Fix linting (#66)

* Fix linting

* Use Python 3.12

* More Python 3.12

* Reformat with black for Python 3.12

.github/workflows/lint.yml

@@ -15,15 +15,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Setup Python 3.10
+      - name: Setup Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Lint with black
         uses: psf/black@stable
-        with:
-            options: "--check --diff --line-length 79"
 
       - name: Check for debugging print statements
         run: |

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = 'setuptools.build_meta'
 
 [tool.black]
 line-length = 79
-target-version = ['py37']
+target-version = ['py312']
 include = '\.pyi?$'
 exclude = '''
 (

spectrum_utils/proforma.py

@@ -378,9 +378,9 @@ def proteoform(self, tree) -> Proteoform:
         self._modifications.sort(key=_modification_sort_key)
         proteoform = Proteoform(
             sequence=sequence,
-            modifications=self._modifications
-            if len(self._modifications) > 0
-            else None,
+            modifications=(
+                self._modifications if len(self._modifications) > 0 else None
+            ),
             charge=charge,
         )
         # Reset class variables.
@@ -664,9 +664,7 @@ def parse(proforma: str) -> List[Proteoform]:
 
 
 @functools.lru_cache
-def _import_cv(
-    cv_id: str, cache: Optional[str]
-) -> Union[
+def _import_cv(cv_id: str, cache: Optional[str]) -> Union[
     Tuple[Dict[str, Tuple[float, str]], Dict[str, Tuple[float, str]]],
     Dict[str, float],
 ]:

tests/spectrum_test.py

@@ -419,7 +419,7 @@ def test_scale_intensity_root():
         intensity_unscaled = spec.intensity.copy()
         spec.scale_intensity(scaling="root", degree=degree)
         np.testing.assert_allclose(
-            spec.intensity ** degree, intensity_unscaled, rtol=1e-5
+            spec.intensity**degree, intensity_unscaled, rtol=1e-5
         )
 
 
@@ -434,7 +434,7 @@ def test_scale_intensity_log():
         intensity_unscaled = spec.intensity.copy()
         spec.scale_intensity(scaling="log", base=base)
         np.testing.assert_allclose(
-            base ** spec.intensity - 1, intensity_unscaled, rtol=1e-5
+            base**spec.intensity - 1, intensity_unscaled, rtol=1e-5
         )