file-systems: Invoke fsck tools with 'system*/tty'.

This ensures those programs, if invoked by shepherd (where standard
input is /dev/null), can still interact with the user if needed.

* gnu/build/file-systems.scm (check-ext2-file-system)
(check-bcachefs-file-system, check-btrfs-file-system):
(check-fat-file-system, check-jfs-file-system):
(check-f2fs-file-system, check-ntfs-file-system):
(check-xfs-file-system): Use 'system*/tty' instead of 'system*'.

mapped-devices: Ensure 'cryptsetup open' gets a tty.

Fixes <https://issues.guix.gnu.org/54770>.
Regression introduced in 400c9ed3d779308e56038305d40cd93acb496180.

Previously, for an encrypted /home (say), "cryptsetup open" would be
invoked by shepherd, with /dev/null as its standard input.  It would
thus run in non-interactive mode and, instead of asking for a
passphrase, fail with:

  Nothing to read on input.

This change ensures it runs in interactive mode.

* gnu/build/file-systems.scm (system*/console, system*/tty): New
procedures.
* gnu/system/mapped-devices.scm (open-luks-device): Use 'system*/tty'
instead of 'system*'.

system: hurd: Fix bogus 'initrd-modules' field.

Reported by kitzman on #guix.

* gnu/system/hurd.scm (%hurd-default-operating-system)[initrd-modules]:
Set to the empty list.

tests: 'guix shell --export-manifest' test no longer needs networking.

* tests/guix-shell-export-manifest.sh: Use '--with-input' rather than
'--with-latest' as the latter would crash in the absence of network
access.

gnu: icedove: Update to 91.8 [fixes CVE-2022-1197].

* gnu/packages/gnuzilla.scm (icedove): Update to 91.8.

gnu: Add cl-jzon.

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

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

gnu: cl-cffi: Remove trailing boolean.

* gnu/packages/lisp-xyz.scm (sbcl-cffi)[arguments]: Remove trailing boolean.

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

gnu: cl-legit: Update to 1.0.0-2.5f8a2d4.

* gnu/packages/lisp-xyz.scm (sbcl-legit): Update to 1.0.0-2.5f8a2d4 and use
  revision variable in let block.
  [arguments]: Add 'patch-git-executable' phase.
  [inputs]: Add formatting and add missing git input.

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

gnu: nginx: Build optimized binaries.

* gnu/packages/web.scm (nginx)[arguments]: Add "-O2 -g" to CFLAGS.

gnu: nginx: Respect #:configure-flags.

* gnu/packages/web.scm (nginx)[arguments]: Add #:configure-flags.  Move
default settings out of the 'configure' phase.

gnu: nginx: Use G-expressions.

* gnu/packages/web.scm (nginx)[arguments]: Rewrite in gexp style.  Remove
trailing #t's.

gnu: uBlock Origin: Update to 1.42.4.

* gnu/packages/browser-extensions.scm (ublock-origin): Update to 1.42.4.

gnu: ungoogled-chromium: Update to 100.0.4896.75-1.

* gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for 100.
(%chromium-version): Set to 100.0.4896.75.
(%debian-revision): Set to debian/100.0.4896.60-1.
(%ungoogled-origin): Update hash.
(%debian-patches): Updates hashes.  Remove obsolete.
(ungoogled-chromium): Update hash.
[arguments]: Remove obsolete substitution.  Patch libvulkan.so.1 in more
files, and add absolute reference to Mesa ICDs.

gnu: ungoogled-chromium: Update to 99.0.4844.84-1.

* gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for 99.
(%chromium-version): Set to 99.0.4844.84.
(%ungoogled-origin): Update hash.
(ungoogled-chromium): Likewise.
[arguments]: Patch absolute file names to GTK libraries.  Patch one more
Opus header inclusion.  Remove labels in wrapping phase.
[native-inputs]: Change from CLANG-13 to CLANG-14.
[inputs]: Add AT-SPI2-ATK.

gnu: LLVM, Clang: Add 14.0.0.

* gnu/packages/llvm.scm (%llvm-monorepo-hashes, %llvm-patches, llvm-monorepo):
New variables.
(clang-runtime-from-llvm): Make HASH optional; use monorepo when not present.
(clang-from-llvm): Likewise.
(llvm-14, clang-runtime-14, clang-14, clang-toolchain-14, lld-14): New variables.
(llvm-13): Inherit from LLVM-14.
(lld-13): Inherit from LLD-14.
(lld): Turn into alias for LLD-14.
* gnu/packages/patches/clang-14.0-libc-search-path.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/zig.scm (zig): Change from LLD to LLD-13.

gnu: radeontop: Simplify inputs.

* gnu/packages/linux.scm (radeontop)[native-inputs]: Simplify.

gnu: Add cura.

* gnu/packages/engineering.scm (cura): New variable.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add python-pynest2d.

* gnu/packages/engineering.scm (python-pynest2d): New variable.

gnu: Add libnest2d-for-cura.

* gnu/packages/engineering.scm (libnest2d-for-cura): New variable.

gnu: Add libsavitar.

* gnu/packages/engineering.scm (libsavitar): New variable.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add libcharon.

* gnu/packages/engineering.scm (libcharon): New variable.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add uranium.

* gnu/packages/engineering.scm (uranium): New variable.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add python-trimesh.

* gnu/packages/python-science.scm (python-trimesh): New variable.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add python-pyinstrument.

* gnu/packages/python-check.scm (python-pyinstrument): New variable.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cura-binary-data.

* gnu/packages/engineering.scm (cura-binary-data): New variable.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cura-engine.

* gnu/packages/engineering.scm (cura-engine): New variable.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add libarcus.

* gnu/packages/engineering.scm (libarcus): New variable.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: cl-slynk: Update to 1.0.43-6.4513c38.

* gnu/packages/lisp-xyz.scm (sbcl-slynk): Update to 1.0.43-6.4513c38.

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

gnu: emacs-sly: Update to 1.0.43-6.4513c38.

* gnu/packages/emacs-xyz.scm (emacs-sly): Update to 1.0.43-6.4513c38.

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

gnu: kicad: Update to 6.0.4.

* gnu/packages/engineering.scm (kicad, kicad-doc, kicad-symbols,
  kicad-footprints, kicad-packages3d, kicad-templates): Update to 6.0.4.

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

gnu: cl-sxql: Update to 0.1.0-3.cc3478c.

* gnu/packages/lisp-xyz.scm (sbcl-sxql): Update to 0.1.0-3.cc3478c and use
  revision variable in let block.
  [inputs]: Add missing sbcl-trivia input.

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

secret-service: Allow cooperative scheduling when Fibers is used.

This lets the 'childhurd' service start in the background, letting
shepherd perform other tasks in the meantime, including serving
clients (such as the 'herd' command).

* gnu/build/secret-service.scm (with-modules): New macro.
(wait-for-readable-fd): Add cooperative implementation when Fibers is in
use.
(secret-service-send-secrets): Define 'sleep' so that it cooperates when
Fibers is in use.

secret-service: Abstract 'wait-for-readable-fd'.

* gnu/build/secret-service.scm (wait-for-readable-fd): New procedure.
(secret-service-send-secrets): Use it instead of 'select'.

services: openssh: Start as an inetd service.

* gnu/services/ssh.scm (openssh-shepherd-service): Use
'make-inetd-constructor' when it is defined.
(<openssh-configuration>)[max-connections]: New field.
* gnu/tests/ssh.scm (run-ssh-test)["sshd PID"]: Adjust to cope with
PID-FILE being #f.
* gnu/tests/ssh.scm (%test-openssh): Pass #f as the 'pid-file'
argument.
* doc/guix.texi (Networking Services): Document 'max-connections'.

home: shepherd: Default to version 0.9.

* gnu/home/services/shepherd.scm (<home-shepherd-configuration>)[shepherd]:
Default to SHEPHERD-0.9.
(home-shepherd-configuration-file): Use 'start-in-the-background' when
it is defined.

services: shepherd: Default to version 0.9.

* gnu/services/shepherd.scm (scm->go): Define 'shepherd&co' and pass it
to 'with-extensions'.
(shepherd-configuration-file): Call 'start-in-the-background' when it is
defined.
(<shepherd-configuration>)[shepherd]: Default to SHEPHERD-0.9.
* gnu/system.scm (hurd-default-essential-services): Use SHEPHERD-0.8.

shepherd: Adjust 'fork+exec-command/container' for the Shepherd 0.9.

* gnu/build/shepherd.scm (exec-command*): New procedure, with code
formerly...
(make-forkexec-constructor/container): ... here.  Use it.
(fork+exec-command/container): Use 'fork+exec-command' only when
CONTAINER-SUPPORT? is false or PID is the current process.

gnu: shepherd: Add 0.9.0.

* gnu/packages/admin.scm (shepherd): Rename to...
(shepherd-0.8): ... this.  New variable.
(shepherd): Define as an alias for SHEPHERD-0.8.
(shepherd-0.9): New variable.
(guile2.2-shepherd): Inherit from SHEPHERD-0.9 and adjust inputs
accordingly.

gnu: lagrange: Update to 1.12.1.

* gnu/packages/web-browsers.scm (lagrange): Update to 1.12.1.

gnu: keepassxc: Update to 2.7.1.

* gnu/packages/password-utils.scm (keepassxc): Update to 2.7.1.

gnu: vim: Update to 8.2.4701.

* gnu/packages/vim.scm (vim): Update to 8.2.4701.
[arguments]: Adjust custom 'skip-or-fix-failing-tests phase to skip
another test.

installer: user: Remove useless filtering.

* gnu/installer/user.scm (users->configuration): Remove root account filtering
that is now performed in the "run-user-add-page" procedure.

installer: user: Forbid root user creation.

Forbid root user creation as it could lead to a system without any
non-priviledged user accouts.

Fixes: <https://issues.guix.gnu.org/54666>.

* gnu/installer/newt/user.scm (run-user-add-page): Forbid it.

gnu: python-pybtex: Update to 0.24.0.

* gnu/packages/python-xyz.scm (python-pybtex): Update to 0.24.0.
[native-inputs]: Remove python-nose; add python-pytest.
[inputs]: Move python-latexcodec, python-pyyaml, and python-six from here...
[propagated-inputs]: ...to here.
[arguments]: Use pytest.

gnu: python-latexcodec: Update to 2.0.1.

* gnu/packages/python-xyz.scm (python-latexcodec): Update to 2.0.1.
[inputs]: Move python-six from here...
[propagated-inputs]: ...to here.

gnu: Add r-rnaseqdtu.

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

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

gnu: Add r-stager.

* gnu/packages/bioconductor.scm (r-stager): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

gnu: Add r-rafalib.

* gnu/packages/cran.scm (r-rafalib): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

gnu: icecat: Update to 91.8.0-guix0-preview1 [security fixes].

Includes fixes for CVE-2022-1097, CVE-2022-1196, CVE-2022-24713,
CVE-2022-28281, CVE-2022-28282, CVE-2022-28285, CVE-2022-28286, and
CVE-2022-28289.

* gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.

gnu: poco: Make description a full sentence.

* gnu/packages/cpp.scm (poco)[description]: Expand into a full sentence.

gnu: u-boot-rockpro64-rk3399: Add support for booting from SCSI/SATA.

* gnu/packages/bootloaders.scm (u-boot-rockpro64-rk3399)[arguments]: Add
  'patch-config phase to support SCSI/SATA disks.

Signed-off-by: Vagrant Cascadian <vagrant@debian.org>

gnu: u-boot: Update to 2022.04.

* gnu/packages/bootloaders.scm (u-boot): Update to 2022.01.
  [native-inputs]: Add gnutls, tinfo, libuuid.
  (u-boot-qemu-riscv64-smode): Drop custom
  patches.
* gnu/packages/patches/u-boot-allow-disabling-openssl.patch: Refresh patch.
* gnu/packages/patches/u-boot-riscv64-fix-extlinux.patch: Remove patch,
  applied upstream.
* gnu/local.mk (dist_patch_DATA): Update with removed patches.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>

gnu: Add ncurses-with-tinfo.

* gnu/packages/ncurses.scm (ncurses/tinfo): New variable.

gnu: l2md: Update to 9db252bc.

[[PGP Signed Part:No public key for 2208D20958C1DEB0 created at 2022-03-28T11:03:48+0200 using RSA]]

* gnu/packages/mail.scm (l2md): Update to 9db252bc.

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

services: messaging: Fix two copy-paste mistakes; avoid warnings.

* gnu/services/messaging.scm (file-name-list, file-object-list): Fix
name in 'define-maybe' instances.

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

gnu: plocate: Build with "--sharedstatedir=/var".

Current plocate package sets the --sharedstatedir to a store directory, which
causes updatedb and plocate to fail by default since the store is immutable.
This will set the default database path to /var/cache/plocate.db instead.

* gnu/packages/search.scm (plocate): Change build options.

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

gnu: phodav: Use libsoup 2 instead of libsoup 3.

Looks like phodav requires libsoup 2. Example of failing build logs,
wanting libsoup 2.4: <https://ci.guix.gnu.org/build/584454/log/raw>

After swapping the dependency, tests were failing due to HOME not being
writable. I added a new build phase to account for this. I also removed
the start-virtual-dir-server phase which no longer seems required, the
tests pass without it.

* gnu/packages/gnome.scm (phodav): Fix build, tests.
[inputs]: Replace libsoup 3 with libsoup 2.
[arguments]<#:phases>[set-temporary-home]: New phase.
[arguments]<#:phases>[start-virtual-dir-server]: Remove phase.

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

gnu: pantheon-calculator: Update to 1.7.2.

* gnu/packages/pantheon.scm (pantheon-calculator): Update to 1.7.2.
[arguments]: Remove trailing boolean.
[inputs]: Use guix style and add libhandy input.

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

gnu: python-w3lib: Fix build.

* gnu/packages/python-web.scm (python-w3lib): Fix build.
  [source]: Add python-w3lib-fix-test-failure.patch.
  [arguments]: Use pytest in the 'check phase.
  [native-inputs]: Add python-pytest.
* gnu/packages/patches/python-w3lib-fix-test-failure.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

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

gnu: python-gst: Fix the concatenation of install path.

Fixes a regression introduced in a5c2e7961c21ef8620ce4cfb3569109fbd694e1e.

* gnu/packages/gstreamer.scm (python-gst):
[arguments]:
<configure-flags>: Add missing leading slash.

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

gnu: python-dotenv: Update to 0.20.0.

* gnu/packages/python-xyz.scm (python-dotenv): Update to 0.20.0.
[home-page]: Update home page.

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

gnu: linux: Allow kconfig options to be strings

* gnu/packages/linux.scm (config->string): add a clause handling strings

Allows for the declarative configuration of kconfig options which accept
strings, such as CONFIG_MODULE_SIG_KEY.

I've enclosed the given string in quotes, but don't do any kind of
escaping. See the kernel mailing list for the current state of escaped
strings upstream:

https://patchwork.kernel.org/project/linux-kbuild/patch/1431003982-992-1-git-send-email-sr@denx.de/

Apologies to those with double-quotes or backslashes in their
CONFIG_SYSTEM_*_KEYS.

Signed-off-by: antlers <autumnalantlers@gmail.com>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: celluloid: Update to 0.23.

* gnu/packages/video.scm (celluloid): Update to 0.23.

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

doc: Update the sample yggdrasil-private.conf.

* doc/guix.texi (Networking Services): Update the sample yggdrasil-private.conf.

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

gnu: curlie: Update to 1.6.9

* gnu/packages/curl.scm (curlie): Update to 1.6.9

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

gnu: xmonad-next: Change #:phases to gexp.

* gnu/packages/wm.scm (xmonad-next)[arguments]: Use #$output, #$name
and #$synopsis instead of %output, name and synopsis.

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

Merge branch 'wip-pyyaml'

gnu: pigx-scrnaseq: Set NUMBA_CACHE_DIR.

This is needed since the update of python-loompy.

* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Rename
'set-PYTHONPATH to 'set-additional-environment-variables and set
NUMBA_CACHE_DIR.

gnu: pigx-scrnaseq: Use new inputs style.

* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use plain list.

gnu: pigx-scrnaseq: Update to 1.1.8.

* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.8.
[patches]: Remove.
[native-inputs]: Remove.
* gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

news: Add 'de' translation.

* etc/news.scm: Add German translation of 'guix shell --export-manifest' entry.

gnu: r-with-tests: Update to 4.1.3.

* gnu/packages/statistics.scm (r-with-tests): Update to 4.1.3.

gnu: git: Update to 2.35.1.

* gnu/packages/version-control.scm (git): Update to 2.35.1.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>

Revert "gnu: git: Update to 2.35.1."

This reverts commit 223a3d7f7fdb6af9c4c090785cab15d38680e887, as it triggered
thousands of rebuilds due to inadvertently touching git-minimal/fixed.

Reported-by: Christopher Baines <mail@cbaines.net>

gnu: python-pyyaml: Update to 6.0.

* gnu/packages/python-xyz.scm (python-pyyaml): Update to 6.0.

gnu: python2-pyyaml: Detach source from python-pyyaml.

* gnu/packages/python-xyz.scm (python2-pyyaml): Override source and version
fields.
(python-pyyaml)[properties]: Add python2-variant.

gnu: eyeD3: Update to 0.9.6.

* gnu/packages/mp3.scm (eyed3): Update to 0.9.6.
[propagated-inputs]: Add python-deprecation and python-filetype.

news: Add entry about 'guix shell --export-manifest'.

* etc/news.scm: Add entry.

shell: Add '--export-manifest'.

* guix/scripts/shell.scm (show-help, %options): Add '--export-manifest'.
(manifest-entry-version-prefix, manifest->code*)
(export-manifest): New procedures.
(guix-shell): Honor '--export-manifest'.
* tests/guix-shell-export-manifest.sh: New file.
* Makefile.am (SH_TESTS): Add it.
* doc/guix.texi (Invoking guix shell): Document '--export-manifest'.
(Invoking guix environment): Link to it.
(Invoking guix pack): Likewise.

environment: Export 'load-manifest'.

* guix/scripts/environment.scm (load-manifest): New procedure.
(options/resolve-packages): Use it.

packages: Add 'package-unique-version-prefix'.

* gnu/packages.scm (package-unique-version-prefix): New procedure.
* guix/scripts/package.scm (manifest-entry-version-prefix): Use it.
* tests/packages.scm ("package-unique-version-prefix, gcc@8")
("package-unique-version-prefix, grep"): New tests.

gnu: Add parole.

* gnu/packages/xfce.scm (parole): New variable.

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

services: Add 'log-cleanup' service to '%base-services' for build logs.

* gnu/services/base.scm (%base-services): Add 'log-cleanup-service-type'
instance.
* doc/guix.texi (Log Rotation): Add example and mention '%base-services'.

services: Add 'log-cleanup-service-type'.

* gnu/services/admin.scm (<log-cleanup-configuration>): New record
type.
(log-cleanup-program, log-cleanup-mcron-jobs): New procedures.
(log-cleanup-service-type): New variable.
* doc/guix.texi (Log Rotation): Document it.

gnu: mediainfo: Update to 22.03.

* gnu/packages/video.scm (mediainfo): Update to 22.03.

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

gnu: libmediainfo: Update to 22.03.

* gnu/packages/video.scm (libmediainfo): Update to 22.03.

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

gnu: gtkmm: Update to 4.6.1.

* gnu/packages/gtk.scm (gtkmm): Update to 4.6.1.
[propagated-inputs]: Remove atkmm because it's no longer needed.
* gnu/packages/gtk.scm (pangomm): Update to 2.50.0.
[propagated-inputs]: Replace 'pango' with 'pango-next'.

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

gnu: Add fcitx5-gtk4.

* gnu/packages/fcitx5.scm (fcitx5-gtk4): New variable.

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

gnu: gtk: Update to 4.6.1.

* gnu/local.mk (dist_patch_DATA): Remove gtk-introspection-test.patch.
* gnu/packages/patches/gtk-introspection-test.patch: Remove.
* gnu/packages/gtk.scm (gtk): Update to 4.6.1.
[source]: Remove stale patch.
[arguments]<phases>: Add 'patch-rst2man' phase, correct the binary name of
rst2man to 'rst2man.py'
[inputs]: Add libjpeg-turbo, libpng, libtiff.
[native-inputs]: Add python-docutils.
[propagated-inputs]: Use pango-next.
* gnu/packages/fcitx5.scm (fcitx5-gtk)[arguments]: Disable GTK4 build.
<configure-flags>: Add "-DENABLE_GTK_IM_MODULE=OFF".
<phases>: In phase "patch-install-prefix", Remove GTK4 code.
[inputs]: Remove package gtk.
[outputs]: Remove output "gtk4".

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

gnu: pango 1.50: Add version 1.50.4.

* gnu/packages/gtk.scm(pango-next): New variable.

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

gnu: freebayes: Fix test suite.

* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Add python.

gnu: smithwaterman: Use new style for phases.

* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Use list
of G-Expressions.

gnu: smithwaterman: Fix cross-compiling.

* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add
make-flag to use cxx-for-target. Adjust custom 'patch-source and
'build-dynamic phases to use cross toolchain binaries when cross
compiling. Remove trailing #t from phases.

gnu: marble-qt: Update to 21.12.3.

* gnu/packages/kde.scm (marble-qt): Update to 21.12.3.
  [inputs]: Add qtwebchannel, qtwebengine.

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

gnu: Add r-zoeppritz.

* gnu/packages/cran.scm (r-zoeppritz): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

gnu: Add python-bip39.

* gnu/packages/python-xyz.scm (python-bip39): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

gnu: parallel: Update to 20220322.

* gnu/packages/parallel.scm (parallel): Update to 20220322.

gnu: stgit: Update to 1.5.

* gnu/packages/version-control.scm (stgit): Update to 1.5.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>

gnu: git: Update to 2.35.1.

* gnu/packages/version-control.scm (git): Update to 2.35.1.
[phases]: Delete trailing #t.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>

gnu: emacs-elpy: Update to 1746e70.

* gnu/packages/emacs-xyz.scm (emacs-elpy): Update to 1746e70.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>