gnu: libstrophe: Update to 0.12.0.

* gnu/packages/messaging.scm (libstrophe): Update to 0.12.0.

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

gnu: emacs-doom-themes: Include extension files.

Newer versions of `emacs-doom-themes' separated extension support into a
separate directory, so this change includes those files.

* gnu/packages/emacs-xyz.scm (emacs-doom-themes)[arguments]: Consider
extensions/*.el files.

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

gnu: public-inbox: Update to 1.8.0.

Some fixes are needed in both the testsuite and the package itself before
tests can pass so disable them for now.

Also, the lei command needs curl to work, so add it to the PATH in
‘wrap-program’.

* gnu/packages/mail.scm (public-inbox)[version]: Change to 1.8.0.
[source]: Update hash.
[arguments]<#:tests?>: Set to #f.
[arguments]<#:phases>{wrap-programs}: Add curl to PATH.
[inputs]: Add curl and perl-socket-msghdr.

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

gnu: Add perl-socket-msghdr

* gnu/packages/perl.scm (perl-socket-msghdr): New variable.

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

gnu: public-inbox: Some packaging fixes

The file ‘script/public-inbox-compact’ doesn't call ‘xapian-compact’ directly
anymore, so the substitution in the ‘qualify-paths’ phase doesn't do anything.

Now there's a reference to ‘xapian-compact’ in ‘lib/PublicInbox/Xapcmd.pm’,
so substitute the path there.

And move xapian from native-inputs to inputs and use its input path in the
substitution, since ‘xapian-compact’ is called during normal execution of
public-inbox.

Also add ‘bash-minimal’ to the package's inputs, since it uses ‘wrap-program’.

Finally, take the opportunity to change build phases to not return #t
unconditionally, since that isn't necessary anymore.

* gnu/packages/mail.scm (public-inbox)[arguments]<#:phases>: Don't return #t
from each phase.
{qualify-paths}: Substitute ‘xapian-compact’ path in the correct file.  Use
‘search-input-file’ rather than ‘which’ to find it.
[native-inputs]: Move ‘xapian’ from here ...
[inputs]: ... to here. Add ‘bash-minimal’.

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

gnu: Add emacs-bfuture.

* gnu/packages/emacs-xyz.scm (emacs-bfuture): New variable.

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

shell: '--export-manifest -D x -D y' generates a valid manifest.

* guix/scripts/shell.scm (manifest->code*): Add missing 'list' in
generated 'concatenate-manifests' call.
* tests/guix-shell-export-manifest.sh: Add test.

gnu: Remove unreferenced patch.

This is a follow-up to a08c21f206d34a42d311e46b495b422188be70eb.

* gnu/packages/patches/libmicrohttpd-0.9.73-test-ssl3.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: LLVM, Clang, LLD: Update to 14.0.4.

* gnu/packages/llvm.scm (%llvm-monorepo-hashes): Adjust for 14.0.4.
(%llvm-patches): Likewise.
(llvm-14, clang-14, lld-14): Update to 14.0.4.
* gnu/packages/patches/clang-14.0-libc-search-path.patch: Adjust for upstream
changes.

daemon: Clarify ‘--check’ error when outputs are missing.

Drop the confusing ‘invalid’ jargon and display a hint like we do
for ‘--fallback’.

* nix/libstore/build.cc (DerivationGoal::outputsSubstituted): Rewrite error message.

gnu: libmicrohttpd: Update to 0.9.75.

* gnu/packages/gnunet.scm (libmicrohttpd): Update to 0.9.75.

gnu: libmicrohttpd: Use G-expressions.

* gnu/packages/gnunet.scm (libmicrohttpd)[arguments]:
Rewrite as G-expressions.

gnu: pgpdump: Update to 0.35.

* gnu/packages/gnupg.scm (pgpdump): Update to 0.35.

gnu: ocrfeeder: Update to 0.8.5.

* gnu/packages/gnome.scm (ocrfeeder): Update to 0.8.5.
[arguments]: Don't explicitly return #t from phases.

gnu: icedove: Use updated clang and llvm.

* gnu/packages/gnuzilla.scm (icedove)[native-inputs]: Replace `clang-11`
and `clang-11` with the default version, which is now 13.

gnu: icedove: Update to 91.10.0 [fixes CVE-2022-1834].

* gnu/packages/gnuzilla.scm (icedove): Update to 91.10.0.

gnu: tractor: Update to 3.13.

* gnu/packages/tor.scm (tractor): Update to 3.13.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>

gnu: fortune-mod: Fix fortune directory.

It now matches the one given in the fortune(6) man page.

* gnu/packages/games.scm (fortune-mode)[arguments]:
Install to /share rather than /local/share/games.
Shorten the 'fix-install-directory phase.

gnu: pigx-scrnaseq: Update to 1.1.9.

* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.9.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove autoconf and automake.

gnu: pigx-bsseq: Update to 0.1.7.

* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.7.
[source]: Remove patch.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove automake and autoconf.
* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove patch.

gnu: pigx-chipseq: Update to 0.1.0.

* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.1.0.
[source]: Remove patch.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove autoconf and automake.
* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove patch.

gnu: vim: Update to 8.2.5048.

* gnu/packages/vim.scm (vim): Update to 8.2.5048.
[arguments]: Patch another instance of '/bin/sh'.

gnu: pigx-rnaseq: Update to 0.1.0.

* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.0.
[arguments]: Remove phase 'patch-knitr.

gnu: pigx-rnaseq: Update to 0.0.21.

* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.21.

gnu: pigx-rnaseq: Fix build.

* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'patch-knitr.

gnu: gnome-commander: Update to 1.14.2.

* gnu/packages/gnome.scm (gnome-commander): Update to 1.14.2.

gnu: angband: Update to 4.2.4.

* gnu/packages/games.scm (angband): Update to 4.2.4.
[arguments]: Don't explicitly return #t from phases.

gnu: freeipmi: Update to 1.6.9.

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

import: minetest: Fix typo.

* guix/import/minetest.scm (important-dependencies): Fix ‘choosen’ typo.

gnu: corefreq: Update to 1.90.1.

* gnu/packages/linux.scm (corefreq): Update to 1.90.1.

bash completion: Fix & unify option parsing.

We now correctly recognise ‘guix -Abcdef’ as equivalent to ‘guix -f’.

* etc/completion/bash/guix (_guix_is_short_option, guix_is_long_option):
New functions.
(_guix_is_dash_f, _guix_is_dash_l, _guix_is_dash_L, _guix_is_dash_m)
(_guix_is_dash_C, _guix_is_dash_p): Use them.

gnu: services: Update setuid service description.

* gnu/services.scm (setuid-program-service-type)[description]:
Remove ‘root’, add ‘setgid’.

gnu: libfprint: Update to 1.94.4.

* gnu/packages/freedesktop.scm (libfprint): Update to 1.94.4.

gnu: fprintd: Update to 1.94.2.

* gnu/packages/freedesktop.scm (fprintd): Update to 1.94.2.

gnu: fprintd: Remove input labels.

* gnu/packages/freedesktop.scm (fprintd)[native-inputs]:
Remove input labels.

gnu: fprintd: Fix build.

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

gnu: beancount: Update to 2.3.5.

* gnu/packages/finance.scm (beancount): Update to 2.3.5.

gnu: caf: Update to 0.18.6.

* gnu/packages/cpp.scm (caf): Update to 0.18.6.

gnu: quazip: Update to 1.3.

* gnu/packages/compression.scm (quazip): Update to 1.3.

gnu: foomatic-filters: Use project home page.

* gnu/packages/cups.scm (foomatic-filters)[home-page]: Point upstream.

gnu: Add sylamer.

* gnu/packages/bioinformatics.scm (sylamer): New variable.

gnu: linux-libre 5.10: Update to 5.10.119.

* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.119.
(linux-libre-5.10-pristine-source): Update hash.

gnu: linux-libre 5.15: Update to 5.15.44.

* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.44.
(linux-libre-5.15-pristine-source): Update hash.

gnu: linux-libre: Update to 5.17.12.

* gnu/packages/linux.scm (linux-libre-5.17-version): Update to 5.17.12.
(linux-libre-5.17-pristine-source): Update hash.

gnu: Add r-gsalib.

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

gnu: Add glibc-locales-2.32.

* gnu/packages/base.scm (glibc-locales-2.32): New variable.

gnu: Add glibc-locales-2.31.

* gnu/packages/base.scm (glibc-locales-2.31): New variable.

gnu: Add glibc-locales-2.30.

* gnu/packages/base.scm (glibc-locales-2.30): New variable.

gnu: Add glibc-2.32.

* gnu/packages/base.scm (glibc-2.32): New variable.

gnu: Remove python2-biopython.

* gnu/packages/bioinformatics.scm (python2-biopython): Delete variable.

gnu: Remove pplacer-scripts.

* gnu/packages/bioinformatics.scm (pplacer-scripts): Delete variable.

gnu: Remove pplacer.

* gnu/packages/bioinformatics.scm (pplacer): Delete variable.

gnu: Remove python2-pytest-cov.

* gnu/packages/check.scm (python2-pytest-cov): Delete variable.

gnu: Remove python2-called-python.

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

gnu: Remove python-prompt-toolkit-2.

* gnu/packages/python-xyz.scm (python-prompt-toolkit-2): Delete variable.
(python-prompt-toolkit)[properties]: Delete field.
(python-jupyter-console): Replace python-prompt-toolkit-2 with
python-prompt-toolkit.

gnu: Remove python2-setuptools.

* gnu/packages/python-xyz.scm (python2-setuptools): Delete variable.
(python-setuptools)[properties]: Delete field.
* gnu/packages/syncthing.scm (syncthing-gtk): Delete commented native input.
* guix/lint.scm (check-inputs-should-not-be-an-input-at-all): Remove obsolete entries.

gnu: Remove python2-checkm-genome.

* gnu/packages/bioinformatics.scm (python2-checkm-genome): Delete variable.

gnu: qtwebengine: Re-style inputs.

* gnu/packages/qt.scm (qtwebengine)[phases]: Delete trailing #t.
{substitute-source}: Use search-input-file.
[inputs, native-inputs]: Use new style.

gnu: Remove python2-backports-csv.

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

gnu: python2-six: Disable tests.

* gnu/packages/python-xyz.scm (python2-six)[native-inputs]: Clear.
[phases]: Delete check phase.

gnu: Remove python2-fonttools.

* gnu/packages/python-xyz.scm (python2-fonttools): Delete variable.
(python-fonttools)[properties]: Delete field.

gnu: Remove python2-py.

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

gnu: Remove python2-pyparsing.

* gnu/packages/python-build.scm (python2-pyparsing): Delete variable.
(python-pyparsing)[properties]: Delete field.

gnu: Remove python2-setuptools-scm.

* gnu/packages/python-xyz.scm (python2-setuptools-scm): Delete variable.
(python-lfdfiles)[properties]: Delete field.

gnu: Remove python2-six-bootstrap.

* gnu/packages/python-build.scm (python2-six-bootstrap): Delete variable.

gnu: Remove python2-pyxdg.

* gnu/packages/freedesktop.scm (python2-pyxdg): Delete variable.

gnu: Remove python2-wcwidth.

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

gnu: openbox: Patch for Python 3.

* gnu/packages/patches/openbox-python3.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/openbox.scm (openbox)[source]: Apply it.
[arguments]: New field.
[propagated-inputs]: Replace python2-pyxdg with python-pyxdg.
[native-inputs]: Replace python-2 with python-wrapper.
Add autoconf, automake, gettext-minimal and libtool.

gnu: Remove python2-pyyaml.

* gnu/packages/python-xyz.scm (python2-pyyaml): Delete variable.
(python-jsonschema)[properties]: Delete field.

gnu: ocaml-dose3: Disable tests to avoid Python 2 dependencies.

* gnu/packages/ocaml.scm (ocaml-dose3)[tests?]: Set to #f.
[native-inputs]: Use new style.  Remove python-2 and python2-pyyaml.

gnu: Remove python2-nose.

* gnu/packages/check.scm (python2-nose): Delete variable.
(python-nose)[properties]: Delete field.

gnu: python-setproctitle: Delete obsolete phase.

* gnu/packages/python-xyz.scm (python-setproctitle)
[phases]{patch-Makefile}: Delete phase.

gnu: pdf2djvu: Disable tests to avoid Python 2 dependencies.

* gnu/packages/djvu.scm (pdf2djvu)[tests]: Set to #f.
[test-target]: Delete argument.
[native-inputs]: Use new style.  Delete python-2 and python2-nose.
[inputs]: Use new style.

gnu: Remove python2-attrs-bootstrap.

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

gnu: Remove python2-libxml2.

* gnu/packages/xml.scm (python2-libxml2): Delete variable.

gnu: Remove 4store.

* gnu/packages/databases.scm (4store): Delete variable.
* gnu/packages/patches/4store-fix-buildsystem.patch: Delete file.
* gnu/packages/patches/4store-unset-preprocessor-directive.patch: Likewise.
* gnu/local.mk (dist_patch_DATA): De-register them.

gnu: libpqxx: Update to 7.7.3.

* gnu/packages/databases.scm (libpqxx): Update to 7.7.3.
[source]: Use git.
[native-inputs]: Replace python-2 with python-wrapper.  Add gcc-11.
[tests?]: Expound comment.
[phases]: Delete argument.

gnu: Remove python2-pyfakefs-bootstrap.

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

gnu: mod-host: Update to 0.10.6-4.cdd30dd.

* gnu/packages/music.scm (mod-host): Update to 0.10.6-4.cdd30dd.
[source]: Use git-version and git-file-name.
[arguments]: Use gexps.
[phases]: Delete trailing #t.
[inputs]: Replace jack-1 with jack-2.
[native-inputs]: replace python-2 with python-wrapper.

gnu: jack-2: Update to 1.9.21.

* gnu/packages/audio.scm (jack-2): Update to 1.9.21.
[source]: Use git.
[phases]: Delete trailing #t.
{wrap-python-scripts}: Use search-input-file.

gnu: icedove: Use new style for inputs.

* gnu/packages/gnuzilla.scm (icecat)[inputs]: Use new style.

gnu: icedove: Delete obsolete Python 2 input.

* gnu/packages/gnuzilla.scm (icedove)[native-inputs]: Replace python-2 with
python-wrapper.  Delete python.
[phases]: Delete trailing #t.

gnu: mozjs: Cleanup to only keep the last version.

* gnu/packages/gnuzilla.scm (mozjs): Preserve only the metadata and otherwise
update fields to use those of mozjs-78.
[arguments]: Use gexps.
[phases]: Delete trailing #t.
[native-inputs]: Use new style.
(mozjs-38, mozjs-52, mozjs-60, mozjs-78): Delete variables.
* gnu/packages/patches/mozjs17-aarch64-support.patch
* gnu/packages/patches/mozjs24-aarch64-support.patch
* gnu/packages/patches/mozjs38-pkg-config-version.patch
* gnu/packages/patches/mozjs38-shell-version.patch
* gnu/packages/patches/mozjs38-tracelogger.patch
* gnu/packages/patches/mozjs38-version-detection.patch
* gnu/packages/patches/mozjs60-riscv64-support.patch: Delete patches.
* gnu/local.mk (dist_patch_DATA): De-register them.
* gnu/packages/games.scm (0ad): Adjust accordingly.
* gnu/packages/gnome.scm (gjs): Likewise.
* gnu/packages/polkit.scm (polkit-mozjs): Likewise.

gnu: Remove python2-cython.

* gnu/packages/python-xyz.scm (python2-cython): Delete variable.
(python-feedgenerator)[properties]: Delete field.

gnu: Remove python2-lirc.

* gnu/packages/lirc.scm (python2-lirc): Delete variable.
(python-lirc)[properties]: Delete field.

gnu: Remove python2-tlsh.

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

gnu: Remove python2-more-itertools.

* gnu/packages/python-xyz.scm (python2-more-itertools): Delete variable.
(python-jsonpatch)[properties]: Delete field.

gnu: gnome-keyring: Use Python 3.

* gnu/packages/gnome.scm (libgnome-keyring)[source]: Fix indentation.
[arguments]: Use gexps.
[phases]{fix-docbook}: Delete phase.
[native-inputs]: Use new style.  Replaec python-2 with python-wrapper.  Use
current docbook-xml.  Add libxml2.

gnu: Remove gnome-doc-utils.

* gnu/packages/gnome.scm (gnome-doc-utils): Delete variable.

gnu: Remove python2-libmpsse.

* gnu/packages/embedded.scm (python2-libmpsse): Delete variable.

gnu: lolcode-lci: Update to 0.11.2-0.6762b72.

* gnu/packages/esolangs.scm (lolcode-lci): Update to 0.11.2-0.6762b72.
[native-inputs]: Replace python-2 with python-wrapper.

gnu: dico: Use Python 3.

* gnu/packages/dico.scm (dico)[source]: Fix indentation.
[phases]: Delete trailing #t.
[inputs]: Use new style.  Replace python-2 with python-wrapper.

gnu: libdbusmenu: Update to 16.04.0-496.

* gnu/packages/gtk.scm (libdbusmenu): Update to 16.04.0-496.
[source]: Fetch using Breezy.
[arguments]: Use gexps.
[phases]: Delete trailing #t.
{remove-deprecated-gnome-common-macros}: New phase.
{patch-paths}: Likewise.
[inputs]: Use new style.
[native-inputs]: Likewise. Replace gnome-doc-utils with gnome-common.  Replace python-2 with
python-wrapper.  Add autoconf, automake, libtool, libxslt and which.

gnu: brasero: Remove obsolete gnome-doc-utils input.

* gnu/packages/gnome.scm (brasero)[inputs]: Delete gnome-doc-utils.

gnu: Remove python2-lxml.

* gnu/packages/xml.scm (python2-lxml): Delete variable.

gnu: mia: Update to 2.4.7.

* gnu/packages/patches/mia-fix-boost-headers.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/image-processing.scm (mia): Update to 2.4.7.
[source]: Apply patch.
[configure-flags]: Use the more conventional OFF option value (instead of 0).
[inputs]: Use new style.  Replace python2-lxml by python-lxml.  Replace vtk by
vtk-7.
[native-inputs]: Use new style.  Replace python-2 with python-wrapper.

gnu: dcmtk: Update to 3.6.7 and build as a shared library.

* gnu/packages/image-processing.scm (dcmtk): Update to 3.6.7.
[arguments]: New field.

gnu: Remove vtk-6.

* gnu/packages/image-processing.scm (vtk-6): Delete variable.

gnu: itk-snap: Fix build.

* gnu/packages/patches/itk-snap-alt-glibc-compat.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/image-processing.scm (itk-snap): Apply it.
[phases]: Delete trailing #t.
[inputs]: Use new style.  Replace vtk-6 with vtk-7.

gnu: Add vtk-7.

* gnu/packages/image-processing.scm: (vtk-7): New variable.
* gnu/packages/patches/vtk-7-gcc-10-compat.patch: New patch.
* gnu/packages/patches/vtk-7-hdf5-compat.patch: Likewise.
* gnu/packages/patches/vtk-7-python-compat.patch: Likewise.
* gnu/local.mk (dist_patch_DATA): Register them.