build: Expand ‘scripts/guix’ at Make time.

This moves the complexity of Autotools variable expansion outside of the
application code.

* scripts/guix.in (config-lookup): Delete.
(maybe-augment-load-paths!, run-guix-main): Use fully expanded variables
instead of calling ‘config-lookup’.
* configure.ac: Don't use AC_CONFIG_FILES for ‘scripts/guix’.
Use AC_PROG_SED.
* Makefile.am (scripts/guix): New rule.
(do_subst): New variable.
(CLEANFILES, EXTRA_DIST): Adapt.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

gnu: parallel: Update source hash.

The upstream tarball changed almost immediately after release.
See https://lists.gnu.org/archive/html/guix-devel/2018-01/msg00319.html.

* gnu/packages/parallel.scm (parallel)[source]: Update hash.

Revert "gnu: wxwidgets: Use webkitgtk-2.4."

This reverts commit 8a58182c12193ae27359591c92febfdd602411f4.

system: Add A20 OLinuXino LIME installer.

* gnu/bootloader/u-boot.scm (u-boot-a20-olinuxino-lime-bootloader):
New exported variable.
* gnu/packages/bootloaders.scm (u-boot-a20-olinuxino-lime):
New exported variable.
* gnu/system/install.scm (a20-olinuxino-lime-installation-os):
New exported variable.

gnu: Add r-argparser.

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

gnu: star: Make reproducible.

* gnu/packages/bioinformatics.scm (star)[arguments]: Add build phase
"make-reproducible".

gnu: python-trytond: End phase in #t.

* gnu/packages/tryton.scm (python-trytond): End phase in #t.

gnu: mpd: Update to 0.20.15.

* gnu/packages/mpd.scm (mpd): Update to 0.20.15.

gnu: aria-maestosa: Add scons-flags.

* gnu/packages/music.scm (aria-maestosa): Add scons-flags.

gnu: python-proteus: Add dependencies.

* gnu/packages/tryton.scm (python-proteus)[propagated-inputs]: Add
python-trytond-party, python-trytond-country, python-trytond,
python-stdnum, python-sql, python-wrapt, python-werkzeug,
python-polib, python-genshi, python-relatorio, python-magic.

gnu: Add python-trytond-party.

* gnu/packages/tryton.scm (define-module): Add (gnu packages finance).
(python-trytond-party): New variable.

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

gnu: Add python-stdnum.

* gnu/packages/finance.scm (python-stdnum, python2-stdnum): New variables.

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

gnu: Add python-trytond-country.

* gnu/packages/tryton.scm (python-trytond-country): New variable.

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

gnu: Rename "trytond" to "python-trytond".

* gnu/packages/tryton.scm (trytond): Rename to...
(python-trytond): ...this.

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

gnu: Add python-proteus.

* gnu/packages/tryton.scm (python-proteus): New variable.

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

gnu: Add python-phonenumbers.

* gnu/packages/python.scm (python-phonenumbers, python2-phonenumbers): New
variables.

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

gnu: tryton: Updated to 4.6.2.

* gnu/packages/tryton.scm (tryton): Update to 4.6.2.

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

gnu: trytond: Updated to 4.6.2.

* gnu/packages/tryton.scm (trytond): Updated to 4.6.2.
[inputs]: Add python-magic.

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

gnu: python-relatorio: Update to 0.8.0.

* gnu/packages/python.scm (python-relatorio): Updated to 0.8.0.

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

gnu: python-magic: Update to 0.4.15.

* gnu/packages/python.scm (python-magic) Updated to 0.4.15.

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

gnu: wxwidgets: Use webkitgtk-2.4.

* gnu/packages/wxwidgets.scm (wxwidgets)[inputs]: Replace "webkitgtk" by
"webkitgtk-2.4".

gnu: aria-maestosa: Use scons-build-system.

* gnu/packages/music.scm (aria-maestosa)[build-system]: Use
scons-build-system.
[native-inputs]: Remove scons-python2.
[arguments]: Use scons-python2.
<#:phases>: Remove custom phases "build" and "install".
Add custom phase "fix-directory-permissions".

gnu: aria-maestosa: Use scons-python2.

* gnu/packages/music.scm (aria-maestosa)[native-inputs]: Replace "scons" by
"scons-python2".

gnu: parallel: Don't end phase with #<undefined>.

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

gnu: parallel: Update to 20180122.

* gnu/packages/parallel.scm (parallel): Update to 20180122.

gnu: guix: Update snapshot to 33988f9.

* gnu/packages/package-management.scm (guix): Update to 33988f9.

publish: Restore gzip compression in cache-less mode.

Fixes <https://bugs.gnu.org/30184>.
Regression introduced in 297e04d66010ada31a40f40143d81bf6b62affcc.
Reported by Christopher Baines <mail@cbaines.net>.

* guix/scripts/publish.scm (nar-response-port): Add 'compression'
parameter and honor it.
(http-write): Get 'x-nar-compression' from the initial RESPONSE.

gnu: python-kivy: Add "git" native-input.

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

gnu: khmer: Add aarch64-linux to supported systems.

* gnu/packages/bioinformatics.scm (khmer)[supported-systems]: Add
aarch64-linux to the supported systems.

gnu: nss-certs: Update to 3.35.

* gnu/packages/certs.scm (nss-certs): Update to 3.35.

gnu: iq80-snappy: Improve synopsis & description.

* gnu/packages/compression.scm (iq80-snappy)[synopsis, description]: Fix
typos and add ‘(de)compressor’ keywords.

gnu: go: Improve description.

* gnu/packages/golang.scm (go-1.4)[description]: Edit for clarity.

gnu: go@1.9: Drop left-over work-around.

* gnu/packages/golang.scm (go-1.9)[arguments]: Remove substitution for
fixed bug from the ‘prebuild’ phase.

gnu: direnv: Edit description.

* gnu/packages/shellutils.scm (direnv)[description]: Edit and use @file.

gnu: direnv: Use HTTPS for home page.

* gnu/packages/shellutils.scm (direnv)[home-page]: Use HTTPS.

gnu: youtube-dl: Return #t from phases.

* gnu/packages/video.scm (youtube-dl)[arguments]: Return #t from
‘fix-the-data-directories’ phase.

gnu: youtube-dl: Update to 2018.01.21.

* gnu/packages/video.scm (youtube-dl): Update to 2018.01.21.
[description]: Update.  ‘A few’ is simply no longer true.

gnu: mktorrent: Add missing @dfn to description.

* gnu/packages/bittorrent.scm (mktorrent)[description]: Add missing @dfn.

gnu: libtorrent-rasterbar: Update home page.

* gnu/packages/bittorrent.scm (libtorrent-rasterbar)[home-page]: Use extant domain.

gnu: newt: Update to 0.52.20.

* gnu/packages/slang.scm (newt): Update to 0.52.20.

gnu: mia: Update to 2.4.6.

* gnu/packages/image-processing.scm (mia): Update to 2.4.6.

gnu: Add python2-graphite-web.

* gnu/packages/monitoring.scm (python2-graphite-web): New variable.

gnu: Add python2-carbon.

* gnu/packages/monitoring.scm (python2-carbon): New variable.

gnu: Add python-whisper.

* gnu/packages/monitoring.scm (python-whisper, python2-whisper): New
variables.

gnu: Add python-django-tagging.

* gnu/packages/django.scm (python-django-tagging, python2-django-tagging): New
variables.

gnu: Add python-txamqp.

* gnu/packages/python.scm (python-txamqp, python2-txamqp): New variables.

gnu: emacs-tiny: Fix indentation.

* gnu/packages/emacs.scm (emacs-tiny): Fix indentation.

gnu: emacs-request: Update to 0.3.0.

* gnu/packages/emacs.scm (emacs-request): Update to 0.3.0.
[source]: Fetch with git.

gnu: Add r-catterplots.

* gnu/packages/statistics.scm (r-catterplots): New variable.

gnu: Add salmon.

* gnu/packages/bioinformatics.scm (libstadenio-for-salmon,
spdlog-for-salmon, bwa-for-salmon, salmon): New variables.

gnu: Add sailfish.

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

gnu: Add libdivsufsort.

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

gnu: Add libgff.

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

gnu: orpheus: Fix build on aarch64-linux.

* gnu/packages/orpheus.scm (orpheus)[arguments]: Explicitly set the
build target when building on aarch64-linux.

gnu: python-kivy: Update to 1.10.0.

* gnu/packages/python.scm (python-kivy): Update to 1.10.0.
[arguments]: Remove custom "build" phase.

gnu: intel-gpu-tools: Use INVOKE.

* gnu/packages/admin.scm (intel-gpu-tools)[arguments]: Substitute INVOKE
for SYSTEM*.

gnu: intel-gpu-tools: Update to 1.21.

* gnu/packages/admin.scm (intel-gpu-tools): Update to 1.21.

gnu: libtorrent-rasterbar: Update to 1.1.6.

* gnu/packages/bittorrent.scm (libtorrent-rasterbar): Update to 1.1.6.

gnu: spice: Use HTTPS for spice-space.org home pages.

* gnu/packages/spice.scm (spice, spice-vdagent)[home-page]: Use HTTPS

gnu: spice-gtk: Update to 0.34.

* gnu/packages/spice.scm (spice-gtk): Update to 0.34.

gnu: babl: Update to 0.1.40.

* gnu/packages/gimp.scm (babl): Update to 0.1.40.

gnu: babl: Parameterise source URI.

* gnu/packages/gimp.scm (babl)[source]: Use VERSION-MAJOR+MINOR.

gnu: babl: Edit description.

* gnu/packages/gimp.scm (babl)[description]: Edit.

gnu: mktorrent: Update to 1.1.

* gnu/packages/bittorrent.scm (mktorrent): Update to 1.1.
[source, home-page]: Use new URI.

doc: Improve ‘fix-runpath’ description.

* doc/guix.texi (Build Systems): Re-write ‘fix-runpath’ documentation
entirely.  Just fixing the typos didn't do much.

services: herd: 'with-shepherd' no longer leaves an open connection.

* gnu/services/herd.scm (with-shepherd): Use 'dynamic-wind' and close
CONNECTION at the end.

doc: No longer mention Wicd in OS examples.

* gnu/system/examples/desktop.tmpl,
gnu/system/examples/lightweight-desktop.tmpl: Mention NetworkManager
instead of Wicd.

services: Missing services are automatically instantiated.

This simplifies OS configuration: users no longer need to be aware of
what a given service depends on.

See the discussion at
<https://lists.gnu.org/archive/html/guix-devel/2018-01/msg00114.html>.

* gnu/services.scm (missing-target-error): New procedure.
(service-back-edges): Use it.
(instantiate-missing-services): New procedure.
* gnu/system.scm (operating-system-services): Call
'instantiate-missing-services'.
* tests/services.scm ("instantiate-missing-services")
("instantiate-missing-services, no default value"): New tests.
* gnu/services/version-control.scm (cgit-service-type)[extensions]: Add
FCGIWRAP-SERVICE-TYPE.
* gnu/tests/version-control.scm (%cgit-os): Remove NGINX-SERVICE-TYPE
and FCGIWRAP-SERVICE-TYPE instances.
* doc/guix.texi (Log Rotation): Remove 'mcron-service-type' in example.
(Miscellaneous Services): Remove 'nginx-service-type' and
'fcgiwrap-service-type' in Cgit example.

tests: Cgit test waits for /var/run/shepherd/socket.

Previously tests sometimes start before the shepherd was listening,
leading to test failures.

* gnu/tests/version-control.scm (run-cgit-test)[test]: Add "shepherd
socket ready" test.  Rename to two "service running" tests for clarity.

services: shepherd: Make 'shepherd-configuration-file' non-monadic.

Suggested by atw on #guix.

* gnu/services/shepherd.scm (shepherd-service-file): Use 'scheme-file'
instead of 'gexp->file'.
(shepherd-configuration-file): Likewise, and adjust to non-monadic
style.
(shepherd-boot-gexp): Adjust accordingly.
* guix/scripts/system.scm (upgrade-shepherd-services): Use
'lower-object' in addition to 'shepherd-service-file'.

gnu: Add mkbootimg.

* gnu/packages/android.scm (mkbootimg): New variable.

gnu: Add abootimg.

* gnu/packages/android.scm (abootimg): New variable.

system: Add Nintendo NES Classic Edition installer.

* gnu/bootloader/u-boot.scm (u-boot-nintendo-nes-classic-edition-bootloader):
New exported variable.
* gnu/packages/bootloaders.scm (u-boot-nintendo-nes-classic-edition):
New exported variable.
* gnu/system/install.scm (nintendo-nes-classic-edition-installation-os):
New exported variable.

system: make-u-boot-package: Replace underscores by dashes in package name.

* gnu/packages/bootloaders.scm (make-u-boot-package): Replace underscores by
dashes in package name.

system: Factor out embedded-installation-os.

* gnu/system/install.scm (embedded-installation-os): New variable.
(beaglebone-black-installation-os): Use it.
(a20-olinuxino-lime2-emmc-installation-os): Use it.
(a20-olinuxino-micro-installation-os): Use it.
(banana-pi-m2-ultra-installation-os): Use it.

system: Factor out agetty-default-service.

* gnu/system/install.scm (agetty-default-service): New variable.
(beaglebone-black-installation-os): Use it.
(a20-olinuxino-lime2-emmc-installation-os): Use it.
(a20-olinuxino-micro-installation-os): Use it.
(banana-pi-m2-ultra-installation-os): Use it.

system: Add A20 OLinuXino MICRO installer.

* gnu/bootloader/u-boot.scm (u-boot-a20-olinuxino-micro-bootloader): New
exported variable.
* gnu/packages/bootloaders.scm (u-boot-a20-olinuxino-micro): New exported
variable.
* gnu/system/install.scm (a20-olinuxino-micro-installation-os): New exported
variable.

system: Add A20 OLinuXino LIME2 installer.

* gnu/bootloader/u-boot.scm (u-boot-a20-olinuxino-lime2-bootloader): New
exported variable.
* gnu/packages/bootloaders.scm (u-boot-a20-olinuxino-lime2): New exported
variable.
* gnu/system/install.scm (a20-olinuxino-lime2-emmc-installation-os): New exported
variable.

gnu: wxsvg: Update to 1.5.12.

* gnu/packages/wxwidgets.scm (wxsvg): Update to 1.5.12.

gnu: video, xml: Fix typo.

* gnu/packages/video.scm (libva)[synopsis]: Fix ‘libary’ typo.
[description]: Use @dfn.
* gnu/packages/xml.scm (libebml): Likewise.

gnu: godot: Fix building on aarch64-linux.

* gnu/packages/game-development.scm (godot)[arguments]: Add a flag when
building for aarch64-linux to build without threads.

gnu: cross-base: Apply gcc 6 patch to gcc >= 6.

* gnu/packages/cross-base.scm (cross-gcc): Apply gcc 6 patch to gcc >= 6.

gnu: u-boot: Update to 2018.01.

* gnu/packages/bootloaders.scm (define-module): Import (gnu packages gcc).
(u-boot): Update to 2018.01.
[native-inputs]: Add swig.  Remove dtc.
(make-u-boot-package): Use gcc-7.

system: Add Banana Pi M2 Ultra installer.

* gnu/bootloader/u-boot.scm (u-boot-banana-pi-m2-ultra-bootloader): New
exported variable.
(install-allwinner-u-boot): New variable.
(u-boot-allwinner-bootloader): New variable.
* gnu/packages/bootloaders.scm (u-boot-banana-pi-m2-ultra): New exported
variable.
* gnu/system/install.scm (banana-pi-m2-ultra-installation-os): New exported
variable.

gnu: graphicsmagick: Update to 1.3.28 [‘security fixes’].

* gnu/packages/imagemagick.scm (graphicsmagick): Update to 1.3.28.

gnu: deutex: Update to 5.1.1.

* gnu/packages/games.scm (deutex): Update to 5.1.1.

gnu: lookingglass: Update to a10.

* gnu/packages/virtualization.scm (lookingglass): Update to a10.

gnu: libexif: Fix CVE-2016-6328.

* gnu/packages/patches/libexif-CVE-2016-6328.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/photo.scm (libexif)[source]: Use it.

gnu: perl-lingua-pt-stemmer: Update URL.

* gnu/packages/language.scm (perl-lingua-pt-stemmer)[source]: Use new
upstream URL.

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

gnu: escpr: Update to 1.6.18.

* gnu/packages/cups.scm (escpr): Update to 1.6.18.

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

gnu: Add Motion.

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

packages: 'package-mapping' maps replacement.

* guix/packages.scm (package-mapping): Apply PROC to 'replacement' as well.

build: Declare “doc/guix.texi“ dependencies.

Fixes <https://bugs.gnu.org/29727>.

* doc/local.mk (%C%_guix_TEXINFOS): New variable containing files included by
“doc/guix.texi”.
(EXTRA_DIST): Remove ‘.texi’ files.

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

gnu: certbot: Update to 0.21.0.

* gnu/packages/tls.scm (certbot): Update to 0.21.0.
(python-acme): Update to 0.21.0.
[propagated-inputs]: Add python-josepy.

gnu: Add python-josepy.

* gnu/packages/python-crypto.scm (python-josepy, python2-josepy): New variables.

gnu: libvirt: Update to 4.0.0.

* gnu/packages/virtualization.scm (libvirt): Update to 4.0.0.
[arguments]: Substitute INVOKE for SYSTEM*.

gnu: Consistently Write ‘file system(s)’.

It is the GNU way.

* doc/guix.texi (Build Systems, DNS Services): Write ‘file system(s)’.
* gnu/build/vm.scm (create-ext-file-system, create-fat-file-system):
Likewise.
* gnu/packages/backup.scm (dirvish, rsnapshot)[description]: Likewise.
* gnu/packages/check.scm (python-testpath)[description]: Likewise.
* gnu/packages/disk.scm (pydf)[description]: Likewise.
* gnu/packages/file-systems.scm (disorderfs)[synopsis, description]: Likewise.
(glusterfs)[description]: Likewise.
* gnu/packages/haskell.scm (ghc-directory, ghc-system-fileio-bootstrap)
(ghc-system-fileio)[synopsis]: Likewise.
(ghc-fsnotify)[description]: Likewise.
* gnu/packages/linux.scm (proot)[description]: Likewise.
(jmtpfs)[synopsis, description]: Likewise.
* gnu/packages/mate.scm (caja, caja-extensions)[description]: Likewise.
* gnu/packages/storage.scm (ceph)[description]: Likewise.
* gnu/packages/sync.scm (lsyncd)[description]: Likewise.
* gnu/packages/syncthing.scm (syncthing)[synopsis]: Likewise.
(go-github-com-zillode-notify)[description]: Likewise.
* gnu/services/nfs.scm (pipefs-service-type): Likewise.
* guix/scripts/system.scm (perform-action): Likewise.

gnu: unbound: Update to 1.6.8 [fixes CVE-2017-15105].

* gnu/packages/dns.scm (unbound): Update to 1.6.8.

gnu: libvpx: Use HTTPS for home page.

* gnu/packages/video.scm (libvpx)[home-page]: Use HTTPS.

gnu: ninja: Update to 1.8.2.

* gnu/packages/ninja.scm (ninja): Update to 1.8.2.
[source]: Remove upstreamed patch.
[arguments]: Substitute INVOKE for SYSTEM*.  Use standard indentation.
* gnu/packages/patches/ninja-zero-mtime.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.