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2018-11-23gnu: pigx-scrnaseq: Use latest snakemake.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-4 with snakemake.
2018-11-23gnu: pigx-bsseq: Use latest snakemake.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake-4 with snakemake.
2018-11-23gnu: pigx-chipseq: Use latest snakemake.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake-4 with snakemake.
2018-11-23gnu: python-gevent: Update to 1.3.7.Ricardo Wurmus
* 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.
2018-11-23gnu: Add python-objgraph.Ricardo Wurmus
* gnu/packages/python.scm (python-objgraph): New variable.
2018-11-23gnu: python-loompy: Remove python-typing.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-loompy)[propagated-inputs]: Remove python-typing.
2018-11-22gnu: podofo: Add patch to fix build.Ricardo Wurmus
* 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.
2018-11-22gnu: jalv: Build with python-2.Efraim Flashner
* gnu/packages/audio.scm (jalv)[arguments]: Build with python-2.
2018-11-22gnu: python-scikit-learn: Update to 0.20.1.Marius Bakke
* 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 $HOME is writable. (python2-scikit-learn): Rewrite in terms of PACKAGE-WITH-PYTHON2.
2018-11-22Merge branch 'master' into core-updatesMarius Bakke
2018-11-22gnu: python-tblib: Fix test failure with Python 3.7.Marius Bakke
* gnu/packages/python.scm (python-tblib)[arguments]: Add 'adjust-tests' phase.
2018-11-21linux-initrd: 'expression->initrd' returns the complete file name.Ludovic Courtès
Previously 'expression->initrd' would return the directory that contains the 'initrd' file; now it returns the complete file name for that file. * gnu/system/linux-initrd.scm (expression->initrd)[builder]: Change output file name to "initrd.cpio.gz". Tail-call 'file-append' to return the complete file name. * gnu/system.scm (operating-system-initrd-file): Remove 'file-append' call. * gnu/build/linux-initrd.scm (write-cpio-archive): Check whether OUTPUT already has the ".gz" suffix; rename if before invoking GZIP if it does, and otherwise after. * gnu/system/vm.scm (expression->derivation-in-linux-vm)[builder]: Do not append "/initrd" to #$initrd.
2018-11-21gnu: python-numpy: Update to 1.15.4.Marius Bakke
* gnu/packages/python.scm (python-numpy): Update to 1.15.4.
2018-11-21gnu: mbedtls-apache: Update to 2.14.0.Marius Bakke
* gnu/packages/tls.scm (mbedtls-apache): Update to 2.14.0.
2018-11-21gnu: termite: Update to 14.Marius Bakke
* gnu/packages/terminals.scm (termite): Update to 14.
2018-11-21gnu: vte-ng: Update to 0.54.2.a.Marius Bakke
* gnu/packages/gnome.scm (vte-ng): Update to 0.54.2.a.
2018-11-21gnu: vte-ng: Fetch source using git.Marius Bakke
* gnu/packages/gnome.scm (vte-ng)[source]: Rewrite in terms of GIT-FETCH.
2018-11-21gnu: vte-ng: Add a home page.Marius Bakke
* gnu/packages/gnome.scm (vte-ng)[home-page]: New field.
2018-11-21gnu: python-numpy: Update to 1.14.6.Marius Bakke
* gnu/packages/python.scm (python-numpy): Update to 1.14.6.
2018-11-21gnu: webkitgtk: Update to 2.22.4.Marius Bakke
* gnu/packages/webkit.scm (webkitgtk-2.22): Update to 2.22.4.
2018-11-21gnu: git: Update to 2.19.2.Marius Bakke
* gnu/packages/version-control.scm (git): Update to 2.19.2.
2018-11-21gnu: feh: Update to 3.1.Marius Bakke
* gnu/packages/image-viewers.scm (feh): Update to 3.1.
2018-11-22gnu: teeworlds: Update to 0.7.0 [fixes CVE-2018-18541].Alex Vong
* 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.
2018-11-22gnu: bam: Update to 0.5.1.Alex Vong
* gnu/packages/build-tools.scm (bam): Update to 0.5.1. [source]: Switch to git-fetch. [arguments]: Use newly provided Makefile. [inputs]: Add lua.
2018-11-22gnu: Add json-parser.Alex Vong
* gnu/packages/web.scm (json-parser): New variable.
2018-11-22gnu: Add pnglite.Alex Vong
* gnu/packages/image.scm (pnglite): New variable.
2018-11-21Merge remote-tracking branch 'origin/master' into core-updatesEfraim Flashner
2018-11-21gnu: libbytesize: Make .mo file builds reproducible.Ludovic Courtès
* gnu/packages/c.scm (libbytesize)[sources](modules, snippet): New fields. [arguments]: Add #:configure-flags and #:phases.
2018-11-21gnu: emacs-pdf-tools: Fix build with recent Poppler.Ludovic Courtès
* 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.
2018-11-21gnu: emacs-pdf-tools: Use 'git-fetch'.Ludovic Courtès
* gnu/packages/emacs.scm (emacs-pdf-tools)[source]: Switch to GIT-FETCH. [arguments]: In 'emacs-patch-variables' phase, make files writable.
2018-11-21gnu: casync: Fix build with glibc 2.28.Ludovic Courtès
* 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.
2018-11-21gnu: ntk: Don't use bundled waf.Efraim Flashner
* gnu/packages/fltk.scm (ntk)[inputs]: Add python-waf. [arguments]: Add custom phase to replace vendored waf.
2018-11-21gnu: python-waf: Use a proper directory structure.Efraim Flashner
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.
2018-11-21gnu: python-waf: Use a proper directory structure.Efraim Flashner
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.
2018-11-21gnu: font-ubuntu: Update url.Jan Nieuwenhuizen
* gnu/packages/fonts.scm (font-ubuntu): Use new url, update hash.
2018-11-21gnu: Add python-wikidata.swedebugia
* gnu/packages/python.scm (python-wikidata): New variable. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2018-11-21gnu: python-astroid: Update to 2.0.4.Efraim Flashner
* 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.
2018-11-21gnu: thermald: Clean up package definition.Efraim Flashner
* gnu/packages/admin.scm (thermald)[arguments]: Remove redundant 'bootstrap phase. Remove unnecessary udev configure flag.
2018-11-21gnu: thermald: Don't use unstable tarball.Efraim Flashner
* gnu/packages/admin.scm (thermald)[source]: Download source using git-fetch.
2018-11-20gnu: emacs-elpy: Update to 1.26.0.Maxim Cournoyer
* gnu/packages/emacs.scm (emacs-elpy): Update to 1.26.0.
2018-11-20gnu: u-boot-pine64-plus: Refactor package definition.Vagrant Cascadian
* 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>
2018-11-20gnu: arm-trusted-firmware-pine64-plus: Rename variable to ↵Vagrant Cascadian
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>
2018-11-20gnu: arm-trusted-firmware-pine64-plus: Update to 2.0-1.cabe0a3.Vagrant Cascadian
* 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>
2018-11-20gnu: Add python-django-debug-toolbar.Christopher Baines
* gnu/packages/django.scm (python-django-debug-toolbar, python2-django-debug-toolbar): New variables.
2018-11-20gnu: Add python-django-jinja.Christopher Baines
* gnu/packages/django.scm (python-django-jinja, python2-django-jinja): New variables.
2018-11-20gnu: Add python-django-pipeline.Christopher Baines
* gnu/packages/django.scm (python-django-pipeline, python2-django-pipeline): New variables.
2018-11-20gnu: Add python-slimit.Christopher Baines
* gnu/packages/python-web.scm (python-slimit, python2-slimit): New variables.
2018-11-20gnu: Add python-jsmin.Christopher Baines
* gnu/packages/python-web.scm (python-jsmin, python2-jsmin): New variables.
2018-11-20gnu: cabextract: Update to 1.9.Kei Kebreau
* gnu/packages/compression.scm (cabextract): Update to 1.9. [arguments]: Add phase "unpack-libmspack". [inputs]: Add libmspack-source.
2018-11-20gnu: libmspack: Update to 0.9.1.Kei Kebreau
* gnu/packages/compression.scm (libmspack): Update to 0.9.1.
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