Add spaces between colons and variables in docstrings and rewrite dic…

…t as Dict
gyorilab · Dec 6, 2023 · 708de13 · 708de13
1 parent 755a01a
commit 708de13
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Showing 3 changed files with 52 additions and 52 deletions.
diff --git a/mira/metamodel/decapodes.py b/mira/metamodel/decapodes.py
@@ -62,15 +62,15 @@ def __init__(self, variables, op1s, op2s, summations, tangent_variables):
 
         Parameters
         ----------
-        variables: Dict[int,Variable]
+        variables : Dict[int,Variable]
             Mapping of Variables.
-        op1s: Dict[int,Op1]
+        op1s : Dict[int,Op1]
             Mapping of Op1s (Operation 1s).
-        op2s: Dict[int,Op2]
+        op2s : Dict[int,Op2]
             Mapping of Op2s (Operation 2s).
-        summations: Dict[int,Summation]
+        summations : Dict[int,Summation]
             Mapping of Summations.
-        tangent_variables: Dict[int,TangentVariable]
+        tangent_variables : Dict[int,TangentVariable]
             Mapping of TangentVariables.
         """
         self.variables = variables
@@ -192,7 +192,7 @@ class TangentVariable:
 
     Attributes
     ----------
-    id: int
+    id : int
         The id of the tangent variable.
     incl_var : Variable
         The variable that is the result of a derivative operation associated

diff --git a/mira/metamodel/template_model.py b/mira/metamodel/template_model.py
@@ -48,9 +48,9 @@ def from_json(cls, data: Dict[str, Any], locals_dict=None) -> "Initial":
         
         Parameters
         ----------
-        data: dict[str,Any]
+        data : Dict[str,Any]
             Mapping of Initial attributes to their values.
-        locals_dict: dict[str,Any]
+        locals_dict : Dict[str,Any]
             Mapping of string symbols to their sympy equivalent.
 
         Returns
@@ -73,9 +73,9 @@ def substitute_parameter(self, name, value):
         
         Parameters
         ----------
-        name: str
+        name : str
             The name of the parameter that will be substituted for.
-        value: Any
+        value : Any
             The number value or expression to substitute for the parameter.
         """
         self.expression = self.expression.subs(sympy.Symbol(name), value)
@@ -86,7 +86,7 @@ def get_parameter_names(self, known_param_names) -> Set[str]:
 
         Parameters
         ----------
-        known_param_names: list[str]
+        known_param_names : list[str]
             List of parameter names.
 
         Returns
@@ -148,9 +148,9 @@ def substitute_parameter(self, name, value):
 
         Parameters
         ----------
-        name: str
+        name : str
             The name of the parameter that will be substituted for.
-        value: Any
+        value : Any
             The number value or expression to substitute for the parameter.
         """
         self.expression = self.expression.subs(sympy.Symbol(name), value)
@@ -161,7 +161,7 @@ def get_parameter_names(self, known_param_names) -> Set[str]:
 
         Parameters
         ----------
-        known_param_names: list[str]
+        known_param_names : list[str]
             List of parameter names.
 
         Returns
@@ -410,7 +410,7 @@ def update_parameters(self, parameter_dict):
 
         Parameters
         ----------
-        parameter_dict: dict[str,float]
+        parameter_dict : Dict[str,float]
             Mapping of parameter name to value.
 
         """
@@ -445,9 +445,9 @@ def eliminate_duplicate_parameter(
 
         Parameters
         ----------
-        redundant_parameter: str
+        redundant_parameter : str
             The name of the parameter to remove.
-        preserved_parameter: str
+        preserved_parameter : str
             The new name of the parameter to preserve.
         """
         # Update the rate laws
@@ -463,7 +463,7 @@ def from_json(cls, data) -> "TemplateModel":
 
         Parameters
         ----------
-        data: dict[str,Any]
+        data : Dict[str,Any]
             Mapping of template model attributes to their values.
 
         Returns
@@ -689,7 +689,7 @@ def get_concepts_map(self):
 
         Returns
         -------
-        : dict[str,Concept]
+        : Dict[str,Concept]
             The mapping of concept keys to concepts that appear in this
             template model's templates.
         """
@@ -702,7 +702,7 @@ def get_concepts_name_map(self):
 
         Returns
         -------
-        :dict[str,Concept]
+        : Dict[str,Concept]
             Mapping of concept names to concepts that appear in this
             template model's templates.
         """
@@ -714,7 +714,7 @@ def get_concept(self, name: str) -> Optional[Concept]:
 
         Parameters
         ----------
-        name:
+        name :
             The name to be queried for.
 
         Returns
@@ -747,7 +747,7 @@ def get_concepts_by_name(self, name: str) -> List[Concept]:
 
         Parameters
         ----------
-        name:
+        name :
             The name to be queried for           
 
         Returns
@@ -774,11 +774,11 @@ def extend(
 
         Parameters
         ----------
-        template_model:
+        template_model :
             The template model to add
-        parameter_mapping:
+        parameter_mapping :
             Mapping of parameter names to `Parameter`
-        initial_mapping:
+        initial_mapping :
             Mapping of initial names to `Initial`
 
         Returns
@@ -881,18 +881,18 @@ def add_transition(
 
         Parameters
         ----------
-        transition_name:
+        transition_name :
             Name of the new transition to be added.
-        subject_concept:
+        subject_concept :
             The subject of the new transition.
-        outcome_concept:
+        outcome_concept :
             The outcome of the new transition.
-        rate_law_sympy:
+        rate_law_sympy :
             The rate law associated with the new transition.
-        params_dict:
+        params_dict :
             Mapping of parameter attribute to their respective
             values.
-        mass_action_parameter:
+        mass_action_parameter :
             The mass action parameter that will be set to the transition's
             mass action rate law if provided.
         Returns
@@ -971,9 +971,9 @@ def substitute_parameter(self, name, value=None):
 
         Parameters
         ----------
-        name: str
+        name : str
             Name of the parameter to be substituted.
-        value:
+        value :
             The value to substitute for the parameter.
 
 
@@ -1009,18 +1009,18 @@ def add_parameter(
 
         Parameters
         ----------
-        parameter_id:
+        parameter_id :
             The id of the parameter.
-        name:
+        name :
             The name of the  parameter.
-        description:
+        description :
             The description of the parameter.
-        value:
+        value :
             The value of the newly added parameter.
-        distribution: dict[str,Any]
+        distribution : Dict[str,Any]
             Dictionary of distribution attributes to their values to be
             passed into the `Distribution` constructor.
-        units_mathml:
+        units_mathml :
             The unit of the parameter in mathml form.
 
         """
@@ -1053,7 +1053,7 @@ def eliminate_parameter(self, name):
         
         Parameters
         ----------
-        name:str
+        name : str
             The name of the parameter to be eliminated.
         """
         self.substitute_parameter(name, value=0)
@@ -1064,7 +1064,7 @@ def set_parameters(self, param_dict):
 
         Parameters
         ----------
-        param_dict: dict[str,float]
+        param_dict : Dict[str,float]
             Mapping of parameter name to its new value.
 
         """
@@ -1078,7 +1078,7 @@ def set_initials(self, initial_dict):
         
         Parameters
         ----------
-        initial_dict: dict[str,SympyExprStr]
+        initial_dict : Dict[str,SympyExprStr]
             Mapping of initial name to its new expression.
         """
         for name, expression in initial_dict.items():
@@ -1145,11 +1145,11 @@ def model_has_grounding(
     
     Parameters
     ----------
-    template_model:
+    template_model :
         The TemplateModel to query.
-    prefix:
+    prefix :
         The prefix of the search curie.
-    identifier:
+    identifier :
         The identifier of the search curie.
     Returns
     -------

diff --git a/mira/sources/util.py b/mira/sources/util.py
@@ -18,22 +18,22 @@ def transition_to_templates(
 
     Parameters
     ----------
-    input_concepts: list[Concept]
+    input_concepts : list[Concept]
         A list of Concepts serving as input to a transition.
     output_concepts : list[Concept]
         A list of Concepts serving as output to a transition.
-    controller_concepts: list[Concept]
+    controller_concepts : list[Concept]
         A list of Concepts serving as controllers towards a transition.
-    transition_rate: sympy.Expr
+    transition_rate : sympy.Expr
         The rate law associated with the transition.
-    transition_id: str
+    transition_id : str
         The id of the transition.
-    transition_name: str
+    transition_name : str
         The name of the transition.
 
     Returns
     -------
-    list[Template]
+    : list[Template]
         A list containing Templates.
     """
     if not controller_concepts:
@@ -128,7 +128,7 @@ def parameter_to_mira(parameter) -> Parameter:
 
     Parameters
     ----------
-    parameter:Dict[str,Any]
+    parameter : Dict[str,Any]
         A mapping containing MIRA Parameter attributes to values.
 
     Returns