[pre-commit.ci] auto fixes from pre-commit.com hooks

pre-commit-ci[bot] · pre-commit-ci[bot] · commit d1d9a10a3aa2 · 2026-02-19T19:56:27.000Z
for more information, see https://pre-commit.ci
diff --git a/mh_utils/csv_parser/classes.py b/mh_utils/csv_parser/classes.py
@@ -218,7 +218,7 @@ def to_dict(self):
 				da_method=self.da_method,
 				irm_cal_status=self.irm_cal_status,
 				filename=self.filename,
-				results=self.results_list
+				results=self.results_list,
 				)
 
 
@@ -750,7 +750,7 @@ def filter(  # noqa: A003  # pylint: disable=redefined-builtin
 		sample_names: Iterable[str],
 		key: str = "sample_name",
 		exclude: bool = False,
-		) -> _SL:
+	) -> _SL:
 		"""
 		Filter the list to only contain sample_names whose name is in ``sample_names``.
 
diff --git a/mh_utils/csv_parser/utils.py b/mh_utils/csv_parser/utils.py
@@ -113,12 +113,17 @@ def drop_columns(df: pandas.DataFrame, *, axis: int = 1, inplace: bool = True, *
 
 	lib_cols = ["Lib/DB", "Score (Lib)"]
 
-	new_df = df.drop([
-			*unknown_cols,
-			*db_cols,
-			*mfg_cols,
-			*lib_cols,
-			], axis=axis, inplace=inplace, **kwargs)
+	new_df = df.drop(
+			[
+					*unknown_cols,
+					*db_cols,
+					*mfg_cols,
+					*lib_cols,
+					],
+			axis=axis,
+			inplace=inplace,
+			**kwargs,
+			)
 
 	if inplace:
 		return df
diff --git a/mh_utils/pcdl.py b/mh_utils/pcdl.py
@@ -160,23 +160,25 @@ def compound_list_2_pandas(compound_list: List[PCDLCompound]) -> DataFrame:
 			data.append(compound.as_list())
 
 	df = DataFrame(data, columns=columns)
-	df = df.reindex([
-			"Name",
-			"Formula",
-			"Mass",
-			"Retention Time",
-			"Retention Index",
-			"Cation",
-			"Anion",
-			"CAS",
-			"ChemSpider",
-			"PubChem",
-			"Synonyms",
-			"IUPAC",
-			"NumSpectra",
-			"CCS Count",
-			],
-					axis=1)
+	df = df.reindex(
+			[
+					"Name",
+					"Formula",
+					"Mass",
+					"Retention Time",
+					"Retention Index",
+					"Cation",
+					"Anion",
+					"CAS",
+					"ChemSpider",
+					"PubChem",
+					"Synonyms",
+					"IUPAC",
+					"NumSpectra",
+					"CCS Count",
+					],
+			axis=1,
+			)
 
 	names = df["IUPAC"]
 	sort_order = get_IUPAC_sort_order(names)
diff --git a/mh_utils/worklist_parser/classes.py b/mh_utils/worklist_parser/classes.py
@@ -273,7 +273,7 @@ def from_xml(cls, element: lxml.objectify.ObjectifiedElement) -> "Checksum":
 		return cls(
 				SchemaVersion=element.attrib["SchemaVersion"],
 				ALGO_VERSION=element.attrib["ALGO_VERSION"],
-				HASHCODE=element.MAIN.attrib["HASHCODE"]
+				HASHCODE=element.MAIN.attrib["HASHCODE"],
 				)
 
 
diff --git a/tests/common.py b/tests/common.py
@@ -16,10 +16,11 @@
 
 def any_type_parametrize():
 	return pytest.mark.parametrize(
-			f"value, expects", [
+			f"value, expects",
+			[
 					("foo", "foo"),
 					(1234, 1234),
 					(12.34, 12.34),
 					(True, True),
-					]
+					],
 			)
diff --git a/tests/test_cef_parser/test_compound.py b/tests/test_cef_parser/test_compound.py
@@ -49,10 +49,12 @@ def test_algo(self):
 
 	def test_location(self):
 		assert Compound(
-				algo="FindByFormula", location={'m': 169.0893, "rt": 13.649, 'a': 29388223, 'y': 3377289}
+				algo="FindByFormula",
+				location={'m': 169.0893, "rt": 13.649, 'a': 29388223, 'y': 3377289},
 				).location == {'m': 169.0893, "rt": 13.649, 'a': 29388223, 'y': 3377289}
 		assert Compound(
-				algo="FindByFormula", location={'m': 169.0893, "rt": 13.649, 'a': 29388223, 'y': 3377289}
+				algo="FindByFormula",
+				location={'m': 169.0893, "rt": 13.649, 'a': 29388223, 'y': 3377289},
 				).location == {'m': 169.0893, "rt": 13.649, 'a': 29388223, 'y': 3377289}
 		assert Compound(algo="FindByFormula").location == {}
 
@@ -63,7 +65,7 @@ def test_location(self):
 					{"fbf": Score(82.53, flag_string="No H adduct", flag_severity=2)},
 					{"fbf": Score(60.62, flag_string="low score", flag_severity=2)},
 					{"fbf": Score(62.90, flag_string="low score", flag_severity=2)},
-					]
+					],
 			)
 	def test_compound_scores(self, scores):
 		assert Compound(algo="FindByFormula", compound_scores=scores).compound_scores == copy.deepcopy(scores)
@@ -222,11 +224,13 @@ def expected_compound(fbf_spectrum, tof_spectrum):
 			compound_scores={"fbf": score},
 			results=[
 					Molecule(
-							name="Diphenylamine", formula="C12 H11 N", matches={
+							name="Diphenylamine",
+							formula="C12 H11 N",
+							matches={
 									"overall": score,
 									"tgt": score,
-									}
-							)
+									},
+							),
 					],
 			spectra=[fbf_spectrum, tof_spectrum],
 			)
@@ -260,7 +264,7 @@ def test_parse_cef(tmpdir, expected_compound):
 	{raw_xml}
 </CompoundList>
 </CEF>
-"""
+""",
 			)
 
 	cef = parse_cef(PathPlus(tmpdir) / "demo.cef")
diff --git a/tests/test_cef_parser/test_device.py b/tests/test_cef_parser/test_device.py
@@ -7,10 +7,11 @@
 
 
 @pytest.mark.parametrize(
-		"device_type, device_type_expects", [
+		"device_type, device_type_expects",
+		[
 				("hello world", "hello world"),
 				("An Instrument", "An Instrument"),
-				]
+				],
 		)
 @pytest.mark.parametrize(
 		"number, number_expects",
diff --git a/tests/test_cef_parser/test_molecule.py b/tests/test_cef_parser/test_molecule.py
@@ -14,10 +14,12 @@ def test_name(self):
 
 	def test_formula(self):
 		assert Molecule(
-				name="Dimethyl Phthalate", formula="C10 H10 O4"
+				name="Dimethyl Phthalate",
+				formula="C10 H10 O4",
 				).formula == Formula({'C': 10, 'H': 10, 'O': 4})
 		assert Molecule(
-				name="Dimethyl Phthalate", formula=Formula({'C': 10, 'H': 10, 'O': 4})
+				name="Dimethyl Phthalate",
+				formula=Formula({'C': 10, 'H': 10, 'O': 4}),
 				).formula == Formula({'C': 10, 'H': 10, 'O': 4})
 		assert Molecule(name="Dimethyl Phthalate").formula == Formula()
 
@@ -47,7 +49,7 @@ def test_dict():
 							"overall": Score(62.90),
 							"tgt": Score(62.90, flag_string="low score", flag_severity=2),
 							},
-					)
+					),
 			) == {
 					"name": "Dimethyl Phthalate",
 					"formula": Formula({'C': 10, 'H': 10, 'O': 4}),
@@ -126,7 +128,7 @@ def test_from_xml(raw_xml, expects):
 				(raw_xml_5, {"fbf": Score(62.90, flag_string="low score", flag_severity=2)}),
 				(
 						raw_xml_multiline,
-						{"fbf": Score(62.90, flag_string="low score", flag_severity=2), "abc": Score(12.34)}
+						{"fbf": Score(62.90, flag_string="low score", flag_severity=2), "abc": Score(12.34)},
 						),
 				],
 		)
diff --git a/tests/test_cef_parser/test_parse_compound_scores.py b/tests/test_cef_parser/test_parse_compound_scores.py
@@ -33,7 +33,7 @@
 				(raw_xml_5, {"fbf": Score(62.90, flag_string="low score", flag_severity=2)}),
 				(
 						raw_xml_multiline,
-						{"fbf": Score(62.90, flag_string="low score", flag_severity=2), "abc": Score(12.34)}
+						{"fbf": Score(62.90, flag_string="low score", flag_severity=2), "abc": Score(12.34)},
 						),
 				],
 		)
diff --git a/tests/test_cef_parser/test_peak.py b/tests/test_cef_parser/test_peak.py
@@ -93,7 +93,7 @@ def test_creation(
 						170.0964,
 						890559.25,
 						1,
-						"M+H"
+						"M+H",
 						),
 				(
 						'<p x="171.0998" rx="171.0996" y="114286.09" z="1" s="M+H+1" />',
@@ -109,15 +109,15 @@ def test_creation(
 						172.1028,
 						7151.12,
 						1,
-						"M+H+2"
+						"M+H+2",
 						),
 				(
 						'<p x="192.0831" rx="192.0784" y="490.62" z="1" s="M+Na" />',
 						192.0831,
 						192.0784,
 						490.62,
 						1,
-						"M+Na"
+						"M+Na",
 						),
 				],
 		)
diff --git a/tests/test_cef_parser/test_spectrum.py b/tests/test_cef_parser/test_spectrum.py
@@ -29,7 +29,8 @@ def test_ionisation(self):
 		assert Spectrum(ionisation="Esi").ionisation == "Esi"
 
 	@pytest.mark.parametrize(
-			"polarity, expected", [
+			"polarity, expected",
+			[
 					('+', 1),
 					("positive", 1),
 					(1, 1),
@@ -38,7 +39,7 @@ def test_ionisation(self):
 					(-1, -1),
 					(0, 0),
 					(22, 22),
-					]
+					],
 			)
 	def test_polarity(self, polarity, expected):
 		assert Spectrum(polarity=polarity).polarity == expected
@@ -55,7 +56,7 @@ def test_rt_ranges(self):
 		assert Spectrum().rt_ranges == []
 		assert Spectrum(rt_ranges=[]).rt_ranges == []
 		assert Spectrum(rt_ranges=()).rt_ranges == []
-		assert Spectrum(rt_ranges=[RTRange(12, 34)], ).rt_ranges == [RTRange(12, 34)]
+		assert Spectrum(rt_ranges=[RTRange(12, 34)]).rt_ranges == [RTRange(12, 34)]
 
 	@pytest.mark.parametrize(
 			"voltage, expected",
@@ -67,7 +68,7 @@ def test_rt_ranges(self):
 					(1234.0, 1234.0),
 					(1234, 1234.0),
 					("ABCDEFG", 0),
-					]
+					],
 			)
 	def test_voltage(self, voltage, expected):
 		assert Spectrum(voltage=voltage).voltage == expected
@@ -193,10 +194,13 @@ def test_repr(spectrum):
 		)
 
 
-@pytest.mark.parametrize("raw_xml, expects", [
-		(raw_xml_fbf, fbf_expects),
-		(raw_xml_tof, tof_expects),
-		])
+@pytest.mark.parametrize(
+		"raw_xml, expects",
+		[
+				(raw_xml_fbf, fbf_expects),
+				(raw_xml_tof, tof_expects),
+				],
+		)
 def test_from_xml(raw_xml, expects):
 	tree = lxml.objectify.fromstring(raw_xml)
 	spec = Spectrum.from_xml(tree)
diff --git a/tests/test_pcdl.py b/tests/test_pcdl.py
@@ -261,16 +261,18 @@ def pcdl_cassette(request: FixtureRequest):
 				pytest.param(
 						"<=3.8",
 						marks=pytest.mark.skipif(
-								sys.version_info >= (3, 9), reason="Output changes after Python 3.8"
-								)
+								sys.version_info >= (3, 9),
+								reason="Output changes after Python 3.8",
+								),
 						),
 				pytest.param(
 						">=3.9",
 						marks=pytest.mark.skipif(
-								sys.version_info < (3, 9), reason="Output changes after Python 3.8"
-								)
+								sys.version_info < (3, 9),
+								reason="Output changes after Python 3.8",
+								),
 						),
-				]
+				],
 		)
 @pytest.mark.usefixtures("pcdl_cassette", "python_version")
 def test_make_pcdl_csv(
diff --git a/tests/test_worklist_parser/test_attribute.py b/tests/test_worklist_parser/test_attribute.py
@@ -39,10 +39,11 @@ def __init__(self):
 
 
 @pytest.mark.parametrize(
-		"data", [
+		"data",
+		[
 				pytest.param(data_from_init, id="from init"),
 				pytest.param(data_from_element, id="from element"),
-				]
+				],
 		)
 def test_attribute(data):
 
diff --git a/tests/test_worklist_parser/test_checksum.py b/tests/test_worklist_parser/test_checksum.py
@@ -5,16 +5,22 @@
 from mh_utils.worklist_parser.classes import Checksum
 
 
-@pytest.mark.parametrize("SchemaVersion, SchemaVersion_expects", [
-		(1, 1),
-		('1', 1),
-		(1.2, 1),
-		])
-@pytest.mark.parametrize("ALGO_VERSION, ALGO_VERSION_expects", [
-		(2, 2),
-		('2', 2),
-		(2.5, 2),
-		])
+@pytest.mark.parametrize(
+		"SchemaVersion, SchemaVersion_expects",
+		[
+				(1, 1),
+				('1', 1),
+				(1.2, 1),
+				],
+		)
+@pytest.mark.parametrize(
+		"ALGO_VERSION, ALGO_VERSION_expects",
+		[
+				(2, 2),
+				('2', 2),
+				(2.5, 2),
+				],
+		)
 def test_creation(SchemaVersion, SchemaVersion_expects, ALGO_VERSION, ALGO_VERSION_expects):
 	data = Checksum(
 			SchemaVersion=SchemaVersion,
diff --git a/tests/test_worklist_parser/test_columns.py b/tests/test_worklist_parser/test_columns.py
diff --git a/tests/test_worklist_parser/test_parser.py b/tests/test_worklist_parser/test_parser.py
diff --git a/tests/test_worklist_parser/test_worklist.py b/tests/test_worklist_parser/test_worklist.py

Original file line number	Diff line number	Diff line change
`@@ -273,7 +273,7 @@ def from_xml(cls, element: lxml.objectify.ObjectifiedElement) -> "Checksum":`
`273`	`273`	`return cls(`
`274`	`274`	`SchemaVersion=element.attrib["SchemaVersion"],`
`275`	`275`	`ALGO_VERSION=element.attrib["ALGO_VERSION"],`
`276`		`- HASHCODE=element.MAIN.attrib["HASHCODE"]`
	`276`	`+ HASHCODE=element.MAIN.attrib["HASHCODE"],`
`277`	`277`	`)`
`278`	`278`
`279`	`279`
Original file line number	Diff line number	Diff line change
`@@ -33,7 +33,7 @@`
`33`	`33`	`(raw_xml_5, {"fbf": Score(62.90, flag_string="low score", flag_severity=2)}),`
`34`	`34`	`(`
`35`	`35`	`raw_xml_multiline,`
`36`		`- {"fbf": Score(62.90, flag_string="low score", flag_severity=2), "abc": Score(12.34)}`
	`36`	`+ {"fbf": Score(62.90, flag_string="low score", flag_severity=2), "abc": Score(12.34)},`
`37`	`37`	`),`
`38`	`38`	`],`
`39`	`39`	`)`