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2020-03-06gnu: fmt: Fix home page.Tobias Geerinckx-Rice
* gnu/packages/pretty-print.scm (fmt)[home-page]: Update.
2020-03-06gnu: Order module imports in (gnu packages audio).Tobias Geerinckx-Rice
* gnu/packages/audio.scm: Order module imports alphabetically.
2020-03-06gnu: carla: Partially fix start-up.Tobias Geerinckx-Rice
This fixes <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=39942> but carla still fails to start. Reported by Nathan Dehnel <ncdehnel@gmail.com>. * gnu/packages/audio.scm (carla)[arguments]: Add ‘make-carla-executable’ phase.
2020-03-06gnu: dovecot: Update to 2.3.10.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (dovecot): Update to 2.3.10.
2020-03-06gnu: Add gnome-boxes.Pierre Neidhardt
* gnu/packages/gnome.scm (gnome-boxes): New variable.
2020-03-06gnu: tracker-miners: Update to 2.3.2.Pierre Neidhardt
* gnu/packages/gnome.scm (tracker-miners): Update to 2.3.2.
2020-03-06gnu: tracker: Update to 2.3.2.Pierre Neidhardt
* gnu/packages/gnome.scm (tracker): Update to 2.3.2. [arguments]: Fix tests properly. [native-inputs]: Remove unneeded native-inputs. [inputs]: Remove unneeded inputs. [description]: Replace unclear description with more down to earth use cases. [license]: Replace lgpl2.0+ with bsd-3 to reflect update.
2020-03-06gnu: libvirt-glib: Update to 3.0.0.Pierre Neidhardt
* gnu/packages/virtualization.scm (libvirt-glib): Update to 3.0.0.
2020-03-06gnu: python-pygit2: Update to 1.1.0.Marius Bakke
* gnu/packages/python-xyz.scm (python-pygit2): Update to 1.1.0. [propagated-inputs]: Remove PYTHON-SIX and PYTHON-TOX. Add PYTHON-CACHED-PROPERTY. (python2-pygit2): Remove variable (Python 2 is no longer supported).
2020-03-06gnu: gitg: Remove redundant input.Marius Bakke
* gnu/packages/gnome.scm (gitg)[inputs]: Remove LIBGIT2.
2020-03-06gnu: libgit2-glib: Adjust inputs.Marius Bakke
* gnu/packages/gnome.scm (libgit2-glib)[native-inputs]: Move LIBSSH2 ... [inputs]: ... here. Move LIBGIT2 ... [propagated-inputs]: ... here. New field.
2020-03-06gnu: libgit2-glib: Update to 0.99.0.1.Marius Bakke
* gnu/packages/gnome.scm (libgit2-glib): Update to 0.99.0.1. [native-inputs]: Remove INTLTOOL.
2020-03-06gnu: r-modeltools: Update to 0.2-23.Ricardo Wurmus
* gnu/packages/statistics.scm (r-modeltools): Update to 0.2-23.
2020-03-06gnu: r-ggplot2: Update to 3.3.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-ggplot2): Update to 3.3.0. [propagated-inputs]: Remove r-lazyeval, r-reshape2, and r-viridislite; add r-glue and r-isoband.
2020-03-06gnu: Add r-isoband.Ricardo Wurmus
* gnu/packages/cran.scm (r-isoband): New variable.
2020-03-06gnu: r-bookdown: Update to 0.18.Ricardo Wurmus
* gnu/packages/cran.scm (r-bookdown): Update to 0.18.
2020-03-06gnu: r-fs: Update to 1.3.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-fs): Update to 1.3.2.
2020-03-06gnu: r-flextable: Update to 0.5.9.Ricardo Wurmus
* gnu/packages/cran.scm (r-flextable): Update to 0.5.9.
2020-03-06gnu: r-lava: Update to 1.6.7.Ricardo Wurmus
* gnu/packages/cran.scm (r-lava): Update to 1.6.7.
2020-03-06gnu: Update python-scikit-learn to 0.22.1.Roel Janssen
* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 0.22.1; Add python-joblib to native-inputs to run the test suite.
2020-03-06gnu: Add soci.Pierre Neidhardt
* gnu/packages/databases.scm (soci): New variable.
2020-03-06gnu: fmt: Update to 6.1.2.Pierre Neidhardt
* gnu/packages/pretty-print.scm (fmt): Update to 6.1.2.
2020-03-06gnu: fmt: Use HTTPS and git-fetch.Pierre Neidhardt
* gnu/packages/pretty-print.scm (fmt)[source]: Use git-fetch. [home-page]: Use HTTPS.
2020-03-06gnu: python-aiohttp: Update to 3.6.2.Ricardo Wurmus
* gnu/packages/python-web.scm (python-aiohttp): Update to 3.6.2.
2020-03-06gnu: python-scanpy: Update to 1.4.5.1.Ricardo Wurmus
* 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.
2020-03-06gnu: Add python-legacy-api-wrap.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-legacy-api-wrap): New variable.
2020-03-06gnu: Add python-get-version.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-get-version): New variable.
2020-03-06gnu: Add python-pytest-black.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-pytest-black): New variable.
2020-03-06gnu: python-black: Update to 19.10b0.Ricardo Wurmus
* 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.
2020-03-06gnu: Add python-pathspec.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-pathspec): New variable.
2020-03-06gnu: python-tables: Use later hdf5 version.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-tables)[inputs]: Replace hdf5 with hdf5-1.10.
2020-03-06gnu: python-tables: Do not detect CPU features.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-tables)[arguments]: Add phase "disable-tuning".
2020-03-06scripts: Show disk-space warning when under the min of the thresholds.Pierre Neidhardt
Follow-up to 71c3c3df92375ca9b4bd28b2be90dda67288fa5c 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.
2020-03-05ci: Adjust 'channel-build-system' for when the source is a file name.Ludovic Courtès
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.
2020-03-05hydra: Remove uses of _IOLBF.Ludovic Courtès
_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.
2020-03-05tests: install: Add %test-gui-installed-os-encrypted.Mathieu Othacehe
* gnu/tests/install.scm (%test-gui-installed-os-encrypted): New variable, (guided-installation-test): set a swap-device only if there is no encryption.
2020-03-05installer: Fix cow-store umount.Mathieu Othacehe
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.
2020-03-05tests: install: Add "gui-installed-os".Ludovic Courtès
* 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.
2020-03-05installer: Honor /tmp/installer-system-init-options.Ludovic Courtès
* gnu/installer/final.scm (install-system): Honor "/tmp/installer-system-init-options".
2020-03-05installer: Run commands without hopping through the shell.Ludovic Courtès
* 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.
2020-03-05installer: Bypass connectivity check when /tmp/installer-assume-online exists.Ludovic Courtès
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?'.
2020-03-05installer: Implement a dialog on /var/guix/installer-socket.Ludovic Courtès
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.
2020-03-05installer: Use a Guile-Newt snapshot that supports 'form-watch-fd'.Ludovic Courtès
* gnu/installer.scm (guile-newt): New variable.
2020-03-05tests: 'run-basic-test' can enter a root password.Ludovic Courtès
* gnu/tests/base.scm (run-basic-test): Add #:root-password and honor it.
2020-03-05gnu: java-openjfx-build: Add snippet.Björn Höfling
* gnu/packages/java.scm (java-openjfx-build)[source]: Add snippet to remove bundled gradle.
2020-03-05gnu: python-anndata: Update to 0.7.1.Ricardo Wurmus
* 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.
2020-03-05gnu: Add python-zarr.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-zarr): New variable.
2020-03-05gnu: Add python-asciitree.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-asciitree): New variable.
2020-03-05gnu: Add python-numcodecs.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-numcodecs): New variable.
2020-03-05gnu: python-h5py: Update to 2.10.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-h5py): Update to 2.10.0. [inputs]: Use hdf5-1.10. [native-inputs]: Add pkg-config.
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