Support numpy 2 in tests

[cbkerr]

Description

Apply changes from https://numpy.org/doc/stable//numpy_2_0_migration_guide.html#changes-to-namespaces

Motivation and Context

Checklist:

• I am familiar with the Contributing Guidelines.
• I agree with the terms of the Contributor Agreement.
• My name is on the list of contributors.
• The changes introduced by this pull request are covered by existing or newly introduced tests.
• The package documentation and framework documentation in signac-docs are up to date with these changes.
• I have updated the changelog and added any related issue and pull request numbers for future reference.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.01%. Comparing base (24035c6) to head (fd76019).

Additional details and impacted files

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  Coverage   86.01%   86.01%           
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  Files          20       20           
  Lines        3503     3503           
  Branches      770      770           
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  Hits         3013     3013           
  Misses        333      333           
  Partials      157      157           

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[bdice]

Test failures appear to be related to PyTables/PyTables#1172

It's fine with me if you want to add an exception to the warnings-as-errors options in pyproject.toml to ignore these. edit: Hmm, these appear to be actual errors and not warnings. I thought this was typically raised as a warning. Not sure.

[bdice]

Overall, our dependency on PyTables has been really hard to keep working. PyTables is usually the last of signac's dependencies to support new Python versions and such. I'd be okay with softening this dependency and not requiring it in our tests. Let me know if you want more specific input on that possibility.

[cbkerr]

I see PyTables has a PR for fixing this, so I vote we wait a couple weeks and check back

[joaander]

I see PyTables has a PR for fixing this, so I vote we wait a couple weeks and check back

The latest pull request on PyTables refactors the CI and specifically pins numpy < 2. The numpy 2 support PR has been closed and a new one has been created by an outside contributor. It appears that we will be waiting MANY weeks, if not months.

I suggest you update the signac tests to optionally skip pytables tests so that we can move forward.

[cbkerr]

The tests already have pandas and tables in a separate list requirements-test-optional.txt, and we see that only the "newest" tests fail. "Minimal" and "oldest" tests work, but those do not include numpy 2.0 either.

I considered making yet another list of requirements like requirements-test-optional-tables.txt, but I'm not sure how that affects building the wheels in the publish-packages github action:

    - name: Install dependencies
      run: |
        # We must explicitly install the requirements so that we can force
        # installation of the local wheel below in case the version conflicts
        # with published wheels (typically only possible during testing).
        python -m pip install \
        -r requirements.txt \
        -r requirements/requirements-test.txt \
        -r requirements/requirements-test-optional.txt

[joaander]

The failure to import pytables is a catchable ValueErorr exception.

The simplest fix is to use

tables = pytest.importorskip("tables")

in place of

import tables

https://docs.pytest.org/en/6.2.x/reference.html#pytest.importorskip

However, it appears that exceptions other than ModuleNotFoundError will be considered errors in a future version of pytest: https://github.com/pytest-dev/pytest/blob/8509fe8be58ea1c093b4b0ac89382bfdacea0083/src/_pytest/outcomes.py#L288-L298

The more complex alternative is

try:
    import tables
    skip_tables = False
except ValueError:
    skip_tables = True

skip_tables = pytest.mark.skipif(skip_tables,
                              reason="The tables package is non-functional.")

Then, decorate individual test functions (and/or classes) that use tables with:

@skip_tables

[joaander]

Thanks!