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Fix KeyError('wyckoff_spglib') in fetch_process_wbm_dataset.py #34

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Merged
merged 2 commits into from
May 9, 2023
Merged

Fix KeyError('wyckoff_spglib') in fetch_process_wbm_dataset.py #34

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5dff77f
fix Generating Aflow labels raised exception=KeyError('wyckoff_spglib…
janosh May 9, 2023
58f5eb2
move out_dir of site-stats.json.gz to data/(wbm|mp) (closes #33)
janosh May 9, 2023
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4 changes: 2 additions & 2 deletions data/wbm/fetch_process_wbm_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -595,11 +595,11 @@ def fix_bad_struct_index_mismatch(material_id: str) -> str:

wyckoff_col = "wyckoff_spglib"
if wyckoff_col not in df_wbm:
df_wbm[wyckoff_col] = None
df_summary[wyckoff_col] = None

for idx, struct in tqdm(df_wbm.initial_structure.items(), total=len(df_wbm)):
if not pd.isna(df_summary.loc[idx, wyckoff_col]):
continue
continue # Aflow label already computed
try:
struct = Structure.from_dict(struct)
df_summary.loc[idx, wyckoff_col] = get_aflow_label_from_spglib(struct)
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1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up @@ -96,6 +96,7 @@ select = [
"PYI", # flakes8-pyi
"Q", # flake8-quotes
"RET", # flake8-return
"RSE", # flake8-raise
"RUF", # Ruff-specific rules
"SIM", # flake8-simplify
"TID", # tidy imports
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2 changes: 1 addition & 1 deletion scripts/compute_struct_fingerprints.py
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Expand Up @@ -36,7 +36,7 @@
slurm_array_task_id = int(os.getenv("SLURM_ARRAY_TASK_ID", 0))
slurm_array_task_count = 100

out_dir = f"{ROOT}/data/{data_name}/structure-fingerprints"
out_dir = f"{ROOT}/data/{data_name}"
os.makedirs(out_dir, exist_ok=True)

slurm_vars = slurm_submit(
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