This is a followup to d0a2db47.

* doc/guix.texi (Application Setup)[The GCC toolchain]: Adjust bit
about GUIX_LD_WRAPPER_ALLOW_IMPURITIES.

* 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.

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.

* gnu/packages/package-management.scm (guix-devel): Remove.

* gnu/packages/bioinformatics.scm (pepr)[source]: Use PYPI-URI.

* gnu/packages/bioinformatics.scm (python2-warpedlmm)[source]: Use PYPI-URI.

* gnu/packages/backup.scm (attic)[source]: Use PYPI-URI.

* gnu/packages/admin.scm (graphios)[source]: Use PYPI-URI.

* gnu/packages/databases.scm (python-sqlalchemy)[source]: Use PYPI-URI.

* gnu/packages/audio.scm (python-pyaudio)[source]: Use PYPI-URI.

* gnu/packages/scheme.scm (femtolisp)[arguments]: Remove "bootstrap" phase;
use INVOKE and return #T unconditionally.

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: d453b0e1

* 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.

* gnu/packages/maths.scm (dealii-openmpi)[arguments]: Add 'mpi-setup' phase.

* 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.

* 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.

* 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.

Follow-up to 1a5f4662.

* gnu/build/linux-modules.scm (module-soft-dependencies): Remove colon from
section names.

* gnu/build/linux-modules.scm (not-softdep-whitespace): New variable.
(module-soft-dependencies): New procedure.

* gnu/packages/games.scm (stepmania):
* gnu/packages/video.scm (ffmpeg-for-stepmania): New variables.

* gnu/packages/kde-frameworks.scm (kcoreaddons)[arguments]: Add build phase
"fix-broken-test".

* gnu/packages/fabric-management.scm (infiniband-diags)[arguments]: Remove
"autotools" phase.

* gnu/packages/gnupg.scm (gpgme): Update to 1.12.0.

* gnu/packages/gnupg.scm (gpgme)[source]: Add upstream patch.

* gnu/packages/engineering.scm (pcb-rnd)[arguments]: Use INVOKE.

* gnu/packages/embedded.scm (proplib)[arguments]: Use INVOKE.

* gnu/packages/embedded.scm (jimtcl)[arguments]: Use INVOKE.

* gnu/packages/display-managers.scm (greenisland)[arguments]: Use INVOKE in
check phase.

* gnu/packages/password-utils.scm (assword)[arguments]: Use INVOKE.

* gnu/packages/openstack.scm (python-oslosphinx)[arguments]: Use INVOKE.

* gnu/packages/openstack.scm (python-reno)[arguments]: Use INVOKE.
[native-inputs]: Replace "git" with "git-minimal".

* gnu/packages/haskell.scm (ghc-libmpd): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

* 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.

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'.

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).

* guix/scripts/weather.scm (all-packages): Pass #:select? to
'fold-packages'.

* guix/packages.scm (package-closure): New procedure.
* tests/packages.scm ("package-closure"): New test.

* gnu/packages/python-crypto.scm (python-pyopenssl): Update to 19.0.0.
[arguments]: Use INVOKE.

* gnu/packages/qt.scm (python2-pyqt-4)[arguments]: Use INVOKE.

* gnu/packages/qt.scm (qwt)[arguments]: Use INVOKE.

* gnu/packages/samba.scm (ldb)[arguments]: Use INVOKE.