unfreeze nodes

Author: FynnBe

bioimageio/spec/_internal/base_nodes.py

@@ -4,21 +4,16 @@
 import collections.abc
 import inspect
 import os
-import sys
 from abc import ABC
 from typing import (
     Any,
     ClassVar,
     Dict,
     FrozenSet,
-    Generic,
-    Iterator,
     List,
     Optional,
-    Set,
     Tuple,
     Type,
-    TypeVar,
     Union,
     cast,
     get_type_hints,
@@ -30,6 +25,7 @@
     DirectoryPath,
     Field,
     GetCoreSchemaHandler,
+    PrivateAttr,
     StringConstraints,
     TypeAdapter,
     ValidationInfo,
@@ -40,27 +36,15 @@
 
 from bioimageio.spec._internal.constants import IN_PACKAGE_MESSAGE
 from bioimageio.spec._internal.types import NotEmpty, RdfContent, Version, YamlValue
-from bioimageio.spec._internal.types.field_validation import is_valid_yaml_mapping
 from bioimageio.spec._internal.utils import unindent
 from bioimageio.spec._internal.validation_context import InternalValidationContext, get_internal_validation_context
 from bioimageio.spec.summary import ValidationSummary
 
-K = TypeVar("K", bound=str)
-V = TypeVar("V")
-
-if sys.version_info < (3, 9):
-
-    class FrozenDictBase(collections.abc.Mapping, Generic[K, V]):  # pyright: ignore[reportMissingTypeArgument]
-        pass
-
-else:
-    FrozenDictBase = collections.abc.Mapping[K, V]
-
 
 class Node(
     pydantic.BaseModel,
     extra="forbid",
-    frozen=True,
+    frozen=False,
     populate_by_name=True,
     revalidate_instances="always",
     validate_assignment=True,
@@ -134,7 +118,7 @@ def _set_undefined_field_descriptions_from_field_name(cls):
                 info.description = name
 
 
-class NodeWithExplicitlySetFields(Node, frozen=True):
+class NodeWithExplicitlySetFields(Node):
     fields_to_set_explicitly: ClassVar[FrozenSet[LiteralString]] = frozenset()
     """set set these fields explicitly with their default value if they are not set,
     such that they are always included even when dumping with 'exlude_unset'"""
@@ -150,13 +134,13 @@ def set_fields_explicitly(cls, data: Union[Any, Dict[Any, Any]]) -> Union[Any, D
         return data
 
 
-class ResourceDescriptionBase(NodeWithExplicitlySetFields, frozen=True):
+class ResourceDescriptionBase(NodeWithExplicitlySetFields):
     """base class for all resource descriptions"""
 
-    __slots__ = ("_internal_validation_context", "_validation_summaries")
-
     type: str
     format_version: str
+    _internal_validation_context: InternalValidationContext
+    _validation_summaries: List[ValidationSummary] = PrivateAttr(default_factory=list)
 
     fields_to_set_explicitly: ClassVar[FrozenSet[LiteralString]] = frozenset({"type", "format_version"})
     implemented_format_version: ClassVar[str]
@@ -184,11 +168,7 @@ def update_context_and_data(cls, data: RdfContent, info: ValidationInfo):
 
     @model_validator(mode="after")
     def remember_internal_validation_context(self, info: ValidationInfo) -> Self:
-        self.model_config["frozen"] = False
-        self._validation_summaries: List[ValidationSummary] = []  # type: ignore[frozen]
-        self._internal_validation_context: InternalValidationContext
-        self._internal_validation_context = get_internal_validation_context(info.context)  # type: ignore[frozen]
-        self.model_config["frozen"] = True
+        self._internal_validation_context = get_internal_validation_context(info.context)
         return self
 
     @classmethod
@@ -314,42 +294,5 @@ def _serialize(self) -> str:
         return self.data
 
 
-D = TypeVar("D")
-
-
-class FrozenDictNode(Node, FrozenDictBase[K, V], frozen=True):
-    def __getitem__(self, item: K) -> V:
-        try:
-            return getattr(self, item)
-        except AttributeError:
-            raise KeyError(item) from None
-
-    def __iter__(self) -> Iterator[K]:  # type: ignore  iterate over keys like a dict, not (key, value) tuples
-        yield from self.model_fields_set  # type: ignore
-
-    def __len__(self) -> int:
-        return len(self.model_fields_set)
-
-    def keys(self) -> Set[K]:  # type: ignore
-        return set(self.model_fields_set)  # type: ignore
-
-    def __contains__(self, key: Any):
-        return key in self.model_fields_set
-
-    def get(self, item: Any, default: D = None) -> Union[V, D]:
-        return getattr(self, item, default)
-
-    @model_validator(mode="after")
-    def validate_raw_mapping(self) -> Self:
-        if not is_valid_yaml_mapping(self):
-            raise AssertionError(f"{self} contains values unrepresentable in YAML")
-
-        return self
-
-
-class ConfigNode(FrozenDictNode[NotEmpty[str], YamlValue], frozen=True):
-    model_config = {**Node.model_config, "extra": "allow"}
-
-
-class Kwargs(FrozenDictNode[NotEmpty[str], YamlValue], frozen=True):
-    model_config = {**Node.model_config, "extra": "allow"}
+ConfigNode = Dict[NotEmpty[str], YamlValue]
+Kwargs = Dict[NotEmpty[str], YamlValue]

bioimageio/spec/application/v0_2.py

@@ -12,7 +12,7 @@
 from bioimageio.spec.generic.v0_2 import Maintainer as Maintainer
 
 
-class Application(GenericBase, frozen=True, title="bioimage.io application specification"):
+class Application(GenericBase, title="bioimage.io application specification"):
     """Bioimage.io description of an application."""
 
     type: Literal["application"] = "application"

bioimageio/spec/application/v0_3.py

@@ -12,7 +12,7 @@
 from bioimageio.spec.generic.v0_3 import Maintainer as Maintainer
 
 
-class Application(GenericBase, frozen=True, title="bioimage.io application specification"):
+class Application(GenericBase, title="bioimage.io application specification"):
     """Bioimage.io description of an application."""
 
     type: Literal["application"] = "application"

bioimageio/spec/collection/v0_2.py

@@ -36,7 +36,7 @@
 EntryNode = Union[Annotated[Union[Model, Dataset, Application, Notebook], Field(discriminator="type")], Generic]
 
 
-class CollectionEntryBase(Node, extra="allow", frozen=True):
+class CollectionEntryBase(Node, extra="allow"):
     entry_adapter: ClassVar[TypeAdapter[Any]]
 
     rdf_source: Annotated[
@@ -89,13 +89,11 @@ def set_entry(self, info: ValidationInfo) -> Self:
         if type_ == "collection":
             raise ValueError("Collections may not be nested!")
 
-        self.model_config["frozen"] = False
-        self._entry = self.entry_adapter.validate_python(entry_data)  # type: ignore[frozen]
-        self.model_config["frozen"] = True
+        self._entry = self.entry_adapter.validate_python(entry_data)
         return self
 
 
-class CollectionEntry(CollectionEntryBase, frozen=True):
+class CollectionEntry(CollectionEntryBase):
     """A valid resource description (RD).
     The entry RD is based on the collection description itself.
     Fields are added/overwritten by the content of `rdf_source` if `rdf_source` is specified,
@@ -113,7 +111,7 @@ def entry(self) -> EntryNode:
         return self._entry
 
 
-class Collection(GenericBase, extra="allow", frozen=True, title="bioimage.io collection specification"):
+class Collection(GenericBase, extra="allow", title="bioimage.io collection specification"):
     """A bioimage.io collection describes several other bioimage.io resources.
     Note that collections cannot be nested; resources listed under `collection` may not be collections themselves.
     """

bioimageio/spec/collection/v0_3.py

@@ -37,7 +37,7 @@
 ]
 
 
-class CollectionEntry(v0_2.CollectionEntryBase, frozen=True):
+class CollectionEntry(v0_2.CollectionEntryBase):
     """A valid resource description (RD).
     The entry RD is based on the collection description itself.
     Fields are added/overwritten by the content of `rdf_source` if `rdf_source` is specified,
@@ -55,7 +55,7 @@ def entry(self) -> EntryNode:
         return self._entry
 
 
-class Collection(GenericBase, extra="allow", frozen=True, title="bioimage.io collection specification"):
+class Collection(GenericBase, extra="allow", title="bioimage.io collection specification"):
     """A bioimage.io collection resource description file (collection RDF) describes a collection of bioimage.io
     resources.
     The resources listed in a collection RDF have types other than 'collection'; collections cannot be nested.

bioimageio/spec/dataset/v0_2.py

@@ -10,15 +10,15 @@
 from bioimageio.spec.generic.v0_2 import Maintainer as Maintainer
 
 
-class Dataset(GenericBase, frozen=True, title="bioimage.io dataset specification"):
+class Dataset(GenericBase, title="bioimage.io dataset specification"):
     """A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage
     processing.
     """
 
     type: Literal["dataset"] = "dataset"
 
 
-class LinkedDataset(LinkedResource, frozen=True):
+class LinkedDataset(LinkedResource):
     """Reference to a bioimage.io dataset."""
 
     id: DatasetId

bioimageio/spec/dataset/v0_3.py

@@ -12,15 +12,15 @@
 from bioimageio.spec.generic.v0_3 import RelativeFilePath as RelativeFilePath
 
 
-class Dataset(GenericBase, frozen=True, title="bioimage.io dataset specification"):
+class Dataset(GenericBase, title="bioimage.io dataset specification"):
     """A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage
     processing.
     """
 
     type: Literal["dataset"] = "dataset"
 
 
-class LinkedDataset(LinkedResource, frozen=True):
+class LinkedDataset(LinkedResource):
     """Reference to a bioimage.io dataset."""
 
     id: DatasetId

bioimageio/spec/description.py

@@ -88,7 +88,7 @@
 """Any of the implemented resource descriptions"""
 
 
-class InvalidDescription(ResourceDescriptionBase, frozen=True, extra="allow", title="An invalid resource description"):
+class InvalidDescription(ResourceDescriptionBase, extra="allow", title="An invalid resource description"):
     type: Any = "unknown"
     format_version: Any = "unknown"
     fields_to_set_explicitly: ClassVar[FrozenSet[LiteralString]] = frozenset()

bioimageio/spec/generic/v0_2.py

@@ -34,14 +34,14 @@
 )
 
 
-class Attachments(Node, frozen=True):
+class Attachments(Node):
     model_config = {**Node.model_config, "extra": "allow"}
     """update pydantic model config to allow additional unknown keys"""
     files: Tuple[FileSource, ...] = ()
     """∈📦 File attachments"""
 
 
-class _Person(Node, frozen=True):
+class _Person(Node):
     name: Optional[Annotated[str, Predicate(lambda s: "/" not in s and "\\" not in s)]]
     """Full name"""
 
@@ -68,17 +68,17 @@ def convert_name(cls, name: Any, info: FieldValidationInfo):
     """
 
 
-class Author(_Person, frozen=True):
+class Author(_Person):
     name: Annotated[str, Predicate(lambda s: "/" not in s and "\\" not in s)]
     github_user: Optional[str] = None
 
 
-class Maintainer(_Person, frozen=True):
+class Maintainer(_Person):
     name: Optional[Annotated[str, Predicate(lambda s: "/" not in s and "\\" not in s)]] = None
     github_user: str
 
 
-class Badge(Node, title="Custom badge", frozen=True):
+class Badge(Node, title="Custom badge"):
     """A custom badge"""
 
     label: Annotated[str, Field(examples=["Open in Colab"])]
@@ -100,7 +100,7 @@ class Badge(Node, title="Custom badge", frozen=True):
     """target URL"""
 
 
-class CiteEntry(Node, frozen=True):
+class CiteEntry(Node):
     text: str
     """free text description"""
 
@@ -132,14 +132,14 @@ def check_doi_or_url(cls, value: Optional[str], info: FieldValidationInfo) -> Op
         return value
 
 
-class LinkedResource(Node, frozen=True):
+class LinkedResource(Node):
     """Reference to a bioimage.io resource"""
 
     id: ResourceId
     """A valid resource `id` from the bioimage.io collection."""
 
 
-class GenericBaseNoSource(ResourceDescriptionBase, frozen=True):
+class GenericBaseNoSource(ResourceDescriptionBase):
     """GenericBaseNoFormatVersion without a source field
 
     (needed because `model.v0_4.Model` and `model.v0_5.Model` have no `source` field)
@@ -326,7 +326,7 @@ def warn_about_tag_categories(cls, value: Tuple[str, ...], info: FieldValidation
 ResourceDescriptionType = TypeVar("ResourceDescriptionType", bound=GenericBaseNoSource)
 
 
-class GenericBaseNoFormatVersion(GenericBaseNoSource, frozen=True):
+class GenericBaseNoFormatVersion(GenericBaseNoSource):
     """A generic node base without format version
     to allow a derived resource description to define its format_version independently."""
 
@@ -336,7 +336,7 @@ class GenericBaseNoFormatVersion(GenericBaseNoSource, frozen=True):
     """The primary source of the resource"""
 
 
-class GenericBase(GenericBaseNoFormatVersion, frozen=True):
+class GenericBase(GenericBaseNoFormatVersion):
     format_version: Literal["0.2.3"] = "0.2.3"
 
     @classmethod
@@ -346,7 +346,7 @@ def convert_from_older_format(cls, data: RdfContent, context: InternalValidation
         convert_from_older_format(data, context)
 
 
-class Generic(GenericBase, extra="ignore", frozen=True, title="bioimage.io generic specification"):
+class Generic(GenericBase, extra="ignore", title="bioimage.io generic specification"):
     """Specification of the fields used in a generic bioimage.io-compliant resource description file (RDF).
 
     An RDF is a YAML file that describes a resource such as a model, a dataset, or a notebook.

bioimageio/spec/generic/v0_3.py

@@ -32,20 +32,20 @@
 KNOWN_SPECIFIC_RESOURCE_TYPES = ("application", "collection", "dataset", "model", "notebook")
 
 
-class Attachment(Node, frozen=True):
+class Attachment(Node):
     source: FileSource
     """∈📦 """
     sha256: Annotated[Optional[Sha256], warn(Sha256, "Missing SHA-256 hash value.")] = None
 
 
-class LinkedResource(Node, frozen=True):
+class LinkedResource(Node
     """Reference to a bioimage.io resource"""
 
     id: ResourceId
     """A valid resource `id` from the official bioimage.io collection."""
 
 
-class GenericBaseNoSource(ResourceDescriptionBase, frozen=True):
+class GenericBaseNoSource(ResourceDescriptionBase ):
     """GenericBaseNoFormatVersion without a source field
 
     (because `bioimageio.spec.model.v0_5.ModelDescription has no source field)
@@ -230,14 +230,14 @@ def warn_about_tag_categories(cls, value: Tuple[str, ...], info: FieldValidation
 ResourceDescriptionType = TypeVar("ResourceDescriptionType", bound=GenericBaseNoSource)
 
 
-class GenericBaseNoFormatVersion(GenericBaseNoSource, frozen=True):
+class GenericBaseNoFormatVersion(GenericBaseNoSource ):
     """GenericBase without a format version"""
 
     source: Optional[FileSource] = None
     """The primary source of the resource"""
 
 
-class GenericBase(GenericBaseNoFormatVersion, frozen=True, extra="ignore"):
+class GenericBase(GenericBaseNoFormatVersion , extra="ignore"):
     format_version: Literal["0.3.0"] = "0.3.0"
 
     @classmethod
@@ -247,7 +247,7 @@ def convert_from_older_format(cls, data: RdfContent, context: InternalValidation
         convert_from_older_format(data, context)
 
 
-class Generic(GenericBase, frozen=True, title="bioimage.io generic specification"):
+class Generic(GenericBase , title="bioimage.io generic specification"):
     """Specification of the fields used in a generic bioimage.io-compliant resource description file (RDF).
 
     An RDF is a YAML file that describes a resource such as a model, a dataset, or a notebook.