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Petr Hodina 2f2b4a0f81
gnu: Add rust-spotify-tui-0.25. 
* gnu/packages/crates-io.scm (rust-spotify-tui-0.25): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:29 +01:00
Petr Hodina f15b6ae03a
gnu: rust-arboard-1: Update to 1.2.1. 
* gnu/packages/crates-io.scm (rust-arboard-1): Update to 1.2.1.
  [arguments](cargo-inputs): Add rust-env-logger-0.8, rust-simple-logger-1,
  rust-wl-clipboard-rs-0.4 and rust-x11rb-0.8. Remove rust-xcb-0.9.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:28 +01:00
Petr Hodina 04cb4fcb5e
gnu: Add rust-wl-clipboard-rs-0.4. 
* gnu/packages/crates-io.scm (rust-wl-clipboard-rs-0.4): New variable.
* gnu/packages/patches/rust-wl-clipboard-rs-newer-wl.patch: New file.
* gnu/local.mk: Add patch.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:28 +01:00
Petr Hodina cf42c98929
gnu: Add rust-stderrlog-0.4. 
* gnu/packages/crates-io.scm (rust-stderrlog-0.4): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:27 +01:00
Petr Hodina cbd745912c
gnu: Add rust-thread-local-0.3.4. 
* gnu/packages/crates-io.scm (rust-thread-local-0.3.4): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:27 +01:00
Petr Hodina fe8f7651d1
gnu: Add rust-simple-logger-1. 
* gnu/packages/crates-io.scm (rust-simple-logger-1): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:26 +01:00
Petr Hodina 149dd92888
gnu: Add rust-atty-0.2.11. 
* gnu/packages/crates-io.scm (rust-atty-0.2.11): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:26 +01:00
Petr Hodina 1c7305adff
gnu: rust-anyhow-1: Update to 1.0.46. 
* gnu/packages/crates-io.scm (rust-anyhow-1): Update to 1.0.46.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:26 +01:00
Petr Hodina bff2009149
gnu: Add rust-tree-magic-0.2. 
* gnu/packages/crates-io.scm (rust-tree-magic-0.2): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:25 +01:00
Petr Hodina 35cba1790f
gnu: Add rust-x11rb-0.8. 
* gnu/packages/crates-graphics.scm (rust-x11rb-0.8): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:25 +01:00
Petr Hodina f6f285270a
gnu: Add rust-winapi-wsapoll-0.1. 
* gnu/packages/crates-io.scm (rust-winapi-wsapoll-0.1): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:24 +01:00
Petr Hodina 4f38c1f57e
gnu: Add rust-rspotify-0.10. 
* gnu/packages/crates-io.scm (rust-rspotify-0.10): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:24 +01:00
Petr Hodina 76eadbeb89
gnu: Add rust-derive-builder-0.7. 
* gnu/packages/crates-io.scm (rust-derive-builder-0.7): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:24 +01:00
Petr Hodina a4d35d0c78
gnu: Add rust-derive-builder-core-0.5. 
* gnu/packages/crates-io.scm (rust-derive-builder-core-0.5): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:23 +01:00
Petr Hodina 39e38804f2
gnu: Add rust-dotenv-0.13 
* gnu/packages/crates-io.scm (rust-dotenv-0.13): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:23 +01:00
Petr Hodina d8c0d955a4
gnu: Add rust-tui-0.16. 
* gnu/packages/crates-io.scm (rust-tui-0.16): New variable.
 (rust-tui-0.15): Inherit from above.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:22 +01:00
Petr Hodina ae01172fb3
gnu: Add rust-argh-0.1. 
* gnu/packages/crates-io.scm (rust-argh-0.1): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:22 +01:00
Petr Hodina 2e625d0b2d
gnu: Add rust-argh-derive-0.1. 
* gnu/packages/crates-io (rust-argh-derive-0.1): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:21 +01:00
Petr Hodina dfdcd375a8
gnu: Add rust-argh-shared-0.1. 
* gnu/packages/crates-io.scm (rust-argh-shared-0.1): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-10 00:11:21 +01:00
Julien Lepiller 4665e6a73b
gnu: opam: Update to 2.1.2. 
* gnu/packages/ocaml.scm (opam): Update to 2.1.2.
 2021-12-09 23:59:21 +01:00
Efraim Flashner 77ea796d1b
gnu: pplacer: Fix build. 
* gnu/packages/bioinformatics.scm (pplacer)[inputs]: Replace gsl with
gsl-static.
* gnu/packages/ocaml.scm (ocaml4.07-gsl-1)[inputs]: Same.
 2021-12-09 23:17:26 +02:00
Efraim Flashner 1da7f9089f
gnu: Add gsl-static. 
* gnu/packages/maths.scm (gsl-static): New variable.
 2021-12-09 23:17:26 +02:00
Efraim Flashner 1e81140cb5
gnu: python-dendropy: Skip additional test. 
* gnu/packages/bioinformatics.scm (python-dendropy)[arguments]: Adjust
custom 'skip-broken-tests phase to skip additional test.
 2021-12-09 22:43:42 +02:00
Ricardo Wurmus 13bc332ed5
gnu: mumi: Update to 0.0.1-6.8a45281. 
* gnu/packages/mail.scm (mumi): Update to 0.0.1-6.8a45281.
[arguments]: Remove trailing #T.
 2021-12-09 19:17:22 +01:00
Ricardo Wurmus 0e8826824c
gnu: python-rich: Remove optional input ipywidgets. 
* gnu/packages/python-xyz.scm (python-rich)[propagated-inputs]: Remove
python-ipywidgets.
 2021-12-09 19:17:21 +01:00
Ricardo Wurmus 4709decb45
gnu: r-minimal: Remove extraneous references. 
* gnu/packages/statistics.scm (r-minimal)[arguments]: Remove references to
native build-time tools.
 2021-12-09 19:17:16 +01:00
Marius Bakke d974b3f860
gnu: uBlock Origin: Update to 1.39.2. 
* gnu/packages/browser-extensions.scm (ublock-origin): Update to 1.39.2.
 2021-12-09 17:39:29 +01:00
Marius Bakke 4cb5f0daf2
gnu: ungoogled-chromium: Update to 96.0.4664.93-1. 
* gnu/packages/chromium.scm (%chromium-version): Set to 96.0.4664.93.
(%ungoogled-origin, ungoogled-chromium): Update hashes.
 2021-12-09 17:39:29 +01:00
Efraim Flashner f0cc0e8f30
gnu: imp: Build with default cmake. 
* gnu/packages/bioinformatics.scm (imp)[arguments]: Remove cmake flag.
 2021-12-09 14:39:22 +02:00
Ricardo Wurmus 2648d3207f
gnu: repeat-masker: Update to 4.1.2-p1. 
* gnu/packages/bioinformatics.scm (repeat-masker): Update to 4.1.2-p1.
 2021-12-09 12:10:18 +01:00
Ricardo Wurmus 0bf3c9abaa
gnu: metabat: Update to 2.15. 
* gnu/packages/bioinformatics.scm (metabat): Update to 2.15.
[source]: Remove patch.
[build-system]: Use cmake-build-system.
[arguments]: Adjust to new build system.
* gnu/packages/patches/metabat-fix-compilation.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-12-09 11:50:10 +01:00
Ricardo Wurmus ab445eb4b7
gnu: python2-scikit-learn: Disable one more test. 
* gnu/packages/machine-learning.scm (python2-scikit-learn)[arguments]: Do not
inherit; remove obsolete 'make-files-writable phase; disable one more failing
test in 'check phase.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus 1c7914009a
gnu: seek: Update to 1-1.196ed4c. 
* gnu/packages/bioinformatics.scm (seek): Update to 1-1.196ed4c.
[source]: Fetch from github.
[build-system]: Use cmake-build-system.
[arguments]: Remove all custom phases; replace 'check phase; disable tests;
set configure flags.
[inputs]: Add apache-thrift:include, apache-thrift:lib, and python.
[native-inputs]: Remove autoconf, automake, and perl; add pkg-config.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus 4fb363c906
gnu: libsvm: Install header and library. 
* gnu/packages/machine-learning.scm (libsvm)[arguments]: Add build phase
'build-lib; also install header file and shared library in the 'install phase.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus 26e26bc819
gnu: miso: Update to 0.5.4-1.b714021. 
* gnu/packages/bioinformatics.scm (miso): Update to 0.5.4-1.b714021.
[source]: Fetch via git; simplify snippet.
[inputs]: Replace samtools with samtools-1.2.
[home-page]: Update to new location.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus 0b8a75cc3a
gnu: Add samtools-1.2. 
* gnu/packages/bioinformatics.scm (samtools-1.2): New variable.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus f505f588a7
gnu: Add htslib-for-samtools-1.2. 
* gnu/packages/bioinformatics.scm (htslib-for-samtools-1.2): New variable.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus 3ebcd637a5
gnu: python2-scipy: Override native inputs. 
* gnu/packages/python-science.scm (python2-scipy)[native-inputs]: Override;
replace gfortran with gfortran-7; add gcc-7.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus 3cd37c94bd
gnu: python2-matplotlib: Fix mpl_toolkits module. 
* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Add phase
'create-init-file; restore 'sanity-check phase.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus b69156ef30
gnu: Add gfortran-7. 
* gnu/packages/gcc.scm (gfortran-7): New variable.
 2021-12-09 11:17:45 +01:00
jgart via Guix-patches via bfaf6c1801
gnu: emacs-evil-magit: Remove deprecated package. 
* gnu/packages/emacs-xyz.scm (emacs-evil-magit): Delete variable.

evil-magit has been consolidated into evil-collection. The package has been
removed from MELPA since February. See here:
<https://github.com/emacs-evil/evil-magit>.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-09 09:17:35 +01:00
Andrew Tropin 1490e02ea2
gnu: Add emacs-dpd. 
* gnu/packages/emacs-xyz.scm (emacs-dpd): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-09 09:13:33 +01:00
Petr Hodina 479742f195
gnu: valeronoi: Update to 0.1.6. 
* gnu/packages/engineering.scm (valeronoi): Update to 0.1.6.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-09 09:07:24 +01:00
terramorpha 38ea869b20
gnu: tiramisu: Update to 2.0.20211107. 
* gnu/packages/gnome-xyz.scm (tiramisu): Update to 2.0.20211107.
[native-inputs]: Add vala.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-12-08 23:10:25 -05:00
Leo Famulari 37186ec462
gnu: isc-dhcp: Update bundled BIND to 9.11.36 [fixes CVE-2021-25219]. 
* gnu/packages/admin.scm (isc-dhcp)[inputs]:
Update bundled BIND to 9.11.36.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2021-12-09 01:24:37 +01:00
Tobias Geerinckx-Rice 4ca0e9d5f7
gnu: bind: Update to 9.16.23 [fixes CVE-2021-25218, CVE-2021-25219]. 
* gnu/packages/dns.scm (isc-bind): Update to 9.16.23.
[source]: Add patch.
* gnu/packages/patches/bind-re-add-attr-constructor-priority.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2021-12-09 01:24:37 +01:00
Tobias Geerinckx-Rice e5e307b676
Revert "installer: Make LUKS2 the default format for encrypted devices" 
This reverts commit a82e9f45fd at the
author's request.  We are not quite ready to boot all resulting
systems.

See <https://logs.guix.gnu.org/guix/2021-12-08.log#231815>.
 2021-12-08 23:23:19 +01:00
Ludovic Courtès 95a4965f2d
gnu: python-slepc4py: Update to 3.16.1. 
This is a followup 5b4d1e57b6.

* gnu/packages/maths.scm (slepc-openmpi)[inputs]: Move ARPACK-NG-OPENMPI to...
[propagated-inputs]: ... here.
(python-slepc4py): Update to 3.16.1.
 2021-12-08 23:04:00 +01:00
Ludovic Courtès fe55ae488b
gnu: python-petsc4py: Update to 3.16.1. 
This is a followup to 07ac13a26a.

* gnu/packages/maths.scm (python-petsc4py): Update to 3.16.1.
 2021-12-08 22:59:44 +01:00
Ludovic Courtès 3b8825421b
gnu: geeqie: Fix X11 error at startup. 
Fixes <https://issues.guix.gnu.org/52089>.
Reported by Maxim Cournoyer <maxim.cournoyer@gmail.com>.
Patch provided by John Kehayias <john.kehayias@protonmail.com>.

* gnu/packages/patches/geeqie-clutter.patch: New file.
* gnu/packages/image-viewers.scm (geeqie)[sources]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2021-12-08 22:35:03 +01:00