What is the best replacement for python setup.py install when Cython needs to be compiled?

Question

With the latest version of setuptools , the python setup.py install command is being deprecated (see https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for more info).

(venv) [jon@dev02 py38]$ python setup.py install
running install
/home/jon/.jenkins/workspace/Farm_revision_linux_py36/TOXENV/py38/venv/lib64/python3.8/site-
packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is 
deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
/home/jon/.jenkins/workspace/Farm_revision_linux_py36/TOXENV/py38/venv/lib64/python3.8/site-
packages/setuptools/command/easy_install.py:156: EasyInstallDeprecationWarning: easy_install 
command is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
running bdist_egg
running egg_info
... etc

It is suggested that you can just pip install. to install a package from source, but this does not compile any Cython code. What is the best method for doing this?

The Cython docs are still recommending use of setup.py and I can't find any better suggestions. It appears that a developer install ( pip install -e. ) does compile the Cython files, or you can python setup.py build_ext --inplace after running pip install. . Neither of these options are ideal, so I would like to know if there is a suggested alternative.

EDIT:

The package setup.py file contains this code, which should compile the Cython files:

try:
    import numpy
    from Cython.Build import cythonize
    cython_files = ["farm/rasters/water_fill.pyx"]
    cython_def = cythonize(cython_files, annotate=True,
                           compiler_directives={'language_level': str(sys.version_info.major)})
    include_dirs = [numpy.get_include()]
except ImportError:
    cython_def = None
    include_dirs = None

When installing with python setup.py install , the farm/rasters directory contains the following files:

water_fill.c
water_fill.cpython-38-x86_64-linux-gnu.so
water_fill.html
water_fill.pyx

When installing with pip install. , the directory does not contain the.so file and when we try and run water_fill tests, we get errors like this

________________________________ TestFlowDown1D.test_distribute_1d_trough_partial_3 _________________________________
farm/rasters/tests/test_flood_enhance.py:241: in test_distribute_1d_trough_partial_3
    actual_arr = water_fill.water_fill_1d(arr, additional_value)
E   AttributeError: 'NoneType' object has no attribute 'water_fill_1d'

Answer 1

I believe the warning should go away if you keep the setup.py but add a pyproject.toml. How to do this is described in https://cython.readthedocs.io/en/latest/src/userguide/source_files_and_compilation.html .

Here is the example pyproject.toml file they give:

[build-system]
requires = ["setuptools", "wheel", "Cython"]