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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".
2020-03-05ci: 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.
2020-03-05tests: 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 <system-test> gexp compiler.Ludovic Courtès
* gnu/tests.scm (compile-system-test): New gexp compiler.
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.
2020-03-05ci: 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.
2020-03-05gnu: squashfs-tools: Update home page URI.Björn Höfling
* gnu/packages/compression.scm (squashfs-tools)[home-page]: Update URI.
2020-03-05gnu: pbzip2: Use archived home-page.Björn Höfling
* gnu/packages/compression.scm (pbzip2)[home-page]: Load from archive.org
2020-03-05gnu: domainfinder: Update home page URI.Björn Höfling
* gnu/packages/chemistry.scm (domainfinder)[home-page]: Update URI.
2020-03-05gnu: nmoldyn: Upate home page URI.Björn Höfling
* gnu/packages/chemistry.scm (nmoldyn)[home-page]: Update URI.
2020-03-04gnu: SuiteSparse: Update to 5.7.1.Felix Gruber
* 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>
2020-03-04gnu: ceph: Update to 14.2.8.Marius Bakke
* 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.
2020-03-04gnu: i3-wm: Update to 4.18.Marius Bakke
* gnu/packages/wm.scm (i3-wm): Update to 4.18.
2020-03-04gnu: kodi: Update to 18.6.Marius Bakke
* gnu/packages/kodi.scm (kodi): Update to 18.6.
2020-03-04gnu: libgit2: Update to 0.99.0.Marius Bakke
* gnu/packages/patches/libgit2-avoid-python.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/version-control.scm (libgit2): Update to 0.99.0. [source](patches): Remove 'libgit2-avoid-python.patch'. [source](snippet): Preserve bundled copy of http-parser. [arguments]: Remove "-DUSE_SHA1DC" from #:configure-flags, which is no longer optional and enabled by default. Add "-DUSE_NTLMCLIENT=OFF" and "-DREGEX_BACKEND=pcre2". Add phase 'fix-pcre2-reference'. [inputs]: Remove HTTP-PARSER. [propagated-inputs]: Add PCRE2. [native-inputs]: Remove GUILE-2.2. Add PYTHON.
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