Explore Updating Biotite and other deps.

[zachcp]

Note: this PR is not intended for inclusion, but for testing the extent of issues in updating the pip deps.

• In response to Biotite Version Bump to 1.X #732
• you can see the test being run outside of blender here
• Current issues seem rather limited and related to renamed classes in biotite.

un pytest with --snapshot-update to delete unused snapshots.
=========================== short test summary info ============================
FAILED tests/test_assembly.py::test_get_transformations[1f2n-cif] - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'PDBxFile'
FAILED tests/test_assembly.py::test_get_transformations[5zng-cif] - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'PDBxFile'
FAILED tests/test_assembly.py::test_get_transformations_cif[1] - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'PDBxFile'
FAILED tests/test_assembly.py::test_get_transformations_cif[2] - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'PDBxFile'
FAILED tests/test_assembly.py::test_get_transformations_cif[3] - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'PDBxFile'
FAILED tests/test_assembly.py::test_get_transformations_cif[4] - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'PDBxFile'
FAILED tests/test_assembly.py::test_get_transformations_cif[5] - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'PDBxFile'
FAILED tests/test_load.py::test_load_small_mol - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'legacy'
==== 8 failed, 373 passed, 2 skipped, 567451 warnings in 170.45s (0:02:50) =====
Read blend: "/tmp/pytest-of-runner/pytest-0/test_save_persistance0/test.blend"

[zachcp]

Added Tests for in-blender here: https://github.com/zachcp/MolecularNodes/actions/runs/13270261007

Those look like the same errors. So.... I think an update in deps that ALSO updates those calls should work in blender and outside of blender (e.g. targeting bpy)

1695 snapshots passed. 2 snapshots unused.
Re-run pytest with --snapshot-update to delete unused snapshots.
=========================== short test summary info ============================
FAILED tests/test_assembly.py::test_get_transformations[1f2n-cif] - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'PDBxFile'
FAILED tests/test_assembly.py::test_get_transformations[5zng-cif] - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'PDBxFile'
FAILED tests/test_assembly.py::test_get_transformations_cif[1] - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'PDBxFile'
FAILED tests/test_assembly.py::test_get_transformations_cif[2] - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'PDBxFile'
FAILED tests/test_assembly.py::test_get_transformations_cif[3] - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'PDBxFile'
FAILED tests/test_assembly.py::test_get_transformations_cif[4] - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'PDBxFile'
FAILED tests/test_assembly.py::test_get_transformations_cif[5] - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'PDBxFile'
FAILED tests/test_load.py::test_load_small_mol - AttributeError: module 'biotite.structure.io.pdbx' has no attribute 'legacy'
==== 8 failed, 386 passed, 1 skipped, 567452 warnings in 247.51s (0:04:07) =====

[zachcp]

Okey. here's the first substantive issue. A difference in key handling for pdbx_struct_assembly_gen.

tests/test_assembly.py:66:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
molecularnodes/entities/molecule/oldcif.py:198: in get_transformations
    assembly_gen_category = self._file["pdbx_struct_assembly_gen"]
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <biotite.structure.io.pdbx.CIFFile object at 0x32e41c710>, key = 'pdbx_struct_assembly_gen'

    def __getitem__(self, key):
>       block = self._blocks[key]
E       KeyError: 'pdbx_struct_assembly_gen'

.pixi/envs/default/lib/python3.11/site-packages/biotite/structure/io/pdbx/cif.py:879: KeyError
---------------------------------------- Captured stdout setup ----------------------------------------
mn.session.get_session().entities={}
list(bpy.data.objects)=[bpy.data.objects['Camera'], bpy.data.objects['Cube'], bpy.data.objects['Light']]
-------------------------------------- Captured stdout teardown ---------------------------------------
Post Test setup:
bpy.app.handlers.frame_change_pre=[<function update_entities at 0x13abfd440>]
mn.session.get_session().entities.keys()=dict_keys([])
list(bpy.data.objects)=[bpy.data.objects['Camera'], bpy.data.objects['Cube'], bpy.data.objects['Light']]
list(o.uuid for o in bpy.data.objects)=['', '', '']
======================================= short test summary info =======================================
FAILED tests/test_assembly.py::test_get_transformations[1f2n-cif] - KeyError: 'pdbx_struct_assembly_gen'
FAILED tests/test_assembly.py::test_get_transformations[5zng-cif] - KeyError: 'pdbx_struct_assembly_gen'
FAILED tests/test_assembly.py::test_get_transformations_cif[1] - KeyError: 'pdbx_struct_assembly_gen'
FAILED tests/test_assembly.py::test_get_transformations_cif[2] - KeyError: 'pdbx_struct_assembly_gen'
FAILED tests/test_assembly.py::test_get_transformations_cif[3] - KeyError: 'pdbx_struct_assembly_gen'
FAILED tests/test_assembly.py::test_get_transformations_cif[4] - KeyError: 'pdbx_struct_assembly_gen'
FAILED tests/test_assembly.py::test_get_transformations_cif[5] - KeyError: 'pdbx_struct_assembly_gen'
===================================== 7 failed, 2 passed in 0.82s =====================================

[zachcp]

@BradyAJohnston I'm sorry but I've managed to unintentionally hang the test suite. Can you cancel the above jobs please?

[zachcp]

Superceded by #737