gnu: Update python-jsonschema to 2.5.1.

* gnu/packages/python.scm (python-jsonschema): Update to 2.5.1.
[inputs]: Add python-vcversioner.

gnu: Add python-vcversioner.

* gnu/packages/python.scm (python-vcversioner, python2-vcversioner): New
variables.

gnu: Add version 2.7 variant of python-requests.

* gnu/packages/python.scm (python-requests-2.7): New variable.

gnu: r-go-db: Add missing input.

* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add
  "r-annotationdbi".

gnu: r-sparsem: Add missing "gfortran" input.

* gnu/packages/statistics.scm (r-sparsem)[inputs]: Add "gfortran".

gnu: bowtie: Update to 2.2.6.

* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6.
[source]: Remove patch; do not set CC and CPP variables.
[inputs]: Add "tbb".
[arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom
"install" phase.
* gnu/packages/patches/bowtie-fix-makefile.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove patch file.

gnu: gnupg: Add TOFU support.

* gnu/packages/gnupg.scm (gnupg)[inputs]: Add sqlite.

import: gem: Beautify description field.

* guix/import/gem.scm (gem->guix-package): Use 'beautify-description'.

import: cran: Move beautify-description to utils module.

* guix/import/cran.scm (beautify-description): Move from here...
* guix/import/utils.scm: ... to here.

emacs: Fix heading face in "Package Info".

Reported by Ludovic Courtès <ludo@gnu.org> on #guix.
This fixes a regression introduced in commit 7171d824.

'insert-text-button' procedure does not allow to override a button face,
so a specialized button type should be used instead.

* emacs/guix-ui-package.el (guix-package-heading): New button type.
  (guix-package-info-insert-heading): Use it.

gnu: orfm: Update to 0.5.3.

* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3.
[native-inputs]: Add inputs required for tests.
[description]: Add commas.

gnu: Add ruby-bio-commandeer.

* gnu/packages/ruby.scm (ruby-bio-commandeer): New variable.

gnu: Add ruby-systemu.

* gnu/packages/ruby.scm (ruby-systemu): New variable.

hydra: Add missing phase and inputs for 'make dist' job.

* build-aux/hydra/guix.scm (tarball-package): Inherit from 'guix-devel'
rather than 'guix'.  Pass #:phases to 'dist-package'.

build-system/gnu: 'dist-package' can be passed the phases.

* guix/build-system/gnu.scm (dist-package): Add #:phases parameter and
honor it.

monad-repl: Close connection when leaving the monad REPL.

* guix/monad-repl.scm (store-monad-language): Add 'store' parameter and
use it.  Remove call to 'open-connection'.
(enter-store-monad): Use 'with-store' and pass the store to
'store-monad-language.

gnu: julia: Update to 0.4.3.

* gnu/packages/julia.scm (julia): Update to 0.4.3.
(libuv-julia): Update to 07730c4bd595.

emacs: Move loading packages to "guix-emacs.el".

* emacs/guix-init.el: Move the code for auto-loading Emacs packages to...
  (guix-package-enable-at-startup): Move to...
* emacs/guix-emacs.el (guix-package-enable-at-startup): ... here.

emacs: Make "guix-emacs.el" independent.

"guix-emacs.el" may be used just for "instructing" Emacs where to find
Emacs packages installed with Guix, so it should have as few
dependencies as possible.

See <http://lists.gnu.org/archive/html/guix-devel/2016-01/msg00022.html>.

* emacs/guix-emacs.el: Require 'guix-profiles' optionally.
  (guix-emacs-load-autoloads): Use 'guix-profile-prompt' only if it is
  available.

emacs: Complete --file in 'guix build' popup.

* emacs/guix-command.el (guix-command-improve-build-argument): Use
  'guix-read-file-name' to complete --file option.