maint: Fix invalid calls to 'info'.

* HACKING <Contributing>: Remove name of the manual from the item argument.
* README <Installation>: Likewise.

gnu: Add r-bsgenome-hsapiens-1000genomes-hs37d5.

* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
  New variable.

gnu: Add light.

* gnu/packages/linux.scm (light): New variable.

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

environment: Fix setting writable? on networking related files

* guix/scripts/environment.scm (launch-environment/container): Include the
  file name in the call to string=? when deciding if the file should be
  writable.

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

gnu: Add font-awesome.

* gnu/packages/fonts.scm (font-awesome): New variable.

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

gnu: Add opencascade-oce.

* gnu/packages/maths.scm (opencascade-oce): New variable.

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

store: Add 'add-data-to-store'.

* guix/serialization.scm (write-bytevector): New procedure.
(write-string): Rewrite in terms of 'write-bytevector'.
* guix/store.scm (write-arg): Add 'bytevector' case.
(add-data-to-store): New procedure, from former 'add-text-to-store'.
(add-text-to-store): Rewrite in terms of 'add-data-to-store'.
* tests/store.scm ("add-data-to-store"): New test.

gnu: Add catimg.

* gnu/packages/image-viewers.scm (catimg): New variable.

Signed-off-by: Kei Kebreau <kei@openmailbox.org>

gnu: Add dub.

* gnu/packages/ldc.scm (dub): New variable.

gnu: khal: Update to 0.9.1.

* gnu/packages/calendar.scm (khal): Update to 0.9.1.

doc: Fix typo.

* doc/guix.texi (ocaml-build-system): Replace ocaml with OCaml.

doc: Document ocaml-build-system.

* doc/guix.texi (Build Systems) [ocaml-build-system]: New definition.

gnu: emacs-org: Update to 20170124.

* gnu/packages/emacs.scm (emacs-org): Update to 20170124.

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

gnu: wireshark: Update to 2.2.4.

* gnu/packages/networking.scm (wireshark): Update to 2.2.4.

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

gnu: asymptote: Update to 2.39

* gnu/packages/plotutils.scm (asymptote): Update to 2.39.

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

gnu: vim: Update to 8.0.0257.

* gnu/packages/vim.scm (vim): Update to 8.0.0257.

gnu: Add GNU Freetalk.

* gnu/packages/messaging.scm (freetalk): New variable.

Signed-off-by: Mathieu Lirzin <mthl@gnu.org>

gnu: exfat-utils: Update to 1.2.6.

* gnu/packages/mtools.scm (exfat-utils): Update to 1.2.6.

gnu: fuse-exfat: Update to 1.2.6.

* gnu/packages/linux.scm (fuse-exfat): Update to 1.2.6.

build-system/python: 'package-with-explicit-python' uses 'eq?' memoization.

* guix/build-system/python.scm (package-with-explicit-python): Use
'mlambdaq' instead of 'mlambda'.  This does not change the <package>
graph and has no visible impact on performance.

gnu-maintenance: 'gnu-package?' uses 'eq?' memoization.

* guix/gnu-maintenance.scm (gnu-package?): Use 'mlambdaq' instead of
'mlambda'.

packages: Remove 'define-memoized/v' and use 'mlambdaq' instead.

* guix/packages.scm (define-memoized/v): Remove.
(package-transitive-supported-systems): Use 'mlambdaq' instead of
'define-memoized/v'.
(package-input-rewriting)[replace]: Likewise.

Use 'mlambda' instead of 'memoize'.

* gnu/packages.scm (find-newest-available-packages): Use 'mlambda'
instead of (memoize (lambda ...) ...).
* gnu/packages/bootstrap.scm (package-with-bootstrap-guile): Likewise.
* guix/build-system/gnu.scm (package-with-explicit-inputs)[rewritten-input]:
Likewise.
* guix/build-system/python.scm (package-with-explicit-python)[transform]:
Likewise.
* guix/derivations.scm (derivation->string): Likewise.
* guix/gnu-maintenance.scm (gnu-package?): Likewise.
* guix/modules.scm (module-file-dependencies): Likewise.
* guix/scripts/graph.scm (standard-package-set): Likewise.
* guix/scripts/lint.scm (official-gnu-packages*): Likewise.
* guix/store.scm (store-regexp*): Likewise.
* guix/utils.scm (location): Likewise.

Add (guix memoization).

* guix/combinators.scm (memoize): Remove.
* guix/memoization.scm: New file.
* Makefile.am (MODULES): Add it.
* gnu/packages.scm, gnu/packages/bootstrap.scm,
guix/build-system/gnu.scm, guix/build-system/python.scm,
guix/derivations.scm, guix/gnu-maintenance.scm,
guix/import/cran.scm, guix/import/elpa.scm,
guix/modules.scm, guix/scripts/build.scm,
guix/scripts/graph.scm, guix/scripts/lint.scm,
guix/store.scm, guix/utils.scm: Adjust imports accordingly.

doc: Fix typos.

Fixes a regression introduced in commit
f31f1acac2efb4bc6558b604a07b56f826423177.

Reported-by roptat on #guix.

* doc/guix.texi (Invoking guix build): Use "@@" instead of "@".

gnu: Add emacs-mu4e-alert.

* gnu/packages/emacs.scm (emacs-mu4e-alert): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>

gnu: Add emacs-alert.

* gnu/packages/emacs.scm (emacs-alert): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>

gnu: Add emacs-gntp.

* gnu/packages/emacs.scm (emacs-gntp): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>

gnu: Add emacs-log4e.

* gnu/packages/emacs.scm (emacs-log4e): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>

gnu: Add emacs-ht.

* gnu/packages/emacs.scm (emacs-ht): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>

gnu: tvtime: Update to 1.0.11.

* gnu/packages/tv.scm (tvtime): Update to 1.0.11.

gnu: manaplus: Update to 1.7.1.21.

* gnu/packages/games.scm (manaplus): Update to 1.7.1.21.

doc: Fix typos.

* doc/guix.texi: Use "@" for package specifications.

gnu: transmission-remote-cli: Superseded by tremc.

* gnu/packages/bittorrent.scm (transmission-remote-cli)[properties]: New field.

gnu: Add tremc.

* gnu/packages/bittorrent.scm (tremc): New variable.

doc: Clarify "Installing GuixSD in a VM".

* doc/guix.texi (Installing GuixSD in a VM): Mention decompressing the
installation image.

gnu: ldc: Add missing patches.

This is a followup to commit 2429dde57d8461cc8e51dbe6c9d47d795fe6fc9a.

* gnu/packages/patches/ldc-1.1.0-disable-dmd-tests.patch,
gnu/packages/patches/ldc-1.1.0-disable-phobos-tests.patch: New files.

doc: Fix networking instructions in "Installing GuixSD in a VM".

This is a followup to commit c8b543741f422ecf41e7635c6a1c40b3bd55947a.

* doc/guix.texi (Installing GuixSD in a VM): Fix typo.

gnu: assword: Wrap with the GObject typelib of GTK+.

Fixes <https://debbugs.gnu.org/25457>.

* gnu/packages/password-utils.scm (assword)[inputs]: Add 'gtk+'.
[arguments]: Add 'wrap-assword' phase.

gnu: python-xdo: Hardcode the path of 'libxdo.so'.

* gnu/packages/python.scm (python-xdo)[arguments]: Add 'patch-libxdo-path'
phase.

gnu: python-xdo: Add 'python-six' to 'propagated-inputs'.

* gnu/packages/python.scm (python-xdo)[propagated-inputs]: New field.

gnu: gtksourceview-2: Adjust inputs.

Fixes <https://debbugs.gnu.org/25537>.

* gnu/packages/gtk.scm (gtksourceview-2): Move 'shared-mime-info' and
'xorg-server' to 'native-inputs'.  Move 'gtk+-2' to 'propagated-inputs'.

gnu: Add ldc@1.1.0-beta6.

* gnu/packages/ldc.scm (ldc-1.1.0-beta6, ldc-beta): New variables.
* gnu/packages/patches/ldc-1.1.0-disable-dmd-tests.patch: New file.
* gnu/packages/patches/ldc-1.1.0-disable-phobos-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add them.

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

tests: Adjust pypi test to recent importer change.

This is a followup to 2f977d92d3ae517788d3dee98f63680ca149aa1a.

* tests/pypi.scm ("pypi->guix-package"): Don't expect 'python-setuptools' in
'propagated-inputs'.
("pypi->guix-package, wheels"): Likewise.

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

doc: Add missing Upstart command for the binary installation.

Fixes <http://bugs.gnu.org/25551>.
Reported by Jason Self <jason@bluehome.net>.

* doc/guix.texi (Binary Installation): Add 'initctl
reload-configuration' command for Upstart.

doc: Add 'cups-configuration' example with 'hplip'.

* doc/guix.texi (Printing Services): Add example with 'hplip'.

packages: Add 'package-upstream-name' and use it.

* guix/packages.scm (package-upstream-name): New procedure.
* guix/gnu-maintenance.scm (gnu-package?, ftp-server/directory)
(latest-release*, latest-gnome-release)
(latest-kde-release): Use it instead of the inline expression.

import: github: Better tolerate unexpected file extensions.

* guix/import/github.scm (find-extension): Add ".tbz".
(updated-github-url): When 'find-extension' returns #f, use "" for EXT.

gnu-maintenance: 'gnu-package?' ignores invalid URLs.

* guix/gnu-maintenance.scm (gnu-package?)[gnu-home-page?]: Add '>>'
threading macro and use it.

gnu: emacs-emms: Add 'upstream-name' property.

* gnu/packages/emacs.scm (emms)[properties]: New field.

gnu-maintenance: GNU updater handles gnu.org-hosted Emacs packages.

* guix/gnu-maintenance.scm (pure-gnu-package?): If an "emacs-" package
matches 'gnu-hosted?', return true.
(gnu-hosted?): New procedure.

gnu-maintenance: Honor 'upstream-name' property in GNU updater.

* guix/gnu-maintenance.scm (gnu-package?): Honor the 'usptream-name'
property of PACKAGE.
(ftp-server/directory): Likewise.

gnu: offlineimap: Update to 7.0.13.

* gnu/packages/mail.scm (offlineimap): Update to 7.0.13.

gnu: btrfs-progs: Update to 4.9.1.

* gnu/packages/linux.scm (btrfs-progs): Update to 4.9.1.

Update .mailmap entries for ng0.

* .mailmap: Update entries for ng0.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>

gnu: extremetuxracer: Update to 0.7.4.

* gnu/packages/games.scm (extremetuxracer): Update to 0.7.4.

gnu: linux-libre: Update to 4.9.6.

* gnu/packages/linux.scm (%linux-libre-version, %linux-libre-hash)
(linux-libre): Update to 4.9.6.

gnu: linux-libre@4.4: Update to 4.4.45.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.45.

gnu: pius: Update to 2.2.3.

* gnu/packages/gnupg.scm (pius): Update to 2.2.3.
[source]: Switch back to using the tarball release.
[arguments]: End 'set-gpg-file-name' phase on #t.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: kakoune: Move reproducibility substitution to source snippet.

* gnu/packages/text-editors.scm (kakoune)[arguments]: Move substitution to ...
[source]: ... here.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: openssl-next: Update to 1.1.0d [fixes CVE-2017-{3730, 3731, 3732}].

* gnu/packages/tls.scm (openssl-next): Update to 1.1.0d.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: openssl: Replace with openssl-1.0.2k [security fixes].

Fix CVE-2016-7055 and CVE-2017-{3731,3732}.

* gnu/packages/tls.scm (openssl)[replacement]: New field.
(openssl-1.0.2k): New variable.
(openssl-next)[replacement]: New field.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: text-editors.scm: Fix imports.

This is a followup to 5613ea79fccc5a5befafea313cb81010c5f5a8dd.

* gnu/packages/text-editors.scm: Import (gnu packages terminals).

gnu: Add kakoune.

* gnu/packages/text-editors.scm (kakoune): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: python-pbr: Update to 1.10.0.

* gnu/packages/python.scm (python-pbr): Update to 1.10.0.

gnu: python-wheel: Update to 0.30.0a0.

* gnu/packages/python.scm (python-wheel): Update to 0.30.0a0.

gnu: awscli: Update to 1.11.43.

* gnu/packages/python.scm (awscli): Update to 1.11.43.
[home-page]: Use HTTPS.

gnu: python-acme: Update to 0.10.2.

* gnu/packages/tls.scm (python-acme): Update to 0.10.2.

gnu: certbot: Update to 0.10.2.

* gnu/packages/tls.scm (certbot): Update to 0.10.2.
[description]: Use present tense; expand acronyms.

gnu: python-certifi: Update to 2017.1.23.

* gnu/packages/python.scm (python-certifi): Update to 2017.1.23.
[arguments]: Remove: run tests if they're ever added.
[home-page]: Fix or update.

gnu: Add xcalc.

* gnu/packages/xorg.scm (xcalc): New variable.

gnu: xf86-input-wacom: Update to 0.34.0.

* gnu/packages/xdisorg.scm (xf86-input-wacom): Update to 0.34.0.

gnu: dnscrypt-proxy: Update to 1.9.4.

* gnu/packages/dns.scm (dnscrypt-proxy): Update to 1.9.4.

bournish: Extend 'rm' command.

* guix/build/bournish.scm (rm-command): New procedure.
(%commands): Use it.
* tests/bournish.scm: Add tests for "rm" and "rm -r".

import: pypi: Don't add setuptools to propagated-inputs.

* guix/import/pypi.scm (compute-inputs): Don't add setuptools to the imported
  package's propagated-inputs.

copy: Use userauth-public-key/auto! for ssh authentification.

* guix/scripts/copy.scm (open-ssh-session): Replace userauth-agent! by
  userauth-public-key/auto!. This way, if ssh-agent is not run,
  default ssh key (~/.ssh/id_rsa) will be used as a fallback.

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

gnu: wine: Update to 2.0.

* gnu/packages/wine.scm (wine): Update to 2.0.

gnu: python-mistune: Fix source URI.

* gnu/packages/python.scm (python-mistune)[source]: Use pypi-uri.

gnu: python-redis: Update to 2.10.5.

* gnu/packages/python.scm (python-redis): Update to 2.10.5.
[source]: Use pypi-uri.

gnu: ruby-minitar: Update to 0.5.4-1.e25205ec.

Fixes the security-related issue reported at
http://seclists.org/oss-sec/2017/q1/178.

* gnu/packages/ruby.scm (ruby-minitar): Update to 0.5.4-1.e25205ec.
[source]: Use GitHub URL.

services: Export guix-configuration getters.

* gnu/services/base.scm (guix-configuration-*): Export.

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

gnu: Add stunnel.

* gnu/packages/web.scm (stunnel): New variable.

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

container: Pass through TERM when calling exec.

* guix/scripts/container/exec.scm (guix-container-exec): Capture the value of
  the TERM environment variable, and pass it through to the container.  This
  means some applications now work where they did not before (e.g. htop), and
  others have more functionality, providing that the terminal was capable of
  enabling that functionality in the first place.

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

services: Fix 'mkdir-p' in activation scripts.

* gnu/services/cups.scm (%cups-activation): Import (guix build utils).
* gnu/services/mail.scm (opensmtpd-activation): Idem.
* gnu/services/networking.scm (ntp-service-activation): Idem.
* gnu/services/spice.scm (spice-vdagent-activation): Idem.
* gnu/services/ssh.scm (openssh-activation): Idem.
  (dropbear-activation): Idem.
* gnu/services/vpn.scm (%openvpn-activation): Idem.

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

grafts: Do not pull derivation outputs not depended on.

Fixes <http://bugs.gnu.org/24886>.

Previously, the grafting derivation of, say, brdf-explorer would pull in
qt:doc even though brdf-explorer depends only on qt:out, not qt:doc.

* guix/grafts.scm (with-cache): Use 'vhash-assoc' and 'vhash-cons'
instead of 'vhash-assq' and 'vhash-consq'.
(cumulative-grafts): Pass #:outputs to 'graft-derivation/shallow'.  Use
OUTPUTS instead of (derivation-output-names drv).
(graft-derivation): Add #:outputs parameter; pass it to
'cumulative-grafts'.
* tests/grafts.scm (make-derivation-input): New variable.
("graft-derivation, replaced derivation has multiple outputs"): Make
sure P2:zzz is not part of the outputs of P3D.
("graft-derivation with #:outputs")
("graft-derivation, unused outputs not depended on"): New tests.

gnu: icecat: Add more fixes from upstream mozilla-esr45.

Includes fixes for CVE-2017-5373, CVE-2017-5375, CVE-2017-5376, CVE-2017-5378,
CVE-2017-5380, CVE-2017-5383, CVE-2017-5386, CVE-2017-5390, and CVE-2017-5396.

* gnu/packages/gnuzilla.scm (icecat)[source]: Rename existing patches to
reflect newly announced CVE assignments.  Add selected fixes from upstream
mozilla-esr45.

gnu: python-debian: Fix URL.

* gnu/packages/python.scm (python-debian)[source]: Use 'pypi-uri'.

gnu: emacs-seq: Update to 2.19.

* gnu/packages/emacs.scm (emacs-seq): Update to 2.19.

gnu: emacs-spinner: Update to 1.7.3.

* gnu/packages/emacs.scm (emacs-spinner): Update to 1.7.3.

gnu: emacs-auctex: Update to 11.90.0.

* gnu/packages/emacs.scm (emacs-auctex): Update to 11.90.0.

gnu: trash-cli: Update to 0.17.1.14.

* gnu/packages/shellutils.scm (trash-cli): Update to 0.17.1.14.

gnu: python2-pysqlite: Update to 2.8.3.

* gnu/packages/python.scm (python2-pysqlite): Update to 2.8.3.

gnu: python-cov-core: Fix & improve synopsis & description.

* gnu/packages/python.scm (python-cov-core)[synopsis]: Capitalise and add
‘coverage’ key-word.
[description]: Use @code.

gnu: python-email-validator: Update to 1.0.2.

* gnu/packages/python.scm (python-email-validator): Update to 1.0.2.

gnu: python-mistune: Update to 0.7.3.

* gnu/packages/python.scm (python-mistune): Update to 0.7.3.

gnu: python-tabulate: Update to 0.7.7.

* gnu/packages/python.scm (python-tabulate): Update to 0.7.7

gnu: python-paste: Update to 2.0.3.

* gnu/packages/python.scm (python-paste): Update to 2.0.3.
[arguments]: Re-enable tests.  They now pass even on Python 3.
[properties]: Remove.
(python2-paste): Use package-with-python2 directly now.

gnu: python-colorama: Fix typo in synopsis.

* gnu/packages/python.scm (python-colorama)[synopsis]: Capitalise.

gnu: python-colorama: Update to 0.3.7.

* gnu/packages/python.scm (python-colorama): Update to 0.3.7.

gnu: python-debian: Update to 0.1.28.

* gnu/packages/python.scm (python-debian): Update to 0.1.28.