Merge pull request #530 from MetaCell/upgrade-python-3.11

Upgrade dependencies and code for pygeppetto to deal with Python 3.11

pygeppetto/pygeppetto/model/geppetto_resource.py

@@ -18,7 +18,8 @@ class GeppettoResource(JsonResource):
                 variables.eClassifiers]
     chain = ChainMap(*packages)
 
-    def serialize_eclass(self, eclass):
+    @staticmethod
+    def serialize_eclass(eclass):
         return eclass.name
 
     @lru_cache()

pygeppetto/pygeppetto/model/model_serializer.py

@@ -46,7 +46,9 @@ def serialize(geppetto_model, onlySerialiseDelta=False):
     # we now create a resource to save the geppetto model and serialize it to a JSON string
     rset = ResourceSet()
     uri = BytesURI('geppetto_model.json')
-    rset.resource_factory['*'] = lambda uri: GeppettoResource(uri, indent=2)
+    JsonGeppettoResource = lambda uri: GeppettoResource(uri, indent=2)
+    rset.resource_factory['json'] = JsonGeppettoResource
+    rset.resource_factory['*'] = JsonGeppettoResource
     resource = rset.create_resource(uri)
     resource.append(geppetto_model)
     if onlySerialiseDelta:
@@ -61,5 +63,7 @@ def serialize(geppetto_model, onlySerialiseDelta=False):
 def load(json):
     rset = ResourceSet()
     uri = BytesURI('geppetto_model.json')
-    rset.resource_factory['*'] = lambda uri: GeppettoResource(uri, indent=2)
+    JsonGeppettoResource = lambda uri: GeppettoResource(uri, indent=2)
+    rset.resource_factory['json'] = JsonGeppettoResource
+    rset.resource_factory['*'] = JsonGeppettoResource
     resource = rset.create_resource(uri)

pygeppetto/pygeppetto/model/utils/pointer_utility.py

@@ -2,7 +2,7 @@
 https://github.com/openworm/org.geppetto.model/blob/master/src/main/java/org/geppetto/model/util/java"""
 import sys
 
-from multimethod import multidispatch
+from multimethod import multimethod
 
 from ..exceptions import GeppettoModelException
 from ..model import GeppettoLibrary, GeppettoModel
@@ -14,8 +14,8 @@
 PointerUtility = sys.modules[__name__]
 
 
-@multidispatch
-def get_pointer(variable: Variable, type_, index):
+@multimethod
+def get_pointer(variable: Variable, type_: Type, index: int):
     pointerElement = PointerElement()
     pointerElement.index = index
     pointerElement.variable = variable
@@ -25,8 +25,8 @@ def get_pointer(variable: Variable, type_, index):
     return pointer
 
 
-@get_pointer.register(GeppettoModel, str)
-def get_pointer_model(model: GeppettoModel, instance_path):
+@get_pointer.register
+def get_pointer_model(model: GeppettoModel, instance_path: str):
     pointer = Pointer(path=instance_path)
 
     st = iter(instance_path.split("."))
@@ -68,7 +68,7 @@ def get_pointer_model(model: GeppettoModel, instance_path):
     return pointer
 
 
-@multidispatch
+@multimethod
 def get_type(model, path):
     st = iter(path.split('.'))
     lastType = None
@@ -100,15 +100,15 @@ def get_type(model, path):
         raise GeppettoModelException("Couldn't find a type for the path " + path)
 
 
-@get_type.register(str)
+@get_type.register
 def get_type_str(token: str):
     if "(" in token:
         return token[token.find("(") + 1: token.find(")")]
     else:
         return None
 
 
-@get_type.register(Pointer)
+@get_type.register
 def get_type_pointer(pointer: Pointer):
     return pointer.elements[-1].type
 
@@ -169,7 +169,7 @@ def find_library(model, libraryId):
 # 	 * @param pointer2
 # 	 * @return true if the two pointers point to the same variables and types
 #
-@multidispatch
+@multimethod
 def equals(pointer: Pointer, pointer2: Pointer):
     if not pointer == pointer2:
         if len(pointer.elements) != len(pointer2.elements):
@@ -190,7 +190,7 @@ def equals(pointer: Pointer, pointer2: Pointer):
 # 	 * @param pointer2
 # 	 * @return
 #
-@equals.register(PointerElement, PointerElement)
+@equals.register
 def equals_pointer(pointer: PointerElement, pointer2: PointerElement):
     sameType = pointer.type == pointer2.type or pointer.type == pointer2.type
     sameVar = pointer.variable == pointer2.variable or pointer.variable == pointer2.variable
@@ -202,12 +202,12 @@ def equals_pointer(pointer: PointerElement, pointer2: PointerElement):
 # 	 * @param pointer
 # 	 * @return
 #
-@multidispatch
+@multimethod
 def get_variable(pointer: Pointer):
     return pointer.elements[-1].variable
 
 
-@get_variable.register(str)
+@get_variable.register
 def get_variable_str(token: str) -> str:
     if "(" in token:
         return token[0: token.find("(")]
@@ -233,7 +233,7 @@ def get_instance_path(variable, type_):
     return variable.id + "(" + type_.id + ")"
 
 
-@multidispatch
+@multimethod
 def find_type(type_, variable: Variable) -> Type:
     if type_ is None:
         types = []
@@ -257,8 +257,8 @@ def find_type(type_, variable: Variable) -> Type:
         raise GeppettoModelException("The type {} was not found in the variable {}".format(type_, variable.id))
 
 
-@find_type.register(str, GeppettoLibrary)
-def find_type_library(typeId, library: GeppettoLibrary):
+@find_type.register
+def find_type_library(typeId: str, library: GeppettoLibrary):
     return next((type_ for type_ in library.types if type_.id == typeId), None)
 
 

pygeppetto/pygeppetto/model/utils/url_reader.py

@@ -1,15 +1,15 @@
 """ generated source for class URLReader """
 SERVER_ROOT_TOKEN = "SERVER_ROOT"
-from multimethod import multidispatch
+from multimethod import multimethod
 
 
-# 
+#
 # 	 * @param urlString
 # 	 * @param baseURL
 # 	 * @return
 #
-@multidispatch
-def getURL(urlString, baseURL):
+@multimethod
+def getURL(urlString: str, baseURL: str | None):
     """ generated source for method getURL """
     url = urlString
 
@@ -22,12 +22,12 @@ def getURL(urlString, baseURL):
     return getURL(url)
 
 
-# 
+#
 # 	 * @param urlString
 # 	 * @return
 #
-@getURL.register(object, str)
-def getURL_0(urlString):
+@getURL.register
+def getURL_0(urlString: str, baseURL: str | None=None):
     """ generated source for method getURL_0 """
     url = None
     if urlString.startsWith("https://") or urlString.startsWith("http://"):

pygeppetto/requirements.txt

@@ -1,5 +1,5 @@
-airspeed==0.5.16
-Deprecated==1.2.10
-multimethod==1.1
-pyecore==0.11.6
-requests==2.23.0
+airspeed==0.6.0
+Deprecated==1.2.14
+multimethod==1.11.2
+pyecore==0.15.1
+requests==2.31.0