tests: cuirass: Remove "cuirass running" test.

* gnu/tests/cuirass.scm ("cuirass running"): Remove it as it fails if all the
dependencies are not started yet.

services: cuirass: Fix services requirements.

* gnu/services/cuirass.scm (cuirass-shepherd-service): Add "postgres-roles" to
cuirass requirements. Set cuirass-web requirements to cuirass only. Remove
"guix-daemon" and "networking" from cuirass-remote-server requirements as are
already required by cuirass.

services: postgresql-roles: Fix race condition.

Make sure that the postgresql-roles script is completed before declaring the
postgresql-roles service as started.

* gnu/services/databases.scm (postgresql-create-roles): Return the command
line instead of a program-file.
(postgresql-role-shepherd-service): Use fork+exec-command to start the role
creation script and wait for its completion before returning.

services: cuirass: Improve simple-cuirass-services.

Instead of returning multiple services in simple-cuirass-services, rely on the
instantiate-missing-services procedure to instantiate postgresql and
postgresql-role-service-type when missing.

Turn simple-cuirass-services procedure into
simple-cuirass-configuration->specs, that takes a simple-cuirass-configuration
record and returns a Cuirass specification.

Suggested-by: Ludovic Courtès <ludo@gnu.org>
* gnu/services/cuirass.scm (%default-cuirass-config): Remove it.
(simple-cuirass-services): Rename it to ...
(simple-cuirass-configuration->specs): ... this procedure.
* gnu/tests/cuirass.scm (cuirass-services): Remove postgresql and
postgresql-role services that are automatically instantiated.
(simple-cuirass-service): New variable.
(%cuirass-simple-test): Adapt it to use simple-cuirass-configuration->specs
instead of simple-cuirass-services.
* doc/guix.texi (Simple Cuirass): Update it.

gnu: sbcl-common-lisp-jupyter: Update to 20210217.

* gnu/packages/lisp-xyz.scm (sbcl-common-lisp-jupyter): Update to 20210217.

gnu: sbcl-trivial-clipboard: Update to 20210219.

* gnu/packages/lisp-xyz.scm (sbcl-trivial-clipboard): Update to 20210219.

gnu: youtube-dl: Update to 2021.02.22.

* gnu/packages/video.scm (youtube-dl): Update to 2021.02.22.

scripts: Don't trigger option hints for short options.

Previously, 'guix install foo -r bar' would crash with a backtrace
because NAME would be #\r (a character instead of a string).

* guix/scripts.scm (parse-command-line)[parse-options-from]: Call
'option-hint' only when NAME is a string.

profiles: Fix typo in manifest comment.

* guix/build/profiles.scm (build-profile): Fix typo.

describe: Fix typo in 'manifest-entry-with-provenance'.

* guix/describe.scm (manifest-entry-with-provenance): Fix first argument
to 'assq'.

gnu: ocaml-llvm: Remove duplicate package.

Commit 8f710cc598fb675d267f49a82cffc197f03ad52c introduced a duplicate
ocaml-llvm@9.0.1 package, which was flagged by a test failure in
tests/packages.scm.

* gnu/packages/ocaml.scm (make-ocaml-llvm): Define as 'mlambdaq'.

gnu: linux-libre-headers@5.11: Refer to 5.11, not 5.10.

Fixes a typo introduced in b819512ca2cce1051c5fea26328da2e5d6a9a101.

* gnu/packages/linux.scm (linux-libre-headers-5.11): Really refer to 5.11.

packages: 'package-field-location' preserves the original file name.

This fixes a regression introduced in
9a38bed2cf32e9462badfa43e74cdd4580e804fc.

* guix/packages.scm (package-field-location): Do not shadow the 'file'
variable.

gnu: isync: Update to 1.3.5 [fixes CVE-2021-20247].

* gnu/packages/mail.scm (isync): Update to 1.3.5.

gnu: Add temper-exporter.

* gnu/packages/monitoring.scm (temper-exporter): New variable.

system: hurd: Have the static networking provision 'networking.

Some services require networking, I'm looking at the Guix Build Coordinator
agent.  Networking seems to work in the childhurd VM, so I think this change
makes sense.

* gnu/system/hurd.scm (%base-services/hurd): Add 'networking to the provision
parameter for the static-networking service.

substitute: Rework connection error handling.

This is part of trying to reduce the interdependency of code within the
substitute module.

This commit addresses some of the error handling that was performed through
open-connection-for-uri/maybe. The new approach is to use
call-with-connection-error-handling, and wrap calls to http-multiple-get and
http-fetch with that procedure, which takes care of handling connection
errors.

I think this is even slightly more rigerous than the previous setup, because
this approach handles connection errors that occur when http-multiple-get
reconnects to a host.

* guix/scripts/substitute.scm (open-connection-for-uri/maybe): Transform in to
call-with-connection-error-handling.
(fetch-narinfos): Use call-with-connection-error-handling.
(process-query): Replace open-connection-for-uri/maybe with
open-connection-for-uri/cached.
(open-connection-for-uri/cached): Set a default timeout, matching the
behaviour in open-connection-for-uri/maybe.
(process-substitution): Use call-with-connection-error-handling.

substitute: Remove fetch-narinfos use open-connection-for-uri/maybe.

At least by default.  Instead, make the open-connection procedure a parameter,
and make the default guix:open-connection-for-uri.  Do so similarly for
lookup-narinfos and lookup-narinfos/diverse which work towards calling
fetch-narinfos.

This means this code can be moved to a different module, without having
use/move the connection caching code.

* guix/scripts/substitute.scm (fetch-narinfos): Add #:open-connection
argument, and call http-multiple-get with it.
(lookup-narinfos) Add #:open-connection argument, and call fetch-narinfos with
it.
(lookup-narinfos/diverse): Add #:open-connection argument, and call
lookup-narinfos with it.
(process-query): Call lookup-narinfos/diverse with #:open-connection
open-connection-for-uri/maybe.

substitute: Inline fetch in to process-substitutes.

As it's only called in one place, and this should make the code easier to
read.

* guix/scripts/substitute.scm (fetch): Move procedure inside…
(process-substitution): …here.

substitute: Remove redundant fetch arguments.

It's just called in one place, with hardcoded argument values, so just inline
them.

* guix/scripts/substitute.scm (fetch): Remove arguments that don't vary, copy
the values from the call site in process-substitution.
(process-substitution): Remove unnecessary argument values from fetch call.

substitute: Remove now redundant connection caching helpers.

Failures now should be handled where they occur, and if there's a problem
that's symptomatic of an issue with the connection, the port should be closed.

* guix/scripts/substitute.scm (call-with-cached-connection): Remove procedure.
(with-cached-connection): Remove syntax rule.

substitute: Change connection cache handling in process-substitution.

Just pass open-connection-for-uri/maybe to http-fetch, this removes the need
for with-cached-connection and passing the port in.

* guix/scripts/substitute.scm (fetch): Don't take a port as an argument, and
pass open-connection-for-uri/maybe to http-fetch.
(process-substitution): Don't call fetch with with-cached-connection.

http-client: Accept #:open-connection in http-fetch.

So that an alternative procedure can be passed in, perhaps to perform
connection caching.

* guix/http-client.scm (http-fetch): Add an #:open-connection keyword
argument.

substitute: Stop using call-with-cached-connection in fetch-narinfos.

Instead, just pass open-connection-for-uri/maybe to http-multiple-get. This
code should be functionaly similar to the previous code. The eventual aim of
this is to make the connection caching not mandatory in fetch-narinfos.

* guix/scripts/substitute.scm (fetch-narinfos): Remove use of
call-with-cached-connection.

substitute: open-connection-for-uri/maybe add #:verify-certificate?.

As this is used by http-fetch and http-multiple-get when they call the
specified open connection procedure.

* guix/scripts/substitute.scm (open-connection-for-uri/maybe): Support
 #:verify-certificate?.

http-client: Add error handling to http-multiple-get.

Making sure to close the port if it looks to be unusable. This closing of the
port will allow for caching connections, without caching broken connections,
as the cache can avoid handing out closed ports.

* guix/http-client.scm (http-multiple-get): Try to catch exceptions that
happen if the port is unusable, this is a adaptation of code within the (guix
scripts substitute) module.

guix: Move http-multiple-get to (guix http-client).

From (guix scripts substitute). This will make it easier to reuse this code.

* guix/scripts/substitute.scm (http-multiple-get): Remove, and move to…
* guix/http-client.scm (http-multiple-get): …here.

substitute: Remove redundant let block from fetch.

* guix/scripts/substitute.scm (fetch): Remove redundant let block.

substitute: Remove connection handling from fetch.

http-fetch does this, so just use that code instead.

* guix/scripts/substitute.scm (fetch): Remove connection handling when the
port is closed.

substitute: Remove buffer handling from fetch.

http-fetch does this, so just set the right option.

* guix/scripts/substitute.scm (fetch): Remove buffering code, and pass
 #:buffered? to http-fetch.

gnu: star: Update to 2.7.8a.

* gnu/packages/bioinformatics.scm (star): Update to 2.7.8a.

gnu: Add dstask.

* gnu/packages/task-management.scm (dstask): New variable.

Signed-off-by: Léo Le Bouter <lle-bout@zaclys.net>

gnu: gnome-keyring: Propagate gcr to fix unlock prompts.

On desktop environments other than GNOME, it is not obvious gcr package needs
to be installed in the profile for gnome-keyring unlock prompts to
work. Propagating it ensures no one will need to figure this out in the future.

* gnu/packages/gnome.scm (gnome-keyring)[propagated-inputs]: Add "gcr".

gnu: gita: Update to 0.12.9.

* gnu/packages/version-control.scm (gita): Update to 0.12.9.

Signed-off-by: Léo Le Bouter <lle-bout@zaclys.net>

gnu: python-sane: Correct the license.

This is a followup to commit f500905ce1baf85a2407c5ccde148ee6c2ea2584.

* gnu/packages/python-xyz.scm (python-sane)[license]: Describe the
license.

gnu: Add python-screenkey.

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

Co-authored-by: Léo Le Bouter <lle-bout@zaclys.net>

doc: Fix build.

This is a follow-up of b309a28678664c295e97a70607def02b0c9b4296.

* doc/guix.texi (Tor): Fix build.

gnu: cuirass: Add missing dependency.

* gnu/packages/ci.scm (cuirass)[inputs]: Add gnutls.
[arguments]: Adapt accordingly.

services: postgresql: Define a default value.

* gnu/services/databases.scm (postgresql-service-type): Define a default value.

services: cuirass: Instantiate postgresql service.

* gnu/services/cuirass.scm (cuirass-service-type): Instantiate postgresql
service when missing.

services: tor: Add control-socket? option.

* doc/guix.texi (Networking Services): Document new `control-socket?'
option for `tor-configuration`.
* gnu/services/networking.scm (<tor-configuration>):
(tor-configuration->torrc):

gnu: ruby-omniauth-oauth2: Update to 1.7.1.

* gnu/packages/ruby.scm (ruby-omniauth-oauth2): Update to 1.7.1.

gnu: ruby-omniauth: Update to 2.0.3.

* gnu/packages/ruby.scm (ruby-omniauth): Update to 2.0.3.
[arguments]: Don't skip tests.
[propagated-inputs]: Add ruby-rack-protector.
[native-inputs]: Add ruby-rspec.

gnu: cuirass: Update to 0.0.1-72.543e26a.

* gnu/packages/ci.scm (guile-mastodon-dev): New variable.
(guile-mastodon-dev): Update to 0.0.1-72.543e26a.
[inputs]: Use guile-mastodon-dev instead of guile-mastodon.

gnu: Fix "license:" prefix in scanner.scm.

* gnu/packages/scanner.scm: Change "licence:" to "license:".

gnu: Add python-sane.

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

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

gnu: guile-dsv: Update to 0.4.0.

* gnu/packages/guile-xyz.scm (guile-dsv): Update to 0.4.0
[arguments]: Remove phase "configure-support-guile3.0".

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

news: Add 'zh' translation.

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

packages: 'package-field-location' handles 'search-path' returning #f.

Fixes <https://bugs.gnu.org/46390>.
Reported by zimoun <zimon.toutoune@gmail.com>.

This is similar to the fix in d10474c38d58bdc676e64336769dc2e00cdfa8ed.

* guix/packages.scm (package-field-location): Handle FILE not in %LOAD-PATH.
* tests/guix-lint.sh: Add test.

gnu: emacs-selectrum: Update to 3.1.

* gnu/packages/emacs-xyz.scm (emacs-selectrum): Update to 3.1.

gnu: cuirass: Update to 0.0.1-71.3e65617.

* gnu/packages/ci.scm (cuirass): Update to 0.0.1-71.3e65617.

gnu: nixfmt: Fix name.

* gnu/packages/haskell-apps.scm (nixfmt): Fix name.

gnu: Rename ghc-nixfmt into nixfmt

* gnu/packages/haskell-xyz.scm (ghc-nixfmt): Move to...
* gnu/packages/haskell-apps.scm (nixfmt): ... here.

This is a followup to 703ccd583611b6efa689b7a2d1daf35d6cd83c35.

gnu: cuirass: Update dependencies.

* gnu/packages/ci.scm (cuirass)[inputs]: Add "guile-mastodon" and "mailutils".
[arguments]: Adapt accordingly.

gnu: guile-mastodon: Build with Guile 3.0.

* gnu/packages/guile-xyz.scm (guile-mastodon)[source]: Modify configure.ac to
add Guile 3.0 support.
[native-inputs]: Add "emacs" and "texinfo".
[inputs]: Use Guile 3.0 and Guile Json 4.0.

services: cuirass: Add parameters support.

* gnu/services/cuirass.scm (<cuirass-configuration>)[parameters]: New field.
[zabbix-uri]: Remove it.
(cuirass-shepherd-service): Honor it.

gnu: cuirass: Update to 0.0.1-70.342c5ed

* gnu/packages/ci.scm (cuirass): Update to 0.0.1-70.342c5ed.

gnu: autoconf-archive: Update to 2021.02.19.

* gnu/packages/autotools.scm (autoconf-archive): Update to 2021.02.19.

gnu: git: Add credential-libsecret output.

* gnu/packages/version-control.scm (git)[native-inputs]: Add pkg-config.
[inputs]: Add glib and libsecret.
[outputs]: Add "credential-libsecret".
[arguments]: Add 'install-credential-libsecret phase to #:phases to build and
install "git-credential-libsecret" to "credential-libsecret" output.
(git-minimal)[arguments]: Delete the 'install-credential-libsecret phase.

Signed-off-by: Chris Marusich <cmmarusich@gmail.com>

gnu: diffoscope: Update to 167.

* gnu/packages/diffoscope.scm (diffoscope): Update to 167.

gnu: Add HDF5 1.12.0.

* gnu/packages/maths.scm (hdf5-1.12): New variable.

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

gnu: ffmpeg: Update to 4.3.2.

* gnu/packages/video.scm (ffmpeg): Update to 4.3.2.

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

image: Add rock64 support.

* gnu/system/images/rock64.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly.

gnu: ungoogled-chromium: Update default preferences.

* gnu/packages/aux-files/chromium/master-preferences.json: Adjust for upstream
changes.

gnu: ungoogled-chromium: Update to 88.0.4324.182-0.b98f2d5.

* gnu/packages/chromium.scm (%chromium-version): Set to -88.0.4324.182.
(%ungoogled-revision): Set to 27c9e9fabd38001b32d148f7b3f99b4d31e67277.
(%ungoogled-origin, ungoogled-chromium): Update hashes.

gnu: emacs-helm-pass: Update to 0.4.

* gnu/packages/emacs-xyz.scm (emacs-helm-pass): Update to 0.4.

gnu: ir: Remove whitespace at end of line.

* gnu/packages/audio.scm (ir): Remove whitespace at end of line.

Signed-off-by: Léo Le Bouter <lle-bout@zaclys.net>

gnu: ruby-rack-protection: Update to 2.0.8.1.

* gnu/packages/ruby.scm (ruby-rack-protection): Update to 2.0.8.1.

gnu: exiv2-0.26: Remove variable.

* gnu/packages/image.scm (exiv2-0.26): Remove variable.
* gnu/packages/patches/exiv2-CVE-2017-14859-14862-14864.patch:
* gnu/packages/patches/exiv2-CVE-2017-14860.patch: Remove files.
* gnu/local.mk (dist_patch_DATA): Apply removal.

gnu: hugin: Update to 2020.0.0.

* gnu/packages/photo.scm (hugin): Update to 2020.0.0.
[inputs]: Use current exiv2.

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

gnu: Add cli11.

* gnu/packages/cpp.scm (cli11): New variable.

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

gnu: screen: Patch CVE-2021-26937.

* gnu/packages/screen.scm (screen)[source]: Add patch.
* gnu/packages/patches/screen-CVE-2021-26937.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.

gnu: sbcl-utm-ups: Update to 1.1-0.ffcb7b6.

* gnu/packages/lisp-xyz.scm (sbcl-utm-ups): Update to 1.1-0.ffcb7b6.

gnu: asymptote: Update to 2.69.

* gnu/packages/plotutils.scm (asymptote): Update to 2.69.

gnu: Add ghc-nixfmt.

* gnu/packages/haskell-xyz.scm (ghc-nixfmt): New variable.

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

gnu: Add vmtouch.

* gnu/packages/admin.scm (vmtouch): New variable.

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

gnu: fontmanager: Update to 0.8.4.

* gnu/packages/fontutils.scm (fontmanager): Update to 0.8.3.
[inputs]: Add libsoup and webkitgtk.
[native-inputs]: Remove vala; add vala-0.50.

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

gnu: herbstluftwm: Update to 0.9.2.

* gnu/packages/wm.scm (herbstluftwm): Update to 0.9.2.
[inputs]: Add libxft.
[native-inputs]: Add python.

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

gnu: python-onnx: Update to 1.8.1.

* gnu/packages/machine-learning.scm (python-onnx): Update to 1.8.1.

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

gnu: libredwg: Update to 0.12.1.

* gnu/packages/engineering.scm (libredwg): Update to 0.12.1.

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

gnu: darktable: Update to 3.4.1.

* gnu/packages/photo.scm (darktable): Update to 3.4.1.

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

gnu: setzer: Update to 0.4.1.

* gnu/packages/gnome.scm (setzer): Update to 0.4.1.
[inputs]: Add python-pdfminer-six.

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

gnu: Add python-pdfminer-six.

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

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

gnu: Add imgp.

* gnu/packages/image.scm (imgp): New variable.

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

gnu: Add python-pillow-simd.

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

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

gnu: Add asdf (Advanced Scientific Data Format)

* gnu/packages/astronomy.scm (python-asdf): New variable

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

gnu: wcslib: Update to 7.4

* gnu/packages/astronomy.scm (wcslib): Update to 7.4

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

gnu: xfce4-cpugraph-plugin: Update to 1.2.2.

* gnu/packages/xfce.scm (xfce4-cpugraph-plugin): Update to 1.2.2.

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

gnu: Add transcrypt.

* gnu/packages/crypto.scm (transcrypt): New variable.

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

gnu: frrouting: Update to 7.5.

* gnu/packages/networking.scm (frrouting): Update to 7.5.
[inputs]: Add libcap and libyang.

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

gnu: Add libyang

* gnu/packages/networking.scm (libyang): New variable.

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

gnu: artyfx: Update to 1.3.1.

* gnu/packages/music.scm (artyfx): Update to 1.3.1.

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

gnu: lrzip: Update to 0.640.

* gnu/packages/compression.scm (lrzip): Update to 0.640.
[source]: Remove obsolete patch 'lrzip-CVE-2017-8842.patch'.
[inputs]: Add lz4.
* gnu/packages/patches/lrzip-CVE-2017-8842.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

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

gnu: lynis: Update to 3.0.3.

* gnu/packages/admin.scm (lynis): Update to 3.0.3.
[native-inputs]: Update lynis-sdk accordingly.

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

gnu: Add libretro-lowresnx.

* gnu/packages/emulators.scm (libretro-lowresnx): New variable.

doc: Fix typography.

* doc/guix.texi (Continuous Integration): Use @pxref appropriately.  Remove
`quote' from code examples.

gnu: emacs-oauth2: Update to 0.16.

* gnu/packages/emacs-xyz.scm (emacs-oauth2): Update to 0.16.

gnu: Python 3.9: Fix CVE-2021-3177.

* gnu/packages/patches/python-3.9-CVE-2021-3177.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/python.scm (python-3.9)[source]: Use it.

gnu: nanopolish: Fix script wrapping.

* gnu/packages/bioinformatics.scm (nanopolish)[arguments]: Fix wrap-programs
phase.
[inputs]: Add Guile for wrap-script; add bioperl and perl-getopt-long for Perl
scripts.

gnu: python-scikit-learn: Update to 0.24.1.

* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 0.24.1.
[propagated-inputs]: Add python-threadpoolctl.
(python2-scikit-learn)[inputs,native-inputs,propagated-inputs]: Do not
inherit these fields.