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39591 Commits

Author SHA1 Message Date
Ludovic Courtès 280e9c2a26
doc: Update bit about GUIX_LD_WRAPPER_ALLOW_IMPURITIES. 
This is a followup to d0a2db47fb.

* doc/guix.texi (Application Setup)[The GCC toolchain]: Adjust bit
about GUIX_LD_WRAPPER_ALLOW_IMPURITIES.
 2019-01-26 00:06:55 +01:00
Ludovic Courtès 1379319fe7
doc: Switch from "GuixSD" to "Guix System". 
* doc/guix.texi (Introduction): Add footnote about the change from
"GuixSD" to "Guix System".
Replace occurrences of "GuixSD" with "Guix System", "Guix", "system", or
other appropriate phrases.
 2019-01-26 00:06:55 +01:00
Ludovic Courtès 9b104bfeef
doc: Make /dev/kvm note more visible. 
Suggested by Giovanni Biscuolo <g@xelera.eu>.

* doc/guix.texi (Invoking guix system): Move note about /dev/kvm access
to the beginning of the 'vm' action description.
 2019-01-26 00:06:55 +01:00
Ludovic Courtès 008883561f
gnu: guix: Remove 'guix-devel' variable. 
* gnu/packages/package-management.scm (guix-devel): Remove.
 2019-01-26 00:06:55 +01:00
Ricardo Wurmus fdb0b40b0e
gnu: pepr: Use PYPI-URI. 
* gnu/packages/bioinformatics.scm (pepr)[source]: Use PYPI-URI.
 2019-01-25 23:27:25 +01:00
Ricardo Wurmus 4cd7c58cf1
gnu: python2-warpedlmm: Use PYPI-URI. 
* gnu/packages/bioinformatics.scm (python2-warpedlmm)[source]: Use PYPI-URI.
 2019-01-25 23:26:50 +01:00
Ricardo Wurmus 99d1744611
gnu: attic: Use PYPI-URI. 
* gnu/packages/backup.scm (attic)[source]: Use PYPI-URI.
 2019-01-25 23:21:20 +01:00
Ricardo Wurmus 4267aa75a3
gnu: graphios: Use PYPI-URI. 
* gnu/packages/admin.scm (graphios)[source]: Use PYPI-URI.
 2019-01-25 23:20:17 +01:00
Ricardo Wurmus aeec4a8fc1
gnu: python-sqlalchemy: Use PYPI-URI. 
* gnu/packages/databases.scm (python-sqlalchemy)[source]: Use PYPI-URI.
 2019-01-25 23:18:55 +01:00
Ricardo Wurmus 7d4dae6a8d
gnu: python-pyaudio: Use PYPI-URI. 
* gnu/packages/audio.scm (python-pyaudio)[source]: Use PYPI-URI.
 2019-01-25 23:17:39 +01:00
Ricardo Wurmus 723f332551
gnu: femtolisp: Use INVOKE. 
* gnu/packages/scheme.scm (femtolisp)[arguments]: Remove "bootstrap" phase;
use INVOKE and return #T unconditionally.
 2019-01-25 23:11:21 +01:00
Christopher Baines dd7bc92afc
gnu: linkchecker: Fix most test failures. 
Add a patch to skip more tests that require the network. Along with some other
changes, this gets all but of one of the tests passing.

The remaining test is broken due to a problem with the Python package in Guix,
which is fixed by [1] which is currently on the core-updates branch. This
patch doesn't work on core-updates due to python2-miniboa not being present.

1: d453b0e11d

* gnu/packages/python.scm (linkchecker)[source]: Add patch.
[native-inputs]: Add more inputs required for the tests.
[arguments]: Enable the tests, move the 'check phase after 'install. Test
using the installed software, and use py.test.
 2019-01-25 22:00:05 +00:00
Eric Bavier 7e309e8a8d
gnu: dealii-openmpi: Setup MPI for tests. 
* gnu/packages/maths.scm (dealii-openmpi)[arguments]: Add 'mpi-setup' phase.
 2019-01-25 13:10:05 -06:00
Eric Bavier 6161141e91
superlu-dist: Upgrade to 6.1.0. 
* gnu/packages/patches/superlu-dist-awpm-grid.patch: New file.
* gnu/packages/maths.scm (superlu-dist)[source]: Upgrade to 6.0.0.  Remove
extraneous 'use-modules' in snippet.
[build-system]: Change to cmake-build-system.
[propagated-inputs]:   Replace pt-scotch with pt-scotch32 to match integer
sizes.  Add "parmetis" input, from pt-scotch32.  Move lapack to ...
[inputs]: ...here.  Add openblas and combinatorial-blas.
[arguments]: Replace 'configure' phase with #:configure-flags.  Add
'set-c++-standard' and 'omp-setup' phases.  Remove
'create-install-directories, 'check', and 'install' phases, which are now
handled by cmake.
* gnu/local.mk (dist_patch_DATA): Add patch.
 2019-01-25 13:10:05 -06:00
Eric Bavier fd3733432b
scotch: Upgrade to 6.0.6. 
* gnu/packages/maths.scm (scotch): Upgrade to 6.0.6.
[source]: Remove patches that have been fixed upstream.
[arguments]: Add 'install-metis' phase.
[outputs]: New field.
(pt-scotch, pt-scotch32)[arguments]: Add 'mpi-setup' phase.  Use 'invoke'.
* gnu/packages/patches/scotch-graph-diam-64.patch,
gnu/packages/patches/scotch-graph-induce-type-64.patch,
gnu/packages/patches/scotch-test-threading.patch: Delete files.
* gnu/packages/patches/scotch-integer-declarations.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust as necessary.
 2019-01-25 13:10:05 -06:00
Eric Bavier a6b9ebc2fc
gnu: Add Combinatorial BLAS. 
* gnu/packages/maths.scm (combinatorial-blas): New variable.
* gnu/packages/patches/combinatorial-blas-awpm.patch,
gnu/packages/patches/combinatorial-blas-io-fix.patch: New files
* gnu/local.mk(dist_patch_DATA): Add them.
 2019-01-25 13:09:47 -06:00
Danny Milosavljevic 519be98c35
linux-modules: module-soft-dependencies: Remove colon from section names. 
Follow-up to 1a5f46621b.

* gnu/build/linux-modules.scm (module-soft-dependencies): Remove colon from
section names.
 2019-01-25 18:24:00 +01:00
Danny Milosavljevic 1a5f46621b
linux-modules: Add module-soft-dependencies. 
* gnu/build/linux-modules.scm (not-softdep-whitespace): New variable.
(module-soft-dependencies): New procedure.
 2019-01-25 18:14:16 +01:00
Nicolas Goaziou 1faf0a0459
gnu: Add stepmania. 
* gnu/packages/games.scm (stepmania):
* gnu/packages/video.scm (ffmpeg-for-stepmania): New variables.
 2019-01-25 18:08:21 +01:00
Ricardo Wurmus 81cf0174b5
gnu: kcoreaddons: Fix broken test. 
* gnu/packages/kde-frameworks.scm (kcoreaddons)[arguments]: Add build phase
"fix-broken-test".
 2019-01-25 15:37:23 +01:00
Ricardo Wurmus fd007bebdd
gnu: infiniband-diags: Remove custom bootstrap phase. 
* gnu/packages/fabric-management.scm (infiniband-diags)[arguments]: Remove
"autotools" phase.
 2019-01-25 15:20:53 +01:00
Ricardo Wurmus 776248419f
gnu: gpgme: Update to 1.12.0. 
* gnu/packages/gnupg.scm (gpgme): Update to 1.12.0.
 2019-01-25 15:17:47 +01:00
Ricardo Wurmus 1d7b8a2452
gnu: gpgme: Add patch to fix qgpgme tests. 
* gnu/packages/gnupg.scm (gpgme)[source]: Add upstream patch.
 2019-01-25 15:17:47 +01:00
Ricardo Wurmus a8416e6951
gnu: pcb-rnd: Use INVOKE. 
* gnu/packages/engineering.scm (pcb-rnd)[arguments]: Use INVOKE.
 2019-01-25 15:17:47 +01:00
Ricardo Wurmus 5cb9754cf4
gnu: proplib: Use INVOKE. 
* gnu/packages/embedded.scm (proplib)[arguments]: Use INVOKE.
 2019-01-25 15:17:47 +01:00
Ricardo Wurmus 78854b3849
gnu: jimtcl: Use INVOKE. 
* gnu/packages/embedded.scm (jimtcl)[arguments]: Use INVOKE.
 2019-01-25 15:17:47 +01:00
Ricardo Wurmus 3af2708881
gnu: greenisland: Use INVOKE. 
* gnu/packages/display-managers.scm (greenisland)[arguments]: Use INVOKE in
check phase.
 2019-01-25 15:17:47 +01:00
Ricardo Wurmus 3692cffed4
gnu: assword: Use INVOKE. 
* gnu/packages/password-utils.scm (assword)[arguments]: Use INVOKE.
 2019-01-25 15:17:47 +01:00
Ricardo Wurmus c9a65d5c37
gnu: python-oslosphinx: Use INVOKE. 
* gnu/packages/openstack.scm (python-oslosphinx)[arguments]: Use INVOKE.
 2019-01-25 15:17:47 +01:00
Ricardo Wurmus c8780a1038
gnu: python-reno: Use INVOKE. 
* gnu/packages/openstack.scm (python-reno)[arguments]: Use INVOKE.
[native-inputs]: Replace "git" with "git-minimal".
 2019-01-25 15:17:47 +01:00
Gabriel Hondet 4ad7d037ad
gnu: Add ghc-libmpd. 
* gnu/packages/haskell.scm (ghc-libmpd): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-01-25 14:06:38 +01:00
Ludovic Courtès bd414e273c
weather: Add '--coverage'. 
* guix/scripts/weather.scm (show-help, %options): Add '--coverage'.
(package-partition-boundary, package->output-mapping)
(substitute-oracle, report-package-coverage-per-system)
(report-package-coverage): New procedures.
(guix-weather): Honor '--coverage'.
* doc/guix.texi (Invoking guix weather): Document it.
 2019-01-25 14:06:37 +01:00
Ludovic Courtès af77219e8a
refresh: Better account for private and generated packages. 
Until now, private and generated packages (e.g., those created by
'texlive-union') we missing from the list passed to 'node-back-edges',
which would lead to inaccurate dependent counts.

Previously we'd get:

  $ guix refresh -l texlive-fonts-cm
  Building the following 80 packages would ensure 116 dependent packages
  are rebuilt: …

Now we have:

  $ Building the following 240 packages would ensure 597 dependent
  packages are rebuilt: …

* guix/scripts/refresh.scm (list-dependents): Call 'package-closure'.
 2019-01-25 14:06:37 +01:00
Ludovic Courtès 4d6ce0f12c
refresh: Fix format string that would lead '-l' to print incorrect numbers. 
The skip "~*" argument was misplaced, leading the number of dependents
to be skipped (instead of the number of covering packages.)  Thus, we'd
get:

  $ guix refresh -l ocaml4.02-ppx-deriving@4.1
  Building the following package would ensure 1 dependent packages are rebuilt: bap@1.3.0

instead of:

  Building the following package would ensure 26 dependent packages are rebuilt: bap@1.3.0

* guix/scripts/refresh.scm (list-dependents): Move "~*" in the right
place, to skip (length covering) rather than (length dependents).
 2019-01-25 14:06:37 +01:00
Ludovic Courtès 731c1a20bc
weather: Ignore deprecated packages but not hidden packages. 
* guix/scripts/weather.scm (all-packages): Pass #:select? to
'fold-packages'.
 2019-01-25 14:06:37 +01:00
Ludovic Courtès 3e223a22a7
packages: Add 'package-closure'. 
* guix/packages.scm (package-closure): New procedure.
* tests/packages.scm ("package-closure"): New test.
 2019-01-25 14:06:37 +01:00
Ricardo Wurmus c6e33df90f
gnu: python-pyopenssl: Update to 19.0.0. 
* gnu/packages/python-crypto.scm (python-pyopenssl): Update to 19.0.0.
[arguments]: Use INVOKE.
 2019-01-25 14:02:04 +01:00
Ricardo Wurmus 39df4d1992
gnu: python2-pyqt-4: Use INVOKE. 
* gnu/packages/qt.scm (python2-pyqt-4)[arguments]: Use INVOKE.
 2019-01-25 13:59:53 +01:00
Ricardo Wurmus 41173df9f8
gnu: qwt: Use INVOKE. 
* gnu/packages/qt.scm (qwt)[arguments]: Use INVOKE.
 2019-01-25 13:53:04 +01:00
Ricardo Wurmus 5b8484635f
gnu: ldb: Use INVOKE. 
* gnu/packages/samba.scm (ldb)[arguments]: Use INVOKE.
 2019-01-25 13:44:13 +01:00
Ricardo Wurmus ed0d6ed9a6
gnu: tevent: Use INVOKE. 
* gnu/packages/samba.scm (tevent)[arguments]: Use INVOKE.
 2019-01-25 13:42:58 +01:00
Ricardo Wurmus d83c52c6bb
gnu: talloc/static: Use INVOKE. 
* gnu/packages/samba.scm (talloc/static)[arguments]: Use INVOKE in the build
phase.
 2019-01-25 13:39:12 +01:00
Ricardo Wurmus ed5900890e
gnu: tre: Use INVOKE. 
* gnu/packages/regex.scm (tre)[arguments]: Use INVOKE.
 2019-01-25 13:37:36 +01:00
Ricardo Wurmus 4255818d1c
gnu: python-rdflib: Use PYPI-URI. 
* gnu/packages/rdf.scm (python-rdflib)[source]: Use PYPI-URI.
[arguments]: Use INVOKE in commented build phase.
 2019-01-25 13:36:14 +01:00
Ricardo Wurmus 48b11025b7
gnu: ocaml-utop: Use INVOKE. 
* gnu/packages/ocaml.scm (ocaml-utop)[arguments]: Use INVOKE.
 2019-01-25 13:32:41 +01:00
Ricardo Wurmus c6aaa7bed6
gnu: ocaml-zed: Use INVOKE. 
* gnu/packages/ocaml.scm (ocaml-zed)[arguments]: Use INVOKE in build phases.
 2019-01-25 13:32:04 +01:00
Ricardo Wurmus 04daa1ed72
gnu: ocaml-zarith: Use INVOKE. 
* gnu/packages/ocaml.scm (ocaml-zarith)[arguments]: Use INVOKE.
 2019-01-25 13:31:29 +01:00
Ricardo Wurmus 2c0234e78e
gnu: camlp4-4.02: Use INVOKE. 
* gnu/packages/ocaml.scm (camlp4-4.02)[arguments]: Use INVOKE in build phases.
 2019-01-25 13:26:24 +01:00
Ricardo Wurmus fa5d6e4c6f
gnu: ocaml-4.01: Use INVOKE. 
* gnu/packages/ocaml.scm (ocaml-4.01)[arguments]: Use INVOKE in build phases.
 2019-01-25 13:23:27 +01:00
Ricardo Wurmus bb29e855da
gnu: ocaml-4.02: Use INVOKE. 
* gnu/packages/ocaml.scm (ocaml-4.02)[arguments]: Use INVOKE in build phases.
 2019-01-25 13:22:34 +01:00