Merge pull request #355 from tcmitchell/301-singleton-initial-value

Progress on implicit list wrapping for singleton initial values

sbol3/attachment.py

@@ -1,4 +1,4 @@
-from typing import List, Any
+from typing import List, Any, Optional
 
 from . import *
 
@@ -11,7 +11,8 @@ class Attachment(TopLevel):
     """
 
     def __init__(self, identity: str, source: str,
-                 *, format: str = None, size: int = None,
+                 *, format: Optional[str] = None,
+                 size: int = None,
                  hash: str = None, hash_algorithm: str = None,
                  namespace: str = None,
                  attachments: List[str] = None,

sbol3/combderiv.py

@@ -1,5 +1,5 @@
 import math
-from typing import Union, List, Any
+from typing import Union, List, Any, Optional
 
 from . import *
 
@@ -18,7 +18,7 @@ class properties template, hasVariableFeature, and strategy.
     """
 
     def __init__(self, identity: str, template: Union[Component, str],
-                 *, strategy: str = None,
+                 *, strategy: Optional[str] = None,
                  variable_features: List[str] = None,
                  namespace: str = None,
                  attachments: List[str] = None,

sbol3/component.py

@@ -1,33 +1,39 @@
+from __future__ import annotations
+
 import math
-from typing import List, Union, Any
+from typing import Any, Optional
+import typing
 
 from . import *
+from .typing import *
 
 
 class Component(TopLevel):
 
-    def __init__(self, identity: str, types: Union[List[str], str],
-                 *, roles: List[str] = None,
-                 sequences: List[str] = None,
-                 features: List[Feature] = None,
-                 constraints: List[Constraint] = None,
-                 interactions: List[Interaction] = None,
-                 interface: Interface = None,
-                 models: List[str] = None,
-                 namespace: str = None,
-                 attachments: List[str] = None,
-                 name: str = None, description: str = None,
-                 derived_from: List[str] = None, generated_by: List[str] = None,
-                 measures: List[SBOLObject] = None, type_uri: str = SBOL_COMPONENT):
+    def __init__(self, identity: str, types: Optional[Union[str, typing.Sequence[str]]],
+                 *,  # Keywords only after this
+                 roles: Optional[Union[str, typing.Sequence[str]]] = None,
+                 sequences: Optional[refobj_list_arg] = None,
+                 features: Union[Feature, typing.Sequence[Feature]] = None,
+                 constraints: Union[Constraint, typing.Sequence[Constraint]] = None,
+                 interactions: Union[Interaction, typing.Sequence[Interaction]] = None,
+                 interface: Union[Interface, typing.Sequence[Interface]] = None,
+                 models: Optional[refobj_list_arg] = None,
+                 namespace: Optional[str] = None,
+                 attachments: Optional[refobj_list_arg] = None,
+                 name: Optional[str] = None,
+                 description: Optional[str] = None,
+                 derived_from: Optional[Union[str, typing.Sequence[str]]] = None,
+                 generated_by: Optional[refobj_list_arg] = None,
+                 measures: Optional[ownedobj_list_arg] = None,
+                 type_uri: str = SBOL_COMPONENT) -> None:
         super().__init__(identity=identity, type_uri=type_uri,
                          namespace=namespace,
                          attachments=attachments, name=name,
                          description=description, derived_from=derived_from,
                          generated_by=generated_by, measures=measures)
-        if isinstance(types, str):
-            types = [types]
-        self.types: Union[List, Property] = URIProperty(self, SBOL_TYPE, 1, math.inf,
-                                                        initial_value=types)
+        self.types = URIProperty(self, SBOL_TYPE, 1, math.inf,
+                                 initial_value=types)
         self.roles = URIProperty(self, SBOL_ROLE, 0, math.inf,
                                  initial_value=roles)
         self.sequences = ReferencedObject(self, SBOL_SEQUENCES, 0, math.inf,

sbol3/document.py

@@ -6,7 +6,7 @@
 
 # import typing for typing.Sequence, which we don't want to confuse
 # with sbol3.Sequence
-import typing
+import typing as pytyping
 
 import pyshacl
 import rdflib
@@ -284,7 +284,7 @@ def assign_document(x: Identified):
         obj.traverse(assign_document)
         return obj
 
-    def _add_all(self, objects: typing.Sequence[TopLevel]) -> typing.Sequence[TopLevel]:
+    def _add_all(self, objects: pytyping.Sequence[TopLevel]) -> pytyping.Sequence[TopLevel]:
         # Perform type check of all objects.
         # We do this to avoid finding out part way through that an
         # object can't be added. That would leave the document in an
@@ -302,7 +302,8 @@ def _add_all(self, objects: typing.Sequence[TopLevel]) -> typing.Sequence[TopLev
         # return the passed argument
         return objects
 
-    def add(self, objects: Union[TopLevel, typing.Sequence[TopLevel]]) -> Union[TopLevel, typing.Sequence[TopLevel]]:
+    def add(self,
+            objects: Union[TopLevel, pytyping.Sequence[TopLevel]]) -> Union[TopLevel, pytyping.Sequence[TopLevel]]:
         # objects must be TopLevel or iterable. If neither, raise a TypeError.
         #
         # Note: Python documentation for collections.abc says "The only

sbol3/extdef.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import math
 from typing import Any
 
@@ -15,7 +16,7 @@ class ExternallyDefined(Feature):
 
     """
 
-    def __init__(self, types: List[str], definition: str,
+    def __init__(self, types: Union[str, list[str]], definition: str,
                  *, roles: List[str] = None, orientation: str = None,
                  name: str = None, description: str = None,
                  derived_from: List[str] = None,

sbol3/feature.py

@@ -1,26 +1,30 @@
+from __future__ import annotations
 import abc
 import math
-from typing import List
+from typing import List, Optional
 
 from . import *
 
+from .typing import *
+
 
 class Feature(Identified, abc.ABC):
     """Feature is an abstract base class."""
 
     def __init__(self, identity: str, type_uri: str,
-                 *, roles: List[str] = None, orientation: str = None,
+                 *, roles: Optional[str, list[str]] = None,
+                 orientation: Optional[str] = None,
                  name: str = None, description: str = None,
                  derived_from: List[str] = None,
                  generated_by: List[str] = None,
                  measures: List[SBOLObject] = None) -> None:
         super().__init__(identity=identity, type_uri=type_uri, name=name,
                          description=description, derived_from=derived_from,
                          generated_by=generated_by, measures=measures)
-        self.roles = URIProperty(self, SBOL_ROLE, 0, math.inf,
-                                 initial_value=roles)
-        self.orientation = URIProperty(self, SBOL_ORIENTATION, 0, 1,
-                                       initial_value=orientation)
+        self.roles: uri_list = URIProperty(self, SBOL_ROLE, 0, math.inf,
+                                           initial_value=roles)
+        self.orientation: uri_singleton = URIProperty(self, SBOL_ORIENTATION, 0, 1,
+                                                      initial_value=orientation)
 
     def validate(self, report: ValidationReport = None) -> ValidationReport:
         report = super().validate(report)

sbol3/identified.py

@@ -1,12 +1,14 @@
-import abc
+from __future__ import annotations
 import math
 import posixpath
-from typing import Union, List, Callable, Any
+from typing import Callable, Any, Optional
+import typing
 from urllib.parse import urlparse
 
 import rdflib
 
 from . import *
+from .typing import *
 from .utils import parse_class_name
 
 
@@ -20,9 +22,11 @@ class Identified(SBOLObject):
     """
 
     def __init__(self, identity: str, type_uri: str,
-                 *, name: str = None, description: str = None,
-                 derived_from: List[str] = None, generated_by: List[str] = None,
-                 measures: List[SBOLObject] = None) -> None:
+                 *, name: Optional[str] = None,
+                 description: Optional[str] = None,
+                 derived_from: Optional[Union[str, typing.Sequence[str]]] = None,
+                 generated_by: Optional[refobj_list_arg] = None,
+                 measures: Optional[ownedobj_list_arg] = None) -> None:
         """
         :param identity: this object's Uniform Resource Identifier (URI).
             this URI MUST be globally unique among all other Identified
@@ -235,7 +239,6 @@ def serialize(self, graph: rdflib.Graph):
                 graph.add((identity, rdf_prop, rdflib.URIRef(item.identity)))
                 item.serialize(graph)
 
-    @abc.abstractmethod
     def accept(self, visitor: Any) -> Any:
         """
         An abstract method for concrete classes to override. This

sbol3/interaction.py

@@ -1,7 +1,9 @@
+from __future__ import annotations
 import math
 from typing import List, Any
 
 from . import *
+from .typing import *
 
 
 class Interaction(Identified):
@@ -19,7 +21,7 @@ class Interaction(Identified):
 
     """
 
-    def __init__(self, types: List[str],
+    def __init__(self, types: Union[str, list[str]],
                  *, participations: List[Participation] = None,
                  name: str = None, description: str = None,
                  derived_from: List[str] = None,
@@ -31,8 +33,8 @@ def __init__(self, types: List[str],
                          name=name, description=description,
                          derived_from=derived_from, generated_by=generated_by,
                          measures=measures)
-        self.types = URIProperty(self, SBOL_TYPE, 1, math.inf,
-                                 initial_value=types)
+        self.types: uri_list = URIProperty(self, SBOL_TYPE, 1, math.inf,
+                                           initial_value=types)
         self.participations = OwnedObject(self, SBOL_PARTICIPATIONS, 0, math.inf,
                                           initial_value=participations,
                                           type_constraint=Participation)

sbol3/localsub.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import math
 from typing import Any
 
@@ -15,7 +16,7 @@ class LocalSubComponent(Feature):
 
     """
 
-    def __init__(self, types: List[str],
+    def __init__(self, types: Union[str, list[str]],
                  *, locations: List[Location] = None,
                  roles: List[str] = None, orientation: str = None,
                  name: str = None, description: str = None,

sbol3/location.py

@@ -1,7 +1,8 @@
 import abc
-from typing import Union, Any
+from typing import Union, Any, Optional
 
 from . import *
+from .typing import uri_singleton
 
 int_property = Union[IntProperty, int]
 
@@ -15,11 +16,11 @@ class Location(Identified, abc.ABC):
 
     def __init__(self, sequence: Union[Sequence, str],
                  identity: str, type_uri: str,
-                 *, orientation: str = None,
+                 *, orientation: Optional[str] = None,
                  order: int = None) -> None:
         super().__init__(identity, type_uri)
-        self.orientation = URIProperty(self, SBOL_ORIENTATION, 0, 1,
-                                       initial_value=orientation)
+        self.orientation: uri_singleton = URIProperty(self, SBOL_ORIENTATION, 0, 1,
+                                                      initial_value=orientation)
         self.order = IntProperty(self, SBOL_ORDER, 0, 1,
                                  initial_value=order)
         self.sequence = ReferencedObject(self, SBOL_SEQUENCES, 1, 1,

sbol3/model.py

@@ -1,6 +1,7 @@
 from typing import List, Any
 
 from . import *
+from .typing import uri_singleton
 
 
 class Model(TopLevel):
@@ -27,12 +28,12 @@ def __init__(self, identity: str, source: str, language: str,
                          attachments=attachments, name=name,
                          description=description, derived_from=derived_from,
                          generated_by=generated_by, measures=measures)
-        self.source = URIProperty(self, SBOL_SOURCE, 1, 1,
-                                  initial_value=source)
-        self.language = URIProperty(self, SBOL_LANGUAGE, 1, 1,
-                                    initial_value=language)
-        self.framework = URIProperty(self, SBOL_FRAMEWORK, 1, 1,
-                                     initial_value=framework)
+        self.source: uri_singleton = URIProperty(self, SBOL_SOURCE, 1, 1,
+                                                 initial_value=source)
+        self.language: uri_singleton = URIProperty(self, SBOL_LANGUAGE, 1, 1,
+                                                   initial_value=language)
+        self.framework: uri_singleton = URIProperty(self, SBOL_FRAMEWORK, 1, 1,
+                                                    initial_value=framework)
 
     def validate(self, report: ValidationReport = None) -> ValidationReport:
         report = super().validate(report)

sbol3/om_unit.py

@@ -1,9 +1,11 @@
+from __future__ import annotations
 import abc
 import math
-from typing import Union, List, Any
+from typing import Union, List, Any, Optional
 
 from . import *
 from .om_prefix import Prefix
+from .typing import *
 
 
 class Unit(CustomTopLevel, abc.ABC):
@@ -55,7 +57,7 @@ class Measure(CustomIdentified):
     """
 
     def __init__(self, value: float, unit: str,
-                 *, types: List[str] = None,
+                 *, types: Optional[str, list[str]] = None,
                  name: str = None, description: str = None,
                  derived_from: List[str] = None,
                  generated_by: List[str] = None,
@@ -68,10 +70,10 @@ def __init__(self, value: float, unit: str,
                          measures=measures)
         self.value = FloatProperty(self, OM_HAS_NUMERICAL_VALUE, 1, 1,
                                    initial_value=value)
-        self.types = URIProperty(self, SBOL_TYPE, 0, math.inf,
-                                 initial_value=types)
-        self.unit = URIProperty(self, OM_HAS_UNIT, 1, 1,
-                                initial_value=unit)
+        self.types: uri_list = URIProperty(self, SBOL_TYPE, 0, math.inf,
+                                           initial_value=types)
+        self.unit: uri_singleton = URIProperty(self, OM_HAS_UNIT, 1, 1,
+                                               initial_value=unit)
 
     def accept(self, visitor: Any) -> Any:
         """Invokes `visit_measure` on `visitor` with `self` as the only

sbol3/ownedobject.py

@@ -98,6 +98,10 @@ def __init__(self, property_owner: Any, property_uri: str,
         # to accept unknown keyword arguments.
         self.type_constraint = type_constraint
         if initial_value is not None:
+            if isinstance(initial_value, SBOLObject):
+                # coerce the singleton into a list
+                # see https://github.com/SynBioDex/pySBOL3/issues/301
+                initial_value = [initial_value]
             self.set(initial_value)
 
     def validate(self, name: str, report: ValidationReport):

sbol3/participation.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import math
 from typing import Any
 
@@ -11,7 +12,7 @@ class Participation(Identified):
 
     """
 
-    def __init__(self, roles: List[str],
+    def __init__(self, roles: Union[str, list[str]],
                  participant: Union[SBOLObject, str],
                  *, name: str = None, description: str = None,
                  derived_from: List[str] = None,