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Author SHA1 Message Date
Leo Famulari
f08c7cb0c7
gnu: Python 3.9: Fix CVE-2021-3177. 
* gnu/packages/patches/python-3.9-CVE-2021-3177.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/python.scm (python-3.9)[source]: Use it.
 2021-02-19 17:58:54 -05:00
Ricardo Wurmus
f310b06685
gnu: nanopolish: Fix script wrapping. 
* gnu/packages/bioinformatics.scm (nanopolish)[arguments]: Fix wrap-programs
phase.
[inputs]: Add Guile for wrap-script; add bioperl and perl-getopt-long for Perl
scripts.
 2021-02-19 23:35:04 +01:00
Ricardo Wurmus
96193caaa1
gnu: python-scikit-learn: Update to 0.24.1. 
* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 0.24.1.
[propagated-inputs]: Add python-threadpoolctl.
(python2-scikit-learn)[inputs,native-inputs,propagated-inputs]: Do not
inherit these fields.
 2021-02-19 23:24:05 +01:00
Ricardo Wurmus
15c0cc4aa2
gnu: Add prinseq. 
* gnu/packages/bioinformatics.scm (prinseq): New variable.
 2021-02-19 23:14:59 +01:00
Ricardo Wurmus
113dabe831
gnu: Add perl-statistics-pca. 
* gnu/packages/perl.scm (perl-statistics-pca): New variable.
 2021-02-19 23:14:59 +01:00
Ricardo Wurmus
1c701708a7
gnu: Add perl-math-cephes. 
* gnu/packages/perl-maths.scm (perl-math-cephes): New variable.
 2021-02-19 23:14:56 +01:00
Leo Famulari
80986c6ab6
gnu: Add butt. 
* gnu/packages/audio.scm (butt): New variable.
 2021-02-19 16:51:17 -05:00
Leo Famulari
ffe4f87c87
gnu: Add xoscope. 
* gnu/packages/electronics.scm (xoscope): New variable.
 2021-02-19 15:45:18 -05:00
Leo Famulari
c35157f78e
gnu: Add comedilib. 
* gnu/packages/electronics.scm (comedilib): New variable.
 2021-02-19 15:45:18 -05:00
Leo Famulari
319470bb3b
gnu: Add GtkDatabox. 
* gnu/packages/gtk.scm (gtkdatabox): New variable.
 2021-02-19 15:45:18 -05:00
Mathieu Othacehe
e9bf511082
services: cuirass: Add "simple-cuirass-services". 
* gnu/services/cuirass.scm (<build-manifest>,
<simple-cuirass-configuration>): New records.
(build-manifest, build-manifest?, simple-cuirass-configuration,
simple-cuirass-configuration?, simple-cuirass-services): New procedures.
(%default-cuirass-config): New variable.
* gnu/tests/cuirass.scm (%cuirass-simple-test): New variable.
* doc/guix.texi (Continuous Integration): Document it.
 2021-02-19 20:10:09 +01:00
Mathieu Othacehe
25ad6e1d8e
tests: cuirass: Add an operating system argument. 
Rewrite so that "run-cuirass-test" takes an operating-system argument. This is
functionally equivalent.

* gnu/tests/cuirass.scm (%derivation-file, git-service, cow-service,
%cuirass-specs): New variables.
(cuirass-services): New procedure.
(run-cuirass-test): Add an "operating-system" argument.
(%cuirass-test): Adapt it.
(%cuirass-remote-test): Ditto.
 2021-02-19 20:10:08 +01:00
Mathieu Othacehe
f57b7cea74
tests: Export %simple-os. 
* gnu/tests.scm (%simple-os): Export it.
 2021-02-19 20:10:08 +01:00
Ricardo Wurmus
fceda92f86
gnu: Add perl-contextual-return. 
* gnu/packages/perl.scm (perl-contextual-return): New variable.
 2021-02-19 18:04:37 +01:00
Ricardo Wurmus
0d9c950269
gnu: Add perl-want. 
* gnu/packages/perl.scm (perl-want): New variable.
 2021-02-19 18:04:03 +01:00
Ricardo Wurmus
f3318fefe4
gnu: Add perl-math-matrixreal. 
* gnu/packages/perl-maths.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2021-02-19 17:57:43 +01:00
Ricardo Wurmus
80d3150c94
gnu: Add ngshmmalign. 
* gnu/packages/bioinformatics.scm (ngshmmalign): New variable.
 2021-02-19 17:24:52 +01:00
Maxim Cournoyer
8999d2b44c
gnu: python-locust: Update to 1.4.3. 
* gnu/packages/benchmark.scm (python-locust): Update to 1.4.3.
[phases]: Remove trailing #t.
{check}: Disable the 'test_html_report_option', 'test_custom_exit_code' and
'test_webserver' tests.
 2021-02-19 10:01:02 -05:00
Maxim Cournoyer
28a2c9c9e1
doc: Add an example of how the open file descriptors limit can be raised. 
* doc/guix.texi (Base Services)[pam-limits-service]: Add an example and
explanation of how the 'nofile', or open file descriptors value, can be
configured.
 2021-02-19 10:01:02 -05:00
Maxim Cournoyer
a386d29c18
gnu: python-psutil: Update to 5.8.0. 
* gnu/packages/python-xyz.scm (python-psutil): Update to 5.8.0.
[home-page]: Update.
[description]: Please lint and re-flow text.
 2021-02-19 10:01:01 -05:00
Maxim Cournoyer
5363d3751b
gnu: python-geventhttpclient: Adjust to build with updated gevent. 
* gnu/packages/python-web.scm (python-geventhttpclient): Delete trailing #t.
[phases]{fix-compatibility-issue}: New phase.
{check}: Adjust comment and remove the extraneous string-append.
 2021-02-19 10:01:01 -05:00
Maxim Cournoyer
c2baa33e4b
gnu: python-greenlet: Update to 1.0.0. 
* gnu/packages/python-xyz.scm (python-greenlet): Update to 1.0.0.
 2021-02-19 10:01:01 -05:00
Maxim Cournoyer
ae66756a69
gnu: python-gevent: Update to 21.1.2. 
* gnu/packages/python-xyz.scm (python-gevent): Update to 21.1.2.  Delete
trailing #t.
 2021-02-19 10:01:01 -05:00
Brice Waegeneire
8a452e156e
ui: Fix typo in description. 
* guix/ui.scm (switch-to-generation*): Fix typo in description.
 2021-02-19 13:35:01 +01:00
Sharlatan Hellseher
19e081138b
gnu: Add stackistry. 
* gnu/packages/astronomy.scm (stackistry): New variable.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-02-19 11:05:34 +01:00
Sharlatan Hellseher
87530f7b4d
gnu: Add libskry. 
* gnu/packages/astronomy.scm (libskry): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-02-19 11:05:34 +01:00
Sharlatan Hellseher
d6996fa052
gnu: Add python-astroalign. 
* gnu/packages/astronomy.scm (python-astroalign): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-02-19 11:05:34 +01:00
Sharlatan Hellseher
d1bd22b9fb
gnu: Add python-sep. 
* gnu/packages/astronomy.scm (python-sep): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-02-19 11:05:33 +01:00
Sharlatan Hellseher
56ec8d6281
gnu: Add python-pyerfa. 
* gnu/packages/astronomy.scm (python-pyerfa): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-02-19 11:05:33 +01:00
Sharlatan Hellseher
4fac8b8f9b
gnu: Add erfa. 
* gnu/packages/astronomy.scm (erfa): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-02-19 11:05:33 +01:00
Sharlatan Hellseher
c1563fc116
gnu: Add qfits. 
* gnu/packages/astronomy.scm (qfits): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-02-19 11:05:33 +01:00
Sharlatan Hellseher
8fa76b836d
gnu: Add python-skyfield. 
* gnu/packages/astronomy.scm (python-skyfield): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-02-19 11:05:33 +01:00
Sharlatan Hellseher
74acb300a3
gnu: Add python-extension-helpers. 
* gnu/packages/python-xyz.scm (python-extension-helpers): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-02-19 11:05:33 +01:00
Sharlatan Hellseher
ac7d2eef80
gnu: Add python-pytest-astropy. 
* gnu/packages/python-check.scm (python-pytest-astropy): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-02-19 11:05:33 +01:00
Sharlatan Hellseher
9daa9f2a6f
gnu: Add python-pytest-astropy-header. 
* gnu/packages/python-check.scm (python-pytest-astropy-header): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-02-19 11:05:33 +01:00
Nicolas Goaziou
f90bbba4cc
gnu: nushell: Update to 0.27.1. 
* gnu/packages/shells.scm (nushell): Update to 0.27.1.
[arguments]: Add rust-serial-test to Cargo development inputs.
(rust-nu-cli-0.27):
(rust-nu-command-0.27):
(rust-nu-data-0.27):
(rust-nu-engine-0.27):
(rust-nu-errors-0.27):
(rust-nu-json-0.27):
(rust-nu-parser-0.27):
(rust-nu-plugin-0.27):
(rust-nu-plugin-binaryview-0.27):
(rust-nu-plugin-chart-0.27):
(rust-nu-plugin-fetch-0.27):
(rust-nu-plugin-from-bson-0.27):
(rust-nu-plugin-from-sqlite-0.27):
(rust-nu-plugin-inc-0.27):
(rust-nu-plugin-match-0.27):
(rust-nu-plugin-post-0.27):
(rust-nu-plugin-ps-0.27):
(rust-nu-plugin-s3-0.27):
(rust-nu-plugin-selector-0.27):
(rust-nu-plugin-start-0.27):
(rust-nu-plugin-sys-0.27):
(rust-nu-plugin-textview-0.27):
(rust-nu-plugin-to-bson-0.27):
(rust-nu-plugin-to-sqlite-0.27):
(rust-nu-plugin-tree-0.27):
(rust-nu-plugin-xpath-0.27):
(rust-nu-protocol-0.27):
(rust-nu-source-0.27):
(rust-nu-stream-0.27):
(rust-nu-table-0.27):
(rust-nu-test-support-0.27):
(rust-nu-value-ext-0.27): Update to 0.27.1.
 2021-02-19 10:42:05 +01:00
Sharlatan Hellseher
0ce63d11b5
gnu: Add cl-glsl-packing. 
* gnu/packages/lisp-xyz.scm (cl-glsl-packing, ecl-glsl-packing,
  sbcl-glsl-packing): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-02-19 09:11:28 +01:00
Stefan Reichör
a30f250d74
gnu: Add vitetris. 
* gnu/packages/games.scm (vitetris): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-02-18 22:09:47 +01:00
Maxim Cournoyer
5fccdbc079
gnu: emacs-elpy: Fix build. 
Fixes <https://issues.guix.gnu.org/46516>, which was caused by commit
41abf3b3a0.

* gnu/packages/emacs-xyz.scm (emacs-elpy)[phases]
{patch-ffip-project-search-call}: New phase.

Reported-by: Simon Streit <simon@netpanic.org> and others.
 2021-02-18 15:37:34 -05:00
Raghav Gururajan
13de685877
gnu: webrtc-for-telegram-desktop: Adjust native inputs. 
This fixes a segmentation fault in telegram-desktop.

* gnu/packages/telegram.scm (webrtc-for-telegram-desktop) [native-inputs]:
Add gcc-9 and perl.

Signed-off-by: Leo Prikler <leo.prikler@student.tugraz.at>
 2021-02-18 21:16:06 +01:00
Yurii Kholodkov
690aa1c59d
gnu: Add emacs-kbd. 
* gnu/packages/emacs-xyz.scm (emacs-kbd): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-02-18 21:01:19 +01:00
Leo Famulari
11feecc23a
gnu: BIND: Point out where to find the release notes. 
The isc.org web page is hard to navigate and designed to steer users
into support contracts, so let's give a hint for Guix packagers.

* gnu/packages/dns.scm (bind): Add comment.
 2021-02-18 13:25:56 -05:00
Leo Famulari
caf8f369b0
gnu: isc-dhcp: Update bundled BIND to 9.11.28 [fixes CVE-2020-8625]. 
* gnu/packages/admin.scm (isc-dhcp)[inputs]: Update bundled BIND to 9.11.28.
 2021-02-18 13:25:56 -05:00
Greg Hogan
7cd0247eb4
gnu: gperftools: Update to 2.8.1. 
* gnu/packages/cpp.scm (gperftools): Update to 2.8.1.
[arguments]: Set '#:parallel-tests? #f'.

Co-authored-by: Leo Famulari <leo@famulari.name>
 2021-02-18 13:03:48 -05:00
Nicolas Goaziou
ac19e83b52
gnu: emacs-eldev: Update to 0.8.1. 
* gnu/packages/emacs-xyz.scm (emacs-eldev): Update to 0.8.1.
[arguments]: Skip failing tests in an additional phase.
 2021-02-18 17:59:56 +01:00
Ricardo Wurmus
a03a3ab043
gnu: r-shiny: Update to 1.6.0. 
* gnu/packages/cran.scm (r-shiny): Update to 1.6.0.
[source]: Remove minified JavaScript files in a snippet.
[arguments]: Update phase replace-bundled-minified-JavaScript.
[propagated-inputs]: Add r-bslib, r-cachem, r-commonmark, r-ellipsis, r-glue,
and r-lifecycle.
[inputs]: Remove js-html5shiv, js-json2, js-respond, and js-es5-shim.
[native-inputs]: Add js-bootstrap-accessibility.
 2021-02-18 17:52:05 +01:00
Ricardo Wurmus
22f78a3c81
gnu: Add r-bslib. 
* gnu/packages/cran.scm (r-bslib): New variable.
 2021-02-18 17:52:05 +01:00
Ricardo Wurmus
281df0d225
gnu: Add r-sass. 
* gnu/packages/cran.scm (r-sass): New variable.
 2021-02-18 17:52:05 +01:00
Ricardo Wurmus
8dac2e0d1e
gnu: Add r-jquerylib. 
* gnu/packages/cran.scm (r-jquerylib): New variable.
 2021-02-18 17:52:05 +01:00
Nicolas Goaziou
359e905352
gnu: emacs-execline: Fix version string. 
* gnu/packages/emacs-xyz.scm (emacs-execline): Use version tag matching commit
chosen.
 2021-02-18 16:41:21 +01:00