branch core-updates updated (bb8afbf -> afe9f40)

[Mark H. Weaver]

mhw pushed a change to branch core-updates
in repository guix.

      from  bb8afbf   gnu: Add dependency on Perl's 'Module::Build' as needed.
      adds  7c033c4   gnu: Add ruby-systemu.
      adds  3d84a99   gnu: Add ruby-bio-commandeer.
      adds  6b6f7d6   gnu: orfm: Update to 0.5.3.
      adds  6b3a1ce   emacs: Fix heading face in "Package Info".
      adds  2028a2c   import: cran: Move beautify-description to utils module.
      adds  869cda5   import: gem: Beautify description field.
      adds  2d12284   gnu: gnupg: Add TOFU support.
      adds  0047d26   gnu: bowtie: Update to 2.2.6.
      adds  d7786ce   gnu: r-sparsem: Add missing "gfortran" input.
      adds  3141b83   gnu: r-go-db: Add missing input.
      adds  e900518   gnu: Add version 2.7 variant of python-requests.
      adds  ea521b4   gnu: Add python-vcversioner.
      adds  b3667af   gnu: Update python-jsonschema to 2.5.1.
      adds  210bf49   gnu: Add python-texttable.
      adds  67c52bb   gnu: Add python-websocket-client.
      adds  d020bfc   gnu: Add python-docker-py.
      adds  b42c9c8   gnu: Add python-dockerpty.
      adds  df1f1d6   gnu: Add docker-compose.
      adds  6d139e5   gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778].
      adds  1beec63   Revert "gnu: openssh: Update to 7.1p2 [fixes 
CVE-0216-0778]."
      adds  45f2ffb   gnu: openssh: Update to 7.1p2.
      adds  f5ca44b   gnu: glade: Update to 3.18.5.
      adds  5c6eea2   gnu: Add python-atomicwrites.
      adds  561bb3c   gnu: Add python-requests-toolbelt.
      adds  d1deb90   gnu: Add python-click-threading.
      adds  7b17cab   gnu: Add python-click-log.
      adds  7b3a4ee   gnu: Add python-apipkg.
      adds  848964f   gnu: Add python-execnet.
      adds  6720dbb   gnu: Add python-pytest-cache.
      adds  d7e729f   gnu: Add python-pytest-localserver.
      adds  28cecbb   gnu: Add python-wsgi-intercept.
      adds  89b8a55   gnu: Add python-pytest-xprocess.
      adds  f75bbb0   gnu: Add radicale.
      adds  a2f6a3d   gnu: Add vdirsyncer.
      adds  5c299bf   gnu: Add python-icalendar.
      adds  6bbbb53   gnu: Add python-sphinxcontrib-newsfeed.
      adds  226d333   gnu: Update python-tzlocal to 1.2.
      adds  b97c1bf   gnu: python-urwid: Disable failing test 
test_remove_watch_file.
      adds  78e6c4a   gnu: Add khal.
      adds  2216e15   gnu: Add python-args.
      adds  c06a3de   gnu: Add python-clint.
      adds  4ecdeef   gnu: Add python-astor.
      adds  e224b7d   gnu: Add python-rply.
      adds  c3e919d   gnu: Add python-hy.
      adds  b830049   Move <boot-parameters> to (gnu system).
      adds  a0ad8ab   emacs: profiles: Add 'guix-system-profile'.
      adds  2df17bd   emacs: Find packages in system profiles.
      adds  54c3c28   emacs: Replace 'generation-diff' search with 
'profile-diff'.
      adds  5672866   emacs: Remove 'generation' search type.
      adds  67cedc4   emacs: Add interface for system generations.
      adds  7ba903b   linux-modules: Support 'modprobe.blacklist' on the 
command line.
      adds  e90cf6c   doc: Document command-line options honored by the initrd.
      adds  2309ed6   gnu: samtools-0.1: Adapt to changes in "samtools" 
variable.
      adds  90907a2   gnu: unison: Add "doc" output.
      adds  f5a8491   gnu: hevea: Update to 2.28.
      adds  2328b47   gnu: Add autojump.
      adds  d5650f8   gnu: Add libvdpau.
      adds  3161d32   gnu: Add vdpauinfo.
      adds  81c29cc   gnu: mpv: Add features.
      adds  cfac127   gnu: drumstick: Update to 1.0.2.
      adds  fb492b9   gnu: vmpk: Update to 0.6.2a.
      adds  c9e330d   gnu: Add python-keystoneclient.
      adds  7a5b944   gnu: Add python-futures.
      adds  8f0cc2f   gnu: Add python-swiftclient.
      adds  81f7f29   gnu: Add python-rauth.
      adds  5988c29   gnu: Add python-pyasn1-modules.
      adds  1abe448   gnu: Add python2-functools32.
      adds  1046863   gnu: python-pytest-cov: Clarify description.
      adds  e1ba074   gnu: python-wheel: Clarify description.
      adds  c18f636   gnu: Add python-urllib3.
      adds  e8d2168   gnu: Add git-annex-remote-hubic.
      adds  b153f9f   linux-initrd: Remove "usbkbd" from the default set of 
modules.
      adds  18ef998   gnu: bristol: Remove SSE flags on platforms other than 
x86_64 and i686.
      adds  e830929   gnu: solfege: Build scores with Lilypond.
      adds  51a277d   gnu: rsync: Update to 3.1.2.
      adds  8047d13   gnu: mariadb: Update to 10.0.23.
      adds  de6af32   build: Speed up .go compilation.
      adds  058247e   gnu: datamash: Update to 1.1.0.
      adds  264ae68   python2-jsonschema: Add python2-functools32 to inputs.
      adds  e119ba9   emacs: Rename 'guix-search-by-name' to 
'guix-packages-by-name'.
      adds  27a2e48   emacs: Add 'guix-search-by-name'.
      adds  a887fd8   doc: Explain how to run a subset of the tests.
      adds  44ad338   derivations: Add test for #:leaked-env-vars.
      adds  e0c941f   doc: Document 'http_proxy'.
      adds  4c896c9   gnu: manaplus: Update to 1.6.1.16.
      adds  d44d60d   gnu: sxiv: Update to 1.3.2.
      adds  60edbe2   gnu: magit: Update to 2.4.0.
      adds  26da7c2   gnu: mpv: Update to 0.15.0.
      adds  aac783c   build: Remove traces of 'NIX_SETUID_HELPER'.
      adds  1348185   gnu: Add linux-libre-4.2.5
       new  afe9f40   Merge branch 'master' into core-updates

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 Makefile.am                                    |   32 +-
 NEWS                                           |    1 +
 build-aux/compile-all.scm                      |   82 +++
 doc/emacs.texi                                 |   15 +-
 doc/guix.texi                                  |   64 ++
 emacs.am                                       |    1 +
 emacs/guix-base.el                             |   25 +-
 emacs/guix-main.scm                            |   77 ++-
 emacs/guix-messages.el                         |   42 +-
 emacs/guix-profiles.el                         |    7 +-
 emacs/guix-ui-generation.el                    |   62 ++-
 emacs/guix-ui-package.el                       |   24 +-
 emacs/guix-ui-system-generation.el             |  105 ++++
 gnu-system.am                                  |    3 +-
 gnu/build/linux-modules.scm                    |   78 ++-
 gnu/packages/admin.scm                         |   61 ++-
 gnu/packages/bioinformatics.scm                |   77 ++--
 gnu/packages/calendar.scm                      |   77 +++-
 gnu/packages/databases.scm                     |    6 +-
 gnu/packages/datamash.scm                      |    5 +-
 gnu/packages/dav.scm                           |  108 ++++
 gnu/packages/docker.scm                        |  107 ++++
 gnu/packages/emacs.scm                         |    6 +-
 gnu/packages/games.scm                         |    6 +-
 gnu/packages/gnome.scm                         |   27 +-
 gnu/packages/gnupg.scm                         |    6 +-
 gnu/packages/linux.scm                         |   17 +
 gnu/packages/music.scm                         |   29 +-
 gnu/packages/ocaml.scm                         |  105 +++-
 gnu/packages/openstack.scm                     |  155 +++++-
 gnu/packages/patches/bowtie-fix-makefile.patch |   31 -
 gnu/packages/python.scm                        |  756 ++++++++++++++++++++++--
 gnu/packages/rsync.scm                         |    5 +-
 gnu/packages/ruby.scm                          |   64 ++
 gnu/packages/ssh.scm                           |    6 +-
 gnu/packages/statistics.scm                    |    4 +-
 gnu/packages/sxiv.scm                          |    6 +-
 gnu/packages/version-control.scm               |   31 +
 gnu/packages/video.scm                         |   60 ++-
 gnu/system.scm                                 |   41 ++
 gnu/system/linux-initrd.scm                    |    4 +-
 guix/import/cran.scm                           |   11 -
 guix/import/gem.scm                            |    3 +-
 guix/import/utils.scm                          |   14 +-
 guix/scripts/system.scm                        |   85 +--
 test-env.in                                    |   11 +-
 tests/derivations.scm                          |   18 +-
 47 files changed, 2158 insertions(+), 402 deletions(-)
 create mode 100644 build-aux/compile-all.scm
 create mode 100644 emacs/guix-ui-system-generation.el
 create mode 100644 gnu/packages/dav.scm
 create mode 100644 gnu/packages/docker.scm
 delete mode 100644 gnu/packages/patches/bowtie-fix-makefile.patch