Further manual updates, update protected namespace for Header class

mira/modeling/acsets/petri.py

@@ -148,7 +148,7 @@ def __init__(self, model: Model):
  continue
  key = p.key if p.key else f"p_petri_{idx + 1}"
  _parameters[key] = p.value
- _distributions[key] = p.distribution.dict() \
+ _distributions[key] = p.distribution.model_dump() \
  if p.distribution else None
  transition_dict["tprop"]["mira_parameters"] = \
  json.dumps(_parameters, sort_keys=True)
@@ -186,7 +186,7 @@ def __init__(self, model: Model):
  key = sanitize_parameter_name(
  p.key) if p.key else f"p_petri_{idx + 1}"
  _parameters[key] = p.value
- _distributions[key] = p.distribution.dict() \
+ _distributions[key] = p.distribution.model_dump() \
  if p.distribution else None
  obs_dict = {
  'concept': json.dumps(concept_data),

mira/modeling/amr/petrinet.py

@@ -10,7 +10,7 @@
 from copy import deepcopy
 from typing import Dict, List, Optional
 
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, ConfigDict
 
 from mira.metamodel import expression_to_mathml, TemplateModel, SympyExprStr
 from mira.sources.amr import sanity_check_amr
@@ -462,6 +462,7 @@ class Ode(BaseModel):
 
 
 class Header(BaseModel):
+ model_config = ConfigDict(protected_namespaces=())
  name: str
  schema_url: str = Field(..., alias='schema')
  schema_name: str

mira/modeling/amr/regnet.py

@@ -11,8 +11,7 @@
 from collections import defaultdict
 from typing import Dict, List, Optional, Union
 
-import sympy
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, ConfigDict
 
 from mira.metamodel import *
 
@@ -508,6 +507,7 @@ class RegNetModel(BaseModel):
 
 
 class Header(BaseModel):
+ model_config = ConfigDict(protected_namespaces=())
  name: str
  schema_name: str
  schema_url: str = Field(..., alias='schema')

mira/modeling/amr/utils.py

@@ -4,7 +4,7 @@ def add_metadata_annotations(metadata, model):
  return
  annotations_subset = {
  k: (str(v) if k in ["time_start", "time_end"] and v is not None else v)
- for k, v in model.template_model.annotations.dict().items()
+ for k, v in model.template_model.annotations.model_dump().items()
  if k not in ["name", "description"]
  # name and description already have a privileged place
  # in the petrinet schema so don't get added again