gnu: Add python-pytest-cov.

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

gnu: Add libconfig.

* gnu/packages/textutils.scm (libconfig): New variable.

gnu: python-pytz: Update to 2015.7.

* gnu/packages/python.scm (python-pytz): Update to 2015.7.
[source]: Change uri to pypi's location.
[home-page]: Change to new website.
[license]: Change to expat.

gnu: ghc-cryptonite: Update description.

* gnu/packages/haskell.scm (ghc-cryptonite)[description]: Shorten overly
  technical package description.

gnu: python-biopython, python2-biopython: Update to 1.66.

* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): Update to 1.66.
[source]: Use PyPi instead of biopython.org.

gnu: Add ghc-pandoc.

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

gnu: Add ghc-http-client-tls.

* gnu/packages/haskell.scm (ghc-http-client-tls): New variable.

gnu: Add ghc-connection.

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

gnu: Add ghc-socks.

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

gnu: Add ghc-tls.

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

gnu: Add ghc-x509-system.

* gnu/packages/haskell.scm (ghc-x509-system): New variable.

gnu: Add ghc-x509-validation.

* gnu/packages/haskell.scm (ghc-x509-validation): New variable.

gnu: Add ghc-x509-store.

* gnu/packages/haskell.scm (ghc-x509-store): New variable.

gnu: Add ghc-x509.

* gnu/packages/haskell.scm (ghc-x509): New variable.

gnu: Add ghc-memory.

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

gnu: Add ghc-cryptonite.

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

gnu: Add ghc-tasty-kat.

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

gnu: Add ghc-asn1-parse.

* gnu/packages/haskell.scm (ghc-asn1-parse): New variable.

gnu: Add ghc-asn1-encoding.

* gnu/packages/haskell.scm (ghc-asn1-encoding): New variable.

gnu: Add ghc-asn1-types.

* gnu/packages/haskell.scm (ghc-asn1-types): New variable.

gnu: Add ghc-pem.

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

gnu: Add ghc-hourglass.

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

gnu: Add ghc-byteable.

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

gnu: Add ghc-http-client.

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

gnu: Add ghc-mime-types.

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

gnu: Add ghc-hslua.

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

gnu: Add ghc-sha.

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

gnu: Add ghc-juicypixels.

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

gnu: Add ghc-mmap.

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

gnu: Add ghc-filemanip.

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

gnu: Add ghc-yaml.

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

gnu: Add ghc-mockery.

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

gnu: Add ghc-logging-facade.

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

gnu: Add ghc-conduit.

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

gnu: Add ghc-hspec-contrib.

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

gnu: Add ghc-aeson-qq.

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

gnu: Add ghc-haskell-src-meta.

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

gnu: Add ghc-th-orphans.

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

gnu: Add ghc-th-reify-many.

* gnu/packages/haskell.scm (ghc-th-reify-many): New variable.

gnu: Add ghc-th-expand-syns.

* gnu/packages/haskell.scm (ghc-th-expand-syns): New variable.

gnu: Add ghc-th-lift.

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

gnu: Add ghc-packedstring.

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

gnu: Add ghc-enclosed-exceptions.

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

gnu: Add ghc-executable-path.

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

gnu: Add ghc-cmark.

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

gnu: Add ghc-highlighting-kate.

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

gnu: Add ghc-diff.

* gnu/packages/haskell.scm (ghc-diff): Add variable.

gnu: Add ghc-regex-pcre-builtin.

* gnu/packages/haskell.scm (ghc-regex-pcre-builtin): New variable.

gnu: Add ghc-texmath.

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

gnu: Add ghc-pandoc-types.

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

gnu: Add ghc-deepseq-generics.

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

gnu: ghc-aeson: Propagate input.

* gnu/packages/haskell.scm (ghc-aeson)[inputs]: Move
  "ghc-unordered-containers" from here ...
[propagated-inputs]: ... to here.

gnu: ghc-haskell-src-exts: Propagate some inputs.

* gnu/packages/haskell.scm (ghc-haskell-src-exts)[inputs]: Remove field.
[propagated-inputs]: Move "cpphs", "ghc-mtl", "ghc-happy", and "ghc-syb"
from inputs field here.
[native-inputs]: Move "ghc-smallcheck", "ghc-tasty",
"ghc-tasty-smallcheck", and "ghc-tasty-golden" from inputs field here.

gnu: emacs-w3m: Update to 1.4.538+0.20141022.

* gnu/packages/emacs.scm (emacs-w3m): Update to 1.4.538+0.20141022.
  [arguments]: Use '--without-compress-install' configure flag.

gnu: emacs-w3m: Use 'modify-syntax'.

* gnu/packages/emacs.scm (emacs-w3m)[arguments]: Use 'modify-syntax'.

doc: rephrase code of conduct.

* doc/contributing.texi (Contributing): Rephrase 'code of conduct'
  section.

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

gnu-maintenance: Really find the latest GNOME releases.

Reported by Efraim Flashner <efraim@flashner.co.il>
at <https://lists.gnu.org/archive/html/guix-devel/2015-12/msg00202.html>.

* guix/gnu-maintenance.scm (latest-ftp-release): Call KEEP-FILE? on
directories too.
(latest-gnome-release)[even-minor-version?]: Protect again MINOR being
false; change pattern to match VERSION with two or more numbers.  Remove
use of 'version-major+minor'.
[even-numbered-tarball?]: Rename to...
[even-numbered?]: ... this.  Use 'package-name->name+version'.  When
VERSION is #f, check NAME.

build: Always check for gzip/bzip2/xz.

This allows (guix config) to contain valid values of %GZIP et al. even
when configured with --disable-daemon.

* config-daemon.ac: Move 'AC_PATH_PROG' invocations for
gzip & co. to...
* configure.ac: ... here.

gnu: youtube-dl: Update to 2015.12.09.

* gnu/packages/video.scm (youtube-dl): Update to 2015.12.09.
[native-inputs]: Move python-setuptools here.

gnu: vte: Update to 0.42.1.

* gnu/packages/gnome.scm (vte): Update to 0.42.1.

gnu: libsecret: Update to 0.18.3.

* gnu/packages/gnome.scm (libsecret): Update to 0.18.3.

gnu: libgnome-keyring: Update to 3.12.0.

* gnu/packages/gnome.scm (libgnome-keyring): Update to 3.12.0.

emacs: Fix '--rounds' option in command popups.

* emacs/guix-command.el (guix-command-improve-common-build-argument):
  Use "R" key for '--rounds' option to avoid conflicts with "r" key in
  'build' popup (--root) and 'package' popup (--remove).

emacs: Add 'guix-build-log-find-file'.

* emacs/guix-build-log.el (guix-build-log-find-file): New procedure.
* emacs/guix-command.el (guix-run-view-build-log): Use it.

emacs: list: Fontify time stamps.

* emacs/guix-list.el (guix-list-time): New face.
  (guix-list-get-time): Use it.

emacs: info: Add 'guix-info-heading' face.

* emacs/guix-info.el (guix-info-heading): New face.
  (guix-package-info-heading): Inherit it.

Add "Contributor Covenant".

* CODE-OF-CONDUCT: New file, adapted from
  <http://contributor-covenant.org/version/1/3/0/code_of_conduct.txt>.
* doc/contributing.texi (Contributing): Mention it.
* Makefile.am (EXTRA_DIST): Add it.

daemon: Use deterministic $TMPDIR in chroot.

Rather than using $<host-TMPDIR>/nix-build-<drvname>-<number>, the
temporary directory is now always /tmp/nix-build-<drvname>-0. This
improves bitwise-exact reproducibility for builds that store $TMPDIR
in their build output. (Of course, those should still be fixed...)

* nix/libstore/build.cc (DerivationGoal)[tmpDirInSandbox]: New field.
(DerivationGoal::startBuilder): Initialize 'useChroot' earlier.  Compute
'tmpDirInSandbox', and use it when populating 'dirsInChroot'.
* doc/guix.texi (Build Environment Setup): Document it.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

guix build: Add '--check'.

* guix/derivations.scm (build-derivations): Add optional 'mode'
parameter.
* guix/scripts/build.scm (%default-options): Add 'build-mode'.
(show-help, %options): Add '--check'.
(guix-build): Honor 'build-mode' key of OPTS.  Pass it to
'show-what-to-build' and 'build-derivations'.
* doc/guix.texi (Invoking guix build): Document it.
(Substitutes): Mention it.

derivations: Determine what's built in 'check' mode.

* guix/derivations.scm (substitution-oracle): Add #:mode parameter and
honor it.
(derivation-prerequisites-to-build): Likewise.
[derivation-built?]: Take it into account.
* guix/ui.scm (show-what-to-build): Add #:mode parameter.  Pass it to
'substitute-oracle' and 'derivations-prerequisites-to-build'.
* tests/derivations.scm ("derivation-prerequisites-to-build in 'check'
mode"): New test.

gnu: gmime: Update to 2.6.20.

* gnu/packages/mail.scm (gmime): Update to 2.6.20.
[arguments]: Use modify-phases syntax.

gnu: guile-sly: Use HTTPS URL.

* gnu/packages/guile.scm (guile-sly)[source]: Use 'https'.  Failing to
do that, we get redirected to 'https', which fails because GnuTLS is
missing.

guix build: Add '--rounds'.

* guix/scripts/build.scm (show-build-options-help)
(%standard-build-options): Add --rounds.
(set-build-options-from-command-line): Honor it.
* doc/guix.texi (Invoking guix build): Document it.
* doc/contributing.texi (Submitting Patches): Mention it.

store: Allow clients to request multiple builds.

* guix/store.scm (set-build-options): Add #:rounds parameter and honor it.
* tests/store.scm ("build multiple times"): New test.

daemon: Allow builds to be repeated.

This makes it easy to detect non-deterministic builds.

* nix/libstore/build.cc (DerivationGoal): Remove 'InodesSeen'; add
'curRound', 'nrRound', and 'prevInfos'.
(DerivationGoal::inputsRealised): Initialize 'nrRound'.
(NotDeterministic): New error type.
(DerivationGoal::buildDone): Check whether we need to repeat.
(DerivationGoal::startBuilder): Adjust message.
(DerivationGoal::registerOutputs): Check whether we get the same result.
* nix/libstore/globals.cc (Settings::get(const string & name, int def)):
New method.
* nix/libstore/globals.hh (Settings): Add it.
* nix/libstore/store-api.hh (ValidPathInfo): Add operator ==.
* nix/nix-daemon/nix-daemon.cc (performOp): Allow "build-repeat" for
"untrusted" users.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

gnu: python-pillow: Update to 3.0.0.

* gnu/packages/python.scm (python-pillow, python2-pillow): Update to 3.0.0.

gnu: numactl: Update to 2.0.10.

* gnu/packages/linux.scm (numactl)[source]: Update to 2.0.10.
  [arguments]: Adapt phases to use the autotools machinery.
  [native-inputs]: Add autotools packages.

gnu-maintenance: Exclude development releases from GNOME update candidates.

Suggested by Efraim Flashner <efraim@flashner.co.il>.

* guix/gnu-maintenance.scm (latest-ftp-release): Add #:keep-file?
parameter and honor it.
(latest-gnome-release)[%not-dot]: New variable.
[even-minor-version?, even-numbered-tarball?]: New procedures.
Pass EVEN-NUMBERED-TARBALL? as #:keep-file? argument.

gnu: glade3: Update to 3.8.5.

* gnu/packages/gnome.scm (glade3): Update to 3.8.5.

gnu: autogen: Update to 5.18.7.

* gnu/packages/autogen.scm (autogen): Update to 5.18.7.

gnu-maintenance: ftp.gnome.org does not provide signatures.

* guix/gnu-maintenance.scm (latest-ftp-release): Add #:file->signature
parameter.  Honor it.
(latest-gnome-release): Pass #:file->signature.
* guix/upstream.scm (coalesce-sources): Keep 'signature-urls' as #f
unless both sources provide it.

gnu-maintenance: Add GNOME updater.

* guix/gnu-maintenance.scm (ftp-server/directory)[quirks]: Remove glib.
(false-if-ftp-error): New macro.
(latest-release*): Use it.
(non-emacs-gnu-package?): Rename to...
(pure-gnu-package?): ... this.  Add call to 'gnome-package?'.
(%gnu-updater): Adjust accordingly.
(gnome-package?, latest-gnome-release): New procedures.
(%gnome-updater): New variable.
* guix/scripts/refresh.scm (%updaters): Add %GNOME-UPDATER.
* doc/guix.texi (Invoking guix refresh): Mention it.

gnu-maintenance: Generalize 'latest-ftp-release'.

* guix/gnu-maintenance.scm (latest-release): Rename to...
(latest-ftp-release): ... this.  Add #:server and #:directory
parameters.
(latest-release): New procedure.

refresh: Bail out when asked for a nonexistent updater.

* guix/scripts/refresh.scm (lookup-updater): Call 'leave' when 'find'
returns #f.

gnu-maintenance: Do not look for releases in "w32" sub-directories.

* guix/gnu-maintenance.scm (latest-release): Filter out "w32"
directories.

gnu-maintenance: Add tests for 'release-file?'.

* tests/gnu-maintenance.scm: New file.
* Makefile.am (SCM_TESTS): Add it.
* guix/gnu-maintenance.scm (release-file?): Export.

gnu-maintenance: Properly handle TeXmacs.

* guix/gnu-maintenance.scm (ftp-server/directory): Add comment.
(release-file?): Use 'string-ci=?' instead of 'equal?' when comparing
project names.

gnu-maintenance: Adjust tarball regexp for IceCat tarballs.

* guix/gnu-maintenance.scm (%tarball-rx): Tweak to match IceCat tarball
patterns.

gnu-maintenance: Fix URLs returned by 'latest-release' for deep trees.

With this, (latest-release "gcc") returns an <upstream-source> with URL:

  ftp://ftp.gnu.org/gnu/gcc/gcc-5.3.0/gcc-5.3.0.tar.gz

Previous it would omit "gcc-5.3.0/" from the URL.

Fixes a regression introduced in 0a7c5a0.

* guix/gnu-maintenance.scm (latest-release)[file->url, file->source]:
Add 'directory' parameter.  Update users.

doc: 'guix environment --container' does not create '/env'.

* doc/guix.texi (Invoking guix environment): Remove outdated mention of
'/env' for '--container'.

gnu: node: Do not use bundled dependencies.

The Node build system was previously building its own copies of
OpenSSL (yikes!), libuv, and zlib.

* gnu/packages/node.scm (node)[inputs]: Add openssl, libuv, and zlib.
  [arguments]: Add configure flags for using system libraries.  Use
  'modify-phases' syntax.

gnu: util-linux: Make description more descriptive.

* gnu/packages/linux.scm (util-linux)[description]: Give some more
  information about the package.

Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: pcre: Update to 8.38.

* gnu/packages/pcre.scm (pcre): Update to 8.38.  Add source URI for
  main FTP site.

gnu: libxml2: Update to 2.9.3.

* gnu/packages/patches/libxml2-CVE-2015-1819.patch,
  gnu/packages/patches/libxml2-CVE-2015-7941-pt1.patch,
  gnu/packages/patches/libxml2-CVE-2015-7941-pt2.patch,
  gnu/packages/patches/libxml2-CVE-2015-7942-pt1.patch,
  gnu/packages/patches/libxml2-CVE-2015-7942-pt2.patch,
  gnu/packages/patches/libxml2-CVE-2015-8035.patch,
  gnu/packages/patches/libxml2-bug-737840.patch,
  gnu/packages/patches/libxml2-bug-738805.patch,
  gnu/packages/patches/libxml2-bug-746048.patch,
  gnu/packages/patches/libxml2-bug-747437.patch,
  gnu/packages/patches/libxml2-bug-751603.patch,
  gnu/packages/patches/libxml2-bug-751631.patch,
  gnu/packages/patches/libxml2-bug-754946.patch,
  gnu/packages/patches/libxml2-bug-754947.patch,
  gnu/packages/patches/libxml2-bug-755857.patch,
  gnu/packages/patches/libxml2-fix-catalog-corruption.patch,
  gnu/packages/patches/libxml2-id-attrs-in-xmlSetTreeDoc.patch,
  gnu/packages/patches/libxml2-node-sort-order-pt1.patch,
  gnu/packages/patches/libxml2-node-sort-order-pt2.patch: Delete files.
* gnu-system.am (dist_patch_DATA): Remove them.
* gnu/packages/xml.scm (libxml2): Update to 2.9.3.  Remove patches.

gnu: openssl: Update to 1.0.2e [fixes CVE-2015-{3193,3194,3195}].

* gnu/packages/tls.scm (openssl): Update to 1.0.2e.
  [arguments]: Rename 'fix-man-dir' phase to 'patch-Makefile.org',
  and patch SHELL in Makefile.org.  Add 'fix-broken-symlinks' phase.
  Return #t from 'patch-tests' phase.

gnu: keepassx: Update to 2.0.

* gnu/packages/password-utils.scm (keepassx): Update to 2.0.
[source]: Change to official release location.

gnu: python2-zope-security: Use python2-zope-testrunner.

* gnu/packages/python.scm (python2-zope-security): Do it.

gnu: help2man: Update to 1.47.3.

* gnu/packages/man.scm (help2man): Update to 1.47.3.

gnu: libmicrohttpd: Update to 0.9.47.

* gnu/packages/gnunet.scm (libmicrohttpd): Update to 0.9.47.

gnu: mp3info: Update URL.

* gnu/packages/mp3.scm (mp3info): Update source URL.

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