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"""Script for regenerating data found in the tests/data directory, using |
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whatever version of average-minimum-distance is installed to Python. |
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""" |
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import numpy as np |
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import amd |
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import pickle |
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import pathlib |
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_parent = pathlib.Path(__file__).absolute().parent |
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def regenerate(name, generator): |
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"""Regenerate and overwrite ``PeriodicSet``s, AMDs and PDDs for a |
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testing dataset from a ``generator`` of ``PeriodicSet``s. |
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""" |
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data = [] |
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for s in generator: |
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pdd = amd.PDD(s, 100, lexsort=False) # No lexsort to avoid FP problems |
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data.append({"PeriodicSet": s, "AMD100": amd.PDD_to_AMD(pdd), "PDD100": pdd}) |
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with open(str(_parent / f"{name}.pkl"), "wb") as f: |
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pickle.dump(data, f) |
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if len(data) > 1: |
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cdm = amd.PDD_pdist([d["PDD100"] for d in data]) |
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np.savez_compressed(str(_parent / f"{name}_cdm.npz"), cdm=cdm) |
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def regenerate_cifs_test_data(): |
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"""Regenerate and overwrite all test data using cifs in tests/data. |
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Does not apply to test data extracted with ``csd-python-api``. |
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""" |
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for name in ("cubic", "T2_experimental"): |
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path = _parent / f"{name}.cif" |
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regenerate(name, amd.CifReader(path, show_warnings=False)) |
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def regenerate_CSD_families_test_data(): |
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"""Regenerate and overwrite all test data for 'CSD_families' using |
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``csd-python-api``. |
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""" |
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csd_families = ["DEBXIT", "GLYCIN", "HXACAN", "ACSALA"] |
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reader = amd.CSDReader(csd_families, refcode_families=True, show_warnings=False) |
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regenerate("CSD_families", reader) |
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if __name__ == "__main__": |
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regenerate_cifs_test_data() |
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regenerate_CSD_families_test_data() |
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dwiddo /
average-minimum-distance
