* gnu/packages/chemistry.scm (mmtf-cpp): Delete variable.

Fixes: guix/guix#4485

* gnu/packages/chemistry.scm (python-pymol)[inputs]: Remove mmtf-cpp
and python-pyqt; add python-pyqt-6.

* gnu/packages/chemistry.scm (avogadro2): Update to 1.102.1.
[inputs]: Remove molequeue. Add jkqtplotter and bash-minimal.
Replace qtbase-5 by qtbase, qtsvg-5 by qtsvg and qtwayland-5 by qtwayland.
[arguments]: Add #:configure-flags.

Signed-off-by: Andreas Enge <andreas@enge.fr>

* gnu/packages/chemistry.scm (avogadrolibs): Update to 1.201.1.
[native-inputs]: Replace pybind11-2 by pybind11. Add patchelf.
Remove mmtf-cpp.
[inputs]: Add hdf5, jkqtplotter and spglib. Remove molequeue.
Replace qtbase-5 by qtbase and qtsvg-5 by qtsvg.
Update avogadro-molecules, avogadro-crystals and avogadro-fragments.
[arguments]<#:configure-flags>: Add -DQT_VERSION=6, -DUSE_HDF5=ON and
-DUSE_PYTHON=ON.
<#:phases>{extend-python-rpath}: New phase.

Co-authored-by: Andreas Enge <andreas@enge.fr>

* gnu/packages/chemistry.scm (rdkit)[native-inputs]: Replace
catch2-3.5 with catch2.
[arguments]: Update ’check #:phase.

* gnu/packages/check.scm (catch2-3): Rename to and define as deprecated
by...
(catch2-3.5): ...this.
(trompeloeil): Adapt input.
* gnu/packages/chemistry.scm (rdkit),
* gnu/packages/cpp.scm (immer),
* gnu/packages/enchant.scm (nuspell),
* gnu/packages/games.scm (fuzzylite, endless-sky)
* gnu/packages/gnome.scm (gnome-system-monitor),
* gnu/packages/logging.scm (spdlog-1.15),
* gnu/packages/luanti.scm (luanti),
* gnu/packages/maths.scm (highfive),
* gnu/packages/networking.scm (restinio),
* gnu/packages/package-management.scm (libmamba),
* gnu/packages/physics.scm (python-brille),
* gnu/packages/potassco.scm (clingo, clingo-lpx, clingcon),
* gnu/packages/xdisorg.scm (j4-dmenu-desktop): Adapt inputs.

Change-Id: I69fac4ec6d3914a6dc7d86f2454f410db937a83f

* gnu/packages/check.scm (catch2): Rename to...
(catch2-2): ...this.
(rapidcheck): Adapt inputs.
* gnu/packages/animation.scm (pencil2d),
* gnu/packages/audio.scm (libkeyfinder),
* gnu/packages/chemistry.scm (python-pymol),
gnu/packages/cpp.scm (xdgpp, icecream-cpp, span, chaiscript, json-dto,
rapidfuzz-cpp, libexpected, zug, lager, cli11, cpp-mustache,
tl-optional, type-safe),
* gnu/packages/engineering.scm (valeronoi, libigl),
* gnu/packages/geo.scm (mapnik),
* gnu/packages/maths.scm (osqp),
* gnu/packages/networking.scm (cppzmq),
* gnu/packages/python-science.scm (python-openpmd-api),
* gnu/packages/security-token.scm (libnitrokey): Adapt inputs.

Change-Id: Icd92b5aa0491911d5eeb5faf7b1d467e1e85fdc7

* gnu/packages/chemistry.scm (ringdecomposerlib)
[arguments]<#:phases>: Add phase 'patch-cython.
[native-inputs]: Replace python-cython-0 by python-cython.

Relates-to: guix/guix!9270
Reviewed-by: Cayetano Santos <csantosb@inventati.org>
Change-Id: Ie16dc9982390cb3ec910f0a6f9fb3a1260f68277
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

* 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>