Fix #434, pydantic fixes

release-notes/0.8.5.md

@@ -0,0 +1,13 @@
+# Release notes for sbmlutils 0.8.5
+![sbmlutils](https://github.com/matthiaskoenig/sbmlutils/raw/develop/docs_builder/images/sbmlutils-logo-60.png)
+
+We are pleased to release the next version of sbmlutils including the 
+following changes:
+
+# Features
+
+- fix #434, pydantic breaking changes
+- minor fixes in type comparison
+- bump pydantic version to >2.1 via pymetadata>=0.3.10
+
+Your sbmlutils team

setup.cfg

@@ -47,14 +47,15 @@ keywords =
 zip_safe = True
 python_requires = >=3.9
 install_requires =
-	pymetadata>=0.3.9
+	pymetadata>=0.3.10
 
 	depinfo
 	rich
 	lxml
 	requests
 	jinja2
 	xmltodict
+    pydantic
 
 	numpy>=1.21.1
 	python-libsbml>=5.20.1

src/sbmlutils/comp/comp.py

@@ -124,13 +124,13 @@ def create_ports(
         data = metaIdRefs
 
     # dictionary, port ids are provided
-    if type(data) == dict:
+    if isinstance(data, dict):
         for pid, ref in data.items():
             kwargs = {"pid": pid, ptype: ref}
             ports.append(_create_port(model, portType=portType, **kwargs))
 
     # only a list of references, port ids created via suffix appending
-    elif type(data) in [list, tuple]:
+    elif isinstance(data, (list, tuple)):
         for ref in data:
             pid = ref + suffix
             kwargs = {"pid": pid, ptype: ref}

src/sbmlutils/converters/odefac.py

@@ -443,7 +443,7 @@ def to_custom_template(self, output_file: Path, template_file: Path) -> None:
             template_file=template_file.name,
             index_offset=0,
             replace_symbols=False,
-            template_dir=template_file.parent
+            template_dir=template_file.parent,
         )
         with open(output_file, "w") as f:
             f.write(content)

src/sbmlutils/factory.py

@@ -25,14 +25,25 @@
 from dataclasses import dataclass
 from enum import Enum
 from pathlib import Path
-from typing import Any, Dict, Iterable, List, Optional, Set, Tuple, Type, Union
+from typing import (
+    Any,
+    ClassVar,
+    Dict,
+    Iterable,
+    List,
+    Optional,
+    Set,
+    Tuple,
+    Type,
+    Union,
+)
 
 import libsbml
 import numpy as np
 import xmltodict  # type: ignore
 from numpy import NaN
 from pint import UndefinedUnitError, UnitRegistry
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 from pymetadata.core.creator import Creator
 
 from sbmlutils.console import console
@@ -751,11 +762,6 @@ def __init__(
         if not self.name:
             self.name = self.definition
 
-    class Config:
-        """Pydantic configuration."""
-
-        arbitrary_types_allowed = True
-
     def create_sbml(self, model: libsbml.Model) -> Optional[libsbml.UnitDefinition]:
         """Create libsbml.UnitDefinition."""
         if isinstance(self.definition, int):
@@ -3103,6 +3109,11 @@ class ModelDict(TypedDict, total=False):
 class Model(Sbase, FrozenClass, BaseModel):
     """Model."""
 
+    model_config = ConfigDict(
+        extra="allow",
+        arbitrary_types_allowed=True,
+    )
+
     sid: str
     name: Optional[str]
     sboTerm: Optional[str]
@@ -3140,12 +3151,7 @@ class Model(Sbase, FrozenClass, BaseModel):
     # layout
     layouts: Optional[List]
 
-    class Config:
-        """Pydantic configuration."""
-
-        arbitrary_types_allowed = True
-
-    _keys = {
+    _keys: ClassVar[Dict[str, Any]] = {
         "sid": None,
         "name": None,
         "sboTerm": None,
@@ -3181,7 +3187,7 @@ class Config:
         "layouts": list,
     }
 
-    _supported_packages = {
+    _supported_packages: ClassVar[Set[str]] = {
         Package.COMP,
         Package.COMP_V1,
         Package.DISTRIB,
@@ -3193,8 +3199,10 @@ class Config:
 
     def __str__(self) -> str:
         """Get string."""
-        field_str = ", ".join(f"{a}={v!r}" for a, v in self.__repr_args__() if a and v)
-        return f"{self.__class__.__name__}({field_str})"
+        # FIXME: issue with access
+        # field_str = ", ".join(f"{a}={v!r}" for a, v in self.__repr_args__() if a and v and not a.startswith("_"))
+        # return f"{self.__class__.__name__}({field_str})"
+        return f"{self.__class__.__name__}"
 
     def __init__(
         self,

src/sbmlutils/report/sbmlinfo.py

@@ -343,7 +343,7 @@ def sbase_dict(cls, sbase: libsbml.SBase) -> Dict[str, Any]:
 
         # comp
         item_comp = sbase.getPlugin("comp")
-        if item_comp and type(item_comp) == libsbml.CompSBasePlugin:
+        if item_comp and isinstance(item_comp, libsbml.CompSBasePlugin):
             # ReplacedBy
             if item_comp.isSetReplacedBy():
                 replaced_by = item_comp.getReplacedBy()