* gnu/packages/simulation.scm (python-meshio)[arguments]:
Update #:test-flags.

hdf5-parallel-openmpi can't be built without openmpi when it's used as
input in other packages, which force to include openmpi every time
hdf5-parallel-openmpi is used, this change propagates openmpi to
simplify the packaging.

* gnu/packages/maths.scm (hdf5-parallel-openmpi)[propagated-inputs]:
Add openmpi.

* gnu/packages/bioinformatics.scm (lammps)[inputs]: Remove openmpi.
(lammps-serial)[inputs]: Drop deletion of openmpi.
* gnu/packages/lisp-xyz.scm (sbcl-cl-ana)[native-inputs]: Remove openmpi.
* gnu/packages/maths.scm (netcdf-cxx4-parallel-openmpi, petsc-openmpi):
[inputs]: Remove openmpi.
* gnu/packages/simulation.scm (fenics-dolfin)[inputs]: Remove openmpi.

Relates-to: guix/guix#7638, guix/guix!7946

* gnu/packages/patches/esmini-use-pkgconfig.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Unregister it.
* gnu/packages/simulation.scm (esmini): Update to 3.5.0.
[source]<snippet>: Also patch CMakeLists to use pkg-config.
Allow “yaml” to be vendored.
[arguments]<#:configure-flags>: Add “-DDOWNLOAD_EXTERNALS=FALSE”.
[inputs]: Add fmt.  Use one line per input.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>

* gnu/packages/simulation.scm (sumo): Update to 1.27.1.
[native-inputs]: Replace googletest-1.8 by googletest.

* 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>

* gnu/packages/simulation.scm (fenics): Fix Python 3.12 build.
[arguments]<#:test-flags>: Ignore failing test.

Fixes: guix/guix#8602
Merges: guix/guix!8801
Change-Id: I022ff73170fa0b451d3a44e9bab981f180e74ac3
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

* gnu/packages/simulation.scm (fenics-dolfin):
[native-inputs]: Add python-setuptools.

Change-Id: Id0cd4c11f192a7055839f482fc72575d306e4fa5

* gnu/packages/simulation.scm (python-fenics-dijitso)
[native-inputs]: Re-introduce python-pytest-cov.

Change-Id: I8ade39f8dbac62eea8f978c70d88310a00ad7581
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

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/astronomy.scm (python-wiimatch)
* gnu/packages/audio.scm (python-resampy, python-librosa)
* gnu/packages/backup.scm (borgmatic)
* gnu/packages/bioinformatics.scm (python-bed-reader, python-pysnptool)
(python-pairtools):
* gnu/packages/check.scm (python-pytest-nunit, python-pytest-perf)
* gnu/packages/dav.scm (vdirsyncer, radicale)
* gnu/packages/django.scm (python-django-redis)
* gnu/packages/engineering.scm (python-scikit-rf)
* gnu/packages/fediverse.scm (python-mastodon-py)
* gnu/packages/fontutils.scm (psautohint)
* gnu/packages/geo.scm (python-pyogrio)
* gnu/packages/graphviz.scm (python-uqbar)
* gnu/packages/jupyter.scm (python-jupyterlab-server python-nbclient,
python-jupyterlite-core, python-ipydatawidgets)
* gnu/packages/machine-learning.scm
(python-pymanopt, python-tensorly, python-torchmetrics)
* gnu/packages/maths.scm (python-libensemble)
* gnu/packages/music.scm (stargate)
* gnu/packages/python-check.scm (python-atpublic, python-vcrpy)
* gnu/packages/python-compression.scm (python-zipstream-ng)
* gnu/packages/python-science.scm (python-plotnine,
python-pandaparallel, python-pyts, python-pingouin)
* gnu/packages/python-web.scm (python-devpi-process, python-cheroot,
python-jsonpickle, python-flask-babel, python-url-normalize,
python-elasticsearch, python-hupper, python-simple-websocket,
python-apiron, python-huggingface-hub, python-aiosignal, python-ovh,
python-cbor2, python-zeep, hypercorn, python-warcio, python-aioftp,
python-oauthlib, python-tinycss2, python-cssselect2, python-httpcore,
python-wsgiprox, python-venusian, gunicorn)
* gnu/packages/python-xyz.scm (python-janus, python-affine,
python-contourpy, python-echo, python-rasterio, python-rich-tables,
python-babel, python-pymarshal, python-portalocker, python-expandvars,
python-mizani, python-cligj, autokey,
python-robotframework-pythonlibcore, python-lsp-jsonrpc,
python-numpydoc, python-pillow, python-manimpango, python-cairocffi,
python-pubmed-parser, python-sentry-sdk, python-prettytable,
python-sniffio, python-ipywidgets, python-pyproject-api,
python-pymemcache, python-async-lru, python-numcodecs, python-mwclient,
python-cmd2, python-pyan3, python-platformdirs, python-multipart,
python-shtab, python-scooby)
* gnu/packages/rdf.scm (python-rdflib-6)
* gnu/packages/simulation.scm (python-fenics-dijitso)
* gnu/packages/sphinx.scm (python-sphinx-design)
* gnu/packages/statistics.scm (python-patsy, python-rchitect)
* gnu/packages/task-management.scm (todoman)
* gnu/packages/vpn.scm (sshuttle)
* gnu/packages/web.scm (anonip, python-tibanna)
[native-inputs]: Remove python-pytest-cov.

Change-Id: I32f027794e90333c27fdff5871180779f603846c
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>