gnu: mingw: Add mingw-w64 reproducibility patches.

These patches were originally found at the debian mingw-w64 team's
mingw-w64 repo, and should improve the reproducibility of our mingw-w64
toolchain.

* gnu/packages/patches/mingw-w64-dlltool-temp-prefix.patch: New file.
* gnu/packages/patches/mingw-w64-reproducible-gendef.patch: New file.
* gnu/local.mk (dist_patch_DATA): Update accordingly.
* gnu/packages/mingw.scm (make-mingw-w64): Apply patches.

gnu: gparted: Make some inputs native.

* gnu/packages/disk.scm (gparted)[inputs]: Move yelp-tools from here...
[native-inputs]: ...to here.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

system: Don’t create a module database when no modules are available.

* gnu/system.scm (operating-system-directory-base-entries): Don't create
a module database when no modules are available.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: rubber: Make some inputs native.

* gnu/packages/tex.scm (rubber)[inputs]: Move texinfo from here...
[native-inputs]: ...to this new field.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: scotch: Make some inputs native.

* gnu/packages/math.scm (scotch)[inputs]: Move flex & bison from here...
[native-inputs]: ...to this new field.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: telegram-purple: Make some inputs native.

* gnu/packages/telephony.scm (telegram-purple)[inputs]: Move gettext from here...
[native-inputs]: ...to here.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: jami: Make some inputs native.

* gnu/packages/telephony.scm (jami)[inputs]: Move gettext from here...
[native-inputs]: ...to here.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: libkate: Make some inputs native.

* gnu/packages/xiph.scm (libkate)[inputs]: Move bison from here...
[native-inputs]: ...to here.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: man-db: Make some inputs native.

* gnu/packages/man.scm (man-db)[inputs]: Move flex from here...
[native-inputs]: ...to here.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: qgis: Fix some plugins.

* gnu/packages/geo.scm (qgis)[arguments]: Add a 'wrap-gis' phase to set the
  environment variables required by some plugins.

tests: Adjust '--with-commit' test for tags.

This is a followup to efa578ecaece67366b4b0e2266de7c2faaa4ae54.

* tests/guix-build-branch.sh: Adjust '--with-commit=guile-gcrypt=v0.1.0'
test to expect the tag ID rather than the commit ID.

store: 'with-store' doesn't close the store upon abort.

Fixes <https://bugs.gnu.org/40428>.
Reported by Marius Bakke <mbakke@fastmail.com> and 白い熊.

Regression introduced with the first uses of 'with-build-handler' in
commit 62195b9a8fd6846117c5d7698842748300d13e31 and subsequent.

* guix/store.scm (call-with-store): Use 'catch #t' instead of
'dynamic-wind'.  This ensures STORE remains open when a non-local exit
other than an exception occurs, such as an abort to the build handler
prompt.
* tests/store.scm ("with-build-handler + with-store"): New test.

maint: Remove unsupported cross-compilation jobs from 'release-manifest.scm'.

* etc/release-manifest.scm (%packages-to-cross-build-for-mingw): New
variable.
(%cross-manifest): Use it.  Remove "riscv64-linux-gnu" from %CROSS-TARGETS.

gnu: ocaml-menhir: Update to 20190626.

* gnu/packages/ocaml.scm (ocaml-menhir): Update to 20190626.

gnu: Replace uses of 'gettext' with 'gettext-minimal'.

* gnu/packages/cdrom.scm (dvdstyler)[native-inputs]: Change from GNU-GETTEXT
to GETTEXT-MINIMAL.
* gnu/packages/emulators.scm (dolphin-emu)[native-inputs]: Likewise.
* gnu/packages/engineering.scm (lepton-eda, kicad, kicad-i18l)[native-inputs]:
Likewise.
* gnu/packages/games.scm (quadrapassel, edgar)[native-inputs]: Likewise.
* gnu/packages/gnome.scm (eog-plugins, workrave, geary)[native-inputs]: Likewise.
* gnu/packages/guile-xyz.scm (guile-gi, emacsy)[native-inputs]: Likewise.
* gnu/packages/image.scm (gpick)[native-inputs]: Likewise.
* gnu/packages/messaging.scm (telegram-purple)[native-inputs]: Likewise.
* gnu/packages/music.scm (fmit)[native-inputs]: Likewise.
* gnu/packages/package-management.scm (flatpak)[native-inputs]: Likewise.
* gnu/packages/patchutils.scm (quilt)[native-inputs]: Likewise.
* gnu/packages/photo.scm (hugin)[native-inputs]: Likewise.
* gnu/packages/security-token.scm (eid-mw)[native-inputs]: Likewise.
* gnu/packages/telephony.scm (jami)[native-inputs]: Likewise.
* gnu/packages/texinfo.scm (pinfo)[native-inputs]: Likewise.
* gnu/packages/vulkan.scm (vkd3d)[native-inputs]: Likewise.
* gnu/packages/web.scm (cadaver)[native-inputs]: Likewise.

gnu: cadaver: Build with OpenSSL 1.0.

* gnu/packages/web.scm (cadaver)[inputs]: Change from OPENSSL to OPENSSL-1.0.

gnu: Add r-asd.

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

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: c-reduce: Make some inputs native.

* gnu/packages/debug.scm (c-reduce)[inputs]: Move flex from here...
[native-inputs]: ...to this new field.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>

gnu: ell: Make some inputs native.

* gnu/packages/linux.scm (ell)[inputs]: Move libtool from here...
[native-inputs]: ...to here.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>

gnu: dico: Make some inputs native.

* gnu/packages/dico.scm (dico)[inputs]: Move groff from here...
[native-inputs]: ...to this new field.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>

gnu: a2ps: Make some inputs native.

* gnu/packages/pretty-print.scm (a2ps)[inputs]: Move groff from here...
[native-inputs]: ...to here.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>

gnu: gnome-online-accounts: Update to 3.36.0.

* gnu/packages/gnome.scm (gnome-online-accounts): Update to 3.36.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: gnome-online-miners: Update to 3.34.0.

* gnu/packages/gnome.scm (gnome-online-miners): Update to 3.34.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: Deprecate emacs-modus-themes.

* gnu/package/emacs-xyz.scm (emacs-modus-themes): Deprecate it.

gnu: Add emacs-modus-operandi-theme.

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

gnu: Add emacs-modus-vivendi-theme.

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

gnu: spandsp: Disable parallel build.

The build could otherwise fail non-deterministically.

Reported-by: Raghav Gururajan <raghavgururajan@disroot.org>
* gnu/packages/telephony.scm (spandsp)[arguments]: Set parallel-build? to
false.

gnu: icecat: Update to 68.6.1-guix0-preview1 [security fixes].

Includes fixes for CVE-2020-6819 and CVE-2020-6820.

* gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.
* gnu/packages/patches/icecat-makeicecat.patch: Adapt to new version.

gnu: Add linux-libre-arm64-generic-5.6.

* gnu/packages/linux (linux-libre-arm64-generic-5.6): New variable.

gnu: Add linux-libre-arm-generic-5.6.

* gnu/packages/linux (linux-libre-arm-generic-5.6): New variable.

gnu: Add linux-libre 5.6.2.

* gnu/packages/linux (deblob-scripts-5.6): New variable.
  (linux-libre-5.6-version): New variable.
  (linux-libre-5.6-pristine-source): New variable.
  (linux-libre-5.6-source): New variable.
  (linux-libre-headers-5.6): New variable.
  (linux-libre-5.6): New variable.

gnu: linux-libre: Update to 5.4.30.

* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.30.
(linux-libre-5.4-pristine-source): Update hash.

gnu: linux-libre@4.19: Update to 4.19.114.

* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.114.
(linux-libre-4.19-pristine-source): Update hash.

gnu: linux-libre@4.14: Update to 4.14.175.

* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.175.
(linux-libre-4.14-pristine-source): Update hash.

gnu: linux-libre@4.9: Update to 4.9.218.

* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.218.
(linux-libre-4.9-pristine-source): Update hash.

gnu: linux-libre@4.4: Update to 4.4.218.

* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.218.
(linux-libre-4.4-pristine-source): Update hash.

gnu: cross-base: Add 'package-with-patches'.

This is a followup to c1c50cb5b099897a18e4cd8c27970cb45a7c3a94.

* gnu/packages/cross-base.scm (package-with-patch): Rename to...
(package-with-patches): ... this, and take a list of patches.
(package-with-extra-patches): Use it.
(cross-binutils): Use 'search-patches' instead of 'search-patch'.

pack: Pass the cross-compilation target to 'run-with-store'.

This ensures '%current-target-system' is correctly bound upfront, which
some packages rely on.

* guix/scripts/pack.scm (guix-pack): Pass #:target to 'run-with-store'.

gnu: cross-base: Fix PACKAGE-WITH-EXTRA-PATCHES

This also removes the execute bit from the patches added. Not sure how
or why those were set in the first place.

* gnu/packages/cross-base.scm (package-with-extra-patches): Imitate
PACKAGE-WITH-PATCH instead of using it.
* gnu/packages/patches/binutils-mingw-w64-reproducible-import-libraries.patch:
Remove execute bit.
* gnu/packages/patches/binutils-mingw-w64-specify-timestamp.patch:
Remove execute bit.

gnu: ungoogled-chromium: Update to 80.0.3987.163-0.516e2d9.

* gnu/packages/chromium.scm (%chromium-version): Set to 80.0.3987.163.
(%chromium-origin): Update hash.

gnu: Add python-cantools.

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

gnu: Add python-bitstruct.

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

gnu: Add python-diskcache.

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

gnu: Add python-can.

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

gnu: Add python-aenum.

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

gnu: Add python-textparser.

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

gnu: Add perl-data-entropy.

* gnu/packages/perl.scm (perl-data-entropy): New variable.

gnu: Add perl-crypt-rijndael.

* gnu/packages/perl.scm (perl-crypt-rijndael): New variable.

gnu: Add perl-data-float.

* gnu/packages/perl.scm (perl-data-float): New variable.

gnu: Add perl-http-lite.

* gnu/packages/web.scm (perl-http-lite): New variable.

gnu: Remove bctoolbox and ortp.

* gnu/packages/telephony.scm (bctoolbox): Delete variable.
(ortp): Delete variable.
* gnu/packages/audio.scm (bluez-alsa)[inputs]: Update ortp reference.
* gnu/packages/kde-internet.scm (kopete)[inputs]: Update ortp reference.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: Add qalculate-gtk.

* gnu/packages/maths.scm (qalculate-gtk): New variable.

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

gnu: Add libqalculate.

* gnu/packages/maths.scm (libqalculate): New variable.

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

gnu: gnome-initial-setup: Record file name of 'gsd-keyboard-display'.

* gnu/packages/gnome.scm (gnome-initial-setup)[arguments]: Add
'set-gkbd-file-name' phase.
[inputs]: Add LIBGNOMEKBD.

gnu: clipnotify: Update to 6.0.1.

* gnu/packages/xdisorg.scm (clipnotify): Update to 6.0.1.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: calibre: Fix build with python-msgpack >= 1.0.

* gnu/packages/patches/calibre-msgpack-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/ebook.scm (calibre)[source](patches): Add it.

gnu: Add bzrtp.

* gnu/packages/linphone.scm (bzrtp): New variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: Add ortp.

* gnu/packages/linphone.scm (ortp): New variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: Add bcg729.

* gnu/packages/linphone.scm (bcg729): New variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

guix system: Mention 'herd restart' when reconfigure completes.

* guix/scripts/system.scm (with-shepherd-error-handling): Use 'mbegin'
instead of 'begin'.
(perform-action): Print a message after 'upgrade-shepherd-services'.
That message had disappeared in commit
5c8c8c455420af27189d6045b3599fe6e27ad012.

guix system: Remove unused procedure.

This procedure was unused since
5c8c8c455420af27189d6045b3599fe6e27ad012.

* guix/scripts/system.scm (call-with-service-upgrade-info): Remove.

reconfigure: Silence Guile warnings.

Fixes <https://bugs.gnu.org/39301>.
Reported by strypsteen@posteo.net.

* guix/scripts/system/reconfigure.scm (switch-to-system)
(upgrade-shepherd-services, install-bootloader): Wrap 'primitive-load'
call in 'parameterize'.

Revert "reconfigure: Run the effect scripts as separate processes."

This reverts commit 5517750344be05c91bc2979c1a0e2348a9ae902d.
That commit would remove all sorts of error checking when running those
programs.

gnu: Add bcmatroska2.

* gnu/packages/linphone.scm (bcmatroska2): New variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: Add belcard.

* gnu/packages/linphone.scm (belcard): New variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: Add belr.

* gnu/packages/linphone.scm (belr): New variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: Add bctoolbox.

* gnu/packages/linphone.scm (bctoolbox): New variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: Add bcunit.

* gnu/packages/linphone.scm (bcunit): New variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

gnu: Add muchsync.

* gnu/packages/mail.scm (muchsync): New variable.

gnu: gpsd: Update to 3.20.

* gnu/packages/gps.scm (gpsd): Update to 3.20.
  [inputs]: Add gtk+.

gnu: txr: Update to 234.

* gnu/packages/lisp.scm (txr): Update to 234.

gnu: lollypop: Peel off duplicate wrapper.

* gnu/packages/gnome.scm (lollypop)[arguments]: Take down some at-ats
with proper module imports and prefixing.  Remove the redundant
‘wrap-glib-or-gtk’ phaseis already run by the MESON-BUILD-SYSTEM.

gnu: cross-base: Hotfix for paren

* gnu/packages/cross-base.scm (package-with-extra-patches): Add trailing
paren.

gnu: cross-base: Add mingw-w64 specific binutils patches.

These patches were originally found at the debian mingw-w64 team's
binutils repo, and should improve the reproducibility of our mingw-w64
toolchain.

* gnu/packages/patches/binutils-mingw-w64-reproducible-import-libraries.patch:
New file.
* gnu/packages/patches/binutils-mingw-w64-specify-timestamp.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Update accordingly.
* gnu/packages/cross-base.scm (cross-binutils): Apply relevant patches
if target is mingw-w64.
(package-with-extra-patches): New procedure.

reconfigure: Run the effect scripts as separate processes.

Fixes <https://bugs.gnu.org/39301>.
Reported by strypsteen@posteo.net.

* guix/scripts/system/reconfigure.scm (switch-to-system)
(upgrade-shepherd-services, install-bootloader): Use 'system*' instead
of 'primitive-load'.

guix system: Do not import the user's (guix config).

Previously, 'switch-to-system.drv' and 'install-bootloader.drv' would
depend on the user's (guix config) module.  This is no longer the case.

* guix/scripts/system/reconfigure.scm (not-config?): New procedure.
(switch-system-program): Do not import the user's (guix config).  Use
'make-config.scm' instead.
(install-bootloader-program): Likewise.

git: Don't try to resolve tags with 'tag-lookup'.

Fixes <https://bugs.gnu.org/40377>.
Reported by Brice Waegeneire <brice@waegenei.re>.

* guix/git.scm (switch-to-ref): In the 'tag case, remove call to
'tag-lookup'.

gnu: Add synapse.

* gnu/packages/matrix.scm (synapse): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-matrix-synapse-ldap3.

* gnu/packages/matrix.scm: New file.
(python-matrix-synapse-ldap3): New variable.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add matrix.scm.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-pysaml2.

* gnu/packages/python-xyz.scm: (python-pysaml2) New variable.

Co-authored-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-txacme.

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

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-txsni.

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

Co-authored-by: Alex ter Weele <alex.ter.weele@gmail.com>

gnu: Add python-pem.

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

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-eliot.

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

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-boltons.

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

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-ldap3.

* gnu/packages/python-xyz.scm (python-ldap3): New variable.

Co-authored-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-prometheus-client.

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

Co-authored-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-pymacaroons.

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

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-daemonize.

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

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-signedjson.

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

Co-authored-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-canonicaljson.

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

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-unpaddedbase64.

* gnu/packages/python-xyz.scm (python-unpaddedbase64): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-frozendict.

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

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

services: murmur: Add missing newline in murmur-configuration.

* gnu/services/telephony.scm (default-murmur-config): Add newline after
"max-user-bandwidth".

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add font-iosevka-term.

* gnu/packages/fonts.scm (font-iosevka-term): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add font-iosevka-term-slab.

* gnu/packages/fonts.scm (font-iosevka-term-slab): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: proof-general: Update home-page.

* gnu/packages/coq.scm (proof-general):[home-page] update to proofgeneral.github.io

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: proof-general: Update to 4.4.

* gnu/packages/coq.scm (proof-general): Update to 4.4.
[source]: Change to GIT-FETCH.
[arguments]: Remove obsolete substitutions.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: gnome-default-applications: Change defaults.list to gnome-mimeapps.list.

* gnu/packages/gnome.scm (gnome-default-applications)[arguments]: Change
deprecated defaults.list filename to gnome-mimeapps.list.  The old
defaults.list was changed to mimeapps.list in the mime spec. The gnome- prefix
makes the file only be read when XDG_CURRENT_DESKTOP=GNOME.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add xwallpaper.

* gnu/packages/xdisorg.scm (xwallpaper): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>