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37404 Commits

Author SHA1 Message Date
Ricardo Wurmus d57ec906ba
gnu: pigx-scrnaseq: Use latest snakemake. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-4
with snakemake.
 2018-11-23 16:30:48 +01:00
Ricardo Wurmus 92d9a1e2c6
gnu: pigx-bsseq: Use latest snakemake. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake-4
with snakemake.
 2018-11-23 16:30:16 +01:00
Ricardo Wurmus c068d00746
gnu: pigx-chipseq: Use latest snakemake. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake-4
with snakemake.
 2018-11-23 16:29:35 +01:00
Ricardo Wurmus 936ea3d664
gnu: python-gevent: Update to 1.3.7. 
* gnu/packages/python.scm (python-gevent): Update to 1.3.7.
[arguments]: Find headers for greenlet in phase "do-not-use-bundled-sources".
[propagated-inputs]: Add python-objgraph.
 2018-11-23 16:01:21 +01:00
Ricardo Wurmus 72ffb51231
gnu: Add python-objgraph. 
* gnu/packages/python.scm (python-objgraph): New variable.
 2018-11-23 16:01:07 +01:00
Ricardo Wurmus 93d229cb86
gnu: python-loompy: Remove python-typing. 
* gnu/packages/bioinformatics.scm (python-loompy)[propagated-inputs]: Remove
python-typing.
 2018-11-23 15:59:44 +01:00
Ricardo Wurmus 37751b480f
gnu: podofo: Add patch to fix build. 
* gnu/packages/patches/podofo-cmake-3.12.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/pdf.scm (podofo)[source]: Add patch.
 2018-11-22 21:56:41 +01:00
Efraim Flashner 691d39a267
gnu: jalv: Build with python-2. 
* gnu/packages/audio.scm (jalv)[arguments]: Build with python-2.
 2018-11-22 22:06:29 +02:00
Marius Bakke 7ff3f3d22c
gnu: python-scikit-learn: Update to 0.20.1. 
* gnu/packages/patches/python-scikit-learn-fix-test-non-determinism.patch:
Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 0.20.1.
[source](patches): Remove.
[arguments]: Skip network tests with pytest instead of deleting files.  Make
sure $HOME is writable.
(python2-scikit-learn): Rewrite in terms of PACKAGE-WITH-PYTHON2.
 2018-11-22 17:02:47 +01:00
Marius Bakke ec8130eb23
Merge branch 'master' into core-updates 2018-11-22 00:10:44 +01:00
Marius Bakke 437c78bcfb
gnu: python-tblib: Fix test failure with Python 3.7. 
* gnu/packages/python.scm (python-tblib)[arguments]: Add 'adjust-tests' phase.
 2018-11-22 00:00:44 +01:00
Ludovic Courtès d422cbb3d6
linux-initrd: 'expression->initrd' returns the complete file name. 
Previously 'expression->initrd' would return the directory that contains
the 'initrd' file; now it returns the complete file name for that file.

* gnu/system/linux-initrd.scm (expression->initrd)[builder]: Change
output file name to "initrd.cpio.gz".  Tail-call 'file-append' to return
the complete file name.
* gnu/system.scm (operating-system-initrd-file): Remove 'file-append'
call.
* gnu/build/linux-initrd.scm (write-cpio-archive): Check whether OUTPUT
already has the ".gz" suffix; rename if before invoking GZIP if it does,
and otherwise after.
* gnu/system/vm.scm (expression->derivation-in-linux-vm)[builder]: Do
not append "/initrd" to #$initrd.
 2018-11-21 23:26:59 +01:00
Ludovic Courtès a29ce1f97d
guix system: Fix 'init' again. 
Fixes a regression introduced in
52ee4479ef, whereby 'install' would now be
passed a procedure instead of a lowerable object.

* guix/scripts/system.scm (perform-action): Pass BOOTLOADER-SCRIPT as
the #:bootloader-installer argument of 'install'.
 2018-11-21 23:26:58 +01:00
Marius Bakke 148caae049
gnu: python-numpy: Update to 1.15.4. 
* gnu/packages/python.scm (python-numpy): Update to 1.15.4.
 2018-11-21 23:15:21 +01:00
Marius Bakke d9f8e846b6
gnu: mbedtls-apache: Update to 2.14.0. 
* gnu/packages/tls.scm (mbedtls-apache): Update to 2.14.0.
 2018-11-21 23:06:08 +01:00
Marius Bakke b344a3a937
gnu: termite: Update to 14. 
* gnu/packages/terminals.scm (termite): Update to 14.
 2018-11-21 23:01:38 +01:00
Marius Bakke b069c30b52
gnu: vte-ng: Update to 0.54.2.a. 
* gnu/packages/gnome.scm (vte-ng): Update to 0.54.2.a.
 2018-11-21 22:59:27 +01:00
Marius Bakke 6bc00737b0
gnu: vte-ng: Fetch source using git. 
* gnu/packages/gnome.scm (vte-ng)[source]: Rewrite in terms of GIT-FETCH.
 2018-11-21 22:57:48 +01:00
Marius Bakke afd90f8d62
gnu: vte-ng: Add a home page. 
* gnu/packages/gnome.scm (vte-ng)[home-page]: New field.
 2018-11-21 22:57:14 +01:00
Marius Bakke b96386501f
gnu: python-numpy: Update to 1.14.6. 
* gnu/packages/python.scm (python-numpy): Update to 1.14.6.
 2018-11-21 22:42:25 +01:00
Marius Bakke da15325e36
gnu: webkitgtk: Update to 2.22.4. 
* gnu/packages/webkit.scm (webkitgtk-2.22): Update to 2.22.4.
 2018-11-21 22:24:51 +01:00
Marius Bakke dca7d8a25c
gnu: git: Update to 2.19.2. 
* gnu/packages/version-control.scm (git): Update to 2.19.2.
 2018-11-21 22:24:35 +01:00
Marius Bakke aa9eb25983
gnu: feh: Update to 3.1. 
* gnu/packages/image-viewers.scm (feh): Update to 3.1.
 2018-11-21 22:23:47 +01:00
Alex Vong f9e5caf9ba
gnu: teeworlds: Update to 0.7.0 [fixes CVE-2018-18541]. 
* gnu/packages/games.scm (teeworlds): Update to 0.7.0.
[source]: Switch to git-fetch. Remove all bundled libraries except md5.
[arguments]: Adjust accordingly.
[inputs]: Use sdl2 instead of sdl and python-wrapper instead of python-2.
Add json-parser and pnglite.
* gnu/packages/patches/teeworlds-use-latest-wavpack.patch: Update it.
 2018-11-22 03:21:29 +08:00
Alex Vong 53367e17b6
gnu: bam: Update to 0.5.1. 
* gnu/packages/build-tools.scm (bam): Update to 0.5.1.
[source]: Switch to git-fetch.
[arguments]: Use newly provided Makefile.
[inputs]: Add lua.
 2018-11-22 03:21:05 +08:00
Alex Vong 078e2edf1d
gnu: Add json-parser. 
* gnu/packages/web.scm (json-parser): New variable.
 2018-11-22 03:20:49 +08:00
Alex Vong 6e35bad0a9
gnu: Add pnglite. 
* gnu/packages/image.scm (pnglite): New variable.
 2018-11-22 03:20:11 +08:00
Efraim Flashner 9cf4ff199c
Merge remote-tracking branch 'origin/master' into core-updates 2018-11-21 19:41:43 +02:00
Ludovic Courtès bf6859e45a
gnu: libbytesize: Make .mo file builds reproducible. 
* gnu/packages/c.scm (libbytesize)[sources](modules, snippet): New
fields.
[arguments]: Add #:configure-flags and #:phases.
 2018-11-21 17:38:00 +01:00
Ludovic Courtès e555bbfc48
gnu: emacs-pdf-tools: Fix build with recent Poppler. 
* gnu/packages/patches/emacs-pdf-tools-poppler.patch: New file.
* gnu/packages/emacs.scm (emacs-pdf-tools)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-11-21 17:38:00 +01:00
Ludovic Courtès c3d8c6ac7e
gnu: emacs-pdf-tools: Use 'git-fetch'. 
* gnu/packages/emacs.scm (emacs-pdf-tools)[source]: Switch to
GIT-FETCH.
[arguments]: In 'emacs-patch-variables' phase, make files writable.
 2018-11-21 17:38:00 +01:00
Ludovic Courtès e1f7912761
gnu: casync: Fix build with glibc 2.28. 
* gnu/packages/patches/casync-renameat2-declaration.patch: New file.
* gnu/packages/sync.scm (casync)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-11-21 17:38:00 +01:00
Efraim Flashner 4cf879fefb
gnu: ntk: Don't use bundled waf. 
* gnu/packages/fltk.scm (ntk)[inputs]: Add python-waf.
[arguments]: Add custom phase to replace vendored waf.
 2018-11-21 15:43:23 +02:00
Efraim Flashner 24a2e19c43
gnu: python-waf: Use a proper directory structure. 
Fixes <https://bugs.gnu.org/25634>.

* gnu/packages/python.scm (python-waf): Replace custom 'install phase to
install "waf" binary into the bin directory. Remove the 'wrap phase.
* gnu/packages/video.scm (mpv)[arguments]: Adjust the 'setup-waf phase
accordingly.
 2018-11-21 15:43:23 +02:00
Efraim Flashner a2aa746cfe
gnu: python-waf: Use a proper directory structure. 
Fixes <https://bugs.gnu.org/25634>.

* gnu/packages/python.scm (python-waf): Replace custom 'install phase to
install "waf" binary into the bin directory. Remove the 'wrap phase.
* gnu/packages/video.scm (mpv)[arguments]: Adjust the 'setup-waf phase
accordingly.
 2018-11-21 15:20:20 +02:00
Jan Nieuwenhuizen 96cae1b48c
gnu: font-ubuntu: Update url. 
* gnu/packages/fonts.scm (font-ubuntu): Use new url, update hash.
 2018-11-21 14:06:07 +01:00
Oleg Pykhalov 1255400faa
describe: Add profile option. 
* guix/scripts/describe.scm (%options): Add profile option.
(show-help): Document this.
(display-checkout-info): Check for profile argument.
* doc/guix.texi (Invoking guix describe): Document this.
 2018-11-21 14:41:13 +03:00
Oleg Pykhalov 3dd28aa37c
describe: Fix 'format' option. 
Fix ‘guix describe’ ignores ‘--format=FORMAT’ option.

* guix/scripts/describe.scm (%options): Fix 'format' option.
 2018-11-21 14:41:13 +03:00
swedebugia ab5d91dd50
gnu: Add python-wikidata. 
* gnu/packages/python.scm (python-wikidata): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-21 11:55:57 +01:00
Ludovic Courtès 1e5b79e5d0
build: Add missing Clojure modules to the distribution. 
* Makefile.am (MODULES): Add guix/build-system/clojure.scm and
guix/build/clojure-build-system.scm
 2018-11-21 11:55:57 +01:00
Efraim Flashner 4e94cdb652
gnu: python-astroid: Update to 2.0.4. 
* gnu/packages/python.scm (python-astroid): Update to 2.0.4.
[source]: Switch to pypi source.
[native-inputs]: Add python-dateutil, python-nose, python-pytest,
python-pytest-runner.
[arguments]: Add phase to remove spurious test failure. Update custom
'check phase.
(python2-astroid): Update to 1.6.5.
[source]: Use pypi source.
[arguments]: Add phase to remove spurious test failure.
 2018-11-21 12:00:01 +02:00
Efraim Flashner 1200783972
gnu: thermald: Clean up package definition. 
* gnu/packages/admin.scm (thermald)[arguments]: Remove redundant
'bootstrap phase. Remove unnecessary udev configure flag.
 2018-11-21 10:13:07 +02:00
Efraim Flashner d09e84c271
gnu: thermald: Don't use unstable tarball. 
* gnu/packages/admin.scm (thermald)[source]: Download source using
git-fetch.
 2018-11-21 10:13:06 +02:00
Maxim Cournoyer 56ddcf0414
gnu: emacs-elpy: Update to 1.26.0. 
* gnu/packages/emacs.scm (emacs-elpy): Update to 1.26.0.
 2018-11-20 23:57:58 -05:00
Vagrant Cascadian 0da3526d58
gnu: u-boot-pine64-plus: Refactor package definition. 
* gnu/packages/bootloaders.scm (make-u-boot-sunxi64-package): New procedure.
(u-boot-pine64-plus): Use it.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-11-20 23:39:41 +01:00
Vagrant Cascadian 95d9198606
gnu: arm-trusted-firmware-pine64-plus: Rename variable to arm-trusted-firmware-sun50i-a64. 
* gnu/packages/firmware (arm-trusted-firmware-pine64-plus): Rename to...
(arm-trusted-firmware-sun50i-a64): ...this.
* gnu/packages/bootloaders (u-boot-pine64-plus)[native-inputs]: Use it.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-11-20 23:34:31 +01:00
Vagrant Cascadian 725b077e40
gnu: arm-trusted-firmware-pine64-plus: Update to 2.0-1.cabe0a3. 
* gnu/packages/firmware.scm (arm-trusted-firmware-pine64-plus):
Use platform name from upstream ("sun50i_a64").
[version]: Update to 2.0-1.cabe0a3,
[source](uri): Use upstream git repository.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-11-20 23:32:55 +01:00
Christopher Baines be02d4df84
gnu: Add python-django-debug-toolbar. 
* gnu/packages/django.scm (python-django-debug-toolbar,
python2-django-debug-toolbar): New variables.
 2018-11-20 19:48:03 +00:00
Christopher Baines a2e9259697
gnu: Add python-django-jinja. 
* gnu/packages/django.scm (python-django-jinja, python2-django-jinja): New
variables.
 2018-11-20 19:48:02 +00:00
Christopher Baines 6cd1bbd0b1
gnu: Add python-django-pipeline. 
* gnu/packages/django.scm (python-django-pipeline, python2-django-pipeline):
New variables.
 2018-11-20 19:48:02 +00:00