Fix multiprocessing pickling error

Author: ulido

src/annotations/annotations.py

@@ -120,6 +120,10 @@ def __hash__(self):
         return hash((self.term, self.modifiers))
 
 
+def _annotation_factory(a_str: str, *args):
+    return Annotation(a_str)
+
+
 class AnnotationCollection(Set):
     """Object that parses and processes localisation (or other) annotation
     strings of the form ".
@@ -130,8 +134,9 @@ def __init__(
         self,
         annotations_string: str,
         annotation_factory: Callable[[str], Annotation] = (
-            lambda a_str: Annotation(a_str)
+            _annotation_factory
         ),
+        annotation_factory_extra_args: tuple = (),
     ):
         """Creates a new `AnnotationCollection` from the given annotation
         string.
@@ -147,13 +152,14 @@ def __init__(
         """
         if annotations_string != "":
             self._annotations = frozenset([
-                annotation_factory(a_str)
+                annotation_factory(a_str, *annotation_factory_extra_args)
                 for a_str in ANNOT_SPLIT_RE.split(annotations_string)
             ])
         else:
             self._annotations = frozenset([])
 
         self._annotation_factory = annotation_factory
+        self._annotation_factory_extra_args = annotation_factory_extra_args
 
     def __contains__(self, item: str | Annotation):
         """Returns whether the annotation collection contains the given
@@ -165,7 +171,8 @@ def __contains__(self, item: str | Annotation):
                 converted to an `Annotation` object.
         """
         if isinstance(item, str):
-            annot = self._annotation_factory(item)
+            annot = self._annotation_factory(
+                item, *self._annotation_factory_extra_args)
         else:
             annot = item
         term_re = re.compile(annot.term)

src/annotations/ontology.py

@@ -108,6 +108,10 @@ def _match_term(self, term, recursive: bool = True):
         return self.ontology_entry.match_term(term, recursive=recursive)
 
 
+def _ontology_annotation_factory(a_str: str, ontology: Ontology):
+    return OntologyAnnotation(a_str, ontology)
+
+
 class OntologyAnnotationCollection(AnnotationCollection):
     """Annotation collection that is connected to an annotation ontology.
     """
@@ -122,7 +126,8 @@ def __init__(self, annotations_string: str, ontology: Ontology):
         self.ontology = ontology
         super().__init__(
             annotations_string,
-            lambda a_str: OntologyAnnotation(a_str, ontology)
+            _ontology_annotation_factory,
+            (ontology,),
         )
 
     def __and__(self, other: OntologyAnnotationCollection):