services: postgresql: Use "/tmp" host directory.

This is a follow-up of c311147bd16aa0e5746d9cbf31502f5fd61e470c.

* gnu/services/databases.scm (<postgresql-role-configuration>)[host]: Set to
"/tmp" which the default Postgresql socket directory.

services: mysql: Add extra-environment as configuration option.

* gnu/services/databases.scm (mysql-configuration): Add extra-environment
(mysql-service): Use #:log-file and #:environment-variables
* doc/guix.texi: Document it.

Signed-off-by: Leo Prikler <leo.prikler@student.tugraz.at>

gnu: Add r-randomforestsrc.

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

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

nls: Add Slovak translation.

* po/guix/LINGUAS: Add 'sk'.
* po/guix/sk.po: New file.

gnu: openconnect-sso: Update to 0.7.2.

* gnu/packages/vpn.scm (openconnect-sso): Update to 0.7.2.
[arguments]: Remove 'adjust-package-version-requirements phase.

gnu: Add r-hmm.

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

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

gnu: python-tinycss2: Enable tests.

* gnu/packages/python-web.scm (python-tinycss2)[source]: Fetch from git
repository to include tests.
[arguments]: Build from source with flit.
[native-inputs]: Add python-flit, python-pytest, python-pytest-cov,
python-pytest-flake8, and python-pytest-isort.

gnu: python-ipywidgets: Update to 7.6.3.

* gnu/packages/python-xyz.scm (python-ipywidgets): Update to 7.6.3.
[propagated-inputs]: Add python-ipython, python-jupyterlab-widgets, and
python-nbformat.
[native-inputs]: Remove python-nose; add python-mock and ptyhon-pytest-cov.

gnu: python-widgetsnbextension: Remove unnecessary inputs.

* gnu/packages/python-xyz.scm (python-widgetsnbextension)[propagated-inputs]:
Remove python-argon2-cffi, python-ipykernel, and python-terminado.
[native-inputs]: Remove python-certifi and python-nose.

gnu: Add python-jupyterlab-widgets.

* gnu/packages/jupyter.scm (python-jupyterlab-widgets): New variable.

gnu: Add python-jupyter-packaging.

* gnu/packages/jupyter.scm (python-jupyter-packaging): New variable.

gnu: Add python-deprecation.

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

gnu: python-testpath: Update to 0.4.4.

* gnu/packages/check.scm (python-testpath): Update to 0.4.4.
[arguments]: Build the package as intended with flit.
[native-inputs]: Add python-flit.

gnu: python-flit: Update to 3.2.0.

* gnu/packages/python-xyz.scm (python-flit): Update to 3.2.0.
[source]: Fetch from git repository to include flit_core.
[arguments]: Add phases to bootstrap the build.
[propagated-inputs]: Add python-pytoml and python-toml.
[native-inputs]: Add python-docutils, python-responses,
python-pygments-github-lexers, python-pytest, python-pytest-cov,
python-sphinx, python-sphinxcontrib-github-alt, and python-testpath.

gnu: Add python-sphinxcontrib-github-alt.

* gnu/packages/sphinx.scm (python-sphinxcontrib-github-alt): New variable.

gnu: Add python-requests-unixsocket.

* gnu/packages/python-web.scm (python-requests-unixsocket): New variable.

gnu: Add python-pygments-github-lexers.

* gnu/packages/python-xyz.scm (python-pygments-github-lexers): New variable.

gnu: Add python-pytoml.

* gnu/packages/python-build.scm (python-pytoml): New variable.

gnu: Remove python2-ipykernel.

* gnu/packages/python-xyz.scm (python2-ipykernel): Remove variable.
(python-ipykernel)[properties]: Remove python2-variant.

gnu: Remove python2-jupyter-console.

* gnu/packages/python-xyz.scm (python2-jupyter-console): Remove variable.
(python-jupyter-console)[properties]: Remove python2-variant.

gnu: Remove python2-jupyter-core.

* gnu/packages/python-xyz.scm (python2-jupyter-core): Remove variable.

gnu: Remove python2-ipyparallel.

* gnu/packages/python-xyz.scm (python2-ipyparallel): Remove variable.

gnu: Remove python2-matplotlib-documentation.

* gnu/packages/python-xyz.scm (python2-matplotlib-documentation): Remove variable.

gnu: python-nbformat: Update to 5.1.3.

* gnu/packages/python-xyz.scm (python-nbformat): Update to 5.1.3.
[arguments]: Remove to enable tests.
[native-inputs]: Add python-pytest.
[properties]: Add python2-variant.
(python2-nbformat): Keep at version 4.4.0; override version and source field.

gnu: python-nbconvert: Update to 6.0.7.

* gnu/packages/python-xyz.scm (python-nbconvert): Update to 6.0.7.
[arguments]: Remove configure flags, enable tests, override check phase.
[propagated-inputs]: Add python-defusedxml, python-nbclient,
python-pandocfilters, python-jupyterlab-pygments, and python-testpath.
[properties]: Add python2-variant.
(python2-nbconvert): Override version, source, arguments, and
propagated-inputs.

gnu: Add python-nbclient.

* gnu/packages/jupyter.scm (python-nbclient): New variable.

gnu: Add python-jupyterlab-pygments.

* gnu/packages/jupyter.scm (python-jupyterlab-pygments): New variable.

gnu: Add python-nest-asyncio.

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

gnu: python-notebook: Update inputs.

* gnu/packages/python-xyz.scm (python-notebook)[propagated-inputs]: Add
python-argon2-cffi, python-ipykernel, python-ipython-genutils, python-jinja2,
python-jupyter-client, python-pyzmq, python-tornado-6, and python-traitlets.
[native-inputs]: Remove python-nose and python-sphinx; add python-coverage,
python-nbval, python-pytest, python-pytest-cov, and
python-requests-unixsocket.
[arguments]: Use pytest instead of nosetests.

gnu: python-notebook: Update to 6.3.0.

* gnu/packages/python-xyz.scm (python-notebook): Update to 6.3.0.

gnu: python-widgetsnbextension: Add missing inputs.

* gnu/packages/python-xyz.scm (python-widgetsnbextension)[propagated-inputs]:
Add python-argon2-cffi and python-terminado.

gnu: python-ipykernel: Update to 5.5.3.

* gnu/packages/python-xyz.scm (python-ipykernel): Update to 5.5.3.

gnu: python-jupyter-client: Update to 6.1.12.

* gnu/packages/python-xyz.scm (python-jupyter-client): Update to 6.1.12.
[propagated-inputs]: Add python-dateutil and python-tornado-6.
[native-inputs]: Add python-pytest.

gnu: python-jupyter-core: Update to 4.7.1.

* gnu/packages/python-xyz.scm (python-jupyter-core): Update to 4.7.1.

gnu: python-terminado: Update to 0.9.4.

* gnu/packages/python-web.scm (python-terminado): Update to 0.9.4.
[propagated-inputs]: Replace python-tornado with python-tornado-6.
[native-inputs]: Replace python-nose with python-pytest.
[home-page]: Follow redirect.
[arguments]: Update check phase.

gnu: esbuild: Update to 0.11.9.

* gnu/packages/web.scm (esbuild): Update to 0.11.9.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: visidata: Update to 2.4.

* gnu/packages/visidata.scm (visidata): Update to 2.4.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: gnu-standards: Update to 2020-11-25.

* gnu/packages/gnu-doc.scm (gnu-standards): Update to 2020-11-25.
[source]: Make file-name more descriptive. Use version variable for
revision.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add texlive-xcharter.

* gnu/packages/tex.scm: New variable.

tests: halt: Fix it.

This fixes: <https://issues.guix.gnu.org/47727>.  The OCR prompt detection is
failing, so remove it altogether.  It looks like the test doesn't need the
prompt detection delay to work properly.

* gnu/tests/base.scm (run-halt-test): Remove failing OCR detection.

services: postgresql: Change service default socket directory.

Fixes <https://bugs.gnu.org/46737>.

PostgreSQL running with a different socket directory to the default one in the
package itself breaks some services, this commit restores the previous
behaviour where PostgreSQL by default will run with a socket directory that
matches the default used by PostgreSQL packaged for Guix.

Switching to a different default value can happen, but only alongside changing
the PostgreSQL package.

* gnu/services/databases.scm (<postgresql-config-file>)[socket-directory]:
Change default to #false.
* doc/guix.texi (Database Services): Update documentation, and specify a
different value for disabling connections via sockets.
* gnu/tests/guix.scm (%guix-data-service-os): Use default PostgreSQL
behaviour.
* gnu/tests/monitoring.scm (%zabbix-os): Likewise.
* gnu/tests/web.scm (patchwork-os): Likewise.

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

gnu: guile-picture-language: Update to 0.0.1-5.a1322bf.

* gnu/packages/guile-xyz.scm (guile-picture-language): Update to
0.0.1-5.a1322bf.

etc/committer: Add missing newline.

* etc/committer.scm.in (main): Add newline to message.

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

etc/committer: Use git plumbing instead of porcelain.

* etc/committer.scm.in (diff-info): Use "git diff-files" instead of "git diff".
(old-sexp): Use "git cat-file" instead of "git show".

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

doc: Document 'gnu-build-system' keyword parameters.

* doc/guix.texi (Build Systems): Document keyword parameters of
'gnu-build-system'.

doc: Move list of build phases to "Build Phases".

Before this change, the 'gnu-build-system' phases were listed in the
"Build Systems" section, and then summarized in the "Build Phases"
section.  This moves everything to "Build Phases".

* doc/guix.texi (Build Systems): Move phase table to...
(Build Phases): ... here.  Rearrange surrounding text.

channels: Build user channels with '-O1'.

This should noticeably speed up compilation for channels with many files.

* guix/channels.scm (standard-module-derivation)[build]: Define
'optimizations-for-level' and '-O1'.  Pass #:optimization-options to
'compile-files'.

services: ipfs: Tweak description.

* gnu/services/networking.scm (ipfs-service-type)[description]: Avoid
abbreviation.

gnu: tests: Test basic funtionality of the IPFS service.

It is tested whether the IPFS service listens
at the gateway and API ports and whether it
is possible to upload and download a bytevector.

* gnu/tests/networking.scm
  (%ipfs-os): New variable.
  (run-ipfs-test): New procedure.
  (%test-ipfs): New system test.

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

tests: Support package extensions in the backdoor REPL.

* gnu/tests.scm
  (<marionette-configuration>): Add 'extensions' field.
  (marionette-shepherd-service): Honour the field.
  (with-import-modules-and-extensions): Define a combination
  of 'with-import-modules' and 'with-extensions'.

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

Add (guix ipfs).

This module allows for communicating with the IPFS
gateway over the HTTP interface.  The commit has been
cherry-picked from <https://issues.guix.gnu.org/33899>.

The procedures for adding and restoring file trees have
been removed as according to a reply issue 33899, a different
format will be used.  The procedure 'add-data' has been
exported as it will be used in the system test for IPFS.

* guix/ipfs.scm: New file.
* Makefile.am (MODULES): Add it.

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

services: Add ipfs-service-type

* gnu/services/networking.scm (ipfs-service-type)
  (%ipfs-home-mapping, %ipfs-environment)
  (%ipfs-accounts, %ipfs-home): New variables.
  (ipfs-configuration, ipfs-configuration?)
  (ipfs-configuration-package, ipfs-configuration-gateway)
  (ipfs-configuration-api, ipfs-shepherd-service)
  (ipfs-binary, %ipfs-activation): New procedures.
* doc/guix.texi (Networking Services): Document it.

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

gnu: racket: Don't inject store paths into Racket files.

Apparently, during grafting, Guix can somehow mangle compiled
Racket CS files (.zo) such that Racket will refuse to load them.
(Maybe it has something to do with compression?)
So, we stop patching Racket sources with absolute paths to store
files (i.e. for foreign libraries to dlopen).
Instead, we put them in a data file that doesn't get compiled or,
in one case, embed it in C.

Fixes https://issues.guix.gnu.org/47064

* gnu/packages/patches/racket-sh-via-rktio.patch: New file.
Adds a special case at the C level, controlled by a preprocessor macro,
to handle attempts to execute "/bin/sh".
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/scheme.scm (racket)[source](patches): Apply it.
(racket)[arguments](#:configure-flags): Add the CPP flag to enable it.
(racket)[arguments](#:modules): Use srfi-1.
(racket)[arguments](#:phases): Remove 'patch-/bin/sh and 'pre-configure.
Change 'pre-configure-minimal to just change directory.
Add 'patch-config.rktd-lib-search-dirs after 'build and before 'install
to configure Racket's "lib-search-dirs".
(racket, racket-minimal)[inputs]: Add bash-minimal as an explicit input.
(racket-minimal)[source]: Adjust to inherit patches from racket.
(racket-minimal)[arguments]: Inherit from racket: changes no longer needed.

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

gnu: Add r-txdb-dmelanogaster-ucsc-dm6-ensgene.

* gnu/packages/bioconductor.scm (r-txdb-dmelanogaster-ucsc-dm6-ensgene):
New variable.

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

services: Support DELETE in MODIFY-SERVICES macro.

* gnu/services.scm (%modify-service): Add clause for DELETE syntax.
(modify-services): Use FILTER-MAP; adjust docstring.
* doc/guix.texi (System Services): Mention alternative syntax.
(X Window): Use MODIFY-SERVICES syntax.

gnu: Add cl-bodge-queue.

* gnu/packages/lisp-xyz.scm (sbcl-bodge-queue, cl-bodge-queue,
  ecl-bodge-queue): New variables.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: hydrogen: Update to 1.0.2.

* gnu/packages/music.scm (hydrogen): Update to 1.0.2.

gnu: Add openvdb.

* gnu/packages/graphics.scm (openvdb): New variable.

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

gnu: Add texlive-newtx.

* gnu/packages/tex.scm: New variable.

gnu: java-eclipse-jetty-util: Update to 9.4.39 [security fixes].

Fixes CVE-2021-28165 - jetty server high CPU when client send data length >
17408, CVE-2021-28164 - Normalize ambiguous URIs and CVE-2021-28163 - Exclude
webapps directory from deployment scan.

* gnu/packages/java.scm (java-eclipse-jetty-util): Update to 9.4.39.
(java-eclipse-jetty-util-ajax): New variable.
(java-eclipse-jetty-util, java-eclipse-jetty-io, java-eclipse-jetty-http)
(java-eclipse-jetty-jmx, java-eclipse-jetty-server)
(java-eclipse-jetty-security, java-eclipse-jetty-servlet)
(java-eclipse-jetty-xml, java-eclipse-jetty-webapp): Disable tests.
[native-inputs]: Remove test dependencies.

gnu: hangups: Run test suite.

* gnu/packages/messaging.scm (hangups)[arguments]: Use custom 'check
phase.

gnu: hangups: Loosen version restrictions further.

* gnu/packages/messaging.scm (hangups)[arguments]: Adjust custom
'relax-dependencies phase to allow more dependency versions.

gnu: python-mechanicalsoup: Update to 1.0.0.

* gnu/packages/python-web.scm (python-mechanicalsoup): Update to
1.0.0.
[arguments]: Enable tests.
[native-inputs]: Add python-pytest-flake8, python-pytest-httpbin,
python-pytest-cov, python-pytest-mock, python-pytest-runner,
python-requests-mock.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

tests: docker: Increase VM building memory size to 1024MiB.

This fixes the following error when running the "docker-system" test:

In ice-9/ftw.scm:
   553:30  1 (_ #<directory stream db6660>)
In unknown file:
           0 (readdir #<directory stream db6660>)

ERROR: In procedure readdir:
In procedure readdir: Cannot allocate memory

* gnu/tests/docker.scm (%test-docker-system): Bump image building VM memory
size to 1024 MiB.

system: vm: Add a memory-size argument to system-docker-image.

* gnu/system/vm.scm (system-docker-image): Add a memory-size argument and pass
it to expression->derivation-in-linux-vm.

gnu: renpy: Update to 7.4.4.

* gnu/packages/game-development.scm (python2-renpy): Update to 7.4.4.
(python2-pygame-sdl2)[renpy-version]: Likewise.

gnu: nginx: Enable stream module.

* gnu/packages/web.scm (nginx)[arguments]: Add --with-stream option in the 'configure phase.

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

gnu: Add prips.

gnu/packages/admin.scm (prips): New variable.

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

gnu: blis: Add deprecated aliases.

Add deprecated aliases for packages removed in the parent commit.

* gnu/packages/maths.scm (blis-sandybridge, blis-haswell, blis-knl): New
variables.

gnu: blis: Update to 0.8.1.

* gnu/packages/maths.scm (make-blis): Remove internal function.
Inline into ...
(bliss): ... this variable. Update to 0.8.1.
[native-inputs]: Add "python" and "perl".
[arguments]: Adjust 'configure' phase to take advantage of new support
for "configuration families" with runtime hardware detection. Select
configuration automatically based on target systems, and allow
"--blis-config=" in #:configure-flags to override the default.
When building for x86_64, include all supported microarchetecture
specializations. Add "--enable-verbose-make" configure flag for better
build logs. Stop ignoring other flags from #:configure-flags.
Remove explicit #:substitutable? argument: the package is now always
substitutable. Add (srfi srfi-1) to #:modules.
(blis/x86_64): Remove internal macro.
(blis-sandybridge): Remove package: included in 'blis'.
(blis-haswell): Remove package: included in 'blis'.
(blis-knl): Remove package: included in 'blis'.

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

ci: Fix system-tests subset.

* gnu/ci.scm (system-test-jobs): Make sure that "all-system-tests" is also
covered by the "current-guix-package" parameter.

gnu: monero-gui: Update to 0.17.2.0.

* gnu/packages/finance.scm (monero-gui): Update to 0.17.2.0.

gnu: monero: Update to 0.17.2.0.

* gnu/packages/finance.scm (monero): Update to 0.17.2.0.

gnu: newlib-nano: Fix nano lib and header paths.

* gnu/packages/embedded.scm (newlib-nano-arm-none-eabi)[arguments]: Hard link
library files from *.a to *_nano.a. Hard link newlib.h to a common location.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: electron-cash: Add missing input.

Fixes <https://bugs.gnu.org/47654>.

* gnu/packages/finance.scm (electron-cash)[inputs]: Add python-pathvalidate.

gnu: Add python-pathvalidate.

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

gnu: Add python-allpairspy.

* gnu/packages/python-check.scm (python-allpairspy): New variable.

scripts: system: Default to -v3 when building a system.

This is a followup to 8f9052d5434a3a11e7b4ff14d6b0090256e08aa4.

* guix/scripts/system.scm (verbosity-level): Change the default
from 2 to 3 when building a system.

gnu: Syncthing: Update to 1.15.1 [fixes CVE-2021-21404].

* gnu/packages/syncthing.scm (syncthing): Update to 1.15.1.
[source]: Use bundled dependencies.
[inputs]: Remove field.
[arguments]: Adjust the custom 'build' and 'install' phases for 1.15.1.

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

gnu: python-cython: Update to 0.29.22.

* gnu/packages/python-xyz.scm (python-cython): Update to 0.29.22.

gnu: python-fastimport: Update to 0.9.9.

* gnu/packages/python-xyz.scm (python-fastimport): Update to 0.9.9.

gnu: minetest: Update to 5.4.1.

* gnu/packages/games.scm (minetest, minetest-data): Update to 5.4.1.

gnu: ghq: Update to 1.1.7.

* gnu/packages/version-control.scm (ghq): Update to 1.1.7.

gnu: lagrange: Update to 1.3.2.

* gnu/packages/web-browsers.scm (lagrange): Update to 1.3.2.

gnu: irssi: Update to 1.2.3.

* gnu/packages/irc.scm (irssi): Update to 1.2.3.

gnu: edgar: Update to 1.34.

* gnu/packages/games.scm (edgar): Update to 1.34.

gnu: libime: Update to 1.0.6.

* gnu/packages/fcitx5.scm (libime): Update to 1.0.6.

gnu: acpica: Update to 20210331.

* gnu/packages/admin.scm (acpica): Update to 20210331.

gnu: python-skyfield: Update to 1.38.

* gnu/packages/astronomy.scm (python-skyfield): Update to 1.38.

gnu: librsync: Update to 2.3.2.

* gnu/packages/rsync.scm (librsync): Update to 2.3.2.

.guix-authorizations: Add raghavgururajan.

* .guix-authorizations: Add raghavgururajan to the committers.

gnu: Add python-pysctp.

* gnu/packages/networking.scm(python-pysctp): New variable.

gnu: lksctp-tools: Fix build of include file.

* gnu/packages/patches/lksctp-tools-1.0.18-fix-header-file-name.patch:
  New file.
* gnu/local.mk[patches]: Add it.
* gnu/packages/networking.scm(/lksctp-tools)[source]: Use this patch.

gnu: gpodder: Update to 3.10.18.

* gnu/packages/gpodder.scm (gpodder): Update to 3.10.18.
[native-inputs]: Add python-pytest, python-pytest-cov,
python-pytest-httpserver and which.
[inputs]: Add python-requests.

gnu: Add python-pytest-httpserver.

* gnu/packages/check.scm (python-pytest-httpserver): New variable.

gnu: scintilla: Update to 5.0.1.

* gnu/packages/text-editors.scm (scintilla): Update to 5.0.1.

gnu: emacs-ivy-posframe: Update to 0.6.0.

* gnu/packages/emacs-xyz.scm (emacs-ivy-posframe): Update to 0.6.0.

gnu: emacs-posframe: Update to 1.0.0.

* gnu/packages/emacs-xyz.scm (emacs-posframe): Update to 1.0.0.

gnu: Add abook.

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

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

gnu: Add python-plumbum.

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

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