setup.py test does not work after a fresh new installation

[miqueleg]

I just installed a new conda enviroment for OpenMM-GaMD following the instalation instructions (OpenMM using cuda-13.0, ambertools, setuptools)

Then, I did python setup.py install and it seems to be working, but I got this comment:

/home/mestevez/miniconda3/envs/OpenMM-GaMD/lib/python3.14/site-packages/setuptools/command/build_py.py:212: _Warning: Package 'gamd.tests.data' is absent from the `packages` configuration.
!!

        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'gamd.tests.data' as an importable package[^1],
        but it is absent from setuptools' `packages` configuration.

        This leads to an ambiguous overall configuration. If you want to distribute this
        package, please make sure that 'gamd.tests.data' is explicitly added
        to the `packages` configuration field.

        Alternatively, you can also rely on setuptools' discovery methods
        (for example by using `find_namespace_packages(...)`/`find_namespace:`
        instead of `find_packages(...)`/`find:`).

        You can read more about "package discovery" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

        If you don't want 'gamd.tests.data' to be distributed and are
        already explicitly excluding 'gamd.tests.data' via
        `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
        you can try to use `exclude_package_data`, or `include-package-data=False` in
        combination with a more fine grained `package-data` configuration.

        You can read more about "package data files" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


        [^1]: For Python, any directory (with suitable naming) can be imported,
              even if it does not contain any `.py` files.
              On the other hand, currently there is no concept of package data
              directory, all directories are treated like packages.
        ********************************************************************************

!!
  check.warn(importable)

Then this is my output for python setup.py test:

>python setup.py test
/home/mestevez/miniconda3/envs/OpenMM-GaMD/lib/python3.14/site-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

        ********************************************************************************
        Requirements should be satisfied by a PEP 517 installer.
        If you are using pip, you can try `pip install --use-pep517`.

        This deprecation is overdue, please update your project and remove deprecated
        calls to avoid build errors in the future.
        ********************************************************************************

!!
  dist.fetch_build_eggs(dist.setup_requires)
/home/mestevez/Programs/gamd-openmm/.eggs/pytest_runner-6.0.1-py3.12.egg/ptr/__init__.py:13: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources
/home/mestevez/Programs/gamd-openmm/.eggs/pytest_runner-6.0.1-py3.12.egg/ptr/__init__.py:81: SetuptoolsDeprecationWarning: The test command is disabled and references to it are deprecated.
!!

        ********************************************************************************
        Please remove any references to `setuptools.command.test` in all supported versions of the affected package.

        This deprecation is overdue, please update your project and remove deprecated
        calls to avoid build errors in the future.
        ********************************************************************************

!!
  class PyTest(orig.test):
running pytest
Traceback (most recent call last):
  File "/home/mestevez/Programs/gamd-openmm/setup.py", line 28, in <module>
    setup(
    ~~~~~^
        # Self-descriptive entries which should always be present
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    ...<35 lines>...
    
    
    )
    ^
  File "/home/mestevez/miniconda3/envs/OpenMM-GaMD/lib/python3.14/site-packages/setuptools/__init__.py", line 115, in setup
    return distutils.core.setup(**attrs)
           ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
  File "/home/mestevez/miniconda3/envs/OpenMM-GaMD/lib/python3.14/site-packages/setuptools/_distutils/core.py", line 186, in setup
    return run_commands(dist)
  File "/home/mestevez/miniconda3/envs/OpenMM-GaMD/lib/python3.14/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
    dist.run_commands()
    ~~~~~~~~~~~~~~~~~^^
  File "/home/mestevez/miniconda3/envs/OpenMM-GaMD/lib/python3.14/site-packages/setuptools/_distutils/dist.py", line 1002, in run_commands
    self.run_command(cmd)
    ~~~~~~~~~~~~~~~~^^^^^
  File "/home/mestevez/miniconda3/envs/OpenMM-GaMD/lib/python3.14/site-packages/setuptools/dist.py", line 1102, in run_command
    super().run_command(command)
    ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
  File "/home/mestevez/miniconda3/envs/OpenMM-GaMD/lib/python3.14/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
    cmd_obj.run()
    ~~~~~~~~~~~^^
  File "/home/mestevez/Programs/gamd-openmm/.eggs/pytest_runner-6.0.1-py3.12.egg/ptr/__init__.py", line 195, in run
    setattr(dist, attr, getattr(self.distribution, attr))
                        ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'Distribution' object has no attribute 'tests_require'. Did you mean: 'extras_require'?

[MiaoLab20]

@miqueleg: Thanks for reporting the issue.
@dyelar @lvotapka @hungd238: Could you help to take a look? Thanks!