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

pre-commit-ci[bot] · pre-commit-ci[bot] · commit d71131ffe5f5 · 2025-01-20T22:47:54.000Z
for more information, see https://pre-commit.ci
diff --git a/backend/config/settings/production.py b/backend/config/settings/production.py
@@ -199,7 +199,7 @@
     "disable_existing_loggers": True,
     "root": {"level": "WARNING"},
     "formatters": {
-        "verbose": {"format": "%(levelname)s %(asctime)s %(module)s " "%(process)d %(thread)d %(message)s"},
+        "verbose": {"format": "%(levelname)s %(asctime)s %(module)s %(process)d %(thread)d %(message)s"},
     },
     "handlers": {
         "console": {
diff --git a/backend/fpbase/forms.py b/backend/fpbase/forms.py
@@ -29,7 +29,7 @@ def friendly_email(self):
 
     def send_email(self):
         EmailMessage(
-            f'FPbase contact from {self.cleaned_data["name"]}',
+            f"FPbase contact from {self.cleaned_data['name']}",
             self.cleaned_data["message"],
             to=[a[1] for a in settings.ADMINS],
             headers={"Reply-To": self.friendly_email()},
diff --git a/backend/fpseq/__init__.py b/backend/fpseq/__init__.py
@@ -6,12 +6,12 @@
 
 __all__ = [
     "FPSeq",
-    "from_fpbase",
-    "SkbSequence",
-    "ParasailAlignment",
-    "align_seqs",
     "Mutation",
     "MutationSet",
+    "ParasailAlignment",
+    "SkbSequence",
+    "align_seqs",
+    "from_fpbase",
     "get_mutations",
     "mutate_sequence",
     "protein_weight",
diff --git a/backend/fpseq/skbio_protein.py b/backend/fpseq/skbio_protein.py
@@ -138,7 +138,7 @@ def _munge_to_sequence(self, other, method):
         if isinstance(other, SkbSequence):
             if type(other) is not type(self):
                 raise TypeError(
-                    f"Cannot use {self.__class__.__name__} and " f"{other.__class__.__name__} together with `{method}`"
+                    f"Cannot use {self.__class__.__name__} and {other.__class__.__name__} together with `{method}`"
                 )
             else:
                 return other
@@ -362,6 +362,6 @@ def _slices_from_iter(array, indexables):
         elif _is_single_index(i):
             i = _single_index_to_slice(i)
         else:
-            raise IndexError("Cannot slice sequence from iterable " f"containing {i!r}.")
+            raise IndexError(f"Cannot slice sequence from iterable containing {i!r}.")
 
         yield array[i]
diff --git a/backend/proteins/extrest/entrez.py b/backend/proteins/extrest/entrez.py
@@ -129,9 +129,9 @@ def fetch_ipg_sequence(protein_name=None, uid=None):
     assert len(record) == 1, "More than one record returned from protein database"
     record = record[0]
     prot_seq = record["GBSeq_sequence"].upper()
-    assert len(prot_seq) == int(
-        seq_len
-    ), f"Protein database sequence different length {len(prot_seq)} than IPG database{int(seq_len)}"
+    assert len(prot_seq) == int(seq_len), (
+        f"Protein database sequence different length {len(prot_seq)} than IPG database{int(seq_len)}"
+    )
     return (ipg_uid, prot_seq)
 
 
diff --git a/backend/proteins/forms/forms.py b/backend/proteins/forms/forms.py
@@ -390,7 +390,7 @@ def clean(self):
         parent = self.cleaned_data.get("parent")
         mutation = self.cleaned_data.get("mutation")
         if (parent and not mutation) or (mutation and not parent):
-            raise forms.ValidationError("Both parent and mutation are " "required when providing lineage information")
+            raise forms.ValidationError("Both parent and mutation are required when providing lineage information")
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
diff --git a/backend/proteins/forms/microscope.py b/backend/proteins/forms/microscope.py
@@ -205,7 +205,7 @@ def _getpromise(fname):
             else:
                 self.add_error(
                     "optical_configs",
-                    "Filter not found in database or at Chroma/Semrock: " f"{fname}",
+                    f"Filter not found in database or at Chroma/Semrock: {fname}",
                 )
                 return None
 
@@ -269,7 +269,7 @@ def lookup(fname, n=None):
                 if len(splt) not in (4, 5):
                     self.add_error(
                         "optical_configs",
-                        "Lines must have 4 or 5 comma-separated fields but this one " f"has {len(splt)}: {line}",
+                        f"Lines must have 4 or 5 comma-separated fields but this one has {len(splt)}: {line}",
                     )
                 for n, f in enumerate(splt):
                     if n == 0:
diff --git a/backend/proteins/forms/spectrum.py b/backend/proteins/forms/spectrum.py
@@ -111,11 +111,11 @@ def clean(self):
         if not (cleaned_data.get("data") or self.files):
             self.add_error(
                 "data",
-                "Please either fill in the data field or " "select a file to upload.",
+                "Please either fill in the data field or select a file to upload.",
             )
             self.add_error(
                 "file",
-                "Please either fill in the data field or " "select a file to upload.",
+                "Please either fill in the data field or select a file to upload.",
             )
 
     def save(self, commit=True):
diff --git a/backend/proteins/models/__init__.py b/backend/proteins/models/__init__.py
@@ -12,23 +12,23 @@
 from .transition import StateTransition
 
 __all__ = [
-    "Protein",
-    "Organism",
     "BleachMeasurement",
-    "OSERMeasurement",
-    "State",
+    "Camera",
     "Dye",
+    "Excerpt",
+    "Filter",
+    "FilterPlacement",
     "Fluorophore",
-    "StateTransition",
-    "ProteinCollection",
-    "Spectrum",
-    "Camera",
     "Light",
-    "Filter",
+    "Lineage",
     "Microscope",
-    "OpticalConfig",
-    "FilterPlacement",
-    "Excerpt",
+    "OSERMeasurement",
     "OcFluorEff",
-    "Lineage",
+    "OpticalConfig",
+    "Organism",
+    "Protein",
+    "ProteinCollection",
+    "Spectrum",
+    "State",
+    "StateTransition",
 ]
diff --git a/backend/proteins/models/collection.py b/backend/proteins/models/collection.py
@@ -41,7 +41,7 @@ class ProteinCollection(OwnedCollection):
     private = models.BooleanField(
         default=False,
         verbose_name="Private Collection",
-        help_text="Private collections can not be seen " "by or shared with other users",
+        help_text="Private collections can not be seen by or shared with other users",
     )
 
     def get_absolute_url(self):
diff --git a/backend/proteins/models/microscope.py b/backend/proteins/models/microscope.py
@@ -295,7 +295,7 @@ def add_filter(self, filter, path, reflects=False):
 
     def __repr__(self):
         fltrs = sorted_ex2em(self.filters.all())
-        return f'<{self.__class__.__name__}: {", ".join([f.name for f in fltrs])}>'
+        return f"<{self.__class__.__name__}: {', '.join([f.name for f in fltrs])}>"
 
     def __str__(self):
         return super().__str__() or self.__repr__().lstrip("<").rstrip(">")
@@ -325,7 +325,7 @@ def __str__(self):
         return self.__repr__().lstrip("<").rstrip(">")
 
     def __repr__(self):
-        return f'<{self.path.title()} Filter: {self.filter.name}{" (reflecting)" if self.reflects else ""}>'
+        return f"<{self.path.title()} Filter: {self.filter.name}{' (reflecting)' if self.reflects else ''}>"
 
 
 def quick_OC(name, filternames, scope, bs_ex_reflect=True):
diff --git a/backend/proteins/models/protein.py b/backend/proteins/models/protein.py
@@ -408,7 +408,7 @@ def em_css(self):
                 if _hex == "#000":
                     sub = 18
                 bgs.append(f"{_hex} {(i + 1) * stepsize - sub}%")
-            return f'linear-gradient(90deg, {", ".join(bgs)})'
+            return f"linear-gradient(90deg, {', '.join(bgs)})"
         elif self.default_state:
             return self.default_state.emhex
         else:
diff --git a/backend/proteins/util/__init__.py b/backend/proteins/util/__init__.py
@@ -1,4 +1,4 @@
 from .blurb import long_blurb
 from .helpers import getprot
 
-__all__ = ["long_blurb", "getprot"]
+__all__ = ["getprot", "long_blurb"]
diff --git a/backend/proteins/validators.py b/backend/proteins/validators.py
@@ -44,7 +44,7 @@ def validate_mutation(code):
 def cdna_sequence_validator(seq):
     badletters = [letter for letter in seq if letter not in UNAMBIGUOUS_DNA_LETTERS]
     if len(badletters):
-        raise ValidationError(f'Invalid DNA letters: {"".join(set(badletters))}')
+        raise ValidationError(f"Invalid DNA letters: {''.join(set(badletters))}")
     try:
         Seq.Seq(seq, UNAMBIGUOUS_DNA_LETTERS).translate()
     except Data.CodonTable.TranslationError as e:
@@ -56,7 +56,7 @@ def protein_sequence_validator(seq):
     badletters = [letter for letter in seq if letter not in IUPAC_PROTEIN_LETTERS]
     if len(badletters):
         badletters = set(badletters)
-        raise ValidationError(f'Invalid letter(s) found in amino acid sequence: {"".join(badletters)}')
+        raise ValidationError(f"Invalid letter(s) found in amino acid sequence: {''.join(badletters)}")
 
 
 def validate_spectrum(value):
diff --git a/backend/proteins/views/protein.py b/backend/proteins/views/protein.py
@@ -97,7 +97,7 @@ def formset_changes(formset):
     for obj, _fields in formset.changed_objects:
         form = next(_form for _form in formset.forms if _form.instance == obj)
         frm_chg = form_changes(form)
-        changes.append(f'Changed {model} {obj}: ({"; ".join(frm_chg)})')
+        changes.append(f"Changed {model} {obj}: ({'; '.join(frm_chg)})")
     return changes
 
 
diff --git a/backend/proteins/views/spectra.py b/backend/proteins/views/spectra.py
@@ -112,7 +112,7 @@ def form_valid(self, form):
             {form.cleaned_data}
             """
             EmailMessage(
-                subject=f'[FPbase] Spectrum needs validation: {form.cleaned_data["owner"]}',
+                subject=f"[FPbase] Spectrum needs validation: {form.cleaned_data['owner']}",
                 body=dedent(body),
                 to=[a[1] for a in settings.ADMINS],
                 headers={"X-Mailgun-Track": "no"},

Original file line number	Diff line number	Diff line change
`@@ -111,11 +111,11 @@ def clean(self):`
`111`	`111`	`if not (cleaned_data.get("data") or self.files):`
`112`	`112`	`self.add_error(`
`113`	`113`	`"data",`
`114`		`- "Please either fill in the data field or " "select a file to upload.",`
	`114`	`+ "Please either fill in the data field or select a file to upload.",`
`115`	`115`	`)`
`116`	`116`	`self.add_error(`
`117`	`117`	`"file",`
`118`		`- "Please either fill in the data field or " "select a file to upload.",`
	`118`	`+ "Please either fill in the data field or select a file to upload.",`
`119`	`119`	`)`
`120`	`120`
`121`	`121`	`def save(self, commit=True):`
Original file line number	Diff line number	Diff line change
`@@ -41,7 +41,7 @@ class ProteinCollection(OwnedCollection):`
`41`	`41`	`private = models.BooleanField(`
`42`	`42`	`default=False,`
`43`	`43`	`verbose_name="Private Collection",`
`44`		`- help_text="Private collections can not be seen " "by or shared with other users",`
	`44`	`+ help_text="Private collections can not be seen by or shared with other users",`
`45`	`45`	`)`
`46`	`46`
`47`	`47`	`def get_absolute_url(self):`