gnu: Add fcitx-qt5.

* gnu/packages/fcitx.scm (fcitx-qt5): New variable.

Signed-off-by: Leo Prikler <leo.prikler@student.tugraz.at>

gnu: Add c++-gsl.

* gnu/packages/cpp.scm (c++-gsl): New variable.
* gnu/packages/patches/c++-gsl-find-system-gtest.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Leo Prikler <leo.prikler@student.tugraz.at>

gnu: linux-libre 4.4: Update to 4.4.254.

* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.254.
(linux-libre-4.4-pristine-source): Update hash.

gnu: linux-libre 4.9: Update to 4.9.254.

* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.254.
(linux-libre-4.9-pristine-source): Update hash.

gnu: linux-libre 4.14: Update to 4.14.218.

* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.218.
(linux-libre-4.14-pristine-source): Update hash.

gnu: linux-libre 4.19: Update to 4.19.172.

* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.172.
(linux-libre-4.19-pristine-source): Update hash.

gnu: linux-libre 5.4: Update to 5.4.94.

* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.94.
(linux-libre-5.4-pristine-source): Update hash.

gnu: linux-libre: Update to 5.10.12.

* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.12.
(linux-libre-5.10-pristine-source): Update hash.

gnu: cmst: Update to 2020.11.01.

* gnu/packages/connman.scm (cmst): Update to 2020.11.01.

gnu: slurm-18.08: Update to 18.08.9.

Fixes CVE-2019-{12838,19727,19728}.

* gnu/packages/parallel.scm (slurm-18.08): Update to 18.08.9.

gnu: slurm-19.05: Update to 19.05.8.

Fixes CVE-2020-{12693,27745,27746,19727,19728}.

* gnu/packages/parallel.scm (slurm-19.05): Update to 19.05.8.

gnu: slurm: Update to 20.11.3.

* gnu/packages/parallel.scm (slurm): Update to 20.11.3.

gnu: slurm: Update note about slurm versions.

* gnu/packages/parallel.scm: Update note about what slurm versions
should be kept.

gnu: parallel: Update to 20210122.

* gnu/packages/parallel.scm (parallel): Update to 20210122.

gnu: blender-2.79: Fix build.

* gnu/packages/graphics.scm (blender-2.79)[inputs]: Add pugixml.

guix system: Adjust 'upgrade-shepherd-services' to shepherd service change.

Fixes a regression introduced in 95f72dcd7aece05e9252c93bef5a831f96cb5393.

* guix/scripts/system/reconfigure.scm (upgrade-shepherd-services)[target-services]:
Add call to 'shepherd-configuration-services'.

gnu: blender: Fix build.

* gnu/packages/graphics.scm (openimageio): Update to 2.2.10.1.
[arguments]: Do not use system pugixml.
[inputs]: Add fmt.
* gnu/packages/graphics.scm (blender)[inputs]: Add "pugixml".

gnu: alacritty: Fix build.

This is a follow-up of 880e6334b7aeda04ad8572f9c68a9055de15aeb8.

* gnu/packages/terminals.scm (alacritty)[arguments]: Rename "rust-dirs-2.0"
into "rust-dirs-2" and "rust-embed-resource-1.3" into "rust-embed-resource-1".

gnu: cuirass: Update to 0.0.1-61.6838ec2.

* gnu/packages/ci.scm (cuirass): Update to 0.0.1-61.6838ec2.

guix system: Test 'extension-graph' and 'shepherd-graph'.

* tests/guix-system.sh: Test 'guix system extension-graph' and 'guix
system shepherd-graph'.

services: shepherd: Allow custom 'shepherd' package.

* gnu/services/shepherd.scm (<shepherd-configuration>): New record.
(shepherd-boot-gexp, shepherd-root-service-type): Use it.
(scm->go, shepherd-configuration-file): Allow passing custom
shepherd package.
* gnu/system.scm (operating-system-shepherd-service-names): Use the new
record.
* guix/scripts/system.scm (export-shepherd-graph): Adjust accordingly.
* doc/guix.texi (Shepherd Services). Document it.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add julia-json.

* gnu/packages/julia-xyz.scm (julia-json): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add julia-offsetarrays.

* gnu/packages/julia-xyz.scm (julia-offsetarrays): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add julia-adapt.

* gnu/packages/julia-xyz.scm (julia-adapt): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add julia-parsers.

* gnu/packages/julia-xyz.scm (julia-parsers): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add julia-fixedpointnumbers.

* gnu/packages/julia-xyz.scm (julia-fixedpointnumbers): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add julia-datastructures.

* gnu/packages/julia-xyz.scm (julia-datastructures): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add julia-orderedcollections.

* gnu/packages/julia-xyz.scm (julia-orderedcollections): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: julia-compat: Update to 3.25.0.

* gnu/packages/julia-xyz.scm (julia-compat): Update to 3.25.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: julia-compat: Set file name according to standards.

* gnu/packages/julia-xyz.scm (julia-compat)[source]: Set 'file-name'
to (git-file-name ...).

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

build-system/julia: Don't rely on file name to set module name.

* guix/build/julia-build-system.scm (project.toml->name): New procedure.
  (precompile, check, julia-build): Accept new key argument #:julia-package-name.
* guix/build-system/julia.scm (julia-build): ... add it.
* doc/guix.texi (julia-build-system): Update julia-package-name accordingly.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

build-system/julia: Enable tests.

* guix/build-system/julia.scm (julia-build): Set tests? default to #t.
* guix/build/julia-build-system.scm (check): Respect tests? and fix julia
  invocation.
  (%standard-phases): Add check phase after install.
* doc/guix.texi (julia-build-system): Update accordingly.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: rust-embed-resource-1: Drop minor version from name.

* gnu/packages/crates-io.scm (rust-embed-resource-1): Drop minor version from
name.
* gnu/packages/rust-apps.scm (watchexec): Apply renaming.

gnu: rust-dirs-2: Drop minor version from name.

* gnu/packages/crates-io.scm (rust-dirs-2): Drop minor version from name.
(rust-dirs-1.0):
(rust-term-0.6):
* gnu/packages/rust-apps.scm (fd):
* gnu/packages/sequoia.scm (sequoia):
* gnu/packages/web.scm (castor): Apply renaming.

gnu: rust-downcast-rs-1: Drop minor version from name.

* gnu/packages/crates-io.scm (rust-downcast-rs-1): Drop minor version from
name.
* gnu/packages/crates-graphics.scm (rust-wayland-client-0.23):
(rust-wayland-client-0.21):
(rust-wayland-server-0.23):
(rust-wayland-server-0.21): Apply renaming.

gnu: rust-downcast-rs-1.1: Remove variable.

* gnu/packages/crates-io.scm (rust-downcast-rs-1.1): Remove variable.
* gnu/packages/crates-graphics.scm (rust-wayland-client-0.23):
(rust-wayland-client-0.21):
(rust-wayland-server-0.23):
(rust-wayland-server-0.21): Refer to rust-downcast-rs-1.2 instead.

gnu: rust-expat-sys-2: Drop minor version from name.

* gnu/packages/crates-io.scm (rust-expat-sys-2): Drop minor version from name.
(rust-servo-fontconfig-sys-4): Apply renaming.

gnu: cuirass: Update to 0.0.1-60.1e8d075.

* gnu/packages/ci.scm (cuirass): Update to 0.0.1-60.1e8d075.

gnu: picocom: Fix cross-compilation.

* gnu/packages/terminals.scm (picocom)[arguments]: Use CC-FOR-TARGET instead
of "gcc".

gnu: uBlock Origin: Update to 1.33.0.

* gnu/packages/browser-extensions.scm (uassets): Update to commit a5b1e3cae.
(ublock-origin): Update to 1.33.0.

gnu: foot: Update to 1.6.2.

* gnu/packages/terminals.scm (foot): Update to 1.6.2.
[native-inputs]: Remove GCC-10.

gnu: ungoogled-chromium: Update to 88.0.4324.104-0.4e2679c.

* gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for 88.
(%chromium-version): Set to 88.0.4324.104.
(%ungoogled-revision): Set to 4e2679ce15a53925b34a95aa3e1731751530dc22.
(%ungoogled-origin): Update hash.
(libvpx/chromium): New variable.
(ungoogled-chromium): Update hash.
[arguments]: Patch one file for compatibility with system ICU.
[inputs]: Change from ICU4C-67 to ICU4C-68.  Change from LIBVPX to
LIBVPX/CHROMIUM.

gnu: Add cl-out123.

* gnu/packages/lisp-xyz.scm (cl-out123, ecl-cl-out123, sbcl-cl-out123): New
  variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add nq.

* gnu/packages/admin.scm (nq): New variable.

doc: Update guidance about Rust package naming.

* doc/contributing.texi (Rust Crates): Explain versions suffix based on
  packages version and Crate "caret" versioning.

gnu: Remove avogadro.

This package fails to build and has been superseded by avogadro2.

* gnu/packages/chemistry.scm (avogadro): Remove variable.
* gnu/packages/patches/avogadro-boost148.patch,
gnu/packages/patches/avogadro-eigen3-update.patch,
gnu/packages/patches/avogadro-python-eigen-lib.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.

gnu: grocsvs: Remove package.

This package depends on Python 2 and doesn't build anymore.  Upstream doesn't
seem active, but if they ever port it to Python 3, they should let people know
here: https://github.com/grocsvs/grocsvs/issues/6.

* gnu/packages/bioinformatics.scm (grocsvs): Delete.

gnu: syncthing-gtk: Switch source to use Debian's Python 3 port.

* gnu/packages/syncthing.scm (syncthing-gtk)[source]: Adjust to use the Debian
Python 3 port.
[phases]{remove-windows.py}: New phase.

gnu: python2-virtualenv: Remove package.

* gnu/packages/python-xyz.scm (python2-virtualenv): Delete.

gnu: python2-pbr: Remove package.

* gnu/packages/python-xyz.scm (python2-pbr-minimal)
(python2-pbr): Delete variables.

gnu: python2-fixtures: Remove package.

* gnu/packages/check.scm (python2-fixtures-bootstrap)
(python2-fixtures): Delete variables.

gnu: python2-testtools: Remove package.

* gnu/packages/check.scm (python2-testtools-bootstrap)
(python2-testtools): Delete variables.

gnu: python2-testscenarios: Remove package.

* gnu/packages/check.scm (python2-testscenarios-bootstrap)
(python2-testscenarios): Delete variables.

gnu: python2-subunit: Remove package.

* gnu/packages/check.scm (python2-subunit-bootstrap)
(python2-subunit): Delete variables.

gnu: python2-testrepository: Remove package.

* gnu/packages/check.scm (python2-testrepository-bootstrap)
(python2-testrepository): Delete variables.

gnu: python2-requests-mock: Remove package.

* gnu/packages/python-xyz.scm (python2-requests-mock): Delete.

gnu: python2-tox: Remove package.

* gnu/packages/python-xyz.scm (python2-tox): Delete.

gnu: python2-pathpy: Remove package.

* gnu/packages/python-xyz.scm (python2-pathpy): Delete.

gnu: python2-lockfile: Remove package.

* gnu/packages/python-xyz.scm (python2-lockfile): Delete.

gnu: python2-requests-oauthlib: Remove package.

* gnu/packages/python-web.scm (python2-requests-oauthlib):

gnu: python2-git-review: Remove package.

* gnu/packages/openstack.scm (python2-git-review): Delete.

gnu: python2-os-client-config: Remove package.

* gnu/packages/openstack.scm (python2-os-client-config): Delete.

gnu: python2-debtcollector: Remove package.

* gnu/packages/openstack.scm (python2-debtcollector): Delete.

gnu: python2-honcho: Remove package.

* gnu/packages/python-xyz.scm (python2-honcho): Delete.

gnu: python2-fasteners: Remove package.

* gnu/packages/python-xyz.scm (python2-fasteners): Delete.

gnu: python2-xenon: Remove package.

* gnu/packages/python-xyz.scm (python2-xenon): Delete.

gnu: python2-apache-libcloud: Remove package.

* gnu/packages/python-xyz.scm (python2-apache-libcloud): Delete.

gnu: python2-mwclient: Remove package.

* gnu/packages/python-xyz.scm (python2-mwclient): Delete.

gnu: python2-cachecontrol: Remove package.

* gnu/packages/python-web.scm (python2-cachecontrol): Delete.

gnu: python2-falcon-cors: Remove package.

* gnu/packages/python-web.scm (python2-falcon-cors): Delete.

gnu: python2-falcon: Remove package.

* gnu/packages/python-web.scm (python2-falcon): Delete.

gnu: python2-oslotest: Remove package.

* gnu/packages/openstack.scm (python2-oslotest: Delete.

gnu: python2-stevedore: Remove package.

* gnu/packages/openstack.scm (python2-stevedore: Delete.

gnu: python2-os-testr: Remove package.

* gnu/packages/openstack.scm (python2-os-testr): Delete.

gnu: python2-behave-web-api: Remove package.

* gnu/packages/check.scm (python2-behave-web-api): Delete.

gnu: python2-pylint: Remove package.

* gnu/packages/check.scm (python2-pylint): Delete.

gnu: python2-testresources: Remove package.

* gnu/packages/check.scm (python2-testresources-bootstrap)
(python2-testresources): Delete.

gnu: python-pikepdf: Update to 2.5.0.

* gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.5.0.

gnu: wine: Update to 6.0.

* gnu/packages/wine.scm (wine): Update to 6.0.
[inputs]: Add libusb.  Remove glu, ncurses and zlib.

gnu: vkd3d: Update to 1.2.

* gnu/packages/vulkan.scm (vkd3d): Update to 1.2.

gnu: Add python-typer.

* gnu/packages/python-xyz.scm (python-typer): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add python-inotify-simple.

* gnu/packages/python-xyz.scm (python-inotify-simple): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add emacs-scad-mode.

* gnu/packages/engineering.scm (emacs-scad-mode): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

inferior: Speed up 'cached-channel-instance' for cache hits.

That way a command like:

  guix time-machine --commit=5aeee07cc9 -- describe

goes from 3.4s to 0.5s on a cache hit, even slightly less when passing
the full commit ID.

* guix/inferior.scm (channel-full-commit): New procedure.
(cached-channel-instance): Remove 'instances' top-level variable.  Add
'commits' and use it for 'key'.  Move 'latest-channel-instances' call to
the cache miss case.

tests: cuirass: Increase delay.

* gnu/tests/cuirass.scm (run-cuirass-test): Increase "cuirass-web build
queued" test delay.

tests: cuirass: Add Cuirass remote test.

* gnu/tests/cuirass.scm (run-cuirass-test): Add "name" and "remote-build?"
arguments.
(%cuirass-test): Adapt it.
(%cuirass-remote-test): New variable.

gnu: Add weightwatcher.

* gnu/packages/astronomy.scm (weightwatcher): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add swarp.

* gnu/packages/astronomy.scm (swarp): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add stuff.

* gnu/packages/astronomy.scm (stuff): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

ci: Raise max-silent-time to 3600.

* gnu/ci.scm (image-jobs, system-test-jobs): Raise max-silent-time to 3600
seconds.

gnu: emacs-repology: Update to 1.1.0.

* gnu/packages/emacs-xyz.scm (emacs-repology): Update to 1.1.0.

doc: Fix mapped devices example in the manual.

Reported by Raghav Gururajan <rg@raghavgururajan.name> and Mikhail Tsykalov
<tsymsh@gmail.com>.

* doc/guix.texi (Mapped Devices): Replace target with targets.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add r-demultiplex.

* gnu/packages/bioinformatics.scm (r-demultiplex): New variable.

gnu: xfce4-statusnotifier-plugin: Update to 0.2.3.

* gnu/packages/xfce.scm (xfce4-statusnotifier-plugin): Update to 0.2.3.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: xfce4-panel: Update to 4.16.1.

* gnu/packages/xfce.scm (xfce4-panel): Update to 4.16.1.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: libfabric: Update to 0.11.2.

* gnu/packages/linux.scm (libfabric): Update to 0.11.2.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: rdma-core: Update to 33.1.

* gnu/packages/linux.scm (rdma-core): Update to 33.1.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: fcitx5-configtool: Update to 5.0.2.

* gnu/packages/fcitx5.scm(fcitx5-configtool): Update to 5.0.2.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: fcitx5-qt: Update to 5.0.2.

* gnu/packages/fcitx5.scm(fcitx5-qt): Update to 5.0.2.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: fcitx5-gtk: Update to 5.0.3.

* gnu/packages/fcitx5.scm(fcitx5-gtk): Update to 5.0.3.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>