futurile/guix-play
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
135,955 Commits 3 Branches 0 Tags 412 MiB
8db1cd28aa
Commit Graph

119976 Commits

Author SHA1 Message Date
Ricardo Wurmus
128d0ead08
gnu: r-adimpute: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-adimpute): Update to 1.14.0.

Change-Id: I888c1281fe44b7877fe01ad10cbca63a30ba337c
 2024-05-08 12:53:17 +02:00
Ricardo Wurmus
6a698c1162
gnu: r-adamgui: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-adamgui): Update to 1.20.0.

Change-Id: I16b63e3e98eddfe0e038b40062d38524881b8e41
 2024-05-08 12:53:17 +02:00
Ricardo Wurmus
21b9cd0355
gnu: r-adam: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-adam): Update to 1.20.0.

Change-Id: I417244fa99e124a285fb020e758ba471d6620d4e
 2024-05-08 12:53:17 +02:00
Ricardo Wurmus
e28ff2ed30
gnu: r-adacgh2: Update to 2.44.0. 
* gnu/packages/bioconductor.scm (r-adacgh2): Update to 2.44.0.
[propagated-inputs]: Remove r-snapcgh.

Change-Id: I47c7a0d00d32cf71ec2f16844ab3a60d120cfc3f
 2024-05-08 12:53:17 +02:00
Ricardo Wurmus
5d1d4936b1
gnu: r-absseq: Update to 1.58.0. 
* gnu/packages/bioconductor.scm (r-absseq): Update to 1.58.0.

Change-Id: I9433d9307416e967a70587eee5b5d891c270f8ee
 2024-05-08 12:53:17 +02:00
Ricardo Wurmus
1fdc5eba8a
gnu: r-abarray: Update to 1.72.0. 
* gnu/packages/bioconductor.scm (r-abarray): Update to 1.72.0.

Change-Id: I207f652b0c5f6d9069de675f245f4fb471d560e9
 2024-05-08 12:53:17 +02:00
Ricardo Wurmus
6dbc09c6d0
gnu: r-tximportdata: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-tximportdata): Update to 1.32.0.

Change-Id: If18a4d7d8b6877beedec24cb17a989e7485af8c8
 2024-05-08 12:53:17 +02:00
Ricardo Wurmus
6332e4ed23
gnu: r-tcgabiolinksgui-data: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-tcgabiolinksgui-data): Update to 1.24.0.

Change-Id: Ie34a052ff74d193f7472ef25fa9fabf6dbbb19a7
 2024-05-08 12:53:17 +02:00
Ricardo Wurmus
0148d18e4b
gnu: r-sesamedata: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-sesamedata): Update to 1.22.0.

Change-Id: I7b57169a24d3f210f9d5373d375c1fcdc8a32b76
 2024-05-08 12:53:17 +02:00
Ricardo Wurmus
49912ae08e
gnu: r-parathyroidse: Update to 1.42.0. 
* gnu/packages/bioconductor.scm (r-parathyroidse): Update to 1.42.0.

Change-Id: I1ee5d4eb8d2f511cd437851aa6fd17b23f85b548
 2024-05-08 12:53:17 +02:00
Ricardo Wurmus
8c4929306f
gnu: r-curatedtcgadata: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.26.0.

Change-Id: Ia96fe42b0b41043879cff80d99c56b48afb06e5b
 2024-05-08 12:53:17 +02:00
Ricardo Wurmus
a14d5f02b9
gnu: r-gagedata: Update to 2.42.0. 
* gnu/packages/bioconductor.scm (r-gagedata): Update to 2.42.0.

Change-Id: I3a8be1fb8255f621b6481dabdeac5460b90ebbb7
 2024-05-08 12:53:17 +02:00
Ricardo Wurmus
eca80e2bf7
gnu: r-affydata: Update to 1.52.0. 
* gnu/packages/bioconductor.scm (r-affydata): Update to 1.52.0.

Change-Id: Ibbdeca7d8ed91da88d14f547403d43c8b9e45775
 2024-05-08 12:53:17 +02:00
Ricardo Wurmus
aa538cc886
gnu: r-all: Update to 1.46.0. 
* gnu/packages/bioconductor.scm (r-all): Update to 1.46.0.

Change-Id: I20d1f918a24e47cee853668b736639369c1e904e
 2024-05-08 12:53:17 +02:00
Ricardo Wurmus
f27c6caa8c
gnu: r-hsmmsinglecell: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-hsmmsinglecell): Update to 1.24.0.

Change-Id: Ie94c7cd87ac4cdaad47035cb110fb58bb6f68126
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
5b5c134658
gnu: r-pasilla: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-pasilla): Update to 1.32.0.

Change-Id: I90a11b64f4cba746c9d5d70bd7746497fe3781a6
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
7d5f112600
gnu: r-msigdb: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-msigdb): Update to 1.12.0.

Change-Id: Ia63cb5d074afcd5b6c597d22c4e5c4f14b59303d
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
46eb71b653
gnu: r-msexperiment: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-msexperiment): Update to 1.6.0.
[propagated-inputs]: Add r-biocgenerics and r-dbi.

Change-Id: I1acadf9e878f4593baf583933c5ccca3daf7ec0d
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
7e05fa61b0
gnu: r-msdata: Update to 0.44.0. 
* gnu/packages/bioconductor.scm (r-msdata): Update to 0.44.0.

Change-Id: I479c861eceb1f50c91d589118a68e217236e89e4
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
27c00a789e
gnu: r-minfidata: Update to 0.50.0. 
* gnu/packages/bioconductor.scm (r-minfidata): Update to 0.50.0.

Change-Id: I6504e8f6ffe57ba1cdf538d2f60c21ff26b06407
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
efc85dfb4d
gnu: r-mousegastrulationdata: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-mousegastrulationdata): Update to 1.18.0.

Change-Id: I4b005c54451d7c306cb4137e4fe668c6e53c840a
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
16e58db1ba
gnu: r-methylclockdata: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-methylclockdata): Update to 1.12.0.

Change-Id: Ibfa765d93c0ed2005f7fb6f630c3104cd30e8371
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
3b1f4f041d
gnu: r-macrophage: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-macrophage): Update to 1.20.0.

Change-Id: I589dd25948fedd3bbe91fddada8e155567cf2d93
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
89a647662c
gnu: r-jaspar2016: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-jaspar2016): Update to 1.32.0.

Change-Id: I826a8a93e0adce98b7ad767c8fbaa7ffb957c554
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
5c28a456e7
gnu: r-italicsdata: Update to 2.42.0. 
* gnu/packages/bioconductor.scm (r-italicsdata): Update to 2.42.0.

Change-Id: I10947b136b273e06b9ac88bf1786b62b0a6739f5
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
cd0b5d0892
gnu: r-illumina450probevariants-db: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-illumina450probevariants-db): Update to 1.40.0.

Change-Id: Ic18b5dcdda0e002375bb9ed43944168f78eb2906
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
3f122a9a1a
gnu: r-hdcytodata: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-hdcytodata): Update to 1.24.0.

Change-Id: Icf2ad5519ee710c3b275f2f608a2bc7674bf3805
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
38d81984dc
gnu: r-genomationdata: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-genomationdata): Update to 1.36.0.

Change-Id: Idf6dbb8e87ed124d9dd3ae10ff3ea78c58b22496
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
66f99b50e5
gnu: r-genelendatabase: Update to 1.39.0. 
* gnu/packages/bioconductor.scm (r-genelendatabase): Update to 1.39.0.

Change-Id: I0630a8fed9f28ad5883a8bb1e4f3c77f16e7ac34
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
76805a5744
gnu: r-flowsorted-blood-epic: Update to 2.8.0. 
* gnu/packages/bioconductor.scm (r-flowsorted-blood-epic): Update to 2.8.0.

Change-Id: I000d233d1a78f36e8daed08f0112cc592b2f99f6
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
aded842e92
gnu: r-flowsorted-blood-450k: Update to 1.42.0. 
* gnu/packages/bioconductor.scm (r-flowsorted-blood-450k): Update to 1.42.0.

Change-Id: I07c3a8640e8b7ca9e36b0a3e81d9831fc4d7299e
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
f5a724eb16
gnu: r-copyhelper: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-copyhelper): Update to 1.36.0.

Change-Id: I4726f8bf6c654b03ee4eb84ae697e7844d06e164
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
b53302805e
gnu: r-chromstardata: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-chromstardata): Update to 1.30.0.

Change-Id: I19aa49ac9d6499d2cea91b0d45fd04f10511b18f
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
cfb000d7e5
gnu: r-champdata: Update to 2.36.0. 
* gnu/packages/bioconductor.scm (r-champdata): Update to 2.36.0.

Change-Id: I5387b2e3722e95911a5355cc56d83086ef205a4c
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
9e2ac92d2f
gnu: r-celldex: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-celldex): Update to 1.14.0.
[propagated-inputs]: Add r-alabaster-base, r-alabaster-matrix, r-alabaster-se, r-dbi,
r-gypsum, r-jsonlite, r-matrix, and r-rsqlite.

Change-Id: Iba166c14dae781e14a9762dc3480ece5ba12a802
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
4bcc9c836d
gnu: r-breastcancervdx: Update to 1.42.0. 
* gnu/packages/bioconductor.scm (r-breastcancervdx): Update to 1.42.0.

Change-Id: I52de3659b7d07d03491091ef0de4ee5d305ec4eb
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
0e2bfbce09
gnu: r-breakpointrdata: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-breakpointrdata): Update to 1.22.0.

Change-Id: I111126dae913bd01e5a3f87551108e6ba1733b89
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
9d1c351076
gnu: r-biscuiteerdata: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-biscuiteerdata): Update to 1.18.0.

Change-Id: Icc31cf376b8f2f085cc045c02383164128f0f009
 2024-05-08 12:53:16 +02:00
Ricardo Wurmus
a4e4f9cf21
gnu: r-bodymaprat: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-bodymaprat): Update to 1.20.0.

Change-Id: I8eb8b9e71cb1068e058b3e827096f25607ac5f01
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
62e7c74453
gnu: r-bladderbatch: Update to 1.42.0. 
* gnu/packages/bioconductor.scm (r-bladderbatch): Update to 1.42.0.

Change-Id: I49350259fef502e59368e4dc0894dcf52db33917
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
5b87013c93
gnu: r-bcellviper: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-bcellviper): Update to 1.40.0.

Change-Id: I5d7af04599d79147eaa2626aead238179e78cfde
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
6ac2448400
gnu: r-arrmdata: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-arrmdata): Update to 1.40.0.

Change-Id: I4695eec74200dd5deac20a71c020a9517e56f9a7
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
fa4635d3ad
gnu: r-aneufinderdata: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-aneufinderdata): Update to 1.32.0.

Change-Id: I91727bf7974078374a2bf9ca935b9df2ca60201f
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
4add20468d
gnu: r-adductdata: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-adductdata): Update to 1.20.0.

Change-Id: I9f795cf931e90fa5f8331a5d3ffa855b56355ca6
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
378904acf5
gnu: r-pfam-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-pfam-db): Update to 3.19.1.

Change-Id: If95fa52bdfeb87ed606b9b7564ce73606a8616c8
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
7eabe6d69d
gnu: r-escape: Update to 2.0.0. 
* gnu/packages/bioconductor.scm (r-escape): Update to 2.0.0.
[propagated-inputs]: Remove r-broom, r-data-table, r-matrix, and r-rlang; add r-aucell,
r-ggdist, r-ggpointdensity, and r-seuratobject.

Change-Id: I7fa2ea581a85a579feeac50e1e4b32ac4fa83d7b
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
a5729ea6ae
gnu: r-org-mm-eg-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-mm-eg-db): Update to 3.19.1.

Change-Id: I3ae90e3d60941caf901d49c91662f38900588a27
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
afb439ddf1
gnu: r-org-hs-eg-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-hs-eg-db): Update to 3.19.1.

Change-Id: Ib120639d743ba4abd0a129f968bd09a3f9c62775
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
b0cd3610d3
gnu: r-org-dr-eg-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-dr-eg-db): Update to 3.19.1.

Change-Id: Ib5d87389f017f2a4ed106ecaef01f82a689ad46e
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
1e295ff0d3
gnu: r-org-dm-eg-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-dm-eg-db): Update to 3.19.1.

Change-Id: I3c19de819fe694d9af11c4263132338340fccc47
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
30be3f2fc8
gnu: r-org-ce-eg-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-ce-eg-db): Update to 3.19.1.

Change-Id: If5ae28c7f68194c7e6dc1b849932417ec1679ec9
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
d85a5a2047
gnu: r-go-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-go-db): Update to 3.19.1.

Change-Id: I894831796ac3121795d76df059b10680e9545ba0
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
5cac1ec6c5
gnu: r-genomeinfodbdata: Update to 1.2.12. 
* gnu/packages/bioconductor.scm (r-genomeinfodbdata): Update to 1.2.12.

Change-Id: I185d52161ec45de7d03fedeb51f2a28864df9903
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
44c5036af2
gnu: r-reactome-db: Update to 1.88.0. 
* gnu/packages/bioconductor.scm (r-reactome-db): Update to 1.88.0.

Change-Id: I80b58a45e8265e82e7a84d8d428fc4339fd926a7
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
43b32ab2e6
gnu: r-org-sc-sgd-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-sc-sgd-db): Update to 3.19.1.

Change-Id: Iee6d57797bb3dde152ce0e22a3ed25c30c039a09
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
487cf830ae
gnu: r-org-bt-eg-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-bt-eg-db): Update to 3.19.1.

Change-Id: If37dc4be3287f0729b2e2d4aecef6745700b429c
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
37696fafac
gnu: r-org-eck12-eg-db: Update to 3.19.1. 
* gnu/packages/bioconductor.scm (r-org-eck12-eg-db): Update to 3.19.1.

Change-Id: I0f3a84abd0dff114231c341e776b542a7b047176
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
a1852df9ff
gnu: r-mafh5-gnomad-v3-1-2-grch38: Update to 3.15.1. 
* gnu/packages/bioconductor.scm (r-mafh5-gnomad-v3-1-2-grch38): Update to 3.15.1.

Change-Id: I6b83a3701c2a4282864bf648677b258c1315598c
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
8d531f9afb
gnu: Add r-ucsc-utils. 
* gnu/packages/bioconductor.scm (r-ucsc-utils): New variable.

Change-Id: I02eebaa69a57b8bbd97b38ae7d62799971f70d45
 2024-05-08 12:53:15 +02:00
Ricardo Wurmus
61a5676a9d
gnu: r-biocpkgtools: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.22.0.

Change-Id: I4afb2530597279d9f2b6c01fc7d76c95c88aa629
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
b9040cb312
gnu: r-debcam: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-debcam): Update to 1.22.0.

Change-Id: Iec96dd28f8adc4d8c070f2e50098a02a4582ec33
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
45b4f78687
gnu: Add r-txdbmaker. 
* gnu/packages/bioconductor.scm (r-txdbmaker): New variable.

Change-Id: I2e236b42117525a48917604ea14396ff661b72f7
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
cf3471cc9e
gnu: Add r-pwalign. 
* gnu/packages/bioconductor.scm (r-pwalign): New variable.

Change-Id: I6a12f48c5de948292af7c6888b12e849e1f42db7
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
155ac301f7
gnu: Add r-psmatch. 
* gnu/packages/bioconductor.scm (r-psmatch): New variable.

Change-Id: I7b3071424563b713912016301f551ce00aceddea
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
6e126301b4
gnu: Add r-gypsum. 
* gnu/packages/bioconductor.scm (r-gypsum): New variable.

Change-Id: Id3bdf044d9a885605b1b2b2ceba32398da6ddec0
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
2c6bd40baf
gnu: Add r-alabaster-se. 
* gnu/packages/bioconductor.scm (r-alabaster-se): New variable.

Change-Id: I698a2d678e4819d9ac4b2668a2f7ef2063f8d674
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
1dd2cce88f
gnu: Add r-alabaster-sce. 
* gnu/packages/bioconductor.scm (r-alabaster-sce): New variable.

Change-Id: I8121614d5b93922555b6cb5fd7a05d68980aff20
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
092609b36a
gnu: Add r-alabaster-ranges. 
* gnu/packages/bioconductor.scm (r-alabaster-ranges): New variable.

Change-Id: I99e1e6549537acb37de2788961dbd17ef6c1de27
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
ba8fbb89e4
gnu: Add r-alabaster-matrix. 
* gnu/packages/bioconductor.scm (r-alabaster-matrix): New variable.

Change-Id: If5b438983a70f8f81e3442d8a1cb3821f4e3489a
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
8031162607
gnu: Add r-alabaster-base. 
* gnu/packages/bioconductor.scm (r-alabaster-base): New variable.

Change-Id: Ifb9fe95fb237d12dadf134278f130e614925b5ec
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
9bd400722d
gnu: Add r-alabaster-schemas. 
* gnu/packages/bioconductor.scm (r-alabaster-schemas): New variable.

Change-Id: I3d9218af9b4408e3375f9ccd98a4c95935b2c273
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
1117e96d9f
gnu: r-cytoml: Update to 2.16.0. 
* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.16.0.

Change-Id: I14ae3ae0d5ff8d66b964651b6fe3753d934f1554
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
c29bc85ec6
gnu: Add r-jsonvalidate. 
* gnu/packages/cran.scm (r-jsonvalidate): New variable.

Change-Id: I1393fb3b4034f870663dc887be783e8aaf4c9884
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
66e179ac18
gnu: r-xts: Remove vignette outputs. 
* gnu/packages/cran.scm (r-xts)[source]: Add snippet to remove generated
files.

Change-Id: Iba82b900e632e2cf5a99c9deb807bae6cf3dabcd
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
628d007b83
gnu: r-desctools: Set HOME variable. 
* gnu/packages/statistics.scm (r-desctools)[argumonts]: Add phase 'pre-check.

Change-Id: Icec222a5cdcb2c95ad7bd600ce5188bd5588bb4e
 2024-05-08 12:53:14 +02:00
Ricardo Wurmus
79c2b32337
gnu: r-with-tests: Update to 4.4.0. 
* gnu/packages/statistics.scm (r-with-tests): Update to 4.4.0.

Change-Id: If77c95867cc16141c397e48c899a9ade3e89876d
 2024-05-08 12:53:14 +02:00
Artyom V. Poptsov
2bea3f2562
gnu: kubo: Unbundle go-cidutil, go-log and go-ipfs-util. 
* gnu/packages/ipfs.scm (kubo) [source]: Delete "go-cidutil", "go-log",
  "go-ipfs-util" from bundled packages.
  [inputs]: Add go-github-com-ipfs-go-cidutil, go-github-com-ipfs-go-log,
  go-github-com-ipfs-go-log-v2, and go-github-com-ipfs-go-ipfs-util.

Change-Id: I3e49deb9572c6ac471210a392a52117fd0b9ce1a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-08 00:07:21 +01:00
Artyom V. Poptsov
231ffaf1ac
gnu: Add go-github-com-ipfs-go-cidutil. 
* gnu/packages/ipfs.scm (go-github-com-ipfs-go-cidutil): New variable.

Change-Id: I6077fc00d22b541a959a6623c8666c35288ca105
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-08 00:05:05 +01:00
Artyom V. Poptsov
6f60f90c15
gnu: Add go-github-com-ipfs-go-log. 
* gnu/packages/ipfs.scm (go-github-com-ipfs-go-log): New variable.

Change-Id: I5b5b1d594b5458a7ca156346c6a6dc3c8d5bd69d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-08 00:05:05 +01:00
Artyom V. Poptsov
58cc52f2dc
gnu: Add go-github-com-ipfs-go-log-v2. 
* gnu/packages/ipfs.scm (go-github-com-ipfs-go-log-v2): New variable.

Change-Id: Id6d85bfa883670345420c21937681ae2844f6263
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-08 00:03:02 +01:00
Artyom V. Poptsov
8cb146a3e6
gnu: Add go-github-com-ipfs-go-detect-race. 
* gnu/packages/ipfs.scm (go-github-com-ipfs-go-detect-race): New variable.

Change-Id: Ic65c12a717a50c4309bc89d29d158a43fbc0c81a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-07 23:51:25 +01:00
Artyom V. Poptsov
f669a24a95
gnu: Add go-github-com-ipfs-go-ipfs-util. 
* gnu/packages/ipfs.scm (go-github-com-ipfs-go-ipfs-util): New variable.

Change-Id: Ic496282dc62b7c0d5bd9017aff6a3818b2661309
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-07 23:51:16 +01:00
Sharlatan Hellseher
2795d0f3e7
gnu: kubo: Unbundle go-bazil-org-fuse. 
* gnu/packages/ipfs.scm (kubo) [source]: Remove vendor/bazil.org.
[inputs]: Add go-bazil-org-fuse.

Change-Id: Ie55e609c15a6eaca7ec32521a55620bf674af240
 2024-05-07 23:18:48 +01:00
Sharlatan Hellseher
1f6c4f226d
gnu: Add go-bazil-org-fuse. 
* gnu/packages/golang-xyz.scm (go-bazil-org-fuse): New variable.

Change-Id: I933d90dca50110f53831febc81d587c14973934f
 2024-05-07 23:18:48 +01:00
Sharlatan Hellseher
330a133b85
gnu: go-git-sr-ht-emersion-go-scfg: Move to golang-xyz. 
* gnu/packages/golang.scm: (go-git-sr-ht-emersion-go-scfg): Move from here ...
* gnu/packages/golang-xyz.scm: ... to here

Change-Id: I75cc680543313e41abc86e71d48a9be9e9ce694a
 2024-05-07 23:18:48 +01:00
Sharlatan Hellseher
74b2a9d5a4
gnu: go-git-sr-ht-emersion-gqlclient: Move to golang-web. 
* gnu/packages/golang.scm (go-git-sr-ht-emersion-gqlclient): Move from
here ...
* gnu/packages/golang-web.scm: ... to here.

Change-Id: I2b07dc198f6710680da0430e5f302893060e37b8
 2024-05-07 23:18:47 +01:00
Sharlatan Hellseher
072b06f2f3
gnu: go-git-sr-ht-sircmpwn-getopt: Move to golang-xyz. 
* gnu/packages/golang.scm (go-git-sr-ht-sircmpwn-getopt): Move from here ...
* gnu/packages/golang-xyz.scm: ... to here.

Change-Id: Ic53ec6828f7389326191b659dd16b623e6d1af43
 2024-05-07 23:18:47 +01:00
Sharlatan Hellseher
9716914d4e
gnu: web: Remove syncthing module from used modules. 
There is no more mudule from syncthing which needs to be imported
anymore.

* gnu/packages/web.scm: Remove (gnu packages syncthing) module.

Change-Id: I688e72009e2daa5e75eaeaaeff9026ca888b266b
 2024-05-07 23:17:46 +01:00
Sharlatan Hellseher
fb44cd89df
gnu: go-github-com-nbrownus-go-metrics-prometheus: Disable tests. 
* gnu/packages/golang-xyz.scm (go-github-com-nbrownus-go-metrics-prometheus):
Disable all tests.

Change-Id: I7f340fd1e58edc0203068c762a1bbc798003a84b
 2024-05-07 21:33:45 +01:00
Sharlatan Hellseher
aa1090713a
gnu: tmsu: Enable test suite. 
* gnu/packages/file-systems.scm (tmsu): Fail over to the project's
Makefile targets.
[arguments]: <#:go>: Use go-1.21.
<#:phases>: Add 'adjust-makefile' phase. Use custom 'build, 'check and
'install phases.

Change-Id: Ice920f2196123f1a1f1561879ab919bc0d4e8512
 2024-05-07 21:33:44 +01:00
Sharlatan Hellseher
c7bd735bc4
gnu: sqls: Use go-1.21. 
Merge all inputs into native-inputs since the output result of the
package is an executable that does not require sources from Golang
modules to be available after installation.

* gnu/packages/databases.scm (sqls):
[arguments]: <#:go>: Use go-1.21.
[inputs]: Remove go-github-com-go-sql-driver-mysql,
go-github-com-lib-pq, go-github-com-mattn-go-runewidth,
go-github-com-mattn-go-sqlite3, go-github-com-olekukonko-tablewriter,
go-github-com-pkg-errors, go-github-com-sourcegraph-jsonrpc2,
go-golang-org-x-crypto, go-golang-org-x-xerrors, and
go-gopkg-in-yaml-v2.
[native-inputs]: Add go-github-com-go-sql-driver-mysql,
go-github-com-lib-pq, go-github-com-mattn-go-runewidth,
go-github-com-mattn-go-sqlite3, go-github-com-olekukonko-tablewriter,
go-github-com-pkg-errors, go-github-com-sourcegraph-jsonrpc2,
go-golang-org-x-crypto, go-golang-org-x-xerrors, and
go-gopkg-in-yaml-v2.

Change-Id: I9312a483dfa954b5f0ad4cfac04b5153570bf571
 2024-05-07 21:33:44 +01:00
Sharlatan Hellseher
e582f27a53
gnu: Add go-github-com-msteinert-pam-v2. 
* gnu/packages/golang-xyz.scm (go-github-com-msteinert-pam-v2): New variable.

Change-Id: I7dfcb72703722f894eb52c603f02e64e7350f53a
 2024-05-07 21:33:44 +01:00
Jesse Eisses
243ff41195
gnu: Add soju. 
* gnu/packages/irc.scm (soju): New variable..

Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: I18b7e574339e98fdf2623338aac1635c8e727699
 2024-05-07 21:33:44 +01:00
Jesse Eisses
13912821a2
gnu: go-github-com-matttproud-golang-protobuf-extensions-pbutil: Update to 2.0.0. 
* gnu/packages/syncthing.scm (go-github-com-matttproud-golang-protobuf-extensions-pbutil):
Update to 2.0.0.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: Ia9f1acacd337b95526ee0b9b7b31f1de598f30d3
 2024-05-07 21:33:44 +01:00
Jesse Eisses
b2054615da
gnu: go-github-com-prometheus-client-golang: Update to 1.17.0. 
* gnu/packages/golang.scm (go-github-com-prometheus-client-golang):
Update to 1.17.0.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: I4d3e9d3e61991f94fc2a7bd4b85e7d4010c4b508
 2024-05-07 21:32:36 +01:00
Jesse Eisses
2359feb658
gnu: go-github-com-prometheus-common: Update to 0.45.0. 
* gnu/packages/golang.scm (go-github-com-prometheus-common): Update to
0.45.0.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: Ic03cdaf87253df869e1d791336189032fac0d625
 2024-05-07 15:38:28 +01:00
Jesse Eisses
b7800aa34f
gnu: go-github-com-prometheus-client-model: Update to 0.5.0. 
* gnu/packages/golang.scm (go-github-com-prometheus-client-model):
Update to 0.5.0.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: Iebb57390b99a4ed2567588872a9745a69aae9ced
 2024-05-07 15:38:28 +01:00
Jesse Eisses
881f9630c9
gnu: Add go-gopkg-in-irc-v4. 
* gnu/packages/irc.scm (go-gopkg-in-irc-v4): New variable.

Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: Ie1afdde3d1a23154e592445b5ce91e5918c6c822
 2024-05-07 15:38:28 +01:00
Sharlatan Hellseher
b6a8c4c142
gnu: go-gopkg-in-irc-v3: Enable tests. 
* gnu/packages/irc.scm (go-gopkg-in-irc-v3): Enable tests, remove input
lables.
[propagated-inputs]: Remove go-github-com-stretchr-testify.
[native-inputs]: Add go-github-com-stretchr-testify and
python-irc-parser-tests.

Change-Id: I83c8094e9417052781993c3cde900c47875a2029
 2024-05-07 15:38:28 +01:00
Sharlatan Hellseher
bb49060039
gnu: Add python-irc-parser-tests. 
* gnu/packages/irc.scm (python-irc-parser-tests): New variable.

Change-Id: Iaffea626ed06e228562b3c92123d30c9712de7c3
 2024-05-07 15:38:28 +01:00
Jesse Eisses
4f4034bb46
gnu: Add go-git-sr-ht-emersion-go-sqlite3-fts5. 
* gnu/packages/golang-xyz.scm (go-git-sr-ht-emersion-go-sqlite3-fts5):
New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: Icb6f77b306ff5c8a816d8a42e90a1bf23115b38f
 2024-05-07 15:38:28 +01:00
Jesse Eisses
bb1beff54d
gnu: Add go-git-sr-ht-sircmpwn-go-bare. 
* gnu/packages/golang-xyz.scm (go-git-sr-ht-sircmpwn-go-bare): New variable.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: Iea3ac2489549fe4cb1b1ce216a998c30c9f996d6
 2024-05-07 15:38:28 +01:00
Sharlatan Hellseher
2799f6c6e1
gnu: go-github-com-mattn-go-sqlite3: Update to 1.14.22. 
* gnu/packages/golang-xyz.scm (go-github-com-mattn-go-sqlite3): Update to 1.14.22.

Change-Id: I01bf397b7d74db812883994deb2c2249adf14d1f
 2024-05-07 15:38:27 +01:00
Jesse Eisses
bea3defe23
gnu: Add go-github-com-pires-go-proxyproto. 
* gnu/packages/golang-xyz.scm (go-github-com-pires-go-proxyproto): New variable.

Change-Id: Iec8e8ead7e18cbbd9be00ec398d11e632e4b2ac4
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-07 15:38:27 +01:00
Jesse Eisses
e78fb8223f
gnu: Add go-nhooyr-io-websocket. 
* gnu/packages/golang-web.scm (go-nhooyr-io-websocket): New variable.

Change-Id: Ifced88b4d916b8593e4b65022cf419c8ae18a769
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-07 15:38:27 +01:00
Jesse Eisses
c9bbfc9f3c
gnu: Add go-github-com-msteinert-pam. 
* gnu/packages/golang-xyz.scm (go-github-com-msteinert-pam): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: Id84648d258d2f1c7f2c9902e80dccb06642d7787
 2024-05-07 15:38:27 +01:00
Jesse Eisses
d12456bebd
gnu: Add go-github-com-sherclockholmes-webpush-go. 
* gnu/packages/golang-web.scm (go-github-com-sherclockholmes-webpush-go): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: Ida07915e1659b79353dd267991bcb615ee5cc837
 2024-05-07 15:38:27 +01:00
Jesse Eisses
223c531ec4
gnu: Add go-github-com-golang-jwt-jwt. 
* gnu/packages/golang-crypto.scm (go-github-com-golang-jwt-jwt-v4): New variable.
(go-github-com-golang-jwt-jwt-v4): Inherit from go-github-com-golang-jwt-jwt.

Change-Id: I2382208434859b7a9b9a314930fa8769072964c7
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-05-07 15:38:25 +01:00
Efraim Flashner
014875b29e
gnu: psascan: Limit to 64-bit systems. 
* gnu/packages/cpp.scm (psascan)[supported-systems]: New field.

Change-Id: I19eef41449a16b4440f3dd73cdb181c7c3383e84
 2024-05-07 01:44:28 +03:00
Efraim Flashner
51c711a328
gnu: bitmapperbs: Limit to x86_64-linux. 
* gnu/packages/bioinformatics.scm (bitmapperbs)[supported-systems]: New
field.

Change-Id: I03484413e5af8e779fe0e5199e456eaab124e8b7
 2024-05-07 01:31:20 +03:00
Efraim Flashner
cc051064c5
gnu: grantlee: Fix build on some architectures. 
* gnu/packages/qt.scm (grantlee)[source]: Add patch.
* gnu/packages/patches/grantlee-register-metaenumvariable.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.

Change-Id: Iecef53baeb023a80139ac70b9caefcfa7b79a3c6
 2024-05-07 00:43:24 +03:00
Efraim Flashner
0a5929033f
gnu: minimap2: Fix make-flags. 
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Adjust the
make-flags to contain actual build flags for all architectures.

Change-Id: I5b4077a25d6d46172ff566ceaa16629ebf066721
 2024-05-06 23:53:04 +03:00
Efraim Flashner
6571231f2d
gnu: minimap2: Update to 2.28. 
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.28.
[arguments]: Adjust custom 'install phase to not delete non-existent
file.  Remove trailing #t from phase.

Change-Id: Ie6cc21f2b761532f08967efea54d3a12b944f213
 2024-05-06 23:42:22 +03:00
Efraim Flashner
a4c0a58594
gnu: proteinortho: Add tunable property. 
* gnu/packages/bioinformatics.scm (proteinortho)[properties]: Add
tunable? flag.

Change-Id: If59d5785c8c8e4aedb5b88479da6fba0e9754640
 2024-05-06 23:16:57 +03:00
Efraim Flashner
dd23efe020
gnu: proteinortho: Update to 6.3.2. 
* gnu/packages/bioinformatics.scm (proteinortho): Update to 6.3.2.
[source]: Adjust snippet to also delete lapack source tarball.
[arguments]: Rewrite using g-expressions.  Add flag to run tests
sequentially.  Adjust make-flags for cross-compiling and to set PREFIX.
Delete 'configure and custom 'configure phase.  Remove trailing #t from
phases.

Change-Id: I40249e5ac92c26223119b81b4677c08d5ab230e6
 2024-05-06 23:16:56 +03:00
Efraim Flashner
d967ffb367
gnu: python-http-client: Fix test suite. 
* gnu/packages/python-web.scm (python-http-client)[arguments]: Add a
phase to adjust the tests to not be dependant on the current date.

Change-Id: I94f512c9b019173f6e15e04791dbfc662fc93c89
 2024-05-06 23:16:56 +03:00
Efraim Flashner
a9c89cd11b
gnu: r-lpsymphony: Fix building on some architectures. 
* gnu/packages/bioconductor.scm (r-lpsymphony) [arguments]: When
building for aarch64-linux or riscv64-linux replace all the config.guess
and config.sub files with newer ones.
[native-inputs]: When building for aarch64-linux or riscv64-linux add
config.

Change-Id: Iaddda8c6d7330fb02bdd83733e7fa70b851a82f2
 2024-05-06 23:16:55 +03:00
Efraim Flashner
3053c40995
gnu: mouseloupe: Update the package style. 
* gnu/packages/accessibility.scm (mouseloupe)[arguments]: Switch to
g-expressions.

Change-Id: I9af4433b2effbcbd9c0178ea3f02d81e202f4c05
 2024-05-06 23:16:55 +03:00
Efraim Flashner
2d5b779b45
gnu: mouseloupe: Don't hardcode building for i686. 
* gnu/packages/accessibility.scm (mouseloupe)[source]: Add snippet to
remove flag from the Makefile explicitly building for i686.

Change-Id: Iec5a5002a51ff7f2be469f6815e6ff6166b32876
 2024-05-06 23:16:54 +03:00
Efraim Flashner
284938bb72
gnu: wolf-shaper: Add tunable property. 
* gnu/packages/music.scm (wolf-shaper)[properties]: Add tunable? flag.

Change-Id: I32b26effaa18b814fcca8f4cd88b083969682a81
 2024-05-06 23:16:54 +03:00
Efraim Flashner
f4c954e314
gnu: wolf-shaper: Fix building on more architectures. 
* gnu/packages/music.scm (wolf-shaper)[arguments]: Add make-flag to
disable optimizations.

Change-Id: I2976d1769324765df3f0aa8b636f528526bdfd78
 2024-05-06 23:16:53 +03:00
Efraim Flashner
5a69a52d74
gnu: solidity: Update to 0.8.25. 
* gnu/packages/solidity.scm (solidity): Update to 0.8.25.
[arguments]: Add configure-flag to allow an older version of z3.
[inputs]: Replace fmt-8.0 with fmt.

Change-Id: I1501d16323566c066c58c1c4bbf90dd17a23f021
 2024-05-06 23:16:53 +03:00
Efraim Flashner
614bd4a777
gnu: solidity: Allow a newer version of jsoncpp. 
* gnu/packages/solidity.scm (solidity)[arguments]: Add a phase to allow
newer versions of jsoncpp.

Change-Id: I4f7b5b3685f8d784da221ccb0eea1ba297e3e0b8
 2024-05-06 23:16:53 +03:00
Efraim Flashner
d3bfc94271
gnu: galera: Update to 26.4.18. 
* gnu/packages/databases.scm (galera): Update to 26.4.18.
[inputs]: Move check from here ...
[native-inputs]: ... to here.

Change-Id: Iac2ce8e1ebbe0e4059b26b7e83afbdafea19641b
 2024-05-06 23:16:52 +03:00
Efraim Flashner
f55af58045
gnu: strongswan: Remove pre-generated files. 
* gnu/packages/vpn.scm (strongswan)[source]: Add snippet to remove some
pre-generated files.
[native-inputs]: Add bison, flex, perl.

Change-Id: Ifc316a1c309f8687418455189457cee83b06bfa1
 2024-05-06 23:16:52 +03:00
Efraim Flashner
2423b0bb2d
gnu: strongswan: Fix building on non-x86 architectures. 
* gnu/packages/vpn.scm (strongswan)[arguments]: When building for
not-x86 architectures disable aesni support.  Also adjust the test suite
so we skip the RSA tests.

Change-Id: Idbc7bb229b83b0f43f3286b94fa4da077711c0ed
 2024-05-06 23:16:51 +03:00
Efraim Flashner
38733b5039
gnu: gnome-js-common: Fix build on some architectures. 
* gnu/packages/gnome.scm (gnome-js-common)[arguemnts]: When building for
aarch64-linux or riscv64-linux replace the config.guess and config.sub
files.
[native-inputs]: When building for aarch64-linux or riscv64-linux add
config.

Change-Id: Ia27b0fec7d0b50e9e4ab7ea7329d390ddc482795
 2024-05-06 23:16:51 +03:00
Efraim Flashner
c6d99eb371
gnu: theorafile: Fix cross-compiling. 
* gnu/packages/video.scm (theorafile)[arguments]: Use cc-for-target.

Change-Id: I191bd177263e57f1193fce1d360ba161726f39b9
 2024-05-06 23:16:50 +03:00
Efraim Flashner
ee926b19ad
gnu: theorafile: Use test-target. 
* gnu/packages/video.scm (theorafile)[arguments]: Add test-target.
Remove custom 'check phase.

Change-Id: Ia741bc7c202a418801672ffcf88bd7b8577c359e
 2024-05-06 23:16:50 +03:00
Efraim Flashner
9a19c50b9b
gnu: theorafile: Update to 0.0.0-2.ea5fd6d. 
* gnu/packages/video.scm (0.0.0-2.ea5fd6d): Update to 0.0.0-2.ea5fd6d.
[arguments]: Remove trailing #t from phases.

Change-Id: I5dc34627d3d3e264743fa65c480872da2182ada0
 2024-05-06 23:16:49 +03:00
Efraim Flashner
88a4a46ed4
gnu: elisa: Update to 23.08.5. 
* gnu/packages/kde-multimedia.scm (elisa): Update to 23.08.5.
[arguments]: Remove trailing #t from phases.

Change-Id: I4de0b34ce52baefeed5aaeb493fa54d14515fcef
 2024-05-06 23:16:49 +03:00
Efraim Flashner
ad330f7d08
gnu: rednotebook: Correctly wrap the binary. 
* gnu/packages/rednotebook.scm (rednotebook)[arguments]: Adjust the
'wrap-with-library-paths phase to use the correct webkitgtk input.
Remove trailing #t.

Change-Id: I3d245f279ca704ab34023a8977a2c6f1003302ab
 2024-05-06 23:16:48 +03:00
Efraim Flashner
af8ad9148f
gnu: libvisual-plugins: Reformat with 'guix style'. 
* gnu/packages/gstreamer.scm (libvisual-plugins): Reformat package using
'guix style'.

Change-Id: I91cb02b22bc50c71ad314d2a48207a77e3700a41
 2024-05-06 23:16:48 +03:00
Efraim Flashner
a2f81c1b9d
gnu: libvisual-plugins: Build with librsvg-for-system. 
* gnu/packages/gstreamer.scm (libvisual-plugins)[inputs]: Replace
librsvg with librsvg-for-system.

Change-Id: Ie4199e6f52236dfae086b1425607b6e0f1f9129b
 2024-05-06 23:16:47 +03:00
Efraim Flashner
f1efd142b6
gnu: libvisual-plugins: Disable oinksie plugin. 
* gnu/packages/gstreamer.scm (libvisual-plugins)[arguments]: Add a
configure-flag to disable the oinksie plugin.

Change-Id: I6181384c715eeeceba81d196960e4cd0148cc55a
 2024-05-06 23:16:47 +03:00
Efraim Flashner
2b6ca9db79
gnu: darkice: Fix build. 
* gnu/packages/audio.scm (darkice)[arguments]: Add a make-flag to use an
earlier C++ standard.

Change-Id: I2b7be09be9deb4637e996a9a697e31efed5c5508
 2024-05-06 23:16:46 +03:00
Efraim Flashner
d5d2963826
gnu: wmfire: Fix build. 
* gnu/packages/gnustep.scm (wmfire)[source]: Add patch.
* gnu/packages/patches/wmfire-dont-inline-draw-fire.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.

Change-Id: I3e937c5e9dbd8a5e2eebfd92213407d9477a47ab
 2024-05-06 23:16:46 +03:00
Efraim Flashner
ae1873558c
gnu: varnish: Fix build on i686-linux. 
* gnu/packages/web.scm (varnish)[arguments]: When building for
i686-linux add a make-flag to adjust the CFLAGS.

Change-Id: I9dbd9566de33f2ad7445e3a7ee8bc2d01e430cc9
 2024-05-06 23:16:45 +03:00
Efraim Flashner
600860e8ac
gnu: varnish-modules: Update to 0.22.0. 
* gnu/packages/web.scm (varnish-module): Update to 0.22.0.

Change-Id: I0bd60aed1d4243887a6501f4561ec5c83f1a3c06
 2024-05-06 23:16:45 +03:00
Efraim Flashner
f14513b660
gnu: graphene: Fix build on armhf-linux. 
* gnu/packages/gtk.scm (graphene)[arguments]: When building for
armhf-linux add a configure-flag to disable neon optimizations.

Change-Id: I42b412d3f7536180e959e268b68f2c292edda749
 2024-05-06 23:16:31 +03:00
Ricardo Wurmus
c5db054e64
gnu: guile-jwt: Update to 0.3.0. 
* gnu/packages/guile-xyz.scm (guile-jwt): Update to 0.3.0.
[propagated-inputs]: Add guile-gcrypt.

Change-Id: I694b63437f51121dd3440ccb32ce279583596586
 2024-05-06 21:56:59 +02:00
Ricardo Wurmus
752c089b4a
Revert "gnu: pcsc-lite: Update to 2.1.0." 
This reverts commit a8f0e8a31d.

It leads to 3799 dependent packages being rebuilt, so it's not suitable for
the master branch.
 2024-05-06 19:01:38 +02:00
Nicolas Goaziou
28e74f49fe
Revert "gnu: hwdata: Update to 0.378." 
This reverts commit 7ed5a336bd.

This introduces too many rebuilds. It should be applied onte "core-updates" instead.

Change-Id: I088b123776a8914be2d22762afcce5b48f346bf0
 2024-05-06 14:29:25 +02:00
Aleksandr Vityazev
f89d06d13b
gnu: Add emacs-devicetree-ts-mode. 
* gnu/packages/emacs-xyz.scm (emacs-devicetree-ts-mode): New variable.
Update copyright.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Change-Id: I6ab5a52d1aa045794f72edd3c810255f2e432038
 2024-05-06 14:14:31 +02:00
Aleksandr Vityazev
03de08d3b6
gnu: Add tree-sitter-devicetree. 
* gnu/packages/tree-sitter.scm (tree-sitter-devicetree): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Change-Id: Ia73316fa422be84a79e16f2fa40371853ae83570
 2024-05-06 14:14:03 +02:00
Daniel Ziltener
a2d4a64d04
gnu: emacs-xyz: Add emacs-xref-union. 
* gnu/packages/emacs-xyz.scm (emacs-xref-union): New variable.

Change-Id: Idea12ce6869f5244a873e933cf1135db284d2391
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2024-05-06 14:12:24 +02:00
Picnoir
fa6716e080
gnu: waybar: Update to 0.10.2. 
* gnu/packages/wm.scm (waybar): Update to 0.10.2.
0.10.1 changelog: https://github.com/Alexays/Waybar/releases/tag/0.10.1.
0.10.2 changelog: https://github.com/Alexays/Waybar/releases/tag/0.10.2.
The meson build has been stable for these two releases, no new/removed
dependencies.

Change-Id: I2359a2111a35041860172232722e6d91a1ff35e7
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2024-05-06 13:48:38 +02:00
Andy Tai
1cb70ce152
gnu: wxmaxima: Update to 24.02.2. 
* gnu/packages/maths.scm (wxmaxima): Update to 24.02.2.

Change-Id: I33cd6a3230a7d1672aadf942ad0b089dfa8603b0
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2024-05-06 13:47:25 +02:00
Andy Tai
29db98ec67
gnu: tenacity: Update to 1.3.1. 
* gnu/packages/audio.scm (tenacity): Update to 1.3.1.

Change-Id: Id06fb3e9283524341f30d961854d8e6f6df1543e
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2024-05-06 13:46:59 +02:00
宋文武
2c299b338a
gnu: retroarch: Fix OpenGL core and Vulkan drivers. 
* gnu/packages/emulators.scm (retroarch)[arguments]: Ignore check result for
HAVE_GLSLANG_HLSL in the configure phase.

Change-Id: I3ba110b834acca25ada0e680a6bcb879b4db96f4
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2024-05-06 13:46:26 +02:00
Wilko Meyer
81743c54a3
gnu: qutebrowser: Add python-tldextract to inputs. 
* gnu/packages/web-browsers.scm (qutebrowser)[inputs]: Add python-tldextract.

Change-Id: I2c1cf1c71cf0e6ba01711d36fd38d3b09e242caa
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2024-05-06 13:45:30 +02:00
chris
d6a39f3e89
gnu: highlight: Update to 4.11. 
* gnu/packages/pretty-print.scm (highlight): Update to 4.11.
[source]: Switch to git-fetch.
[home-page]: Switch to html page.
[arguments]<#:make-flags>: Use #$output replace %output.
<#:phases>: Use ‘this-package-input‘ to find lua and perl.

Reviewed-by: Dale Mellor <guix-devel-0brg6a@rdmp.org>
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

Change-Id: I0c402fcea5708c4882b52309b3e072301f0a5614
 2024-05-06 13:44:24 +02:00
Daniel Ziltener
7ed5a336bd
gnu: hwdata: Update to 0.378. 
* gnu/packages/pciutils.scm (hwdata): Update to 0.378.

Reviewed-by: Dale Mellor <guix-devel-0brg6a@rdmp.org>
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Change-Id: I7200477ce06280913802e94cd5ef6d9639b8de9f
 2024-05-06 13:42:50 +02:00
Arjan Adriaanse
a8f0e8a31d
gnu: pcsc-lite: Update to 2.1.0. 
* gnu/packages/security-token.scm (pcsc-lite): Update to 2.1.0.

Reviewed-by: Christina O'Donnell <cdo@mutix.org>

Change-Id: I133fd056afb84259cf5cb1f3e9c664ac336e50b9
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2024-05-06 13:41:57 +02:00
Rovanion Luckey
3bc4f32058
gnu: musescore: Propagate alsa-plugins pulseaudio to runtime. 
In order for libasound_module_conf_pulse.so to be present at runtime of
MuseScore the alsa-plugins output "pulseaudio" must be present.

Playback of scores was not working, at least on a foreign distro like
Debian. When running on Debian, MuseScore complained that
libasound_module_conf_pulse.so was missing at startup. This patch was
tested on Debian 12 and fixed the issue.

* gnu/packages/music.scm (musescore): Propagate alsa-plugins pulseaudio to runtime

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Change-Id: I4e2db8e45fdf33987817cef41bcd336526b16d90
 2024-05-06 13:41:11 +02:00
James Smith
20cb45a502
gnu: leocad: Update to 23.03 
* gnu/packages/lego.scm (leocad): Update to 23.03

Change-Id: I0fc566e0325aa992440cf4f895b5780df7e49632
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-05-06 13:26:16 +02:00
Timotej Lazar
e4090a558f
gnu: msmtp: Update to 1.8.26. 
* gnu/packages/mail.scm (msmtp): Update to 1.8.26.

Change-Id: I85eea2d64944a3e1b7b4ed3022772190ee5787c2
 2024-05-06 13:24:42 +02:00
Sergey Trofimov
bdba291a72
gnu: emacs-telega: Update to 0.8.255. 
* gnu/packages/emacs-xyz.scm (emacs-telega): Update to 0.8.255.
* gnu/packages/patches/emacs-telega-path-placeholder.patch: Update patch.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I8cec5a5170318f0ae99116a98afcefe31203b585
 2024-05-06 13:22:29 +02:00
Ricardo Wurmus
f736a784e1
gnu: trust4: Update to 1.1.0. 
* gnu/packages/bioinformatics.scm (trust4): Update to 1.1.0.

Change-Id: I4780038a5db110514e27f07a576166def4063da7
 2024-05-06 12:36:53 +02:00
Mădălin Ionel Patrașcu
709e87caff
gnu: Add trust4. 
gnu/packages/bioinformatics.scm (trust4): New variable.

Change-Id: I6a0fd339a0f761a473f50c7da74c26cfac7b1caf
 2024-05-06 11:47:05 +02:00
Mădălin Ionel Patrașcu
57769fb0b3
gnu: Add r-seraster. 
* gnu/packages/bioinformatics.scm (r-seraster): New variable.

Change-Id: I9f9fd24a9aa563f7c74154e613b85dee46bdcf79
 2024-05-06 11:38:17 +02:00
Mădălin Ionel Patrașcu
fc51a747fa
gnu: Add r-rearrr. 
* gnu/packages/cran.scm (r-rearrr): New variable.

Change-Id: I41e06b24e565a4070f570b7fd5c656f185aacfa9
 2024-05-06 11:38:08 +02:00
Mădălin Ionel Patrașcu
64fcc49dc5
gnu: Add r-metadeconfoundr. 
* gnu/packages/bioinformatics.scm (r-metadeconfoundr): New variable.

Change-Id: I733fb464d2a3c7fd1335826be9f23e2610e6fd60
 2024-05-06 11:26:54 +02:00
Mădălin Ionel Patrașcu
2c52bbd16d
gnu: Add r-detectseparation. 
* gnu/packages/cran.scm (r-detectseparation): New variable.

Change-Id: I6c795719c22a6ff929785e799f749ce053e83fbe
 2024-05-06 11:24:57 +02:00
Mădălin Ionel Patrașcu
458cd1e1d8
gnu: Add r-roi-plugin-lpsolve. 
* gnu/packages/cran.scm (r-roi-plugin-lpsolve): New variable.

Change-Id: Ia3f47ba0b414ecd9273c101977ec8d14916fa656
 2024-05-06 11:24:56 +02:00
Mădălin Ionel Patrașcu
112ecacba3
gnu: Add r-roi. 
* gnu/packages/cran.scm (r-roi): New variable.

Change-Id: I58cbb4be238a5cc9f861ee9dafea03a133f7c0f1
 2024-05-06 11:24:56 +02:00
Mădălin Ionel Patrașcu
2b7e9239c0
gnu: Add r-lpsolveapi. 
* gnu/packages/cran.scm (r-lpsolveapi): New variable.

Change-Id: I6a93603a5814df0eb43a214b5c2a0f4865901bcd
 2024-05-06 11:24:56 +02:00
nafkhamdc
00aa6b5a3c
gnu: Add python-pyrodigal. 
* gnu/packages/bioinformatics.scm (python-pyrodigal): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>

Change-Id: Iaa0bdb4b918d93f990d5b904f1df3a3f910726b0
 2024-05-06 10:37:41 +02:00
nafkhamdc
a5fef66b34
gnu: Add python-archspec. 
* gnu/packages/python-xyz.scm (python-archspec): New variable.

Change-Id: Icb15a681d7f339ab25cb0a91feeaacc6a3e8cd6a
 2024-05-06 10:37:41 +02:00
Wilko Meyer
da41a8f5e8
gnu: linux-libre 4.19: Update to 4.19.313. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.313.
(linux-libre-4.19-pristine-source): Update hash.

Change-Id: I22e9d175b537164efcde4cec5188c26bae8d2fca
Signed-off-by: Leo Famulari <leo@famulari.name>
 2024-05-05 23:15:59 -04:00
Wilko Meyer
44d28d102b
gnu: linux-libre 5.4: Update to 5.4.275. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.275.
(linux-libre-5.4-pristine-source): Update hash.

Change-Id: Ifcd296510ae1c7e81a4a5fa3c8eb6e304e2d662d
Signed-off-by: Leo Famulari <leo@famulari.name>
 2024-05-05 23:15:59 -04:00
Wilko Meyer
5d51f8897c
gnu: linux-libre 5.10: Update to 5.10.216. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.216.
(linux-libre-5.10-pristine-source): Update hashes.

Change-Id: Ia14fa905e109c81cc8397d1151cc327d6e1ea25a
Signed-off-by: Leo Famulari <leo@famulari.name>
 2024-05-05 23:15:58 -04:00
Wilko Meyer
5ea5d677fe
gnu: linux-libre 5.15: Update to 5.15.158. 
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.158.
(linux-libre-5.15-pristine-source): Update hash.

Change-Id: Ib2b12fac8301ced17e6e068a1e68768e200d5a24
Signed-off-by: Leo Famulari <leo@famulari.name>
 2024-05-05 23:15:58 -04:00
Wilko Meyer
ef0cf6ae85
gnu: linux-libre 6.1: Update to 6.1.90. 
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.90.
(linux-libre-6.1-pristine-source): Update hash.

Change-Id: Ic1ef7176af2055db78b58458bb9327bce5789d48
 2024-05-05 23:15:58 -04:00
Wilko Meyer
98e368f660
gnu: linux-libre 6.6: Update to 6.6.30. 
* gnu/packages/linux.scm (linux-libre-6.6-version): Update to 6.6.30.
(linux-libre-6.6-pristine-source): Update hash.

Change-Id: Ic261985e2c199a80068e2898684d522939b98a89
 2024-05-05 23:15:58 -04:00
Wilko Meyer
c2fdac2262
gnu: linux-libre-6.8-gnu-revision: Update to 6.8.9. 
* gnu/packages/linux.scm (linux-libre-6.8-version): Update to 6.8.9.
(linux-libre-6.8-pristine-source): Update hash.

Signed-off-by: Leo Famulari <leo@famulari.name>
Change-Id: I4f8031b1db5e19e98e5f61377a45912f91d403f7
 2024-05-05 23:15:57 -04:00
Maxim Cournoyer
dae5eecd47
gnu: Add mupen64plus-video-gliden64. 
* gnu/packages/emulators.scm (mupen64plus-video-gliden64): New variable.

Change-Id: I09782d0c793062c3fa448b5376a97a5f3356ea5c
 2024-05-05 22:58:13 -04:00
Maxim Cournoyer
79a51c910c
gnu: mupen64plus-ui-console: Modernize. 
* gnu/packages/emulators.scm (mupen64plus-ui-console)
[propagated-inputs]: Remove legacy mupen64plus-video-glide64 plugin.
[arguments]: Use gexps.

Change-Id: I33ce0ef1e7ea87b382f74aae07098bcf0e5f30e0
 2024-05-05 22:58:13 -04:00
Maxim Cournoyer
3a1737aaa2
gnu: mupen64plus-video-rice: Adjust synopsis. 
* gnu/packages/emulators.scm (mupen64plus-video-rice): Adjust synopsis.

Change-Id: I3708c46593a096f632d9268200c312a434525331
 2024-05-05 22:58:13 -04:00
Maxim Cournoyer
726b076658
gnu: mupen64plus-video-glide64mk2: Fix synopsis. 
* gnu/packages/emulators.scm (mupen64plus-video-glide64mk2): Fix synopsis.

Change-Id: I6f41e9a4b70faa0e2342a4ffc2803873a8dc8f08
 2024-05-05 22:58:13 -04:00
Maxim Cournoyer
8c25cab988
gnu: mupen64plus-video-glide64: Fix synopsis. 
* gnu/packages/emulators.scm (mupen64plus-video-glide64): Fix synopsis.

Change-Id: I0b2b4630dcf3c5dc5ee385e82c71f92694cf2abe
 2024-05-05 22:58:12 -04:00
Maxim Cournoyer
e21c9f337e
gnu: mupen64plus-video-arachnoid: Fix synopsis. 
* gnu/packages/emulators.scm (mupen64plus-video-arachnoid): Fix synopsis.

Change-Id: Ic560e6780965526723907aff9d2af6c48f580508
 2024-05-05 22:58:12 -04:00
Maxim Cournoyer
8fbc8e7a65
gnu: mupen64plus-rsp-z64: Fix synopsis. 
* gnu/packages/emulators.scm (mupen64plus-rsp-z64): Fix synopsis.

Change-Id: I97d5b8e70949f2a5198ce45b0a1fe24a089078ba
 2024-05-05 22:58:12 -04:00
Maxim Cournoyer
376fe82015
gnu: mupen64plus-rsp-hle: Fix synopsis. 
* gnu/packages/emulators.scm (mupen64plus-rsp-hle): Fix synopsis.

Change-Id: I7235da472ecd1856fdc33ed08d92f9f05b29ba3a
 2024-05-05 22:58:12 -04:00
Maxim Cournoyer
721e44d419
gnu: mupen64plus-audio-sdl: Fix synopsis. 
* gnu/packages/emulators.scm (mupen64plus-audio-sdl): Fix synopsis.

Change-Id: I08b2778cf625699d72d5fbab2b23d86ff06a1be0
 2024-05-05 22:58:12 -04:00
nafkhamdc
e33bf0bbe6
gnu: Add python-pyahocorasick. 
* gnu/packages/bioinformatics.scm (python-pyahocorasick): New variable.

Change-Id: I468bed450351b49cf81344a328841cd77f67cb4e
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-05-06 00:07:40 +02:00
nafkhamdc
a710ebec1d
gnu: Add r-memes. 
* gnu/packages/bioconductor.scm (r-memes): New variable.

Change-Id: Ibdf5173d35ef81d27da6831148e66be83f856deb
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-05-06 00:06:19 +02:00
Ricardo Wurmus
a4ad0a46ef
gnu: python-graphtools: Fix tests. 
* gnu/packages/graph.scm (python-graphtools)[arguments]: Add 'patch-tests
phase.

Change-Id: I5ffb4321ddd7e33e812bcb1cf67cee069b07b5f8
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
1b44a23503
gnu: python-gpy: Update to 1.13.1. 
* gnu/packages/python-science.scm (python-gpy): Update to 1.13.1.
[source]: Remove snippet.
[build-system]: Use pyproject-build-system.
[arguments]: Remove phase 'remove-plotting-tests; add phase 'compatibility.
[native-inputs]: Remove python-nose and python-climin; add python-pytest,
python-matplotlib, and python-pods.

Change-Id: I1ed95e3ad2e8444979fd2cf272d7f3104b1bf2ec
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
a4039b6994
gnu: python-pygsp: Add missing input. 
* gnu/packages/graph.scm (python-pygsp)[native-inputs]: Add python-pytest.

Change-Id: I94cd4e160dcbecfbb491c0d101bcbeb761189876
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
9d615b915b
gnu: python-paramz: Update to 0.9.6. 
* gnu/packages/python-science.scm (python-paramz): Update to 0.9.6.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-nose.

Change-Id: I62a2f7ecf600f48da74f4d233e108360a583d5ca
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
041ea43a86
gnu: python-pingouin: Update to 0.5.4. 
* gnu/packages/python-science.scm (python-pingouin): Update to 0.5.4.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add 'sklearn-compatibility phase;
skip one test.

Change-Id: I8d13f15558eadee0547f04bc4bb89a0fd0e0767b
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
99bf1b1002
gnu: python-liana-py: Update to 1.1.0. 
* gnu/packages/bioinformatics.scm (python-liana-py): Update to 1.1.0.
[arguments]: Adjust tests; add phase 'relax-requirements.
[propagated-inputs]: Remove python-mofax; add python-numpy.
[native-inputs]: Remove python-numpy; add python-poetry-core.

Change-Id: I279be08ac3ac73d9a724f59652f2f0d333607696
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
4d65083bf8
gnu: python-plotnine: Fix version string. 
* gnu/packages/python-science.scm (python-plotnine)[native-inputs]: Add
python-setuptools-scm.

Change-Id: I0fc2f3ad7edcdaaa5e3bf9774bc6840c8fbeb727
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
02ca781c03
gnu: python-plotnine: Disable test because of harmless warning. 
* gnu/packages/python-science.scm (python-plotnine)[arguments]: Disable
test_save_method which prints an unexpected warning..

Change-Id: I28a20b85ee549311bed534efbf801db930419ca9
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
f678884b4a
gnu: python-mapie: Disable strict tests. 
* gnu/packages/statistics.scm (python-mapie)[arguments]: Disable two tests.

Change-Id: I2c72f6f2d0136db5f97ba709a468a3aebd447d5d
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
c226d12856
gnu: python-scikit-learn-extra: Disable a validation test. 
* gnu/packages/machine-learning.scm (python-scikit-learn-extra)[arguments]:
Disable one test.

Change-Id: I1309cb6a82dee1a714ddec59aa90692ccfcd885b
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
1ea0e3e6dd
gnu: python-cooltools: Update to 0.7.0. 
* gnu/packages/bioinformatics.scm (python-cooltools): Update to 0.7.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.

Change-Id: I4112bf0cbc309df551087b8bb3cb1d37af7f751d
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
d14d5147b1
gnu: python-bioframe: Update to 0.6.4. 
* gnu/packages/bioinformatics.scm (python-bioframe): Update to 0.6.4.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add 'pre-check phase.  Use
 #:test-flags to disable tests that require internet access.
[native-inputs]: Add python-hatchling.
[propagated-inputs]: Add python-pyyaml.

Change-Id: Iad1c8c6ef8f52886e398e9c4d2d384c5fce075c6
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
317be75d1d
gnu: python-verde: Add missing input. 
* gnu/packages/geo.scm (python-verde)[native-inputs]: Add python-pytest.

Change-Id: I82b844627f27cfe60e42050bb37d092b3d9a43c1
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
ffffc0227a
gnu: python-statmake: Adjust tests and version checks. 
* gnu/packages/fontutils.scm (python-statmake)[arguments]: Disable broken
test; relax check for cattrs.

Change-Id: Ibd479743160d3591088d17635e26484e7de5250f
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
cb9ec4c5c5
gnu: python-decoupler-py: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (python-decoupler-py): Update to 1.6.0.
[arguments]: Do not disable test_plot_volcano test.

Change-Id: I44a31d30e8a03d2d1ffd86383c8bc6db79628def
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
0e24635033
gnu: python-omnipath: Update to 1.0.8. 
* gnu/packages/python-web.scm (python-omnipath): Update to 1.0.8.
[arguments]: Disable tests that need internet access.
[native-inputs]: Add python-pytest-socket.

Change-Id: Ib5856a1a25835d43918d9fe565d0262dded70eed
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
7c938c232c
gnu: barectf: Use python-termcolor-1. 
* gnu/packages/instrumentation.scm (barectf)[propagated-inputs]: Use
python-termcolor-1.

Change-Id: I8284db970d3cee8988318be7f1180aa933ab461a
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
1f5eef8391
gnu: Add python-termcolor-1. 
* gnu/packages/python-xyz.scm (python-termcolor-1): New variable.

Change-Id: I1aca97b6b7976cb698131c3a0be73e4798bef6d6
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
79d13482e4
gnu: python-pytest-shutil: Disable a test. 
* gnu/packages/python-check.scm (python-pytest-shutil)[build-system]: Use
pyproject-build-system.
[arguments]: Disable test_pretty_formatter.

Change-Id: I862320feab5b3c6e375bf652deced6a631dfc575
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
360f9ea421
gnu: python-cleanlab: Update to 2.6.3. 
* gnu/packages/machine-learning.scm (python-cleanlab): Update to 2.6.3.
[arguments]: Disable tests that require "datasets" package; add phase
'remove-datasets.

Change-Id: I6af99e3e749a10515328db4874974a3504658352
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
714baf2295
gnu: python-termcolor: Update to 2.4.0. 
* gnu/packages/python-xyz.scm (python-termcolor): Update to 2.4.0.
[build-system]: Use pyproject-build-system.
[arguments]: Add 'fix-pyproject build phase.
[native-inputs]: Add python-hatch-vcs, python-hatchling, python-pytest, and
python-pytest-cov.

Change-Id: I1b824ca6f125305169c3f64f00dbacbeb77d0ed0
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
31f57ae7df
gnu: python-hicexplorer: Update to 3.7.4. 
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.4.
[source]: Remove obsolete snippet.
[arguments]: Remove obsolete phase 'scipy-compatibility.
[propagated-inputs]: Replace python-cleanlab-1 with python-cleanlab.

Change-Id: Iac9a24cc4551b7d7e1d41d1f07a6db6d620b119e
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
9692e2bb7c
gnu: snakemake-5: Patch version string. 
* gnu/packages/python-xyz.scm (snakemake-5)[arguments]: Add phase
'patch-version.

Change-Id: I647625e9d26b2ee06274a0c5bb844ccb87035537
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
8d14b1cbb6
gnu: snakemake-5: Make compatible with tabulate 0.9.0. 
* gnu/packages/python-xyz.scm (snakemake-5)[arguments]: Add phase
'tabulate-compatibility.

Change-Id: I0b0ddafe9c2da91dbe10a584eb6fa0a3d5d62e87
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
36a1e76173
gnu: snakemake: Fetch from git repository. 
* gnu/packages/python-xyz.scm (snakemake)[source]: Fetch from git repository
to include tests.
[arguments]: Enable tests; add 'pre-check phase.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add git-minimal, python-wrapper, python-pytest,
python-pandas, and python-requests-mock.

Change-Id: I32e9d36752cc91eacb8f05138d969834dbbce817
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
6095e5b436
gnu: snakemake-7: Make compatible with tabulate 0.9.0. 
* gnu/packages/python-xyz.scm (snakemake-7)[arguments]: Add phase
'tabulate-compatibility.

Change-Id: Ie6b2a7d65bc76e3df7c3946ba4533b301f5a3610
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
6244177e79
gnu: snakemake-6: Make compatible with tabulate 0.9.0. 
* gnu/packages/python-xyz.scm (snakemake-6)[arguments]: Add phase
'tabulate-compatibility.

Change-Id: I0471726e2000af76871e2542ed347cd1727bf0c9
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
ee9720b2f0
gnu: python-jsonpickle: Update to 3.0.4. 
* gnu/packages/python-web.scm (python-jsonpickle): Update to 3.0.4.
[build-system]: Use pyproject-build-system.
[arguments]: Use test-flags; add 'pre-check phase.
[propagated-inputs]: Add python-importlib-metadata.
[native-inputs]: Add python-bson, python-ecdsa, python-feedparser,
python-pymongo, python-pytest, python-pytest-benchmark, python-pytest-cov,
python-pytest-enabler, python-setuptools, python-setuptools-scm,
python-simplejson, python-sqlalchemy, python-ujson, and tzdata-for-tests.

Change-Id: I99e41ae2652ce02b090ee2b99a7b850a19b5f353
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
d5424b12af
gnu: python-imbalanced-learn: Update to 0.12.2. 
* gnu/packages/machine-learning.scm (python-imbalanced-learn): Update to
0.12.2.
[native-inputs]: Remove python-numpydoc.

Change-Id: I8af0017f76d5ab3a2d55a96c0ace6be22d57fb66
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
2d8c81a8d7
gnu: tadbit: Add R to inputs. 
* gnu/packages/bioinformatics.scm (tadbit)[inputs]: Add r-minimal.

Change-Id: I4929dd89ddd27b4fcbd8b3a00b8ab8f3586945d2
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
93a397f8b7
gnu: tadbit: Patch for compatibility with latest scipy. 
* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Add phase
'scipy-compatibility.

Change-Id: Ib25b9cde75f0505c347c4ff470e61f06fb162839
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
453b7a267b
gnu: tadbit: Update to 1.0.1-2.2838129. 
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-2.2838129.

Change-Id: I2c220ae37cd196ca508d30aefc24938cce985527
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
332a8fa4bc
gnu: python-cooler: Update to 0.9.3. 
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.9.3.

Change-Id: I4b89d552a424e74f76cda0c527dc7b712b8c9f31
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
57f265f1ea
gnu: python-dask: Do not reference pyarrow_hotfix. 
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Add 'patch-pyproject
phase.

Change-Id: Idd173b72b1467540c295224072f3740c7f42b0a8
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
262df6c607
gnu: python-dask: Disable some tests. 
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Disable ORC tests and
those that fail due to differences in job id.

Change-Id: I272a77c8291b121b57b02750916f520b52185bbe
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
78d5fb1720
gnu: python-dask: Propagate python-dask-expr. 
* gnu/packages/python-xyz.scm (python-dask/bootstrap): New variable.
(python-dask)[propagated-inputs]: Add python-dask-expr.
* gnu/packages/python-science.scm (python-dask-expr)[propagated-inputs]:
Remove python-dask.
[native-inputs]: Add python-dask/bootstrap.

Change-Id: I1196641425421c7dde94c6fea8d573e78db9c402
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
a237ba5378
gnu: python-umap-learn: Disable failing test. 
* gnu/packages/machine-learning.scm (python-umap-learn)[arguments]: Disable
one failing test.

Change-Id: Ic8f5f60f7d7bea0c24b417932daab3d54813d5fd
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
ba92122e53
gnu: python-umap-learn: Update to 0.5.6. 
* gnu/packages/machine-learning.scm (python-umap-learn): Update to 0.5.6.

Change-Id: If05cf1a9c7ad1d9fd0439bc888983608d70aea75
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
3c0579849c
gnu: python-pandas-stubs: Accept numpy 1.23. 
* gnu/packages/python-science.scm (python-pandas-stubs)[arguments]: Add phase
'relax-requirements.

Change-Id: I62e04574d53abd7d67068d08475522dd8989dcca
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
22eeb8f16e
gnu: python-dask: Disable all tokenize tests. 
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Ignore the test file.

Change-Id: Icbd4845361aa57c493f473ab87a15ade8a20a65f
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
1295abd0af
Revert "gnu: python-numpy: Update to 1.26.0." 
numba cannot use numpy > 1.24.

This reverts commit 6b8efd211fbd619e80628d2a78f99c6afc18723e.
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
5450886934
gnu: python-numpy: Update to 1.26.0. 
* gnu/packages/python-xyz.scm (python-numpy): Update to 1.26.0.
[build-system]: Use pyproject-build-system.
[arguments]: Move test flags to #:test-flags; add phase
'use-setuptools-backend.
[native-inputs]: Remove gfortran; add replace python-cython with
python-cython-3; add meson/newer and ninja.

Change-Id: I783bbca58624bf6f047056ba21d838f5ecb09ac2
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
2a7e513803
gnu: python-tabulate: Enable tests and fix version string. 
* gnu/packages/python-xyz.scm (python-tabulate)[arguments]: Enable tests.
[native-inputs]: Add python-pytest and python-setuptools-scm.

Change-Id: I14073151916fd637d83905c03e76b96c390db917
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
92259a5d4b
gnu: python-pandas-stubs: Update tests. 
This is a follow-up to adding ORC support to pyarrow.

* gnu/packages/python-science.scm (python-pandas-stubs)[arguments]: Disable
more tests that are due to enabling ORC support to pyarrow.

Change-Id: I8c3ca6afff8128792738251c85a1dba3dc3b0569
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
53b2fe2973
gnu: python-scikit-bio: Update to 0.6.0. 
* gnu/packages/patches/python-scikit-bio-1887.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.6.0.
[source]: Remove patch.
[arguments]: Disable skbio.diversity doctest; remove 'compatibility phase.
[propagated-inputs]: Add python-biom-format; remove python-ipython and
python-matplotlib.

Change-Id: I9bd9e0fd72f5f1b80ef6ff61c52da5fd56a715ed
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
e9d70b85eb
gnu: python-biom-format: Untangle from python-scikit-bio. 
* gnu/packages/bioinformatics.scm (python-biom-format)[arguments]: Add phase
'pandas-compatibility; disable tests that need sciki-bio.
[propagated-inputs]: Remove python-scikit-bio.

Change-Id: Ifd528d256a1c75962fb05aef5602edbf67a5af26
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
24bf2329a4
gnu: python-anndata: Update to 0.10.7. 
* gnu/packages/python-xyz.scm (python-anndata): Update to 0.10.7.
[arguments]: Patch conftest.py; adjust tests; remove old patch for version
string; add phase 'set-numba-cache-dir.
[native-inputs]: Add python-awkward, python-dask, python-distributed,
python-hatchling, python-hatch-vcs, python-loompy, python-matplotlib,
python-pytest-doctestplus, and python-pytest-xdist.
[propagated-inputs]: Add python-array-api-compat and python-exceptiongroup.

Change-Id: I3099cbfbb1865743c75d32243be9e5a59df1507d
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
eb866b3699
gnu: Add python-array-api-compat. 
* gnu/packages/python-xyz.scm (python-array-api-compat): New variable.

Change-Id: Ibfd701630b41f860c7ad4df57fd3624d9c5b7752
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
a3ff747a48
gnu: Add python-awkward. 
* gnu/packages/python-xyz.scm (python-awkward): New variable.

Change-Id: Ie4f9b12d3662b9029f6e042f9c3a4d547073a6e7
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
fe780b55b4
gnu: Add python-awkward-cpp. 
* gnu/packages/python-xyz.scm (python-awkward-cpp): New variable.

Change-Id: I68f7e314aa6b575eb7135aa5308c327d5f6bf3ea
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
d4c62ff301
gnu: Add python-scikit-build-core. 
* gnu/packages/python-science.scm (python-scikit-build-core): New variable.

Change-Id: If234d19d720afe88f6893bdd36fcc4955a45c5d3
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
07c7b342bb
gnu: python-distributed: Update to 2024.4.2. 
* gnu/packages/python-science.scm (python-distributed): Update to 2024.4.2.
[propagated-inputs]: Add python-dask-expr.
[arguments]: Adjust tests.

Change-Id: I9d3b45d14ae052f3a5a5dec3587bc01d13e4b71f
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
f3a80df770
gnu: Add python-dask-expr. 
* gnu/packages/python-science.scm (python-dask-expr): New variable.

Change-Id: I691593ab713fe865c771aa68b5521c4c10cc58f6
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
cc67370ca1
gnu: python-partd: Update to 1.4.1. 
* gnu/packages/python-xyz.scm (python-partd): Update to 1.4.1.
[propagated-inputs]: Remove python-blosc.

Change-Id: I3aff28899339f9ffaa47b6f5c81e0e68ce660963
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
dff3357bb6
gnu: python-dask: Update to 2024.4.2. 
* gnu/packages/python-xyz.scm (python-dask): Update to 2024.4.2.
[arguments]: Disable a few tests.

Change-Id: I759ddee2ec49fbf74f368c3313f7215906b0e5a2
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
fef6edecbc
gnu: python-tables: Update to 3.7.0. 
* gnu/packages/python-xyz.scm (python-tables): Update to 3.7.0.
[propagated-inputs]: Add python-packaging and python-py-cpuinfo.

Change-Id: I8653bef9a07bb898933b249aad92ddb2b79b8d85
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
dd6f87e492
gnu: python-pyarrow: Build with ORC support. 
* gnu/packages/databases.scm (python-pyarrow)[propagated-inputs]: Add
apache-orc.
[arguments]: Set PYARROW_WITH_ORC variable.

Change-Id: Ic35cd1db75349ecb51d35815d710d8ca3a303b00
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
8647aaaa14
gnu: apache-arrow: Build with ORC. 
* gnu/packages/databases.scm (apache-arrow)[arguments]: Set options needed to
build with ORC support; remove unused options
-DBENCHMARK_ENABLE_GTEST_TESTS=OFF and -DARROW_GLOG=ON.
[inputs]: Add apache-orc.

Change-Id: Icabe6e3a73478c8464ea1e8efc103899da8e5a86
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
442eba98be
gnu: Add apache-orc. 
* gnu/packages/databases.scm (apache-orc): New variable.

Change-Id: I9e7df4a03a5d2f258ff44d9705f539f9fc925a99
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
adf54dea4e
gnu: python-pandas-stub: Update to 2.1.1.230928. 
This is a follow-up to commit ff2d0ecfca.

* gnu/packages/python-science.scm (python-pandas-stub): Update to
2.1.1.230928.

Change-Id: I2e8ce18bd25399b467a6ff2a6fb846f8bb969e4c
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
9953207f3e
gnu: python-tabulate: Update to 0.9.0. 
* gnu/packages/python-xyz.scm (python-tabulate): Update to 0.9.0.
[build-system]: Use pyproject-build-system.

Change-Id: If360e5be6433b35308b76bd1284bb6ddb74008e8
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
5e7da50260
gnu: python-pandas-2: Fix version. 
* gnu/packages/python-science.scm (python-pandas-2)[arguments]: Write version
string to "_version.py", not "_version_meson.py" to avoid reporting the
version as "0+unknown".

Change-Id: I1a18814e37c023102714326bc8bd505705234205
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
b343aef5aa
gnu: python-scikit-learn: Update to 1.4.2. 
* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 1.4.2.
[native-inputs]: Replace python-cython-0.29.35 with python-cython-3.

Change-Id: Id8be08f931bf250a8ecb8bc46b44d7148b4c4a2f
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
6be3c24d82
gnu: python-cython-3: Update to 3.0.8. 
* gnu/packages/python-xyz.scm (python-cython-3): Update to 3.0.8.

Change-Id: I9129a7837cefea0b95b0a3c3cdf73997d91f7484
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
6962b32a2b
gnu: python-pyjanitor: Update to 0.27.0. 
* gnu/packages/python-science.scm (python-pyjanitor): Update to 0.27.0.
[arguments]: Disable a few more tests; add phase 'pandas-compat.

Change-Id: Ia8891971a687342166f30ded11f9e341a208d95e
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
5def84031f
gnu: tadbit: Use G-expression. 
* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Use G-expression.

Change-Id: I4fe4afc41eb3442f243b0e415ddcb363be36ce7f
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
8f8cee9ed9
gnu: r-reticulate: Update to 1.36.1. 
* gnu/packages/cran.scm (r-reticulate): Update to 1.36.1.

Change-Id: I7119ca05b8411209c617be318806b3ff4bc3b530
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
297e88edff
gnu: python-xarray: Disable tests that are known to fail. 
* gnu/packages/python-science.scm (python-xarray)[arguments]: Disable two
tests.

Change-Id: I70954173e0aca5a377cf19476e9390a97febadc7
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
74dd2def7f
gnu: python-pandas: Default to version 2.x. 
* gnu/packages/python-science.scm (python-pandas): Define as alias for
python-pandas-2; rename existing definition to...
(python-pandas-1): ...this new variable.

Change-Id: If359e3b2d42c683d7d0152b1757bbc5a979c999b
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
d85a19a29c
gnu: python-scikit-opt: Add missing input. 
* gnu/packages/python-science.scm (python-scikit-opt)[propagated-inputs]: Add
python-pytorch.

Change-Id: I037cc43bedeaebb05bf038c0bca72919f8c27c40
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
da4006d474
gnu: python-plastid: Replace nose with pytest. 
* gnu/packages/bioinformatics.scm (python-plastid)[native-inputs]: Replace
python-nose with python-pytest.

Change-Id: Ie0e5362d2304d3af0bcb1405fa0c1ad36fb2ace6
 2024-05-05 22:38:15 +02:00
Marco Baggio
854c42e30c
gnu: Add python-metacells. 
* gnu/packages/bioinformatics.scm (python-metacells): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I4fc760dc4317bde79c815f441ad0cc453248990a
 2024-05-05 22:38:15 +02:00
Marco Baggio
da18b8620f
gnu: Add python-cvxpy. 
* gnu/packages/python-science.scm (python-cvxpy): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I440ab3768cbc4e78364dc31cf9484effd9670f49
 2024-05-05 22:38:15 +02:00
Marco Baggio
2c0cf38f04
gnu: Add python-ecos. 
* gnu/packages/python-science.scm (python-ecos): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I83d9b746f5f3563f417efc5d18911f2eb04f201c
 2024-05-05 22:38:15 +02:00
Marco Baggio
a0971243bc
gnu: Add python-osqp. 
* gnu/packages/python-science.scm (python-osqp): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: Id6f1665505469fd6543046636b82d0730b319df3
 2024-05-05 22:38:15 +02:00
Marco Baggio
d051ef0913
gnu: Add python-qdldl. 
* gnu/packages/python-science.scm (python-qdldl): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I523ecb2292c9b514b548e2130d0d43bb77317b00
 2024-05-05 22:38:15 +02:00
Marco Baggio
d470a9aa54
gnu: Add python-scs. 
* gnu/packages/python-science.scm (python-scs): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I6c5ecdac4b558aab4b8ee396dff1dfc9cdec07f0
 2024-05-05 22:38:15 +02:00
Marco Baggio
670dcc8e4c
gnu: Add python-fastcluster. 
* gnu/packages/python-science.scm (python-fastcluster): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: Ifc5229a4d00f581eb358a1f41fc3479fd1c33c2e
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
c4eccd2066
gnu: Add python-clarabel. 
* gnu/packages/python-science.scm (python-clarabel): New variable.

Change-Id: I28459162460ca9bf9e9557122f611c677afadc27
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
94ea83d9ef
gnu: Add rust-amd-0.2. 
* gnu/packages/crates-io.scm (rust-amd-0.2): New variable.

Change-Id: I28d4e0d6bd9b590ca61df9152f91641408e48e5a
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
d1eda517f3
gnu: Add python-param. 
* gnu/packages/python-xyz.scm (python-param): New variable.

Change-Id: Idad928488d7c306c969b4484a3cd22661c41d488
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
83262c971e
gnu: Add python-multiscale-spatial-image. 
* gnu/packages/python-xyz.scm (python-multiscale-spatial-image): New variable.

Change-Id: I05a0b3a93091148917fade831faefb88c13bbc6f
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
407fcd510b
gnu: Add python-colorcet. 
* gnu/packages/python-xyz.scm (python-colorcet): New variable.

Change-Id: I8b3f6d9a132d028f56330308b034d263e162f0f9
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
859953f60a
gnu: Add python-nbmake. 
* gnu/packages/python-check.scm (python-nbmake): New variable.

Change-Id: If062d0e34329e99b5bb87588e7ddf149c65bfdfb
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
5f186e2f79
gnu: Add python-pyct. 
* gnu/packages/python-xyz.scm (python-pyct): New variable.

Change-Id: Ia207d5aa9d66fd2bf3616049c042fbb12e50928d
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
6f71c4ab01
gnu: Add rust-blas-0.22. 
* gnu/packages/crates-io.scm (rust-blas-0.22): New variable.

Change-Id: Ic7bcbde20b6552659255f4ff11adde8fb1eeea45
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
aed5e5965f
gnu: Add rust-blas-sys-0.7. 
* gnu/packages/crates-io.scm (rust-blas-sys-0.7): New variable.

Change-Id: Ibfa2ab61256527e34e9ff9a8f7d871990ffbeda7
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
95478222c0
gnu: Add rust-lapack-0.19. 
* gnu/packages/crates-io.scm (rust-lapack-0.19): New variable.

Change-Id: I2c32db5e4028432e030005c7ee16773d0f052d21
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
82f83cafb9
gnu: Add rust-lapack-sys-0.14. 
* gnu/packages/crates-io.scm (rust-lapack-sys-0.14): New variable.

Change-Id: Id8fa94a06c231f3864040d2c428ac81042803adf
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
c9d9b9572b
gnu: Add python-xarray-schema. 
* gnu/packages/python-science.scm (python-xarray-schema): New variable.

Change-Id: I4ca650f2c2872698fc22392add169f44b9e2e035
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
061885faec
gnu: python-xarray-datatree: Add missing input. 
* gnu/packages/python-science.scm (python-xarray-datatree)[native-inputs]:
Add python-setuptools-scm.

Change-Id: I86a7280ba687385edb15f30dae1a20e3811a0beb
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
536228e65e
gnu: python-pooch: Update to 1.8.1. 
* gnu/packages/python-xyz.scm (python-pooch): Update to 1.8.1.
[arguments]: Enable tests, but not all of them.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-pytest and python-setuptools-scm.
[propagated-inputs]: Add python-platformdirs; remove python-appdirs and
python-packaging.

Change-Id: I3a0f73db5c0d78c9cee24c73402e9b1e34e26b4a
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus
749cb3c520
gnu: Add python-dask-image. 
* gnu/packages/python-xyz.scm (python-dask-image): New variable.

Change-Id: I77c22bba69d73ce39681064bfdcc05b2b360ea26
 2024-05-05 22:38:14 +02:00
Sharlatan Hellseher
d6c95d4208
gnu: Revmoe go-github-com-syndtr-goleveldb. 
This package is a duplicate to go-github-com-syndtr-goleveldb-leveldb.

* gnu/packages/ipfs.scm: Revmoe (gnu packages syncthing) module.
(kubo) [inputs]: Replace go-github-com-syndtr-goleveldb with
go-github-com-syndtr-goleveldb-leveldb.

* gnu/packages/syncthing.scm (go-github-com-syndtr-goleveldb): Remove
variable.

Change-Id: I8641a18a3d97f570f3bbbd849f7dabdea4e41b01
 2024-05-05 21:24:10 +01:00
Sharlatan Hellseher
b2dbd7ca8a
gnu: go-go-uber-org-atomic: Update to 1.11.0. 
The upstream suggested to update to the latest version to resolve
failing tests on RISK-V, see
<https://github.com/uber-go/atomic/issues/164>.

* gnu/packages/golang-xyz.scm (go-go-uber-org-atomic): Update to 1.11.0.
[arguments]: <#:tests?>: Enable tests on all platforms.

Change-Id: I6df21cfaebb9e4d4a609e93f3fe4bfea2bff5e8d
 2024-05-05 21:11:02 +01:00
Maxim Cournoyer
79c597c0ee
gnu: zsnes: Relocate to (gnu packages emulator). 
* gnu/packages/games.scm (zsnes): Move to...
* gnu/packages/emulators.scm (zsnes): ... here.

Change-Id: I739e0f3b221790b6f780362d884209fff0aed3d7
 2024-05-05 14:03:17 -04:00
Maxim Cournoyer
e276f5ed19
gnu: mupen64plus-ui-console: Update to 2.5.9. 
* gnu/packages/emulators.scm (mupen64plus-ui-console): Update to 2.5.9.

Change-Id: I9794dc81e0417c9879820400dbdb002faec35cdc
 2024-05-05 14:03:16 -04:00
Maxim Cournoyer
8521d0b81e
gnu: mupen64plus-video-z64: Update to 2.5.9. 
* gnu/packages/emulators.scm (mupen64plus-video-z64): Update to 2.5.9.
[source]: Delete patches.
* gnu/packages/patches/mupen64plus-video-z64-glew-correct-path.patch: Delete
file.
* gnu/local.mk (dist_patch_DATA): De-register it.

Change-Id: Ic8022c3a88f88f48644cc694e0a18c0b0a6745a1
 2024-05-05 14:03:16 -04:00
Maxim Cournoyer
71e99742ab
gnu: mupen64plus-video-rice: Update to 2.5.9. 
* gnu/packages/emulators.scm (mupen64plus-video-rice): Update to 2.5.9.

Change-Id: Ie2d26d6c62a09c0077e4c28869bf33b2c275d01f
 2024-05-05 14:03:16 -04:00
Maxim Cournoyer
925b95ff23
gnu: mupen64plus-video-glide64mk2: Update to 2.5.9. 
* gnu/packages/emulators.scm (mupen64plus-video-glide64mk2): Update to 2.5.9.

Change-Id: I77afdd1c954411203e75248d0d4bf4709db375bb
 2024-05-05 14:03:16 -04:00
Maxim Cournoyer
52bfa64956
gnu: mupen64plus-video-arachnoid: Update to 2.5.9. 
* gnu/packages/emulators.scm (mupen64plus-video-arachnoid): Update to 2.5.9.

Change-Id: I2751cca9a553029fbceba59762e498931a1f9946
 2024-05-05 14:03:16 -04:00
Maxim Cournoyer
9cab740594
gnu: mupen64plus-rsp-z64: Update to 2.5.9. 
* gnu/packages/emulators.scm (mupen64plus-rsp-z64): Update to 2.5.9.

Change-Id: Ibf9b67d37506f742c50397ff269586df1636af4d
 2024-05-05 14:03:15 -04:00
Maxim Cournoyer
9f11f67043
gnu: mupen64plus-rsp-hle: Update to 2.5.9. 
* gnu/packages/emulators.scm (mupen64plus-rsp-hle): Update to 2.5.9.

Change-Id: I68c1f92fd2be820ba437696d61d064a97ed4581e
 2024-05-05 14:03:15 -04:00
Maxim Cournoyer
506425d6bd
gnu: mupen64plus-input-sdl: Update to 2.5.9. 
* gnu/packages/emulators.scm (mupen64plus-input-sdl): Update to 2.5.9.

Change-Id: Idec4c3633767d151101beeba3ef2317e54d3f6f4
 2024-05-05 14:03:15 -04:00
Maxim Cournoyer
2b25208c81
gnu: mupen64plus-audio-sdl: Update to 2.5.9. 
* gnu/packages/emulators.scm (mupen64plus-audio-sdl): Update to 2.5.9.

Change-Id: If888cf62ee2247438d47cd385d7812ad22fb8068
 2024-05-05 14:03:15 -04:00
Maxim Cournoyer
4e6701a09a
gnu: mupen64plus-core: Update to 2.5.9. 
* gnu/packages/emulators.scm (mupen64plus-core): Update to 2.5.9.
[native-inputs]: Add nasm.

Change-Id: I9960b697124c130e75f765d55e1ce8a56dda168b
 2024-05-05 14:03:15 -04:00
Maxim Cournoyer
e89763682e
gnu: mupen64plus-video-glide64: Update to 2.5.9. 
* gnu/packages/emulators.scm (mupen64plus-video-glide64): Update to 2.5.9.
[phases]: Delete use-sdl2 phase.

Change-Id: Ic7359fb764f40fa25c553ab15e39f47963d3301b
 2024-05-05 14:03:14 -04:00
Steve George
dde37247fa
gnu: gnucash: Update to 5.6. 
* gnu/packages/gnucash.scm (gnucash): Update to 5.6.

Change-Id: I3646082d628470327fbd9deec6111de8c1eec921
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2024-05-04 19:14:27 +02:00
Steve George
aa9e639216
gnu: perl-finance-quote: Update perl-finance-quote. 
* gnu/packages/web.scm (perl-finance-quote): Update to 1.59.
[source] remove patch
* gnu/packages/patches/perl-finance-quote-unuse-mozilla-ca.patch: Remove file.

Change-Id: I3646082d628470327fbd9deec6111de8c1eec921

Change-Id: Ibe50f9736bcbe4e628c05f86c0e0be8bd335d4c8
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2024-05-04 19:14:26 +02:00
Steve George
ec9c5a8ff5
gnu: Add perl-spreadsheet-xlsx. 
* gnu/packages/perl.scm (perl-spreadsheet-xlsx): New variable.

Change-Id: Iec4fc26945bd2f154587d4b13b593fd947bb0e5a
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2024-05-04 19:14:26 +02:00
Steve George
92641467b4
gnu: Add perl-spreadsheet-parseexcel. 
* gnu/packages/perl.scm (perl-spreadsheet-parseexcel): New variable.

Change-Id: I0dfbf49f4b8b1865a738edc805d3dc83b038a124
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2024-05-04 19:14:26 +02:00
Steve George
6a23664cd8
gnu: Add perl-digest-perl-md5. 
* gnu/packages/perl.scm (perl-digest-perl-md5): New variable.

Change-Id: Ic656fef7bbc77790d114812f0c9dcafa1586e357
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2024-05-04 19:14:26 +02:00
Steve George
e175175a11
gnu: Add perl-html-tokeparser-simple. 
* gnu/packages/web.scm (perl-html-tokeparser-simple): New variable.

Change-Id: If779dbe29de05697d87143b38d986d5ff7fa2c8f
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2024-05-04 19:14:26 +02:00