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85685 Commits

Author SHA1 Message Date
Tobias Geerinckx-Rice
f36a0908f2
gnu: clzip: Update to 1.13. 
* gnu/packages/compression.scm (clzip): Update to 1.13.
 2022-05-01 02:00:20 +02:00
Tobias Geerinckx-Rice
2e99cb15e6
gnu: lunzip: Update to 1.13. 
* gnu/packages/compression.scm (lunzip): Update to 1.13.
 2022-05-01 02:00:20 +02:00
Tobias Geerinckx-Rice
c12095c680
gnu: lrzip: Update to 0.651. 
* gnu/packages/compression.scm (lrzip): Update to 0.651.
 2022-05-01 02:00:20 +02:00
Tobias Geerinckx-Rice
fcab7ac841
gnu: lziprecover: Update to 1.23. 
* gnu/packages/compression.scm (lziprecover): Update to 1.23.
 2022-05-01 02:00:20 +02:00
Tobias Geerinckx-Rice
28741adda9
gnu: audit: Update to 3.0.8. 
* gnu/packages/admin.scm (audit): Update to 3.0.8.
 2022-05-01 02:00:19 +02:00
Tobias Geerinckx-Rice
69fff28de8
gnu: libshout: Update to 2.4.6. 
* gnu/packages/xiph.scm (libshout): Update to 2.4.6.
 2022-05-01 02:00:19 +02:00
Tobias Geerinckx-Rice
0bb0984724
gnu: acpica: Update to 20220331. 
* gnu/packages/admin.scm (acpica): Update to 20220331.
 2022-05-01 02:00:19 +02:00
Tobias Geerinckx-Rice
110ed3433d
gnu: rasdaemon: Update to 0.6.8. 
* gnu/packages/linux.scm (rasdaemon): Update to 0.6.8.
 2022-05-01 02:00:19 +02:00
Tobias Geerinckx-Rice
73b0b298bf
gnu: mcelog: Update to 181. 
* gnu/packages/linux.scm (mcelog): Update to 181.
 2022-05-01 02:00:19 +02:00
Tobias Geerinckx-Rice
4e27e4652f
gnu: nsd: Update to 4.4.0. 
* gnu/packages/dns.scm (nsd): Update to 4.4.0.
 2022-05-01 02:00:19 +02:00
Tobias Geerinckx-Rice
cb75465645
gnu: gptfdisk: Correct gettext input type. 
* gnu/packages/disk.scm (gptfdisk)[inputs]: Move gettext-minimal from here…
[native-inputs]: …to here.
 2022-05-01 02:00:19 +02:00
Tobias Geerinckx-Rice
4e3d04a33b
gnu: gptfdisk: Use new input style. 
* gnu/packages/disk.scm (gptfdisk)[inputs]: Use new style.
Move field to its conventional location.
 2022-05-01 02:00:18 +02:00
Tobias Geerinckx-Rice
fdeb2479aa
gnu: gptfdisk: Update to 1.0.9. 
* gnu/packages/disk.scm (gptfdisk): Update to 1.0.9.
[arguments]: Don't explicitly return #t from phases.
 2022-05-01 02:00:18 +02:00
Tobias Geerinckx-Rice
ad99a09abe
gnu: epson-inkjet-printer-escpr: Use new style. 
* gnu/packages/cups.scm (epson-inkjet-printer-escpr)[arguments]:
Rewrite with (guix gexp).
[inputs]: Use new style.
 2022-05-01 02:00:18 +02:00
Tobias Geerinckx-Rice
20456fd016
gnu: epson-inkjet-printer-escpr: Use HTTPS home page. 
* gnu/packages/cups.scm (epson-inkjet-printer-escpr)[home-page]: Use HTTPS.
 2022-05-01 02:00:18 +02:00
Tobias Geerinckx-Rice
04544c8f1c
gnu: epson-inkjet-printer-escpr: Update to 1.7.18. 
* gnu/packages/cups.scm (epson-inkjet-printer-escpr): Update to 1.7.18.
 2022-05-01 02:00:18 +02:00
Tobias Geerinckx-Rice
cc796dc320
gnu: tor: Use G-expressions. 
* gnu/packages/tor.scm (tor)[arguments]: Rewrite using (guix gexp).
(tor-client)[arguments]: SUBSTITUTE-KEYWORD-ARGUMENTS accordingly.
 2022-05-01 02:00:18 +02:00
Tobias Geerinckx-Rice
be6d5783ba
gnu: tor: Update to 0.4.7.7. 
* gnu/packages/tor.scm (tor): Update to 0.4.7.7.
[source]: Remove patch.
* gnu/packages/patches/tor-sandbox-i686.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2022-05-01 02:00:18 +02:00
Tobias Geerinckx-Rice
51b716f7f2
gnu: enblend-enfuse: Fix build. 
* gnu/packages/photo.scm (enblend-enfuse)[arguments]: Rewrite as a
keyword/gexp list.  Add a new 'add-missing-include phase to build with a
recent GCC.
 2022-05-01 02:00:17 +02:00
Tobias Geerinckx-Rice
db5c49fc62
gnu: enblend-enfuse: Remove input labels. 
* gnu/packages/photo.scm (enblend-enfuse)[native-inputs, inputs]:
Remove input labels.
 2022-05-01 02:00:17 +02:00
Tobias Geerinckx-Rice
4b08526865
gnu: Remove linux-libre@4.4 configuration files. 
This follows up on commit bc54947410.

* gnu/packages/aux-files/linux-libre/4.4-i686.conf,
gnu/packages/aux-files/linux-libre/4.4-x86_64.conf: Delete files.
* Makefile.am (AUX_FILES): Remove them.
 2022-05-01 02:00:00 +02:00
Guillaume Le Vaillant
5320ba2054
gnu: flrig: Update to 1.4.05. 
* gnu/packages/radio.scm (flrig): Update to 1.4.05.
 2022-05-07 13:50:27 +02:00
Guillaume Le Vaillant
ffcec65878
gnu: fldigi: Update to 4.1.22. 
* gnu/packages/radio.scm (fldigi): Update to 4.1.22.
 2022-05-07 13:48:01 +02:00
Rostislav Svoboda
02182c623e
gnu: openjdk17: Update to 17.0.2 
* gnu/packages/java.scm (openjdk17): Update to 17.0.2.
 2022-05-07 11:22:19 +02:00
Julien Lepiller
513f54dc5d
gnu: ocaml-cmdliner: Update to 1.1.1. 2022-05-07 08:16:31 +02:00
Julien Lepiller
fe794295ab
gnu: ocaml-reactivedata: Update to 0.3. 
* gnu/packages/ocaml.scm (ocaml-reactivedata): Update to 0.3.
 2022-05-07 08:16:17 +02:00
Ricardo Wurmus
ee70ed5bf5
gnu: Add rust-blake3-1. 
* gnu/packages/crypto.scm (rust-blake3-1): New variable.
 2022-05-06 23:13:29 +02:00
Jan (janneke) Nieuwenhuizen
0e9429544f
gnu: dezyne: Use new package style. 
* gnu/packages/dezyne.scm (dezyne)[arguments]: Convert to list of
G-Expressions.
[inputs]: Drop labels.
 2022-05-06 15:56:11 +02:00
Christopher Baines
83c1f017a6
gnu: nar-herder: Update to 0-6.ea997c6. 
* gnu/packages/package-management.scm (nar-herder): Update to 0-6.ea997c6.
 2022-05-06 14:38:52 +01:00
Ricardo Wurmus
4f15745b95
gnu: Add rust-page-size-0.4. 
* gnu/packages/crates-io.scm (rust-page-size-0.4): New variable.
 2022-05-06 15:34:31 +02:00
Ricardo Wurmus
6f5cbac67d
gnu: pigx-sars-cov-2: Update to 0.0.7. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.7.
[inputs]: Remove bbmap and prinseq; add r-viridis.
[arguments]: Remove autoreconf phase.
 2022-05-06 15:34:31 +02:00
Ricardo Wurmus
f550c0ccb0
gnu: Add pigx-sars-cov-2. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): New variable.
(pigx-sars-cov2-ww): Deprecate this package in favor of the former.
 2022-05-06 15:34:31 +02:00
Ricardo Wurmus
bec6bf64bc
gnu: rust-instant-0.1: Update to 0.1.9. 
* gnu/packages/crates-io.scm (rust-instant-0.1): Update to 0.1.9.
 2022-05-06 15:34:31 +02:00
Ricardo Wurmus
70f6d2302c
gnu: rust-lock-api-0.4: Update to 0.4.5. 
* gnu/packages/crates-io.scm (rust-lock-api-0.4): Update to 0.4.5.
 2022-05-06 15:34:31 +02:00
Ricardo Wurmus
f02f8db381
gnu: rust-parking-lot-0.11: Update to 0.11.2. 
* gnu/packages/crates-io.scm (rust-parking-lot-0.11): Update to 0.11.2.
 2022-05-06 15:34:31 +02:00
Ricardo Wurmus
d16298196c
gnu: rust-parking-lot-core-0.8: Update to 0.8.4. 
* gnu/packages/crates-io.scm (rust-parking-lot-core-0.8): Update to 0.8.4.
 2022-05-06 15:34:31 +02:00
Ludovic Courtès
8079bd3da8
gnu: tcl-tls: Use a gexp. 
* gnu/packages/tcl.scm (tcl-tls)[arguments]: Use a gexp.
 2022-05-06 15:23:07 +02:00
Ludovic Courtès
4a3f8994f4
gnu: tcl-tls: Add 'release-monitoring-url' and 'upstream-name' properties. 
* gnu/packages/tcl.scm (tcl-tls)[properties]: New field.
 2022-05-06 15:23:07 +02:00
Daniel Lowe
06d244197b
gnu: tcl: Add tcl-tls to packages. 
* gnu/packages/tcl.scm (tcl-tls): Added 1.7.22

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:07 +02:00
Paul A. Patience
e606e02844
gnu: python-vedo: Update to 2022.2.0. 
* gnu/packages/python-science.scm (python-vedo): Update to 2022.2.0.
[arguments]: Add 'fix-tests' phase.
[inputs]: Move fenics and python-matplotlib to propagated-inputs.
Move python-pkgconfig from here...
[native-inputs]: ...to here.
[propagated-inputs]: Add python-deprecated (and fenics and
python-matplotlib).
[description]: Make description more accurate.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:06 +02:00
Paul A. Patience
9edc0f3dbb
gnu: python-vedo: Disable sanity check. 
* gnu/packages/python-science.scm (python-vedo)[arguments]: Disable
sanity check.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:06 +02:00
Paul A. Patience
a5fec06868
gnu: python-vedo: Remove input labels. 
* gnu/packages/python-science.scm (python-vedo)[inputs]: Remove labels
and sort the inputs.
[propagated-inputs]: Remove labels.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:06 +02:00
Paul A. Patience
34f49d15e6
gnu: python-vedo: Honor #:tests? flag. 
* gnu/packages/python-science.scm (python-vedo)[arguments]: Adjust
custom 'check' phase to honor the #:tests? flag. Also remove its
trailing boolean.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:06 +02:00
Paul A. Patience
b7d2644cd0
gnu: fenics: Fix sanity check. 
* gnu/packages/simulation.scm (fenics)[arguments]: Relax pybind11
requirement to appease the sanity check.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:06 +02:00
Paul A. Patience
9d5160bc8a
gnu: fenics: Honor #:tests? flag. 
* gnu/packages/simulation.scm (fenics)[arguments]: Adjust custom 'check'
phase to honor the #:tests? flag.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:06 +02:00
Paul A. Patience
69505bec93
gnu: fenics-dolfin: Honor #:tests? flag. 
* gnu/packages/simulation.scm (fenics-dolfin)[source]: Remove trailing
boolean.
[arguments]: Adjust custom 'check' phase to honor the #:tests? flag. While
here, remove trailing booleans.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:06 +02:00
Ludovic Courtès
a2d44231ea
gnu: Add Guix-Modules. 
* gnu/packages/package-management.scm (guix-modules): New variable.
 2022-05-06 15:23:05 +02:00
Guillaume Le Vaillant
5e27c54e08
gnu: monero-gui: Update to 0.17.3.2. 
* gnu/packages/finance.scm (monero-gui): Update to 0.17.3.2.
 2022-05-06 15:08:41 +02:00
Guillaume Le Vaillant
4188d211c7
gnu: monero: Update to 0.17.3.2. 
* gnu/packages/finance.scm (monero): Update to 0.17.3.2.
  [source]: Remove obsolete part of snippet.
  [arguments]: Remove trailing booleans.
 2022-05-06 15:08:41 +02:00
Jan (janneke) Nieuwenhuizen
53628d6e3b
gnu: Add dezyne. 
* gnu/packages/dezyne.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2022-05-06 14:39:50 +02:00
Jan (janneke) Nieuwenhuizen
984add419c
gnu: mescc-tools: Update supported-systems. 
* gnu/packages/mes.scm (mescc-tools)[supported-systems]: Add riscv32-linux,
riscv64-linux, remove powerpc64le-linux.
 2022-05-06 14:39:45 +02:00
Efraim Flashner
22b794a4a7
gnu: links: Use gexps. 
* gnu/packages/web-browsers.scm (links)[arguments]: Rewrite using gexps.
 2022-05-06 14:36:08 +03:00
Efraim Flashner
d540c6792b
gnu: links: Remove input labels. 
* gnu/packages/web-browsers.scm (links)[inputs]: Remove input labels.
 2022-05-06 14:36:08 +03:00
Efraim Flashner
1123da369d
gnu: links: Use configure-flags. 
* gnu/packages/web-browsers.scm (links)[arguments]: Add configure-flags
field. Adjust custom 'configure phase to use configure-flags.
 2022-05-06 14:36:08 +03:00
Efraim Flashner
5cf81294c0
gnu: links: Update to 2.26. 
* gnu/packages/web-browsers.scm (links): Update to 2.26.
 2022-05-06 14:36:07 +03:00
Efraim Flashner
166e0dfc44
gnu: ncdu-2: Update to 2.1.2. 
* gnu/packages/ncdu.scm (ncdu-2): Update to 2.1.2.
 2022-05-06 14:36:07 +03:00
Ricardo Wurmus
549e478f23
gnu: Add python-ipydatawidgets. 
* gnu/packages/jupyter.scm (python-ipydatawidgets): New variable.
 2022-05-06 13:02:59 +02:00
Ricardo Wurmus
221bf543e8
gnu: Add python-xyzservices. 
* gnu/packages/python-xyz.scm (python-xyzservices): New variable.
 2022-05-06 13:02:59 +02:00
Ricardo Wurmus
0d73287d97
gnu: Add python-mercantile. 
* gnu/packages/python-xyz.scm (python-mercantile): New variable.
 2022-05-06 13:02:59 +02:00
Ricardo Wurmus
ea3cfeb665
gnu: Add python-ipympl. 
* gnu/packages/jupyter.scm (python-ipympl): New variable.
 2022-05-06 13:02:58 +02:00
Ricardo Wurmus
e47b080474
gnu: Add python-traittypes. 
* gnu/packages/python-science.scm (python-traittypes): New variable.
 2022-05-06 13:02:55 +02:00
Daniel Meißner
27fc4ae397
gnu: cava: Fix build failure 
* gnu/packages/audio.scm (cava)[source]: Remove bundled iniparser.
(cava)[inputs]: Add iniparser.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 10:32:06 +02:00
Daniel Meißner
de4e4506c1
gnu: cava: Use G-expressions. 
* gnu/packages/audio.scm (cava)[arguments]: Use G-expressions.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 10:32:06 +02:00
kiasoc5
253fc14777
gnu: nftables: Update to 1.0.2. 
* gnu/packages/patches/nftables-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/linux.scm (nftables): Update to 1.0.2.
[source]: Add patch.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 10:32:06 +02:00
Vincent Prat
9e630a362d
gnu: Add python-arpeggio. 
* gnu/packages/python-xyz.scm (python-arpeggio): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 10:32:06 +02:00
Michael Rohleder
7727757a73
gnu: ytfzf: Update to 2.3. 
* gnu/packages/patches/ytfzf-programs.patch,
* gnu/packages/patches/ytfzf-updates.patch: Delete patches.
* gnu/local.mk (dist_patch_DATA): Unregister them.
* gnu/packages/image-viewers.scm (ytfzf): Update to 2.3.
[source]: Delete patches.
[arguments]: Remove phase 'patch-script. Add phase 'install-addons,
'wrap-program.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 10:32:06 +02:00
Ludovic Courtès
3d05105705
gnu: slurm: Add 21.08.8. 
* gnu/packages/parallel.scm (slurm): Update to 21.08.8.
(slurm-20.11): New variable.
 2022-05-06 10:32:05 +02:00
Ludovic Courtès
c018871c04
gnu: slurm: Update to 20.11.9 [fixes CVE-2022-{29500,29501,29502}]. 
* gnu/packages/parallel.scm (slurm): Update to 20.11.9.
 2022-05-06 10:32:05 +02:00
Ricardo Wurmus
a2fb35e43d
gnu: python-ipython: Add missing input. 
* gnu/packages/python-xyz.scm (python-ipython)[propagated-inputs]: Add
python-decorator.
 2022-05-06 10:15:04 +02:00
Ricardo Wurmus
ce1746819b
gnu: python-traitlets: Update to 5.1.1. 
* gnu/packages/python-xyz.scm (python-traitlets): Update to 5.1.1.
[propagated-inputs]: Remove python-ipython-genutils, python-decorator, and
python-six.
 2022-05-06 10:15:04 +02:00
Ricardo Wurmus
471f650498
gnu: Add python-kneed. 
* gnu/packages/python-xyz.scm (python-kneed): New variable.
 2022-05-06 10:15:04 +02:00
Ricardo Wurmus
b4da7c2133
gnu: Add python-databases. 
* gnu/packages/databases.scm (python-databases): New variable.
 2022-05-06 10:15:04 +02:00
Ricardo Wurmus
43992cdbea
gnu: python-anyio: Update to 3.5.0. 
* gnu/packages/python-xyz.scm (python-anyio): Update to 3.5.0.
[arguments]: Remove phase 'fix-compatibility; disable one more test.
[propagated-inputs]: Add python-contextvars and python-dataclasses.
[native-inputs]: Add python-contextlib2 and python-trio; remove
python-iniconfig.
 2022-05-06 10:15:04 +02:00
Ricardo Wurmus
b95e3dc17c
gnu: python-multipart: Fix test failure due to PyYAML 6. 
* gnu/packages/python-xyz.scm (python-multipart)[arguments]: Patch instance of
yaml.load.
 2022-05-06 10:15:00 +02:00
Foo Chuan Wei
312879fddc
gnu: Add byacc. 
* gnu/packages/c.scm (byacc): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-05 23:56:58 +02:00
Ludovic Courtès
0780164f1f
gnu: b4: Update to 0.8.0. 
* gnu/packages/version-control.scm (b4): Update to 0.8.0.
 2022-05-05 23:56:58 +02:00
Pierre-Antoine Bouttier
6829d61bc5
gnu: Add n2p2. 
* gnu/packages/maths.scm (n2p2): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-05 23:56:58 +02:00
Jonathan Brielmaier
34dbbb9172
gnu: icedove: Update to 91.9.0 [fixes CVE-2022-1520]. 
* gnu/packages/gnuzilla.scm (icedove): Update to 91.9.0.
 2022-05-05 23:09:48 +02:00
Andreas Enge
d809e71df2
gnu: python-pari-jupyter: Update to 1.4.1. 
* gnu/packages/python-xyz.scm (python-pari-jupyter): Update to 1.4.1.
  [home-page]: Update after maintainer change.
 2022-05-05 16:14:43 +02:00
Andreas Enge
a1b0fc8133
gnu: cm: Update to 0.4.0. 
* gnu/packages/algebra.scm (cm): Update to 0.4.0.
 2022-05-05 16:10:16 +02:00
Marius Bakke
b80ca672de
gnu: ungoogled-chromium: Update to 101.0.4951.54-1. 
* gnu/packages/chromium.scm (%chromium-version): Set to 101.0.4951.54.
(%ungoogled-origin, ungoogled-chromium): Update hashes.
 2022-05-03 22:35:12 +02:00
Mark H Weaver
9916933a04
gnu: icecat: Update to 91.9.0-guix0-preview1 [security fixes]. 
Includes fixes for CVE-2022-29909, CVE-2022-29911, CVE-2022-29912,
CVE-2022-29914, CVE-2022-29916, and CVE-2022-29917.

* gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.
 2022-05-03 14:56:54 -04:00
Paul A. Patience
8b2d266607
gnu: dealii: Update to 9.3.3. 
* gnu/packages/maths.scm (dealii): Update to 9.3.3.
* gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch:
Delete file.
* gnu/packages/patches/dealii-fix-sundials.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:28 +02:00
Paul A. Patience
240b604eda
gnu: dealii: Add SUNDIALS dependency. 
* gnu/packages/maths.scm (dealii)[propagated-inputs]: Add sundials-5.
Reformat list to clarify comment.
(dealii-openmpi)[propagated-inputs]: Add sundials-openmpi-5.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:28 +02:00
Paul A. Patience
d34f941c33
gnu: dealii-openmpi: Remove input labels. 
* gnu/packages/maths.scm (dealii-openmpi)[inputs]: Remove labels.
[propagated-inputs]: Same.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:28 +02:00
Paul A. Patience
e131f705dd
gnu: dealii: Remove trailing booleans. 
* gnu/packages/maths.scm (dealii)[snippet]: Remove trailing boolean (and
therefore the 'begin').
[native-inputs, inputs]: Reindent.
[arguments]<#:phases>: Remove trailing boolean.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:28 +02:00
Paul A. Patience
e648957b7b
gnu: sundials: Add 5.8.0. 
* gnu/packages/maths.scm (sundials-5, sundials-openmpi-5): New
variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:27 +02:00
Paul A. Patience
d1a6a795b3
gnu: sundials: Update to 6.2.0. 
* gnu/packages/maths.scm (sundials): Update to 6.2.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:27 +02:00
Paul A. Patience
4c509a73b7
gnu: sundials-openmpi: Add HYPRE dependency. 
* gnu/packages/maths.scm (sundials-openmpi)[propagated-inputs]: Add
hypre-openmpi.
[arguments]<#:configure-flags>: Add -DENABLE_HYPRE, -DHYPRE_INCLUDE_DIR
and -DHYPRE_LIBRARY_DIR.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:27 +02:00
Paul A. Patience
0d3c2c9543
gnu: sundials: Fix various issues. 
This commit fixes various issues. First, some of SUNDIALS's CMake
variables were renamed at some point between 5.2.0 and 5.7.0, in
particular KLU_ENABLE, which was changed to ENABLE_KLU. Since
sundials-julia is essentially SUNDIALS 5.2.0, its configure flags need
to be different from those of the sundials package. Second, commit
61bcd648ca, which updated SUNDIALS to
6.1.1, accidentally completely disabled PETSc support for
sundials-openmpi (PETSc is supported only with MPI) by removing the
relevant configure flags. Third, SUNDIALS's default index size is
64 bits, but PETSc's is 32 bits, and they need to be the same; this
issue is discussed in the next three paragraphs.

The default index size in SUNDIALS 3.1.1 (which was the sundials
package's version previous to the aforementioned commit) was also
64 bits (though it was configured through the SUNDIALS_INDEX_TYPE CMake
variable, which could take the values INT64_T or INT32_T), but
SUNDIALS's configure script didn't warn of any incompatibility with
PETSc's 32-bit indices. I don't know if this was an accidental omission
from the configure script or if SUNDIALS's index size didn't have to
correspond to PETSc's at the time.

Keeping 64-bit indices in SUNDIALS would require adding a package for
PETSc with 64-bit indices (using the --with-64-bit-indices configure
flag), possibly named petsc64-openmpi (to follow the style of the SCOTCH
packages, i.e., scotch, scotch32, etc., though there the unadorned
package name represents the 64-bit version, unlike the unadorned petsc),
which would in turn require a package for METIS with 64-bit
indices (using IDXTYPEWIDTH=64). However, SUNDIALS is an optional
dependency of deal.II, both of which have PETSc as an optional
dependency, and deal.II's index size (which defaults to 32 bits) must
match PETSc's. In other words, the current deal.II package can build
with SUNDIALS only if SUNDIALS has 32-bit indices.

Furthermore, users needing 64-bit indices in SUNDIALS probably also need
them in PETSc and other libraries. If and when 64-bit indices are deemed
necessary, we can add all the package variations at once (for SUNDIALS,
PETSc, METIS, deal.II and any others).

* gnu/packages/maths.scm (sundials)[source]: Reuse version in URL.
[native-inputs]: Capitalize and punctuate comment.
[inputs]: Remove petsc, now unnecessary gfortran, and obsolete
comment. Move TODO item to sundials-openmpi.
[arguments]<#:configure-flags>: Add -DSUNDIALS_INDEX_SIZE=32 to match
PETSc's 32-bit indices. Remove obsolete -DEXAMPLES_ENABLE_F77,
-DEXAMPLES_ENABLE_F90 and -DFCMIX_ENABLE. Mention new but currently
unusable -DBUILD_FORTRAN_MODULE_INTERFACE and
-DEXAMPLES_ENABLE_F2003. Rename KLU_ENABLE to ENABLE_KLU.
(sundials-openmpi): Use package/inherit.
[inputs]: Move openmpi and petsc-openmpi from here...
[propagated-inputs]: ...to here. Clarify comment.
[arguments]<#:configure-flags>: Add -DENABLE_PETSC and -DPETSC_DIR, the
equivalents of which were accidentally removed in commit
61bcd648ca.
<#:phases>: Replace a tab with spaces.
[synopsis]: Replace OpenMPI with MPI to conform to other package
synopses.
(sundials-julia)[inputs]: Add gfortran.
[arguments]<#:configure-flags>: Set only, and manually, -DCMAKE_C_FLAGS,
-DSUNDIALS_INDEX_SIZE, -DKLU_ENABLE, -DKLU_INCLUDE_DIR,
-DKLU_LIBRARY_DIR and -DLAPACK_ENABLE instead of inheriting from the
sundials package, because some of SUNDIALS's CMake variables have
changed name.
[synopsis]: Capitalize “LAPACK”.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:27 +02:00
Paul A. Patience
a3b6a4df6c
gnu: petsc-openmpi: Fix header inclusions. 
* gnu/packages/maths.scm (petsc-openmpi)[arguments]: Add
'patch-header-inclusions' phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:27 +02:00
Ludovic Courtès
7855a9366b
services: pipefs: Correctly handle lack of extensions. 
Previously, in the absence of extensions of 'pipefs-service-type', we'd
get a wrong-type-arg exception while folding services:

  In gnu/services/nfs.scm:
     134:37  1 (_ #<<pipefs-configuration> mount-point: "/var/lib/nfs…> …)
  In ice-9/boot-9.scm:
    1685:16  0 (raise-exception _ #:continuable? _)
  In procedure car: Wrong type argument in position 1 (expecting pair): ()

* gnu/services/nfs.scm (pipefs-service-type)[extend]: Gracefully handle
the case where VALUES is the empty list, as done in 'gss-service-type'.
 2022-05-03 18:02:27 +02:00
Leo Famulari
654f878f0b
gnu: Mutt: Update to 2.2.4. 
* gnu/packages/mail.scm (mutt): Update to 2.2.4.
 2022-05-02 19:31:42 -04:00
Leo Famulari
39bdf71db1
gnu: linux-libre 4.19: Update to 4.19.241. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.241.
(linux-libre-4.19-pristine-source): Update hash.
 2022-05-02 18:57:38 -04:00
Leo Famulari
ac2857e042
gnu: linux-libre 5.15: Update to 5.15.37. 
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.37.
(linux-libre-5.15-pristine-source): Update hash.
 2022-05-02 18:57:38 -04:00
Jan (janneke) Nieuwenhuizen
6b588da368
gnu: mes: Update to 0.24. 
* gnu/packages/mes.scm (mes-next)[source]: Update to 0.24.
[native-inputs]: Add m2-planet.
 2022-05-02 19:07:06 +02:00
Jan (janneke) Nieuwenhuizen
c14f1e3195
gnu: m2-planet: Update to 1.9.0. 
* gnu/packages/mes.scm (m2-planet): Update to 1.9.0.
 2022-05-02 19:07:04 +02:00
Jan (janneke) Nieuwenhuizen
954ff74bc8
gnu: mescc-tools: Update to 1.4.0. 
* gnu/packages/mes.scm (mescc-tools): Update to 1.4.0.
 2022-05-02 19:07:02 +02:00
Konstantinos Agiannis
f49b1a10f3
gnu: Add xschem. 
* gnu/packages/engineering.scm (xschem): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 18:03:06 +02:00
Ludovic Courtès
2a37f174be
services: Make sure Shepherd destructors match constructors. 
This is a followup to b06ecc5751,
211fe3f66e, and
fd57ce267c.

* gnu/services/base.scm (guix-publish-shepherd-service): Change 'stop'
method to use 'make-systemd-destructor' when 'make-systemd-constructor'
is used.
* gnu/services/dict.scm (dicod-shepherd-service): Change 'stop' method
to use 'make-inetd-destructor' when 'make-inetd-constructor' is used.
* gnu/services/messaging.scm (bitlbee-shepherd-service): Likewise.
 2022-05-02 17:57:30 +02:00
Ricardo Wurmus
39d6c13fda
gnu: python-hic2cool: Fix build. 
* gnu/packages/bioinformatics.scm (python-hic2cool)[arguments]: Fix
incompatibility with h5py 3; disable two tests.
 2022-05-02 17:33:31 +02:00
Mădălin Ionel Patrașcu
7494f4b4ab
gnu: Add r-agimicrorna. 
* gnu/packages/bioconductor.scm (r-agimicrorna): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-05-02 15:23:50 +02:00
Mădălin Ionel Patrașcu
9c19db8c1d
gnu: Add r-adductomicsr. 
* gnu/packages/bioconductor.scm (r-adductomicsr): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-05-02 15:17:28 +02:00
Mădălin Ionel Patrașcu
495bc9f962
gnu: Add r-orgmassspecr. 
* gnu/packages/cran.scm (r-orgmassspecr): New variable.
 2022-05-02 15:17:28 +02:00
Mădălin Ionel Patrașcu
290934c8fc
gnu: Add r-adductdata. 
* gnu/packages/bioconductor.scm (r-adductdata): New variable.
 2022-05-02 15:17:28 +02:00
Felix Gruber
f455c1e313
gnu: Add python-scrapy. 
* gnu/packages/python-web.scm (python-scrapy): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:46 +02:00
Felix Gruber
d9a7f652e2
gnu: Add python-itemloaders. 
* gnu/packages/python-xyz.scm (python-itemloaders): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:46 +02:00
Felix Gruber
76b6337650
gnu: Add python-parsel. 
* gnu/packages/python-web.scm (python-parsel): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:46 +02:00
Felix Gruber
d219d48cce
gnu: Add python-protego. 
* gnu/packages/python-web.scm (python-protego): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:46 +02:00
Felix Gruber
c0c16d6b84
gnu: Add python-itemadapter. 
* gnu/packages/python-xyz.scm (python-itemadapter): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:45 +02:00
Felix Gruber
fce913281f
gnu: Add python-queuelib. 
* gnu/packages/python-xyz.scm (python-queuelib): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:45 +02:00
Felix Gruber
f728d1dcd2
gnu: Add python-pydispatcher. 
* gnu/packages/python-xyz.scm (python-pydispatcher): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:45 +02:00
Felix Gruber
919fdd6fcc
gnu: Add python-sybil. 
* gnu/packages/python-check.scm (python-sybil): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:45 +02:00
Greg Hogan
8ffd8fc64e
gnu: bear: Update to 3.0.19. 
* gnu/packages/build-tools.scm (bear): Update to 3.0.19.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:45 +02:00
Greg Hogan
9bf9da2571
gnu: spdlog: Update to 1.10.0. 
* gnu/packages/logging.scm (spdlog): Update to 1.10.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:45 +02:00
Greg Hogan
c152174ca2
gnu: fmt: Update to 8.1.1. 
* gnu/packages/pretty-print.scm (fmt): Update to 8.1.1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:44 +02:00
Paul A. Patience
67b10f18c7
gnu: apl: Use G-expressions. 
* gnu/packages/apl.scm (apl)[arguments]: Use G-expressions.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:44 +02:00
Paul A. Patience
fe6ba5e902
gnu: apl: Remove input labels. 
* gnu/packages/apl.scm (apl)[inputs]: Remove labels and sort.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:44 +02:00
Paul A. Patience
94b1905580
gnu: apl: Update to 1.8-r1550. 
This commit fixes a failing build caused by -Werror (the configure
script no longer sets the -Werror compilation flag).

* gnu/packages/apl.scm (apl): Update to 1.8-r1550.
[arguments]: Add 'fix-configure' phase.
[license]: Prefix with 'license:'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:44 +02:00
Niklas Eklund
35e5d2ce56
gnu: Add emacs-git-email. 
* gnu/packages/emacs-xyz.scm (emacs-git-email): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:44 +02:00
kiasoc5
75b7f495d0
gnu: ugrep: Update to 3.7.9. 
* gnu/packages/search.scm (ugrep): Update to 3.7.9.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:44 +02:00
Greg Hogan
a8fde99e80
gnu: aws-sdk-cpp: Remove openssl input. 
* gnu/packages/cpp.scm (aws-sdk-cpp):
[inputs]: Remove openssl.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:43 +02:00
Greg Hogan
af856afb6c
gnu: s2n: Link to aws-lc as libcrypto dependency. 
* gnu/packages/tls.scm (s2n):
[arguments]: Fix for openssl as replacement input for aws-lc.
[propagated-inputs]: Add aws-lc and remove openssl.
[supported-systems]: Only support x86_64-linux.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:43 +02:00
Greg Hogan
a5a408c3a7
gnu: aws-lc: Fix checksum and enable tests. 
* gnu/packages/tls.scm (aws-lc):
[source]: Fix checksum.
[arguments]: Enable tests.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:43 +02:00
Greg Hogan
fec71efeae
gnu: aws-crt-cpp: Fix comment formatting. 
* gnu/packages/cpp.scm (aws-crt-cpp): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:43 +02:00
Greg Hogan
a822f3e2d0
gnu: aws-c-mqtt: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-mqtt): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:43 +02:00
Greg Hogan
b62d4872ba
gnu: aws-c-s3: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-s3): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:43 +02:00
Greg Hogan
d62c101991
gnu: aws-c-auth: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-auth): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:43 +02:00
Greg Hogan
b8c4bb3e0d
gnu: aws-c-compression: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-compression): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:42 +02:00
Greg Hogan
d7c8a83549
gnu: aws-c-http: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-http): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:42 +02:00
Greg Hogan
e8f2855d73
gnu: aws-c-sdkutils: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-sdkutils): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:42 +02:00
Greg Hogan
c7805de435
gnu: aws-c-cal: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-cal): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:42 +02:00
Greg Hogan
d230c67068
gnu: aws-c-io: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-io): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:42 +02:00
Greg Hogan
4dbb1520e2
gnu: aws-c-event-stream: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-event-stream): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:42 +02:00
Greg Hogan
a9b4d69c9c
gnu: aws-checksums: Fix comment formatting. 
* gnu/packages/c.scm (aws-checksums): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:42 +02:00
Greg Hogan
acbf5b1022
gnu: aws-c-common: Only support i686 and x86_64. 
* gnu/packages/c.scm (aws-c-common):
[supported-systems]: Only support i686-linux and x86_64-linux.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:41 +02:00
Ludovic Courtès
6075d25143
services: bitlbee: Preserve 'PURPLE_PLUGIN_PATH'. 
Fixes a regression introduced in
211fe3f66e whereby, in inetd mode, and
when using 'bitlbee-purple', libpurple plugins would not be found.

* gnu/services/messaging.scm (bitlbee-shepherd-service): Pass
 #:preserved-environment-variables to 'least-authority-wrapper'.
 2022-05-02 15:14:41 +02:00
Ricardo Wurmus
b1dd32d8e3
gnu: htslib-for-stringtie: Inherit from htslib-1.12. 
* gnu/packages/bioinformatics.scm (htslib-for-stringtie): Inherit from
htslib-1.12.
 2022-05-02 14:35:26 +02:00
Ricardo Wurmus
4571b218b5
gnu: Remove python-xlrd-1. 
* gnu/packages/python-xyz.scm (python-xlrd-1): Remove variable.
 2022-05-02 13:49:57 +02:00
Ricardo Wurmus
4642a50d52
gnu: Remove python-cytoolz-for-cooler. 
* gnu/packages/python-xyz.scm (python-cytoolz-for-cooler): Remove variable.
 2022-05-02 13:35:03 +02:00
Ricardo Wurmus
5caad9f252
gnu: python-cooler: Use more recent cytoolz. 
* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace
python-cytoolz-for-cooler with python-cytoolz.
 2022-05-02 13:33:16 +02:00
Ricardo Wurmus
9dafaf1635
gnu: python-anndata: Remove python-xlrd-1. 
* gnu/packages/python-xyz.scm (python-anndata)[propagated-inputs]: Remove
python-xlrd-1.
 2022-05-02 12:39:02 +02:00
Marius Bakke
098f2eea33
gnu: ungoogled-chromium: Update to 101.0.4951.41-1. 
* gnu/packages/chromium.scm (%preserved-third-party-files): Include bundled
Vulkan headers.
(%chromium-version): Set to 101.0.4951.41.
(%debian-revision): Set to debian/101.0.4951.41-2.
(%debian-patches): Add one new patch.
(%ungoogled-origin, ungoogled-chromium): Update hashes.
* gnu/packages/patches/ungoogled-chromium-system-nspr.patch: Refresh.
 2022-05-01 22:28:31 +02:00
Ludovic Courtès
fee06d5aaa
services: opendht: Use 'least-authority-wrapper'. 
* gnu/services/networking.scm (opendht-configuration->command-line-arguments):
Use 'least-authority-wrapper'.
(opendht-shepherd-service): Use 'make-forkexec-constructor'.
 2022-05-01 21:30:36 +02:00
Ludovic Courtès
dac4efc466
services: quassel: Use 'least-authority-wrapper'. 
* gnu/services/messaging.scm (quassel-shepherd-service): Use
'least-authority-wrapper' instead of
'make-forkexec-constructor/container'.
 2022-05-01 21:30:36 +02:00
Ludovic Courtès
53dbc6fd9a
services: wesnothd: Use 'least-authority-wrapper'. 
* gnu/services/games.scm (wesnothd-shepherd-service): Use
'least-authority-wrapper' instead of
'make-forkexec-constructor/container'.
 2022-05-01 21:30:36 +02:00
Ludovic Courtès
19df5f2423
services: wesnothd: Grant write access to /var/run/wesnothd. 
* gnu/services/games.scm (wesnothd-shepherd-service): Augment 'modules'
field.  Pass #:mappings argument to 'make-forkexec-constructor/container'.
(wesnothd-activation): New variable.
(wesnothd-service-type): Extend ACTIVATION-SERVICE-TYPE.
 2022-05-01 21:30:36 +02:00
Ludovic Courtès
f5ef68ba98
services: ipfs: Use 'least-authority-wrapper'. 
* gnu/services/networking.scm (ipfs-binary): Call
'least-authority-wrapper'.
(%ipfs-home-mapping): Remove surrounding gexp.
(ipfs-shepherd-service)[exec-command]: New procedure.
[ipfs-config-command, set-config!-gexp, shepherd&co]
[container-gexp, container-script]: Remove.
[inner-gexp]: Use 'exec-command'.
 2022-05-01 21:30:35 +02:00
Ludovic Courtès
211fe3f66e
services: bitlbee: Use 'make-inetd-constructor'. 
* gnu/services/messaging.scm (bitlbee-shepherd-service): Add call to
'least-authority-wrapper'.  In 'start' method, use
'make-inetd-constructor' when available.
* gnu/tests/messaging.scm (run-bitlbee-test)["valid PID"]: Remove test.
 2022-05-01 21:30:35 +02:00
Ludovic Courtès
fd57ce267c
services: dicod: Use 'make-inetd-constructor'. 
* gnu/services/dict.scm (dicod-shepherd-service): Use
'make-inetd-constructor' in the 'start' method when available.
 2022-05-01 21:30:35 +02:00