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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.
2020-03-05gnu: Add emacs-ddskk.Masaya Tojo
* gnu/packages/emacs-xyz.scm (emacs-ddskk): New variable.
2020-03-05gnu: libraqm: Parametrize version.Nicolas Goaziou
* gnu/packages/fontutils.scm (libraqm)[source]: Parametrize version.
2020-03-05gnu: Add libraqm.Nicolas Goaziou
* gnu/packages/fontutils.scm (libraqm): New variable.
2020-03-05tests: Add a manifest for system tests.Ludovic Courtès
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'.
2020-03-05tests: Add <system-test> gexp compiler.Ludovic Courtès
* gnu/tests.scm (compile-system-test): New gexp compiler.
2020-03-05weather: Parameterize '%graft?' upfront.Ludovic Courtès
* guix/scripts/weather.scm (guix-weather): Parameterize %GRAFT? upfront.
2020-03-05guix build: Parameterize '%graft?' upfront.Ludovic Courtès
* guix/scripts/build.scm (guix-build): Add 'graft?' variable and parameterize %GRAFT?.
2020-03-05tests: "make check-system" includes the current commit ID, if any.Ludovic Courtès
* 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'.
2020-03-05tests: "make check-system" no longer interns source upfront.Ludovic Courtès
* 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.
2020-03-05weather: Allow non-package objects in manifest.Ludovic Courtès
* guix/scripts/weather.scm (package-outputs)[lower-object/no-grafts]: New procedure. Use it instead of 'package->derivation'.
2020-03-05guix build: Allow non-package objects in manifest.Ludovic Courtès
* 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.
2020-03-05ci: Move 'cross-jobs' procedure to the top level.Ludovic Courtès
* gnu/ci.scm (cross-jobs): New procedure. Moved from... (hydra-jobs): ... here.
2020-03-05gnu: sbcl-cl-webkit: Update to 20200227.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (sbcl-cl-webkit): Update to 20200227.
2020-03-05gnu: Add guile-xapian.Arun Isaac
* gnu/packages/guile-xyz.scm (guile-xapian, guile3.0-xapian): New variables.
2020-03-05gnu: emacs-tldr: Update to 0-1.7203d1b.Arun Isaac
* gnu/packages/emacs-xyz.scm (emacs-tldr): Update to 0-1.7203d1b. [propagated-inputs]: Add emacs-request.
2020-03-05gnu: coq-mathcomp: Update home page URI.Björn Höfling
* gnu/packages/coq.scm (coq-mathcomp)[home-page]: Update URI.
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