fix final linting

Author: JaGeo

src/atomate2/utils/testing/lobster.py

@@ -4,7 +4,6 @@
 
 import logging
 import shutil
-from collections.abc import Callable, Generator
 from pathlib import Path
 from typing import TYPE_CHECKING
 
@@ -15,7 +14,7 @@
 import atomate2.lobster.run
 
 if TYPE_CHECKING:
-    from collections.abc import Sequence
+    from collections.abc import Callable, Generator, Sequence
 
 logger = logging.getLogger("atomate2")
 
@@ -26,7 +25,7 @@
 
 
 @pytest.fixture(scope="session")
-def lobster_test_dir(test_dir) -> Path:
+def lobster_test_dir(test_dir: str | Path) -> Path:
     """Fixture to provide the test directory for LOBSTER tests.
 
     Args:
@@ -36,7 +35,7 @@ def lobster_test_dir(test_dir) -> Path:
     -------
         Path: The test directory for LOBSTER tests.
     """
-    return test_dir / "lobster"
+    return Path(test_dir) / "lobster"
 
 
 def monkeypatch_lobster(
@@ -52,34 +51,54 @@ def monkeypatch_lobster(
     It replaces calls to run_lobster with a mock function that copies reference files
     instead of running LOBSTER.
 
-    The primary idea is that instead of running LOBSTER to generate the output files,
-    reference files will be copied into the directory instead. This ensures that the
-    calculation inputs are generated correctly and that the outputs are parsed properly.
+    The primary idea is that instead of running LOBSTER to
+    generate the output files, reference files will be copied
+    into the directory instead. This ensures that the calculation
+    inputs are generated correctly and that the outputs are
+    parsed properly.
 
     To use the fixture successfully, follow these steps:
-    1. Include "mock_lobster" as an argument to any test that would like to use its functionality.
-    2. For each job in your workflow, prepare a reference directory containing two folders:
-       "inputs" (containing the reference input files expected to be produced by
-       Lobsterin.standard_calculations_from_vasp_files) and "outputs" (containing the expected
-       output files to be produced by run_lobster). These files should reside in a subdirectory
+    1. Include "mock_lobster" as an argument to any test that
+    would like to use its functionality.
+    2. For each job in your workflow, prepare a reference
+    directory containing two folders:
+       "inputs" (containing the reference input files expected
+       to be produced by Lobsterin.standard_calculations_from_vasp_files)
+       and "outputs" (containing the expected
+       output files to be produced by run_lobster).
+       These files should reside in a subdirectory
        of "tests/test_data/lobster".
-    3. Create a dictionary mapping each job name to its reference directory. Note that you should
-       supply the reference directory relative to the "tests/test_data/lobster" folder. For example,
-       if your calculation has one job named "lobster_run_0" and the reference files are present in
-       "tests/test_data/lobster/Si_lobster_run_0", the dictionary would look like:
+    3. Create a dictionary mapping each job name
+        to its reference directory. Note that you should
+       supply the reference directory relative
+       to the "tests/test_data/lobster" folder. For example,
+       if your calculation has one job named
+       "lobster_run_0" and the reference files are present in
+       "tests/test_data/lobster/Si_lobster_run_0",
+       the dictionary would look like:
        {"lobster_run_0": "Si_lobster_run_0"}.
-    4. Optionally, create a dictionary mapping each job name to custom keyword arguments that will be
-       supplied to fake_run_lobster. This way you can configure which lobsterin settings are expected
-       for each job. For example, if your calculation has one job named "lobster_run_0" and you wish
-       to validate that "basisfunctions" is set correctly in the lobsterin, your dictionary would look like:
-       {"lobster_run_0": {"lobsterin_settings": {"basisfunctions": Ba 5p 5s 6s}}.
-    5. Inside the test function, call `mock_lobster(ref_paths, fake_lobster_kwargs)`, where ref_paths is the
-       dictionary created in step 3 and fake_lobster_kwargs is the dictionary created in step 4.
+    4. Optionally, create a dictionary mapping each
+       job name to custom keyword arguments that will be
+       supplied to fake_run_lobster. This way you can
+       configure which lobsterin settings are expected
+       for each job. For example, if your calculation
+       has one job named "lobster_run_0" and you wish
+       to validate that "basisfunctions" is set correctly
+       in the lobsterin, your dictionary would look like:
+       {"lobster_run_0": {"lobsterin_settings":
+        {"basisfunctions": Ba 5p 5s 6s}}.
+    5. Inside the test function, call
+        `mock_lobster(ref_paths, fake_lobster_kwargs)`,
+        where ref_paths is the
+       dictionary created in step 3 and
+       fake_lobster_kwargs is the dictionary created in step 4.
     6. Run your LOBSTER job after calling `mock_lobster`.
 
     Args:
-        monkeypatch (pytest.MonkeyPatch): The pytest monkeypatch fixture.
-        lobster_test_dir (Path): The directory containing reference files for LOBSTER tests.
+        monkeypatch (pytest.MonkeyPatch):
+            The pytest monkeypatch fixture.
+        lobster_test_dir (Path):
+            The directory containing reference files for LOBSTER tests.
     """
 
     def mock_run_lobster(*_args, **_kwargs) -> None:
@@ -110,7 +129,7 @@ def fake_run_lobster(
     check_lobster_inputs: Sequence[str] = _LFILES,
     check_dft_inputs: Sequence[str] = _DFT_FILES,
     lobsterin_settings: Sequence[str] = (),
-):
+) -> None:
     """
     Emulate running LOBSTER and validate LOBSTER input files.
 

tutorials/force_fields/__init__.py

@@ -1 +1 @@
-"""Forcefield-based tutorials"""
+"""Forcefield-based tutorials."""

tutorials/lobster_workflow.ipynb

@@ -143,17 +143,15 @@
     "    load=True,\n",
     ")\n",
     "\n",
-    "for number, (key, cohp) in enumerate(\n",
-    "    result[\"output\"][\"lobsterpy_data\"][\"cohp_plot_data\"][\"data\"].items()\n",
-    "):\n",
+    "for key, cohp in result[\"output\"][\"lobsterpy_data\"][\"cohp_plot_data\"][\"data\"].items():\n",
     "    plotter = CohpPlotter()\n",
     "    cohp_obj = Cohp.from_dict(cohp)\n",
     "    plotter.add_cohp(key, cohp_obj)\n",
-    "    plotter.save_plot(f\"plots_all_bonds{number}.pdf\")\n",
+    "    plotter.show()\n",
     "\n",
-    "for number, (key, cohp) in enumerate(\n",
-    "    result[\"output\"][\"lobsterpy_data_cation_anion\"][\"cohp_plot_data\"][\"data\"].items()\n",
-    "):\n",
+    "for key, cohp in result[\"output\"][\"lobsterpy_data_cation_anion\"][\"cohp_plot_data\"][\n",
+    "    \"data\"\n",
+    "].items():\n",
     "    plotter = CohpPlotter()\n",
     "    cohp_obj = Cohp.from_dict(cohp)\n",
     "    plotter.add_cohp(key, cohp_obj)\n",