gnu: Add ocaml4.07-alcotest.

* gnu/packages/ocaml.scm (ocaml4.07-alcotest): New variable.

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

gnu: Add ocaml4.07-re.

* gnu/packages/ocaml.scm (ocaml4.07-re): New variable.

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

gnu: Add texlive-latex-textpos.

* gnu/packages/tex.scm (texlive-latex-textpos): New variable.

gnu: Add texlive-translator.

* gnu/packages/tex.scm (texlive-translator): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>

home: Adjust 'guix home import' test for shell aliases.

This is a followup to 4b96998292442ec03024481c911d88f86c7c36b5.

* tests/home-import.scm (match-home-environment-bash-service): Match the
'aliases' field.

home: services: bash: Emit 'extra-content' first again.

Fixes a regression introduced in
4b96998292442ec03024481c911d88f86c7c36b5 that would less to a
'tests/guix-home.sh' failure.

* gnu/home/services/shells.scm (add-bash-configuration)[file-if-not-empty]:
Move EXTRA-CONTENT first.

home: services: Fix typo.

Reinstates 4dcec60fa6a93dbc93bef2cdb91e3633c705579e, minus the
regression it introduced.

* gnu/home/services.scm (compute-on-first-login-script): Use
'program-file', not 'gexp->script'.

daemon: Do not deduplicate files smaller than 8 KiB.

Files smaller than 8 KiB typically represent ~70% of the entries in
/gnu/store/.links but only contribute to ~4% of the space savings
afforded by deduplication.

Not considering these files for deduplication speeds up file insertion
in the store and, more importantly, leaves 'removeUnusedLinks' with
fewer entries to traverse, thereby speeding it up proportionally.

Partly fixes <https://issues.guix.gnu.org/24937>.

* config-daemon.ac: Remove symlink hard link check and CAN_LINK_SYMLINK
definition.
* guix/store/deduplication.scm (%deduplication-minimum-size): New
variable.
(deduplicate)[loop]: Do not recurse when FILE's size is below
%DEDUPLICATION-MINIMUM-SIZE.
(dump-port): New procedure.
(dump-file/deduplicate)[hash]: Turn into...
[dump-and-compute-hash]: ... this thunk.
Call 'deduplicate' only when SIZE is greater than
%DEDUPLICATION-MINIMUM-SIZE; otherwise call 'dump-port'.
* nix/libstore/gc.cc (LocalStore::removeUnusedLinks): Drop files where
st.st_size < deduplicationMinSize.
* nix/libstore/local-store.hh (deduplicationMinSize): New declaration.
* nix/libstore/optimise-store.cc (deduplicationMinSize): New variable.
(LocalStore::optimisePath_): Return when PATH is a symlink or smaller
than 'deduplicationMinSize'.
* tests/derivations.scm ("identical files are deduplicated"): Produce
files bigger than %DEDUPLICATION-MINIMUM-SIZE.
* tests/nar.scm ("restore-file-set with directories (signed, valid)"):
Likewise.
* tests/store-deduplication.scm ("deduplicate, below %deduplication-minimum-size"):
New test.
("deduplicate", "deduplicate, ENOSPC"): Produce files bigger than
%DEDUPLICATION-MINIMUM-SIZE.
* tests/store.scm ("substitute, deduplication"): Likewise.

tests: Factorize 'file=?'.

* guix/tests.scm (file=?): Add optional 'stat' parameter.  Add fast
patch comparing inode numbers.
* tests/gexp.scm ("imported-files with file-like objects"): Remove
'file=?' procedure and use the one from (guix tests).

services: openssh: Collect all keys for all users.

Fixes <https://issues.guix.gnu.org/51487>

* gnu/services/ssh.scm (extend-openssh-authorized-keys): ensure that no key is forgotten.

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

Revert "home-services: Demonadify 'on-first-login' handling."

This commit breaks building guix home
guix home: error: reference to invalid output 'out' of derivation \
    '/gnu/store/86zc4rijsswmfqnaq8rwixcxjl2zyl1c-on-first-login.drv'

This reverts commit 4dcec60fa6a93dbc93bef2cdb91e3633c705579e.

gnu: Add julia-sundials-jull

* gnu/packages/julia-jll.scm (julia-sundials-jll): New variable.
* gnu/packages/maths.scm (sundials-julia): New variable.

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

Revert "gnu: Add cl-https-everywhere."

With thanks to jlicht on IRC:
sbcl-package->cl-source-package assumes all inputs are packages
which isn't the case here.

This reverts commit e31d48d8db09e723727eeadbeea22d677f5d1d52.

gnu: julia-pycall: Update to 1.92.5.

* gnu/packages/julia-xyz.scm (julia-pycall): Update to 1.92.5.

build-system/julia: Enable Julia Pkg to find installed packages.

Julia's built-in package manager (Pkg) looks for packages in
JULIA_DEPOT_PATH/packages/PACKAGENAME/XXXX, where XXXX is a string
encoding package UUID and SHA1 of files.  The link-depot phase creates
a link at the correct location to allow Pkg to find packages that were
already installed by Guix.

* guix/build/julia-build-system.scm (link-depot): New phase.
(%package-path): Modified package path from packages/ to loadpath/.
(project.toml->uuid): New procedure, retrive package uuid from TOML file.
(precompile, check): Adjust to the change in paths.
(%standard-phases): Add link-depot phase.
(julia-build): Add julia-package-uuid keyword.
* guix/build-system/julia.scm (julia-build): Also use the
julia-package-uuid keyword.
* gnu/packages/julia-jll.scm (julia-bzip2-jll, julia-cairo-jll,
julia-compilersupportlibraries-jll, julia-expat-jll, julia-ffmpeg-jll,
julia-fontconfig-jll, julia-freetype2-jll, julia-fribidi-jll,
julia-gettext-jll, julia-glib-jll, julia-gr-jll, julia-gumbo-jll,
julia-imagemagick-jll, julia-jllwrappers-jll, julia-jpegturbo-jll,
julia-lame-jll, julia-libass-jll, julia-libfdk-aac-jll,
julia-libffi-jll, julia-libgcrypt-jll, julia-libglvnd-jll,
julia-libgpg-error-jll, juli-libiconv-jll, julia-libmount-jll,
julia-libpng-jll, julia-libsass-jll, julia-libtiff-jll,
julia-libuuid-jll, julia-libvorbis-jll, julia-lzo-jll,
julia-mbedtls-jll, julia-ogg-jll, julia-openspecfun-jll,
julia-openssl-jll, julia-opus-jll, julia-pcre-jll, julia-pixman-jll,
julia-qt5base-jll, julia-wayland-jll, julia-wayland-protocols-jll,
julia-x264-jll, julia-x265-jll, julia-xkbcommon-jll, julia-xml2-jll,
julia-xorg-libpthread-stubs-jll, julia-xorg-libx11-jll,
julia-xorg-libxau-jll, julia-xorg-libxcb-jll, julia-xorg-libxcursor-jll,
julia-xorg-libxdmcp-jll, julia-xorg-libxext-jll,
julia-xorg-libxfixes-jll, julia-xorg-libxi-jll,
julia-xorg-libxinerama-jll, julia-xorg-libxkbfile-jll,
julia-xorg-libxrandr-jll, julia-xorg-libxrender-jll,
julia-xorg-xcb-util-jll, julia-xorg-xcb-util-keysyms-jll,
julia-xorg-xcb-util-renderutil-jll, julia-xorg-xcb-util-wm-jll,
julia-xorg-xkbcomp-jll, julia-xorg-xkeyboard-config-jll,
julia-xorg-xtrans-jll, julia-xslt-jll, julia-zlib-jll, julia-zstd-jll)
[argument]: Adjust the order of the phases to the change in the
julia-build-system.
* gnu/packages/julia-xyz.scm (julia-bufferedstreams, julia-calculus,
julia-dataframes, julia-datavalues, julia-distances, julia-documenter,
julia-dualnumbers, julia-ellipsisnotation, julia-expronicon,
julia-fileio, julia-fixedpointnumbers, julia-functionwrappers,
julia-fuzzycompletions, julia-genericlinearalgebra, julia-genericschur,
julia-geometrybasics, julia-imagemagick, julia-infinity,
julia-matrixfactorizations, julia-media, julia-missings, julia-nnlib,
julia-optimtestproblems, julia-orderedcollections, julia-prettytables,
julia-pycall, julia-quadmath, julia-safetests, julia-stackviews)
[arguments]: Correct paths to reflect change of %package-path modify
order of phases as link-depot needs to run on an unmodified src
directory add package-name-uuid keyword argument to packages without
Project.toml file.
* gnu/packages/julia.scm (julia)[native-search-paths]: Correct paths to
reflect change of %package-path modify order of phases as link-depot
needs to run on an unmodified src directory.

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

gnu: Add cl-https-everywhere.

* gnu/packages/lisp-xyz.scm (cl-https-everywhere, sbcl-cl-https-everywhere):
New variables.

gnu: Add vernacular.

* gnu/packages/lisp-xyz.scm (cl-vernacular, sbcl-vernacular): New variables.

gnu: Add fxml.

* gnu/packages/lisp-xyz.scm (cl-fxml, sbcl-fxml): New variables.

gnu: Add xpath.

* gnu/packages/lisp-xyz.scm (cl-xpath, sbcl-xpath): New variables.

gnu: Add overlord.

* gnu/packages/lisp-xyz.scm (cl-overlord, sbcl-overlord): New variables.