc4b191
 2025-05-12 08:55:48 +02:00
Ricardo Wurmus
f6d49bd518
gnu: r-paws-database: Update to 0.9.0. 
* gnu/packages/cran.scm (r-paws-database): Update to 0.9.0.

Change-Id: I5bf56853d9984abece401cc7909d4e8db5138b5a
 2025-05-12 08:55:48 +02:00
Ricardo Wurmus
e610ae78d4
gnu: r-paws-networking: Update to 0.9.0. 
* gnu/packages/cran.scm (r-paws-networking): Update to 0.9.0.

Change-Id: I364ee0d82cfaf9706d980f6119db00296016328c
 2025-05-12 08:55:48 +02:00
Ricardo Wurmus
1cbd59b198
gnu: r-paws-management: Update to 0.9.0. 
* gnu/packages/cran.scm (r-paws-management): Update to 0.9.0.

Change-Id: Ie87d855a601fc1146c34cebc4ff30cfd68b3f745
 2025-05-12 08:55:48 +02:00
Ricardo Wurmus
c70e1a1e54
gnu: r-paws-machine-learning: Update to 0.9.0. 
* gnu/packages/cran.scm (r-paws-machine-learning): Update to 0.9.0.

Change-Id: I321de81ad18bf8d9919c25c6c97a180816e04d3a
 2025-05-12 08:55:48 +02:00
Ricardo Wurmus
73df3b555c
gnu: r-paws-analytics: Update to 0.9.0. 
* gnu/packages/cran.scm (r-paws-analytics): Update to 0.9.0.

Change-Id: If0e0c6f51ac8d1ea787e14165c4ff513022355ff
 2025-05-12 08:55:47 +02:00
Ricardo Wurmus
c4a03a8b93
gnu: r-paws-security-identity: Update to 0.9.0. 
* gnu/packages/cran.scm (r-paws-security-identity): Update to 0.9.0.

Change-Id: I4ae29cb687826150c9da708e42c357919b1fb659
 2025-05-12 08:55:47 +02:00
Ricardo Wurmus
ec40675256
gnu: r-paws-application-integration: Update to 0.9.0. 
* gnu/packages/cran.scm (r-paws-application-integration): Update to 0.9.0.

Change-Id: Id85247e94a1854019ca57beb584b790f593a0eb1
 2025-05-12 08:55:47 +02:00
Ricardo Wurmus
a9cf139610
gnu: r-paws-end-user-computing: Update to 0.9.0. 
* gnu/packages/cran.scm (r-paws-end-user-computing): Update to 0.9.0.

Change-Id: Id316b69b2e4d8acbe6e6aa8c7dc5d306075d2a0a
 2025-05-12 08:55:47 +02:00
Ricardo Wurmus
71fbc534a4
gnu: r-paws-developer-tools: Update to 0.9.0. 
* gnu/packages/cran.scm (r-paws-developer-tools): Update to 0.9.0.

Change-Id: Ibf2875c0b0d37a6f544019a85be3a8e69f4b7ba2
 2025-05-12 08:55:47 +02:00