* gnu/packages/sagemath.scm (sage)[inputs]: Remove flint-3.3; add flint.

* gnu/packages/sagemath.scm (sage): Update to 10.9.

Change-Id: If8f93389ffe8bb8449476e61bfcb83d61c2c3839

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>

See https://github.com/sagemath/sage/pull/41141.

* gnu/packages/sagemath.scm (sage)[arguments]: Add a patch that removes
an outdated function.

Merges guix/guix!7737

Change-Id: Ie38eca12dceb92e95596687d9e15b826c3712184
Signed-off-by: Cayetano Santos <csantosb@inventati.org>
Modified-by: Cayetano Santos <csantosb@inventati.org>

* gnu/packages/sagemath.scm (sage)[native-inputs]: Replace meson-python
by python-meson.

Change-Id: I9231e35f54b11153b0fb7b85911dda5d7521b556

* gnu/packages/sagemath.scm (sage)[native-inputs]: Replace
python-setuptools by meson-python.  Add python-sphinx.
[arguments]<#:phases>{patch-source}: Patch out checks for maxima from ecl.
It is not found by meson, but will be found by sage due to our patching
of src/sage/env.py.
[setup]: Do not chdir into src, so that the higher level pyproject.toml
is used for the build with meson.

Change-Id: Id3f8fbc4e9097f31a5e56ee8a49d2d2772620cf5

* gnu/packages/sagemath.scm (sage)[inputs]: Add python-cvxopt,
python-lrcalc, python-mpmath, python-networkx, python-primecountpy,
python-scipy, python-sympy.

Change-Id: I6531b2c4e6ac14b1eed838bc51035ce84621a349
Signed-off-by: Andreas Enge <andreas@enge.fr>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

* gnu/packages/patches/sage-safeguard-sage-getargspec-cython.patch:
Remove file.
* gnu/local.mk (dist_patch_DATA): Unregister patch.
* gnu/packages/sagemath.scm (sage): Update to 10.7.
[origin]: Remove patch.

Change-Id: I64093e73369bd378b2553df589f0e2c6e5097aef

* gnu/packages/algebra.scm (flint): Update to 3.4.0.
(flint-3.3): New variable.
(python-flint)[inputs]: Replace flint by flint-3.3.
* gnu/packages/sagemath.scm (sage)[inputs]: Replace flint by flint-3.3.

Change-Id: I4a9e0a4bf70be54f165183959ef1cd4652387c27

This is a followup to 941b6ff1c11be3ba73e4e67bc661bd0eed3e9d58 commit.

Replace all python-cython-3 occurrences with python-cython.

* gnu/packages/python-xyz.scm (python-cython-3): Deprecate variable.

* gnu/packages/algebra.scm (python-fpylll, python-flint)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/astronomy.scm (python-astropy, python-astroscrappy,
python-halotools, python-healpy, python-libstempo, python-lofar-h5plot,
python-losoto, python-photutils, python-pyxsim, python-regions,
python-reproject, python-sncosmo, python-sndata, python-stcal,
python-yt)[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/bioinformatics.scm (macs-3, python-pyrodigal):
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/build-tools.scm (meson-python)[propagated-inputs]: Remove
python-cython-3; add python-cython.
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/databases.scm: (python-adbc-driver-manager,
python-psycopg, python-pyarrow)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/finance.scm (python-ta-lib)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/game-development.scm (python-pygame-ce)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/geo.scm (python-pyogrio, python-cf-units)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/machine-learning.scm: (python-scikit-learn,
python-opentsne)[native-inputs]: Remove python-cython-3; add
python-cython.

* gnu/packages/maths.scm: (python-cylp, python-petsc4py,
python-primecountpy, python-slepc4py)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/python-check.scm (python-line-profiler)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/python-compression.scm (python-blosc2)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/python-graphics.scm (python-vispy)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/python-science.scm: (python-pykdtree, python-qutip,
python-scikit-misc, python-scikit-surprise, python-pandas-2,
python-vaex-core)[native-inputs]: Remove python-cython-3; add
python-cython.

* gnu/packages/python-web.scm: (python-aiohttp, python-falcon,
python-yarl, python-uvloop)[native-inputs]: Remove python-cython-3; add
python-cython.

* gnu/packages/python-xyz.scm: (python-logbook, python-netcdf4,
python-pyyaml, python-propcache, python-pywavelets, python-symengine,
python-cysignals, python-pyemd, python-rbfly)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/sagemath.scm: (python-cypari2, python-pplpy, sage)
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/sphinx.scm (python-sphinx)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/statistics.scm: (python-statsmodels, python-pyreadstat):
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/tor.scm (onionshare-cli)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/xorg.scm (xpra)[native-inputs]: Remove python-cython-3;
add python-cython.

Change-Id: I38038d2ab18e6a7b549070083d6e4c5beb8b0293