profiles: Compute manual database entries in parallel.

This provides a 36% speedup on an SSD and 4 cores for the 1.5K man pages
in the manual database derivation of:

  guix environment --ad-hoc jupyter python-ipython python-ipykernel

* guix/profiles.scm (manual-database)[build]: Add 'print-string',
'print', and 'compute-entry'.  Change 'compute-entries' to call
'compute-entry' in 'n-par-map'.

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

gnu: coreutils: Fix cross-compilation to i586-pc-gnu.

Until now cross-compilation would fail with:

  i586-pc-gnu-ld: src/copy.o: undefined reference to symbol 'file_chauthor'
  i586-pc-gnu-ld: /gnu/store/…-glibc-cross-i586-pc-gnu-2.29/lib/libhurduser.so.0.3: error adding symbols: DSO missing from command line
  collect2: error: ld returned 1 exit status

* gnu/packages/base.scm (coreutils)[arguments]: When 'hurd-target?', add
 #:configure-flags.

ci: Fix 'evaluation-spec' binding.

* guix/ci.scm (<evaluation>)[spec]: Add "specification", which is what
the JSON field is actually called.

gnu: hwloc@2: Update to 2.2.0.

* gnu/packages/mpi.scm (hwloc-2): Update to 2.2.0.

gnu: hwloc@2: Skip test that fails on emulated hardware.

Works around <https://bugs.gnu.org/40342>.

* gnu/packages/mpi.scm (hwloc-2)[arguments]: Add
'skip-test-that-fails-on-qemu' phase.

gnu: scdoc: Update to 1.10.1.

* gnu/packages/man.scm (scdoc): Update to 1.10.1.

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

gnu: Order module imports in (gnu packages ntp).

This shouldn't cause any conflicts :-)

* gnu/packages/ntp.scm: Order module imports alphabetically.

gnu: sonic: Fix installation directories.

* gnu/packages/speech.scm (sonic)[arguments]: Replace erroneous use of
DESTDIR with PREFIX.  Add the required ‘rpath’ LDFLAGS together with a
‘respect-LDFLAGS’ phase.

gnu: hexchat: Fix typo in synopsis.

* gnu/packages/messaging.scm (hexchat)[synopsis]: Lowercase ‘client’.

gnu: gmime: Update to 3.2.7.

* gnu/packages/mail.scm (gmime): Update to 3.2.7.

gnu: font-rachana: Don't use unstable tarball.

* gnu/packages/fonts.scm (font-rachana)[source]: Use GIT-FETCH and
GIT-FILE-NAME.

gnu: font-rachana: Update to 7.0.3.

* gnu/packages/fonts.scm (font-rachana): Update to 7.0.3.

gnu: mumi: Update to 0.0.0-8.9f66dbc.

* gnu/packages/mail.scm (mumi): Update to 0.0.0-8.9f66dbc.

gnu: procenv: Make some inputs native & make multiline.

* gnu/packages/linux.scm (procenv)[native-inputs]: New field.
[inputs]: Move groff to native-inputs, move each remaining item on its own line.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>

gnu: nftables: Make some inputs native.

* gnu/packages/linux.scm (procenv)[native-inputs]: New field.
[inputs]: Move bison & flex to native-inputs.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>

gnu: sudo: Make some inputs native.

* gnu/packages/admin.scm (sudo)[native-inputs]: New field.
[inputs]: Move groff to native-inputs.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>

gnu: privoxy: Make some inputs native.

* gnu/packages/tor.scm (privoxy)[native-inputs]: New field.
[inputs]: Move autoconf & automake to native-inputs.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>

gnu: antlr3: Make antlr3-3.3 public.

This is done in preparation of adding Linphone, which transitively requires
antlr3-3.3 through its belle-sip dependency.

* gnu/packages/java.scm (antlr3): Make antlr3-3.3 public.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>

gnu: Add emacs-flycheck-elm.

* gnu/packages/emacs-xyz.scm (emacs-flycheck-elm): New variable.

pack: Adjust test to '--dry-run' changes.

This is a followup to 131f50cdc9dbb7183023f4dae759876a9e700bef.

* tests/guix-pack.sh: Use '--no-grafts' in conjunction with '-n' and '-d'.

guix package: Do not misdiagnose upgrades when there are propagated inputs.

Fixes <https://bugs.gnu.org/35872>.
Reported by Andy Tai <atai@atai.org>.

* guix/profiles.scm (list=?, manifest-entry=?): New procedures.
* guix/scripts/package.scm (transaction-upgrade-entry): In the '=' case,
use 'manifest-entry=?' to determine whether it's an upgrade.
* tests/packages.scm ("transaction-upgrade-entry, zero upgrades,
propagated inputs"): New test.

guix package: Add 'transaction-upgrade-entry' test.

* tests/packages.scm ("transaction-upgrade-entry, zero upgrades, equivalent package"):
New test.

profiles: 'lower-manifest-entry' recurses on dependencies.

* guix/profiles.scm (lower-manifest-entry)[recurse]: New procedure.
Call it on dependencies and set the 'dependencies' field accordingly.

guix package: 'transaction-upgrade-entry' swallows build requests.

Fixes a regression introduced in
131f50cdc9dbb7183023f4dae759876a9e700bef whereby the install/upgrade
message would not be displayed:

  $ guix upgrade -n
  2.1 MB would be downloaded:
     /gnu/store/…-something-1.2
     /gnu/store/…-its-dependency-2.3

This is because we'd directly abort from 'transaction-upgrade-entry' to
the build handler of 'build-notifier'.

* guix/scripts/package.scm (transaction-upgrade-entry): Call 'string=?'
expression in 'with-build-handler'.
* tests/packages.scm ("transaction-upgrade-entry, grafts"): New test.

guix package: 'transaction-upgrade-entry' uses 'lower-manifest-entry'.

* guix/profiles.scm (lower-manifest-entry): Export.
* guix/scripts/package.scm (transaction-upgrade-entry)[lower-manifest-entry*]
[upgrade]: New procedures.
Use 'lower-manifest-entry*' instead of 'package-derivation' to compute
the output file name of PKG.

gnu: emacs-stumpwm-mode: Bump revision.

* gnu/packages/emacs-xyz.scm (emacs-stumpwm-mode): Bump revision.  This is
a followup to 31ee29161c1b9451b68366e653c7858d8135f8d1.

gnu: Add emacs-dhall-mode.

* gnu/packages/emacs-xyz.scm (emacs-dhall-mode): New variable.

gnu: Add emacs-haskell-snippets.

* gnu/packages/emacs-xyz.scm (emacs-haskell-snippets): New variable.

gnu: Add stumpish.

* gnu/packages/wm.scm (stumpish): New variable.

gnu: Add sbcl-stumpwm-ttf-fonts.

* gnu/packages/wm.scm (sbcl-stumpwm-ttf-fonts): New variable.
* doc/guix-cookbook.texi (Customizing a Window Manager): Document
SBCL-STUMPWM-TTF-FONTS installation and configuration.

gnu: emacs-stumpwm-mode: Update to 0.0.1-1.dd5b037.

* gnu/packages/emacs-xyz.scm (emacs-stumpwm-mode): Update to 0.0.1-1.dd5b037.

gnu: Add sbcl-clx-truetype.

* gnu/packages/lisp-xyz.scm (sbcl-clx-truetype): New variable.

Revert "system: Move nanorc to XDG_CONFIG_HOME."

This reverts commit bd71818df31364bbd04f3f13b3bbb251636748b4.

This changed caused system reconfiguration to fail like this:

------
building /gnu/store/y1x8asbzw624ywgkpin35p1i4bqnyfy2-skel.drv...
Backtrace:
           4 (primitive-load "/gnu/store/2x7d0jsbgf2ndb5fsk0nj07rhsx?")
In ice-9/eval.scm:
    619:8  3 (_ #f)
In ice-9/boot-9.scm:
   260:13  2 (for-each #<procedure 7ffff6ad8100 at ice-9/eval.scm:3?> ?)
In guix/build/utils.scm:
   343:27  1 (_ "/gnu/store/ajrgkj1s9vdcq00drn703f4zj9dvfrsv-nanorc" ?)
In unknown file:
           0 (copy-file "/gnu/store/ajrgkj1s9vdcq00drn703f4zj9dvfrs?" ?)

ERROR: In procedure copy-file:
In procedure copy-file: No such file or directory
`/gnu/store/v1grsca743phw41lyf63dzmh9nz5jlpn-bash_profile' -> `.bash_profile'
`/gnu/store/xdsaw0mj6axj427hyi6ysrnsxi21n7d5-bashrc' -> `.bashrc'
`/gnu/store/6i0b236dyar78zc5k5hrj5dv3vr4zb9w-zprofile' -> `.zprofile'
`/gnu/store/ajrgkj1s9vdcq00drn703f4zj9dvfrsv-nanorc' -> `.config/nano/nanorc'
builder for `/gnu/store/y1x8asbzw624ywgkpin35p1i4bqnyfy2-skel.drv' failed with exit code 1
------

gnu: reprotest: Update to 0.7.14.

* gnu/packages/diffoscope (reprotest): Update to 0.7.14.
* gnu/packages/patches/reprotest-support-guix.patch: Remove file.
* gnu/local.mk [dist_patch_DATA]: Update accordingly.

gnu: diffoscope: Update to 138.

* gnu/packages/diffoscope (diffoscope): Update to 138.

gnu: Add python-tortoise-orm.

* gnu/packages/databases.scm (python-tortoise-orm): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add python-ciso8601.

* gnu/packages/time.scm (python-ciso8601): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add python-pypika.

Not to be confused with python-pika, which is a different package.

* gnu/packages/databases.scm (python-pypika): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add python-aiosqlite.

* gnu/packages/databases.scm (python-aiosqlite): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add python-aiounittest.

* gnu/packages/check.scm (python-aiounittest): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add emacs-flycheck-rust.

* gnu/packages/emacs-xyz.scm (emacs-flycheck-rust): New variable.

gnu: sbcl-cl-containers: Update to 20200328.

* gnu/packages/lisp-xyz.scm (sbcl-cl-containers): Update to 20200328.

gnu: sbcl-serapeum: Update to 20200330.

* gnu/packages/lisp-xyz.scm (sbcl-serapeum): Update to 20200330.

gnu: Add emacs-racer.

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

gnu: Add emacs-evil-escape.

* gnu/packages/emacs-xyz.scm (emacs-evil-escape): New variable.

system: Move nanorc to XDG_CONFIG_HOME.

* gnu/system/shadow.scm (default-skeletons): Move .nanorc to
.config/nano/nanorc.

gnu: Add emacs-company-coq.

* gnu/packages/emacs-xyz.scm (emacs-company-coq): New variable.

gnu: Add emacs-elm-mode.

* gnu/packages/emacs-xyz.scm (emacs-elm-mode): New variable.

gnu: Add emacs-caps-lock.

* gnu/packages/emacs-xyz.scm (emacs-caps-lock): New variable.

gnu: emacs-arduino-mode: Change to a maintained fork.

* gnu/packages/emacs-xyz.scm (emacs-arduino-mode)[source]: Update URI.
[arguments]: Add phase to fix obsolete warnings.
[home-page]: Update home page.

.gitignore: Ignore test results in tests/services.

This is a follow-up to commit d3e439e355284f136ff13eb3e6fffb4661552f3b.

* .gitignore: Add /tests/services/*.trs.

gnu: ath9k-htc-firmware: Correct home-page url.

* gnu/packages/firmware.scm (ath9k-htc-firmware)[home-page]: Correct url.

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

gnu: antlr3: Don't use unstable tarball.

* gnu/packages/java.scm (antlr3)[source]: Download using git-fetch.

gnu: java-javaewah: Don't use unstable tarball.

* gnu/packages/java.scm (java-javaewah)[source]: Download using
git-fetch.

gnu: java-jmock: Don't use unstable tarball.

* gnu/packages/java.scm (java-jmock)[source]: Download using git-fetch.

gnu: java-jmock-1: Don't use unstable tarball.

* gnu/packages/java.scm (java-jmock-1)[source]: Download using git-fetch.
[home-page]: Update home-page.

gnu: java-easymock: Don't use unstable tarball.

* gnu/packages/java.scm (java-easymock)[source]: Download using git-fetch.
[home-page]: Use https.

gnu: java-objenesis: Don't use unstable tarball.

* gnu/packages/java.scm (java-objenesis)[source]: Download using
git-fetch.

gnu: java-asm: Download using https.

* gnu/packages/java.scm (java-asm)[source]: Use https URL.

gnu: java-modello-core: Don't use unstable tarball.

* gnu/packages/java.scm (java-modello-core)[source]: Download using
git-fetch.

gnu: java-sisu-build-api: Don't use unstable tarball.

* gnu/packages/java.scm (java-sisu-build-api)[source]: Download using
git-fetch.

gnu: java-plexus-sec-dispatcher: Don't use unstable tarball.

* gnu/packages/java.scm (java-plexus-sec-dispatcher)[source]: Download
using git-fetch.

gnu: java-plexus-compiler-api: Don't use unstable tarball.

* gnu/packages/java.scm (java-plexus-compiler-api)[source]: Download
using git-fetch.

gnu: java-plexus-cipher: Don't use unstable tarball.

* gnu/packages/java.scm (java-plexus-cipher)[source]: Download using
git-fetch.

gnu: java-plexus-io: Don't use unstable tarball.

* gnu/packages/java.scm (java-plexus-io)[source]: Download using git-fetch.

gnu: java-plexus-container-default-bootstrap: Don't use unstable tarball.

* gnu/packages/java.scm (java-plexus-container-default-bootstrap)
[source]: Download using git-fetch.

gnu: java-plexus-classworlds: Don't use unstable tarball.

* gnu/packages/java.scm (java-plexus-classworlds)[source]: Download
using git-fetch.

gnu: java-plexus-interpolation: Don't use unstable tarball.

* gnu/packages/java.scm (java-plexus-interpolation)[source]: Download
using git-fetch.

gnu: java-plexus-utils: Don't use unstable tarball.

* gnu/packages/java.scm (java-plexus-utils)[source]: Download using
git-fetch.

gnu: java-junit: Don't use unstable tarball.

* gnu/packages/java.scm (java-junit)[source]: Download using git-fetch.
[home-page]: Update home-page.

gnu: java-hamcrest-core: Don't use unstable tarball.

* gnu/packages/java.scm (java-hamcrest-core)[source]: Download using
git-fetch.

gnu: gmp: Build fix for mingw.

* gnu/packages/multiprecision.scm (gmp) [arguments]: Add `setenv' phase for
mingw target.

gnu: commencement: Micro-optimize the package graph.

This removes 2 'add-data-to-store-cache' lookups.

* gnu/packages/commencement.scm (flex-boot0): Move (package (inherit …))
outside the 'propagated-inputs' field to avoid creating a new node each
time the field is accessed.

build-system/gnu: Optimize the package graph.

With this change, the output of:

  guix graph -e '(@@ (gnu packages commencement) coreutils-final)' |grep 'label = ' | wc -l

drops from 76 nodes to 68 nodes, and the "add-data-to-store-cache" hit
rate for:

  guix build libreoffice -d --no-grafts

drops from 3.9% to 2.6%.

* guix/build-system/gnu.scm (package-with-explicit-inputs*)[cut?]:
Adjust condition to exclude packages with build systems other than
GNU-BUILD-SYSTEM, such as 'ld-wrapper-boot3'.

packages: 'package->bag' keys cache by replacement.

* guix/packages.scm (package->bag): When GRAFT? is true, use PACKAGE's
replacement as the cache key.  Remove GRAFT? from the list of
secondary cache keys.

deploy: Use 'map/accumulate-builds'.

* guix/scripts/deploy.scm (guix-deploy): Use 'map/accumulate-builds'
instead of 'for-each'.

deploy: Factorize machine deployment.

* guix/scripts/deploy.scm (deploy-machine*): New procedure.
(guix-deploy): Call it in 'for-each'.

gnu: MPD: Update to 0.21.21.

* gnu/packages/mpd.scm (mpd): Update to 0.21.21.

gnu: Add parlatype.

* gnu/packages/gnome.scm (parlatype): New variable.

gnu: font-jetbrains-mono: Update to 1.0.3.

* gnu/packages/fonts.scm (font-jetbrains-mono): update to 1.0.3

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

gnu: emacs-helm-org-contacts: Update to 20200319.

* gnu/packages/emacs-xyz.scm (emacs-helm-org-contacts): update to 20200310

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

gnu: Add fogpad.

* gnu/packages/music.scm (fogpad): New variable.

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

gnu: Add regrader.

* gnu/packages/music.scm (regrader): New variable.

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

gnu: Add vl1-emulator.

* gnu/packages/music.scm (vl1-emulator): New variable.

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

gnu: python-typing-extensions: Update to 3.7.4.1.

* gnu/packages/python-xyz (python-typing-extensions): Update to 3.7.4.1.

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

gnu: emacs-next: Add harfbuzz (text shaping engine) to inputs.

* gnu/packages/emacs.scm (emacs-next)[inputs]: Add harfbuzz.
[arguments]: Enable harfbuzz in #:configure-flags.

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

gnu: ghc-esqueleto: Update to 3.3.1.1.

* gnu/packages/haskell-xyz.scm (ghc-esqueleto): Update to 3.3.1.1.

gnu: ghc-yesod-persistent: Update to 1.6.0.4.

* gnu/packages/haskell-web.scm (ghc-yesod-persistent): Update to 1.6.0.4.

gnu: ghc-scalpel: Fix typo in description.

* gnu/packages/haskell-web.scm (ghc-scalpel)[description]: Add punctuation.

gnu: ghc-persistent-sqlite: Update to 2.10.5.2.

* gnu/packages/haskell-xyz.scm (ghc-persistent-sqlite): Update to 2.10.5.2.
[inputs]: Remove GHC-OLD-LOCALE.
[native-inputs]: Add GHC-PERSISTENT-TEST, GHC-EXCEPTIONS, GHC-FAST-LOGGER,
GHC-HUNIT, GHC-QUICKCHECK, GHC-SYSTEM-FILEIO, and GHC-SYSTEM-FILEPATH.

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

gnu: Add ghc-persistent-test.

* gnu/packages/haskell-xyz.scm (ghc-persistent-test): New variable.

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

gnu: ghc-persistent-template: Update to 2.8.0.

* gnu/packages/haskell-xyz.scm (ghc-persistent-template): Update to 2.8.0.

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

gnu: ghc-persistent: Update to 2.10.4.

* gnu/packages/haskell-xyz.scm (ghc-persistent): Update to 2.10.4.

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

gnu: Add ghc-html-conduit.

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

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

gnu: Add ghc-pwstore-fast.

* gnu/packages/haskell-xyz.scm (ghc-pwstore-fast): New variable.

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

gnu: Add ghc-nonce.

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

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

gnu: Add ghc-basic-prelude.

* gnu/packages/haskell-xyz.scm (ghc-basic-prelude): New variable.

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

gnu: Add ghc-project-template.

* gnu/packages/haskell-xyz.scm (ghc-project-template): New variable.

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

gnu: Add emacs-hlint-refactor-mode.

* gnu/packages/emacs-xyz.scm (emacs-hlint-refactor-mode): New variable.

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

gnu: Add apply-refact.

* gnu/packages/haskell-apps.scm (apply-refact): New variable.

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