gnu: Add r-enrichplot.

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

gnu: Add r-dose.

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

gnu: Add r-ggraph.

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

gnu: Add r-europepmc.

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

gnu: Add r-ggforce.

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

gnu: Add r-urltools.

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

gnu: Add r-polyclip.

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

gnu: Add r-tweenr.

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

gnu: Add r-triebeard.

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

gnu: Add r-ggplotify.

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

gnu: Add r-farver.

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

gnu: Add r-gridgraphics.

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

gnu: Add r-do-db.

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

gnu: Add r-fgsea.

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

gnu: Add r-msigdbr.

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

gnu: Add r-xkcd.

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

gnu: Add r-extrafont.

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

gnu: Add r-extrafontdb.

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

gnu: Add r-rttf2pt1.

* gnu/packages/cran.scm (r-rttf2pt1): New variable.

gnu: emacs-debbugs: Update to 0.17.

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

refresh: Update the source code URL.

Reported by Tobias Geerinckx-Rice <me@tobias.gr>
in <https://bugs.gnu.org/35010>.

* guix/upstream.scm (update-package-source): Take 'source' instead of
'version' as the second argument.
[update-expression]: Change to take 'replacements', a list of
replacement pairs.
Compute OLD-URL and NEW-URL and replace the dirname of the OLD-URL with
that of NEW-URL.
* guix/scripts/refresh.scm (update-package): Adjust call to
'update-package-source' accordingly.

upstream: 'package-update' returns the <upstream-source> object.

Fixes a regression introduced in
abd4d6b33dba4de228e90ad15a8efb456fcf7b6e, where CHANGES would no longer
be a thunk.

Reported by Ricardo Wurmus.

* guix/upstream.scm (package-update/url-fetch): Return SOURCE as the
third value instead of CHANGES.
* guix/scripts/refresh.scm (update-package): Adjust accordingly.

gnu: Add r-xyz.

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

scripts: Skip 'guix pull' suggestion when running code from a checkout.

* guix/scripts.scm (warn-about-old-distro): Do not warn when
GUIX_UNINSTALLED is set.

vm: Ask QEMU for more RAM in the VM that makes ISO9660 images.

* gnu/system/vm.scm (iso9660-image): Pass #:memory-size to
'expression->derivation-in-linux-vm'.

services: Deprecate 'xfce-desktop-service'.

* gnu/services/desktop.scm (xfce-desktop-service-type)[default-value]
[description]: New fields.
(xfce-desktop-service): Deprecate.
* gnu/system/examples/desktop.tmpl: Use the (service …) form.
* gnu/installer/services.scm (%desktop-environments): Add TODO comment.
* doc/guix.texi (Desktop Services): Adjust accordingly, and fix spelling
of "Xfce" throughout.

services: Deprecate 'gnome-desktop-service'.

* gnu/services/desktop.scm (gnome-desktop-service-type)[default-value]:
New field.
(gnome-desktop-service): Deprecate.
* gnu/installer/services.scm (%desktop-environments): Use the (service …)
form for GNOME.
* gnu/system/examples/desktop.tmpl: Likewise.
* doc/guix.texi (Desktop Services): Adjust accordingly.

installer: Use the (service …) form for MATE.

* gnu/installer/services.scm (%desktop-environments): Use
'mate-desktop-service-type' for MATE.

installer: Ask for confirmation before formatting partitions.

* gnu/installer/newt/page.scm (run-confirmation-page): New procedure.
* gnu/installer/newt/partition.scm (draw-formatting-page): Call it.

installer: Produce an 'initrd-modules' field if needed.

* gnu/installer/parted.scm (root-user-partition?): New procedure.
(bootloader-configuration): Use it.
(user-partition-missing-modules, initrd-configuration): New procedures.
(user-partitions->configuration): Call 'initrd-configuration'.o
* gnu/installer.scm (not-config?): Rename to...
(module-to-import?): ... this.  Add cases to exclude non-installer and
non-build (gnu …) modules.
(installer-program)[installer-builder]: Add GUIX to the extension list.

installer: Emit 'bootloader' field before 'swap-devices'.

* gnu/installer/parted.scm (user-partitions->configuration): Move
'bootloader' section above 'swap-devices'.

gnu: Add emacs-webfeeder.

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

gnu: trim-galore: Add pigz.

* gnu/packages/bioinformatics.scm (trim-galore)[inputs]: Add pigz.
[arguments]: Embed reference to pigz.

gnu: trim-galore: Fix test for Python.

* gnu/packages/bioinformatics.scm (trim-galore)[arguments]: Replace
"configure" phase to skip ill-advised test for Python.

gnu: hdf-java: Adjust indentation.

* gnu/packages/maths.scm (hdf-java): Adjust indentation.

gnu: hdf-java: Fix build.

* gnu/packages/maths.scm (hdf-java)[arguments]: Fix copying from automake;
substitute embedded hdf5 version number.

gnu: hdf-java: Use INVOKE.

* gnu/packages/maths.scm (hdf-java)[arguments]: Unconditionally return #T from
build phases.

gnu: r-rhdf5lib: Update to 1.4.3.

* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.3.

gnu: r-genomicfeatures: Update to 1.34.7.

* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.7.

gnu: r-hdf5r: Update to 1.1.1.

* gnu/packages/cran.scm (r-hdf5r): Update to 1.1.1.

gnu: r-caret: Update to 6.0-82.

* gnu/packages/statistics.scm (r-caret): Update to 6.0-82.

gnu: r-gtable: Update to 0.3.0.

* gnu/packages/statistics.scm (r-gtable): Update to 0.3.0.

gnu: grantlee: Delete broken tests.

* gnu/packages/qt.scm (grantlee)[arguments]: Add phase "delete-broken-tests".

gnu: Add adanaxis-mush and adanaxisgpl.

* gnu/packages/games.scm (adanaxis-mush, adanaxisgpl): New variables.

gnu: qjackctl: Re-enable xunique.

Version 0.5.6 of qjackctl appears to have fixed the xunique
bug that was causing X hanging when using tiling window managers.

See https://github.com/rncbc/qjackctl/blob/d54a1da43fa197da04d676a110f36a1d4c062252/ChangeLog#L9

* gnu/packages/audio.scm (qjackctl)[arguments]: Remove "--disable-xunique"
from configure-flags.

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

gnu: python-django-overextends: Use INVOKE.

* gnu/packages/django.scm (python-django-overextends)[arguments]: Use INVOKE.

gnu: python-django-contact-form: Use INVOKE.

* gnu/packages/django.scm (python-django-contact-form)[arguments]: Use INVOKE.

gnu: fritzing: Update to 0.9.3b.

* gnu/packages/engineering.scm (fritzing): Update to 0.9.3b.
[source]: Fetch from git.
[arguments]: Use INVOKE and adjust configure phase.
[inputs]: Add libgit2; fetch fritzing-parts-db via git.

gnu: ldc: Use INVOKE.

* gnu/packages/dlang.scm (ldc)[arguments]: Use INVOKE.

gnu: ldc-bootstrap: Use INVOKE.

* gnu/packages/dlang.scm (ldc-bootstrap)[arguments]: Use INVOKE and
unconditionally return #T from build phase.

gnu: open-adventure: Use INVOKE.

* gnu/packages/games.scm (open-adventure)[arguments]: Use INVOKE.

gnu: 0ad: Use INVOKE.

* gnu/packages/games.scm (0ad)[arguments]: Use INVOKE.

gnu: Add jami-client-gnome.

* gnu/packages/telephony.scm (jami-client-gnome): New variable.

gnu: Add libringclient.

* gnu/packages/telephony.scm (libringclient): New variable.

gnu: Add libring.

* gnu/packages/telephony.scm (libring): New variable.

gnu: Add pjproject-jami.

* gnu/packages/telephony.scm (pjproject-jami): New variable.

gnu: Add pjproject.

* gnu/packages/telephony.scm (pjproject): New variable.

environment: Create /etc/group in containers.

Reported by Pierre Neidhardt <mail@ambrevar.xyz>.

* guix/scripts/environment.scm (launch-environment/container): Create
GROUPS and call 'write-group'.
* tests/guix-environment-container.sh: Test it.

environment: Use (gnu build accounts) for /etc/passwd handling.

* guix/scripts/environment.scm (launch-environment/container): Remove
call to 'mock-passwd'; instantiate a <password-entry> instead.  Call
'write-passwd' to write the pasword database instead of using custom
code.
(mock-passwd): Remove.
* tests/guix-environment-container.sh: Test 'getpwuid'.

build-self: Disable position recording.

'guix pull -n' goes roughly from 40s to 35s.

* build-aux/build-self.scm (build-program): Add call to 'read-disable'.

gnu: current-guix: Delay effectful bits.

* gnu/packages/package-management.scm (current-guix): Delay 'repository-root'.

gnu: python-scanpy: Update to 1.4.

* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.
[source]: Fetch from git.
[arguments]: Disable broken tests.
[native-inputs]: Add python-pytest.
[home-page]: Use HTTPS.

gnu: python-anndata: Update to 0.6.18.

* gnu/packages/python-xyz.scm (python-anndata): Update to 0.6.18.

gnu: trim-galore: Update to 0.6.1.

* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.6.1.
[arguments]: Adjust patching.

gnu: cutadapt: Update to 2.1.

* gnu/packages/bioinformatics.scm (cutadapt): Update to 2.1.
[source]: Fetch from pypi.
[native-inputs]: Add python-setuptools-scm.

gnu: python-xopen: Update to 0.5.0.

* gnu/packages/python-xyz.scm (python-xopen): Update to 0.5.0.

etc: Add "rename" snippet.

* etc/snippets/text-mode/guix-commit-message-rename-package: New file.

gnu: edgar: Rename package to the-legend-of-edgar.

* gnu/packages/games.scm (edgar): Define in terms of
'deprecated-package'.
(the-legend-of-edgar): New variable, formerly known as "edgar".

gnu: btanks: Rename package to battle-tanks.

* gnu/packages/games.scm (btanks): Define in terms of
'deprecated-package'.
(battle-tanks): New variable, formerly known as "btanks".

gnu: tome4: Rename package to tales-of-maj-eyal.

* gnu/packages/games.scm (tome4): Define in terms of
'deprecated-package'.
(tales-of-maj-eyal): New variable, formerly known as "tome4".

gnu: crawl-tiles: Rename package to dungeon-crawl-stone-soup-tiles.

* gnu/packages/games.scm (crawl-tiles): Define in terms of
'deprecated-package'.
(dungeon-crawl-stone-soup-tiles): New variable, formerly known as "crawl-tiles".

gnu: crawl: Rename package to dungeon-crawl-stone-soup.

* gnu/packages/games.scm (crawl): Define in terms of
'deprecated-package'.
(dungeon-crawl-stone-soup): New variable, formerly known as "crawl".

gnu: fillets-ng: Rename package to fish-fillets-ng.

* gnu/packages/games.scm (fillets-ng): Define in terms of
'deprecated-package'.
(fish-fillets-ng): New variable, formerly known as "fillets-ng".

gnu: kiki: Rename package to kiki-the-nano-bot.

* gnu/packages/games.scm (kiki): Define in terms of
'deprecated-package'.
(kiki-the-nano-bot): New variable, formerly known as "kiki".

gnu: starfighter: Rename package to project-starfighter.

* gnu/packages/games.scm (starfighter): Define in terms of
'deprecated-package'.
(project-starfighter): New variable, formerly known as "starfighter".

gnu: wesnoth-server: Rename package to the-battle-for-wesnoth-server.

* gnu/packages/games.scm (wesnoth-server): Define in terms of
'deprecated-package'.
(the-battle-for-wesnoth-server): New variable, formerly known as "wesnoth-server".

gnu: wesnoth: Rename package to the-battle-for-wesnoth.

* gnu/packages/games.scm (wesnoth): Define in terms of
'deprecated-package'.
(the-battle-for-wesnoth): New variable, formerly known as "wesnoth".

gnu: abbaye: Rename package to l-abbaye-des-morts.

* gnu/packages/games.scm (abbaye): Define in terms of
'deprecated-package'.
(l-abbaye-des-morts): New variable, formerly known as "abbaye".

gnu: gnubg: Rename package to gnubackgammon.

* gnu/packages/games.scm (gnubg): Define in terms of
'deprecated-package'.
(gnubackgammon): New variable, formerly known as "gnubg".

gnu: cataclysm-dda: Rename package to cataclysm-dark-days-ahead.

* gnu/packages/games.scm (cataclysm-dda): Define in terms of
'deprecated-package'.
(cataclysm-dark-days-ahead): New variable, formerly known as "cataclysm-dda".

gnu: armagetronad: Rename package to armagetron-advanced.

* gnu/packages/games.scm (armagetronad): Define in terms of
'deprecated-package'.
(armagetron-advanced): New variable, formerly known as "armagetronad".

gnu: docker: Use disjunct temp directories for probing.

* gnu/packages/patches/docker-use-fewer-modprobes.patch: Use disjunct temp
directories for probing.

gnu: docker: Add comment.

* gnu/packages/patches/docker-use-fewer-modprobes.patch: Add comment.

packages: Adjust to new calling convention for "thunked" fields.

Fixes <https://bugs.gnu.org/34995>.

This is a followup to abd4d6b33dba4de228e90ad15a8efb456fcf7b6e.

* guix/packages.scm (package->bag): Adjust calls to INPUTS,
PROPAGATED-INPUTS, NATIVE-INPUTS, and ARGS, passing them SELF as an
argument.
* gnu/packages/gnucash.scm (gnucash)[arguments]: Use (package-inputs
this-record) intead of (inputs).
* gnu/packages/version-control.scm (git)[arguments]: Likewise.

gnu: gzdoom: Update to 3.7.2.

* gnu/packages/games.scm (gzdoom): Update to 3.7.2.
[source](uri): Update path.
[source](snippet): Bundled libjpeg directory has been renamed.

Signed-off-by: Kei Kebreau <kkebreau@posteo.net>

system: Add 'essential-services' field to <operating-system>.

* gnu/system.scm (<operating-system>)[essential-services]: New field.
(operating-system-directory-base-entries): Remove #:container? keyword
and keep only the not-container branch.
(essential-services): Likewise.
(operating-system-services): Likewise, and call
'operating-system-essential-services' instead of 'essential-services'.
(operating-system-activation-script): Remove #:container?.
(operating-system-boot-script): Likewise.
(operating-system-derivation): Likewise.
* gnu/system/linux-container.scm (container-essential-services): New procedure.
(containerized-operating-system): Use it and set the
'essential-services' field.
(container-script): Remove call to 'operating-system-derivation'.
* gnu/system/vm.scm (system-docker-image): Likewise.
* doc/guix.texi (operating-system Reference): Document 'essential-services'.

accounts: Add default value for the 'home-directory' field of <user-account>.

* gnu/system/accounts.scm (<user-account>)[home-directory]: Mark as
thunked and add a default value.
(default-home-directory): New procedure.
* doc/guix.texi (User Accounts): Remove 'home-directory' from example.
* gnu/system/examples/bare-bones.tmpl: Likewise.
* gnu/system/examples/beaglebone-black.tmpl: Likewise.
* gnu/system/examples/desktop.tmpl: Likewise.
* gnu/system/examples/docker-image.tmpl: Likewise.
* gnu/system/examples/lightweight-desktop.tmpl: Likewise.
* gnu/system/install.scm (installation-os): Likewise.
* gnu/tests.scm (%simple-os): Likewise.
* gnu/tests/install.scm (%minimal-os, %minimal-os-on-vda):
(%separate-home-os, %encrypted-root-os, %btrfs-root-os): Likewise.
* tests/accounts.scm ("allocate-passwd")
("allocate-passwd with previous state"): Likewise.

records: Allow thunked fields to refer to 'this-record'.

* guix/records.scm (this-record): New syntax parameter.
(make-syntactic-constructor)[wrap-field-value]: When F is thunked,
return a one-argument lambda instead of a thunk, and parameterize
THIS-RECORD.
(define-record-type*)[thunked-field-accessor-definition]: Pass X
to (real-get X).
* tests/records.scm ("define-record-type* & thunked & this-record")
("define-record-type* & thunked & default & this-record")
("define-record-type* & thunked & inherit & this-record"): New tests.

installer: Set the system's 'keyboard-layout' field.

* gnu/installer/newt/keymap.scm (keyboard-layout->configuration): New
procedure.
* gnu/installer.scm (compute-keymap-step): Return RESULT.
(installer-steps) <'keymap>: Add 'configuration-formatter' field.
(installer-program): Use (gnu installer newt keymap).
* gnu/installer/parted.scm (bootloader-configuration): Set
'keyboard-layout'.

gnu: guix: Update to f970946.

* gnu/packages/package-management.scm (guix): Update to f970946.

gnu: docker: Use fewer modprobes.

Fixes <https://bugs.gnu.org/34333>.
Reported by Allan Adair <allan@adair.io>.

* gnu/packages/patches/docker-use-fewer-modprobes.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/docker.scm (docker)[source]: Use it.

gnu: nano: Update to 4.0.

* gnu/packages/nano.scm (nano): Update to 4.0.

services: SDDM: Specify absolute path to the X server.

I'm not sure how this service ever worked, but SDDM started consistently
failing on one machine seemingly because of this setting.

* gnu/services/sddm.scm (sddm-configuration-file): Append /bin/X to the
ServerPath setting.

gnu: Add r-svmisc.

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

gnu: Add r-rjava.

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

gnu: Add r-r2html.

* gnu/packages/cran.scm (r-r2html): New variable.

gnu: Add r-sampling.

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

gnu: r-gsl: Update to 2.1-6.

* gnu/packages/cran.scm (r-gsl): Update to 2.1-6.

gnu: Add r-sigpathway.

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

gnu: Add r-anota.

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