fix linting

Author: JaGeo

src/atomate2/utils/testing/lobster.py

@@ -1,9 +1,11 @@
+"""Utilities for testing LOBSTER calculations."""
+
 from __future__ import annotations
 
 import logging
 import shutil
 from pathlib import Path
-from typing import TYPE_CHECKING, Literal
+from typing import TYPE_CHECKING
 
 import pytest
 from pymatgen.io.lobster import Lobsterin
@@ -18,8 +20,8 @@
 
 _LFILES = "lobsterin"
 _DFT_FILES = ("WAVECAR", "POSCAR", "INCAR", "KPOINTS", "POTCAR")
-_LOBS_REF_PATHS = {}
-_FAKE_RUN_LOBSTER_KWARGS = {}
+_LOBS_REF_PATHS: dict[str, str | Path] = {}
+_FAKE_RUN_LOBSTER_KWARGS: dict[str, dict[str, Sequence]] = {}
 
 
 @pytest.fixture(scope="session")
@@ -91,8 +93,8 @@ def _run(ref_paths, fake_run_lobster_kwargs):
 
 def fake_run_lobster(
     ref_path: str | Path,
-    check_lobster_inputs: Sequence[Literal["lobsterin"]] = _LFILES,
-    check_dft_inputs: Sequence[Literal["WAVECAR", "POSCAR"]] = _DFT_FILES,
+    check_lobster_inputs: Sequence[str] = _LFILES,
+    check_dft_inputs: Sequence[str] = _DFT_FILES,
     lobsterin_settings: Sequence[str] = (),
 ):
     """
@@ -105,6 +107,8 @@ def fake_run_lobster(
         and output files in the folder named 'outputs'.
     check_lobster_inputs
         A list of lobster input files to check. Supported options are "lobsterin.gz".
+    check_dft_inputs
+        A list of VASP files that need to be copied to start the LOBSTER runs.
     lobsterin_settings
         A list of LOBSTER settings to check.
     """
@@ -131,15 +135,15 @@ def verify_inputs(ref_path: str | Path, lobsterin_settings: Sequence[str]):
     user = Lobsterin.from_file("lobsterin")
 
     # Check lobsterin
-    ref = Lobsterin.from_file(ref_path / "inputs" / "lobsterin")
+    ref = Lobsterin.from_file(Path(ref_path) / "inputs" / "lobsterin")
 
     for key in lobsterin_settings:
         if user.get(key) != ref.get(key):
             raise ValueError(f"lobsterin value of {key} is inconsistent!")
 
 
 def copy_lobster_outputs(ref_path: str | Path):
-    output_path = ref_path / "outputs"
+    output_path = Path(ref_path) / "outputs"
     for output_file in output_path.iterdir():
         if output_file.is_file():
             shutil.copy(output_file, ".")

tutorials/lobster_workflow.ipynb

@@ -5,7 +5,7 @@
    "id": "0",
    "metadata": {},
    "source": [
-    "The first lines are needed to ensure that we can mock VASP and LOBSTER runs."
+    "The first lines are needed to ensure that we can mock VASP and LOBSTER runs. The test files here might not belong to the same calculation but are good enough for testing."
    ]
   },
   {