Fix failing ruff PT001 on master (#4003)

* bump ruff version in pre-commit

* fix PT001

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.7
+    rev: v0.6.0
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
@@ -65,6 +65,6 @@ repos:
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.375
+    rev: v1.1.376
     hooks:
       - id: pyright

tests/core/test_xcfunc.py

@@ -53,12 +53,11 @@ def test_pickle_serialize(self):
         # Test if object can be serialized with Pickle
         self.serialize_with_pickle(self.ixc_11)
 
-    @pytest.mark.skip()
+    @pytest.mark.skip(reason="TODO:")
     def test_msonable(self):
         # Test if object supports MSONable
-        # TODO
         self.ixc_11.x.as_dict()
-        self.assertMSONable(self.ixc_11)
+        self.assert_msonable(self.ixc_11)
 
     def test_from(self):
         # GGA-PBE from ixc given in abinit-libxc mode

tests/entries/test_mixing_scheme.py

@@ -156,7 +156,7 @@ def all_entries(self):
         return self.gga_entries + self.scan_entries
 
 
-@pytest.fixture()
+@pytest.fixture
 def mixing_scheme_no_compat():
     """Get an instance of MaterialsProjectDFTMixingScheme with no additional
     compatibility schemes (e.g., compat_1=None). Used by most of the tests where
@@ -205,7 +205,7 @@ def mixing_scheme_no_compat():
 )
 
 
-@pytest.fixture()
+@pytest.fixture
 def ms_complete():
     """Mixing state where we have R2SCAN for all GGA."""
     gga_entries = [
@@ -370,7 +370,7 @@ def ms_complete():
     return MixingState(gga_entries, scan_entries, mixing_state)
 
 
-@pytest.fixture()
+@pytest.fixture
 def ms_scan_only(ms_complete):
     """Mixing state with only R2SCAN entries."""
     gga_entries = []
@@ -391,7 +391,7 @@ def ms_scan_only(ms_complete):
     return MixingState(gga_entries, scan_entries, mixing_state)
 
 
-@pytest.fixture()
+@pytest.fixture
 def ms_gga_only(ms_complete):
     """Mixing state with only GGA entries."""
     gga_entries = ms_complete.gga_entries
@@ -412,7 +412,7 @@ def ms_gga_only(ms_complete):
     return MixingState(gga_entries, scan_entries, mixing_state)
 
 
-@pytest.fixture()
+@pytest.fixture
 def ms_gga_1_scan(ms_complete):
     """
     Mixing state with all GGA entries and one R2SCAN, corresponding to the GGA
@@ -434,7 +434,7 @@ def ms_gga_1_scan(ms_complete):
     return MixingState(gga_entries, scan_entries, mixing_state)
 
 
-@pytest.fixture()
+@pytest.fixture
 def ms_gga_1_scan_novel(ms_complete):
     """
     Mixing state with all GGA entries and 1 R2SCAN, corresponding to a composition
@@ -464,7 +464,7 @@ def ms_gga_1_scan_novel(ms_complete):
     return MixingState(gga_entries, scan_entries, mixing_state)
 
 
-@pytest.fixture()
+@pytest.fixture
 def ms_gga_2_scan_same(ms_complete):
     """
     Mixing state with all GGA entries and 2 R2SCAN, corresponding to the GGA
@@ -486,7 +486,7 @@ def ms_gga_2_scan_same(ms_complete):
     return MixingState(gga_entries, scan_entries, mixing_state)
 
 
-@pytest.fixture()
+@pytest.fixture
 def ms_gga_2_scan_diff_match(ms_complete):
     """
     Mixing state with all GGA entries and 2 R2SCAN entries corresponding to
@@ -510,7 +510,7 @@ def ms_gga_2_scan_diff_match(ms_complete):
     return MixingState(gga_entries, scan_entries, mixing_state)
 
 
-@pytest.fixture()
+@pytest.fixture
 def ms_gga_2_scan_diff_no_match(ms_complete):
     """
     Mixing state with all GGA entries and 2 R2SCAN, corresponding to the GGA
@@ -552,7 +552,7 @@ def ms_gga_2_scan_diff_no_match(ms_complete):
     return MixingState(gga_entries, scan_entries, mixing_state)
 
 
-@pytest.fixture()
+@pytest.fixture
 def ms_all_gga_scan_gs(ms_complete):
     """
     Mixing state with all GGA entries and R2SCAN entries corresponding to all GGA
@@ -576,7 +576,7 @@ def ms_all_gga_scan_gs(ms_complete):
     return MixingState(gga_entries, scan_entries, mixing_state)
 
 
-@pytest.fixture()
+@pytest.fixture
 def ms_all_gga_scan_gs_plus_novel(ms_all_gga_scan_gs):
     """
     Mixing state with all GGA entries and R2SCAN entries corresponding to all GGA
@@ -617,7 +617,7 @@ def ms_all_gga_scan_gs_plus_novel(ms_all_gga_scan_gs):
     return MixingState(gga_entries, scan_entries, mixing_state)
 
 
-@pytest.fixture()
+@pytest.fixture
 def ms_all_scan_novel(ms_complete):
     """
     Mixing state with all GGA entries and all R2SCAN, with an additional unstable
@@ -658,7 +658,7 @@ def ms_all_scan_novel(ms_complete):
     return MixingState(gga_entries, scan_entries, mixing_state)
 
 
-@pytest.fixture()
+@pytest.fixture
 def ms_incomplete_gga_all_scan(ms_complete):
     """Mixing state with an incomplete GGA phase diagram."""
     gga_entries = [entry for entry in ms_complete.gga_entries if entry.reduced_formula != "Sn"]
@@ -678,7 +678,7 @@ def ms_incomplete_gga_all_scan(ms_complete):
     return MixingState(gga_entries, scan_entries, mixing_state)
 
 
-@pytest.fixture()
+@pytest.fixture
 def ms_scan_chemsys_superset(ms_complete):
     """
     Mixing state where we have R2SCAN for all GGA, and there is an additional R2SCAN
@@ -709,7 +709,7 @@ def ms_scan_chemsys_superset(ms_complete):
     return MixingState(gga_entries, scan_entries, mixing_state)
 
 
-@pytest.fixture()
+@pytest.fixture
 def ms_complete_duplicate_structs(ms_complete):
     """
     Mixing state where we have R2SCAN for all GGA, plus extra entries that duplicate

tests/io/aims/test_aims_parsers.py

@@ -23,7 +23,7 @@
 parser_file_dir = Path(__file__).parent / "parser_checks"
 
 
-@pytest.fixture()
+@pytest.fixture
 def default_chunk():
     lines = ["TEST", "A", "TEST", "| Number of atoms: 200 atoms"]
     return AimsOutChunk(lines)
@@ -50,7 +50,7 @@ def test_search_parse_scalar(default_chunk):
     assert default_chunk.parse_scalar("n_electrons") is None
 
 
-@pytest.fixture()
+@pytest.fixture
 def empty_header_chunk():
     return AimsOutHeaderChunk([])
 
@@ -89,7 +89,7 @@ def test_default_header_k_point_weights(empty_header_chunk):
     assert empty_header_chunk.k_point_weights is None
 
 
-@pytest.fixture()
+@pytest.fixture
 def initial_lattice():
     return np.array(
         [
@@ -100,7 +100,7 @@ def initial_lattice():
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def header_chunk():
     with gzip.open(f"{parser_file_dir}/header_chunk.out.gz", mode="rt") as hc_file:
         lines = hc_file.readlines()
@@ -155,7 +155,7 @@ def test_header_n_k_points(header_chunk):
     assert header_chunk.n_k_points == 8
 
 
-@pytest.fixture()
+@pytest.fixture
 def k_points():
     return np.array(
         [
@@ -203,7 +203,7 @@ def test_header_header_summary(header_chunk, k_points):
             assert val == header_summary[key]
 
 
-@pytest.fixture()
+@pytest.fixture
 def empty_calc_chunk(header_chunk):
     return AimsOutCalcChunk([], header_chunk)
 
@@ -288,7 +288,7 @@ def test_default_calc_converged(empty_calc_chunk):
     assert not empty_calc_chunk.converged
 
 
-@pytest.fixture()
+@pytest.fixture
 def calc_chunk(header_chunk):
     with gzip.open(f"{parser_file_dir}/calc_chunk.out.gz", mode="rt") as file:
         lines = file.readlines()
@@ -298,7 +298,7 @@ def calc_chunk(header_chunk):
     return AimsOutCalcChunk(lines, header_chunk)
 
 
-@pytest.fixture()
+@pytest.fixture
 def numerical_stress_chunk(header_chunk):
     with gzip.open(f"{parser_file_dir}/numerical_stress.out.gz", mode="rt") as file:
         lines = file.readlines()
@@ -419,7 +419,7 @@ def test_calc_hirshfeld_dipole(calc_chunk):
     assert calc_chunk.hirshfeld_dipole is None
 
 
-@pytest.fixture()
+@pytest.fixture
 def molecular_header_chunk():
     with gzip.open(f"{parser_file_dir}/molecular_header_chunk.out.gz", mode="rt") as file:
         lines = file.readlines()
@@ -451,7 +451,7 @@ def test_molecular_header_initial_structure(molecular_header_chunk, molecular_po
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def molecular_calc_chunk(molecular_header_chunk):
     with gzip.open(f"{parser_file_dir}/molecular_calc_chunk.out.gz", mode="rt") as file:
         lines = file.readlines()
@@ -461,7 +461,7 @@ def molecular_calc_chunk(molecular_header_chunk):
     return AimsOutCalcChunk(lines, molecular_header_chunk)
 
 
-@pytest.fixture()
+@pytest.fixture
 def molecular_positions():
     return np.array([[-0.00191785, -0.00243279, 0], [0.97071531, -0.00756333, 0], [-0.25039746, 0.93789612, 0]])
 

tests/io/qchem/test_outputs.py

@@ -301,7 +301,7 @@ def _test_property(self, key, single_outs, multi_outs):
                     else:
                         assert_allclose(sub_output.data.get(key), multi_job_dict[filename][idx].get(key), atol=1e-6)
 
-    @pytest.mark.skip()  # self._test_property(key, single_outs, multi_outs) fails with
+    @pytest.mark.skip  # self._test_property(key, single_outs, multi_outs) fails with
     # ValueError: The truth value of an array with more than one element is ambiguous
     @pytest.mark.skipif(openbabel is None, reason="OpenBabel not installed.")
     def test_all(self):

tests/io/test_openff.py

@@ -26,7 +26,7 @@
 pybel = pytest.importorskip("openbabel.pybel")
 
 
-@pytest.fixture()
+@pytest.fixture
 def mol_files():
     return {
         "CCO_xyz": f"{TEST_DIR}/CCO.xyz",

tests/test_cli.py

@@ -14,7 +14,7 @@
     from pytest import MonkeyPatch
 
 
-@pytest.fixture()
+@pytest.fixture
 def cd_tmp_path(tmp_path: Path, monkeypatch: MonkeyPatch):
     monkeypatch.chdir(tmp_path)
     return tmp_path