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3e84503cb2bd926dca191bc25e885df2967eeb69
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55367 Commits

Author SHA1 Message Date
Edouard Klein
3e84503cb2 gnu: Add python-daemux. 
* gnu/packages/tmux.scm (python-daemux): New variable.

Signed-off-by: Marius Bakke <marius@gnu.org>
 2020-06-22 23:52:54 +02:00
Edouard Klein
3565a30f70 gnu: Add python-libtmux. 
* gnu/packages/tmux.scm (python-libtmux): New variable.

Signed-off-by: Marius Bakke <marius@gnu.org>
 2020-06-22 23:52:54 +02:00
Edouard Klein
9d0e87f8ed gnu: Add python-pyfiglet. 
* gnu/packages/python-xyz.scm (python-pyfiglet): New variable.

Signed-off-by: Marius Bakke <marius@gnu.org>
 2020-06-22 23:52:54 +02:00
Edouard Klein
24297a9a9c gnu: Add python-flask-restx. 
* gnu/packages/python-web.scm (python-flask-restx): New variable.

Signed-off-by: Marius Bakke <marius@gnu.org>
 2020-06-22 23:52:54 +02:00
Edouard Klein
85acb5f53d gnu: Add python-pytest-flask. 
* gnu/packages/python-check.scm (python-pytest-flask): New variable.

Signed-off-by: Marius Bakke <marius@gnu.org>
 2020-06-22 23:52:54 +02:00
Edouard Klein
857c63fe03 gnu: Add python-pytest-benchmark. 
* gnu/packages/python-check.scm (python-pytest-benchmark): New variable.

Signed-off-by: Marius Bakke <marius@gnu.org>
 2020-06-22 23:52:54 +02:00
Edouard Klein
bb7e9ab755 gnu: Add python-py-cpuinfo. 
* gnu/packages/python-xyz.scm (python-py-cpuinfo): New variable.

Signed-off-by: Marius Bakke <marius@gnu.org>
 2020-06-22 23:52:53 +02:00
Nicolas Goaziou
68a6070bc3 gnu: Add abe. 
* gnu/packages/games.scm (abe): New variable.
 2020-06-22 22:06:06 +02:00
Jonathan Brielmaier
5d9540ddcf gnu: mate: Don't propagate glib:bin. 
* gnu/packages/mate.scm (mate)[propagated-inputs]: Remove as the
proper fix arrived from core-updates.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2020-06-22 21:28:12 +03:00
Jonathan Brielmaier
a2ebd098d7 gnu: mate-common: Update to 1.24.1. 
* gnu/packages/mate.scm (mate-common): Update to 1.24.1.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2020-06-22 21:27:38 +03:00
Vinicius Monego
bf2ffbcd77 gnu: Add python-pytest-lazy-fixture. 
* gnu/packages/check.scm (python-pytest-lazy-fixture): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2020-06-22 21:18:40 +03:00
Ricardo Wurmus
af02327856 gnu: r-with-tests, r-minimal: Update to 4.0.2. 
* gnu/packages/statistics.scm (r-with-tests, r-minimal): Update to 4.0.2.
 2020-06-22 18:28:52 +02:00
Mathieu Othacehe
7f75a7ec08 system: image: Remove "image-root" when building raw disk-images. 
The "image-root" derivation output is used as a temporary directory that is
passed to mke2fs and mkdosfs later on. By merging the creation of this
directory and the production of partition images, we can get rid of the
derivation.

As mke2fs and mkdosfs are not able to override file permissions, call those
commands with fakeroot. This way, all the image files will be owned by root,
even if image generation is done in an unprivilegded context.

* gnu/system/image.scm (system-disk-image): Merge "image-root" and
"iso9660-image" derivations so that we spare an extra derivation. Also add
"fakeroot" and its runtime dependencies to the inputs.
* gnu/build/image.scm (make-ext-image, make-vfat-image): Make sure that mke2fs
and mkdosfs are respectively called by fakeroot.
 2020-06-22 17:49:19 +02:00
Marius Bakke
cf14e67963 gnu: gn: Update to 0.0-1794.eb997b5. 
* gnu/packages/build-tools.scm (gn): Update to 0.0-1794.eb997b5.
 2020-06-22 17:16:39 +02:00
Marius Bakke
75527eb1cb gnu: ungoogled-chromium: Update to 83.0.4103.106-0.f08ce8b [security fixes]. 
This fixes CVE-2020-6465, CVE-2020-6466, CVE-2020-6467, CVE-2020-6468,
CVE-2020-6469, CVE-2020-6470, CVE-2020-6471, CVE-2020-6472, CVE-2020-6473,
CVE-2020-6474, CVE-2020-6475, CVE-2020-6476, CVE-2020-6477, CVE-2020-6478,
CVE-2020-6479, CVE-2020-6480, CVE-2020-6481, CVE-2020-6482, CVE-2020-6483,
CVE-2020-6484, CVE-2020-6485, CVE-2020-6486, CVE-2020-6487, CVE-2020-6488,
CVE-2020-6489, CVE-2020-6490, CVE-2020-6491, CVE-2020-6493, CVE-2020-6494,
CVE-2020-6495, CVE-2020-6496, CVE-2020-6497, and CVE-2020-6498.

* gnu/packages/patches/ungoogled-chromium-system-jsoncpp.patch,
gnu/packages/patches/ungoogled-chromium-system-zlib.patch: New files.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for 83.
(%chromium-version): Set to 83.0.4103.106.
(%ungoogled-revision): Set to f08ce8b3f1300ef0750b5d6bf967b9cbbfd9a56d.
(%gentoo-revision, %gentoo-patches, %debian-patches): New variables.
(gentoo-patch, debian-patch): New procedures.
(%chromium-origin, %ungoogled-origin): Update hashes.
(ungoogled-chromium-source): Don't apply patches from %DEBIAN-ORIGIN, but take
%GENTOO-PATCHES, %DEBIAN-PATCHES, and the local patch files.
(ungoogled-chromium)[arguments]: Remove "enable_swiftshader=false" from
 #:configure-flags.  Add "icu_use_data_file=false".  Set CFLAGS in phase.
Remove obsolete substitution.  Adjust install phase to install .so files for
ANGLE and Swiftshader.
[native-inputs]: Change from CLANG-9 to CLANG-10.
[inputs]: Replace ICU4C with ICU4C-67.
(ungoogled-chromium/wayland): Remove obsolete substitution.  Add
"ozone_platform_x11=true" in #:configure-flags.
 2020-06-22 17:16:39 +02:00
Marius Bakke
8169cc736a gnu: icu4c: Add 67.1. 
* gnu/packages/icu4c.scm (icu4c-67): New public variable.
 2020-06-22 17:16:39 +02:00
Marius Bakke
acac3b94d7 gnu: ungoogled-chromium: Specify CPE name. 
* gnu/packages/chromium.scm (ungoogled-chromium)[properties]: Add CPE-NAME.
 2020-06-22 17:16:39 +02:00
Marius Bakke
cafc5f8927 gnu: ungoogled-chromium: Remove non-free file. 
* gnu/packages/chromium.scm (ungoogled-chromium-source): Remove (unused) SVG
file that is licensed under a NoDerivatives license.
 2020-06-22 17:16:39 +02:00
Marius Bakke
3d5a217d5e gnu: ungoogled-chromium: Build with ffmpeg@4.2. 
Fixes <https://bugs.gnu.org/41987>.
Reported by Jonathan Brielmaier <jonathan.brielmaier@web.de>.

* gnu/packages/video.scm (ffmpeg-4.2): New public variable.
* gnu/packages/chromium.scm (ungoogled-chromium)[inputs]: Change from FFMPEG
to FFMPEG-4.2.
 2020-06-22 17:16:38 +02:00
Marius Bakke
402d03751c gnu: ffmpeg: Enable rav1e on x86_64 only. 
Fixes <https://bugs.gnu.org/41993>.
Reported by Kurt I <gitlabcanada@runbox.com>.

* gnu/packages/video.scm (ffmpeg)[inputs]: Conditionally add RAV1E.
[arguments]: Adjust #:configure-flags accordingly.
 2020-06-22 17:16:38 +02:00
Mathieu Othacehe
1cb9effc3e system: image: Remove "image-root" derivation when building ISO. 
The "image-root" derivation output is used as a temporary directory that is
passed to GNU Xorriso later on. By merging the creation of this directory and
the production of an ISO image, we can get rid of the derivation.

* gnu/system/image.scm (system-iso9660-image): Merge "image-root" and
"iso9660-image" derivations so that we spare an extra derivation.
 2020-06-22 17:07:22 +02:00
Mathieu Othacehe
0919d6148f gnu: xl2tpd: Fix build. 
* gnu/packages/vpn.scm (xl2tpd)[arguments]: Substitute hardcoded pppd path
instead of trying to set CFLAGS variable.
 2020-06-22 16:48:58 +02:00
Pierre Langlois
6e31d6f3c4 gnu: python-plotly: Update to 4.8.1. 
But keep version 2.4.1 around for packages that still need it and for python2
support.

* gnu/packages/graph.scm (python-plotly): Update to 4.8.1.
[source]: Use git-fetch so that tests are also included.
[arguments]: Enable tests.
[home-page]: Follow redirect.
(python-plotly-2.4.1): New variable.
(python2-plotly): Inherit from python-plotly-2.4.1.
* gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Depend on
python-plotly-2.4.1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-22 15:44:16 +02:00
Pierre Langlois
3417a25156 gnu: Add python-xarray. 
From 27ec21904f769c1e8114f767972d9037e1e9f68a Mon Sep 17 00:00:00 2001
From: Pierre Langlois <pierre.langlois@gmx.com>
Date: Thu, 18 Jun 2020 00:58:02 +0200
Subject: [PATCH 4/5] gnu: Add python-xarray.

* gnu/package/python-science.scm (python-xarray): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-22 15:44:14 +02:00
Pierre Langlois
7fd33283df gnu: Add python-retrying. 
* gnu/packages/python-xyz.scm (python-retrying): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-22 15:44:12 +02:00
Pierre Langlois
20b545f768 gnu: python-pandas: Update to 1.0.5. 
But also keep version 0.25.3 around for packages requiring an earlier
versions, as well as version 0.24.2 for a version with python2.

* gnu/packages/python-science.scm (python-pandas): Update to 1.0.5.
[arguments]: Adapt 'patch-which phase.  Add new 'prepare-x phase.  Do not
delete tests that depend on "moto", they are skipped automatically.
[propagated-inputs]: Add python-jinja2.
[inputs]: Add xsel and xclip.
[native-inputs]: Add xorg-server-for-tests so we can test clipboard support.
(python-pandas-0.24): New variable.
(python2-pandas): Inherit from python-pandas-0.25.
* gnu/packages/bioinformatics.scm (python-biom-format)[propagated-inputs]:
Switch to python-pandas-0.25.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-22 15:44:08 +02:00
Pierre Langlois
3a79adab41 gnu: deeptools: Deprecate in favor of python-deeptools. 
And make sure python-deeptools's tests are running.

* gnu/packages/bioinformatics.scm (python-deeptools): Fetch source using git.
[native-inputs]: Add python-mock and python-nose.
(deeptools): Mark as deprecated.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-22 15:43:59 +02:00
Ludovic Courtès
955caaab26 self: Build with Guile 3.0.3. 
* gnu/packages/guile.scm (guile-3.0/libgc-7): Inherit from GUILE-3.0.3.
 2020-06-22 15:42:56 +02:00
Pierre Neidhardt
a0dccc71a6 gnu: emacs-helm: Update to 3.6.3. 
* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.6.3.
 2020-06-22 15:05:46 +02:00
Pierre Neidhardt
561aeefb0b gnu: emacs-helm-fish-completion: Update to 0.5. 
* gnu/packages/emacs-xyz.scm (emacs-helm-fish-completion): Update to 0.5.
 2020-06-22 15:01:09 +02:00
Guillaume Le Vaillant
69b82c6078 gnu: js8call: Fix build. 
* gnu/packages/radio.scm (js8call)[inputs]: Use regular hamlib.
 2020-06-22 14:50:50 +02:00
Guillaume Le Vaillant
09e27115d6 gnu: wsjtx: Update to 2.2.1. 
* gnu/packages/radio.scm (wsjtx-hamlib): Update to 2.2.1.
  [arguments]: Add a 'fix-tests' phase.
  (wsjtx): Update to 2.2.1.
 2020-06-22 14:50:50 +02:00
Guillaume Le Vaillant
0213f0940e gnu: qgis: Disable some failing tests. 
* gnu/packages/geo.scm (qgis)[arguments]: Disable a few more failing tests.
 2020-06-22 14:50:50 +02:00
Ricardo Wurmus
c89afe7516 gnu: Add r-rgreat. 
* gnu/packages/bioconductor.scm (r-rgreat): New variable.
 2020-06-22 14:39:03 +02:00
Efraim Flashner
277ac1f242 gnu: rust-libc-0.2: Don't skip build. 
* gnu/packages/crates-io.scm (rust-libc-0.2)[arguments]: Don't skip
build.
 2020-06-22 14:15:34 +03:00
Efraim Flashner
a1b79c09ee gnu: rust-libc-0.2: Update to 0.2.71. 
* gnu/packages/crates-io.scm (rust-libc-0.2): Update to 0.2.71.
 2020-06-22 14:15:34 +03:00
Efraim Flashner
a56305539f gnu: rust-rayon-1.3: Rename to rust-rayon-1. 
* gnu/packages/crates-io.scm (rust-rayon-1.3): Rename to rust-rayon-1.
(rust-criterion-0.3, rust-criterion-0.2, rust-gimli-0.18,
rust-hashbrown-0.5, rust-indexmap-1.3, rust-jpeg-decoder-0.1,
rust-nasm-rs-0.1, rust-scroll-0.9, rust-syn-1.0, rust-syn-0.15)
[arguments]: Adjust accordingly.
* gnu/packages/gnome.scm (librsvg-next)[arguments]: Same.
* gnu/packages/rust-apps.scm (tokei)[arguments]: Same.
* gnu/packages/video.scm (rav1e)[arguments]: Same.
 2020-06-22 14:15:34 +03:00
Efraim Flashner
6c2189c858 gnu: Remove rust-rayon-1.1. 
* gnu/packages/crates-io.scm (rust-rayon-1.1): Remove variable.
(rust-criterion-0.2, rust-gimli-0.18, rust-hashbrown-0.5,
rust-jpeg-decoder-0.1, rust-scroll-0.9, rust-syn-0.15)
[arguments]: Replace rust-rayon-1.1 with 1.3.
 2020-06-22 14:15:34 +03:00
Efraim Flashner
8781c8edd2 gnu: rust-rayon-core-1.7: Rename to rust-rayon-core-1. 
* gnu/packages/crates-io.scm (rust-rayon-core-1.7): Rename to
rust-rayon-core-1.
(rust-criterion-0.2, rust-rayon-1.3, rust-rayon-1.1, rust-rayon-0.8)
[arguments]: Adjust accordingly.
 2020-06-22 14:15:34 +03:00
Efraim Flashner
4f76fbfcd9 gnu: Remove rust-rayon-core-1.5. 
* gnu/packages/crates-io.scm (rust-rayon-core-1.5): Remove variable.
(rust-criterion-0.2, rust-rayon-1.1) [arguments]: Replace
rust-rayon-core-1.5 with 1.7.
 2020-06-22 14:15:33 +03:00
Efraim Flashner
df4d2ddaee gnu: sequoia: Fix typos. 
* gnu/packages/sequoia.scm (sequoia)[arguments]: Move unquote next to
the expression it applies to.
 2020-06-22 14:15:33 +03:00
Efraim Flashner
6cd7b35544 gnu: rust-regex-1.3: Rename to rust-regex-1. 
* gnu/packages/crates-io.scm (rust-regex-1.3): Rename to rust-regex-1.
(rust-ansi-term-0.12, rust-bindgen-0.52, rust-bindgen-0.51,
rust-bindgen-0.50, rust-bindgen-0.37, rust-bindgen-0.49, rust-clap-2,
rust-compiletest-rs-0.3, rust-console-0.9, rust-console-0.7,
rust-docopt-1.1, rust-env-logger-0.7, rust-env-logger-0.6,
rust-env-logger-0.5, rust-gimli-0.18, rust-globset-0.4,
rust-grep-cli-0.1, rust-grep-matcher-0.1, rust-grep-regex-0.1,
rust-grep-searcher-0.1, rust-ignore-0.4, rust-lalrpop-0.17,
rust-lalrpop-util-0.17, rust-locale-config-0.3, rust-localeconfig-0.2,
rust-nom-5, rust-nom-4.2, rust-once-cell-1.2, rust-proptest-0.9,
rust-proptest-0.8, rust-pulldown-cmark-0.4, rust-regex-automata-0.1,
rust-rusqlite-0.19, rust-scan-fmt-0.2, rust-syn-1.0, rust-syn-0.15,
rust-ucd-parse-0.1, rust-version-sync-0.8) [arguments]: Adjust accordingly.
* gnu/packages/gnome.scm (librsvg-next)[arguments]: Same.
* gnu/packages/rust-apps.scm (fd, ripgrep, tokei, rust-cargo-c)
[arguments]: Same.
* gnu/packages/sequoia.scm (sequoia)[arguments]: Same.
 2020-06-22 14:15:33 +03:00
Efraim Flashner
9c13497df4 gnu: Remove rust-regex-1.1. 
* gnu/packages/crates-io.scm (rust-regex-1.1): Remove variable.
(rust-bindgen-0.50, rust-bindgen-0.49, rust-clap-2,
rust-compiletest-rs-0.2, rust-console-0.7, rust-docopt-1.1,
rust-env-logger-0.7, rust-env-logger-0.6, rust-env-logger-0.5,
rust-gimli-0.18, rust-globset-0.4, rust-grep-cli-0.1,
rust-grep-matcher-0.1, rust-grep-regex-0.1, rust-grep-searcher-0.1,
rust-ignore-0.4, rust-nom-5, rust-nom-4.2, rust-once-cell-1.2,
rust-proptest-0.9, rust-proptest-0.8, rust-pulldown-cmark-0.4,
rust-regex-automata-0.1, rust-rusqlite-0.19, rust-syn-0.15,
rust-ucd-parse-0.1, rust-version-sync-0.8) [arguments]: Replace
rust-regex-1.1 with 1.3.
* gnu/packages/rust-apps.scm (ripgrep)[arguments]: Same.
 2020-06-22 14:15:33 +03:00
Efraim Flashner
80cfe5458c gnu: Add rust-once-cell-0.1. 
* gnu/packages/crates-io.scm (rust-once-cell-0.1): New variable.
 2020-06-22 14:15:33 +03:00
Efraim Flashner
f4022d8549 gnu: Add rust-gettext-rs-0.4. 
* gnu/packages/crates-io.scm (rust-gettext-rs-0.4): New variable.
 2020-06-22 14:15:32 +03:00
Efraim Flashner
e1240cb249 gnu: Add rust-gettext-sys-0.19. 
* gnu/packages/crates-io.scm (rust-gettext-sys-0.19): New variable.
 2020-06-22 14:15:32 +03:00
Efraim Flashner
b3987cd3d2 gnu: Add rust-locale-config-0.2. 
* gnu/packages/crates-io.scm (rust-locale-config-0.2): New variable.
 2020-06-22 14:15:32 +03:00
Efraim Flashner
d77146e9fe gnu: Add rust-proptest-0.7. 
* gnu/packages/crates-io.scm (rust-proptest-0.7): New variable.
 2020-06-22 14:15:32 +03:00
Efraim Flashner
eba1524df2 gnu: Add rust-regex-syntax-0.4. 
* gnu/packages/crates-io.scm (rust-regex-syntax-0.4): New variable.
 2020-06-22 14:15:32 +03:00
Efraim Flashner
5247f79db6 gnu: Add rust-section-testing-0.0. 
* gnu/packages/crates-io.scm (rust-section-testing-0.0): New variable.
 2020-06-22 14:15:31 +03:00