* doc/guix.texi (Invoking guix pull): Change "run" to "ran".

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

* gnu/packages/xfce.scm (thunar-volman): Update to 0.9.5.

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

This is a followup to 81c3dc32.

Since that commit, when /releases returned an empty JSON array, we would
not fall back to /tags because of the incorrect match.

* guix/import/github.scm (fetch-releases-or-tags): Match the empty
vector instead of the empty list.

* gnu/packages/xfce.scm (tumbler)[inputs]: Remove gstreamer.

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

* gnu/packages/xfce.scm (tumbler)[inputs]: Add cairo.

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

* gnu/packages/cluster.scm (libraft)[source]: Switch to GIT-FETCH.

* gnu/packages/cluster.scm (libraft): New variable.

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

* gnu/packages/package-management.scm (guix): Update to cc98b008.
(guix-daemon)[arguments]: Remove 'install' phase; add
'change-default-guix' phase.

* gnu/packages/python.scm (micropython): Update to 1.11.

* gnu/packages/wget.scm (wget2): Update to 1.99.2.
[source]: Download from gnu mirrors.
[arguments]: Remove custom 'bootstrap phase, update custom
'skip-network-tests phase. Don't build static library.
[inputs]: Add bzip2, gpgme, zlib.
[native-inputs]: Remove autoconf, automake, flex, gettext-minimal,
libtool, python-2.

* gnu/packages/wget.scm (wget, wgetpaste, wget2)[license]: Use
'license:' prefix.

* etc/guix-daemon.cil.in: Remove references to libexec/guix*.

* nix/libstore/globals.hh (Settings)[nixLibexecDir]: Remove.
* nix/libstore/globals.cc (Settings::processEnvironment): Remove
reference to 'nixLibexecDir'.
* nix/local.mk (libstore_a_CPPFLAGS): Remove -DNIX_LIBEXEC_DIR flag.
* build-aux/pre-inst-env.in: Remove references to 'NIX_LIBEXEC_DIR'.

The daemon had a mechanism that allows it to handle a list of
substituters and try them sequentially; this removes it.

* nix/scripts/substitute.in: Remove.
* nix/local.mk (nodist_pkglibexec_SCRIPTS): Remove.
* config-daemon.ac: Don't output 'nix/scripts/substitute'.
* nix/libstore/build.cc (SubstitutionGoal)[subs, sub, hasSubstitute]:
Remove.
[tryNext]: Make private.
(SubstitutionGoal::SubstitutionGoal, SubstitutionGoal::init): Remove now
unneeded initializers.
(SubstitutionGoal::tryNext): Adjust to assume a single substituter: call
'amDone' upfront when we couldn't find substitutes.
(SubstitutionGoal::tryToRun): Adjust to run 'guix substitute' via
'settings.guixProgram'.
(SubstitutionGoal::finished): Call 'amDone(ecFailed)' upon failure
instead of setting 'state' to 'tryNext'.
* nix/libstore/globals.hh (Settings)[substituters]: Remove.
* nix/libstore/local-store.cc (LocalStore::~LocalStore): Adjust to
handle a single substituter.
(LocalStore::startSubstituter): Remove 'path' parameter.  Adjust to
invoke 'settings.guixProgram'.  Don't refer to 'run.program', which no
longer exists.
(LocalStore::querySubstitutablePaths): Adjust for 'runningSubstituters'
being a singleton instead of a list.
(LocalStore::querySubstitutablePathInfos): Likewise, and remove
'substituter' parameter.
* nix/libstore/local-store.hh (RunningSubstituter)[program]: Remove.
(LocalStore)[runningSubstituters]: Remove.
[runningSubstituter]: New field.
[querySubstitutablePathInfos]: Remove 'substituter' parameter.
[startSubstituter]: Remove 'substituter' parameter.
* nix/nix-daemon/guix-daemon.cc (main): Remove references to
'settings.substituters'.
* nix/nix-daemon/nix-daemon.cc (performOp): Ignore the user's
"build-use-substitutes" value when 'settings.useSubstitutes' is false.

* nix/scripts/offload.in: Remove.
* nix/local.mk (nodist_pkglibexec_SCRIPTS) [BUILD_DAEMON_OFFLOAD]:
Remove 'scripts/offload'.
* config-daemon.ac: Don't output 'nix/scripts/offload'.
* build-aux/pre-inst-env.in: Don't set 'NIX_BUILD_HOOK'.
* nix/libstore/build.cc (HookInstance::HookInstance): Run 'guix
offload'.
(DerivationGoal::tryBuildHook): Remove reference to 'NIX_BUILD_HOOK'.
* nix/nix-daemon/guix-daemon.cc (main) [HAVE_DAEMON_OFFLOAD_HOOK]: Don't
set 'NIX_BUILD_HOOK'.
* nix/nix-daemon/nix-daemon.cc (performOp) [!HAVE_DAEMON_OFFLOAD_HOOK]:
Leave 'settings.useBuildHook' unchanged.

* nix/scripts/download.in: Remove.
* nix/local.mk (nodist_pkglibexec_SCRIPTS): Remove 'scripts/download'.
* config-daemon.ac: Don't output 'nix/scripts/download'.
* nix/libstore/builtins.cc (builtinDownload): Invoke 'guix
perform-download' directly.

* nix/scripts/authenticate.in: Remove.
* nix/local.mk (nodist_pkglibexec_SCRIPTS): Remove
scripts/authenticate.
* config-daemon.ac: Don't output 'nix/scripts/authenticate'.
* nix/libstore/local-store.cc (runAuthenticationProgram): Run 'guix
authenticate'.

* nix/scripts/list-runtime-roots.in: Remove.
* guix/store/roots.scm (%proc-directory): New variable.
(proc-file-roots, proc-exe-roots, proc-cwd-roots)
(proc-fd-roots, proc-maps-roots, proc-environ-roots)
(referenced-files, canonicalize-store-item, busy-store-items): New
procedures, taken from 'list-runtime-roots.in'.
* nix/libstore/globals.hh (Settings)[guixProgram]: New field.
* nix/libstore/globals.cc (Settings::processEnvironment): Initialize
'guixProgram'.
* nix/libstore/gc.cc (addAdditionalRoots): Drop code related to
'NIX_ROOT_FINDER'.  Run "guix gc --list-busy".
* nix/local.mk (nodist_pkglibexec_SCRIPTS): Remove
'scripts/list-runtime-roots'.
* config-daemon.ac: Don't output nix/scripts/list-runtime-roots.
* build-aux/pre-inst-env.in: Don't set 'NIX_ROOT_FINDER'.
Set 'GUIX'.
* doc/guix.texi (Invoking guix gc): Document '--list-busy'.
* guix/scripts/gc.scm (show-help, %options): Add "--list-busy".
(guix-gc)[list-busy]: New procedure.
Handle the 'list-busy' action.

* gnu/packages/music.scm (fmit): New variable.

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

* gnu/packages/haskell-xyz.scm (ghc-attoparsec-bootstrap,
ghc-integer-logarithms-bootstrap, ghc-scientific-bootstrap,
ghc-semigroups-bootstrap, ghc-unordered-containers-bootstrap,
ghc-wcwidth-bootstrap)[properties]: Fix typo, make 'hidden?' a tuple.

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

* gnu/packages/textutils (odt2txt): New variable.
* gnu/packages/package-management (diffoscope)[native-inputs]: Add odt2txt.
  [use-modules]: Remove accidentally added libreoffice package module.

* gnu/packages/images (sng): New variable.
* gnu/packages/package-management (diffoscope)[native-inputs]: Add sng.

* gnu/packages/image (pngsuite): New variable.

* gnu/packages/package-management (diffoscope)[native-inputs]: Add additional
  dependencies for tests.
  [use-module]: Add corresponding package modules.

* gnu/packages/package-management (diffoscope) [native-inputs]: Add additional
  packages used for tests.

* gnu/packages/package-management (diffoscope): Update to 123.
  [arguments]: Update phase writable-test-data to include tests directory.
    Add phase remove-ocaml-test.

* gnu/packages/python-xyz (python-debian): Update to 0.1.36.
  [source]: Switch to using git-fetch.
  [arguments]: Add phase to delete tests depending on tools not yet present in
  guix.
  [propagated-inputs]: Add python-chardet.

* gnu/packages/bioconductor.scm (r-rsubread): Update to 1.34.7.

* gnu/packages/bioconductor.scm (r-regioner): Update to 1.16.3.

* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.8.

* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.16.1.

* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.8.

* gnu/packages/cran.scm (r-ggraph): Update to 2.0.0.
[propagated-inputs]: Add r-graphlayouts, r-rlang, and r-tidygraph; remove
r-plyr.

* gnu/packages/cran.scm (r-msigdbr): Update to 7.0.1.

* gnu/packages/cran.scm (r-ggeffects): Update to 0.12.0.

* gnu/packages/cran.scm (r-ggformula): Update to 0.9.2.

* gnu/packages/cran.scm (r-insight): Update to 0.5.0.

* gnu/packages/cran.scm (r-ggpubr): Update to 0.2.3.

* gnu/packages/cran.scm (r-geometry): Update to 0.4.4.