Hi, this issue is part of this package's pyOpenSci review at pyOpenSci/software-submission#244

Severity: Moderate

Description

Getting some failing tests on my WIndows laptop:

==== 22 failed, 868 passed, 12 warnings, 787 errors in 290.12s (0:04:50) ===

Most of the errors are PermissionErrors: e.g.,

ERROR tests/test_masking.py::TestMaskingNamedColumnDatasets::test_bool_mask[False] - PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'demo_data\toysnap.hdf5'

Here is a snippet from some of the more detailed tracebacks:

________________________________________________________________________________________________________ TestMaskingSWIFTGalaxy.test_mask_without_spatial_mask ________________________________________________________________________________________________________

self = <test_masking.TestMaskingSWIFTGalaxy object at 0x0000027FAC893910>

def test_mask_without_spatial_mask(self):
    """
    Check that if we have no masks we read everything in the box (and warn about it).
    Then that we can still apply an extra mask, and a second one (there's specific
    logic for applying two consecutively).
    """
    try:
        _create_toysnap()
        sg = SWIFTGalaxy(
            _toysnap_filename,
            None,  # no halo_catalogue is easiest way to get no mask
            transforms_like_coordinates={"coordinates", "extra_coordinates"},
            transforms_like_velocities={"velocities", "extra_velocities"},
        )
        # check that extra mask is blank for all particle types:
        assert sg._extra_mask.gas is None
        assert sg._extra_mask.dark_matter is None
        assert sg._extra_mask.stars is None
        assert sg._extra_mask.black_holes is None
        # check that cell mask is blank for all particle types:
        assert sg._spatial_mask is None
        # check that we read all the particles:
        assert sg.gas.masses.size == _n_g_all
        assert sg.dark_matter.masses.size == _n_dm_all
        assert sg.stars.masses.size == _n_s_all
        assert sg.black_holes.masses.size == _n_bh_all
        # now apply an extra mask
        sg.mask_particles(MaskCollection(gas=np.s_[:1000]))
        assert sg.gas.masses.size == 1000
        # and the second consecutive one
        sg.mask_particles(MaskCollection(gas=np.s_[:100]))
        assert sg.gas.masses.size == 100
    finally:

      _remove_toysnap()

tests\test_masking.py:122:

---

swiftgalaxy\demo_data.py:1078: in _remove_toysnap
Path(snapfile).unlink(missing_ok=True)

---

self = WindowsPath('demo_data/toysnap.hdf5'), missing_ok = True

def unlink(self, missing_ok=False):
    """
    Remove this file or link.
    If the path is a directory, use rmdir() instead.
    """
    try:

      self._accessor.unlink(self)

E PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'demo_data\toysnap.hdf5'

They seem to be related to demo data file handling during breakdown. From my web searching it seems like maybe files need to closed (file.close()) before un-linking on Windows, but I'm not positive if that will fix it.