gnu: emacs: Load package descriptors from packages referenced by subdirs.el

* gnu/packages/aux-files/emacs/guix-emacs.el
(guix-emacs--non-core-load-path): New procedure.
(guix-emacs-autoload-packages): Use it here.
(guix-emacs-load-package-descriptors): New procedure.
* gnu/packages/emacs.scm (emacs)[install-site-start]: Install advice to run
‘guix-emacs-load-package-descriptors’.

build-system: emacs: Keep -pkg.el files.

Partly fixes <https://bugs.gnu.org/48331> -- package descriptions can now be
found in the install directory.

* guix/build/emacs-build-system.scm (%default-exclude): Remove "-pkg\\.el$".

gnu: emacs: Make DocView PDF work out of the box.

* gnu/packages/emacs.scm (emacs)[patch-program-file-names]: Add patches for
the programs “gs”, “dvipdf”, “ps2pdf” and “pdftotext”.
[inputs]: Add ghostscript and poppler.

gnu: emacs: Find real GVFS processes.

* gnu/packages/emacs.scm (emacs)[#:phases]<patch-program-file-names>: Expand
calls to “tramp-compat-process-running-p” so that Guix wrappers are also
matched.

gnu: Add valeronoi.

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

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: st: Install terminfo files.

* gnu/packages/suckless.scm (st)[native-inputs]: Add ncurses.
[make-flags](TERMINFO): New flag.
[phases](inhibit-terminfo-install): Remove phase.

Signed-off-by: Raghav Gururajan <rg@raghavgururajan.name>

gnu: emacs-org: Preserve version information.

* gnu/packages/emacs-xyz.scm (emacs-org)[#:phases]: Prevent install phase from
deleting the version information.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: emacs-consult-notmuch: Update to 0.6.

* gnu/packages/emacs-xyz.scm (emacs-consult-notmuch): Update to 0.6.

gnu: emacs-helm: Update to 3.8.2.

* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.8.2.

gnu: emacs-vertico: Update to 0.17.

* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 0.17.

gnu: python-ont-fast5-api: Update to 4.0.0.

* gnu/packages/bioinformatics.scm (python-ont-fast5-api): Update to 4.0.0.
[source]: Remove bundled plugin binaries.
[arguments]: Install plugin from inputs.
[inputs]: Add vbz-compression.
[propagated-inputs]: Remove python-six; add python-packaging.

gnu: Add vbz-compression.

* gnu/packages/bioinformatics.scm (vbz-compression): New variable.

system: vm: Remove the vga argument.

* gnu/system/vm.scm (common-qemu-options): Remove the "-vga std" argument that
is the default since QEMU 2.2.

Suggested-by: Attila Lendvai <attila@lendvai.name>

guix system vm: Add --no-graphic CLI argument.

It configures QEMU to use the tty it was started in for IO (as opposed to
opening a separate graphical window).  This enables copy-pasting and
scrollback.  Exit QEMU with C-a x.

* gnu/system/vm.scm (system-qemu-image/shared-store-script): Also add the
'-nographic' QEMU argument when called with #:graphic? #false.
* guix/scripts/system.scm (system-derivation-for-action): Propagate
the #:graphic? keyword arg.
(perform-action): Add and propagate the #:graphic? keyword arg.
(show-help): Add --no-graphic CLI arg.
(%options): Process the new --no-graphic CLI arg.
(process-action): Feed in the CLI arg through the #:graphic? keyword arg.
* doc/guix.texi (Invoking guix system): Add example to combine guix system and
invoking the vm start script into one command.  Split the description of the
various options into separate paragraphs.  Add a paragraph to describe
--no-graphic.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>

gnu: cl-coalton: Update to 0.0.1-2.012f6c8.

* gnu/packages/lisp-xyz.scm (sbcl-coalton): Update to 0.0.1-2.012f6c8.

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

gnu: cl-float-features: Update to 1.0.0-2.c1f86ae.

* gnu/packages/lisp-xyz.scm (sbcl-float-features): Update to 1.0.0-2.c1f86ae.

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

gnu: ivar: Disable parallel tests.

* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.

gnu: Remove python2-biom-format.

There are no users of this variant, and the current version of biom-format
does not support Python 2.

* gnu/packages/bioinformatics.scm (python2-biom-format): Remove variable.
(python-biom-format)[properties]: Remove field.

gnu: r-flowclust: Add gsl.

* gnu/packages/bioconductor.scm (r-flowclust)[inputs]: Remove accidentally
committed comment character.

gnu: icecat: Remove vestigial icecat-78-makeicecat.patch.

This is a followup to commit a63231003e7bbeafb0110b077788e47e78685f20.

* gnu/packages/patches/icecat-78-makeicecat.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: cuirass: Update to 1.1.0-6.df8837c.

* gnu/packages/ci.scm (cuirass): Update to 1.1.0-6.df8837c.

gnu: python-pandocfilters: Update to 1.5.0.

* gnu/packages/textutils.scm (python-pandocfilters): Update to 1.5.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>

gnu: icecat: Fix CVE-2021-43527.

* gnu/packages/patches/icecat-CVE-2021-43527.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gnuzilla.scm (icecat-source): Apply it.

gnu: nss: Fix CVE-2021-43527 via graft.

* gnu/packages/patches/nss-CVE-2021-43527.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/nss.scm (nss/fixed): New variable
(nss)[replacement]: New field.

gnu: openjdk16: Use MAKE-FILE-WRITABLE.

* gnu/packages/java.scm (openjdk16)[arguments]: Do not shell out to "chmod".

gnu: Add openjdk17.

* gnu/packages/java.scm (openjdk17): New variable.

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

doc: Give more details about generating patches with base commit information.

* doc/contributing.texi (Submitting Patches): Talk more about '--base'.

gnu: python2-decorator: Downgrade to 4.3.0

* gnu/packages/python-xyz.scm (python2-decorator): Keep at 4.3.0.
(python-decorator)[properties]: Add python2-variant.

gnu: ribodiff: Remove trailing #T.

* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T
from build phase.

gnu: ribodiff: Disable broken test.

* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase
'disable-plot-test.

gnu: python2-statsmodels: Downgrade to 0.9.0.

* gnu/packages/statistics.scm (python2-statsmodels): Downgrade to 0.9.0.

gnu: khmer: Fix build with Python 3.8.

* gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T.
[arguments]: Remove trailing #T from build phases; add build phase
'python-3.8-compatibility.

gnu: python-biom-format: Update to 2.1.10.

* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.10.
[source]: Simplify snippet.
[arguments]: Add phase 'relax; remove trailing #T from other build phases.
[propagated-inputs]: Add python-anndata; replace python-pandas-0.25 with
python-pandas.

gnu: Add trayer-srg.

* gnu/packages/wm.scm (trayer-srg): New variable.

Co-authored-by: Disseminate Dissent <disseminatedissent@protonmail.com>
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>

gnu: pardre: Update to 2.2.5.

* gnu/packages/bioinformatics.scm (pardre): Update to 2.2.5.
[arguments]: Remove trailing #T and update comment about tests.

gnu: pardre: Use C++ bindings for MPI.

* gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with
openmpi-c++.

gnu: Add openmpi-c++.

* gnu/packages/mpi.scm (openmpi-c++): New variable.

gnu: Add libconfini.

* gnu/packages/cpp.scm (libconfini): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>

gnu: shotcut: Update to 21.10.31.

* gnu/packages/video.scm (shotcut): Update to 21.10.31.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>

gnu: kdenlive: Update to 21.08.3.

* gnu/packages/kde.scm (kdenlive): Update to 21.08.3.
[arguments]: Pass "-DBUILD_TESTING=off" to #:configure-flags as tests are
currently disabled.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>

gnu: mlt: Update to 7.2.0.

* gnu/packages/video.scm (mlt): Update to 7.2.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>

gnu: ccls: Update to 0.20210330.

* gnu/packages/cpp.scm (ccls): Update to 0.20210330.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>

gnu: guile-udev: Update to 0.2.0

* gnu/packages/guile-xyz.scm (guile-udev): Update to 0.2.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>

gnu: python-ipython: Update to 7.20.0.

* gnu/packages/python-xyz.scm (python-ipython): Update to 7.20.0.

gnu: python-ipython: Remove trailing #T.

* gnu/packages/python-xyz.scm (python-ipython)[arguments]: Remove trailing #T
from build phases.

gnu: yggdrasil: Simplify build phases.

* gnu/packages/networking.scm (yggdrasil)[arguments]: Rewrite custom
'build phase reusing go-build-system 'build phase. Remove custom
'install phase.

gnu: go-golang-zx2c4-com-wireguard: Fix downloading source.

* gnu/packages/golang.scm (go-golang-zx2c4-com-wireguard)[source]:
Adjust commit string in git-reference.

gnu: go-github-com-vividcortex-ewma: Adjust import-path.

* gnu/packages/golang.scm (go-github-com-vividcortex-ewma)[arguments]:
Adjust import-path to location other go packages expect it to be.

gnu: guix: Update to 8cc099b.

* gnu/packages/package-management.scm (guix): Update to 8cc099b.

gnu: Add python-mygene.

* gnu/packages/bioinformatics.scm (python-mygene): New variable.

gnu: Add python-biothings-client.

* gnu/packages/bioinformatics.scm (python-biothings-client): New variable.

gnu: Add r-scdblfinder.

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

Revert "gnu: godot: Update to 3.4."

This reverts commit dd4365efa1c6fb609de9bd7cd10f9c82e064aed4.

We reverted this commit because it broke the operation of the only
package in Guix that depends on Godot, SuperStarfighter:

https://debbugs.gnu.org/cgi/bugreport.cgi?bug=52233#20

gnu: cl-tooter: Update to 1.0.0-3.ec97bee.

* gnu/packages/lisp-xyz.scm (cl-tooter): Update to 1.0.0-3.ec97bee.

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

gnu: cl-i18n: Update to 0.5.1-1.4216fe9.

* gnu/packages/lisp-xyz.scm (cl-i18n): Update to 0.5.1-1.4216fe9.

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

gnu: godot: Update to 3.4.

* gnu/packages/game-development.scm (godot): Update to 3.4.
[source]: Add new bundled dependencies to the origin snippet.

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

gnu: linux-libre 4.19: Update to 4.19.219.

* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.219.
(linux-libre-4.19-pristine-source): Update hash.

gnu: linux-libre 5.4: Update to 5.4.163.

* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.163.
(linux-libre-5.4-pristine-source): Update hash.

gnu: linux-libre 5.10: Update to 5.10.83.

* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.83.
(linux-libre-5.10-pristine-source): Update hash.

gnu: linux-libre: Update to 5.15.6.

* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.6.
(linux-libre-5.15-pristine-source): Update hash.

gnu: Remove couger.

This package has been moved to the Guix Past channel.

* gnu/packages/bioinformatics.scm (couger): Remove variable.

gnu: randomjungle: Fix compatibility errors.

* gnu/packages/machine-learning.scm (randomjungle)[arguments]: Add build phase
'fix-compatibility-errors to patch type errors.

news: Add entry about Icedove 91.

* etc/news.scm: New entry.

gnu: icecat: Remove leftovers of release 78.

No longer required as icedove is now based on the 91 branch.

* gnu/packages/gnuzilla.scm (mozilla-78-compare-locales): Remove.
(all-mozilla-78-locales): Remove.
(%icecat-78-version): Remove.
(icecat-78-source): Remove.

gnu: icedove: Update to 91.3.2.

The profile folder moved from `~/.icedove` to `~/.thunderbird`. You may
need to migrate (copy) your profile over.

* gnu/packages/gnuzilla.scm (icedove): Update to 91.3.2.
[source]: Switch back to icecat-source.
[arguments]: `obj-x86_64-pc-linux-gnu` folder is now generated during
build, so it can't deleted in front. Remove surounding `'` from
MOZ_DEDICATED_PROFILES to follow source code. MOZ_APP_BASENAME and
MOZ_APP_DISPLAYNAME are no longer set in `comm/mail/confvars.sh`. Update
path of `customizeToolbar.js`.
Delete `'bootstrap` phase and no longer set AUTOCONF variable as the
autoconf build part was removed. Set MACH_USE_SYSTEM_PYTHON and
MOZ_APP_NAME, the latter is the binary name.
`--enable-calendar` flag got removed. Use bundled NSS until
core-updates merge.
[inputs]: Update to `icu4c-69` and `nspr-4.32`. Use bundled NSS for now.
[native-inputs]: Switch to comm-esr91 branch. Remove autoconf, add m4.
Update rust and cargo to 1.51. Use `rust-cbindgen-0.19`.

gnu: Add nspr@4.32.

Required for icecat/icedove 91.

* gnu/packages/nss.scm (nspr-4.32): New variable.

gnu: emacs-citar: Remove unnecessary input.

* gnu/packages/emacs-xyz.scm (emacs-citar)[propagated-inputs]: Remove emacs-helm-bibtex.

gnu: bullet: Update to 3.17.

* gnu/packages/game-development.scm (bullet): Update to 3.17.
[arguments]<#:configure-flags>: Disable access to third-party libs.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Update Trezor support.

* gnu/packages/patches/python-trezor-agent-fix-argv0.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Apply previous removal.
* gnu/packages/finance.scm (python-trezor-agent): Update to 0.14.4.
[source]: Remove now useless patch.
(python-mnemonic): Update to 0.20.
(python-trezor): Update to 0.12.4
(trezor-agent): Update to 0.11.0-1.
[source]: Add file-name field.
[arguments]: Remove trailing #T in phases.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: python-daemon: Update to 2.3.0.

* gnu/packages/python-xyz.scm (python-daemon): Update to 2.3.0.
[native-inputs]: Add python-coverage and python-twine.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: openssh: Add support for ecdsa-sk, ed25519-sk ssh keys.

* gnu/packages/ssh.scm (openssh)[inputs]: Add LIBFIDO2.
[arguments]: Pass "--with-security-key-builtin".

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

gnu: Add libfido2.

* gnu/packages/security-token.scm (libfido2): New variable.

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

gnu: Add libcbor.

* gnu/packages/compression.scm (libcbor): New variable.

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

gnu: Add vim-nerdtree.

* gnu/packages/vim.scm (vim-nerdtree): New variable.

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

build-system: haskell: Add ‘hackage-uri’ procedure.

* guix/build-system/haskell (hackage-uri): New procedure.
* guix/import/hackage.scm (hackage-module->sexp, latest-release): Use it.
* tests/hackage.scm (match-ghc-foo, match-ghc-foo-6, match-ghc-foo-revision,
match-ghc-foo-import): Adjust accordingly.

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

gnu: Add smplayer.

* gnu/packages/video.scm (smplayer): New variable.

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

gnu: Add python-codespell.

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

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

installer: Make LUKS2 the default format for encrypted devices

* gnu/installer/parted.scm (luks-format-and-open): Change it.

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

doc: Document LUKS2 GRUB support and shortcomings

* doc/guix.texi (Keyboard Layout, Networking, and Partitioning)[Disk
Partitioning]: Document it.

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

gnu: system: Add LUKS2 support for the root file system.

* gnu/bootloader/grub.scm (grub-configuration-file): Add 'insmod
luks2'.
* gnu/system/mapped-devices.scm (open-luks-device): Create
'/run/cryptsetup/' directory.

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

inferior: 'cached-channel-instance' does not cache unauthenticated instances.

The comment saying that caching is fine even when AUTHENTICATE? is false
was true in commit 838ac881ec98cb71d4a4e4b20773573f99ecbf25, but it
became incorrect in 7cfd789150f448cf5256b88915bae4163cc9db03, which
no longer calls 'latest-channel-instances' on cache hits.

* guix/inferior.scm (cached-channel-instance): Do not create CACHED when
AUTHENTICATE? is false.

gnu: sdrangel: Add missing input.

QtQuick is required by some runtime features.

* gnu/packages/radio.scm (sdrangel)[inputs]: Add qtquickcontrols2.

gnu: python-language-server: Add deprecated alias.

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

Add deprecated alias for package removed in the parent commit.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add python-lsp-server.

* gnu/packages/python-xyz.scm (python-language-server): Delete variable.
* gnu/packages/python-xyz.scm (python-lsp-server): New variable.

Removes deprecated python-language-server package and adds maintained
fork.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: python-lsp-jsonrpc: Add deprecated alias.

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

Add deprecated alias for package removed in the parent commit.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add python-lsp-jsonrpc.

* gnu/packages/python-xyz.scm (python-jsonrpc-server): Delete variable.
* gnu/packages/python-xyz.scm (python-lsp-jsonrpc): New variable.

Removes deprecated python-jsonrpc-server package and adds maintained
fork.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: python-jedi: Update to 0.18.1.

* gnu/packages/python-xyz.scm (python-jedi): Update to 0.18.1.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: python2-jedi: Remove package.

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

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: python-parso: Update to 0.8.2.

* gnu/packages/python-xyz.scm (python-parso): Update to 0.8.2.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: yggdrasil: Update to 0.4.1.

* gnu/packages/networking.scm (yggdrasil): Update to 0.4.1.
* gnu/packages/patches/yggdrasil-extra-config.patch: Update for new version.

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

gnu: yggdrasil: Update to 0.4.0.

* gnu/packages/patches/yggdrasil-extra-config.patch: Update patch.
* gnu/packages/networking.scm (yggdrasil): Update to 0.4.0.
[arguments]: Also install genkeys.
[propagated-inputs]: Remove go-github-com-cheggaaa-pb; add go-golang-org-x-sys,
go-github-com-mattn-go-runewidth, go-github-com-mattn-go-isatty,
go-github-com-fatih-color, go-github-com-cheggaaa-pb-v3,
go-github-com-vividcortex-ewma, and go-github-com-arceliar-ironwood.

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

gnu: Add go-github-com-arceliar-ironwood.

* gnu/packages/golang.scm (go-github-com-arceliar-ironwood): New variable.

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

gnu: Rename go-github-com-cheggaaa-pb to go-github-com-cheggaaa-pb-v3.

* gnu/packages/golang.scm (go-github-com-cheggaaa-pb): Rename this variable...
(go-github-com-cheggaaa-pb-v3): ...to this variable.
(go-github-com-cheggaaa-pb): New variable for deprecated package.

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

gnu: go-github-com-cheggaaa-pb: Update to 3.0.8.

* gnu/packages/golang.scm (go-github-com-cheggaaa-pb): Update to 3.0.8.
[arguments]: Disable tests; update import path.
[native-inputs]: Move go-github-com-mattn-go-isatty from here...
[propagated-inputs]: ...to here; add go-github-com-vividcortex-ewma and
go-github-com-rivo-uniseg.

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

gnu: Add go-github-com-mattn-go-runewidth.

* gnu/packages/golang.scm (go-github-com-mattn-go-runewidth): New variable.

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

gnu: Add go-github-com-rivo-uniseg.

* gnu/packages/golang.scm (go-github-com-rivo-uniseg): New variable.

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

gnu: Add go-github-com-vividcortex-ewma.

* gnu/packages/golang.scm (go-github-com-vividcortex-ewma): New variable.

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

gnu: Add python-mrkd.

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

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: telescope: Update to 0.6.1.

* gnu/packages/web-browsers.scm (telescope): Update to 0.6.1.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: cl-unix-opts: Update to 0.1.7-1.0e61f34.

* gnu/packages/lisp-xyz.scm (sbcl-unix-opts): Update to 0.1.7-1.0e61f34.
  [source]: Fetch using commit instead of old tag.

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