guix-bioinformatics/guix - guix

Commit Graph

Author	SHA1	Message	Date
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.	2 years ago
Björn Höfling	2c2b1ef854	gnu: java-openjfx-build: Add snippet. * gnu/packages/java.scm (java-openjfx-build)[source]: Add snippet to remove bundled gradle.	2 years ago
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.	2 years ago
Ricardo Wurmus	7032c1cc60	gnu: Add python-zarr. * gnu/packages/python-xyz.scm (python-zarr): New variable.	2 years ago
Ricardo Wurmus	8e04b233f1	gnu: Add python-asciitree. * gnu/packages/python-xyz.scm (python-asciitree): New variable.	2 years ago
Ricardo Wurmus	241409cd8a	gnu: Add python-numcodecs. * gnu/packages/python-xyz.scm (python-numcodecs): New variable.	2 years ago
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.	2 years ago
Masaya Tojo	5d0f33c2ab	gnu: Add emacs-ddskk. * gnu/packages/emacs-xyz.scm (emacs-ddskk): New variable.	2 years ago
Nicolas Goaziou	67c525035f	gnu: libraqm: Parametrize version. * gnu/packages/fontutils.scm (libraqm)[source]: Parametrize version.	2 years ago
Nicolas Goaziou	a1797f3244	gnu: Add libraqm. * gnu/packages/fontutils.scm (libraqm): New variable.	2 years ago
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'.	2 years ago
Ludovic Courtès	c0b726c211	tests: Add <system-test> gexp compiler. * gnu/tests.scm (compile-system-test): New gexp compiler.	2 years ago
Ludovic Courtès	e7671685a8	weather: Parameterize '%graft?' upfront. * guix/scripts/weather.scm (guix-weather): Parameterize %GRAFT? upfront.	2 years ago
Ludovic Courtès	f42f39ad68	guix build: Parameterize '%graft?' upfront. * guix/scripts/build.scm (guix-build): Add 'graft?' variable and parameterize %GRAFT?.	2 years ago
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'.	2 years ago
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.	2 years ago
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'.	2 years ago
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.	2 years ago
Ludovic Courtès	3046e73b4c	ci: Move 'cross-jobs' procedure to the top level. * gnu/ci.scm (cross-jobs): New procedure. Moved from... (hydra-jobs): ... here.	2 years ago
Pierre Neidhardt	94aab844c6	gnu: sbcl-cl-webkit: Update to 20200227. * gnu/packages/lisp-xyz.scm (sbcl-cl-webkit): Update to 20200227.	2 years ago
Arun Isaac	69bb61f128	gnu: Add guile-xapian. * gnu/packages/guile-xyz.scm (guile-xapian, guile3.0-xapian): New variables.	2 years ago
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.	2 years ago
Björn Höfling	6656123d26	gnu: coq-mathcomp: Update home page URI. * gnu/packages/coq.scm (coq-mathcomp)[home-page]: Update URI.	2 years ago
Björn Höfling	c5bb55a844	gnu: squashfs-tools: Update home page URI. * gnu/packages/compression.scm (squashfs-tools)[home-page]: Update URI.	2 years ago
Björn Höfling	1ac624cd5b	gnu: pbzip2: Use archived home-page. * gnu/packages/compression.scm (pbzip2)[home-page]: Load from archive.org	2 years ago
Björn Höfling	7f489c5655	gnu: domainfinder: Update home page URI. * gnu/packages/chemistry.scm (domainfinder)[home-page]: Update URI.	2 years ago
Björn Höfling	357328d2a9	gnu: nmoldyn: Upate home page URI. * gnu/packages/chemistry.scm (nmoldyn)[home-page]: Update URI.	2 years ago
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>	2 years ago
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.	2 years ago
Marius Bakke	d3c1e9272d	gnu: i3-wm: Update to 4.18. * gnu/packages/wm.scm (i3-wm): Update to 4.18.	2 years ago
Marius Bakke	75545401cd	gnu: kodi: Update to 18.6. * gnu/packages/kodi.scm (kodi): Update to 18.6.	2 years ago
Marius Bakke	0a7aa6922b	gnu: libgit2: Update to 0.99.0. * 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.	2 years ago
Marius Bakke	2f894cbc6a	gnu: enchant: Update to 2.2.8. * gnu/packages/enchant.scm (enchant): Update to 2.2.8.	2 years ago
Marius Bakke	3f03643219	gnu: wpebackend-fdo: Update to 1.4.2. * gnu/packages/webkit.scm (wpebackend-fdo): Update to 1.4.2.	2 years ago
Marius Bakke	e26c4a7e4e	gnu: re2: Update to 2020-03-03. * gnu/packages/regex.scm (re2): Update to 2020-03-03.	2 years ago
Marius Bakke	bd65a4cf01	gnu: ibus: Update to 1.5.22. * gnu/packages/ibus.scm (ibus): Update to 1.5.22.	2 years ago
Marius Bakke	16af0dd907	gnu: libsoup: Update to 2.68.4. * gnu/packages/gnome.scm (libsoup): Update to 2.68.4.	2 years ago
Marius Bakke	c1a86b666f	gnu: appstream-glib: Update to 0.7.17. * gnu/packages/patches/appstream-glib-2020.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/glib.scm (appstream-glib): Update to 0.7.17. [source](patches): Remove.	2 years ago
Efraim Flashner	60ce496ad8	gnu: gcc-8: Update to 8.4.0. * gnu/packages/gcc.scm (gcc-8): Update to 8.4.0.	2 years ago
Efraim Flashner	9cedae2aaf	gnu: libgee: Update to 0.20.3. * gnu/packages/gnome.scm (libgee): Update to 0.20.3.	2 years ago
Tobias Geerinckx-Rice	5ba94aa702	gnu: ardour: Use HTTPS home page. * gnu/packages/audio.scm (ardour)[home-page]: Use HTTPS.	2 years ago
Tobias Geerinckx-Rice	e85af13724	gnu: Update pypi.python.org home pages & use HTTPS. * gnu/packages/check.scm (python-unittest2, python-pytest-localserver) (python-discover)[home-page]: Follow (HTTPS) redirections. * gnu/packages/fontutils.scm (python2-defcon)[home-page]: Likewise. * gnu/packages/glib.scm (python2-pygobject-2)[home-page]: Likewise. * gnu/packages/graph.scm (python-igraph)[home-page]: Likewise. * gnu/packages/graphviz.scm (xdot)[home-page]: Likewise. * gnu/packages/pdf.scm (python-poppler-qt5)[home-page]: Likewise. * gnu/packages/python-web.scm (python-zope-event, python-zope-testing) (python-zope-testrunner, python-zope-i18nmessageid, python-zope-schema) (python-zope-configuration, python-zope-proxy, python-zope-location) (python-zope-security))[home-page]: Likewise. * gnu/packages/python-xyz.scm (python-setuptools,python-six) (python2-dogtail, python2-enum, python-enum34, python-unidecode) (python-numpydoc, python-decorator, python-drmaa, python-pathlib2) (python-ly, python-msgpack, python-termcolor, python-colorama) (python-pluggy, python2-pathlib2, python-rfc3987)[home-page]: Likewise.	2 years ago
Tobias Geerinckx-Rice	dbc8a6e750	gnu: python-pyodbc: Update to 4.0.30. * gnu/packages/databases.scm (python-pyodbc): Update to 4.0.30.	2 years ago
Tobias Geerinckx-Rice	e884c20533	gnu: crispy-doom: Update to 5.7.1. * gnu/packages/games.scm (crispy-doom): Update to 5.7.1.	2 years ago
Tobias Geerinckx-Rice	95858abb62	gnu: sg3-utils: Update to 1.45. * gnu/packages/scsi.scm (sg3-utils): Update to 1.45.	2 years ago
Tobias Geerinckx-Rice	8863477245	gnu: girara: Update to 0.3.4. * gnu/packages/gtk.scm (girara): Update to 0.3.4.	2 years ago
Tobias Geerinckx-Rice	13d872234b	gnu: zathura-pdf-poppler: Update to 0.3.0. * gnu/packages/pdf.scm (zathura-pdf-poppler): Update to 0.3.0.	2 years ago
Tobias Geerinckx-Rice	01ebd8617f	gnu: zathura: Update to 0.4.5. * gnu/packages/pdf.scm (zathura): Update to 0.4.5.	2 years ago
Tobias Geerinckx-Rice	c0ba02379e	gnu: weasyprint: Update to 51. * gnu/packages/pdf.scm (weasyprint): Update to 51.	2 years ago
Tobias Geerinckx-Rice	8b5185c6a6	gnu: zathura-djvu: Update to 0.2.9. * gnu/packages/pdf.scm (zathura-djvu): Update to 0.2.9.	2 years ago

1 2 3 4 5 ...

56471 Commits (91ba90c18b9ca3512e3a3ab359119f94f94c5b17) All Branches Search

56471 Commits (91ba90c18b9ca3512e3a3ab359119f94f94c5b17)

All Branches