bump ruff + auto-fixes

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.5.6
+  rev: v0.6.1
   hooks:
   - id: ruff
     args: [--fix]

pyproject.toml

@@ -165,13 +165,10 @@ target-version = "py39"
 [tool.ruff.lint]
 select = ["ALL"]
 ignore = [
-    "ANN002",
-    "ANN003",
-    "ANN101", # missing self type annotation
-    "ANN102", # missing cls annotation
-    "ANN401",
-    "ARG002", # unused method argument
-    # "BLE001",
+    "ANN002",  # Missing type annotation for *arg
+    "ANN003",  # Missing type annotation for **kwargs
+    "ANN401",  # typing.Any disallowed
+    "ARG002",  # unused method argument
     "C408",    # Unnecessary (dict/list/tuple) call - remove call
     "C901",    # function too complex
     "COM812",  # trailing comma missing
@@ -180,7 +177,7 @@ ignore = [
     "FBT001",
     "FBT002",
     "FIX002",
-    "G004",    # logging uses fstring
+    "G004",    # logging uses f-string
     "ISC001",
     "PD011",   # pandas-use-of-dot-values
     "PERF203", # try-except-in-loop

tests/abinit/conftest.py

@@ -27,7 +27,7 @@ def abinit_integration_tests(pytestconfig):
     return pytestconfig.getoption("abinit_integration")
 
 
-@pytest.fixture()
+@pytest.fixture
 def mock_abinit(mocker, abinit_test_dir, abinit_integration_tests):
     """
     This fixture allows one to mock running ABINIT.

tests/aims/conftest.py

@@ -34,7 +34,7 @@ def pytest_addoption(parser):
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def si():
     return Structure(
         lattice=Lattice(
@@ -45,7 +45,7 @@ def si():
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def o2():
     return Molecule(species=["O", "O"], coords=[[0, 0, 0.622978], [0, 0, -0.622978]])
 
@@ -64,15 +64,15 @@ def ref_path():
     return test_dir.resolve()
 
 
-@pytest.fixture()
+@pytest.fixture
 def should_mock_aims(request):
     try:
         return not request.config.getoption("--generate-test-data")
     except ValueError:
         return True
 
 
-@pytest.fixture()
+@pytest.fixture
 def mock_aims(monkeypatch, ref_path, should_mock_aims):
     """
     This fixture allows one to mock (fake) running FHI-aims.

tests/aims/test_files/test_files.py

@@ -7,7 +7,7 @@
 TEST_DIR = Path(__file__).parent
 
 
-@pytest.fixture()
+@pytest.fixture
 def tmp_dir():
     """Same as clean_dir but is fresh for every test"""
     import os

tests/conftest.py

@@ -50,7 +50,7 @@ def clean_dir(debug_mode):
         shutil.rmtree(new_path)
 
 
-@pytest.fixture()
+@pytest.fixture
 def tmp_dir():
     """Same as clean_dir but is fresh for every test"""
 
@@ -79,7 +79,7 @@ def lpad(database, debug_mode):
             lpad.db[coll].drop()
 
 
-@pytest.fixture()
+@pytest.fixture
 def memory_jobstore():
     store = JobStore(MemoryStore(), additional_stores={"data": MemoryStore()})
     store.connect()
@@ -92,27 +92,27 @@ def log_to_stdout_auto_use():
     initialize_logger()
 
 
-@pytest.fixture()
+@pytest.fixture
 def si_structure(test_dir):
     return Structure.from_file(test_dir / "structures" / "Si.cif")
 
 
-@pytest.fixture()
+@pytest.fixture
 def si_diamond(test_dir):
     return Structure.from_file(test_dir / "structures" / "Si_diamond.cif")
 
 
-@pytest.fixture()
+@pytest.fixture
 def al2_au_structure(test_dir):
     return Structure.from_file(test_dir / "structures" / "Al2Au.cif")
 
 
-@pytest.fixture()
+@pytest.fixture
 def sr_ti_o3_structure(test_dir):
     return Structure.from_file(test_dir / "structures" / "SrTiO3.cif")
 
 
-@pytest.fixture()
+@pytest.fixture
 def ba_ti_o3_structure(test_dir):
     return Structure.from_file(test_dir / "structures" / "BaTiO3.cif")
 

tests/cp2k/conftest.py

@@ -56,7 +56,7 @@ def cp2k_test_outputs(test_dir):
     return Path(test_dir / "cp2k").glob("*/outputs")
 
 
-@pytest.fixture()
+@pytest.fixture
 def mock_cp2k(monkeypatch, cp2k_test_dir):
     """
     This fixture allows one to mock (fake) running CP2K.
@@ -169,7 +169,7 @@ def fake_run_cp2k(
     logger.info("Generated fake cp2k outputs")
 
 
-@pytest.fixture()
+@pytest.fixture
 def check_input():
     from pymatgen.io.cp2k.inputs import Cp2kInput
 

tests/qchem/conftest.py

@@ -31,7 +31,7 @@ def qchem_test_dir(test_dir):
     return test_dir / "qchem"
 
 
-@pytest.fixture()
+@pytest.fixture
 def mock_qchem(
     monkeypatch: MonkeyPatch, qchem_test_dir: Path
 ) -> Generator[Callable[[Any, Any], Any], None, None]:

tests/vasp/conftest.py

@@ -44,7 +44,7 @@ def lobster_test_dir(test_dir):
     return test_dir / "lobster"
 
 
-@pytest.fixture()
+@pytest.fixture
 def mock_vasp(
     monkeypatch: MonkeyPatch, vasp_test_dir: Path
 ) -> Generator[Callable[[Any, Any], Any], None, None]:

tests/vasp/lobster/conftest.py

@@ -27,7 +27,7 @@ def lobster_test_dir(test_dir):
     return test_dir / "lobster"
 
 
-@pytest.fixture()
+@pytest.fixture
 def mock_lobster(monkeypatch, lobster_test_dir):
     """
     This fixture allows one to mock (fake) running LOBSTER.

tutorials/blob_storage.ipynb

@@ -6,19 +6,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from atomate2.vasp.flows.core import StaticMaker\n",
     "from jobflow import JobStore, run_locally\n",
     "from maggma.stores import MemoryStore\n",
-    "from pymatgen.core import Structure\n",
-    "from mock_vasp import mock_vasp, TEST_DIR\n",
+    "from mock_vasp import TEST_DIR, mock_vasp\n",
     "from monty.json import MontyDecoder\n",
+    "from pymatgen.core import Structure\n",
     "from pymatgen.io.vasp import Chgcar\n",
-    "import numpy as np\n",
     "\n",
-    "def decode(d):\n",
-    "    return MontyDecoder().process_decoded(d)\n",
+    "from atomate2.vasp.flows.core import StaticMaker\n",
     "\n",
-    "jobstore = JobStore(MemoryStore(), additional_stores={\"data\": MemoryStore()})\n",
+    "job_store = JobStore(MemoryStore(), additional_stores={\"data\": MemoryStore()})\n",
     "si_structure = Structure.from_file(TEST_DIR / \"structures\" / \"Si.cif\")\n",
     "ref_paths = {\"static\": \"Si_band_structure/static\"}"
    ]
@@ -71,7 +68,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "static_maker = StaticMaker(task_document_kwargs={\"store_volumetric_data\": (\"chgcar\",)})\n"
+    "static_maker = StaticMaker(task_document_kwargs={\"store_volumetric_data\": (\"chgcar\",)})"
    ]
   },
   {
@@ -113,13 +110,13 @@
     "# create the job\n",
     "job = static_maker.make(si_structure)\n",
     "# run the job in a mock vasp environment\n",
-    "# make sure to send the results to the temporary jobstore\n",
+    "# make sure to send the results to the temporary job store\n",
     "with mock_vasp(ref_paths=ref_paths) as mf:\n",
     "    responses = run_locally(\n",
     "        job,\n",
     "        create_folders=True,\n",
     "        ensure_success=True,\n",
-    "        store=jobstore,\n",
+    "        store=job_store,\n",
     "        raise_immediately=True,\n",
     "    )"
    ]
@@ -139,11 +136,12 @@
    },
    "outputs": [],
    "source": [
-    "with jobstore as s:\n",
-    "    result = s.get_output(job.uuid, load=True)\n",
+    "with job_store as js:\n",
+    "    result = js.get_output(job.uuid, load=True)\n",
     "\n",
-    "chgcar = decode(result[\"vasp_objects\"][\"chgcar\"])\n",
-    "assert isinstance(chgcar, Chgcar)\n"
+    "chgcar = MontyDecoder().process_decoded(result[\"vasp_objects\"][\"chgcar\"])\n",
+    "if not isinstance(chgcar, Chgcar):\n",
+    "    raise TypeError(f\"{type(chgcar)=}\")"
    ]
   },
   {
@@ -159,9 +157,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "with jobstore as s:\n",
-    "    result_no_obj = s.get_output(job.uuid)\n",
-    "result_no_obj[\"vasp_objects\"]\n"
+    "with job_store as js:\n",
+    "    result_no_obj = js.get_output(job.uuid)\n",
+    "result_no_obj[\"vasp_objects\"]"
    ]
   },
   {
@@ -177,9 +175,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "seach_data = result_no_obj[\"vasp_objects\"][\"chgcar\"]\n",
-    "with jobstore.additional_stores[\"data\"] as s:\n",
-    "    blob_data = s.query_one(criteria={\"blob_uuid\": seach_data[\"blob_uuid\"]})"
+    "search_data = result_no_obj[\"vasp_objects\"][\"chgcar\"]\n",
+    "with job_store.additional_stores[\"data\"] as js:\n",
+    "    blob_data = js.query_one(criteria={\"blob_uuid\": search_data[\"blob_uuid\"]})"
    ]
   },
   {
@@ -195,7 +193,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "chgcar2 = decode(blob_data[\"data\"])"
+    "chgcar2 = MontyDecoder().process_decoded(blob_data[\"data\"])"
    ]
   }
  ],
@@ -210,7 +208,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,