Test suite Windows compatibility

[maurerv]

After PR #25, pytme builds on Windows but does not pass all tests. A few temp files get created with mkstemp and then removed later without closing the file descriptor first, disallowed on Windows.

generate_tempfile_name in matching_utils and mkstemp calls in the tests need to be adapted accordingly. It is also worth checking np.memmap and h5py usage for the same pattern.

Would also be good to add a Windows runner to CI/CD.

[boydcpeters]

Hi @maurerv,

As promised, here are my logs, some parts at the bottom are truncated, but looking at the top, you can find more extensive tracebacks.

I will see whether I have some time the coming days to update some tests and get them to pass and make a PR, but if you already know how to fix the issues and have some time, feel free to implement it yourself of course.

I only get errors/failures in:

• test_density.py
• test_matching_cli.py
• test_matching_utils.py
• test_structure.py

Open to see the logs

============================= test session starts =============================
platform win32 -- Python 3.13.5, pytest-9.1.0, pluggy-1.6.0
rootdir: C:\Users\boydpeters\projects\pyTME
configfile: pyproject.toml
collected 1084 items

tests\preprocessing\test_compose.py ..........                           [  0%]
tests\preprocessing\test_frequency_filters.py .......................... [  3%]
............                                                             [  4%]
tests\preprocessing\test_preprocessor.py ............................... [  7%]
....                                                                     [  7%]
tests\preprocessing\test_utils.py ...................................... [ 11%]
...................................                                      [ 14%]
tests\test_analyzer.py ................................................. [ 18%]
......................                                                   [ 20%]
tests\test_backends.py ................................................. [ 25%]
.....................................................................    [ 31%]
tests\test_density.py .E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E [ 34%]
.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E [ 37%]
.E.EFE.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E [ 40%]
.E.E.E.E.E.E.E                                                           [ 41%]
tests\test_extensions.py ............................................... [ 45%]
........................................................................ [ 52%]
.....                                                                    [ 52%]
tests\test_matching_cli.py ............................................. [ 57%]
...........................FFFFFFFFFF...........                         [ 61%]
tests\test_matching_data.py ...........................                  [ 63%]
tests\test_matching_exhaustive.py ...................................... [ 67%]
                                                                         [ 67%]
tests\test_matching_memory.py .......................................... [ 71%]
................................................                         [ 75%]
tests\test_matching_optimization.py .................................... [ 79%]
.                                                                        [ 79%]
tests\test_matching_utils.py ........................................... [ 83%]
........................................................................ [ 89%]
..............................F.                                         [ 92%]
tests\test_orientations.py .................................             [ 95%]
tests\test_parser.py .....                                               [ 96%]
tests\test_rotations.py ...........                                      [ 97%]
tests\test_structure.py .E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E [ 99%]
.E.E.E.E.E.E                                                             [100%]

=================================== ERRORS ====================================
____________ ERROR at teardown of TestDensity.test_initialization _____________

self = <tests.test_density.TestDensity object at 0x000002CE7FC6D950>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpgss0jlrm'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_initialization_errors[data0-origin0-sampling_rate0-metadata0] _

self = <tests.test_density.TestDensity object at 0x000002CE7FC6DF90>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpj_tj6rpk'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_initialization_errors[data1-origin1-sampling_rate1-metadata1] _

self = <tests.test_density.TestDensity object at 0x000002CE7FC86780>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpl5jndl47'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_initialization_errors[data2-origin2-sampling_rate2-not_a_dict] _

self = <tests.test_density.TestDensity object at 0x000002CE7FC868B0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpkfut56p4'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_initialization_errors[data3-origin3-sampling_rate3-not_a_dict] _

self = <tests.test_density.TestDensity object at 0x000002CE7FD85250>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpotwrbose'

tests\test_density.py:45: PermissionError
_________________ ERROR at teardown of TestDensity.test_repr __________________

self = <tests.test_density.TestDensity object at 0x000002CE7FC76250>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp_q1t7bru'

tests\test_density.py:45: PermissionError
____________ ERROR at teardown of TestDensity.test_to_file[False] _____________

self = <tests.test_density.TestDensity object at 0x000002CE7FC76AD0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpri27h93y'

tests\test_density.py:45: PermissionError
_____________ ERROR at teardown of TestDensity.test_to_file[True] _____________

self = <tests.test_density.TestDensity object at 0x000002CE7FDB4350>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpofi2aq01'

tests\test_density.py:45: PermissionError
_______________ ERROR at teardown of TestDensity.test_from_file _______________

self = <tests.test_density.TestDensity object at 0x000002CE7FDB4450>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpwzwh1o_3'

tests\test_density.py:45: PermissionError
__________ ERROR at teardown of TestDensity.test_from_file_baseline ___________

self = <tests.test_density.TestDensity object at 0x000002CE7FC7A4E0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpnk3mhw_1'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[True-True-True-mrc] ___

self = <tests.test_density.TestDensity object at 0x000002CE7FC7A5D0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpqzjzw3id'

tests\test_density.py:45: PermissionError
___ ERROR at teardown of TestDensity.test_file_format_io[True-True-True-em] ___

self = <tests.test_density.TestDensity object at 0x000002CE7FD8F5B0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp1y37dx28'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[True-True-True-tiff] __

self = <tests.test_density.TestDensity object at 0x000002CE7FD8F770>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpvww2nqku'

tests\test_density.py:45: PermissionError
___ ERROR at teardown of TestDensity.test_file_format_io[True-True-True-h5] ___

self = <tests.test_density.TestDensity object at 0x000002CE10FEC600>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpw5bpgub_'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[True-True-False-mrc] __

self = <tests.test_density.TestDensity object at 0x000002CE7FDB8050>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpl5qks83n'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[True-True-False-em] ___

self = <tests.test_density.TestDensity object at 0x000002CE7FDB81D0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpfmkwn3tq'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_file_format_io[True-True-False-tiff] __

self = <tests.test_density.TestDensity object at 0x000002CE7FD62FC0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpg9d7ayan'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[True-True-False-h5] ___

self = <tests.test_density.TestDensity object at 0x000002CE7FD63070>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpj1f3jpro'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[True-False-True-mrc] __

self = <tests.test_density.TestDensity object at 0x000002CE10FDA210>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpdbs8zu9a'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[True-False-True-em] ___

self = <tests.test_density.TestDensity object at 0x000002CE10FDA0D0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpgf83fil_'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_file_format_io[True-False-True-tiff] __

self = <tests.test_density.TestDensity object at 0x000002CE7FDB0830>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp5o97av1g'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[True-False-True-h5] ___

self = <tests.test_density.TestDensity object at 0x000002CE10FF2C50>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpctxnzjtw'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_file_format_io[True-False-False-mrc] __

self = <tests.test_density.TestDensity object at 0x000002CE10FF2D50>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpaqhohsgj'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[True-False-False-em] __

self = <tests.test_density.TestDensity object at 0x000002CE10FE63C0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp0dc_hy84'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_file_format_io[True-False-False-tiff] _

self = <tests.test_density.TestDensity object at 0x000002CE10FE6510>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpzij6u4jq'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[True-False-False-h5] __

self = <tests.test_density.TestDensity object at 0x000002CE7FDA2750>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp4ywaf07y'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[False-True-True-mrc] __

self = <tests.test_density.TestDensity object at 0x000002CE7FDA2810>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpfhaydom_'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[False-True-True-em] ___

self = <tests.test_density.TestDensity object at 0x000002CE7FDAED50>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpcxp2he9o'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_file_format_io[False-True-True-tiff] __

self = <tests.test_density.TestDensity object at 0x000002CE7FDAEDA0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp9f6gabcz'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[False-True-True-h5] ___

self = <tests.test_density.TestDensity object at 0x000002CE7FDAEE40>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp9gukq941'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_file_format_io[False-True-False-mrc] __

self = <tests.test_density.TestDensity object at 0x000002CE7FDAEE90>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpnqgfkc_u'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[False-True-False-em] __

self = <tests.test_density.TestDensity object at 0x000002CE7FDAEEE0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpddtg1bzk'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_file_format_io[False-True-False-tiff] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAEF30>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpwl_31iuc'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[False-True-False-h5] __

self = <tests.test_density.TestDensity object at 0x000002CE7FDAEF80>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpnvn3_nj8'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_file_format_io[False-False-True-mrc] __

self = <tests.test_density.TestDensity object at 0x000002CE7FDAEFD0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpg4dla3o_'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[False-False-True-em] __

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF020>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpec2m2qyj'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_file_format_io[False-False-True-tiff] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF070>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpkn3s6c6z'

tests\test_density.py:45: PermissionError
__ ERROR at teardown of TestDensity.test_file_format_io[False-False-True-h5] __

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF0C0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpzg5l6un6'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_file_format_io[False-False-False-mrc] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF110>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpwab_qa5d'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_file_format_io[False-False-False-em] __

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF160>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp05lb8kuc'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_file_format_io[False-False-False-tiff] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF1B0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpztnhyosk'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_file_format_io[False-False-False-h5] __

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF200>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpou2s04ee'

tests\test_density.py:45: PermissionError
_______ ERROR at teardown of TestDensity.test__read_binary_subset_error _______

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF2F0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpanm3dxjc'

tests\test_density.py:45: PermissionError
____________ ERROR at teardown of TestDensity.test_from_structure _____________

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF390>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmphp61v6hx'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_from_structure_weight_types[atomic_weight] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF430>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmptuviolci'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_from_structure_weight_types[atomic_number] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF480>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpk955mgwg'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_from_structure_weight_types[van_der_waals_radius] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF4D0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpvqpsubhz'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_from_structure_weight_types[scattering_factors] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF520>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpsd76ol_9'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_from_structure_weight_types[lowpass_scattering_factors] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF570>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpogysbiez'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_from_structure_weight_types[gaussian] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF610>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmprgqwetb4'

tests\test_density.py:45: PermissionError
___ ERROR at teardown of TestDensity.test_from_structure_weight_types_error ___

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF6B0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpgne3q6o_'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_from_structure_scattering[dt1969-scattering_factors] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF840>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpmgzv4dnp'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_from_structure_scattering[dt1969-lowpass_scattering_factors] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF930>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpn3dq5fca'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_from_structure_scattering[wk1995-scattering_factors] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAFA20>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp8m6_eyws'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_from_structure_scattering[wk1995-lowpass_scattering_factors] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAFAC0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp4k7kmcze'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_from_structure_scattering[peng1995-scattering_factors] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAFB60>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp9f5zgp1l'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_from_structure_scattering[peng1995-lowpass_scattering_factors] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAFC00>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpirrqey_9'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_from_structure_scattering[peng1999-scattering_factors] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAFCA0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp5l5989li'

tests\test_density.py:45: PermissionError
_ ERROR at teardown of TestDensity.test_from_structure_scattering[peng1999-lowpass_scattering_factors] _

self = <tests.test_density.TestDensity object at 0x000002CE7FDAFD40>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpdl7em6eg'

tests\test_density.py:45: PermissionError
_________ ERROR at teardown of TestDensity.test_from_structure_error __________

self = <tests.test_density.TestDensity object at 0x000002CE7FDAFDE0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp91rzi80i'

tests\test_density.py:45: PermissionError
_________________ ERROR at teardown of TestDensity.test_empty _________________

self = <tests.test_density.TestDensity object at 0x000002CE7FDAFE80>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmppi8cxgsq'

tests\test_density.py:45: PermissionError
_________________ ERROR at teardown of TestDensity.test_copy __________________

self = <tests.test_density.TestDensity object at 0x000002CE7FDAFF20>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpe9a0qq33'

tests\test_density.py:45: PermissionError
_______________ ERROR at teardown of TestDensity.test_to_memmap _______________

self = <tests.test_density.TestDensity object at 0x000002CE7FDAFFC0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpu4j38t6r'

tests\test_density.py:45: PermissionError
_______________ ERROR at teardown of TestDensity.test_to_numpy ________________

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF7F0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpl45ahfxj'

tests\test_density.py:45: PermissionError
___________ ERROR at teardown of TestDensity.test_to_pointcloud[0] ____________

self = <tests.test_density.TestDensity object at 0x000002CE7FD0ABC0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpq5w2fjuv'

tests\test_density.py:45: PermissionError
__________ ERROR at teardown of TestDensity.test_to_pointcloud[0.5] ___________

self = <tests.test_density.TestDensity object at 0x000002CE7FD780F0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpzkkhpzsy'

tests\test_density.py:45: PermissionError
___________ ERROR at teardown of TestDensity.test_to_pointcloud[1] ____________

self = <tests.test_density.TestDensity object at 0x000002CE7FD78500>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmprpg1eibx'

tests\test_density.py:45: PermissionError
__________ ERROR at teardown of TestDensity.test_to_pointcloud[1.5] ___________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC050>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpox08thup'

tests\test_density.py:45: PermissionError
______________ ERROR at teardown of TestDensity.test__pad_slice _______________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC0A0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmppdwylj0f'

tests\test_density.py:45: PermissionError
______________ ERROR at teardown of TestDensity.test_adjust_box _______________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC0F0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp024szgt2'

tests\test_density.py:45: PermissionError
_______________ ERROR at teardown of TestDensity.test_trim_box ________________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC140>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpirh56sgg'

tests\test_density.py:45: PermissionError
__________________ ERROR at teardown of TestDensity.test_pad __________________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC190>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpss1_rnpz'

tests\test_density.py:45: PermissionError
_________ ERROR at teardown of TestDensity.test_pad_error[new_shape0] _________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC230>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpc74793tq'

tests\test_density.py:45: PermissionError
_________ ERROR at teardown of TestDensity.test_pad_error[new_shape1] _________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC320>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpc967gymg'

tests\test_density.py:45: PermissionError
_________ ERROR at teardown of TestDensity.test_pad_error[new_shape2] _________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC3C0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpwu21ft4o'

tests\test_density.py:45: PermissionError
_________ ERROR at teardown of TestDensity.test_minimum_enclosing_box _________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC410>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp9l5947nh'

tests\test_density.py:45: PermissionError
___________ ERROR at teardown of TestDensity.test_centered[cutoff0] ___________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC460>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpdyf9fcwf'

tests\test_density.py:45: PermissionError
______________ ERROR at teardown of TestDensity.test_centered[0] ______________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC4B0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp2zcpbf5y'

tests\test_density.py:45: PermissionError
___________ ERROR at teardown of TestDensity.test_centered[cutoff2] ___________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC550>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp_b34_q3y'

tests\test_density.py:45: PermissionError
________ ERROR at teardown of TestDensity.test_rigid_transform[1-True] ________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC640>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpcwcf0uun'

tests\test_density.py:45: PermissionError
_______ ERROR at teardown of TestDensity.test_rigid_transform[1-False] ________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC6E0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpnk3ln0pa'

tests\test_density.py:45: PermissionError
________ ERROR at teardown of TestDensity.test_rigid_transform[3-True] ________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC780>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpyly9oilr'

tests\test_density.py:45: PermissionError
_______ ERROR at teardown of TestDensity.test_rigid_transform[3-False] ________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC820>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpvl1tj520'

tests\test_density.py:45: PermissionError
_________ ERROR at teardown of TestDensity.test_resample[spline-2-1] __________

self = <tests.test_density.TestDensity object at 0x000002CE10FDC960>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp1j9w04yw'

tests\test_density.py:45: PermissionError
_________ ERROR at teardown of TestDensity.test_resample[spline-4-3] __________

self = <tests.test_density.TestDensity object at 0x000002CE10FDCA00>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpipobx3_g'

tests\test_density.py:45: PermissionError
_________ ERROR at teardown of TestDensity.test_resample[fourier-2-1] _________

self = <tests.test_density.TestDensity object at 0x000002CE10FDCAA0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp4vz434ck'

tests\test_density.py:45: PermissionError
_________ ERROR at teardown of TestDensity.test_resample[fourier-4-3] _________

self = <tests.test_density.TestDensity object at 0x000002CE10FDCB40>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmphfj4nbey'

tests\test_density.py:45: PermissionError
________ ERROR at teardown of TestDensity.test_density_boundary[0.5-2] ________

self = <tests.test_density.TestDensity object at 0x000002CE10FDCC30>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpr7q_xp2v'

tests\test_density.py:45: PermissionError
_________ ERROR at teardown of TestDensity.test_density_boundary[1-3] _________

self = <tests.test_density.TestDensity object at 0x000002CE10FDCCD0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp3imd5czw'

tests\test_density.py:45: PermissionError
____ ERROR at teardown of TestDensity.test_density_boundary_error[-0.5-0] _____

self = <tests.test_density.TestDensity object at 0x000002CE10FDCDC0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpxs9q0dk0'

tests\test_density.py:45: PermissionError
_____ ERROR at teardown of TestDensity.test_density_boundary_error[1--3] ______

self = <tests.test_density.TestDensity object at 0x000002CE10FDCE60>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmplmt6l737'

tests\test_density.py:45: PermissionError
____ ERROR at teardown of TestDensity.test_surface_coordinates[ConvexHull] ____

self = <tests.test_density.TestDensity object at 0x000002CE10FDCF00>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp8q_iroud'

tests\test_density.py:45: PermissionError
______ ERROR at teardown of TestDensity.test_surface_coordinates[Weight] ______

self = <tests.test_density.TestDensity object at 0x000002CE10FDCFA0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp059z_h6k'

tests\test_density.py:45: PermissionError
______ ERROR at teardown of TestDensity.test_surface_coordinates[Sobel] _______

self = <tests.test_density.TestDensity object at 0x000002CE10FDD090>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp38u5cnef'

tests\test_density.py:45: PermissionError
_____ ERROR at teardown of TestDensity.test_surface_coordinates[Laplace] ______

self = <tests.test_density.TestDensity object at 0x000002CE10FDD130>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp92guagel'

tests\test_density.py:45: PermissionError
_____ ERROR at teardown of TestDensity.test_surface_coordinates[Minimum] ______

self = <tests.test_density.TestDensity object at 0x000002CE10FDD1D0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpvu7wcpvl'

tests\test_density.py:45: PermissionError
_______ ERROR at teardown of TestDensity.test_surface_coordinates_error _______

self = <tests.test_density.TestDensity object at 0x000002CE10FDD220>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp9fi3h866'

tests\test_density.py:45: PermissionError
____________ ERROR at teardown of TestDensity.test_normal_vectors _____________

self = <tests.test_density.TestDensity object at 0x000002CE10FDD270>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpg1_0aylc'

tests\test_density.py:45: PermissionError
_________ ERROR at teardown of TestDensity.test_normal_vectors_error __________

self = <tests.test_density.TestDensity object at 0x000002CE10FDD310>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpum4tnnai'

tests\test_density.py:45: PermissionError
_______________ ERROR at teardown of TestDensity.test_core_mask _______________

self = <tests.test_density.TestDensity object at 0x000002CE10FDD3B0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp77e0vv7q'

tests\test_density.py:45: PermissionError
____________ ERROR at teardown of TestDensity.test_center_of_mass _____________

self = <tests.test_density.TestDensity object at 0x000002CE10FDD450>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpgc79xz54'

tests\test_density.py:45: PermissionError
___ ERROR at teardown of TestDensity.test_match_densities[CrossCorrelation] ___

self = <tests.test_density.TestDensity object at 0x000002CE10FDD590>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpso3vwoqg'

tests\test_density.py:45: PermissionError
---------------------------- Captured stdout call -----------------------------
Niter: 5, success : True (['requested number of basinhopping iterations completed successfully']).
Initial score: -998.7816162109375 - Refined score: -1718.448486328125
_ ERROR at teardown of TestDensity.test_match_densities[NormalizedCrossCorrelation] _

self = <tests.test_density.TestDensity object at 0x000002CE10FDD5E0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp7xdq7n5n'

tests\test_density.py:45: PermissionError
---------------------------- Captured stdout call -----------------------------
Niter: 5, success : True (['requested number of basinhopping iterations completed successfully']).
Initial score: -0.6845981478691101 - Refined score: -0.9983691573143005
______ ERROR at teardown of TestDensity.test_match_structure_to_density _______

self = <tests.test_density.TestDensity object at 0x000002CE10FDD6D0>

    def teardown_method(self):
        del self.density
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpt5qz9kx4'

tests\test_density.py:45: PermissionError
---------------------------- Captured stdout call -----------------------------
Niter: 10, success : True (['requested number of basinhopping iterations completed successfully']).
Initial score: -271.3240966796875 - Refined score: -304.31573486328125
___________ ERROR at teardown of TestStructure.test_initialization ____________

self = <tests.test_structure.TestStructure object at 0x000002CE11AB39D0>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpk458x04y'

tests\test_structure.py:40: PermissionError
_ ERROR at teardown of TestStructure.test_initialization_errors[record_type] __

self = <tests.test_structure.TestStructure object at 0x000002CE11AB3B10>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpklxxb1_i'

tests\test_structure.py:40: PermissionError
_ ERROR at teardown of TestStructure.test_initialization_errors[atom_serial_number] _

self = <tests.test_structure.TestStructure object at 0x000002CE11AD7100>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp1m6fw3e3'

tests\test_structure.py:40: PermissionError
__ ERROR at teardown of TestStructure.test_initialization_errors[atom_name] ___

self = <tests.test_structure.TestStructure object at 0x000002CE11AD7950>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpm0f98n_k'

tests\test_structure.py:40: PermissionError
_ ERROR at teardown of TestStructure.test_initialization_errors[atom_coordinate] _

self = <tests.test_structure.TestStructure object at 0x000002CE11C403B0>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp4c17vdnj'

tests\test_structure.py:40: PermissionError
_ ERROR at teardown of TestStructure.test_initialization_errors[alternate_location_indicator] _

self = <tests.test_structure.TestStructure object at 0x000002CE11AC39B0>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmposdcqelt'

tests\test_structure.py:40: PermissionError
_ ERROR at teardown of TestStructure.test_initialization_errors[residue_name] _

self = <tests.test_structure.TestStructure object at 0x000002CE11AC3AC0>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpi98t67xk'

tests\test_structure.py:40: PermissionError
_ ERROR at teardown of TestStructure.test_initialization_errors[chain_identifier] _

self = <tests.test_structure.TestStructure object at 0x000002CE11B2FA50>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp9ttjru9t'

tests\test_structure.py:40: PermissionError
_ ERROR at teardown of TestStructure.test_initialization_errors[residue_sequence_number] _

self = <tests.test_structure.TestStructure object at 0x000002CE11B2FB50>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpphog3gmz'

tests\test_structure.py:40: PermissionError
_ ERROR at teardown of TestStructure.test_initialization_errors[code_for_residue_insertion] _

self = <tests.test_structure.TestStructure object at 0x000002CE11B53110>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpe0xio3ul'

tests\test_structure.py:40: PermissionError
__ ERROR at teardown of TestStructure.test_initialization_errors[occupancy] ___

self = <tests.test_structure.TestStructure object at 0x000002CE11B53200>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpb1bpi2w1'

tests\test_structure.py:40: PermissionError
_ ERROR at teardown of TestStructure.test_initialization_errors[temperature_factor] _

self = <tests.test_structure.TestStructure object at 0x000002CE11BEBAF0>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpql8oygfv'

tests\test_structure.py:40: PermissionError
_ ERROR at teardown of TestStructure.test_initialization_errors[segment_identifier] _

self = <tests.test_structure.TestStructure object at 0x000002CE11BEB310>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpyd4nibtc'

tests\test_structure.py:40: PermissionError
_ ERROR at teardown of TestStructure.test_initialization_errors[element_symbol] _

self = <tests.test_structure.TestStructure object at 0x000002CE11BA7450>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpeepmuqif'

tests\test_structure.py:40: PermissionError
_____________ ERROR at teardown of TestStructure.test__getitem__ ______________

self = <tests.test_structure.TestStructure object at 0x000002CE11A2ED50>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmps88k2bn_'

tests\test_structure.py:40: PermissionError
_______________ ERROR at teardown of TestStructure.test__repr__ _______________

self = <tests.test_structure.TestStructure object at 0x000002CE11A2EF90>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpopeswax3'

tests\test_structure.py:40: PermissionError
_ ERROR at teardown of TestStructure.test_fromfile[C:\\Users\\boydpeters\\projects\\pyTME\\tests\\data\\Structures\\5khe.cif] _

self = <tests.test_structure.TestStructure object at 0x000002CE11BF6200>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpkbzxypfn'

tests\test_structure.py:40: PermissionError
_ ERROR at teardown of TestStructure.test_fromfile[C:\\Users\\boydpeters\\projects\\pyTME\\tests\\data\\Structures\\5khe.pdb] _

self = <tests.test_structure.TestStructure object at 0x000002CE11BF6360>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp2cyj84kk'

tests\test_structure.py:40: PermissionError
___________ ERROR at teardown of TestStructure.test_fromfile_error ____________

self = <tests.test_structure.TestStructure object at 0x000002CE11C29DB0>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpc23mc2bg'

tests\test_structure.py:40: PermissionError
____________ ERROR at teardown of TestStructure.test_to_file[cif] _____________

self = <tests.test_structure.TestStructure object at 0x000002CE11C2A2B0>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpz3upa13v'

tests\test_structure.py:40: PermissionError
____________ ERROR at teardown of TestStructure.test_to_file[pdb] _____________

self = <tests.test_structure.TestStructure object at 0x000002CE11B01FD0>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpoer_m_qp'

tests\test_structure.py:40: PermissionError
____________ ERROR at teardown of TestStructure.test_to_file[gro] _____________

self = <tests.test_structure.TestStructure object at 0x000002CE11C4EB50>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpee5sforp'

tests\test_structure.py:40: PermissionError
____________ ERROR at teardown of TestStructure.test_to_file_error ____________

self = <tests.test_structure.TestStructure object at 0x000002CE11C4EED0>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpw52__p1i'

tests\test_structure.py:40: PermissionError
___________ ERROR at teardown of TestStructure.test_subset_by_chain ___________

self = <tests.test_structure.TestStructure object at 0x000002CE11C3FD90>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp08nhaavb'

tests\test_structure.py:40: PermissionError
________ ERROR at teardown of TestStructure.test_subset_by_chain_range ________

self = <tests.test_structure.TestStructure object at 0x000002CE11C58130>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp9mpknr44'

tests\test_structure.py:40: PermissionError
___________ ERROR at teardown of TestStructure.test_center_of_mass ____________

self = <tests.test_structure.TestStructure object at 0x000002CE11BA3110>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpsxy4jief'

tests\test_structure.py:40: PermissionError
_______ ERROR at teardown of TestStructure.test__get_atom_weights_error _______

self = <tests.test_structure.TestStructure object at 0x000002CE11BA3170>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp9v9742g2'

tests\test_structure.py:40: PermissionError
_________ ERROR at teardown of TestStructure.test_compare_structures __________

self = <tests.test_structure.TestStructure object at 0x000002CE11C0E490>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpaxft2fql'

tests\test_structure.py:40: PermissionError
______ ERROR at teardown of TestStructure.test_comopare_structures_error ______

self = <tests.test_structure.TestStructure object at 0x000002CE11C0E530>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpe6ez5h7n'

tests\test_structure.py:40: PermissionError
__________ ERROR at teardown of TestStructure.test_align_structures ___________

self = <tests.test_structure.TestStructure object at 0x000002CE11C0E670>

    def teardown_method(self):
        del self.structure
>       remove(self.path)
E       PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpflm2fwzk'

tests\test_structure.py:40: PermissionError
---------------------------- Captured stdout call -----------------------------
Initial RMSD: 22.37634 - Final RMSD: 0.00003
Initial RMSD: 22.37634 - Final RMSD: 0.00003
================================== FAILURES ===================================
__________________________ TestDensity.test_to_numpy __________________________

self = <tests.test_density.TestDensity object at 0x000002CE7FDAF7F0>

    def test_to_numpy(self):
        temp = self.density.copy()
        temp.to_memmap()
>       temp.to_numpy()

tests\test_density.py:258: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tme\density.py:1093: in to_numpy
    self.data = memmap_to_array(self.data)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

arr = array([[[0., 0., 0., ..., 0., 0., 0.],
        [0., 0., 0., ..., 0., 0., 0.],
        [0., 0., 0., ..., 0., 0., 0.],
 ...0.],
        [0., 0., 0., ..., 0., 0., 0.],
        [0., 0., 0., ..., 0., 0., 0.]]], shape=(50, 50, 50), dtype=float32)

    def memmap_to_array(arr: NDArray) -> NDArray:
        """
        Convert a obj:`numpy.memmap` to a obj:`numpy.ndarray` and delete the memmap.
    
        Parameters
        ----------
        arr : obj:`numpy.memmap`
            Input data.
    
        Returns
        -------
        obj:`numpy.ndarray`
            In-memory version of ``arr``.
        """
        if isinstance(arr, np.memmap):
            memmap_filepath = arr.filename
            arr = np.array(arr)
>           os.remove(memmap_filepath)
E           PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmphpupxr9v'

tme\matching_utils.py:188: PermissionError
____ TestPostprocessing.test_postproces_score_formats[orientations-score] _____

self = <tests.test_matching_cli.TestPostprocessing object at 0x000002CE110769E0>
input_format = 'score', output_format = 'orientations'

    @pytest.mark.parametrize("input_format", ("score", "peaks"))
    @pytest.mark.parametrize(
        "output_format",
        ("orientations", "alignment", "average", "relion4", "relion5"),
    )
    def test_postproces_score_formats(self, input_format, output_format):
        self.try_delete(self.tempdir)
        makedirs(self.tempdir, exist_ok=True)
    
        input_file = self.score_pickle
        if input_format == "peaks":
            input_file = self.peak_pickle
    
        argdict = {
            "--input-file": input_file,
            "--output-format": output_format,
            "--output-prefix": f"{self.tempdir}/temp",
            "--num-peaks": 3,
            "--peak-caller": "PeakCallerMaximumFilter",
        }
        cmd = argdict_to_command(argdict, executable="postprocess.py")
        ret = subprocess.run(cmd, capture_output=True, shell=True)
    
        match output_format:
            case "orientations":
>               assert exists(f"{self.tempdir}/temp.tsv")
E               AssertionError: assert False
E                +  where False = exists('C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp3chtibx7/temp.tsv')

tests\test_matching_cli.py:277: AssertionError
____ TestPostprocessing.test_postproces_score_formats[orientations-peaks] _____

self = <tests.test_matching_cli.TestPostprocessing object at 0x000002CE110768F0>
input_format = 'peaks', output_format = 'orientations'

    @pytest.mark.parametrize("input_format", ("score", "peaks"))
    @pytest.mark.parametrize(
        "output_format",
        ("orientations", "alignment", "average", "relion4", "relion5"),
    )
    def test_postproces_score_formats(self, input_format, output_format):
        self.try_delete(self.tempdir)
        makedirs(self.tempdir, exist_ok=True)
    
        input_file = self.score_pickle
        if input_format == "peaks":
            input_file = self.peak_pickle
    
        argdict = {
            "--input-file": input_file,
            "--output-format": output_format,
            "--output-prefix": f"{self.tempdir}/temp",
            "--num-peaks": 3,
            "--peak-caller": "PeakCallerMaximumFilter",
        }
        cmd = argdict_to_command(argdict, executable="postprocess.py")
        ret = subprocess.run(cmd, capture_output=True, shell=True)
    
        match output_format:
            case "orientations":
>               assert exists(f"{self.tempdir}/temp.tsv")
E               AssertionError: assert False
E                +  where False = exists('C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp3chtibx7/temp.tsv')

tests\test_matching_cli.py:277: AssertionError
______ TestPostprocessing.test_postproces_score_formats[alignment-score] ______

self = <tests.test_matching_cli.TestPostprocessing object at 0x000002CE11076940>
input_format = 'score', output_format = 'alignment'

    @pytest.mark.parametrize("input_format", ("score", "peaks"))
    @pytest.mark.parametrize(
        "output_format",
        ("orientations", "alignment", "average", "relion4", "relion5"),
    )
    def test_postproces_score_formats(self, input_format, output_format):
        self.try_delete(self.tempdir)
        makedirs(self.tempdir, exist_ok=True)
    
        input_file = self.score_pickle
        if input_format == "peaks":
            input_file = self.peak_pickle
    
        argdict = {
            "--input-file": input_file,
            "--output-format": output_format,
            "--output-prefix": f"{self.tempdir}/temp",
            "--num-peaks": 3,
            "--peak-caller": "PeakCallerMaximumFilter",
        }
        cmd = argdict_to_command(argdict, executable="postprocess.py")
        ret = subprocess.run(cmd, capture_output=True, shell=True)
    
        match output_format:
            case "orientations":
                assert exists(f"{self.tempdir}/temp.tsv")
            case "alignment":
>               assert exists(f"{self.tempdir}/temp_0.mrc")
E               AssertionError: assert False
E                +  where False = exists('C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp3chtibx7/temp_0.mrc')

tests\test_matching_cli.py:279: AssertionError
______ TestPostprocessing.test_postproces_score_formats[alignment-peaks] ______

self = <tests.test_matching_cli.TestPostprocessing object at 0x000002CE11076990>
input_format = 'peaks', output_format = 'alignment'

    @pytest.mark.parametrize("input_format", ("score", "peaks"))
    @pytest.mark.parametrize(
        "output_format",
        ("orientations", "alignment", "average", "relion4", "relion5"),
    )
    def test_postproces_score_formats(self, input_format, output_format):
        self.try_delete(self.tempdir)
        makedirs(self.tempdir, exist_ok=True)
    
        input_file = self.score_pickle
        if input_format == "peaks":
            input_file = self.peak_pickle
    
        argdict = {
            "--input-file": input_file,
            "--output-format": output_format,
            "--output-prefix": f"{self.tempdir}/temp",
            "--num-peaks": 3,
            "--peak-caller": "PeakCallerMaximumFilter",
        }
        cmd = argdict_to_command(argdict, executable="postprocess.py")
        ret = subprocess.run(cmd, capture_output=True, shell=True)
    
        match output_format:
            case "orientations":
                assert exists(f"{self.tempdir}/temp.tsv")
            case "alignment":
>               assert exists(f"{self.tempdir}/temp_0.mrc")
E               AssertionError: assert False
E                +  where False = exists('C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp3chtibx7/temp_0.mrc')

tests\test_matching_cli.py:279: AssertionError
_______ TestPostprocessing.test_postproces_score_formats[average-score] _______

self = <tests.test_matching_cli.TestPostprocessing object at 0x000002CE11076A30>
input_format = 'score', output_format = 'average'

    @pytest.mark.parametrize("input_format", ("score", "peaks"))
    @pytest.mark.parametrize(
        "output_format",
        ("orientations", "alignment", "average", "relion4", "relion5"),
    )
    def test_postproces_score_formats(self, input_format, output_format):
        self.try_delete(self.tempdir)
        makedirs(self.tempdir, exist_ok=True)
    
        input_file = self.score_pickle
        if input_format == "peaks":
            input_file = self.peak_pickle
    
        argdict = {
            "--input-file": input_file,
            "--output-format": output_format,
            "--output-prefix": f"{self.tempdir}/temp",
            "--num-peaks": 3,
            "--peak-caller": "PeakCallerMaximumFilter",
        }
        cmd = argdict_to_command(argdict, executable="postprocess.py")
        ret = subprocess.run(cmd, capture_output=True, shell=True)
    
        match output_format:
            case "orientations":
                assert exists(f"{self.tempdir}/temp.tsv")
            case "alignment":
                assert exists(f"{self.tempdir}/temp_0.mrc")
            case "average":
>               assert exists(f"{self.tempdir}/temp.mrc")
E               AssertionError: assert False
E                +  where False = exists('C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp3chtibx7/temp.mrc')

tests\test_matching_cli.py:281: AssertionError
_______ TestPostprocessing.test_postproces_score_formats[average-peaks] _______

self = <tests.test_matching_cli.TestPostprocessing object at 0x000002CE11076A80>
input_format = 'peaks', output_format = 'average'

    @pytest.mark.parametrize("input_format", ("score", "peaks"))
    @pytest.mark.parametrize(
        "output_format",
        ("orientations", "alignment", "average", "relion4", "relion5"),
    )
    def test_postproces_score_formats(self, input_format, output_format):
        self.try_delete(self.tempdir)
        makedirs(self.tempdir, exist_ok=True)
    
        input_file = self.score_pickle
        if input_format == "peaks":
            input_file = self.peak_pickle
    
        argdict = {
            "--input-file": input_file,
            "--output-format": output_format,
            "--output-prefix": f"{self.tempdir}/temp",
            "--num-peaks": 3,
            "--peak-caller": "PeakCallerMaximumFilter",
        }
        cmd = argdict_to_command(argdict, executable="postprocess.py")
        ret = subprocess.run(cmd, capture_output=True, shell=True)
    
        match output_format:
            case "orientations":
                assert exists(f"{self.tempdir}/temp.tsv")
            case "alignment":
                assert exists(f"{self.tempdir}/temp_0.mrc")
            case "average":
>               assert exists(f"{self.tempdir}/temp.mrc")
E               AssertionError: assert False
E                +  where False = exists('C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp3chtibx7/temp.mrc')

tests\test_matching_cli.py:281: AssertionError
_______ TestPostprocessing.test_postproces_score_formats[relion4-score] _______

self = <tests.test_matching_cli.TestPostprocessing object at 0x000002CE11076AD0>
input_format = 'score', output_format = 'relion4'

    @pytest.mark.parametrize("input_format", ("score", "peaks"))
    @pytest.mark.parametrize(
        "output_format",
        ("orientations", "alignment", "average", "relion4", "relion5"),
    )
    def test_postproces_score_formats(self, input_format, output_format):
        self.try_delete(self.tempdir)
        makedirs(self.tempdir, exist_ok=True)
    
        input_file = self.score_pickle
        if input_format == "peaks":
            input_file = self.peak_pickle
    
        argdict = {
            "--input-file": input_file,
            "--output-format": output_format,
            "--output-prefix": f"{self.tempdir}/temp",
            "--num-peaks": 3,
            "--peak-caller": "PeakCallerMaximumFilter",
        }
        cmd = argdict_to_command(argdict, executable="postprocess.py")
        ret = subprocess.run(cmd, capture_output=True, shell=True)
    
        match output_format:
            case "orientations":
                assert exists(f"{self.tempdir}/temp.tsv")
            case "alignment":
                assert exists(f"{self.tempdir}/temp_0.mrc")
            case "average":
                assert exists(f"{self.tempdir}/temp.mrc")
            case "relion4":
>               assert exists(f"{self.tempdir}/temp.star")
E               AssertionError: assert False
E                +  where False = exists('C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp3chtibx7/temp.star')

tests\test_matching_cli.py:283: AssertionError
_______ TestPostprocessing.test_postproces_score_formats[relion4-peaks] _______

self = <tests.test_matching_cli.TestPostprocessing object at 0x000002CE11076B20>
input_format = 'peaks', output_format = 'relion4'

    @pytest.mark.parametrize("input_format", ("score", "peaks"))
    @pytest.mark.parametrize(
        "output_format",
        ("orientations", "alignment", "average", "relion4", "relion5"),
    )
    def test_postproces_score_formats(self, input_format, output_format):
        self.try_delete(self.tempdir)
        makedirs(self.tempdir, exist_ok=True)
    
        input_file = self.score_pickle
        if input_format == "peaks":
            input_file = self.peak_pickle
    
        argdict = {
            "--input-file": input_file,
            "--output-format": output_format,
            "--output-prefix": f"{self.tempdir}/temp",
            "--num-peaks": 3,
            "--peak-caller": "PeakCallerMaximumFilter",
        }
        cmd = argdict_to_command(argdict, executable="postprocess.py")
        ret = subprocess.run(cmd, capture_output=True, shell=True)
    
        match output_format:
            case "orientations":
                assert exists(f"{self.tempdir}/temp.tsv")
            case "alignment":
                assert exists(f"{self.tempdir}/temp_0.mrc")
            case "average":
                assert exists(f"{self.tempdir}/temp.mrc")
            case "relion4":
>               assert exists(f"{self.tempdir}/temp.star")
E               AssertionError: assert False
E                +  where False = exists('C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp3chtibx7/temp.star')

tests\test_matching_cli.py:283: AssertionError
_______ TestPostprocessing.test_postproces_score_formats[relion5-score] _______

self = <tests.test_matching_cli.TestPostprocessing object at 0x000002CE11076B70>
input_format = 'score', output_format = 'relion5'

    @pytest.mark.parametrize("input_format", ("score", "peaks"))
    @pytest.mark.parametrize(
        "output_format",
        ("orientations", "alignment", "average", "relion4", "relion5"),
    )
    def test_postproces_score_formats(self, input_format, output_format):
        self.try_delete(self.tempdir)
        makedirs(self.tempdir, exist_ok=True)
    
        input_file = self.score_pickle
        if input_format == "peaks":
            input_file = self.peak_pickle
    
        argdict = {
            "--input-file": input_file,
            "--output-format": output_format,
            "--output-prefix": f"{self.tempdir}/temp",
            "--num-peaks": 3,
            "--peak-caller": "PeakCallerMaximumFilter",
        }
        cmd = argdict_to_command(argdict, executable="postprocess.py")
        ret = subprocess.run(cmd, capture_output=True, shell=True)
    
        match output_format:
            case "orientations":
                assert exists(f"{self.tempdir}/temp.tsv")
            case "alignment":
                assert exists(f"{self.tempdir}/temp_0.mrc")
            case "average":
                assert exists(f"{self.tempdir}/temp.mrc")
            case "relion4":
                assert exists(f"{self.tempdir}/temp.star")
            case "relion5":
>               assert exists(f"{self.tempdir}/temp.star")
E               AssertionError: assert False
E                +  where False = exists('C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp3chtibx7/temp.star')

tests\test_matching_cli.py:285: AssertionError
_______ TestPostprocessing.test_postproces_score_formats[relion5-peaks] _______

self = <tests.test_matching_cli.TestPostprocessing object at 0x000002CE11076BC0>
input_format = 'peaks', output_format = 'relion5'

    @pytest.mark.parametrize("input_format", ("score", "peaks"))
    @pytest.mark.parametrize(
        "output_format",
        ("orientations", "alignment", "average", "relion4", "relion5"),
    )
    def test_postproces_score_formats(self, input_format, output_format):
        self.try_delete(self.tempdir)
        makedirs(self.tempdir, exist_ok=True)
    
        input_file = self.score_pickle
        if input_format == "peaks":
            input_file = self.peak_pickle
    
        argdict = {
            "--input-file": input_file,
            "--output-format": output_format,
            "--output-prefix": f"{self.tempdir}/temp",
            "--num-peaks": 3,
            "--peak-caller": "PeakCallerMaximumFilter",
        }
        cmd = argdict_to_command(argdict, executable="postprocess.py")
        ret = subprocess.run(cmd, capture_output=True, shell=True)
    
        match output_format:
            case "orientations":
                assert exists(f"{self.tempdir}/temp.tsv")
            case "alignment":
                assert exists(f"{self.tempdir}/temp_0.mrc")
            case "average":
                assert exists(f"{self.tempdir}/temp.mrc")
            case "relion4":
                assert exists(f"{self.tempdir}/temp.star")
            case "relion5":
>               assert exists(f"{self.tempdir}/temp.star")
E               AssertionError: assert False
E                +  where False = exists('C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmp3chtibx7/temp.star')

tests\test_matching_cli.py:285: AssertionError
______________________ TestMatchingUtils.test_pickle_io _______________________

src = 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpw5vz4ys1'
dst = 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpytynyrap.mm'
copy_function = <function copy2 at 0x000002CE56448C20>

    def move(src, dst, copy_function=copy2):
        """Recursively move a file or directory to another location. This is
        similar to the Unix "mv" command. Return the file or directory's
        destination.
    
        If dst is an existing directory or a symlink to a directory, then src is
        moved inside that directory. The destination path in that directory must
        not already exist.
    
        If dst already exists but is not a directory, it may be overwritten
        depending on os.rename() semantics.
    
        If the destination is on our current filesystem, then rename() is used.
        Otherwise, src is copied to the destination and then removed. Symlinks are
        recreated under the new name if os.rename() fails because of cross
        filesystem renames.
    
        The optional `copy_function` argument is a callable that will be used
        to copy the source or it will be delegated to `copytree`.
        By default, copy2() is used, but any function that supports the same
        signature (like copy()) can be used.
    
        A lot more could be done here...  A look at a mv.c shows a lot of
        the issues this implementation glosses over.
    
        """
        sys.audit("shutil.move", src, dst)
        real_dst = dst
        if os.path.isdir(dst):
            if _samefile(src, dst) and not os.path.islink(src):
                # We might be on a case insensitive filesystem,
                # perform the rename anyway.
                os.rename(src, dst)
                return
    
            # Using _basename instead of os.path.basename is important, as we must
            # ignore any trailing slash to avoid the basename returning ''
            real_dst = os.path.join(dst, _basename(src))
    
            if os.path.exists(real_dst):
                raise Error("Destination path '%s' already exists" % real_dst)
        try:
>           os.rename(src, real_dst)
E           PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpw5vz4ys1' -> 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpytynyrap.mm'

..\..\AppData\Roaming\uv\python\cpython-3.13.5-windows-x86_64-none\Lib\shutil.py:856: PermissionError

During handling of the above exception, another exception occurred:

self = <tests.test_matching_utils.TestMatchingUtils object at 0x000002CE11B9FB60>

    def test_pickle_io(self):
        _, filename = mkstemp()
    
        data = ["Hello", 123, np.array([1, 2, 3])]
        write_pickle(data=data, filename=filename)
        loaded_data = load_pickle(filename)
        assert all([np.array_equal(a, b) for a, b in zip(data, loaded_data)])
    
        data = 42
        write_pickle(data=data, filename=filename)
        loaded_data = load_pickle(filename)
        assert loaded_data == data
    
        _, filename = mkstemp()
        data = np.memmap(filename, dtype="float32", mode="w+", shape=(3,))
        data[:] = [1.1, 2.2, 3.3]
        data.flush()
        data = np.memmap(filename, dtype="float32", mode="r+", shape=(3,))
        _, filename = mkstemp()
>       write_pickle(data=data, filename=filename)

tests\test_matching_utils.py:126: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tme\matching_utils.py:228: in write_pickle
    future.result()
..\..\AppData\Roaming\uv\python\cpython-3.13.5-windows-x86_64-none\Lib\concurrent\futures\_base.py:456: in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
..\..\AppData\Roaming\uv\python\cpython-3.13.5-windows-x86_64-none\Lib\concurrent\futures\_base.py:401: in __get_result
    raise self._exception
..\..\AppData\Roaming\uv\python\cpython-3.13.5-windows-x86_64-none\Lib\concurrent\futures\thread.py:59: in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

src = 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpw5vz4ys1'
dst = 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpytynyrap.mm'
copy_function = <function copy2 at 0x000002CE56448C20>

    def move(src, dst, copy_function=copy2):
        """Recursively move a file or directory to another location. This is
        similar to the Unix "mv" command. Return the file or directory's
        destination.
    
        If dst is an existing directory or a symlink to a directory, then src is
        moved inside that directory. The destination path in that directory must
        not already exist.
    
        If dst already exists but is not a directory, it may be overwritten
        depending on os.rename() semantics.
    
        If the destination is on our current filesystem, then rename() is used.
        Otherwise, src is copied to the destination and then removed. Symlinks are
        recreated under the new name if os.rename() fails because of cross
        filesystem renames.
    
        The optional `copy_function` argument is a callable that will be used
        to copy the source or it will be delegated to `copytree`.
        By default, copy2() is used, but any function that supports the same
        signature (like copy()) can be used.
    
        A lot more could be done here...  A look at a mv.c shows a lot of
        the issues this implementation glosses over.
    
        """
        sys.audit("shutil.move", src, dst)
        real_dst = dst
        if os.path.isdir(dst):
            if _samefile(src, dst) and not os.path.islink(src):
                # We might be on a case insensitive filesystem,
                # perform the rename anyway.
                os.rename(src, dst)
                return
    
            # Using _basename instead of os.path.basename is important, as we must
            # ignore any trailing slash to avoid the basename returning ''
            real_dst = os.path.join(dst, _basename(src))
    
            if os.path.exists(real_dst):
                raise Error("Destination path '%s' already exists" % real_dst)
        try:
            os.rename(src, real_dst)
        except OSError:
            if os.path.islink(src):
                linkto = os.readlink(src)
                os.symlink(linkto, real_dst)
                os.unlink(src)
            elif os.path.isdir(src):
                if _destinsrc(src, dst):
                    raise Error("Cannot move a directory '%s' into itself"
                                " '%s'." % (src, dst))
                if (_is_immutable(src)
                        or (not os.access(src, os.W_OK) and os.listdir(src)
                            and sys.platform == 'darwin')):
                    raise PermissionError("Cannot move the non-empty directory "
                                          "'%s': Lacking write permission to '%s'."
                                          % (src, src))
                copytree(src, real_dst, copy_function=copy_function,
                         symlinks=True)
                rmtree(src)
            else:
                copy_function(src, real_dst)
>               os.unlink(src)
E               PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\BOYDPE~1\\AppData\\Local\\Temp\\tmpw5vz4ys1'

..\..\AppData\Roaming\uv\python\cpython-3.13.5-windows-x86_64-none\Lib\shutil.py:877: PermissionError
============================== warnings summary ===============================
tests/preprocessing/test_preprocessor.py::TestPreprocessor::test_kaiserb_filter[1]
  C:\Users\boydpeters\projects\pyTME\tme\preprocessor.py:591: RuntimeWarning: invalid value encountered in divide
    arr = beta * np.sqrt(1 - ((window - alpha) / alpha) ** 2.0)

tests/preprocessing/test_preprocessor.py::TestPreprocessor::test_blob_filter[1]
  C:\Users\boydpeters\projects\pyTME\tme\preprocessor.py:622: RuntimeWarning: invalid value encountered in divide
    arr = beta * np.sqrt(1 - ((window - alpha) / alpha) ** 2.0)

tests/test_density.py: 9 warnings
tests/test_matching_cli.py: 4 warnings
  C:\Users\boydpeters\projects\pyTME\tme\density.py:873: UserWarning: Current data type not supported by MRC format. Defaulting to float32.
    warnings.warn(

tests/test_density.py::TestDensity::test_file_format_io[True-True-True-tiff]
tests/test_density.py::TestDensity::test_file_format_io[True-False-True-tiff]
tests/test_density.py::TestDensity::test_file_format_io[False-True-True-tiff]
tests/test_density.py::TestDensity::test_file_format_io[False-False-True-tiff]
  C:\Users\boydpeters\projects\pyTME\tme\density.py:949: FutureWarning: The plugin infrastructure in `skimage.io` is deprecated since version 0.25 and will be removed in 0.27 (or later). To avoid this warning, please do not pass additional keyword arguments for plugins (`**plugin_args`). Instead, use `imageio` or other I/O packages directly. See also `skimage.io.imsave`.
    skio.imsave(fname=swap, arr=self.data.astype("float32"), **kwargs)

tests/test_density.py::TestDensity::test_file_format_io[True-True-True-tiff]
tests/test_density.py::TestDensity::test_file_format_io[True-False-True-tiff]
tests/test_density.py::TestDensity::test_file_format_io[False-True-True-tiff]
tests/test_density.py::TestDensity::test_file_format_io[False-False-True-tiff]
  C:\Users\boydpeters\projects\pyTME\.venv\Lib\site-packages\imageio\plugins\pillow.py:126: UserWarning: Can't determine file format to write as. You _must_ set `format` during write or the call will fail. Use `extension` to supress this warning. 
    warnings.warn(

tests/test_density.py::TestDensity::test_file_format_io[True-True-True-tiff]
tests/test_density.py::TestDensity::test_file_format_io[True-True-False-tiff]
tests/test_density.py::TestDensity::test_file_format_io[True-False-True-tiff]
tests/test_density.py::TestDensity::test_file_format_io[True-False-False-tiff]
tests/test_density.py::TestDensity::test_file_format_io[False-True-True-tiff]
tests/test_density.py::TestDensity::test_file_format_io[False-True-False-tiff]
tests/test_density.py::TestDensity::test_file_format_io[False-False-True-tiff]
tests/test_density.py::TestDensity::test_file_format_io[False-False-False-tiff]
  C:\Users\boydpeters\projects\pyTME\tme\density.py:580: UserWarning: origin and sampling_rate are not yet extracted from non CCP4/MRC files.
    warnings.warn(

tests/test_density.py::TestDensity::test_from_structure
  C:\Users\boydpeters\projects\pyTME\tme\structure.py:1227: UserWarning: 1352/1564 atoms were out of bounds.
    warnings.warn(

tests/test_density.py::TestDensity::test_from_structure
  C:\Users\boydpeters\projects\pyTME\tme\structure.py:1227: UserWarning: 1136/1564 atoms were out of bounds.
    warnings.warn(

tests/test_density.py::TestDensity::test_from_structure
  C:\Users\boydpeters\projects\pyTME\tme\structure.py:1227: UserWarning: 1450/1564 atoms were out of bounds.
    warnings.warn(

tests/test_density.py::TestDensity::test_from_structure_weight_types[lowpass_scattering_factors]
tests/test_density.py::TestDensity::test_from_structure_scattering[dt1969-lowpass_scattering_factors]
tests/test_density.py::TestDensity::test_from_structure_scattering[wk1995-lowpass_scattering_factors]
tests/test_density.py::TestDensity::test_from_structure_scattering[peng1995-lowpass_scattering_factors]
tests/test_density.py::TestDensity::test_from_structure_scattering[peng1999-lowpass_scattering_factors]
  C:\Users\boydpeters\projects\pyTME\tme\preprocessor.py:948: RuntimeWarning: invalid value encountered in log10
    f1_values = np.log10(f_filter_mag[valid_freq_mask] * size_f)

tests/test_density.py::TestDensity::test_from_structure_scattering[wk1995-scattering_factors]
tests/test_density.py::TestDensity::test_from_structure_scattering[wk1995-lowpass_scattering_factors]
  C:\Users\boydpeters\projects\pyTME\tme\preprocessor.py:801: RuntimeWarning: invalid value encountered in sqrt
    temp = a * np.sqrt(np.pi / b) * np.exp(-np.power(dist, 2) / (4 * b))

tests/test_density.py::TestDensity::test_from_structure_scattering[wk1995-scattering_factors]
tests/test_density.py::TestDensity::test_from_structure_scattering[wk1995-lowpass_scattering_factors]
  C:\Users\boydpeters\projects\pyTME\tme\preprocessor.py:801: RuntimeWarning: overflow encountered in exp
    temp = a * np.sqrt(np.pi / b) * np.exp(-np.power(dist, 2) / (4 * b))

tests/test_density.py::TestDensity::test_from_structure_scattering[wk1995-lowpass_scattering_factors]
  C:\Users\boydpeters\projects\pyTME\tme\preprocessor.py:949: RuntimeWarning: invalid value encountered in log10
    f2_values = np.log10(np.divide(T, fourier_form_f[valid_freq_mask]))

tests/test_matching_exhaustive.py: 18 warnings
  C:\Users\boydpeters\projects\pyTME\tme\matching_exhaustive.py:367: UserWarning: Target splitting without padding target edges leads to unreliable similarity estimates around the split border.
    warnings.warn(

tests/test_matching_optimization.py::TestMatchDensityToDensity::test_call[FLC]
  C:\Users\boydpeters\projects\pyTME\tme\backends\matching_backend.py:23: RuntimeWarning: invalid value encountered in divide
    return backend_func(*args, **kwargs)

tests/test_matching_optimization.py::TestMatchCoordinateToCoordinates::test_call[NormalVectorScore]
  C:\Users\boydpeters\projects\pyTME\tme\matching_optimization.py:980: RuntimeWarning: divide by zero encountered in divide
    score = np.mean(numerator / denominator)

tests/test_matching_optimization.py::TestMatchCoordinateToCoordinates::test_call[NormalVectorScore]
  C:\Users\boydpeters\projects\pyTME\tme\matching_optimization.py:980: RuntimeWarning: invalid value encountered in divide
    score = np.mean(numerator / denominator)

tests/test_matching_optimization.py::TestOptimizeMatch::test_call[True-True-differential_evolution]
tests/test_matching_optimization.py::TestOptimizeMatch::test_call[True-False-differential_evolution]
tests/test_matching_optimization.py::TestOptimizeMatch::test_call[False-True-differential_evolution]
tests/test_matching_optimization.py::TestOptimizeMatch::test_call[False-False-differential_evolution]
  C:\Users\boydpeters\projects\pyTME\.venv\Lib\site-packages\scipy\optimize\_differentiable_functions.py:385: UserWarning: delta_grad == 0.0. Check if the approximated function is linear. If the function is linear better results can be obtained by defining the Hessian as zero instead of using quasi-Newton approximations.
    self.H.update(self.x - self.x_prev, self.g - self.g_prev)

tests/test_matching_optimization.py::TestOptimizeMatch::test_call[True-True-differential_evolution]
tests/test_matching_optimization.py::TestOptimizeMatch::test_call[True-True-basinhopping]
tests/test_matching_optimization.py::TestOptimizeMatch::test_call[True-True-minimize]
tests/test_matching_optimization.py::TestOptimizeMatch::test_call[True-False-differential_evolution]
tests/test_matching_optimization.py::TestOptimizeMatch::test_call[True-False-basinhopping]
tests/test_matching_optimization.py::TestOptimizeMatch::test_call[True-False-minimize]
  C:\Users\boydpeters\projects\pyTME\tme\rotations.py:207: UserWarning: Gimbal lock detected. Setting third angle to zero since it is not possible to uniquely determine all angles.
    return Rotation.from_matrix(rotation_matrix).as_euler(seq=seq, degrees=True)

tests/test_matching_optimization.py::TestOptimizeMatch::test_call[True-True-minimize]
tests/test_matching_optimization.py::TestOptimizeMatch::test_call[True-False-minimize]
tests/test_matching_optimization.py::TestOptimizeMatch::test_call[False-True-minimize]
tests/test_matching_optimization.py::TestOptimizeMatch::test_call[False-False-minimize]
  C:\Users\boydpeters\projects\pyTME\tme\matching_optimization.py:1241: UserWarning: Consider initializing score object with return_gradient=True.
    warnings.warn(

tests/test_structure.py::TestStructure::test_to_file[gro]
  C:\Users\boydpeters\projects\pyTME\tme\structure.py:1265: UserWarning: Missing keys: ('label_alt_id', 'occupancy', 'pdbx_PDB_ins_code', 'B_iso_or_equiv', 'pdbx_formal_charge', 'type_symbol') in data - filling with default value.
    warnings.warn(f"Missing keys: ({msg}) in data - filling with default value.")

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ===========================
FAILED tests/test_density.py::TestDensity::test_to_numpy - PermissionError: [...
FAILED tests/test_matching_cli.py::TestPostprocessing::test_postproces_score_formats[orientations-score]
FAILED tests/test_matching_cli.py::TestPostprocessing::test_postproces_score_formats[orientations-peaks]
FAILED tests/test_matching_cli.py::TestPostprocessing::test_postproces_score_formats[alignment-score]
FAILED tests/test_matching_cli.py::TestPostprocessing::test_postproces_score_formats[alignment-peaks]
FAILED tests/test_matching_cli.py::TestPostprocessing::test_postproces_score_formats[average-score]
FAILED tests/test_matching_cli.py::TestPostprocessing::test_postproces_score_formats[average-peaks]
FAILED tests/test_matching_cli.py::TestPostprocessing::test_postproces_score_formats[relion4-score]
FAILED tests/test_matching_cli.py::TestPostprocessing::test_postproces_score_formats[relion4-peaks]
FAILED tests/test_matching_cli.py::TestPostprocessing::test_postproces_score_formats[relion5-score]
FAILED tests/test_matching_cli.py::TestPostprocessing::test_postproces_score_formats[relion5-peaks]
FAILED tests/test_matching_utils.py::TestMatchingUtils::test_pickle_io - Perm...
ERROR tests/test_density.py::TestDensity::test_initialization - PermissionErr...
ERROR tests/test_density.py::TestDensity::test_initialization_errors[data0-origin0-sampling_rate0-metadata0]
ERROR tests/test_density.py::TestDensity::test_initialization_errors[data1-origin1-sampling_rate1-metadata1]
ERROR tests/test_density.py::TestDensity::test_initialization_errors[data2-origin2-sampling_rate2-not_a_dict]
ERROR tests/test_density.py::TestDensity::test_initialization_errors[data3-origin3-sampling_rate3-not_a_dict]
ERROR tests/test_density.py::TestDensity::test_repr - PermissionError: [WinEr...
ERROR tests/test_density.py::TestDensity::test_to_file[False] - PermissionErr...
ERROR tests/test_density.py::TestDensity::test_to_file[True] - PermissionErro...
ERROR tests/test_density.py::TestDensity::test_from_file - PermissionError: [...
ERROR tests/test_density.py::TestDensity::test_from_file_baseline - Permissio...
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-True-True-mrc]
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-True-True-em]
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-True-True-tiff]
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-True-True-h5]
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-True-False-mrc]
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-True-False-em]
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-True-False-tiff]
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-True-False-h5]
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-False-True-mrc]
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-False-True-em]
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-False-True-tiff]
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-False-True-h5]
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-False-False-mrc]
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-False-False-em]
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-False-False-tiff]
ERROR tests/test_density.py::TestDensity::test_file_format_io[True-False-False-h5]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-True-True-mrc]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-True-True-em]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-True-True-tiff]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-True-True-h5]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-True-False-mrc]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-True-False-em]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-True-False-tiff]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-True-False-h5]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-False-True-mrc]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-False-True-em]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-False-True-tiff]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-False-True-h5]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-False-False-mrc]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-False-False-em]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-False-False-tiff]
ERROR tests/test_density.py::TestDensity::test_file_format_io[False-False-False-h5]
ERROR tests/test_density.py::TestDensity::test__read_binary_subset_error - Pe...
ERROR tests/test_density.py::TestDensity::test_from_structure - PermissionErr...
ERROR tests/test_density.py::TestDensity::test_from_structure_weight_types[atomic_weight]
ERROR tests/test_density.py::TestDensity::test_from_structure_weight_types[atomic_number]
ERROR tests/test_density.py::TestDensity::test_from_structure_weight_types[van_der_waals_radius]
ERROR tests/test_density.py::TestDensity::test_from_structure_weight_types[scattering_factors]
ERROR tests/test_density.py::TestDensity::test_from_structure_weight_types[lowpass_scattering_factors]
ERROR tests/test_density.py::TestDensity::test_from_structure_weight_types[gaussian]
ERROR tests/test_density.py::TestDensity::test_from_structure_weight_types_error
ERROR tests/test_density.py::TestDensity::test_from_structure_scattering[dt1969-scattering_factors]
ERROR tests/test_density.py::TestDensity::test_from_structure_scattering[dt1969-lowpass_scattering_factors]
ERROR tests/test_density.py::TestDensity::test_from_structure_scattering[wk1995-scattering_factors]
ERROR tests/test_density.py::TestDensity::test_from_structure_scattering[wk1995-lowpass_scattering_factors]
ERROR tests/test_density.py::TestDensity::test_from_structure_scattering[peng1995-scattering_factors]
ERROR tests/test_density.py::TestDensity::test_from_structure_scattering[peng1995-lowpass_scattering_factors]
ERROR tests/test_density.py::TestDensity::test_from_structure_scattering[peng1999-scattering_factors]
ERROR tests/test_density.py::TestDensity::test_from_structure_scattering[peng1999-lowpass_scattering_factors]
ERROR tests/test_density.py::TestDensity::test_from_structure_error - Permiss...
ERROR tests/test_density.py::TestDensity::test_empty - PermissionError: [WinE...
ERROR tests/test_density.py::TestDensity::test_copy - PermissionError: [WinEr...
ERROR tests/test_density.py::TestDensity::test_to_memmap - PermissionError: [...
ERROR tests/test_density.py::TestDensity::test_to_numpy - PermissionError: [W...
ERROR tests/test_density.py::TestDensity::test_to_pointcloud[0] - PermissionE...
ERROR tests/test_density.py::TestDensity::test_to_pointcloud[0.5] - Permissio...
ERROR tests/test_density.py::TestDensity::test_to_pointcloud[1] - PermissionE...
ERROR tests/test_density.py::TestDensity::test_to_pointcloud[1.5] - Permissio...
ERROR tests/test_density.py::TestDensity::test__pad_slice - PermissionError: ...
ERROR tests/test_density.py::TestDensity::test_adjust_box - PermissionError: ...
ERROR tests/test_density.py::TestDensity::test_trim_box - PermissionError: [W...
ERROR tests/test_density.py::TestDensity::test_pad - PermissionError: [WinErr...
ERROR tests/test_density.py::TestDensity::test_pad_error[new_shape0] - Permis...
ERROR tests/test_density.py::TestDensity::test_pad_error[new_shape1] - Permis...
ERROR tests/test_density.py::TestDensity::test_pad_error[new_shape2] - Permis...
ERROR tests/test_density.py::TestDensity::test_minimum_enclosing_box - Permis...
ERROR tests/test_density.py::TestDensity::test_centered[cutoff0] - Permission...
ERROR tests/test_density.py::TestDensity::test_centered[0] - PermissionError:...
ERROR tests/test_density.py::TestDensity::test_centered[cutoff2] - Permission...
ERROR tests/test_density.py::TestDensity::test_rigid_transform[1-True] - Perm...
ERROR tests/test_density.py::TestDensity::test_rigid_transform[1-False] - Per...
ERROR tests/test_density.py::TestDensity::test_rigid_transform[3-True] - Perm...
ERROR tests/test_density.py::TestDensity::test_rigid_transform[3-False] - Per...
ERROR tests/test_density.py::TestDensity::test_resample[spline-2-1] - Permiss...
ERROR tests/test_density.py::TestDensity::test_resample[spline-4-3] - Permiss...
ERROR tests/test_density.py::TestDensity::test_resample[fourier-2-1] - Permis...
ERROR tests/test_density.py::TestDensity::test_resample[fourier-4-3] - Permis...
ERROR tests/test_density.py::TestDensity::test_density_boundary[0.5-2] - Perm...
ERROR tests/test_density.py::TestDensity::test_density_boundary[1-3] - Permis...
ERROR tests/test_density.py::TestDensity::test_density_boundary_error[-0.5-0]
ERROR tests/test_density.py::TestDensity::test_density_boundary_error[1--3]
ERROR tests/test_density.py::TestDensity::test_surface_coordinates[ConvexHull]
ERROR tests/test_density.py::TestDensity::test_surface_coordinates[Weight] - ...
ERROR tests/test_density.py::TestDensity::test_surface_coordinates[Sobel] - P...
ERROR tests/test_density.py::TestDensity::test_surface_coordinates[Laplace]
ERROR tests/test_density.py::TestDensity::test_surface_coordinates[Minimum]
ERROR tests/test_density.py::TestDensity::test_surface_coordinates_error - Pe...
ERROR tests/test_density.py::TestDensity::test_normal_vectors - PermissionErr...
ERROR tests/test_density.py::TestDensity::test_normal_vectors_error - Permiss...
ERROR tests/test_density.py::TestDensity::test_core_mask - PermissionError: [...
ERROR tests/test_density.py::TestDensity::test_center_of_mass - PermissionErr...
ERROR tests/test_density.py::TestDensity::test_match_densities[CrossCorrelation]
ERROR tests/test_density.py::TestDensity::test_match_densities[NormalizedCrossCorrelation]
ERROR tests/test_density.py::TestDensity::test_match_structure_to_density - P...
ERROR tests/test_structure.py::TestStructure::test_initialization - Permissio...
ERROR tests/test_structure.py::TestStructure::test_initialization_errors[record_type]
ERROR tests/test_structure.py::TestStructure::test_initialization_errors[atom_serial_number]
ERROR tests/test_structure.py::TestStructure::test_initialization_errors[atom_name]
ERROR tests/test_structure.py::TestStructure::test_initialization_errors[atom_coordinate]
ERROR tests/test_structure.py::TestStructure::test_initialization_errors[alternate_location_indicator]
ERROR tests/test_structure.py::TestStructure::test_initialization_errors[residue_name]
ERROR tests/test_structure.py::TestStructure::test_initialization_errors[chain_identifier]
ERROR tests/test_structure.py::TestStructure::test_initialization_errors[residue_sequence_number]
ERROR tests/test_structure.py::TestStructure::test_initialization_errors[code_for_residue_insertion]
ERROR tests/test_structure.py::TestStructure::test_initialization_errors[occupancy]
ERROR tests/test_structure.py::TestStructure::test_initialization_errors[temperature_factor]
ERROR tests/test_structure.py::TestStructure::test_initialization_errors[segment_identifier]
ERROR tests/test_structure.py::TestStructure::test_initialization_errors[element_symbol]
ERROR tests/test_structure.py::TestStructure::test__getitem__ - PermissionErr...
ERROR tests/test_structure.py::TestStructure::test__repr__ - PermissionError:...
ERROR tests/test_structure.py::TestStructure::test_fromfile[C:\\Users\\boydpeters\\projects\\pyTME\\tests\\data\\Structures\\5khe.cif]
ERROR tests/test_structure.py::TestStructure::test_fromfile[C:\\Users\\boydpeters\\projects\\pyTME\\tests\\data\\Structures\\5khe.pdb]
ERROR tests/test_structure.py::TestStructure::test_fromfile_error - Permissio...
ERROR tests/test_structure.py::TestStructure::test_to_file[cif] - PermissionE...
ERROR tests/test_structure.py::TestStructure::test_to_file[pdb] - PermissionE...
ERROR tests/test_structure.py::TestStructure::test_to_file[gro] - PermissionE...
ERROR tests/test_structure.py::TestStructure::test_to_file_error - Permission...
ERROR tests/test_structure.py::TestStructure::test_subset_by_chain - Permissi...
ERROR tests/test_structure.py::TestStructure::test_subset_by_chain_range - Pe...
ERROR tests/test_structure.py::TestStructure::test_center_of_mass - Permissio...
ERROR tests/test_structure.py::TestStructure::test__get_atom_weights_error - ...
ERROR tests/test_structure.py::TestStructure::test_compare_structures - Permi...
ERROR tests/test_structure.py::TestStructure::test_comopare_structures_error
ERROR tests/test_structure.py::TestStructure::test_align_structures - Permiss...
==== 12 failed, 1072 passed, 80 warnings, 134 errors in 373.59s (0:06:13) =====

[maurerv]

Hi, thanks for the logs!

It seems most of these can be addressed by adapting generate_tempfile_name to close the file handle and then replaces occurences of mkstemp in the tests. For the memmap failure, it might be enough to use rename instead of move. As long as you are not invoking match_template with --use-memmap this should not affect you though.

I will integrate these changes into the next version which should come (hopefully) soon :)

[boydcpeters]

Sounds good!