New ruff rules, reduce line length to 99

backend/config/api_router.py

@@ -4,10 +4,7 @@
 import proteins.api.urls
 from fpbase.users.api.views import UserViewSet
 
-if settings.DEBUG:
-    router = DefaultRouter()
-else:
-    router = SimpleRouter()
+router = DefaultRouter() if settings.DEBUG else SimpleRouter()
 
 router.register("users", UserViewSet)
 

backend/config/settings/base.py

@@ -26,7 +26,8 @@
 READ_DOT_ENV_FILE = env.bool("DJANGO_READ_DOT_ENV_FILE", default=False)
 
 if READ_DOT_ENV_FILE:
-    # Operating System Environment variables have precedence over variables defined in the .env file,
+    # Operating System Environment variables have precedence over variables defined in the
+    # .env file,
     # that is to say variables from the .env files will only be used if not defined
     # as environment variables.
     env_file = str(ROOT_DIR / ".env")
@@ -322,7 +323,8 @@
     "DEFAULT_SCHEMA_CLASS": "drf_spectacular.openapi.AutoSchema",
 }
 
-# By Default swagger ui is available only to admin user(s). You can change permission classes to change that
+# By Default swagger ui is available only to admin user(s). You can change permission
+# classes to change that
 # See more configuration options at https://drf-spectacular.readthedocs.io/en/latest/settings.html#settings
 SPECTACULAR_SETTINGS = {
     "TITLE": "fpbase API",
@@ -464,17 +466,18 @@ def add_sentry_context(logger, method_name, event_dict):
     using the ID to find the full exception context in Sentry.
     """
     # Check if sentry_event_id was explicitly passed in extra dict
-    if "sentry_event_id" not in event_dict:
-        # Try to get it from Sentry SDK's last_event_id()
-        # This works if Django/Sentry integration auto-captured an exception
-        if event_dict.get("exc_info") or "exception" in event_dict:
-            try:
-                import sentry_sdk
-
-                if event_id := sentry_sdk.last_event_id():
-                    event_dict["sentry_event_id"] = event_id
-            except (ImportError, AttributeError, Exception):
-                pass  # Sentry not available
+    # Try to get it from Sentry SDK's last_event_id()
+    # This works if Django/Sentry integration auto-captured an exception
+    if "sentry_event_id" not in event_dict and (
+        event_dict.get("exc_info") or "exception" in event_dict
+    ):
+        try:
+            import sentry_sdk
+
+            if event_id := sentry_sdk.last_event_id():
+                event_dict["sentry_event_id"] = event_id
+        except (ImportError, AttributeError, Exception):
+            pass  # Sentry not available
 
     return event_dict
 

backend/config/settings/local.py

@@ -29,7 +29,9 @@
 EMAIL_PORT = 1025
 
 EMAIL_HOST = "localhost"
-EMAIL_BACKEND = env("DJANGO_EMAIL_BACKEND", default="django.core.mail.backends.console.EmailBackend")
+EMAIL_BACKEND = env(
+    "DJANGO_EMAIL_BACKEND", default="django.core.mail.backends.console.EmailBackend"
+)
 
 if env("MAILGUN_API_KEY", default=False) and env("MAILGUN_DOMAIN", default=False):
     INSTALLED_APPS += [

backend/config/settings/production.py

@@ -205,7 +205,9 @@ def WHITENOISE_IMMUTABLE_FILE_TEST(path, url):
     send_default_pii=True,
     release=HEROKU_SLUG_COMMIT,
     traces_sample_rate=env.float("SENTRY_TRACES_SAMPLE_RATE", default=0.1),  # 10% of all requests
-    profiles_sample_rate=env.float("SENTRY_PROFILES_SAMPLE_RATE", default=0.05),  # 5% of traced requests
+    profiles_sample_rate=env.float(
+        "SENTRY_PROFILES_SAMPLE_RATE", default=0.05
+    ),  # 5% of traced requests
 )
 
 # Scout APM Configuration
@@ -322,7 +324,7 @@ def WHITENOISE_IMMUTABLE_FILE_TEST(path, url):
 
 # Enable API and GraphQL rate limiting in production
 REST_FRAMEWORK["DEFAULT_THROTTLE_CLASSES"] = [
-    "fpbase.views.SameOriginExemptAnonThrottle",  # Custom throttle that exempts same-origin requests
+    "fpbase.views.SameOriginExemptAnonThrottle",  # Custom throttle that exempts same-origin
     "rest_framework.throttling.UserRateThrottle",
 ]
 # NOTE: Rate limiting settings are used by both REST API and GraphQL

backend/config/urls.py

@@ -71,7 +71,6 @@
         TemplateView.as_view(template_name="pages/bleaching.html"),
         name="bleaching",
     ),
-    # path('mutations/', TemplateView.as_view(template_name='pages/mutations.html'), name='mutations'),
     path(
         "robots.txt",
         TemplateView.as_view(template_name="robots.txt", content_type="text/plain"),

backend/conftest.py

@@ -61,8 +61,12 @@ def mock_get_organism_info(organism_id: str | int):
         }
 
     # Use unittest.mock.patch for session-scoped mocking
-    patcher1 = unittest.mock.patch("proteins.extrest.entrez.doi_lookup", side_effect=mock_doi_lookup)
-    patcher2 = unittest.mock.patch("proteins.extrest.entrez.get_organism_info", side_effect=mock_get_organism_info)
+    patcher1 = unittest.mock.patch(
+        "proteins.extrest.entrez.doi_lookup", side_effect=mock_doi_lookup
+    )
+    patcher2 = unittest.mock.patch(
+        "proteins.extrest.entrez.get_organism_info", side_effect=mock_get_organism_info
+    )
 
     patcher1.start()
     patcher2.start()

backend/favit/managers.py

@@ -112,7 +112,9 @@ def get_favorite(self, user, obj, model=None):
             return None
 
         try:
-            return self.get_query_set().get(user=user, target_content_type=content_type, target_object_id=obj.id)
+            return self.get_query_set().get(
+                user=user, target_content_type=content_type, target_object_id=obj.id
+            )
         except self.model.DoesNotExist:
             return None
 

backend/favit/models.py

@@ -22,7 +22,9 @@ class Favorite(models.Model):
         on_delete=models.CASCADE,
     )
     target_content_type_id: int
-    target_content_type: models.ForeignKey[ContentType] = models.ForeignKey(ContentType, on_delete=models.CASCADE)
+    target_content_type: models.ForeignKey[ContentType] = models.ForeignKey(
+        ContentType, on_delete=models.CASCADE
+    )
     target_object_id = models.PositiveIntegerField()
     target = GenericForeignKey("target_content_type", "target_object_id")
     timestamp = models.DateTimeField(auto_now_add=True, db_index=True)

backend/fpbase/__init__.py

@@ -3,7 +3,9 @@
 from fpbase.celery import app as celery_app
 
 __version__ = "0.1.0"
-__version_info__ = tuple([int(num) if num.isdigit() else num for num in __version__.replace("-", ".", 1).split(".")])
+__version_info__ = tuple(
+    [int(num) if num.isdigit() else num for num in __version__.replace("-", ".", 1).split(".")]
+)
 
 
 __all__ = ("celery_app",)

backend/fpbase/decorators.py

@@ -44,7 +44,9 @@ def login_required_message_and_redirect(
     message=default_message,
 ):
     if function:
-        return login_required_message(login_required(function, redirect_field_name, login_url), message)
+        return login_required_message(
+            login_required(function, redirect_field_name, login_url), message
+        )
 
     return lambda deferred_function: login_required_message_and_redirect(
         deferred_function, redirect_field_name, login_url, message

backend/fpbase/templatetags/fpbase_tags.py

@@ -13,7 +13,8 @@
 ICON_DIR = Path(__file__).parent.parent / "static" / "icons"
 if not ICON_DIR.exists():
     raise RuntimeError(
-        f"Icon directory does not exist: {ICON_DIR}. Please run 'python scripts/extract_fa_icons.py' to generate it."
+        f"Icon directory does not exist: {ICON_DIR}. Please run "
+        "'python scripts/extract_fa_icons.py' to generate it."
     )
 
 

backend/fpbase/users/admin.py

@@ -117,7 +117,9 @@ def get_queryset(self, request):
             super()
             .get_queryset(request)
             .prefetch_related("socialaccount_set", "proteincollections", "emailaddress_set")
-            .annotate(verified=Exists(EmailAddress.objects.filter(user_id=OuterRef("id"), verified=True)))
+            .annotate(
+                verified=Exists(EmailAddress.objects.filter(user_id=OuterRef("id"), verified=True))
+            )
             .annotate(
                 _collections=Count("proteincollections"),
                 _microscopes=Count("microscopes"),

backend/fpbase/users/models.py

@@ -48,7 +48,9 @@ class UserLogin(models.Model):
     """Represent users' logins, one per record"""
 
     user_id: int
-    user: models.ForeignKey[User] = models.ForeignKey(User, on_delete=models.CASCADE, related_name="logins")
+    user: models.ForeignKey[User] = models.ForeignKey(
+        User, on_delete=models.CASCADE, related_name="logins"
+    )
     timestamp = models.DateTimeField(auto_now_add=True)
 
     def __str__(self) -> str:

backend/fpbase/views.py

@@ -35,7 +35,8 @@ def allow_request(self, request, view):
         # Check if this is a same-origin request by comparing the referer with the host
         referer = request.headers.get("referer", "")
 
-        # If the referer contains our host (accounting for port differences), it's a same-origin request
+        # If the referer contains our host (accounting for port differences), it's a
+        # same-origin request
         # Note: This checks for the host in the referer URL (e.g., "https://www.fpbase.org/...")
         # We strip the port from host comparison to handle localhost:8000 vs fpbase.org
         if referer:

backend/fpseq/align.py

@@ -201,7 +201,9 @@ def __str__(self):
         out = []
         for t, q in zip(a, b):
             out.append(q)
-            out.append("".join(["*" if x != y else (" " if x == " " else "|") for x, y in zip(t, q)]))
+            out.append(
+                "".join(["*" if x != y else (" " if x == " " else "|") for x, y in zip(t, q)])
+            )
             out.append(t + "\n")
         return "\n".join(out)
 

backend/fpseq/mutations.py

@@ -57,7 +57,7 @@
     (?P<new_chars>[{0}*]+)?
     (?:ext(?P<ext>[{0}]+))?
     (?:,|$|/|\s)""".format(r"A-Z*", "{1}"),
-    re.X,
+    re.VERBOSE,
 )
 
 
@@ -129,7 +129,9 @@ def __init__(
         if self.operation == "sub" and (stop_char or self.stop_idx):
             raise ValueError("Substitution mutations cannot specify a range (or a stop_char/idx)")
         if stop_idx and (int(stop_idx) < int(start_idx)):
-            raise ValueError(f"Stop position ({stop_idx}) must be greater than start position ({start_idx})")
+            raise ValueError(
+                f"Stop position ({stop_idx}) must be greater than start position ({start_idx})"
+            )
         if self.operation.endswith("ins"):
             if not (stop_char and self.stop_idx):
                 print(stop_char)
@@ -171,9 +173,7 @@ def __repr__(self):
         return f"<Mutation: {self}>"
 
     def __eq__(self, other):
-        if str(self) == str(other):
-            return True
-        return False
+        return str(self) == str(other)
 
     def __hash__(self):
         return hash(str(self))
@@ -185,7 +185,9 @@ def __call__(self, seq: Sequence, idx0: int = 1) -> tuple[Sequence, int]:
         # self._assert_position_consistency(seq, idx0)
         startpos = self.start_idx - idx0
         if startpos > len(seq):  # allowing one extra position for extensions
-            raise IndexError(f"Starting position {self.start_idx} is outside of sequence with length {len(seq)}")
+            raise IndexError(
+                f"Starting position {self.start_idx} is outside of sequence with length {len(seq)}"
+            )
         if self.operation == "sub":
             end = startpos + 1
             return (seq[:startpos] + self.new_chars + seq[end:], 0)
@@ -230,7 +232,7 @@ def _assert_position_consistency(self, seq, idx0=1):
             )
         if self.stop_idx and self.stop_char:
             stoppos = self.stop_idx - idx0
-            if not seq[stoppos] == self.stop_char:
+            if seq[stoppos] != self.stop_char:
                 beg = stoppos - 3
                 beg2 = stoppos + 1
                 end = stoppos + 4
@@ -248,7 +250,10 @@ def from_str(cls, mutstring, sep="/"):
         if not m:
             raise ValueError(f"Mutation code invalid: {mutstring}")
         if len(m) > 1:
-            raise ValueError("Multiple mutation codes found. For multiple mutations, create a MutationSet instead")
+            raise ValueError(
+                "Multiple mutation codes found. For multiple mutations, "
+                "create a MutationSet instead"
+            )
         return m[0]
 
 
@@ -271,7 +276,9 @@ def clear_insertions(ins_start_idx, insertions, extension=False):
         if extension:
             out.append(f"*{ins_start_idx + 1}{insertions[0]}ext{insertions[1:]}")
         else:
-            out.append(f"{ins_start_char}{ins_start_idx}_{before}{ins_start_idx + 1}ins{insertions}")
+            out.append(
+                f"{ins_start_char}{ins_start_idx}_{before}{ins_start_idx + 1}ins{insertions}"
+            )
 
     def clear_deletions(delstart, numdel, delins, idx):
         string = "{}{}del".format(delstart, f"_{lastchar + str(idx - 1)}" if numdel > 1 else "")
@@ -366,7 +373,9 @@ def __init__(self, muts=None, position_labels=None):
                         mut.stop_label = position_labels[mut.stop_idx - 1]
                 else:
                     try:
-                        mut.start_label = str(len(position_labels) - mut.start_idx + int(position_labels[-1]))
+                        mut.start_label = str(
+                            len(position_labels) - mut.start_idx + int(position_labels[-1])
+                        )
                     except Exception:
                         mut.start_label = str(mut.start_idx)
 
@@ -545,7 +554,9 @@ def __eq__(self, other):
             try:
                 otherm = MutationSet(other).muts
             except Exception as e:
-                raise ValueError(f"Could not compare MutationSet object with other: {other}") from e
+                raise ValueError(
+                    f"Could not compare MutationSet object with other: {other}"
+                ) from e
         if not otherm:
             raise ValueError(f"operation not valid between type MutationSet and {type(other)}")
         else:
@@ -647,10 +658,7 @@ def rand_mut(seq):
     elif operation in ("ins", "delins"):
         new_chars = "".join(choices(AAs, k=randint(1, 6)))
     if operation in ("del", "ins", "delins"):
-        if operation == "ins":
-            stop_idx = start_idx + 1
-        else:
-            stop_idx = start_idx + randint(1, 6)
+        stop_idx = start_idx + 1 if operation == "ins" else start_idx + randint(1, 6)
         while stop_idx > len(seq) - 2:
             stop_idx = start_idx + randint(0, 6)
         stop_char = seq[stop_idx - 1]

backend/fpseq/skbio_protein.py

@@ -138,7 +138,8 @@ 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 {other.__class__.__name__} together with `{method}`"
+                    f"Cannot use {self.__class__.__name__} and "
+                    f"{other.__class__.__name__} together with `{method}`"
                 )
             else:
                 return other
@@ -214,9 +215,14 @@ def __getitem__(self, indexable):
         elif isinstance(indexable, str | bool):
             raise IndexError(f"Cannot index with {type(indexable).__name__} type: {indexable!r}")
 
-        if isinstance(indexable, np.ndarray) and indexable.dtype == bool and len(indexable) != len(self):
+        if (
+            isinstance(indexable, np.ndarray)
+            and indexable.dtype == bool
+            and len(indexable) != len(self)
+        ):
             raise IndexError(
-                f"An boolean vector index must be the same length as the sequence ({len(self)}, not {len(indexable)})."
+                f"An boolean vector index must be the same length as the sequence "
+                f"({len(self)}, not {len(indexable)})."
             )
 
         if isinstance(indexable, np.ndarray) and indexable.size == 0:
@@ -270,7 +276,8 @@ def _gap_codes(cls):
     def _validate(self):
         """https://github.com/biocore/scikit-bio/blob/0.5.4/skbio/sequence/_grammared_sequence.py#L340"""
         invalid_characters = (
-            np.bincount(self._bytes, minlength=self._number_of_extended_ascii_codes) * self._validation_mask
+            np.bincount(self._bytes, minlength=self._number_of_extended_ascii_codes)
+            * self._validation_mask
         )
         if np.any(invalid_characters):
             bad = list(np.where(invalid_characters > 0)[0].astype(np.uint8).view("|S1"))

backend/proteins/admin.py

@@ -284,10 +284,9 @@ def owner(self, obj):
         owner = obj.owner
         # FluorState is a base class - resolve to the actual subclass admin
         if isinstance(owner, FluorState):
-            if owner.entity_type == FluorState.EntityTypes.PROTEIN:
-                model_name = "state"
-            else:
-                model_name = "dyestate"
+            model_name = (
+                "state" if owner.entity_type == FluorState.EntityTypes.PROTEIN else "dyestate"
+            )
         else:
             model_name = owner._meta.model.__name__.lower()
 
@@ -724,7 +723,9 @@ class Meta:
         fields = ("protein", "parent", "mutation", "root_node", "rootmut")
         readonly_fields = "root_node"
 
-    parent = forms.ModelChoiceField(required=False, queryset=Lineage.objects.prefetch_related("protein").all())
+    parent = forms.ModelChoiceField(
+        required=False, queryset=Lineage.objects.prefetch_related("protein").all()
+    )
     root_node = forms.ModelChoiceField(queryset=Lineage.objects.prefetch_related("protein").all())