* gnu/packages/code.scm (cloc): Update to 2.10.

Merges: https://codeberg.org/guix/guix/pulls/9769
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>

* gnu/packages/code.scm (sourcetrail): Update to 2.1.0.
[inputs]: Remove spdlog-1.13; add spdlog.

* gnu/packages/code.scm (scc): Update to 3.7.0.
  [native-inputs]: Remove go-github-com-dbaggerman-cuba,
  go-github-com-minio-blake2b-simd, go-golang-org-x-text,
  go-gopkg-in-yaml-v2.  Add go-github-com-agnivade-levenshtein,
  go-github-com-boyter-gocodewalker, go-github-com-boyter-simplecache,
  go-github-com-rs-zerolog, go-github-com-spf13-pflag,
  go-go-yaml-in-yaml-v2, go-golang-org-x-crypto, go-golang-org-x-text.

Change-Id: Ib2febf40c93211bc99da8434bdc1ade1d05155e1
Merges: https://codeberg.org/guix/guix/pulls/8857
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>

* gnu/packages/c.scm:  Remove references to (gnu packages flex).
* gnu/packages/video.scm: Likewise.
* gnu/packages/web.scm: Likewise.
* gnu/packages/admin.scm: Change (gnu packages flex)
  to (gnu packages compiler-tools).
* gnu/packages/algebra.scm: Likewise.
* gnu/packages/apparmor.scm: Likewise.
* gnu/packages/assembly.scm: Likewise.
* gnu/packages/astronomy.scm: Likewise.
* gnu/packages/audio.scm: Likewise.
* gnu/packages/bioinformatics.scm: Likewise.
* gnu/packages/bison.scm: Likewise.
* gnu/packages/bootloaders.scm: Likewise.
* gnu/packages/cdrom.scm: Likewise.
* gnu/packages/chemistry.scm: Likewise.
* gnu/packages/cluster.scm: Likewise.
* gnu/packages/cobol.scm: Likewise.
* gnu/packages/code.scm: Likewise.
* gnu/packages/commencement.scm: Likewise.
* gnu/packages/coq.scm: Likewise.
* gnu/packages/coreboot.scm: Likewise.
* gnu/packages/databases.scm: Likewise.
* gnu/packages/datalog.scm: Likewise.
* gnu/packages/debug.scm: Likewise.
* gnu/packages/dictionaries.scm: Likewise.
* gnu/packages/dns.scm: Likewise.
* gnu/packages/documentation.scm: Likewise.
* gnu/packages/dotnet.scm: Likewise.
* gnu/packages/education.scm: Likewise.
* gnu/packages/electronics.scm: Likewise.
* gnu/packages/embedded.scm: Likewise.
* gnu/packages/emulators.scm: Likewise.
* gnu/packages/engineering.scm: Likewise.
* gnu/packages/esolangs.scm: Likewise.
* gnu/packages/fabric-management.scm: Likewise.
* gnu/packages/file-systems.scm: Likewise.
* gnu/packages/finance.scm: Likewise.
* gnu/packages/firmware.scm: Likewise.
* gnu/packages/flashing-tools.scm: Likewise.
* gnu/packages/fontutils.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/gcc.scm: Likewise.
* gnu/packages/gdb.scm: Likewise.
* gnu/packages/geo.scm: Likewise.
* gnu/packages/gl.scm: Likewise.
* gnu/packages/glib.scm: Likewise.
* gnu/packages/gnome.scm: Likewise.
* gnu/packages/graph.scm: Likewise.
* gnu/packages/graphics.scm: Likewise.
* gnu/packages/groff.scm: Likewise.
* gnu/packages/gstreamer.scm: Likewise.
* gnu/packages/guile.scm: Likewise.
* gnu/packages/hardware.scm: Likewise.
* gnu/packages/haskell.scm: Likewise.
* gnu/packages/heads.scm: Likewise.
* gnu/packages/hurd.scm: Likewise.
* gnu/packages/image-processing.scm: Likewise.
* gnu/packages/instrumentation.scm: Likewise.
* gnu/packages/kde-frameworks.scm: Likewise.
* gnu/packages/kde-graphics.scm: Likewise.
* gnu/packages/kde-pim.scm: Likewise.
* gnu/packages/kde-sdk.scm: Likewise.
* gnu/packages/kerberos.scm: Likewise.
* gnu/packages/lego.scm: Likewise.
* gnu/packages/lesstif.scm: Likewise.
* gnu/packages/libreoffice.scm: Likewise.
* gnu/packages/lighting.scm: Likewise.
* gnu/packages/linux.scm: Likewise.
* gnu/packages/logging.scm: Likewise.
* gnu/packages/mail.scm: Likewise.
* gnu/packages/man.scm: Likewise.
* gnu/packages/maths.scm: Likewise.
* gnu/packages/mpi.scm: Likewise.
* gnu/packages/multiprecision.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/netpbm.scm: Likewise.
* gnu/packages/networking.scm: Likewise.
* gnu/packages/nickle.scm: Likewise.
* gnu/packages/ocaml.scm: Likewise.
* gnu/packages/package-management.scm: Likewise.
* gnu/packages/parallel.scm: Likewise.
* gnu/packages/plotutils.scm: Likewise.
* gnu/packages/pretty-print.scm: Likewise.
* gnu/packages/profiling.scm: Likewise.
* gnu/packages/qt.scm: Likewise.
* gnu/packages/radio.scm: Likewise.
* gnu/packages/rdesktop.scm: Likewise.
* gnu/packages/rpc.scm: Likewise.
* gnu/packages/rust.scm: Likewise.
* gnu/packages/security-token.scm: Likewise.
* gnu/packages/selinux.scm: Likewise.
* gnu/packages/shellutils.scm: Likewise.
* gnu/packages/simulation.scm: Likewise.
* gnu/packages/statistics.scm: Likewise.
* gnu/packages/telephony.scm: Likewise.
* gnu/packages/toys.scm: Likewise.
* gnu/packages/version-control.scm: Likewise.
* gnu/packages/virtualization.scm: Likewise.
* gnu/packages/vpn.scm: Likewise.
* gnu/packages/vulkan.scm: Likewise.
* gnu/packages/webkit.scm: Likewise.
* gnu/packages/wine.scm: Likewise.
* gnu/packages/wm.scm: Likewise.
* gnu/packages/xdisorg.scm: Likewise.
* gnu/packages/xorg.scm: Likewise.

Merges: https://codeberg.org/guix/guix/pulls/8483
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>

After this commit, when both modules are imported:

- if pyproject is imported before, the warning is 'pypi-uri' is
deprecated, use '(@ (guix build-system pyproject) pypi-uri)' instead

- if python is imported before, the warning is `pypi-uri' imported from
both (guix build-system python) and (guix build-system pyproject)

This seems convenient enough to warn for deprecation in the short term,
while avoiding any breaking changes.

* guix/build-system/pyproject.scm (pypi-uri): Move the procedure from
(guix build-system python) here.

* guix/build-system/python (pypi-uri): Drop definition, import it
from (guix build-system pyproject) and deprecate it.

* gnu/packages/openldap.scm: Reorder modules to get the right warning.

* gnu/packages/pypy.scm: Likewise.

* gnu/packages/*.scm : Drop module (guix build-system python).

* tests/import/pypi.scm: Likewise.

Merges: https://codeberg.org/guix/guix/pulls/7448
Change-Id: Ib42f53bc545052eb7918a25afe9db6d5fc2cb834
Reviewed-by: Nguyễn Gia Phong <cnx@loang.net>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

* gnu/packages/idutils.scm (idutils): Run guix style.
[native-inputs]: Drop input labels.
Move from here ...
* gnu/packages/code.scm: ... to here.

Change-Id: Ie48e1e2ad67d484dbde9d8f5f37cf5bfb6df4a7f
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

* gnu/packages/code.scm (rtags): Delete variable.
* gnu/packages/patches/rtags-separate-rct.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Unregister file.

Change-Id: I37b5d87c928920f4687a1141f24bebacd5d0d8a1

* gnu/packages/code.scm (python-xenon): Delete variable.

Change-Id: I585e70120a7a4057564e5c9dbb5497f40a6119cb

* gnu/packages/code.scm (cloc): Update to 2.08.

Change-Id: I0f667b5fe7c222924624b8764773615d9985c1e2
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

* gnu/packages/boost.scm (boost-for-source-highlight): Rename this ...
(boost-1.83): ... to this.
(boost-numpy): Inherit from boost-1.83.
* gnu/packages/pretty-print.scm (source-highlight): Update accordingly.

* gnu/packages/boost.scm (boost): Update to 1.89.0.
[source]: Remove patches.

* gnu/packages/boost.scm (mdds)
[propagated-inputs]: Replace boost with boost-1.83.

* gnu/packages/astronomy.scm (aoflagger),
* gnu/packages/embedded.scm (cc-tool),
* gnu/packages/games.scm (0ad, vcmi),
* gnu/packages/image.scm (gpick),
* gnu/packages/maths.scm (highfive),
* gnu/packages/plotutils.scm (asymptote)
[native-inputs]: Replace boost with boost-1.83.

* gnu/packages/audio.scm (guitarix, supercollider),
* gnu/packages/bioconductor.scm (r-mzr),
* gnu/packages/bioinformatics.scm (ataqv, bless, express, isolator,
metabat, r-velocytom, rsem, sailfish, salmon),
* gnu/packages/bittorrent.scm (libtorrent-rasterbar),
* gnu/packages/code.scm (sourcetrail),
* gnu/packages/compression.scm (innoextract),
* gnu/packages/cpp.scm (lager),
* gnu/packages/crypto.scm (cryfs),
* gnu/packages/electronics.scm (nextpnr, prjpeppercorn, prjtrellis,
pulseview),
* gnu/packages/emulators.scm (mupen64plus-video-glide64mk2),
* gnu/packages/engineering.scm (cadabra2, freecad, libigl,
openscad, prusa-slicer),
* gnu/packages/file-systems.scm (snapper),
* gnu/packages/finance.scm (ledger),
* gnu/packages/game-development.scm (dds),
* gnu/packages/games.scm (colobot, fifengine, knightsgame, leela-zero,
pokerth, supertux, wesnoth, wesnoth-server),
* gnu/packages/geo.scm (gplates),
* gnu/packages/gnucash.scm (gnucash),
* gnu/packages/graph.scm (python-graph-tool),
* gnu/packages/graphics.scma (openshadinglanguage),
* gnu/packages/i2p.scm (i2pd),
* gnu/packages/image-viewers.scm (luminance-hdr),
* gnu/packages/kde-graphics.scm (krita),
* gnu/packages/mail.scm (astroid),
* gnu/packages/medical.scm (orthanc, orthanc-mysql,
orthanc-postgresql),
* gnu/packages/messaging.scm (libphonenumber),
* gnu/packages/mpd.scm (ncmpcpp),
* gnu/packages/networking.scm (kismet),
* gnu/packages/opencog.scm (cogutil),
* gnu/packages/photo.scm (hugin),
* gnu/packages/poedit.scm (poedit),
* gnu/packages/radio.scm (gnuradio),
* gnu/packages/rdf.scm (lucene++),
* gnu/packages/serialization.scm (avro-cpp),
* gnu/packages/simulation.scm (fenics-dolfin),
* gnu/packages/version-control.scm (gource),
* gnu/packages/video.scm (aegisub, mkvtoolnix),
* gnu/packages/web.scm (websocketpp)
[inputs]: Replace boost with boost-1.83.

* gnu/packages/libreoffice.scm (libcmis): Update to 0.6.2-00a85bf6.
(librevenge): Update to 0.0.5.
[arguments]<#:configure-flags>: Remove reference to boost system
component for which the compatibility stub has been removed.
* gnu/packages/serialization.scm (msgpack-cxx): Update to 7.0.0.

Change-Id: I247f3eaecde3de3fe227586b840f0312b4797ee1