Merge branch 'main' into annotator-structure

src/ga4gh/core/enderef.py

@@ -26,13 +26,13 @@ def ga4gh_enref(o, cra_map, object_store=None, return_id_obj_tuple=False) -> tup
     """Recursively convert "referable attributes" from inlined to
     referenced form.  Returns a new object.
 
-    cra_map: class referrable-attribute map; { o.type: [attr, attr, ...] }
-
-    If `object_store` is provided, it must be an
-    collections.abc.MutableMapping subclass and will be used to store
-    objects as they are referenced.  If `object_store` is not provided
-    (or None), referenced objects will not be stored.
-
+    :param o: VRS object
+    :param cra_map: class referrable-attribute map; { o.type: [attr, attr, ...] }
+    :param object_store: `collections.abc.MutableMapping` subclass that stores
+        objects as they are referenced. If not given, referenced objects are not stored.
+    :param return_id_obj_tuple: include ID with return value or not
+    :return: new, enref'd object, as well as object ID if param set
+    :raise TypeError: if any object IDs are non-GA4GH CURIEs
     """
 
     def _id_and_store(o):  # noqa: ANN202 ANN001
@@ -51,9 +51,11 @@ def _enref(o):  # noqa: ANN202 ANN001
             elif isinstance(v, str):
                 pass
             elif is_curie_type(v):  # already a reference
-                assert is_ga4gh_identifier(v), (  # noqa: S101
-                    "Identifiable attribute CURIE is contains an invalid identifier"
-                )
+                if not is_ga4gh_identifier(v):
+                    msg = (
+                        "Identifiable attribute CURIE is contains an invalid identifier"
+                    )
+                    raise TypeError(msg)
             elif v is not None:
                 _id = _id_and_store(v)
                 if _id:

src/ga4gh/vrs/dataproxy.py

@@ -320,9 +320,13 @@ def _isoformat(o: datetime.datetime) -> str:
     >>> _isoformat(dt)
     '2019-10-15T10:23:41.115927Z'
 
+    :param o: date object to format
+    :return: ISO8601-formatted string equivalent
+    :raise TypeError: if object given isn't a Python datetime instance
     """
     # stolen from connexion flask_app.py
-    assert isinstance(o, datetime.datetime)  # noqa: S101
+    if not isinstance(o, datetime.datetime):
+        raise TypeError
     if o.tzinfo:
         # eg: '2015-09-25T23:14:42.588601+00:00'
         return o.isoformat("T")

src/ga4gh/vrs/normalize.py

@@ -273,11 +273,16 @@ def _normalize_cis_phased_block(o, data_proxy: _DataProxy | None = None):  # noq
 def normalize(vo, data_proxy: _DataProxy | None = None, **kwargs):
     """Normalize given vrs object, regardless of type
 
-    kwargs:
-        rle_seq_limit: If RLE is set as the new state, set the limit for the length
-            of the `sequence`. To exclude `state.sequence`, set to 0.
+    :param vo:
+    :param data_proxy: GA4GH sequence dataproxy instance, if needed
+    :keyword rle_seq_limit: If RLE is set as the new state, set the limit for the length
+        of the `sequence`. To exclude `state.sequence`, set to 0.
+    :return: normalized object
+    :raise TypeError: if given object isn't a pydantic.BaseModel
     """
-    assert is_pydantic_instance(vo)  # noqa: S101
+    if not is_pydantic_instance(vo):
+        msg = f"Object is of class {vo.__class__} (with parents {vo.__class__.__mro__}), but normalize requires objects that inherit from pydantic.BaseModel."
+        raise TypeError(msg)
     vo_type = vo.type
 
     if vo_type in handlers: