.gitignore: Re-add 'authenticate' script.

This is a follow-up to commit 0fe1fba4af41f267c4bb2c006fb37f42422ab703.

* .gitignore: s/guix-authenticate/authenticate/

gnu: Add missing patch to local.mk.

This line was removed by accident in 0a41123f01d5d2466d6f533be3644ac8c9a2bdf9.

* gnu/local.mk (dist_patch_DATA): Add "clang-3.5-libc-search-path.patch".

gnu: libwebp: Update to 1.0.1.

* gnu/packages/image.scm (libwebp): Update to 1.0.1.

gnu: fluidsynth: Update to 2.0.2.

* gnu/packages/audio.scm (fluidsynth): Update to 2.0.2.

gnu: python-joblib: Update home page.

* gnu/packages/python.scm (python-joblib)[home-page]: Update to current.

gnu: python-joblib: Update to 0.13.0.

* gnu/packages/python.scm (python-joblib): Update to 0.13.0.
[source](snippet): Remove.
[arguments]: Remove 'disable-failing-tests' phase.  Add custom check phase.
[native-inputs]: Remove PYTHON-NOSE, PYTHON-SPHINX, PYTHON-DOCUTILS and
PYTHON-NUMPYDOC.  Add PYTHON-PYTEST.

gnu: python-natsort: Update to 5.4.1.

* gnu/packages/python.scm (python-natsort): Update to 5.4.1.
[arguments]: Add #:modules.  Replace 'check' phase with custom pytest
invokation.
[native-inputs]: Remove PYTHON-PYTEST-CACHE, PYTHON-PYTEST-FLAKES and
PYTHON-PYTEST-PEP8.  Add PYTHON-PYTEST and PYTHON-PYTEST-MOCK.
(python2-natsort)[native-inputs]: Remove PYTHON2-ENUM34 and PYTHON2-MOCK.

gnu: z3: Update to 4.8.1.

* gnu/packages/maths.scm (z3): Update to 4.8.1.

gnu: z3: Fetch source using git.

* gnu/packages/maths.scm (z3)[source]: Change to GIT-FETCH.

gnu: xonotic: Symlink to xonotic data instead of copying into xonotic.

* gnu/packages/games.scm (xonotic)[arguments]: Modify the phase
'install-data so it creates a symlink to xonotic's data instead of
copying it into the xonotic package.

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

gnu: Add autotalent.

* gnu/packages/audio.scm (autotalent): New variable.

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

gnu: git-when-merged: Fix license.

Reported by Mark H Weaver <mhw@netris.org>.

* gnu/packages/version-control.scm (git-when-merged)[license]: Change to
GPL2+.

gnu: r-shinyfiles: Update to 0.7.2.

* gnu/packages/web.scm (r-shinyfiles): Update to 0.7.2.

gnu: r-mclust: Update to 5.4.2.

* gnu/packages/statistics.scm (r-mclust): Update to 5.4.2.

gnu: r-openssl: Update to 1.1.

* gnu/packages/statistics.scm (r-openssl): Update to 1.1.

gnu: r-biocmanager: Update to 1.30.4.

* gnu/packages/cran.scm (r-biocmanager): Update to 1.30.4.

gnu: r-ggeffects: Update to 0.7.0.

* gnu/packages/cran.scm (r-ggeffects): Update to 0.7.0.

gnu: r-sjstats: Update to 0.17.2.

* gnu/packages/cran.scm (r-sjstats): Update to 0.17.2.

gnu: r-ggpubr: Update to 0.2.

* gnu/packages/cran.scm (r-ggpubr): Update to 0.2.

gnu: r-recipes: Update to 0.1.4.

* gnu/packages/cran.scm (r-recipes): Update to 0.1.4.

gnu: r-dimred: Update to 0.2.2.

* gnu/packages/cran.scm (r-dimred): Update to 0.2.2.

gnu: r-ensembldb: Update to 2.6.2.

* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.2.

gnu: r-msnbase: Update to 2.8.1.

* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.1.

gnu: r-genomeinfodb: Update to 1.18.1.

* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.1.

gnu: Add clojure-algo-monads.

* gnu/packages/lisp.scm (clojure-algo-monads): New public variable.

gnu: Add clojure-tools-macro.

* gnu/packages/lisp.scm (clojure-tools-macro): New public variable.

gnu: Add clojure-algo-generic.

* gnu/packages/lisp.scm (clojure-algo-generic): New public variable.

gnu: Add clojure-core-match.

* gnu/packages/lisp.scm (clojure-core-match): New public variable.

gnu: Add clojure-instaparse.

* gnu/packages/lisp.scm (clojure-instaparse): New public variable.

build-system: Add 'clojure-build-system'.

* guix/build-system/clojure.scm, guix/build/clojure-build-system.scm: New
files.
* guix/build/clojure-utils.scm (@*, @@*): New macros.
(%source-dirs, %test-dirs, %compile-dir, %main-class, %omit-source?,
%aot-include, %aot-exclude, %tests?, %test-include, %test-exclude,
%clojure-regex): New variables.
(package-name->jar-names, canonicalize-relative-path, find-files*,
file-sans-extension, relative-path->clojure-lib-string, find-clojure-libs,
compiled-from?, include-list\exclude-list, eval-with-clojure, create-jar):
New procedures.
* Makefile.am (MODULES): Add them.
* doc/guix.texi (Build Systems): Document 'clojure-build-system'.

guix: Add clojure-utils.

* guix/build/clojure-utils.scm: New file.
* gnu/packages/lisp.scm (clojure)[arguments]: Use it.
* Makefile.am (MODULES): Add it.

gnu: clojure: Use (guix build java-utils) to simplify build phases.

* gnu/packages/lisp.scm (clojure)[arguments]: Use 'ant-build-javadoc',
'install-jars' and 'install-javadoc' in build phases.

gnu: clojure: Refactor to ensure there's a single list of libraries.

This avoids having to update multiple lists.

* gnu/packages/lisp.scm (clojure)[native-inputs]: Use new local variable.
[arguments]: Adjust build phases accordingly.

gnu: clojure: Remove 'remove-archives' snippet.

This is no longer needed since clojure now makes official source releases
in github.

* gnu/packages/lisp.scm (clojure)[source]: Remove it.
[native-inputs]: Remove it in 'submodule'.
[arguments]: Adjust 'unpack-submodule-sources' phase accordingly.

gnu: clojure: Move from java to lisp.

* gnu/packages/java.scm (clojure): Move from here...
* gnu/packages/lisp.scm (clojure): ...to here.

gnu: python-kivy: Update to 1.10.1

* gnu/packages/python.scm (python-kivy): Update to 1.10.1.

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

gnu: help2man: Add 1.47.8.

* gnu/packages/man.scm (help2man/latest): New variable.

gnu: fuse-exfat: Update to 1.3.0.

* gnu/packages/linux.scm (fuse-exfat): Update to 1.3.0.

gnu: diffoscope: Update to 105.

* gnu/packages/package-management.scm (diffoscope): Update to 105.

guix system: Fix 'init'.

Fixes a regression introduced in
52ee4479ef26826a53b9929cd00ca7738be687b1, whereby 'install' would now be
passed a <computed-file> object instead of a derivation.

* guix/scripts/system.scm (install): Call 'lower-object' on BOOTCFG.

gnu: Add libfdk 'FDK AAC' library.

* gnu/packages/audio.scm (libfdk): New variable.

guix system: Clarify 'perform-action'.

* guix/scripts/system.scm (perform-action): Move non-monadic local
variables outside the 'mlet' form.

guix system: De-monadify bootloader installation script.

* guix/scripts/system.scm (bootloader-installer-derivation): Rename
to...
(bootloader-installer-script): ... this.  Use 'scheme-file' instead of
'gexp->file'.
(perform-action): Adjust accordingly.  Move 'lower-object' call to the
point where DRVS is computed.

guix system: Simplify bootloader package handling.

* guix/scripts/system.scm (perform-action): Remove 'bootloader-package'
variable.  Pass (bootloader-package bootloader) as the 2nd argument to
'bootloader-installer-derivation'.  Remove BOOTLOADER-PACKAGE from DRVS
since it's redundant.

vm: Remove explicit calls to 'operating-system-derivation'.

* gnu/system/vm.scm (iso9660-image): Change 'os-drv' to 'os' and remove
call to 'operating-system-derivation'.
(system-qemu-image): Likewise.
(system-qemu-image/shared-store): Likewise.

system: De-monadify 'operating-system-bootcfg'.

* gnu/system.scm (operating-system-bootcfg): Remove 'mlet*' and
'lower-object' call.
* gnu/system/vm.scm (system-disk-image)
(system-qemu-image/shared-store): Adjust accordingly.
* guix/scripts/system.scm (perform-action): Add 'lower-object' call for
BOOTCFG.

system: Please Emacs.

* gnu/system.scm (operating-system-bootcfg): Remove opening parenthesis
at the beginning of the line in the docstring to placate Emacs.

system: De-monadify 'operating-system-boot-parameters'.

* gnu/system.scm (operating-system-boot-parameters): Turn to direct
style instead of monadic.
(operating-system-bootcfg): Adjust accordingly.
(operating-system-boot-parameters-file): Likewise.

linux-initrd: Return file-like objects instead of monadic values.

This is an incompatible change visible to users via the 'initrd' field
of 'operating-system'.  However, assuming the user's 'initrd' value
tail-calls to 'raw-initrd' or 'base-initrd', the switch to non-monadic
style is invisible.

* gnu/system/linux-initrd.scm (expression->initrd): Use 'computed-file'
instead of 'gexp->derivation'.
(raw-initrd, base-initrd): Adjust docstring to mention non-monadic
return.
* gnu/system/vm.scm (expression->derivation-in-linux-vm): Adjust
accordingly.
* gnu/system.scm (operating-system-directory-base-entries)
(operating-system-initrd-file)
(operating-system-boot-parameters): Adjust accordingly.
* doc/guix.texi (operating-system Reference)
(Initial RAM Disk): Update.

system: Simplify kernel argument handling.

* gnu/system.scm (bootable-kernel-arguments): Remove 'kernel-arguments'
parameter and return only the base list of kernel arguments.  Rename
'system.drv' to 'system'.
(operating-system-kernel-arguments): Adjust accordingly and remove
'system.drv' parameter.
(read-boot-parameters-file): Adjust accordingly.  Remove 'if params'
since dominating code assumed PARAMS is always true.
(operating-system-boot-parameters): Remove 'system.drv' parameter; add
 #:system-kernel-arguments? instead and honor it.
(operating-system-bootcfg): Adjust accordingly.
(operating-system-boot-parameters-file): Likewise.
* gnu/system/vm.scm (system-qemu-image/shared-store-script): Remove
'os-drv' variable.  Adjust call to 'operating-system-kernel-arguments'.

bootloader: De-monadify configuration file generators.

* gnu/bootloader/extlinux.scm: Remove unneeded imports.
(extlinux-configuration-file): Use 'computed-file' instead of
'gexp->derivation'.
* gnu/bootloader/grub.scm (svg->png): Likewise.
(grub-background-image, eye-candy): Adjust accordingly, return
non-monadically.
(grub-configuration-file): Likewise, and use 'computed-file' instead of
'gexp->derivation'.
* gnu/bootloader/u-boot.scm: Remove unneeded imports.
* gnu/system.scm: Add 'lower-object' call.

activation: Aways pass '-d HOME' to 'useradd'.

Fixes <https://bugs.gnu.org/33422>.
Reported by fps.

* gnu/build/activation.scm (add-user): Always pass "-d HOME" when HOME
is true.  Pass "--create-home" only when HOME, CREATE-HOME?, and SYSTEM?
are true.
(activate-users+groups): Pass #:create-home? create-home? to
'ensure-user'.
* gnu/tests/base.scm (run-basic-test)["accounts"]: Test 'passwd:dir' as
well.

gnu: ocaml: Update to 4.7.0.

Update ocaml to the latest version and fixes dependent packages by
updating them or by adding new inputs, such as ocaml-num and ocamlbuild,
that were removed from the core ocaml package. Rename packages that
cannot be built with the new compiler with an ocaml4.02 prefix. Add
ocaml4.02 dependencies.

* gnu/packages/ocaml.scm (ocaml): Update to 4.7.0.
(ocaml-4.02, ocamlbuild, camlp4-4.02, ocaml-num, ocaml4.02-menhir)
(ocaml4.02-lablgtk, ocaml4.02-findlib, ocaml4.02-ounit, ocaml4.02-camlzip)
(ocaml4.02-ocamlmod, ocaml4.02-zarith, ocaml4.02-qcheck, ocaml4.02-qtest)
(ocaml4.02-stringext, ocaml4.02-bisect, dune, ocaml-migrate-parsetree)
(ocaml-ppx-tools-versioned, ocaml-ppx-tools-versioned)
(ocaml4.02-bitstring, ocaml4.02-result, ocaml4.02-topkg, ocaml4.02-rresult)
(ocaml4.02-sqlite3, ocaml4.02-csv, ocaml4.02-mtime, ocaml4.02-cmdliner)
(ocaml4.02-fmt, ocaml4.02-astring, ocaml4.02-alcotest, ocaml4.02-ppx-tools)
(ocaml4.02-react, ocaml4.02-ssl, ocaml4.02-lwt, ocaml-lwt-log)
(ocaml4.02-lwt-log, ocaml4.02-logs, ocaml4.02-fpath, ocaml4.02-bos)
(ocaml4.02-xmlm, ocaml4.02-ulex, ocaml4.02-uchar, ocaml4.02-uutf)
(ocaml4.02-jsonm, ocaml4.02-ocurl, ocaml4.02-base64, ocaml4.02-omake)
(ocaml4.02-batteries, ocaml4.02-pcre, ocaml4.02-oasis)
(ocaml4.02-js-build-tools, ocaml4.02-cppo, ocaml-seq, ocaml4.02-seq)
(ocaml4.02-re, ocaml4.02-ocplib-endian, ocaml4.02-easy-format)
(ocaml4.02-piqilib, ocaml4.02-uuidm, ocaml4.02-graph, ocaml4.02-piqi)
(ocaml4.02-camomile, ocaml4.02-zed, ocaml4.02-lambda-term): New packages.
(opam): Update to 2.0.0.
(camlp4): Update to 4.07+1.
(camlp5): Update to 7.06.
(hevea): Update to 2.32.
(coq)[inputs]: Add ocaml-num.
(emacs-tuareg): Update to 2.2.0.
(ocaml-menhir)[native-inputs]: Add ocamlbuild.
(ocaml-lablgtk): Update to 2.18.6.
(unison)[inputs]: Use ocaml-4.02.
(ocaml-findlib): Update to 1.8.0.
(ocaml-ounit)[native-inputs]: Add ocamlbuild.
(ocamlmod): Update to 0.0.9.
(ocaml-frontc)[arguments]: Use ocaml-4.02.
(ocaml-qcheck)[native-inputs]: Add ocamlbuild.
(ocaml-qtest)[native-inputs]: Remove ocaml-findlib and add ocamlbuild.
(ocaml-stringext)[native-inputs]: Add ocamlbuild.
(ocaml-bisect): Update to 1.3.1.
(ocaml4.01-bisect): Downgrade to 1.3.
(ocaml-bitstring): Update to 3.1.0.
(ocaml-topkg)[native-inputs]: Add ocamlbuild.
(ocaml-rresult)[native-inputs]: Add ocamlbuild.
(ocaml-sqlite3)[native-inputs]: Add ocamlbuild.
(ocaml-csv)[native-inputs]: Add ocamlbuild.
(ocaml-mtime)[native-inputs]: Add ocamlbuild.
(ocaml-cmdliner)[native-inputs]: Add ocamlbuild.
(ocaml-fmt)[native-inputs]: Add ocamlbuild.
(ocaml-astring)[native-inputs]: Add ocamlbuild.
(ocaml-alcotest)[native-inputs]: Add ocamlbuild.
(ocaml-ppx-tools)[native-inputs]: Add ocamlbuild.
(ocaml-react)[native-inputs]: Add ocamlbuild.
(ocaml-ssl)[arguments]: Return #t in phases.
(ocaml-lwt): Update to 4.1.0.
(ocaml-logs)[native-inputs]: Add ocamlbuild.
(ocaml-fpath)[native-inputs]: Add ocamlbuild.
(ocaml-bos)[native-inputs]: Add ocamlbuild.
(ocaml-xmlm): Update to 1.3.0.
(ocaml-ulex): Update to 1.2.0.
(ocaml-uchar)[native-inputs]: Add ocamlbuild.
(ocaml-uutf): Update to 1.0.1.
(ocaml-jsonm): Update to 1.0.1.
(ocaml-ocurl): Update to 0.8.2.
(ocaml-base64)[native-inputs]: Add ocamlbuild.
(ocamlify)[native-inputs]: Use ocaml-4.02.
(omake): Update to 0.10.3.
(ocaml-batteries): Update to 2.9.0.
(ocaml-pcre)[native-inputs]: Add ocamlbuild.
(ocaml-expect): Update 0.0.6.
(ocaml4.02-fileutils): Update to 0.5.3.
(ocaml-oasis): Update 0.4.11.
(ocaml-js-build-tools)[native-inputs]: Add ocamlbuild.
(ocaml-bin-prot): Rename to ocaml4.02-bin-prot.
(ocaml-fieldslib): Rename to ocaml4.02-fieldslib.
(ocaml-ppx-core): Rename to ocaml4.02-ppx-core.
(ocaml-ppx-optcomp): Rename to ocaml4.02-ppx-optcomp.
(ocaml-ppx-driver): Rename to ocaml4.02-ppx-driver.
(ocaml-cppo): Update to 1.6.5.
(ocaml-ppx-deriving): Rename to ocaml4.02-ppx-deriving.
(ocaml-ppx-type-conv): Rename to ocaml4.02-ppx-type-conv.
(ocaml-ppx-inline-test): Rename to ocaml4.02-ppx-inline-test.
(ocaml-ppx-bench): Rename to ocaml4.02-ppx-bench.
(ocaml-ppx-compare): Rename to ocaml4.02-ppx-compare.
(ocaml-sexplib): Rename to ocaml4.02-sexplib.
(ocaml-typerep): Rename to ocaml4.02-typerep.
(ocaml-variantslib): Rename to ocaml4.02-variantslib.
(ocaml-ppx-sexp-conv): Rename to ocaml4.02-ppx-sexp-conv.
(ocaml-ppx-variants-conv): Rename to ocaml4.02-ppx-variants-conv.
(ocaml-ppx-here): Rename to ocaml4.02-ppx-here.
(ocaml-ppx-assert): Rename to ocaml4.02-ppx-assert.
(ocaml-ppx-enumerate): Rename to ocaml4.02-ppx-enumerate.
(ocaml-ppx-let): Rename to ocaml4.02-ppx-let.
(ocaml-ppx-typerep-conv): Rename to ocaml4.02-ppx-typerep-conv.
(ocaml-ppx-sexp-value): Rename to ocaml4.02-ppx-sexp-value.
(ocaml-ppx-pipebang): Rename to ocaml4.02-ppx-pipebang.
(ocaml-ppx-bin-prot): Rename to ocaml4.02-ppx-bin-prot.
(ocaml-ppx-fail): Rename to ocaml4.02-ppx-fail.
(ocaml-ppx-custom-printf): Rename to ocaml4.02-ppx-custom-printf.
(ocaml-ppx-sexp-message): Rename to ocaml4.02-ppx-sexp-message.
(ocaml-ppx-fields-conv): Rename to ocaml4.02-ppx-fields-conv.
(ocaml-re): Update to 1.8.0.
(ocaml-ppx-expect): Rename to ocaml4.02-ppx-expect.
(ocaml-ppx-jane): Rename to ocaml4.02-ppx-jane.
(ocaml-core-kernel): Rename to ocaml4.02-core-kernel.
(ocaml-async-kernel): Rename to ocaml4.02-async-kernel.
(ocaml-async-rpc-kernel): Rename to ocaml4.02-async-rpc-kernel.
(ocaml-core): Rename to ocaml4.02-core.
(ocaml-async-unix): Rename to ocaml4.02-async-unix.
(ocaml-async-extra): Rename to ocaml4.02-async-extra.
(ocaml-async): Rename to ocaml4.02-async.
(ocaml-ocplib-endian)[native-inputs]: Update to 1.0.
(ocaml-cstruct): Rename to ocaml4.02-cstruct.
(ocaml-hex): Rename to ocaml4.02-hex.
(ocaml-ezjsonm): Rename to ocaml4.02-ezjsonm.
(ocaml-uri): Rename to ocaml4.02-uri.
(optcomp): Use ocaml-4.02.
(ocaml-piqilib): Update to 0.6.14.
(ocaml-uuidm)[native-inputs]: Add ocamlbuild.
(ocaml-graph): Update to 1.8.8.
(ocaml-piqi): Update to 0.7.6.
(bap): Update to 1.3.0.
(ocaml-camomile): Update to 1.0.1.
(ocaml-jbuilder): Use ocaml-4.02.
(ocaml-lambda-term): Update to 1.13.
(ocaml-utop): Update to 2.2.0.
(ocaml-integers)[native-inputs]: Add ocamlbuild.
(ocaml-ctypes): Update to 0.14.0.
(ocaml-ocb-stubblr)[native-inputs]: Add ocamlbuild.
(ocaml-tsdl)[native-inputs]: Add ocamlbuild.
* gnu/packages/machine-learning.scm (ocaml-mcl): Use ocaml-4.02.
* gnu/packages/maths.scm (cubicle): Update to 1.1.2.
* gnu/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch:
Update patch.
* guix/build-system/ocaml.scm: (default-ocaml4.02, default-ocaml4.02-findlib)
(package-with-ocaml4.02, strip-ocaml4.02-variant): New variables.

build-system/ocaml: Use invoke and return #t.

* guix/build/ocaml-build-system.scm (configure, build, check, install)
(prepare-install): Use invoke and return #t.

gnu: maxima: Fix tests on i686 and x86_64.

* gnu/packages/maths.scm (maxima)[arguments]: Replace check phase.

gnu: ccl: Include x86-headers and remove missing "contrib" folder.

* gnu/packages/lisp.scm (ccl): Include x86-headers and remove missing "contrib" folder.

gnu: mesa: Stay on RTTI-less LLVM.

* gnu/packages/llvm.scm (llvm-without-rtti): New public variable.
* gnu/packages/gl.scm (mesa)[inputs]: Use that instead of LLVM.

gnu: Add ClamAV.

* gnu/packages/antivirus.scm: New file.
* gnu/packages/patches/clamav-system-tomsfastmath.patch,
gnu/packages/patches/clamav-config-llvm-libs.patch: New files.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add new module.
(dist_patch_DATA): Add patches.

Co-authored-by: Christopher Baines <mail@cbaines.net>

gnu: Add TomsFastMath.

* gnu/packages/multiprecision.scm (tomsfastmath): New variable.
* gnu/packages/patches/tomsfastmath-constness.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Add it.

llvm: Build with RTTI by default.

Increases size of llvm@6 by 2.5MiB (2.5%), but saves building specialized
llvm's with rtti enabled for packages that require RTTI when linking with the
llvm libraries.

* gnu/packages/llvm.scm (llvm-3.8-with-rtti): Remove variable.
(llvm)[arguments]: Add '-DLLVM_REQUIRES_RTTI=1' to #:configure-flags.
* gnu/packages/audio.scm (faust-2)[native-inputs]:
'llvm-3.8-with-rtti' -> 'llvm-3.8'.

gnu: u-boot: Update to 2018.11.

* gnu/packages/bootloaders.scm (u-boot): Update to 2018.11.
(u-boot)[native-inputs]: Add lz4.

doc: Mention that ./pre-inst-env is generated.

Suggested by swedebugia <swedebugia@riseup.net>.

* doc/contributing.texi (Running Guix Before It Is Installed): Mention
that ./pre-inst-env is generated.

gnu: Add git-when-merged.

* gnu/packages/version-control.scm (git-when-merged): New variable.

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

gnu: Add caps-plugins-lv2.

* gnu/packages/audio.scm (caps-plugins-lv2): New variable.

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

doc: Recommend pool.sks-keyservers.net.

pgp.mit.edu appears to be unreliable these days.

* doc/guix.texi (KEY-SERVER): New variable.
(Binary Installation, USB Stick and DVD Installation): Use it in 'gpg
--recv-keys' example.

gnu: tiled: Update to 1.2.1.

* gnu/packages/game-development.scm (tiled): Update to 1.2.1.

progress: Do not display the last 0B transfer when size is unknown.

* guix/progress.scm (display-download-progress): Don't display anything when
both SIZE and TRANSFERRED are null.

progress: Fix crash because of division by zero.

* guix/progress.scm (display-download-progress): Handle the case where SIZE is
null.

guile: newt: Update revision to 2.

* gnu/packages/guile.scm (guile-newt): Update revision to 2.

gnu: Add cmh.

* gnu/packages/algebra.scm (cmh): New variable.

gnu: gp2c: Update to 0.0.11pl1.

* gnu/packages/algebra.scm (gp2c): Update to 0.0.11pl1.

gnu: emacs-realgud: Patch configure.ac to repair the build.

This fixes https://bugs.gnu.org/33196, a build problem caused by a defective
Elisp snippet in a check in configure.ac.

* gnu/packages/patches/emacs-realgud-fix-configure-ac.patch: Add patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/emacs.scm (emacs-realgud)[source]: Use it.

gnu: Add nanopolish.

* gnu/packages/bioinformatics.scm (nanopolish): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

doc: Fix typo in connman config.

* doc/guix.texi (Networking Services): Fix typo in connman config
"disable-vpn?" parameter documentation, semantic is inverted.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: sambamba: Update to 0.6.8.

* gnu/packages/bioinformatics.scm (sambamba): Update to 0.6.8.

gnu: linux-libre: Update to 4.19.2.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.19.2.
(%linux-libre-hash): Update hash.

gnu: linux-libre@4.14: Update to 4.14.81.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.81.
(%linux-libre-4.14-hash): Update hash.

gnu: linux-libre@4.9: Update to 4.9.137.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.137.

gnu: Add fenics.

* gnu/packages/simulation.scm (fenics): New variable.

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

gnu: Add fenics-dolfin.

* gnu/packages/simulation.scm (fenics-dolfin): New variable.

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

gnu: Add python-fenics-ffc.

* gnu/packages/simulation.scm (python-fenics-ffc): New variable.

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

gnu: Add python-fenics-fiat.

* gnu/packages/simulation.scm (python-fenics-fiat): New variable.

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

gnu: Add python-fenics-ufl.

* gnu/packages/simulation.scm (python-fenics-ufl): New variable.

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

gnu: Add python-fenics-dijitso.

* gnu/packages/simulation.scm (python-fenics-dijitso): New varaible.

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

gnu: Add python-slepc4py.

* gnu/packages/maths.scm (python-slepc4py): New variable.

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

gnu: Add python-petsc4py.

* gnu/packages/maths.scm (python-petsc4py): New variable.

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

gnu: Add python-mpi4py.

* gnu/packages/mpi.scm (python-mpi4py): New variable.

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

daemon: Install 'authenticate' script under LIBEXECDIR/guix.

That way it is handled in the same way as other helper scripts.

* nix/scripts/guix-authenticate.in: Rename to...
* nix/scripts/authenticate.in: ... this.
* config-daemon.ac: Adjust accordingly.
* nix/local.mk (libstore_a_CPPFLAGS): Remove -DOPENSSL_PATH.
(nodist_libexec_SCRIPTS): Remove.
(nodist_pkglibexec_SCRIPTS): New variable.
* nix/nix-daemon/guix-daemon.cc (main): Remove 'setenv' call for
"PATH".
* nix/libstore/local-store.cc (runAuthenticationProgram): New function.
(LocalStore::exportPath, LocalStore::importPath): Use it instead of
'runProgram' and OPENSSL_PATH.

gnu: guix-daemon: Install 'guix-authenticate'.

Fixes <https://bugs.gnu.org/33368>.
Reported by Konrad Hinsen <konrad.hinsen@fastmail.net>.

* gnu/packages/package-management.scm (guix-daemon)[arguments]: In
'install' phase, build "install-nodist_libexecSCRIPTS" target to install
'guix-authenticate'.

download: Access content-addressed mirrors over HTTPS.

Bug <http://bugs.gnu.org/22774> is no longer relevant now that we use
"builtin:download" exclusively.

* guix/download.scm (%content-addressed-mirrors): Use "https", not
"http".

download: Add Software Heritage as a content-addressed mirror.

* guix/download.scm (%content-addressed-mirrors): Add Software
Heritage.

gnu: xf86-video-r128: Update to 6.12.0.

* gnu/packages/xorg.scm (xf86-video-r128): Update to 6.12.0.

gnu: mtools: Update to 4.0.20.

* gnu/packages/mtools.scm (mtools): Update to 4.0.20.
[source](uri): Change to 'bz2' compressed tarball.

gnu: nano: Update to 3.2.

* gnu/packages/nano.scm (nano): Update to 3.2.

gnu: sudo: Update to 1.8.26.

* gnu/packages/admin.scm (sudo): Update to 1.8.26.

gnu: feh: Update to 3.0.

* gnu/packages/image-viewers.scm (feh): Update to 3.0.

gnu: Add jamm.

* gnu/packages/bioinformatics.scm (jamm): New variable.

gnu: Add r-ouch.

* gnu/packages/cran.scm (r-ouch): New variable.

gnu: Add r-activity.

* gnu/packages/cran.scm (r-activity): New variable.

gnu: Add r-circular.

* gnu/packages/cran.scm (r-circular): New variable.