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Fix warnings#21

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peteole wants to merge 1 commit intobioinf-jku:masterfrom
peteole:fix-warnings
Open

Fix warnings#21
peteole wants to merge 1 commit intobioinf-jku:masterfrom
peteole:fix-warnings

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@peteole
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@peteole peteole commented Jun 27, 2025

Some numpy and scipy syntax is depreciated, resulting in warnings when running the code. This PR fixes those warnings.

Before:

  /Users/ole/Documents/software/molecule_benchmarks/.venv/lib/python3.12/site-packages/fcd/fcd.py:81: DeprecationWarning: `row_stack` alias is deprecated. Use `np.vstack` directly.
    return np.row_stack(chemnet_activations)

tests/test_benchmarker.py::test_benchmarker
tests/test_benchmarker.py::test_benchmarker
  /Users/ole/Documents/software/molecule_benchmarks/.venv/lib/python3.12/site-packages/fcd/utils.py:200: DeprecationWarning: The `disp` argument is deprecated and will be removed in SciPy 1.18.0.
    covmean, _ = linalg.sqrtm(sigma1.dot(sigma2), disp=False)

After the PR, these warnings disappear and keep the results identical.

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peteole commented Jul 15, 2025

Can we merge this?

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