fix: re-apply verified bug fixes on synced master#180
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MANIFEST.in referenced src/ATLAS/data (wrong case), so config_schema.yaml and the rest of data/ were never shipped, breaking atl_gen_configuration_file in installs.
Read os.environ['XDG_CACHE_HOME'] instead of the literal '$XDG_CACHE_HOME'; update the test that pinned the bug.
The fps data-reduction path passed shifted positional args (int as selected_db) -> TypeError. Pass explicit keywords and an empty selected_db.
__init__/architecture/load_model were at module scope (and nested), so the class was non-functional. Remove a bogus kwargs.pop and flush/seek the temp file before torch.load.
Divided the atom count by len(symbol_string) (1 or 2) instead of len(struct), corrupting the species-fraction feature.
The computed score was discarded, so the function always returned None.
np.max's second positional arg is axis, not a second array; element-wise max needs np.maximum.
is_ase was only set in the ase.Atoms branch, raising UnboundLocalError for ATL/pymatgen inputs.
An ndarray hull has len()==n_vertices, falling through to an empty MultiPolygon so every frame was flagged extrapolating. Add the ndim==2 branch (mirrors concave_hull.py).
The base-skip checked the same empty .info key twice; read base/isolated_atom from the row instead. (The except/continue half is already handled upstream.)
fix: re-apply verified bug fixes on synced master
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Summary
Re-applies the verified bug fixes from the earlier (discarded) bug-fix PR, rebased onto the current synced master. Each fix is its own commit. Two fixes from the original set were dropped because the synced upstream already resolved them.
Applied (10 fixes)
src/ATLAS/data→src/atlas/data) sodata/shipsMANIFEST.inget_cache_pathhonorsXDG_CACHE_HOME(dropped literal$) + testcore/code_utils.py,tests/test_code_utils.pyselect_structures_fpscalled with correct args (was shifted positionals)active_learning/active_learning_utils.pyMLIPModelFileDatamethods defined inside the classworkflows/datatypes/mlip.py/ len(struct)(was/ len(symbol))core/database/diversity_metrics.pyget_vendi_score_db_rbfreturns its resultcore/database/diversity_metrics.pynp.maximumintanimoto_distance(wasnp.max)core/database/diversity_metrics.pyis_aseinitialized before use inapply_replacementcore/utils.pycheck_traj_in_domainactive_learning/md/atl_process_structure.py.infokey)core/filtering/structure_filters.pyDropped (already fixed upstream on the synced master)
clusters.pyis False→ upstream already uses== Falsein the refactoredapply_replacement_cluster_db.can_submit_calculationtuple-as-bool → the buggy fileworkflows/active_learning.pywas deleted upstream; remaining callers already unpack correctly.Test plan
py_compileclean on all changed filespytest tests/→ 157 passed, 0 failed (4 errors aretest_structure_viewer.pymissing optionalPySide6, unrelated)test_gen_db(schema/data/packaging) and theXDG_CACHE_HOMEtest pass