DEP: fix end->stop deprecation warnings in other sectionds of code

src/cogent3/core/alignment.py

@@ -18,6 +18,7 @@
     passed in a stream of two-item label, sequence pairs. However, this can
     cause confusion when testing.
 """
+
 from __future__ import annotations
 
 import functools
@@ -5289,7 +5290,7 @@ def _get_seq_features(
             seqname = seqid_to_seqname[seqid]
             seq = self.named_seqs[seqname]
             # we use parent seqid, stored on SeqView
-            parent_id, start, end, _ = seq.data.parent_coordinates()
+            parent_id, start, stop, _ = seq.data.parent_coordinates()
             offset = seq.data.annotation_offset
 
             for feature in self.annotation_db.get_features_matching(
@@ -5299,7 +5300,7 @@ def _get_seq_features(
                 on_alignment=False,
                 allow_partial=allow_partial,
                 start=start,
-                end=end,
+                stop=stop,
             ):
                 if offset:
                     feature["spans"] = (array(feature["spans"]) - offset).tolist()

src/cogent3/core/annotation.py

@@ -187,14 +187,14 @@ def get_parent(self, **kwargs):
         """generator returns parent features of self optionally matching biotype"""
         offset = getattr(self.parent, "annotation_offset", 0)
         start = self.map.start + offset
-        end = self.map.end + offset
+        stop = self.map.end + offset
 
         make_feature = self.parent.make_feature
         db = self.parent.annotation_db
         for record in db.get_feature_parent(
             name=self.name,
             start=start,
-            end=end,
+            stop=stop,
             **kwargs,
         ):
             record["spans"] = array(record["spans"]) - offset

src/cogent3/core/annotation_db.py

@@ -14,12 +14,13 @@
 import numpy
 import typing_extensions
 
+import cogent3.util.warning as c3warn
+
 from cogent3._version import __version__
 from cogent3.util.deserialise import register_deserialiser
 from cogent3.util.misc import extend_docstring_from, get_object_provenance
 from cogent3.util.progress_display import display_wrap
 from cogent3.util.table import Table
-import cogent3.util.warning as c3warn
 
 
 OptionalInt = typing.Optional[int]
@@ -73,11 +74,14 @@ class FeatureDataType(typing.TypedDict):
 
 @typing.runtime_checkable
 class SerialisableType(typing.Protocol):  # pragma: no cover
-    def to_rich_dict(self) -> dict: ...
+    def to_rich_dict(self) -> dict:
+        ...
 
-    def to_json(self) -> str: ...
+    def to_json(self) -> str:
+        ...
 
-    def from_dict(self, data): ...
+    def from_dict(self, data):
+        ...
 
 
 @typing.runtime_checkable
@@ -99,7 +103,8 @@ def get_features_matching(
         strand: OptionalStr = None,
         attributes: OptionalStr = None,
         on_alignment: OptionalBool = None,
-    ) -> typing.Iterator[FeatureDataType]: ...
+    ) -> typing.Iterator[FeatureDataType]:
+        ...
 
     @c3warn.deprecated_args(
         "2024.9",
@@ -113,7 +118,8 @@ def get_feature_children(
         start: OptionalInt = None,
         stop: OptionalInt = None,
         **kwargs,
-    ) -> typing.List[FeatureDataType]: ...
+    ) -> typing.List[FeatureDataType]:
+        ...
 
     @c3warn.deprecated_args(
         "2024.9",
@@ -127,7 +133,8 @@ def get_feature_parent(
         start: OptionalInt = None,
         stop: OptionalInt = None,
         **kwargs,
-    ) -> typing.List[FeatureDataType]: ...
+    ) -> typing.List[FeatureDataType]:
+        ...
 
     def num_matches(
         self,
@@ -138,7 +145,8 @@ def num_matches(
         strand: OptionalStr = None,
         attributes: OptionalStr = None,
         on_alignment: OptionalBool = None,
-    ) -> int: ...
+    ) -> int:
+        ...
 
     @c3warn.deprecated_args(
         "2024.9",
@@ -155,7 +163,8 @@ def subset(
         stop: OptionalInt = None,
         strand: OptionalStr = None,
         attributes: OptionalStr = None,
-    ): ...
+    ):
+        ...
 
 
 @typing.runtime_checkable
@@ -172,15 +181,17 @@ def add_feature(
         attributes: OptionalStr = None,
         strand: OptionalStr = None,
         on_alignment: bool = False,
-    ) -> None: ...
+    ) -> None:
+        ...
 
     def add_records(
         self,
         *,
         records: typing.Sequence[dict],
         # seqid required for genbank
         seqid: OptionalStr = None,
-    ) -> None: ...
+    ) -> None:
+        ...
 
     def update(self, annot_db, seqids: OptionalStrList = None) -> None:
         # update records with those from an instance of the same type

src/cogent3/core/sequence.py

@@ -10,6 +10,7 @@
 performance reasons, but don't alter the MolType or the sequence data after
 creation.
 """
+
 from __future__ import annotations
 
 import contextlib
@@ -920,7 +921,7 @@ def get_features(
         name
             name of the feature
         start, stop
-            start, end positions to search between, relative to offset
+            start, stop positions to search between, relative to offset
             of this sequence. If not provided, entire span of sequence is used.
 
         Notes
@@ -955,11 +956,11 @@ def get_features(
         query_start = self._seq.absolute_position(start, include_boundary=False)
         # we set include_boundary=True because stop is exclusive indexing,
         # i,e., the stop can be equal to the length of the view
-        query_end = self._seq.absolute_position(stop, include_boundary=True)
+        query_stop = self._seq.absolute_position(stop, include_boundary=True)
 
         rev_strand = strand == -1
         if rev_strand:
-            query_start, query_end = query_end, query_start
+            query_start, query_stop = query_stop, query_start
 
         query_start = max(query_start, 0)
         # in the underlying db, features are always plus strand oriented
@@ -983,7 +984,7 @@ def get_features(
             name=name,
             biotype=biotype,
             start=query_start,
-            end=query_end,  # todo gah end should be stop
+            stop=query_stop,
             allow_partial=allow_partial,
         ):
             # spans need to be converted from absolute to relative positions