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56698 Commits (43d4eb8fc4a6074a872c80bd0b2263b98472f01a)

Author SHA1 Message Date
Ricardo Wurmus 099adcf81f
gnu: r-fs: Update to 1.3.2.
* gnu/packages/cran.scm (r-fs): Update to 1.3.2.
2020-03-06 12:15:51 +01:00
Ricardo Wurmus 36488596b4
gnu: r-flextable: Update to 0.5.9.
* gnu/packages/cran.scm (r-flextable): Update to 0.5.9.
2020-03-06 12:15:51 +01:00
Ricardo Wurmus be01767cb9
gnu: r-lava: Update to 1.6.7.
* gnu/packages/cran.scm (r-lava): Update to 1.6.7.
2020-03-06 12:15:50 +01:00
Roel Janssen 83a483aac7
gnu: Update python-scikit-learn to 0.22.1.
* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 0.22.1;
  Add python-joblib to native-inputs to run the test suite.
2020-03-06 10:45:51 +01:00
Pierre Neidhardt 6d26ee3b67
gnu: Add soci.
* gnu/packages/databases.scm (soci): New variable.
2020-03-06 10:20:55 +01:00
Pierre Neidhardt 8be782c713
gnu: fmt: Update to 6.1.2.
* gnu/packages/pretty-print.scm (fmt): Update to 6.1.2.
2020-03-06 10:15:19 +01:00
Pierre Neidhardt 744f445c92
gnu: fmt: Use HTTPS and git-fetch.
* gnu/packages/pretty-print.scm (fmt)[source]: Use git-fetch.
[home-page]: Use HTTPS.
2020-03-06 10:15:19 +01:00
Ricardo Wurmus fecd32501f
gnu: python-aiohttp: Update to 3.6.2.
* gnu/packages/python-web.scm (python-aiohttp): Update to 3.6.2.
2020-03-06 09:16:48 +01:00
Ricardo Wurmus 858e642e4c
gnu: python-scanpy: Update to 1.4.5.1.
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.5.1.
[source]: Fetch from pypi.
[propagated-inputs]: Add python-legacy-api-wrap, python-packaging,
python-patsy, and python-umap-learn.
[native-inputs]: Add python-setuptools-scm.
2020-03-06 09:16:48 +01:00
Ricardo Wurmus 053ab825be
gnu: Add python-legacy-api-wrap.
* gnu/packages/python-xyz.scm (python-legacy-api-wrap): New variable.
2020-03-06 09:16:48 +01:00
Ricardo Wurmus 2ceff35f07
gnu: Add python-get-version.
* gnu/packages/python-xyz.scm (python-get-version): New variable.
2020-03-06 09:16:48 +01:00
Ricardo Wurmus cc2c2850ce
gnu: Add python-pytest-black.
* gnu/packages/python-xyz.scm (python-pytest-black): New variable.
2020-03-06 09:16:48 +01:00
Ricardo Wurmus 5f603fab23
gnu: python-black: Update to 19.10b0.
* gnu/packages/python-xyz.scm (python-black): Update to 19.10b0.
[arguments]: Patch tests.
[propagated-inputs]: Add python-pathspec, python-regex, and python-typed-ast.
[native-inputs]: Add python-setuptools-scm.
2020-03-06 09:16:48 +01:00
Ricardo Wurmus c777ecb372
gnu: Add python-pathspec.
* gnu/packages/python-xyz.scm (python-pathspec): New variable.
2020-03-06 09:16:48 +01:00
Ricardo Wurmus 538c1a024a
gnu: python-tables: Use later hdf5 version.
* gnu/packages/python-xyz.scm (python-tables)[inputs]: Replace hdf5 with
hdf5-1.10.
2020-03-06 09:16:47 +01:00
Ricardo Wurmus 70b74663b6
gnu: python-tables: Do not detect CPU features.
* gnu/packages/python-xyz.scm (python-tables)[arguments]: Add phase
"disable-tuning".
2020-03-06 09:16:47 +01:00
Pierre Neidhardt 1d24cc6de6
scripts: Show disk-space warning when under the min of the thresholds.
Follow-up to 71c3c3df92 which got the logic
wrong.

* guix/scripts.scm (warn-about-disk-space): Compare AVAILABLE to the min of
RELATIVE-THRESHOLD-IN-BYTES and ABSOLUTE-THRESHOLD-IN-BYTES, not the max.
2020-03-06 08:32:01 +01:00
Ludovic Courtès bc8b2ffdac
ci: Adjust 'channel-build-system' for when the source is a file name.
Fixes an evaluation error introduced in
dd1ee160be8ba4e211432c08e161c24901cd670e: when invoked via
'build-aux/cuirass/gnu-system.scm', SOURCE is a store file name, not a
<local-file> as it is when invoked via 'etc/system-tests.scm'.

* gnu/ci.scm (channel-build-system)[build]: Call 'lower-object' only
when SOURCE is not a string.
2020-03-05 23:40:24 +01:00
Ludovic Courtès 530e31b824
hydra: Remove uses of _IOLBF.
_IOLBF & co. were deprecated in Guile 2.2 and removed in 3.0.

* build-aux/hydra/gnu-system.scm: Pass 'line instead of _IOLBF to 'setvbuf'.
* build-aux/hydra/guix-modular.scm: Likewise.
2020-03-05 23:40:24 +01:00
Mathieu Othacehe e666a92344
tests: install: Add %test-gui-installed-os-encrypted.
* gnu/tests/install.scm (%test-gui-installed-os-encrypted): New variable,
(guided-installation-test): set a swap-device only if there is no encryption.
2020-03-05 23:40:24 +01:00
Mathieu Othacehe 64704be417
installer: Fix cow-store umount.
This fixes <https://bugs.gnu.org/39712>.

The guix-daemon was preventing the cow-store umount, so restart it.  Some
udevd workers, using cow-store files might also still be around, so have some
umount retries.

* gnu/installer/final.scm (kill-cow-users): New procedure,
(umount-cow-store): restart guix-daemon and kill all processes started from
within the cow-store before trying to umount the store overlay. Also try 5
times to umount the overlay in case it is still busy.
2020-03-05 23:40:24 +01:00
Ludovic Courtès ccb1a8c437
tests: install: Add "gui-installed-os".
* gnu/installer/tests.scm: New file.
* gnu/local.mk (INSTALLER_MODULES): Add it.
* gnu/tests/install.scm (run-install): Add #:gui-test.  Add (gnu
installer tests) to the marionette imported modules.  Honor GUI-TEST.
Check whether SCRIPT is true.
(%root-password, %syslog-conf): New variable.
(operating-system-with-console-syslog, gui-test-program)
(guided-installation-test): New procedures.
(%extra-packages, installation-os-for-gui-tests)
(%test-gui-installed-os): New variable.
2020-03-05 23:40:23 +01:00
Ludovic Courtès e458726ab4
installer: Honor /tmp/installer-system-init-options.
* gnu/installer/final.scm (install-system): Honor
"/tmp/installer-system-init-options".
2020-03-05 23:40:23 +01:00
Ludovic Courtès 8a4b11c6a9
installer: Run commands without hopping through the shell.
* gnu/installer/utils.scm (run-shell-command): Rename to...
(run-command): Remove call to 'call-with-temporary-output-file' and hop
through Bash.  Expect COMMAND to be a list of strings rather than a
string.
* gnu/installer/final.scm (install-system): Turn INSTALL-COMMAND into a
list of strings and pass it to 'run-command'.
* gnu/installer/newt/page.scm (edit-file): Likewise.
2020-03-05 23:40:23 +01:00
Ludovic Courtès f901f5d2bc
installer: Bypass connectivity check when /tmp/installer-assume-online exists.
This is useful for automated tests.

* gnu/installer/newt/network.scm (wait-service-online)[online?]: New
procedure.  Check for /tmp/installer-assume-online.
Use it instead of 'connman-online?'.
2020-03-05 23:40:22 +01:00
Ludovic Courtès 63b8c089c1
installer: Implement a dialog on /var/guix/installer-socket.
This will allow us to automate testing of the installer.

* gnu/installer/utils.scm (%client-socket-file)
(current-server-socket, current-clients): New variables.
(open-server-socket, call-with-server-socket): New procedure.
(with-server-socket): New macro.
(run-shell-command): Add call to 'send-to-clients'.  Select on both
current-input-port and current-clients.
* gnu/installer/steps.scm (run-installer-steps): Wrap 'call-with-prompt'
in 'with-socket-server'.  Call 'sigaction' for SIGPIPE.
* gnu/installer/newt/page.scm (watch-clients!, close-port-and-reuse-fd)
(run-form-with-clients, send-to-clients): New procedures.
(draw-info-page): Add call to 'run-form-with-clients'.
(run-input-page): Likewise.  Handle EXIT-REASON equal to 'exit-fd-ready.
(run-confirmation-page): Likewise.
(run-listbox-selection-page): Likewise.  Define 'choice->item' and use it.
(run-checkbox-tree-page): Likewise.
(run-file-textbox-page): Add call to 'run-form-with-clients'.  Handle
'exit-fd-ready'.
* gnu/installer/newt/partition.scm (run-disk-page): Pass
 #:client-callback-procedure to 'run-listbox-selection-page'.
* gnu/installer/newt/user.scm (run-user-page): Call
'run-form-with-clients'.  Handle 'exit-fd-ready'.
* gnu/installer/newt/welcome.scm (run-menu-page): Define
'choice->item' and use it.  Call 'run-form-with-clients'.
* gnu/installer/newt/final.scm (run-install-success-page)
(run-install-failed-page): When (current-clients) is non-empty, call
'send-to-clients' without displaying a choice window.
2020-03-05 23:40:22 +01:00
Ludovic Courtès 5ce84b1713
installer: Use a Guile-Newt snapshot that supports 'form-watch-fd'.
* gnu/installer.scm (guile-newt): New variable.
2020-03-05 23:40:22 +01:00
Ludovic Courtès 91ba90c18b
tests: 'run-basic-test' can enter a root password.
* gnu/tests/base.scm (run-basic-test): Add #:root-password and honor it.
2020-03-05 23:40:22 +01:00
Björn Höfling 2c2b1ef854
gnu: java-openjfx-build: Add snippet.
* gnu/packages/java.scm (java-openjfx-build)[source]: Add snippet to remove
bundled gradle.
2020-03-05 22:10:17 +01:00
Ricardo Wurmus a098b34980
gnu: python-anndata: Update to 0.7.1.
* gnu/packages/python-xyz.scm (python-anndata): Update to 0.7.1.
[arguments]: Move check phase after install phase; delete one test.
[propagated-inputs]: Add python-importlib-metadata, python-numcodecs,
python-packaging, and python-zarr.
[native-inputs]: Add python-joblib, python-pytest, and python-setuptools-scm.
2020-03-05 21:46:12 +01:00
Ricardo Wurmus 7032c1cc60
gnu: Add python-zarr.
* gnu/packages/python-xyz.scm (python-zarr): New variable.
2020-03-05 21:46:05 +01:00
Ricardo Wurmus 8e04b233f1
gnu: Add python-asciitree.
* gnu/packages/python-xyz.scm (python-asciitree): New variable.
2020-03-05 21:45:55 +01:00
Ricardo Wurmus 241409cd8a
gnu: Add python-numcodecs.
* gnu/packages/python-xyz.scm (python-numcodecs): New variable.
2020-03-05 21:45:46 +01:00
Ricardo Wurmus 24ce64216e
gnu: python-h5py: Update to 2.10.0.
* gnu/packages/python-xyz.scm (python-h5py): Update to 2.10.0.
[inputs]: Use hdf5-1.10.
[native-inputs]: Add pkg-config.
2020-03-05 21:45:14 +01:00
Masaya Tojo 5d0f33c2ab
gnu: Add emacs-ddskk.
* gnu/packages/emacs-xyz.scm (emacs-ddskk): New variable.
2020-03-05 19:22:42 +01:00
Nicolas Goaziou 67c525035f
gnu: libraqm: Parametrize version.
* gnu/packages/fontutils.scm (libraqm)[source]: Parametrize version.
2020-03-05 18:43:09 +01:00
Nicolas Goaziou a1797f3244
gnu: Add libraqm.
* gnu/packages/fontutils.scm (libraqm): New variable.
2020-03-05 18:42:02 +01:00
Ludovic Courtès 5ec4156bbc
tests: Add a manifest for system tests.
The manifest can be passed to 'guix build -m', 'guix weather -m', and so
on.  It can also be passed to an installed 'guix' (without
./pre-inst-env), with the exception so far of installation tests.

* build-aux/run-system-tests.scm: Remove.  Move interesting bits move
to...
* etc/system-tests.scm: ... here.  New file.
* Makefile.am (EXTRA_DIST): Remove 'build-aux/run-system-tests.scm' and
add 'etc/system-tests.scm'.
(check-system): Rewrite to run 'guix build -m etc/system-tests.scm'.
2020-03-05 16:33:38 +01:00
Ludovic Courtès c0b726c211
tests: Add <system-test> gexp compiler.
* gnu/tests.scm (compile-system-test): New gexp compiler.
2020-03-05 16:33:37 +01:00
Ludovic Courtès e7671685a8
weather: Parameterize '%graft?' upfront.
* guix/scripts/weather.scm (guix-weather): Parameterize %GRAFT? upfront.
2020-03-05 16:33:37 +01:00
Ludovic Courtès f42f39ad68
guix build: Parameterize '%graft?' upfront.
* guix/scripts/build.scm (guix-build): Add 'graft?' variable and
parameterize %GRAFT?.
2020-03-05 16:33:37 +01:00
Ludovic Courtès c5a3d8f646
tests: "make check-system" includes the current commit ID, if any.
* build-aux/run-system-tests.scm (source-commit): New procedure.
(tests-for-current-guix): Add 'commit' parameter and pass it to
'channel-source->package'.
(run-system-tests): Call 'source-commit' and pass the result to
'tests-for-current-guix'.
2020-03-05 16:33:37 +01:00
Ludovic Courtès dd1ee160be
tests: "make check-system" no longer interns source upfront.
* gnu/ci.scm (channel-build-system)[build, lower]: Honor #:source.
(channel-source->package): New procedure.
(system-test-jobs): Remove 'instance' and call to
'checkout->channel-instance'.  Use 'channel-source->package'.
* build-aux/run-system-tests.scm (tests-for-channel-instance): Rename to...
(tests-for-current-guix): ... this.  Change 'instance' to 'source'.
(run-system-tests): Use 'local-file' instead of 'interned-file' for
SOURCE.
2020-03-05 16:33:37 +01:00
Ludovic Courtès d37b5a1b58
weather: Allow non-package objects in manifest.
* guix/scripts/weather.scm (package-outputs)[lower-object/no-grafts]:
New procedure.
Use it instead of 'package->derivation'.
2020-03-05 16:33:37 +01:00
Ludovic Courtès 5a675b2c67
guix build: Allow non-package objects in manifest.
* guix/scripts/build.scm (options->things-to-build)[manifest->packages]:
Remove.
Inline map of 'manifest-entry-item'.
* tests/guix-build.sh: Add test for "guix build -m" with non-package object.
2020-03-05 16:33:37 +01:00
Ludovic Courtès 3046e73b4c
ci: Move 'cross-jobs' procedure to the top level.
* gnu/ci.scm (cross-jobs): New procedure.  Moved from...
(hydra-jobs): ... here.
2020-03-05 16:33:37 +01:00
Pierre Neidhardt 94aab844c6
gnu: sbcl-cl-webkit: Update to 20200227.
* gnu/packages/lisp-xyz.scm (sbcl-cl-webkit): Update to 20200227.
2020-03-05 15:57:18 +01:00
Arun Isaac 69bb61f128
gnu: Add guile-xapian.
* gnu/packages/guile-xyz.scm (guile-xapian, guile3.0-xapian): New variables.
2020-03-05 19:59:46 +05:30
Arun Isaac 85c3a49a67
gnu: emacs-tldr: Update to 0-1.7203d1b.
* gnu/packages/emacs-xyz.scm (emacs-tldr): Update to 0-1.7203d1b.
[propagated-inputs]: Add emacs-request.
2020-03-05 15:56:32 +05:30
Björn Höfling 6656123d26
gnu: coq-mathcomp: Update home page URI.
* gnu/packages/coq.scm (coq-mathcomp)[home-page]: Update URI.
2020-03-05 10:11:34 +01:00