[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -21,7 +21,7 @@ repos:
       - id: detect-private-key
 
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.8.15
+    rev: 0.9.2
     hooks:
       - id: uv-export
         args: ["--group", "prod", "--no-dev", "--frozen", "--output-file=requirements.txt"]
@@ -39,13 +39,13 @@ repos:
   #     - id: djlint-django
 
   - repo: https://github.com/adamchainz/django-upgrade
-    rev: "1.27.0"
+    rev: "1.29.0"
     hooks:
       - id: django-upgrade
         args: ["--target-version", "4.2"]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.12.11"
+    rev: "v0.14.0"
     hooks:
       - id: ruff
         args: ["--fix", "--unsafe-fixes"]

backend/proteins/extrest/__init__.py

@@ -50,7 +50,7 @@ def execute(self):
         p = Protein.objects.get(id=self.id)  # in case it's changed
         for attr, newval in self.changes.items():
             if attr == "parent_organism" and isinstance(newval, int):
-                org, created = Organism.objects.get_or_create(id=newval)
+                org, _created = Organism.objects.get_or_create(id=newval)
                 p.parent_organism = org
             else:
                 setattr(p, attr, newval)

backend/proteins/forms/forms.py

@@ -542,7 +542,7 @@ def save(self, commit=True):
         obj = super().save(commit=False)
         doi = self.cleaned_data.get("reference_doi")
         if doi:
-            ref, created = Reference.objects.get_or_create(doi=doi)
+            ref, _created = Reference.objects.get_or_create(doi=doi)
             obj.reference = ref
         if commit:
             obj.save()
@@ -635,7 +635,7 @@ def save(self, commit=True):
         obj = super().save(commit=False)
         doi = self.cleaned_data.get("reference_doi")
         if doi:
-            ref, created = Reference.objects.get_or_create(doi=doi)
+            ref, _created = Reference.objects.get_or_create(doi=doi)
             obj.reference = ref
         if commit:
             obj.save()

backend/proteins/forms/spectrum.py

@@ -140,7 +140,7 @@ def clean_file(self):
                         filetext += chunk.decode("utf-8")
                     except AttributeError:
                         filetext += chunk
-                x, y, headers = text_to_spectra(filetext)
+                x, y, _headers = text_to_spectra(filetext)
                 if not len(y):
                     self.add_error("file", "Did not find a data column in the provided file")
                 if not len(x):

backend/proteins/tests/test_forms.py

@@ -105,7 +105,7 @@ def test_ids_already_exist(self):
 
 class TestStateForm(TestCase):
     def setUp(self):
-        self.t, c = Protein.objects.get_or_create(name="Test Protein")
+        self.t, _c = Protein.objects.get_or_create(name="Test Protein")
         State.objects.get_or_create(protein=self.t)
 
     def test_clean_state_success(self):
@@ -132,7 +132,7 @@ def test_nondark_state_exemmax_required(self):
 
 class TestCollectionForm(TestCase):
     def setUp(self):
-        self.p, c = Protein.objects.get_or_create(name="Test Protein")
+        self.p, _c = Protein.objects.get_or_create(name="Test Protein")
         self.userA = self.make_user("userA", "userApassword")
         self.userB = self.make_user("userB", "userBpassword")
 

backend/proteins/util/_local.py

@@ -459,7 +459,7 @@ def import2P():
             with open(infile) as f:
                 text = f.read()
 
-            x, y, headers = text_to_spectra(text)
+            x, y, _headers = text_to_spectra(text)
             D = zip_wave_data(x, y[0])
 
             sf = SpectrumForm(
@@ -477,7 +477,7 @@ def import2P():
                 P.default_state.save()
 
                 # add drobizhev reference
-                ref, created = Reference.objects.get_or_create(doi="10.1038/nmeth.1596")
+                ref, _created = Reference.objects.get_or_create(doi="10.1038/nmeth.1596")
                 P.references.add(ref)
                 P.save()
                 print(f"Successfuly import 2P spectrum for {P.name}")
@@ -965,7 +965,7 @@ def import_chroma():
 
 def import_lights():
     file = os.path.join(BASEDIR, "_data/broadband_light_spectra.csv")
-    objs, errs = import_csv_spectra(file, categories=Spectrum.LIGHT, stypes=Spectrum.PD)
+    objs, _errs = import_csv_spectra(file, categories=Spectrum.LIGHT, stypes=Spectrum.PD)
     for obj in objs:
         obj.owner.created_by = User.objects.first()
         obj.created_by = User.objects.first()

backend/proteins/util/importers.py

@@ -24,7 +24,7 @@ def reimport_filter_spectrum(obj):
         text = fetch_semrock_part(obj.part)
     elif obj.manufacturer.lower() == "chroma":
         text = fetch_chroma_part(obj.part)
-    waves, data, headers = text_to_spectra(text)
+    waves, data, _headers = text_to_spectra(text)
     D = zip_wave_data(waves, data[0])
     obj.spectrum.data = D
     obj.spectrum.save()

backend/proteins/util/spectra.py

@@ -50,7 +50,7 @@ def norm2one(y):
 
 
 def step_size(lol):
-    x, y = zip(*lol)
+    x, _y = zip(*lol)
     s = set(np.subtract(x[1:], x[:-1]))
     if len(s) != 1:  # multiple step sizes
         return 0
@@ -107,7 +107,7 @@ def interp2int(x, y, s=1):
     from proteins.util.importers import text_to_spectra
 
     def file2spectra(file, dtype="", getcol=0):
-        waves, outdata, headers = text_to_spectra(file)
+        waves, outdata, _headers = text_to_spectra(file)
         x = waves
         y = outdata[getcol]
         spectra = [list(i) for i in zip(x, y)]

backend/proteins/views/protein.py

@@ -684,7 +684,7 @@ def add_reference(request, slug=None):
         with reversion.create_revision():
             doi = request.POST.get("reference_doi").lower()
             p = Protein.objects.get(slug=slug)
-            ref, created = Reference.objects.get_or_create(doi=doi)
+            ref, _created = Reference.objects.get_or_create(doi=doi)
             p.references.add(ref)
             if not request.user.is_staff:
                 p.status = "pending"
@@ -712,7 +712,7 @@ def add_protein_excerpt(request, slug=None):
             p = Protein.objects.get(slug=slug)
             content = request.POST.get("excerpt_content")
             if content:
-                ref, created = Reference.objects.get_or_create(doi=doi)
+                ref, _created = Reference.objects.get_or_create(doi=doi)
                 p.references.add(ref)
                 excerpt = Excerpt.objects.create(reference=ref, content=strip_tags(content), created_by=request.user)
                 excerpt.proteins.add(p)