49671 Commits

Author SHA1 Message Date
Ricardo Wurmus
bafedbc362
gnu: Add r-isoband.
* gnu/packages/cran.scm (r-isoband): New variable.
2020-03-06 12:15:51 +01:00
Ricardo Wurmus
858d5d7037
gnu: r-bookdown: Update to 0.18.
* gnu/packages/cran.scm (r-bookdown): Update to 0.18.
2020-03-06 12:15:51 +01:00
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
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
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
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
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
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
Björn Höfling
c5bb55a844
gnu: squashfs-tools: Update home page URI.
* gnu/packages/compression.scm (squashfs-tools)[home-page]: Update URI.
2020-03-05 10:11:34 +01:00
Björn Höfling
1ac624cd5b
gnu: pbzip2: Use archived home-page.
* gnu/packages/compression.scm (pbzip2)[home-page]: Load from archive.org
2020-03-05 10:11:33 +01:00
Björn Höfling
7f489c5655
gnu: domainfinder: Update home page URI.
* gnu/packages/chemistry.scm (domainfinder)[home-page]: Update URI.
2020-03-05 10:11:33 +01:00
Björn Höfling
357328d2a9
gnu: nmoldyn: Upate home page URI.
* gnu/packages/chemistry.scm (nmoldyn)[home-page]: Update URI.
2020-03-05 10:11:32 +01:00
Felix Gruber
aac148a87b
gnu: SuiteSparse: Update to 5.7.1.
* gnu/packages/maths.scm (suitesparse): Update to 5.7.1.
[source]: The latest releases of SuiteSparse have only been published on GitHub.
Fetch from git tag as GitHub releases page only contains autogenerated tarballs
that guix lint complains about. Apply new patch for Mongoose's CMakeList.txt to
find SuiteSparse_config.
[arguments]: Add CMake flags used by new components GraphBLAS and Mongoose.
[native-inputs]: Add CMake and m4 needed to build GraphBLAS and Mongoose.
* gnu/packages/patches/suitesparse-mongoose-cmake.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Leo Famulari <leo@famulari.name>
2020-03-04 18:08:13 -05:00
Marius Bakke
c2d7e800e6
gnu: ceph: Update to 14.2.8.
* gnu/packages/patches/ceph-boost-compat.patch,
gnu/packages/patches/ceph-volume-respect-PATH.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/storage.scm (ceph): Update to 14.2.8.
[source](patches): Remove obsolete.
2020-03-04 22:06:24 +01:00