remove WithGenericFormatVersion mixin

FynnBe · FynnBe · commit 260cac2c1e89 · 2023-11-09T15:23:23.000+01:00
diff --git a/bioimageio/spec/_internal/base_nodes.py b/bioimageio/spec/_internal/base_nodes.py
@@ -5,7 +5,7 @@
 import inspect
 import os
 import traceback
-from abc import ABC
+from abc import ABC, abstractmethod
 from copy import deepcopy
 from typing import (
     Any,
@@ -140,7 +140,7 @@ def set_fields_explicitly(cls, data: Union[Any, Dict[Any, Any]]) -> Union[Any, D
         return data
 
 
-class ResourceDescriptionBase(NodeWithExplicitlySetFields):
+class ResourceDescriptionBase(NodeWithExplicitlySetFields, ABC):
     """base class for all resource descriptions"""
 
     _internal_validation_context: InternalValidationContext = PrivateAttr(
@@ -163,15 +163,15 @@ def validation_summaries(self) -> List[ValidationSummary]:
     def root(self) -> Union[AnyUrl, DirectoryPath]:
         return self._internal_validation_context["root"]
 
+    @abstractmethod
     @classmethod
     def convert_from_older_format(cls, data: BioimageioYamlContent, context: InternalValidationContext) -> None:
-        pass
+        ...
 
     @model_validator(mode="before")
     @classmethod
-    def update_context_and_data(cls, data: BioimageioYamlContent, info: ValidationInfo):
+    def _convert_from_older_format(cls, data: BioimageioYamlContent, info: ValidationInfo):
         context = get_internal_validation_context(info.context)
-        cls._update_context(context, data)
         cls.convert_from_older_format(data, context)
         return data
 
@@ -304,6 +304,10 @@ class InvalidDescription(ResourceDescriptionBase, extra="allow", title="An inval
     format_version: Any = "unknown"
     fields_to_set_explicitly: ClassVar[FrozenSet[LiteralString]] = frozenset()
 
+    @classmethod
+    def convert_from_older_format(cls, data: BioimageioYamlContent, context: InternalValidationContext) -> None:
+        pass
+
 
 class StringNode(collections.UserString, ABC):
     """deprecated! don't use for new spec fields!"""
diff --git a/bioimageio/spec/application/v0_2.py b/bioimageio/spec/application/v0_2.py
@@ -10,12 +10,12 @@
 from bioimageio.spec.generic.v0_2 import Author as Author
 from bioimageio.spec.generic.v0_2 import Badge as Badge
 from bioimageio.spec.generic.v0_2 import CiteEntry as CiteEntry
-from bioimageio.spec.generic.v0_2 import GenericBase, WithGenericFormatVersion
+from bioimageio.spec.generic.v0_2 import GenericBase
 from bioimageio.spec.generic.v0_2 import LinkedResource as LinkedResource
 from bioimageio.spec.generic.v0_2 import Maintainer as Maintainer
 
 
-class Application(GenericBase, WithGenericFormatVersion, title="bioimage.io application specification"):
+class Application(GenericBase, title="bioimage.io application specification"):
     """Bioimage.io description of an application."""
 
     type: Literal["application"] = "application"
diff --git a/bioimageio/spec/application/v0_3.py b/bioimageio/spec/application/v0_3.py
@@ -10,12 +10,12 @@
 from bioimageio.spec.generic.v0_3 import Author as Author
 from bioimageio.spec.generic.v0_3 import Badge as Badge
 from bioimageio.spec.generic.v0_3 import CiteEntry as CiteEntry
-from bioimageio.spec.generic.v0_3 import GenericBase, WithGenericFormatVersion
+from bioimageio.spec.generic.v0_3 import GenericBase
 from bioimageio.spec.generic.v0_3 import LinkedResource as LinkedResource
 from bioimageio.spec.generic.v0_3 import Maintainer as Maintainer
 
 
-class Application(GenericBase, WithGenericFormatVersion, title="bioimage.io application specification"):
+class Application(GenericBase, title="bioimage.io application specification"):
     """Bioimage.io description of an application."""
 
     type: Literal["application"] = "application"
diff --git a/bioimageio/spec/collection/v0_2.py b/bioimageio/spec/collection/v0_2.py
@@ -27,7 +27,7 @@
 from bioimageio.spec.generic.v0_2 import Badge as Badge
 from bioimageio.spec.generic.v0_2 import CiteEntry as CiteEntry
 from bioimageio.spec.generic.v0_2 import Generic as Generic
-from bioimageio.spec.generic.v0_2 import GenericBase, WithGenericFormatVersion
+from bioimageio.spec.generic.v0_2 import GenericBase
 from bioimageio.spec.generic.v0_2 import LinkedResource as LinkedResource
 from bioimageio.spec.generic.v0_2 import Maintainer as Maintainer
 from bioimageio.spec.model.v0_4 import Model as Model
@@ -111,7 +111,7 @@ def entry(self) -> EntryNode:
         return self._entry
 
 
-class Collection(GenericBase, WithGenericFormatVersion, extra="allow", 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.
     """
diff --git a/bioimageio/spec/collection/v0_3.py b/bioimageio/spec/collection/v0_3.py
@@ -17,7 +17,7 @@
 from bioimageio.spec.generic.v0_3 import Author as Author
 from bioimageio.spec.generic.v0_3 import Badge as Badge
 from bioimageio.spec.generic.v0_3 import CiteEntry as CiteEntry
-from bioimageio.spec.generic.v0_3 import Generic, GenericBase, WithGenericFormatVersion
+from bioimageio.spec.generic.v0_3 import Generic, GenericBase
 from bioimageio.spec.generic.v0_3 import LinkedResource as LinkedResource
 from bioimageio.spec.generic.v0_3 import Maintainer as Maintainer
 from bioimageio.spec.model.v0_4 import Model as Model04
@@ -55,7 +55,7 @@ def entry(self) -> EntryNode:
         return self._entry
 
 
-class Collection(GenericBase, WithGenericFormatVersion, extra="allow", 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.
diff --git a/bioimageio/spec/dataset/v0_2.py b/bioimageio/spec/dataset/v0_2.py
@@ -10,11 +10,11 @@
 from bioimageio.spec.generic.v0_2 import Author as Author
 from bioimageio.spec.generic.v0_2 import Badge as Badge
 from bioimageio.spec.generic.v0_2 import CiteEntry as CiteEntry
-from bioimageio.spec.generic.v0_2 import GenericBase, WithGenericFormatVersion
+from bioimageio.spec.generic.v0_2 import GenericBase
 from bioimageio.spec.generic.v0_2 import Maintainer as Maintainer
 
 
-class Dataset(GenericBase, WithGenericFormatVersion, 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.
     """
diff --git a/bioimageio/spec/dataset/v0_3.py b/bioimageio/spec/dataset/v0_3.py
@@ -6,13 +6,13 @@
 from bioimageio.spec.generic.v0_3 import Author as Author
 from bioimageio.spec.generic.v0_3 import Badge as Badge
 from bioimageio.spec.generic.v0_3 import CiteEntry as CiteEntry
-from bioimageio.spec.generic.v0_3 import GenericBase, WithGenericFormatVersion
+from bioimageio.spec.generic.v0_3 import GenericBase
 from bioimageio.spec.generic.v0_3 import HttpUrl as HttpUrl
 from bioimageio.spec.generic.v0_3 import Maintainer as Maintainer
 from bioimageio.spec.generic.v0_3 import RelativeFilePath as RelativeFilePath
 
 
-class Dataset(GenericBase, WithGenericFormatVersion, 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.
     """
diff --git a/bioimageio/spec/generic/v0_2.py b/bioimageio/spec/generic/v0_2.py
@@ -10,6 +10,7 @@
 from bioimageio.spec._internal.field_warning import as_warning, warn
 from bioimageio.spec._internal.types import (
     AbsoluteFilePath,
+    BioimageioYamlContent,
     DeprecatedLicenseId,
     Doi,
     FileSource,
@@ -21,7 +22,8 @@
     Version,
 )
 from bioimageio.spec._internal.types.field_validation import WithSuffix
-from bioimageio.spec._internal.validation_context import get_internal_validation_context
+from bioimageio.spec._internal.validation_context import InternalValidationContext, get_internal_validation_context
+from bioimageio.spec.generic.v0_2_converter import convert_from_older_format
 
 KNOWN_SPECIFIC_RESOURCE_TYPES = ("application", "collection", "dataset", "model", "notebook")
 
@@ -144,7 +146,7 @@ class LinkedResource(Node):
 
 
 class GenericModelBase(ResourceDescriptionBase):
-    """Base with common fields"""
+    """Base for all resource descriptions including of model descriptions"""
 
     name: Annotated[NotEmpty[str], warn(MaxLen(128), "Longer than 128 characters.")]
     """A human-friendly name of the resource description"""
@@ -285,6 +287,19 @@ def warn_about_tag_categories(cls, value: List[str], info: ValidationInfo) -> Li
 
 
 class GenericBase(GenericModelBase):
+    """Base for all resource descriptions except for the model descriptions"""
+
+    format_version: Literal["0.2.3"] = "0.2.3"
+    """The format version of this resource specification
+    (not the `version` of the resource description)
+    When creating a new resource always use the latest micro/patch version described here.
+    The `format_version` is important for any consumer software to understand how to parse the fields.
+    """
+
+    @classmethod
+    def convert_from_older_format(cls, data: BioimageioYamlContent, context: InternalValidationContext) -> None:
+        convert_from_older_format(data, context)
+
     badges: List[Badge] = Field(default_factory=list)
     """badges associated with this resource"""
 
@@ -324,17 +339,7 @@ def deprecated_spdx_license(cls, value: Optional[str]) -> Optional[str]:
 ResourceDescriptionType = TypeVar("ResourceDescriptionType", bound=GenericBase)
 
 
-class WithGenericFormatVersion(Node):
-    format_version: Literal["0.2.3"] = "0.2.3"
-
-    """The format version of this resource specification
-    (not the `version` of the resource description)
-    When creating a new resource always use the latest micro/patch version described here.
-    The `format_version` is important for any consumer software to understand how to parse the fields.
-    """
-
-
-class Generic(GenericBase, WithGenericFormatVersion, extra="ignore", 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.
diff --git a/bioimageio/spec/generic/v0_3.py b/bioimageio/spec/generic/v0_3.py
@@ -11,6 +11,7 @@
 from bioimageio.spec._internal.field_warning import as_warning, warn
 from bioimageio.spec._internal.types import AbsoluteFilePath as AbsoluteFilePath
 from bioimageio.spec._internal.types import (
+    BioimageioYamlContent,
     DeprecatedLicenseId,
     FileSource,
     LicenseId,
@@ -21,11 +22,13 @@
 )
 from bioimageio.spec._internal.types import RelativeFilePath as RelativeFilePath
 from bioimageio.spec._internal.types.field_validation import WithSuffix
+from bioimageio.spec._internal.validation_context import InternalValidationContext
 from bioimageio.spec.generic.v0_2 import VALID_COVER_IMAGE_EXTENSIONS, CoverImageSource
 from bioimageio.spec.generic.v0_2 import Author as Author
 from bioimageio.spec.generic.v0_2 import Badge as Badge
 from bioimageio.spec.generic.v0_2 import CiteEntry as CiteEntry
 from bioimageio.spec.generic.v0_2 import Maintainer as Maintainer
+from bioimageio.spec.generic.v0_3_converter import convert_from_older_format
 
 KNOWN_SPECIFIC_RESOURCE_TYPES = ("application", "collection", "dataset", "model", "notebook")
 
@@ -51,13 +54,8 @@ class LinkedResource(Node):
     """A valid resource `id` from the official bioimage.io collection."""
 
 
-class WithGenericFormatVersion(Node):
-    format_version: Literal["0.3.0"] = "0.3.0"
-    """The **format** version of this resource specification"""
-
-
 class GenericModelBase(ResourceDescriptionBase):
-    """Base with with common fields"""
+    """Base for all resource descriptions including of model descriptions"""
 
     name: Annotated[NotEmpty[str], MaxLen(128)]
     """A human-friendly name of the resource description"""
@@ -203,6 +201,15 @@ def warn_about_tag_categories(cls, value: List[str], info: ValidationInfo) -> Li
 
 
 class GenericBase(GenericModelBase):
+    """Base for all resource descriptions except for the model descriptions"""
+
+    format_version: Literal["0.3.0"] = "0.3.0"
+    """The **format** version of this resource specification"""
+
+    @classmethod
+    def convert_from_older_format(cls, data: BioimageioYamlContent, context: InternalValidationContext) -> None:
+        convert_from_older_format(data, context)
+
     documentation: Annotated[
         Optional[MarkdownSource],
         Field(
@@ -232,7 +239,7 @@ class GenericBase(GenericModelBase):
 ResourceDescriptionType = TypeVar("ResourceDescriptionType", bound=GenericBase)
 
 
-class Generic(GenericBase, WithGenericFormatVersion, 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.
diff --git a/bioimageio/spec/model/v0_4.py b/bioimageio/spec/model/v0_4.py
@@ -916,5 +916,4 @@ def ignore_url_parent(cls, parent: Any):
 
     @classmethod
     def convert_from_older_format(cls, data: BioimageioYamlContent, context: InternalValidationContext) -> None:
-        super().convert_from_older_format(data, context)
         convert_from_older_format(data, context)
diff --git a/bioimageio/spec/notebook/v0_2.py b/bioimageio/spec/notebook/v0_2.py
@@ -10,7 +10,7 @@
 from bioimageio.spec.generic.v0_2 import Author as Author
 from bioimageio.spec.generic.v0_2 import Badge as Badge
 from bioimageio.spec.generic.v0_2 import CiteEntry as CiteEntry
-from bioimageio.spec.generic.v0_2 import GenericBase, WithGenericFormatVersion
+from bioimageio.spec.generic.v0_2 import GenericBase
 from bioimageio.spec.generic.v0_2 import LinkedResource as LinkedResource
 from bioimageio.spec.generic.v0_2 import Maintainer as Maintainer
 
@@ -22,7 +22,7 @@
 ]
 
 
-class Notebook(GenericBase, WithGenericFormatVersion, title="bioimage.io notebook specification"):
+class Notebook(GenericBase, title="bioimage.io notebook specification"):
     """Bioimage.io description of a Jupyter Notebook."""
 
     type: Literal["notebook"] = "notebook"
diff --git a/bioimageio/spec/notebook/v0_3.py b/bioimageio/spec/notebook/v0_3.py
@@ -8,13 +8,13 @@
 from bioimageio.spec.generic.v0_3 import Author as Author
 from bioimageio.spec.generic.v0_3 import Badge as Badge
 from bioimageio.spec.generic.v0_3 import CiteEntry as CiteEntry
-from bioimageio.spec.generic.v0_3 import GenericBase, WithGenericFormatVersion
+from bioimageio.spec.generic.v0_3 import GenericBase
 from bioimageio.spec.generic.v0_3 import LinkedResource as LinkedResource
 from bioimageio.spec.generic.v0_3 import Maintainer as Maintainer
 from bioimageio.spec.notebook.v0_2 import NotebookSource
 
 
-class Notebook(GenericBase, WithGenericFormatVersion, title="bioimage.io notebook specification"):
+class Notebook(GenericBase, title="bioimage.io notebook specification"):
     """Bioimage.io description of a Jupyter notebook."""
 
     type: Literal["notebook"] = "notebook"
diff --git a/scripts/generate_spec_documentation.py b/scripts/generate_spec_documentation.py
@@ -49,7 +49,7 @@
     "They are not always intuitively understandable and merely a hint at more complex validation.|\n"
     r"| \<type\>.v\<major\>_\<minor\>.\<sub spec\> | "
     "Subparts of a spec might be taken from another spec type or format version. |\n"
-    "| `field` ≝ `default` | Default field values are indicated after '=' and make a field optional. "
+    "| `field` ≝ `default` | Default field values are indicated after '≝' and make a field optional. "
     "However, `type` and `format_version` alwyas need to be set for resource descriptions written as YAML files "
     "and determine which bioimage.io specification applies. They are optional only when creating a resource "
     "description in Python code using the appropriate, `type` and `format_version` specific class.|\n"
diff --git a/tests/test_bioimageio_collection.py b/tests/test_bioimageio_collection.py
@@ -9,7 +9,7 @@
 
 from bioimageio.spec._internal.constants import DISCOVER, LATEST
 from bioimageio.spec._internal.types import FormatVersionPlaceholder
-from tests.utils import ParameterSet, check_rdf
+from tests.utils import ParameterSet, check_bioimageio_yaml
 
 BASE_URL = "https://bioimage-io.github.io/collection-bioimage-io/"
 RDF_BASE_URL = BASE_URL + "rdfs/"
@@ -174,24 +174,24 @@ def yield_bioimageio_yaml_paths() -> Iterable[ParameterSet]:
 
     for rdf in collection_registry:
         descr_path = Path(collection.fetch(rdf))
-        rdf_key = descr_path.relative_to(CACHE_PATH).as_posix()
-        yield pytest.param(descr_path, rdf_key, id=rdf_key)
+        key = descr_path.relative_to(CACHE_PATH).as_posix()
+        yield pytest.param(descr_path, key, id=key)
 
 
 @pytest.mark.parametrize("format_version", [DISCOVER, LATEST])
-@pytest.mark.parametrize("rdf_path,rdf_key", list(yield_bioimageio_yaml_paths()))
-def test_rdf(descr_path: Path, rdf_key: str, format_version: FormatVersionPlaceholder):
+@pytest.mark.parametrize("descr_path,key", list(yield_bioimageio_yaml_paths()))
+def test_rdf(descr_path: Path, key: str, format_version: FormatVersionPlaceholder):
     if (
         format_version == DISCOVER
-        and rdf_key in KNOWN_INVALID
+        and key in KNOWN_INVALID
         or format_version == LATEST
-        and rdf_key in KNOWN_INVALID_AS_LATEST
+        and key in KNOWN_INVALID_AS_LATEST
     ):
         pytest.skip("known failure")
 
-    check_rdf(
-        AnyUrl("https://example.com/"),
+    check_bioimageio_yaml(
         descr_path,
+        root=AnyUrl("https://example.com/"),
         as_latest=format_version == LATEST,
-        exclude_fields_from_roundtrip=EXCLUDE_FIELDS_FROM_ROUNDTRIP.get(rdf_key, set()),
+        exclude_fields_from_roundtrip=EXCLUDE_FIELDS_FROM_ROUNDTRIP.get(key, set()),
     )
diff --git a/tests/test_example_specs.py b/tests/test_example_specs.py
diff --git a/tests/utils.py b/tests/utils.py
