Fix DistanceMatrix crash on read-only array from remove_zerors #199

[OmerJauhar]

Description

DistanceMatrix in teaspoon/TDA/PHN.py called np.fill_diagonal(A, 0) on the array returned by network_tools.remove_zeros. That function returns its result via pandas to_numpy(), which is read-only on the numpy/pandas versions resolved for Python 3.11 and 3.12. Since np.fill_diagonal writes in place, it raised ValueError: underlying array is read-only, which failed the CI test suite on 3.11 and 3.12 while 3.9 and 3.10 passed.

The fix wraps the result in np.array(...), which returns a writable copy regardless of the input's read-only flag. The diagonal is still zeroed exactly as before.

Motivation and Context

Closes #199. The Test Installs workflow was red on Python 3.11 and 3.12 (all platforms), which blocked the checks on every pull request. This was pre-existing and not introduced by any recent.

How has this been tested?

• Reproduced the exact failure by forcing remove_zeros to return a read-only array, then confirmed DistanceMatrix raised underlying array is read-only without the fix.
• With the fix, ran both affected tests (test_point_summaries_empty_persistence_diagram, test_point_summaries_non_empty_persistence_diagram`) end-to-end under the same read-only condition — both pass, and no further read-only error appears downstream.
• Ran tests/test_PointSummariesPHN.py normally — 2 passed.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)

Checklist

• My code follows the code style of this project. (make clean)
• My change requires a change to the documentation.
• I have updated the documentation accordingly. (make html)
• I have incremented the version number in the pyproject.toml file.
• I have added tests to cover my changes.
• All new and existing tests passed. (make tests)