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v0_2 ¤

Used by:
CLASS DESCRIPTION
AfterValidator
AttachmentsDescr
Author
BadgeDescr

A custom badge
CiteEntry
DeprecatedLicenseId
Doi

A digital object identifier, see https://www.doi.org/
GenericDescr

Specification of the fields used in a generic bioimage.io-compliant resource description file (RDF).
GenericDescrBase

Base for all resource descriptions except for the model descriptions
GenericModelDescrBase

Base for all resource descriptions including of model descriptions
HttpUrl

A URL with the HTTP or HTTPS scheme.
LicenseId
LinkedResource

Reference to a bioimage.io resource
Maintainer
Node
OrcidId

An ORCID identifier, see https://orcid.org/
RelativeFilePath

A path relative to the rdf.yaml file (also if the RDF source is a URL).
ResourceDescrBase

base class for all resource descriptions
ResourceId
RestrictCharacters
Uploader
ValidatedString
Version

wraps a packaging.version.Version instance for validation in pydantic models
WithSuffix
_Person
FUNCTION DESCRIPTION
_convert_from_older_format

convert raw RDF data of an older format where possible
_remove_slashes
as_warning

turn validation function into a no-op, based on warning level
is_sequence

to avoid Sequence[Unknown]
issue_warning
warn

treat a type or its annotation metadata as a warning condition
wo_special_file_name
ATTRIBUTE DESCRIPTION
BioimageioYamlContent

FilePath

FileSource

FileSource_

A file source that is included when packaging the resource.
FileSource_cover

KNOWN_SPECIFIC_RESOURCE_TYPES

NotEmpty

ResourceDescrType

TAG_CATEGORIES

TYPE: Mapping[str, Mapping[str, Sequence[str]]]

VALID_COVER_IMAGE_EXTENSIONS

YamlValue

include_in_package

DEPRECATED serializer for source fields without corresponding sha256 field.

BioimageioYamlContent module-attribute ¤

BioimageioYamlContent = Dict[str, YamlValue]
Returned by: Used by:

FilePath module-attribute ¤

FilePath = pydantic.FilePath
Used by:

FileSource module-attribute ¤

FileSource = Union[HttpUrl, RelativeFilePath, FilePath]
Used by:

FileSource_ module-attribute ¤

FileSource_ = FileSource

A file source that is included when packaging the resource.

Subclassed by: Used by:

FileSource_cover module-attribute ¤

FileSource_cover = FileSource_

KNOWN_SPECIFIC_RESOURCE_TYPES module-attribute ¤

KNOWN_SPECIFIC_RESOURCE_TYPES = (
    "application",
    "collection",
    "dataset",
    "model",
    "notebook",
)

NotEmpty module-attribute ¤

NotEmpty = S
Used by:

ResourceDescrType module-attribute ¤

ResourceDescrType = TypeVar(
    "ResourceDescrType", bound=GenericDescrBase
)

TAG_CATEGORIES module-attribute ¤

TAG_CATEGORIES: Mapping[
    str, Mapping[str, Sequence[str]]
] = json.load(f)

VALID_COVER_IMAGE_EXTENSIONS module-attribute ¤

VALID_COVER_IMAGE_EXTENSIONS = (
    ".gif",
    ".jpeg",
    ".jpg",
    ".png",
    ".svg",
    ".tif",
    ".tiff",
)

YamlValue module-attribute ¤

YamlValue = Union[
    YamlLeafValue,
    List["YamlValue"],
    Dict[YamlKey, "YamlValue"],
]
Returned by: Used by:

include_in_package module-attribute ¤

include_in_package = PrettyPlainSerializer(
    _package_serializer, when_used="unless-none"
)

DEPRECATED serializer for source fields without corresponding sha256 field.

AfterValidator dataclass ¤

AfterValidator()

Bases: functional_validators.AfterValidator


              flowchart TD
              bioimageio.spec.generic.v0_2.AfterValidator[AfterValidator]

              

              click bioimageio.spec.generic.v0_2.AfterValidator href "" "bioimageio.spec.generic.v0_2.AfterValidator"
METHOD DESCRIPTION
__str__

__str__ ¤

__str__()
Source code in src/bioimageio/spec/_internal/validator_annotations.py 
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def __str__(self):
    return f"AfterValidator({self.func.__name__})"

AttachmentsDescr pydantic-model ¤

Bases: Node

Show JSON schema: 
{
  "$defs": {
    "RelativeFilePath": {
      "description": "A path relative to the `rdf.yaml` file (also if the RDF source is a URL).",
      "format": "path",
      "title": "RelativeFilePath",
      "type": "string"
    }
  },
  "additionalProperties": true,
  "properties": {
    "files": {
      "description": "File attachments",
      "items": {
        "anyOf": [
          {
            "description": "A URL with the HTTP or HTTPS scheme.",
            "format": "uri",
            "maxLength": 2083,
            "minLength": 1,
            "title": "HttpUrl",
            "type": "string"
          },
          {
            "$ref": "#/$defs/RelativeFilePath"
          },
          {
            "format": "file-path",
            "title": "FilePath",
            "type": "string"
          }
        ]
      },
      "title": "Files",
      "type": "array"
    }
  },
  "title": "generic.v0_2.AttachmentsDescr",
  "type": "object"
}

Config:

  • default: {None: Node.model_config, 'extra': 'allow'}

Fields:

files pydantic-field ¤

files: List[FileSource_]

File attachments

model_config class-attribute instance-attribute ¤

model_config = {None: Node.model_config, 'extra': 'allow'}

update pydantic model config to allow additional unknown keys

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self

Validate a pydantic model instance.

PARAMETER DESCRIPTION

obj ¤

The object to validate.

TYPE: Union[Any, Mapping[str, Any]]

strict ¤

Whether to raise an exception on invalid fields.

TYPE: Optional[bool] DEFAULT: None

from_attributes ¤

Whether to extract data from object attributes.

TYPE: Optional[bool] DEFAULT: None

context ¤

Additional context to pass to the validator.

TYPE: Union[ValidationContext, Mapping[str, Any], None] DEFAULT: None

RAISES DESCRIPTION
ValidationError

If the object failed validation.
RETURNS DESCRIPTION
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self:
    """Validate a pydantic model instance.

    Args:
        obj: The object to validate.
        strict: Whether to raise an exception on invalid fields.
        from_attributes: Whether to extract data from object attributes.
        context: Additional context to pass to the validator.

    Raises:
        ValidationError: If the object failed validation.

    Returns:
        The validated description instance.
    """
    __tracebackhide__ = True

    if context is None:
        context = get_validation_context()
    elif isinstance(context, collections.abc.Mapping):
        context = ValidationContext(**context)

    assert not isinstance(obj, collections.abc.Mapping) or is_kwargs(obj), obj

    with context:
        # use validation context as context manager for equal behavior of __init__ and model_validate
        return super().model_validate(
            obj, strict=strict, from_attributes=from_attributes
        )

Author pydantic-model ¤

Bases: _Person

Show JSON schema: 
{
  "additionalProperties": false,
  "properties": {
    "affiliation": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Affiliation",
      "title": "Affiliation"
    },
    "email": {
      "anyOf": [
        {
          "format": "email",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Email",
      "title": "Email"
    },
    "orcid": {
      "anyOf": [
        {
          "description": "An ORCID identifier, see https://orcid.org/",
          "title": "OrcidId",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "An [ORCID iD](https://support.orcid.org/hc/en-us/sections/360001495313-What-is-ORCID\n) in hyphenated groups of 4 digits, (and [valid](\nhttps://support.orcid.org/hc/en-us/articles/360006897674-Structure-of-the-ORCID-Identifier\n) as per ISO 7064 11,2.)",
      "examples": [
        "0000-0001-2345-6789"
      ],
      "title": "Orcid"
    },
    "name": {
      "title": "Name",
      "type": "string"
    },
    "github_user": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Github User"
    }
  },
  "required": [
    "name"
  ],
  "title": "generic.v0_2.Author",
  "type": "object"
}

Fields:

affiliation pydantic-field ¤

affiliation: Optional[str] = None

Affiliation

email pydantic-field ¤

email: Optional[EmailStr] = None

Email

github_user pydantic-field ¤

github_user: Optional[str] = None

name pydantic-field ¤

name: str

orcid pydantic-field ¤

orcid: Optional[OrcidId] = None

An ORCID iD in hyphenated groups of 4 digits, (and valid as per ISO 7064 11,2.)

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self

Validate a pydantic model instance.

PARAMETER DESCRIPTION

obj ¤

The object to validate.

TYPE: Union[Any, Mapping[str, Any]]

strict ¤

Whether to raise an exception on invalid fields.

TYPE: Optional[bool] DEFAULT: None

from_attributes ¤

Whether to extract data from object attributes.

TYPE: Optional[bool] DEFAULT: None

context ¤

Additional context to pass to the validator.

TYPE: Union[ValidationContext, Mapping[str, Any], None] DEFAULT: None

RAISES DESCRIPTION
ValidationError

If the object failed validation.
RETURNS DESCRIPTION
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self:
    """Validate a pydantic model instance.

    Args:
        obj: The object to validate.
        strict: Whether to raise an exception on invalid fields.
        from_attributes: Whether to extract data from object attributes.
        context: Additional context to pass to the validator.

    Raises:
        ValidationError: If the object failed validation.

    Returns:
        The validated description instance.
    """
    __tracebackhide__ = True

    if context is None:
        context = get_validation_context()
    elif isinstance(context, collections.abc.Mapping):
        context = ValidationContext(**context)

    assert not isinstance(obj, collections.abc.Mapping) or is_kwargs(obj), obj

    with context:
        # use validation context as context manager for equal behavior of __init__ and model_validate
        return super().model_validate(
            obj, strict=strict, from_attributes=from_attributes
        )

BadgeDescr pydantic-model ¤

Bases: Node

A custom badge

Show JSON schema: 
{
  "$defs": {
    "RelativeFilePath": {
      "description": "A path relative to the `rdf.yaml` file (also if the RDF source is a URL).",
      "format": "path",
      "title": "RelativeFilePath",
      "type": "string"
    }
  },
  "additionalProperties": false,
  "description": "A custom badge",
  "properties": {
    "label": {
      "description": "badge label to display on hover",
      "examples": [
        "Open in Colab"
      ],
      "title": "Label",
      "type": "string"
    },
    "icon": {
      "anyOf": [
        {
          "format": "file-path",
          "title": "FilePath",
          "type": "string"
        },
        {
          "$ref": "#/$defs/RelativeFilePath"
        },
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "badge icon (included in bioimage.io package if not a URL)",
      "examples": [
        "https://colab.research.google.com/assets/colab-badge.svg"
      ],
      "title": "Icon"
    },
    "url": {
      "description": "target URL",
      "examples": [
        "https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb"
      ],
      "format": "uri",
      "maxLength": 2083,
      "minLength": 1,
      "title": "HttpUrl",
      "type": "string"
    }
  },
  "required": [
    "label",
    "url"
  ],
  "title": "generic.v0_2.BadgeDescr",
  "type": "object"
}

Fields:

icon pydantic-field ¤

icon: Optional[
    Union[
        Union[FilePath, RelativeFilePath],
        Union[HttpUrl, pydantic.HttpUrl],
    ]
] = None

badge icon (included in bioimage.io package if not a URL)

label pydantic-field ¤

label: str

badge label to display on hover

url pydantic-field ¤

url: HttpUrl

target URL

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self

Validate a pydantic model instance.

PARAMETER DESCRIPTION

obj ¤

The object to validate.

TYPE: Union[Any, Mapping[str, Any]]

strict ¤

Whether to raise an exception on invalid fields.

TYPE: Optional[bool] DEFAULT: None

from_attributes ¤

Whether to extract data from object attributes.

TYPE: Optional[bool] DEFAULT: None

context ¤

Additional context to pass to the validator.

TYPE: Union[ValidationContext, Mapping[str, Any], None] DEFAULT: None

RAISES DESCRIPTION
ValidationError

If the object failed validation.
RETURNS DESCRIPTION
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self:
    """Validate a pydantic model instance.

    Args:
        obj: The object to validate.
        strict: Whether to raise an exception on invalid fields.
        from_attributes: Whether to extract data from object attributes.
        context: Additional context to pass to the validator.

    Raises:
        ValidationError: If the object failed validation.

    Returns:
        The validated description instance.
    """
    __tracebackhide__ = True

    if context is None:
        context = get_validation_context()
    elif isinstance(context, collections.abc.Mapping):
        context = ValidationContext(**context)

    assert not isinstance(obj, collections.abc.Mapping) or is_kwargs(obj), obj

    with context:
        # use validation context as context manager for equal behavior of __init__ and model_validate
        return super().model_validate(
            obj, strict=strict, from_attributes=from_attributes
        )

CiteEntry pydantic-model ¤

Bases: Node

Show JSON schema: 
{
  "additionalProperties": false,
  "properties": {
    "text": {
      "description": "free text description",
      "title": "Text",
      "type": "string"
    },
    "doi": {
      "anyOf": [
        {
          "description": "A digital object identifier, see https://www.doi.org/",
          "pattern": "^10\\.[0-9]{4}.+$",
          "title": "Doi",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "A digital object identifier (DOI) is the prefered citation reference.\nSee https://www.doi.org/ for details. (alternatively specify `url`)",
      "title": "Doi"
    },
    "url": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "URL to cite (preferably specify a `doi` instead)",
      "title": "Url"
    }
  },
  "required": [
    "text"
  ],
  "title": "generic.v0_2.CiteEntry",
  "type": "object"
}

Fields:

Validators:

doi pydantic-field ¤

doi: Optional[Doi] = None

A digital object identifier (DOI) is the prefered citation reference. See https://www.doi.org/ for details. (alternatively specify url)

text pydantic-field ¤

text: str

free text description

url pydantic-field ¤

url: Optional[str] = None

URL to cite (preferably specify a doi instead)

accept_prefixed_doi pydantic-validator ¤

accept_prefixed_doi(doi: Any) -> Any
Source code in src/bioimageio/spec/generic/v0_2.py 
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@field_validator("doi", mode="before")
@classmethod
def accept_prefixed_doi(cls, doi: Any) -> Any:
    if isinstance(doi, str):
        for doi_prefix in ("https://doi.org/", "http://dx.doi.org/"):
            if doi.startswith(doi_prefix):
                doi = doi[len(doi_prefix) :]
                break

    return doi

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self

Validate a pydantic model instance.

PARAMETER DESCRIPTION

obj ¤

The object to validate.

TYPE: Union[Any, Mapping[str, Any]]

strict ¤

Whether to raise an exception on invalid fields.

TYPE: Optional[bool] DEFAULT: None

from_attributes ¤

Whether to extract data from object attributes.

TYPE: Optional[bool] DEFAULT: None

context ¤

Additional context to pass to the validator.

TYPE: Union[ValidationContext, Mapping[str, Any], None] DEFAULT: None

RAISES DESCRIPTION
ValidationError

If the object failed validation.
RETURNS DESCRIPTION
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self:
    """Validate a pydantic model instance.

    Args:
        obj: The object to validate.
        strict: Whether to raise an exception on invalid fields.
        from_attributes: Whether to extract data from object attributes.
        context: Additional context to pass to the validator.

    Raises:
        ValidationError: If the object failed validation.

    Returns:
        The validated description instance.
    """
    __tracebackhide__ = True

    if context is None:
        context = get_validation_context()
    elif isinstance(context, collections.abc.Mapping):
        context = ValidationContext(**context)

    assert not isinstance(obj, collections.abc.Mapping) or is_kwargs(obj), obj

    with context:
        # use validation context as context manager for equal behavior of __init__ and model_validate
        return super().model_validate(
            obj, strict=strict, from_attributes=from_attributes
        )

DeprecatedLicenseId ¤

Bases: ValidatedString


              flowchart TD
              bioimageio.spec.generic.v0_2.DeprecatedLicenseId[DeprecatedLicenseId]
              bioimageio.spec._internal.validated_string.ValidatedString[ValidatedString]

                              bioimageio.spec._internal.validated_string.ValidatedString --> bioimageio.spec.generic.v0_2.DeprecatedLicenseId
                


              click bioimageio.spec.generic.v0_2.DeprecatedLicenseId href "" "bioimageio.spec.generic.v0_2.DeprecatedLicenseId"
              click bioimageio.spec._internal.validated_string.ValidatedString href "" "bioimageio.spec._internal.validated_string.ValidatedString"
METHOD DESCRIPTION
__get_pydantic_core_schema__
__get_pydantic_json_schema__
__new__
ATTRIBUTE DESCRIPTION
root_model

TYPE: Type[RootModel[Any]]

root_model class-attribute ¤

root_model: Type[RootModel[Any]] = RootModel[
    DeprecatedLicenseIdLiteral
]

__get_pydantic_core_schema__ classmethod ¤

__get_pydantic_core_schema__(
    source_type: Any, handler: GetCoreSchemaHandler
) -> CoreSchema
Source code in src/bioimageio/spec/_internal/validated_string.py 
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@classmethod
def __get_pydantic_core_schema__(
    cls, source_type: Any, handler: GetCoreSchemaHandler
) -> CoreSchema:
    return no_info_after_validator_function(cls, handler(str))

__get_pydantic_json_schema__ classmethod ¤

__get_pydantic_json_schema__(
    core_schema: CoreSchema, handler: GetJsonSchemaHandler
) -> JsonSchemaValue
Source code in src/bioimageio/spec/_internal/validated_string.py 
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@classmethod
def __get_pydantic_json_schema__(
    cls, core_schema: CoreSchema, handler: GetJsonSchemaHandler
) -> JsonSchemaValue:
    json_schema = cls.root_model.model_json_schema(mode=handler.mode)
    json_schema["title"] = cls.__name__.strip("_")
    if cls.__doc__:
        json_schema["description"] = cls.__doc__

    return json_schema

__new__ ¤

__new__(object: object)
Source code in src/bioimageio/spec/_internal/validated_string.py 
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def __new__(cls, object: object):
    _validated = cls.root_model.model_validate(object).root
    self = super().__new__(cls, _validated)
    self._validated = _validated
    return self._after_validator()

Doi ¤

Bases: ValidatedString


              flowchart TD
              bioimageio.spec.generic.v0_2.Doi[Doi]
              bioimageio.spec._internal.validated_string.ValidatedString[ValidatedString]

                              bioimageio.spec._internal.validated_string.ValidatedString --> bioimageio.spec.generic.v0_2.Doi
                


              click bioimageio.spec.generic.v0_2.Doi href "" "bioimageio.spec.generic.v0_2.Doi"
              click bioimageio.spec._internal.validated_string.ValidatedString href "" "bioimageio.spec._internal.validated_string.ValidatedString"

A digital object identifier, see https://www.doi.org/

METHOD DESCRIPTION
__get_pydantic_core_schema__
__get_pydantic_json_schema__
__new__
ATTRIBUTE DESCRIPTION
root_model

TYPE: Type[RootModel[Any]]

root_model class-attribute ¤

root_model: Type[RootModel[Any]] = RootModel[str]

__get_pydantic_core_schema__ classmethod ¤

__get_pydantic_core_schema__(
    source_type: Any, handler: GetCoreSchemaHandler
) -> CoreSchema
Source code in src/bioimageio/spec/_internal/validated_string.py 
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@classmethod
def __get_pydantic_core_schema__(
    cls, source_type: Any, handler: GetCoreSchemaHandler
) -> CoreSchema:
    return no_info_after_validator_function(cls, handler(str))

__get_pydantic_json_schema__ classmethod ¤

__get_pydantic_json_schema__(
    core_schema: CoreSchema, handler: GetJsonSchemaHandler
) -> JsonSchemaValue
Source code in src/bioimageio/spec/_internal/validated_string.py 
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@classmethod
def __get_pydantic_json_schema__(
    cls, core_schema: CoreSchema, handler: GetJsonSchemaHandler
) -> JsonSchemaValue:
    json_schema = cls.root_model.model_json_schema(mode=handler.mode)
    json_schema["title"] = cls.__name__.strip("_")
    if cls.__doc__:
        json_schema["description"] = cls.__doc__

    return json_schema

__new__ ¤

__new__(object: object)
Source code in src/bioimageio/spec/_internal/validated_string.py 
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def __new__(cls, object: object):
    _validated = cls.root_model.model_validate(object).root
    self = super().__new__(cls, _validated)
    self._validated = _validated
    return self._after_validator()

GenericDescr pydantic-model ¤

Bases: GenericDescrBase

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. Note that those resources are described with a type-specific RDF. Use this generic resource description, if none of the known specific types matches your resource.

Show JSON schema: 
{
  "$defs": {
    "AttachmentsDescr": {
      "additionalProperties": true,
      "properties": {
        "files": {
          "description": "File attachments",
          "items": {
            "anyOf": [
              {
                "description": "A URL with the HTTP or HTTPS scheme.",
                "format": "uri",
                "maxLength": 2083,
                "minLength": 1,
                "title": "HttpUrl",
                "type": "string"
              },
              {
                "$ref": "#/$defs/RelativeFilePath"
              },
              {
                "format": "file-path",
                "title": "FilePath",
                "type": "string"
              }
            ]
          },
          "title": "Files",
          "type": "array"
        }
      },
      "title": "generic.v0_2.AttachmentsDescr",
      "type": "object"
    },
    "Author": {
      "additionalProperties": false,
      "properties": {
        "affiliation": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Affiliation",
          "title": "Affiliation"
        },
        "email": {
          "anyOf": [
            {
              "format": "email",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Email",
          "title": "Email"
        },
        "orcid": {
          "anyOf": [
            {
              "description": "An ORCID identifier, see https://orcid.org/",
              "title": "OrcidId",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "An [ORCID iD](https://support.orcid.org/hc/en-us/sections/360001495313-What-is-ORCID\n) in hyphenated groups of 4 digits, (and [valid](\nhttps://support.orcid.org/hc/en-us/articles/360006897674-Structure-of-the-ORCID-Identifier\n) as per ISO 7064 11,2.)",
          "examples": [
            "0000-0001-2345-6789"
          ],
          "title": "Orcid"
        },
        "name": {
          "title": "Name",
          "type": "string"
        },
        "github_user": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Github User"
        }
      },
      "required": [
        "name"
      ],
      "title": "generic.v0_2.Author",
      "type": "object"
    },
    "BadgeDescr": {
      "additionalProperties": false,
      "description": "A custom badge",
      "properties": {
        "label": {
          "description": "badge label to display on hover",
          "examples": [
            "Open in Colab"
          ],
          "title": "Label",
          "type": "string"
        },
        "icon": {
          "anyOf": [
            {
              "format": "file-path",
              "title": "FilePath",
              "type": "string"
            },
            {
              "$ref": "#/$defs/RelativeFilePath"
            },
            {
              "description": "A URL with the HTTP or HTTPS scheme.",
              "format": "uri",
              "maxLength": 2083,
              "minLength": 1,
              "title": "HttpUrl",
              "type": "string"
            },
            {
              "format": "uri",
              "maxLength": 2083,
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "badge icon (included in bioimage.io package if not a URL)",
          "examples": [
            "https://colab.research.google.com/assets/colab-badge.svg"
          ],
          "title": "Icon"
        },
        "url": {
          "description": "target URL",
          "examples": [
            "https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb"
          ],
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        }
      },
      "required": [
        "label",
        "url"
      ],
      "title": "generic.v0_2.BadgeDescr",
      "type": "object"
    },
    "CiteEntry": {
      "additionalProperties": false,
      "properties": {
        "text": {
          "description": "free text description",
          "title": "Text",
          "type": "string"
        },
        "doi": {
          "anyOf": [
            {
              "description": "A digital object identifier, see https://www.doi.org/",
              "pattern": "^10\\.[0-9]{4}.+$",
              "title": "Doi",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "A digital object identifier (DOI) is the prefered citation reference.\nSee https://www.doi.org/ for details. (alternatively specify `url`)",
          "title": "Doi"
        },
        "url": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "URL to cite (preferably specify a `doi` instead)",
          "title": "Url"
        }
      },
      "required": [
        "text"
      ],
      "title": "generic.v0_2.CiteEntry",
      "type": "object"
    },
    "Maintainer": {
      "additionalProperties": false,
      "properties": {
        "affiliation": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Affiliation",
          "title": "Affiliation"
        },
        "email": {
          "anyOf": [
            {
              "format": "email",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Email",
          "title": "Email"
        },
        "orcid": {
          "anyOf": [
            {
              "description": "An ORCID identifier, see https://orcid.org/",
              "title": "OrcidId",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "An [ORCID iD](https://support.orcid.org/hc/en-us/sections/360001495313-What-is-ORCID\n) in hyphenated groups of 4 digits, (and [valid](\nhttps://support.orcid.org/hc/en-us/articles/360006897674-Structure-of-the-ORCID-Identifier\n) as per ISO 7064 11,2.)",
          "examples": [
            "0000-0001-2345-6789"
          ],
          "title": "Orcid"
        },
        "name": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Name"
        },
        "github_user": {
          "title": "Github User",
          "type": "string"
        }
      },
      "required": [
        "github_user"
      ],
      "title": "generic.v0_2.Maintainer",
      "type": "object"
    },
    "RelativeFilePath": {
      "description": "A path relative to the `rdf.yaml` file (also if the RDF source is a URL).",
      "format": "path",
      "title": "RelativeFilePath",
      "type": "string"
    },
    "Uploader": {
      "additionalProperties": false,
      "properties": {
        "email": {
          "description": "Email",
          "format": "email",
          "title": "Email",
          "type": "string"
        },
        "name": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "name",
          "title": "Name"
        }
      },
      "required": [
        "email"
      ],
      "title": "generic.v0_2.Uploader",
      "type": "object"
    },
    "Version": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "integer"
        },
        {
          "type": "number"
        }
      ],
      "description": "wraps a packaging.version.Version instance for validation in pydantic models",
      "title": "Version"
    },
    "YamlValue": {
      "anyOf": [
        {
          "type": "boolean"
        },
        {
          "format": "date",
          "type": "string"
        },
        {
          "format": "date-time",
          "type": "string"
        },
        {
          "type": "integer"
        },
        {
          "type": "number"
        },
        {
          "type": "string"
        },
        {
          "items": {
            "$ref": "#/$defs/YamlValue"
          },
          "type": "array"
        },
        {
          "additionalProperties": {
            "$ref": "#/$defs/YamlValue"
          },
          "type": "object"
        },
        {
          "type": "null"
        }
      ]
    }
  },
  "description": "Specification of the fields used in a generic bioimage.io-compliant resource description file (RDF).\n\nAn RDF is a YAML file that describes a resource such as a model, a dataset, or a notebook.\nNote that those resources are described with a type-specific RDF.\nUse this generic resource description, if none of the known specific types matches your resource.",
  "properties": {
    "name": {
      "description": "A human-friendly name of the resource description",
      "minLength": 1,
      "title": "Name",
      "type": "string"
    },
    "description": {
      "title": "Description",
      "type": "string"
    },
    "covers": {
      "description": "Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')",
      "examples": [
        [
          "cover.png"
        ]
      ],
      "items": {
        "anyOf": [
          {
            "description": "A URL with the HTTP or HTTPS scheme.",
            "format": "uri",
            "maxLength": 2083,
            "minLength": 1,
            "title": "HttpUrl",
            "type": "string"
          },
          {
            "$ref": "#/$defs/RelativeFilePath"
          },
          {
            "format": "file-path",
            "title": "FilePath",
            "type": "string"
          }
        ]
      },
      "title": "Covers",
      "type": "array"
    },
    "id_emoji": {
      "anyOf": [
        {
          "examples": [
            "\ud83e\udd88",
            "\ud83e\udda5"
          ],
          "maxLength": 1,
          "minLength": 1,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "UTF-8 emoji for display alongside the `id`.",
      "title": "Id Emoji"
    },
    "authors": {
      "description": "The authors are the creators of the RDF and the primary points of contact.",
      "items": {
        "$ref": "#/$defs/Author"
      },
      "title": "Authors",
      "type": "array"
    },
    "attachments": {
      "anyOf": [
        {
          "$ref": "#/$defs/AttachmentsDescr"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "file and other attachments"
    },
    "cite": {
      "description": "citations",
      "items": {
        "$ref": "#/$defs/CiteEntry"
      },
      "title": "Cite",
      "type": "array"
    },
    "config": {
      "additionalProperties": {
        "$ref": "#/$defs/YamlValue"
      },
      "description": "A field for custom configuration that can contain any keys not present in the RDF spec.\nThis means you should not store, for example, a github repo URL in `config` since we already have the\n`git_repo` field defined in the spec.\nKeys in `config` may be very specific to a tool or consumer software. To avoid conflicting definitions,\nit is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,\nfor example:\n```yaml\nconfig:\n    bioimageio:  # here is the domain name\n        my_custom_key: 3837283\n        another_key:\n            nested: value\n    imagej:       # config specific to ImageJ\n        macro_dir: path/to/macro/file\n```\nIf possible, please use [`snake_case`](https://en.wikipedia.org/wiki/Snake_case) for keys in `config`.\nYou may want to list linked files additionally under `attachments` to include them when packaging a resource\n(packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains\nan altered rdf.yaml file with local references to the downloaded files)",
      "examples": [
        {
          "bioimageio": {
            "another_key": {
              "nested": "value"
            },
            "my_custom_key": 3837283
          },
          "imagej": {
            "macro_dir": "path/to/macro/file"
          }
        }
      ],
      "title": "Config",
      "type": "object"
    },
    "download_url": {
      "anyOf": [
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "URL to download the resource from (deprecated)",
      "title": "Download Url"
    },
    "git_repo": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "A URL to the Git repository where the resource is being developed.",
      "examples": [
        "https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad"
      ],
      "title": "Git Repo"
    },
    "icon": {
      "anyOf": [
        {
          "maxLength": 2,
          "minLength": 1,
          "type": "string"
        },
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "$ref": "#/$defs/RelativeFilePath"
        },
        {
          "format": "file-path",
          "title": "FilePath",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "An icon for illustration",
      "title": "Icon"
    },
    "links": {
      "description": "IDs of other bioimage.io resources",
      "examples": [
        [
          "ilastik/ilastik",
          "deepimagej/deepimagej",
          "zero/notebook_u-net_3d_zerocostdl4mic"
        ]
      ],
      "items": {
        "type": "string"
      },
      "title": "Links",
      "type": "array"
    },
    "uploader": {
      "anyOf": [
        {
          "$ref": "#/$defs/Uploader"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The person who uploaded the model (e.g. to bioimage.io)"
    },
    "maintainers": {
      "description": "Maintainers of this resource.\nIf not specified `authors` are maintainers and at least some of them should specify their `github_user` name",
      "items": {
        "$ref": "#/$defs/Maintainer"
      },
      "title": "Maintainers",
      "type": "array"
    },
    "rdf_source": {
      "anyOf": [
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "$ref": "#/$defs/RelativeFilePath"
        },
        {
          "format": "file-path",
          "title": "FilePath",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from.\nDo not set this field in a YAML file.",
      "title": "Rdf Source"
    },
    "tags": {
      "description": "Associated tags",
      "examples": [
        [
          "unet2d",
          "pytorch",
          "nucleus",
          "segmentation",
          "dsb2018"
        ]
      ],
      "items": {
        "type": "string"
      },
      "title": "Tags",
      "type": "array"
    },
    "version": {
      "anyOf": [
        {
          "$ref": "#/$defs/Version"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The version of the resource following SemVer 2.0."
    },
    "version_number": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "version number (n-th published version, not the semantic version)",
      "title": "Version Number"
    },
    "format_version": {
      "const": "0.2.4",
      "description": "The format version of this resource specification\n(not the `version` of the resource description)\nWhen creating a new resource always use the latest micro/patch version described here.\nThe `format_version` is important for any consumer software to understand how to parse the fields.",
      "title": "Format Version",
      "type": "string"
    },
    "badges": {
      "description": "badges associated with this resource",
      "items": {
        "$ref": "#/$defs/BadgeDescr"
      },
      "title": "Badges",
      "type": "array"
    },
    "documentation": {
      "anyOf": [
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "$ref": "#/$defs/RelativeFilePath"
        },
        {
          "format": "file-path",
          "title": "FilePath",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is `README.md`. An `.md` suffix is mandatory.",
      "examples": [
        "https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md",
        "README.md"
      ],
      "title": "Documentation"
    },
    "license": {
      "anyOf": [
        {
          "enum": [
            "0BSD",
            "AAL",
            "Abstyles",
            "AdaCore-doc",
            "Adobe-2006",
            "Adobe-Display-PostScript",
            "Adobe-Glyph",
            "Adobe-Utopia",
            "ADSL",
            "AFL-1.1",
            "AFL-1.2",
            "AFL-2.0",
            "AFL-2.1",
            "AFL-3.0",
            "Afmparse",
            "AGPL-1.0-only",
            "AGPL-1.0-or-later",
            "AGPL-3.0-only",
            "AGPL-3.0-or-later",
            "Aladdin",
            "AMDPLPA",
            "AML",
            "AML-glslang",
            "AMPAS",
            "ANTLR-PD",
            "ANTLR-PD-fallback",
            "Apache-1.0",
            "Apache-1.1",
            "Apache-2.0",
            "APAFML",
            "APL-1.0",
            "App-s2p",
            "APSL-1.0",
            "APSL-1.1",
            "APSL-1.2",
            "APSL-2.0",
            "Arphic-1999",
            "Artistic-1.0",
            "Artistic-1.0-cl8",
            "Artistic-1.0-Perl",
            "Artistic-2.0",
            "ASWF-Digital-Assets-1.0",
            "ASWF-Digital-Assets-1.1",
            "Baekmuk",
            "Bahyph",
            "Barr",
            "bcrypt-Solar-Designer",
            "Beerware",
            "Bitstream-Charter",
            "Bitstream-Vera",
            "BitTorrent-1.0",
            "BitTorrent-1.1",
            "blessing",
            "BlueOak-1.0.0",
            "Boehm-GC",
            "Borceux",
            "Brian-Gladman-2-Clause",
            "Brian-Gladman-3-Clause",
            "BSD-1-Clause",
            "BSD-2-Clause",
            "BSD-2-Clause-Darwin",
            "BSD-2-Clause-Patent",
            "BSD-2-Clause-Views",
            "BSD-3-Clause",
            "BSD-3-Clause-acpica",
            "BSD-3-Clause-Attribution",
            "BSD-3-Clause-Clear",
            "BSD-3-Clause-flex",
            "BSD-3-Clause-HP",
            "BSD-3-Clause-LBNL",
            "BSD-3-Clause-Modification",
            "BSD-3-Clause-No-Military-License",
            "BSD-3-Clause-No-Nuclear-License",
            "BSD-3-Clause-No-Nuclear-License-2014",
            "BSD-3-Clause-No-Nuclear-Warranty",
            "BSD-3-Clause-Open-MPI",
            "BSD-3-Clause-Sun",
            "BSD-4-Clause",
            "BSD-4-Clause-Shortened",
            "BSD-4-Clause-UC",
            "BSD-4.3RENO",
            "BSD-4.3TAHOE",
            "BSD-Advertising-Acknowledgement",
            "BSD-Attribution-HPND-disclaimer",
            "BSD-Inferno-Nettverk",
            "BSD-Protection",
            "BSD-Source-beginning-file",
            "BSD-Source-Code",
            "BSD-Systemics",
            "BSD-Systemics-W3Works",
            "BSL-1.0",
            "BUSL-1.1",
            "bzip2-1.0.6",
            "C-UDA-1.0",
            "CAL-1.0",
            "CAL-1.0-Combined-Work-Exception",
            "Caldera",
            "Caldera-no-preamble",
            "CATOSL-1.1",
            "CC-BY-1.0",
            "CC-BY-2.0",
            "CC-BY-2.5",
            "CC-BY-2.5-AU",
            "CC-BY-3.0",
            "CC-BY-3.0-AT",
            "CC-BY-3.0-AU",
            "CC-BY-3.0-DE",
            "CC-BY-3.0-IGO",
            "CC-BY-3.0-NL",
            "CC-BY-3.0-US",
            "CC-BY-4.0",
            "CC-BY-NC-1.0",
            "CC-BY-NC-2.0",
            "CC-BY-NC-2.5",
            "CC-BY-NC-3.0",
            "CC-BY-NC-3.0-DE",
            "CC-BY-NC-4.0",
            "CC-BY-NC-ND-1.0",
            "CC-BY-NC-ND-2.0",
            "CC-BY-NC-ND-2.5",
            "CC-BY-NC-ND-3.0",
            "CC-BY-NC-ND-3.0-DE",
            "CC-BY-NC-ND-3.0-IGO",
            "CC-BY-NC-ND-4.0",
            "CC-BY-NC-SA-1.0",
            "CC-BY-NC-SA-2.0",
            "CC-BY-NC-SA-2.0-DE",
            "CC-BY-NC-SA-2.0-FR",
            "CC-BY-NC-SA-2.0-UK",
            "CC-BY-NC-SA-2.5",
            "CC-BY-NC-SA-3.0",
            "CC-BY-NC-SA-3.0-DE",
            "CC-BY-NC-SA-3.0-IGO",
            "CC-BY-NC-SA-4.0",
            "CC-BY-ND-1.0",
            "CC-BY-ND-2.0",
            "CC-BY-ND-2.5",
            "CC-BY-ND-3.0",
            "CC-BY-ND-3.0-DE",
            "CC-BY-ND-4.0",
            "CC-BY-SA-1.0",
            "CC-BY-SA-2.0",
            "CC-BY-SA-2.0-UK",
            "CC-BY-SA-2.1-JP",
            "CC-BY-SA-2.5",
            "CC-BY-SA-3.0",
            "CC-BY-SA-3.0-AT",
            "CC-BY-SA-3.0-DE",
            "CC-BY-SA-3.0-IGO",
            "CC-BY-SA-4.0",
            "CC-PDDC",
            "CC0-1.0",
            "CDDL-1.0",
            "CDDL-1.1",
            "CDL-1.0",
            "CDLA-Permissive-1.0",
            "CDLA-Permissive-2.0",
            "CDLA-Sharing-1.0",
            "CECILL-1.0",
            "CECILL-1.1",
            "CECILL-2.0",
            "CECILL-2.1",
            "CECILL-B",
            "CECILL-C",
            "CERN-OHL-1.1",
            "CERN-OHL-1.2",
            "CERN-OHL-P-2.0",
            "CERN-OHL-S-2.0",
            "CERN-OHL-W-2.0",
            "CFITSIO",
            "check-cvs",
            "checkmk",
            "ClArtistic",
            "Clips",
            "CMU-Mach",
            "CMU-Mach-nodoc",
            "CNRI-Jython",
            "CNRI-Python",
            "CNRI-Python-GPL-Compatible",
            "COIL-1.0",
            "Community-Spec-1.0",
            "Condor-1.1",
            "copyleft-next-0.3.0",
            "copyleft-next-0.3.1",
            "Cornell-Lossless-JPEG",
            "CPAL-1.0",
            "CPL-1.0",
            "CPOL-1.02",
            "Cronyx",
            "Crossword",
            "CrystalStacker",
            "CUA-OPL-1.0",
            "Cube",
            "curl",
            "D-FSL-1.0",
            "DEC-3-Clause",
            "diffmark",
            "DL-DE-BY-2.0",
            "DL-DE-ZERO-2.0",
            "DOC",
            "Dotseqn",
            "DRL-1.0",
            "DRL-1.1",
            "DSDP",
            "dtoa",
            "dvipdfm",
            "ECL-1.0",
            "ECL-2.0",
            "EFL-1.0",
            "EFL-2.0",
            "eGenix",
            "Elastic-2.0",
            "Entessa",
            "EPICS",
            "EPL-1.0",
            "EPL-2.0",
            "ErlPL-1.1",
            "etalab-2.0",
            "EUDatagrid",
            "EUPL-1.0",
            "EUPL-1.1",
            "EUPL-1.2",
            "Eurosym",
            "Fair",
            "FBM",
            "FDK-AAC",
            "Ferguson-Twofish",
            "Frameworx-1.0",
            "FreeBSD-DOC",
            "FreeImage",
            "FSFAP",
            "FSFAP-no-warranty-disclaimer",
            "FSFUL",
            "FSFULLR",
            "FSFULLRWD",
            "FTL",
            "Furuseth",
            "fwlw",
            "GCR-docs",
            "GD",
            "GFDL-1.1-invariants-only",
            "GFDL-1.1-invariants-or-later",
            "GFDL-1.1-no-invariants-only",
            "GFDL-1.1-no-invariants-or-later",
            "GFDL-1.1-only",
            "GFDL-1.1-or-later",
            "GFDL-1.2-invariants-only",
            "GFDL-1.2-invariants-or-later",
            "GFDL-1.2-no-invariants-only",
            "GFDL-1.2-no-invariants-or-later",
            "GFDL-1.2-only",
            "GFDL-1.2-or-later",
            "GFDL-1.3-invariants-only",
            "GFDL-1.3-invariants-or-later",
            "GFDL-1.3-no-invariants-only",
            "GFDL-1.3-no-invariants-or-later",
            "GFDL-1.3-only",
            "GFDL-1.3-or-later",
            "Giftware",
            "GL2PS",
            "Glide",
            "Glulxe",
            "GLWTPL",
            "gnuplot",
            "GPL-1.0-only",
            "GPL-1.0-or-later",
            "GPL-2.0-only",
            "GPL-2.0-or-later",
            "GPL-3.0-only",
            "GPL-3.0-or-later",
            "Graphics-Gems",
            "gSOAP-1.3b",
            "gtkbook",
            "HaskellReport",
            "hdparm",
            "Hippocratic-2.1",
            "HP-1986",
            "HP-1989",
            "HPND",
            "HPND-DEC",
            "HPND-doc",
            "HPND-doc-sell",
            "HPND-export-US",
            "HPND-export-US-modify",
            "HPND-Fenneberg-Livingston",
            "HPND-INRIA-IMAG",
            "HPND-Kevlin-Henney",
            "HPND-Markus-Kuhn",
            "HPND-MIT-disclaimer",
            "HPND-Pbmplus",
            "HPND-sell-MIT-disclaimer-xserver",
            "HPND-sell-regexpr",
            "HPND-sell-variant",
            "HPND-sell-variant-MIT-disclaimer",
            "HPND-UC",
            "HTMLTIDY",
            "IBM-pibs",
            "ICU",
            "IEC-Code-Components-EULA",
            "IJG",
            "IJG-short",
            "ImageMagick",
            "iMatix",
            "Imlib2",
            "Info-ZIP",
            "Inner-Net-2.0",
            "Intel",
            "Intel-ACPI",
            "Interbase-1.0",
            "IPA",
            "IPL-1.0",
            "ISC",
            "ISC-Veillard",
            "Jam",
            "JasPer-2.0",
            "JPL-image",
            "JPNIC",
            "JSON",
            "Kastrup",
            "Kazlib",
            "Knuth-CTAN",
            "LAL-1.2",
            "LAL-1.3",
            "Latex2e",
            "Latex2e-translated-notice",
            "Leptonica",
            "LGPL-2.0-only",
            "LGPL-2.0-or-later",
            "LGPL-2.1-only",
            "LGPL-2.1-or-later",
            "LGPL-3.0-only",
            "LGPL-3.0-or-later",
            "LGPLLR",
            "Libpng",
            "libpng-2.0",
            "libselinux-1.0",
            "libtiff",
            "libutil-David-Nugent",
            "LiLiQ-P-1.1",
            "LiLiQ-R-1.1",
            "LiLiQ-Rplus-1.1",
            "Linux-man-pages-1-para",
            "Linux-man-pages-copyleft",
            "Linux-man-pages-copyleft-2-para",
            "Linux-man-pages-copyleft-var",
            "Linux-OpenIB",
            "LOOP",
            "LPD-document",
            "LPL-1.0",
            "LPL-1.02",
            "LPPL-1.0",
            "LPPL-1.1",
            "LPPL-1.2",
            "LPPL-1.3a",
            "LPPL-1.3c",
            "lsof",
            "Lucida-Bitmap-Fonts",
            "LZMA-SDK-9.11-to-9.20",
            "LZMA-SDK-9.22",
            "Mackerras-3-Clause",
            "Mackerras-3-Clause-acknowledgment",
            "magaz",
            "mailprio",
            "MakeIndex",
            "Martin-Birgmeier",
            "McPhee-slideshow",
            "metamail",
            "Minpack",
            "MirOS",
            "MIT",
            "MIT-0",
            "MIT-advertising",
            "MIT-CMU",
            "MIT-enna",
            "MIT-feh",
            "MIT-Festival",
            "MIT-Modern-Variant",
            "MIT-open-group",
            "MIT-testregex",
            "MIT-Wu",
            "MITNFA",
            "MMIXware",
            "Motosoto",
            "MPEG-SSG",
            "mpi-permissive",
            "mpich2",
            "MPL-1.0",
            "MPL-1.1",
            "MPL-2.0",
            "MPL-2.0-no-copyleft-exception",
            "mplus",
            "MS-LPL",
            "MS-PL",
            "MS-RL",
            "MTLL",
            "MulanPSL-1.0",
            "MulanPSL-2.0",
            "Multics",
            "Mup",
            "NAIST-2003",
            "NASA-1.3",
            "Naumen",
            "NBPL-1.0",
            "NCGL-UK-2.0",
            "NCSA",
            "Net-SNMP",
            "NetCDF",
            "Newsletr",
            "NGPL",
            "NICTA-1.0",
            "NIST-PD",
            "NIST-PD-fallback",
            "NIST-Software",
            "NLOD-1.0",
            "NLOD-2.0",
            "NLPL",
            "Nokia",
            "NOSL",
            "Noweb",
            "NPL-1.0",
            "NPL-1.1",
            "NPOSL-3.0",
            "NRL",
            "NTP",
            "NTP-0",
            "O-UDA-1.0",
            "OCCT-PL",
            "OCLC-2.0",
            "ODbL-1.0",
            "ODC-By-1.0",
            "OFFIS",
            "OFL-1.0",
            "OFL-1.0-no-RFN",
            "OFL-1.0-RFN",
            "OFL-1.1",
            "OFL-1.1-no-RFN",
            "OFL-1.1-RFN",
            "OGC-1.0",
            "OGDL-Taiwan-1.0",
            "OGL-Canada-2.0",
            "OGL-UK-1.0",
            "OGL-UK-2.0",
            "OGL-UK-3.0",
            "OGTSL",
            "OLDAP-1.1",
            "OLDAP-1.2",
            "OLDAP-1.3",
            "OLDAP-1.4",
            "OLDAP-2.0",
            "OLDAP-2.0.1",
            "OLDAP-2.1",
            "OLDAP-2.2",
            "OLDAP-2.2.1",
            "OLDAP-2.2.2",
            "OLDAP-2.3",
            "OLDAP-2.4",
            "OLDAP-2.5",
            "OLDAP-2.6",
            "OLDAP-2.7",
            "OLDAP-2.8",
            "OLFL-1.3",
            "OML",
            "OpenPBS-2.3",
            "OpenSSL",
            "OpenSSL-standalone",
            "OpenVision",
            "OPL-1.0",
            "OPL-UK-3.0",
            "OPUBL-1.0",
            "OSET-PL-2.1",
            "OSL-1.0",
            "OSL-1.1",
            "OSL-2.0",
            "OSL-2.1",
            "OSL-3.0",
            "PADL",
            "Parity-6.0.0",
            "Parity-7.0.0",
            "PDDL-1.0",
            "PHP-3.0",
            "PHP-3.01",
            "Pixar",
            "Plexus",
            "pnmstitch",
            "PolyForm-Noncommercial-1.0.0",
            "PolyForm-Small-Business-1.0.0",
            "PostgreSQL",
            "PSF-2.0",
            "psfrag",
            "psutils",
            "Python-2.0",
            "Python-2.0.1",
            "python-ldap",
            "Qhull",
            "QPL-1.0",
            "QPL-1.0-INRIA-2004",
            "radvd",
            "Rdisc",
            "RHeCos-1.1",
            "RPL-1.1",
            "RPL-1.5",
            "RPSL-1.0",
            "RSA-MD",
            "RSCPL",
            "Ruby",
            "SAX-PD",
            "SAX-PD-2.0",
            "Saxpath",
            "SCEA",
            "SchemeReport",
            "Sendmail",
            "Sendmail-8.23",
            "SGI-B-1.0",
            "SGI-B-1.1",
            "SGI-B-2.0",
            "SGI-OpenGL",
            "SGP4",
            "SHL-0.5",
            "SHL-0.51",
            "SimPL-2.0",
            "SISSL",
            "SISSL-1.2",
            "SL",
            "Sleepycat",
            "SMLNJ",
            "SMPPL",
            "SNIA",
            "snprintf",
            "softSurfer",
            "Soundex",
            "Spencer-86",
            "Spencer-94",
            "Spencer-99",
            "SPL-1.0",
            "ssh-keyscan",
            "SSH-OpenSSH",
            "SSH-short",
            "SSLeay-standalone",
            "SSPL-1.0",
            "SugarCRM-1.1.3",
            "Sun-PPP",
            "SunPro",
            "SWL",
            "swrule",
            "Symlinks",
            "TAPR-OHL-1.0",
            "TCL",
            "TCP-wrappers",
            "TermReadKey",
            "TGPPL-1.0",
            "TMate",
            "TORQUE-1.1",
            "TOSL",
            "TPDL",
            "TPL-1.0",
            "TTWL",
            "TTYP0",
            "TU-Berlin-1.0",
            "TU-Berlin-2.0",
            "UCAR",
            "UCL-1.0",
            "ulem",
            "UMich-Merit",
            "Unicode-3.0",
            "Unicode-DFS-2015",
            "Unicode-DFS-2016",
            "Unicode-TOU",
            "UnixCrypt",
            "Unlicense",
            "UPL-1.0",
            "URT-RLE",
            "Vim",
            "VOSTROM",
            "VSL-1.0",
            "W3C",
            "W3C-19980720",
            "W3C-20150513",
            "w3m",
            "Watcom-1.0",
            "Widget-Workshop",
            "Wsuipa",
            "WTFPL",
            "X11",
            "X11-distribute-modifications-variant",
            "Xdebug-1.03",
            "Xerox",
            "Xfig",
            "XFree86-1.1",
            "xinetd",
            "xkeyboard-config-Zinoviev",
            "xlock",
            "Xnet",
            "xpp",
            "XSkat",
            "YPL-1.0",
            "YPL-1.1",
            "Zed",
            "Zeeff",
            "Zend-2.0",
            "Zimbra-1.3",
            "Zimbra-1.4",
            "Zlib",
            "zlib-acknowledgement",
            "ZPL-1.1",
            "ZPL-2.0",
            "ZPL-2.1"
          ],
          "title": "LicenseId",
          "type": "string"
        },
        {
          "enum": [
            "AGPL-1.0",
            "AGPL-3.0",
            "BSD-2-Clause-FreeBSD",
            "BSD-2-Clause-NetBSD",
            "bzip2-1.0.5",
            "eCos-2.0",
            "GFDL-1.1",
            "GFDL-1.2",
            "GFDL-1.3",
            "GPL-1.0",
            "GPL-1.0+",
            "GPL-2.0",
            "GPL-2.0+",
            "GPL-2.0-with-autoconf-exception",
            "GPL-2.0-with-bison-exception",
            "GPL-2.0-with-classpath-exception",
            "GPL-2.0-with-font-exception",
            "GPL-2.0-with-GCC-exception",
            "GPL-3.0",
            "GPL-3.0+",
            "GPL-3.0-with-autoconf-exception",
            "GPL-3.0-with-GCC-exception",
            "LGPL-2.0",
            "LGPL-2.0+",
            "LGPL-2.1",
            "LGPL-2.1+",
            "LGPL-3.0",
            "LGPL-3.0+",
            "Nunit",
            "StandardML-NJ",
            "wxWindows"
          ],
          "title": "DeprecatedLicenseId",
          "type": "string"
        },
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "A [SPDX license identifier](https://spdx.org/licenses/).\nWe do not support custom license beyond the SPDX license list, if you need that please\n[open a GitHub issue](https://github.com/bioimage-io/spec-bioimage-io/issues/new/choose\n) to discuss your intentions with the community.",
      "examples": [
        "CC0-1.0",
        "MIT",
        "BSD-2-Clause"
      ],
      "title": "License"
    },
    "type": {
      "default": "generic",
      "description": "The resource type assigns a broad category to the resource.",
      "title": "Type",
      "type": "string"
    },
    "id": {
      "anyOf": [
        {
          "minLength": 1,
          "title": "ResourceId",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version **un**specific.",
      "title": "Id"
    },
    "source": {
      "anyOf": [
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The primary source of the resource",
      "title": "Source"
    }
  },
  "required": [
    "name",
    "description",
    "format_version"
  ],
  "title": "generic.v0_2.GenericDescr",
  "type": "object"
}

Fields:

Validators:

attachments pydantic-field ¤

attachments: Optional[AttachmentsDescr] = None

file and other attachments

authors pydantic-field ¤

authors: List[Author]

The authors are the creators of the RDF and the primary points of contact.

badges pydantic-field ¤

badges: List[BadgeDescr]

badges associated with this resource

cite pydantic-field ¤

cite: List[CiteEntry]

citations

config pydantic-field ¤

config: Dict[str, YamlValue]

A field for custom configuration that can contain any keys not present in the RDF spec. This means you should not store, for example, a github repo URL in config since we already have the git_repo field defined in the spec. Keys in config may be very specific to a tool or consumer software. To avoid conflicting definitions, it is recommended to wrap added configuration into a sub-field named with the specific domain or tool name, for example: 

config:
    bioimageio:  # here is the domain name
        my_custom_key: 3837283
        another_key:
            nested: value
    imagej:       # config specific to ImageJ
        macro_dir: path/to/macro/file
If possible, please use snake_case for keys in config. You may want to list linked files additionally under attachments to include them when packaging a resource (packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains an altered rdf.yaml file with local references to the downloaded files)

covers pydantic-field ¤

covers: List[FileSource_cover]

Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.

description pydantic-field ¤

description: str

documentation pydantic-field ¤

documentation: Optional[FileSource] = None

URL or relative path to a markdown file with additional documentation. The recommended documentation file name is README.md. An .md suffix is mandatory.

download_url pydantic-field ¤

download_url: Optional[HttpUrl] = None

URL to download the resource from (deprecated)

file_name property ¤

file_name: Optional[FileName]

File name of the bioimageio.yaml file the description was loaded from.

format_version pydantic-field ¤

format_version: Literal['0.2.4'] = '0.2.4'

git_repo pydantic-field ¤

git_repo: Optional[str] = None

A URL to the Git repository where the resource is being developed.

icon pydantic-field ¤

icon: Union[str, FileSource, None] = None

An icon for illustration

id pydantic-field ¤

id: Optional[ResourceId] = None

bioimage.io-wide unique resource identifier assigned by bioimage.io; version unspecific.

id_emoji pydantic-field ¤

id_emoji: Optional[str] = None

UTF-8 emoji for display alongside the id.

implemented_format_version class-attribute ¤

implemented_format_version: Literal['0.2.4'] = '0.2.4'

implemented_format_version_tuple class-attribute ¤

implemented_format_version_tuple: Tuple[int, int, int]

license pydantic-field ¤

license: Union[
    LicenseId, DeprecatedLicenseId, str, None
] = None

A SPDX license identifier. We do not support custom license beyond the SPDX license list, if you need that please open a GitHub issue to discuss your intentions with the community.

links: List[str]

IDs of other bioimage.io resources

maintainers pydantic-field ¤

maintainers: List[Maintainer]

Maintainers of this resource. If not specified authors are maintainers and at least some of them should specify their github_user name

name pydantic-field ¤

name: NotEmpty[str]

A human-friendly name of the resource description

rdf_source pydantic-field ¤

rdf_source: Optional[FileSource] = None

Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from. Do not set this field in a YAML file.

root property ¤

root: Union[RootHttpUrl, DirectoryPath, ZipFile]

The URL/Path prefix to resolve any relative paths with.

source pydantic-field ¤

source: Optional[HttpUrl] = None

The primary source of the resource

tags pydantic-field ¤

tags: List[str]

Associated tags

type pydantic-field ¤

type: str = 'generic'

The resource type assigns a broad category to the resource.

uploader pydantic-field ¤

uploader: Optional[Uploader] = None

The person who uploaded the model (e.g. to bioimage.io)

validation_summary property ¤

validation_summary: ValidationSummary

version pydantic-field ¤

version: Optional[Version] = None

The version of the resource following SemVer 2.0.

version_number pydantic-field ¤

version_number: Optional[int] = None

version number (n-th published version, not the semantic version)

__pydantic_init_subclass__ classmethod ¤

__pydantic_init_subclass__(**kwargs: Any)
Source code in src/bioimageio/spec/_internal/common_nodes.py 
199
200
201
202
203
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207
208
209
210
211
@classmethod
def __pydantic_init_subclass__(cls, **kwargs: Any):
    super().__pydantic_init_subclass__(**kwargs)
    # set classvar implemented_format_version_tuple
    if "format_version" in cls.model_fields:
        if "." not in cls.implemented_format_version:
            cls.implemented_format_version_tuple = (0, 0, 0)
        else:
            fv_tuple = get_format_version_tuple(cls.implemented_format_version)
            assert fv_tuple is not None, (
                f"failed to cast '{cls.implemented_format_version}' to tuple"
            )
            cls.implemented_format_version_tuple = fv_tuple

accept_author_strings classmethod ¤

accept_author_strings(
    authors: Union[Any, Sequence[Any]],
) -> Any

we unofficially accept strings as author entries

Source code in src/bioimageio/spec/generic/v0_2.py 
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@field_validator("authors", mode="before")
@classmethod
def accept_author_strings(cls, authors: Union[Any, Sequence[Any]]) -> Any:
    """we unofficially accept strings as author entries"""
    if is_sequence(authors):
        authors = [{"name": a} if isinstance(a, str) else a for a in authors]

    if not authors:
        issue_warning("missing", value=authors, field="authors")

    return authors

check_specific_types pydantic-validator ¤

check_specific_types(value: str) -> str
Source code in src/bioimageio/spec/generic/v0_2.py 
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@field_validator("type", mode="after")
@classmethod
def check_specific_types(cls, value: str) -> str:
    if value in KNOWN_SPECIFIC_RESOURCE_TYPES:
        raise ValueError(
            f"Use the {value} description instead of this generic description for"
            + f" your '{value}' resource."
        )

    return value

deprecated_spdx_license classmethod ¤

deprecated_spdx_license(
    value: Optional[
        Union[LicenseId, DeprecatedLicenseId, str]
    ],
)
Source code in src/bioimageio/spec/generic/v0_2.py 
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@field_validator("license", mode="after")
@classmethod
def deprecated_spdx_license(
    cls, value: Optional[Union[LicenseId, DeprecatedLicenseId, str]]
):
    if isinstance(value, LicenseId):
        pass
    elif value is None:
        issue_warning("missing", value=value, field="license")
    elif isinstance(value, DeprecatedLicenseId):
        issue_warning(
            "'{value}' is a deprecated license identifier.",
            value=value,
            field="license",
        )
    elif isinstance(value, str):
        issue_warning(
            "'{value}' is an unknown license identifier.",
            value=value,
            field="license",
        )
    else:
        assert_never(value)

    return value

get_package_content ¤

get_package_content() -> Dict[
    FileName, Union[FileDescr, BioimageioYamlContent]
]

Returns package content without creating the package.

Source code in src/bioimageio/spec/_internal/common_nodes.py 
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def get_package_content(
    self,
) -> Dict[FileName, Union[FileDescr, BioimageioYamlContent]]:
    """Returns package content without creating the package."""
    content: Dict[FileName, FileDescr] = {}
    with PackagingContext(
        bioimageio_yaml_file_name=BIOIMAGEIO_YAML,
        file_sources=content,
    ):
        rdf_content: BioimageioYamlContent = self.model_dump(
            mode="json", exclude_unset=True
        )

    _ = rdf_content.pop("rdf_source", None)

    return {**content, BIOIMAGEIO_YAML: rdf_content}

load classmethod ¤

load(
    data: BioimageioYamlContentView,
    context: Optional[ValidationContext] = None,
) -> Union[Self, InvalidDescr]

factory method to create a resource description object

Source code in src/bioimageio/spec/_internal/common_nodes.py 
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@classmethod
def load(
    cls,
    data: BioimageioYamlContentView,
    context: Optional[ValidationContext] = None,
) -> Union[Self, InvalidDescr]:
    """factory method to create a resource description object"""
    context = context or get_validation_context()
    if context.perform_io_checks:
        file_descrs = extract_file_descrs({k: v for k, v in data.items()})
        populate_cache(file_descrs)  # TODO: add progress bar

    with context.replace(log_warnings=context.warning_level <= INFO):
        rd, errors, val_warnings = cls._load_impl(deepcopy_yaml_value(data))

    if context.warning_level > INFO:
        all_warnings_context = context.replace(
            warning_level=INFO, log_warnings=False, raise_errors=False
        )
        # raise all validation warnings by reloading
        with all_warnings_context:
            _, _, val_warnings = cls._load_impl(deepcopy_yaml_value(data))

    format_status = "failed" if errors else "passed"
    rd.validation_summary.add_detail(
        ValidationDetail(
            errors=errors,
            name=(
                "bioimageio.spec format validation"
                f" {rd.type} {cls.implemented_format_version}"
            ),
            status=format_status,
            warnings=val_warnings,
        ),
        update_status=False,  # avoid updating status from 'valid-format' to 'passed', but ...
    )
    if format_status == "failed":
        # ... update status in case of failure
        rd.validation_summary.status = "failed"

    return rd

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self

Validate a pydantic model instance.

PARAMETER DESCRIPTION

obj ¤

The object to validate.

TYPE: Union[Any, Mapping[str, Any]]

strict ¤

Whether to raise an exception on invalid fields.

TYPE: Optional[bool] DEFAULT: None

from_attributes ¤

Whether to extract data from object attributes.

TYPE: Optional[bool] DEFAULT: None

context ¤

Additional context to pass to the validator.

TYPE: Union[ValidationContext, Mapping[str, Any], None] DEFAULT: None

RAISES DESCRIPTION
ValidationError

If the object failed validation.
RETURNS DESCRIPTION
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self:
    """Validate a pydantic model instance.

    Args:
        obj: The object to validate.
        strict: Whether to raise an exception on invalid fields.
        from_attributes: Whether to extract data from object attributes.
        context: Additional context to pass to the validator.

    Raises:
        ValidationError: If the object failed validation.

    Returns:
        The validated description instance.
    """
    __tracebackhide__ = True

    if context is None:
        context = get_validation_context()
    elif isinstance(context, collections.abc.Mapping):
        context = ValidationContext(**context)

    assert not isinstance(obj, collections.abc.Mapping) or is_kwargs(obj), obj

    with context:
        # use validation context as context manager for equal behavior of __init__ and model_validate
        return super().model_validate(
            obj, strict=strict, from_attributes=from_attributes
        )

package ¤

package(
    dest: Optional[
        Union[ZipFile, IO[bytes], Path, str]
    ] = None,
) -> ZipFile

package the described resource as a zip archive

PARAMETER DESCRIPTION

dest ¤

(path/bytes stream of) destination zipfile

TYPE: Optional[Union[ZipFile, IO[bytes], Path, str]] DEFAULT: None

Source code in src/bioimageio/spec/_internal/common_nodes.py 
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def package(
    self, dest: Optional[Union[ZipFile, IO[bytes], Path, str]] = None, /
) -> ZipFile:
    """package the described resource as a zip archive

    Args:
        dest: (path/bytes stream of) destination zipfile
    """
    if dest is None:
        dest = BytesIO()

    if isinstance(dest, ZipFile):
        zip = dest
        if "r" in zip.mode:
            raise ValueError(
                f"zip file {dest} opened in '{zip.mode}' mode,"
                + " but write access is needed for packaging."
            )
    else:
        zip = ZipFile(dest, mode="w")

    if zip.filename is None:
        zip.filename = (
            str(getattr(self, "id", getattr(self, "name", "bioimageio"))) + ".zip"
        )

    content = self.get_package_content()
    write_content_to_zip(content, zip)
    return zip

warn_about_tag_categories classmethod ¤

warn_about_tag_categories(
    value: List[str], info: ValidationInfo
) -> List[str]
Source code in src/bioimageio/spec/generic/v0_2.py 
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@as_warning
@field_validator("tags")
@classmethod
def warn_about_tag_categories(
    cls, value: List[str], info: ValidationInfo
) -> List[str]:
    categories = TAG_CATEGORIES.get(info.data["type"], {})
    missing_categories: List[Mapping[str, Sequence[str]]] = []
    for cat, entries in categories.items():
        if not any(e in value for e in entries):
            missing_categories.append({cat: entries})

    if missing_categories:
        raise ValueError(
            "Missing tags from bioimage.io categories: {missing_categories}"
        )

    return value

GenericDescrBase pydantic-model ¤

Bases: GenericModelDescrBase

Base for all resource descriptions except for the model descriptions

Show JSON schema: 
{
  "$defs": {
    "AttachmentsDescr": {
      "additionalProperties": true,
      "properties": {
        "files": {
          "description": "File attachments",
          "items": {
            "anyOf": [
              {
                "description": "A URL with the HTTP or HTTPS scheme.",
                "format": "uri",
                "maxLength": 2083,
                "minLength": 1,
                "title": "HttpUrl",
                "type": "string"
              },
              {
                "$ref": "#/$defs/RelativeFilePath"
              },
              {
                "format": "file-path",
                "title": "FilePath",
                "type": "string"
              }
            ]
          },
          "title": "Files",
          "type": "array"
        }
      },
      "title": "generic.v0_2.AttachmentsDescr",
      "type": "object"
    },
    "Author": {
      "additionalProperties": false,
      "properties": {
        "affiliation": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Affiliation",
          "title": "Affiliation"
        },
        "email": {
          "anyOf": [
            {
              "format": "email",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Email",
          "title": "Email"
        },
        "orcid": {
          "anyOf": [
            {
              "description": "An ORCID identifier, see https://orcid.org/",
              "title": "OrcidId",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "An [ORCID iD](https://support.orcid.org/hc/en-us/sections/360001495313-What-is-ORCID\n) in hyphenated groups of 4 digits, (and [valid](\nhttps://support.orcid.org/hc/en-us/articles/360006897674-Structure-of-the-ORCID-Identifier\n) as per ISO 7064 11,2.)",
          "examples": [
            "0000-0001-2345-6789"
          ],
          "title": "Orcid"
        },
        "name": {
          "title": "Name",
          "type": "string"
        },
        "github_user": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Github User"
        }
      },
      "required": [
        "name"
      ],
      "title": "generic.v0_2.Author",
      "type": "object"
    },
    "BadgeDescr": {
      "additionalProperties": false,
      "description": "A custom badge",
      "properties": {
        "label": {
          "description": "badge label to display on hover",
          "examples": [
            "Open in Colab"
          ],
          "title": "Label",
          "type": "string"
        },
        "icon": {
          "anyOf": [
            {
              "format": "file-path",
              "title": "FilePath",
              "type": "string"
            },
            {
              "$ref": "#/$defs/RelativeFilePath"
            },
            {
              "description": "A URL with the HTTP or HTTPS scheme.",
              "format": "uri",
              "maxLength": 2083,
              "minLength": 1,
              "title": "HttpUrl",
              "type": "string"
            },
            {
              "format": "uri",
              "maxLength": 2083,
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "badge icon (included in bioimage.io package if not a URL)",
          "examples": [
            "https://colab.research.google.com/assets/colab-badge.svg"
          ],
          "title": "Icon"
        },
        "url": {
          "description": "target URL",
          "examples": [
            "https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb"
          ],
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        }
      },
      "required": [
        "label",
        "url"
      ],
      "title": "generic.v0_2.BadgeDescr",
      "type": "object"
    },
    "CiteEntry": {
      "additionalProperties": false,
      "properties": {
        "text": {
          "description": "free text description",
          "title": "Text",
          "type": "string"
        },
        "doi": {
          "anyOf": [
            {
              "description": "A digital object identifier, see https://www.doi.org/",
              "pattern": "^10\\.[0-9]{4}.+$",
              "title": "Doi",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "A digital object identifier (DOI) is the prefered citation reference.\nSee https://www.doi.org/ for details. (alternatively specify `url`)",
          "title": "Doi"
        },
        "url": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "URL to cite (preferably specify a `doi` instead)",
          "title": "Url"
        }
      },
      "required": [
        "text"
      ],
      "title": "generic.v0_2.CiteEntry",
      "type": "object"
    },
    "Maintainer": {
      "additionalProperties": false,
      "properties": {
        "affiliation": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Affiliation",
          "title": "Affiliation"
        },
        "email": {
          "anyOf": [
            {
              "format": "email",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Email",
          "title": "Email"
        },
        "orcid": {
          "anyOf": [
            {
              "description": "An ORCID identifier, see https://orcid.org/",
              "title": "OrcidId",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "An [ORCID iD](https://support.orcid.org/hc/en-us/sections/360001495313-What-is-ORCID\n) in hyphenated groups of 4 digits, (and [valid](\nhttps://support.orcid.org/hc/en-us/articles/360006897674-Structure-of-the-ORCID-Identifier\n) as per ISO 7064 11,2.)",
          "examples": [
            "0000-0001-2345-6789"
          ],
          "title": "Orcid"
        },
        "name": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Name"
        },
        "github_user": {
          "title": "Github User",
          "type": "string"
        }
      },
      "required": [
        "github_user"
      ],
      "title": "generic.v0_2.Maintainer",
      "type": "object"
    },
    "RelativeFilePath": {
      "description": "A path relative to the `rdf.yaml` file (also if the RDF source is a URL).",
      "format": "path",
      "title": "RelativeFilePath",
      "type": "string"
    },
    "Uploader": {
      "additionalProperties": false,
      "properties": {
        "email": {
          "description": "Email",
          "format": "email",
          "title": "Email",
          "type": "string"
        },
        "name": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "name",
          "title": "Name"
        }
      },
      "required": [
        "email"
      ],
      "title": "generic.v0_2.Uploader",
      "type": "object"
    },
    "Version": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "integer"
        },
        {
          "type": "number"
        }
      ],
      "description": "wraps a packaging.version.Version instance for validation in pydantic models",
      "title": "Version"
    },
    "YamlValue": {
      "anyOf": [
        {
          "type": "boolean"
        },
        {
          "format": "date",
          "type": "string"
        },
        {
          "format": "date-time",
          "type": "string"
        },
        {
          "type": "integer"
        },
        {
          "type": "number"
        },
        {
          "type": "string"
        },
        {
          "items": {
            "$ref": "#/$defs/YamlValue"
          },
          "type": "array"
        },
        {
          "additionalProperties": {
            "$ref": "#/$defs/YamlValue"
          },
          "type": "object"
        },
        {
          "type": "null"
        }
      ]
    }
  },
  "additionalProperties": false,
  "description": "Base for all resource descriptions except for the model descriptions",
  "properties": {
    "name": {
      "description": "A human-friendly name of the resource description",
      "minLength": 1,
      "title": "Name",
      "type": "string"
    },
    "description": {
      "title": "Description",
      "type": "string"
    },
    "covers": {
      "description": "Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')",
      "examples": [
        [
          "cover.png"
        ]
      ],
      "items": {
        "anyOf": [
          {
            "description": "A URL with the HTTP or HTTPS scheme.",
            "format": "uri",
            "maxLength": 2083,
            "minLength": 1,
            "title": "HttpUrl",
            "type": "string"
          },
          {
            "$ref": "#/$defs/RelativeFilePath"
          },
          {
            "format": "file-path",
            "title": "FilePath",
            "type": "string"
          }
        ]
      },
      "title": "Covers",
      "type": "array"
    },
    "id_emoji": {
      "anyOf": [
        {
          "examples": [
            "\ud83e\udd88",
            "\ud83e\udda5"
          ],
          "maxLength": 1,
          "minLength": 1,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "UTF-8 emoji for display alongside the `id`.",
      "title": "Id Emoji"
    },
    "authors": {
      "description": "The authors are the creators of the RDF and the primary points of contact.",
      "items": {
        "$ref": "#/$defs/Author"
      },
      "title": "Authors",
      "type": "array"
    },
    "attachments": {
      "anyOf": [
        {
          "$ref": "#/$defs/AttachmentsDescr"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "file and other attachments"
    },
    "cite": {
      "description": "citations",
      "items": {
        "$ref": "#/$defs/CiteEntry"
      },
      "title": "Cite",
      "type": "array"
    },
    "config": {
      "additionalProperties": {
        "$ref": "#/$defs/YamlValue"
      },
      "description": "A field for custom configuration that can contain any keys not present in the RDF spec.\nThis means you should not store, for example, a github repo URL in `config` since we already have the\n`git_repo` field defined in the spec.\nKeys in `config` may be very specific to a tool or consumer software. To avoid conflicting definitions,\nit is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,\nfor example:\n```yaml\nconfig:\n    bioimageio:  # here is the domain name\n        my_custom_key: 3837283\n        another_key:\n            nested: value\n    imagej:       # config specific to ImageJ\n        macro_dir: path/to/macro/file\n```\nIf possible, please use [`snake_case`](https://en.wikipedia.org/wiki/Snake_case) for keys in `config`.\nYou may want to list linked files additionally under `attachments` to include them when packaging a resource\n(packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains\nan altered rdf.yaml file with local references to the downloaded files)",
      "examples": [
        {
          "bioimageio": {
            "another_key": {
              "nested": "value"
            },
            "my_custom_key": 3837283
          },
          "imagej": {
            "macro_dir": "path/to/macro/file"
          }
        }
      ],
      "title": "Config",
      "type": "object"
    },
    "download_url": {
      "anyOf": [
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "URL to download the resource from (deprecated)",
      "title": "Download Url"
    },
    "git_repo": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "A URL to the Git repository where the resource is being developed.",
      "examples": [
        "https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad"
      ],
      "title": "Git Repo"
    },
    "icon": {
      "anyOf": [
        {
          "maxLength": 2,
          "minLength": 1,
          "type": "string"
        },
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "$ref": "#/$defs/RelativeFilePath"
        },
        {
          "format": "file-path",
          "title": "FilePath",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "An icon for illustration",
      "title": "Icon"
    },
    "links": {
      "description": "IDs of other bioimage.io resources",
      "examples": [
        [
          "ilastik/ilastik",
          "deepimagej/deepimagej",
          "zero/notebook_u-net_3d_zerocostdl4mic"
        ]
      ],
      "items": {
        "type": "string"
      },
      "title": "Links",
      "type": "array"
    },
    "uploader": {
      "anyOf": [
        {
          "$ref": "#/$defs/Uploader"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The person who uploaded the model (e.g. to bioimage.io)"
    },
    "maintainers": {
      "description": "Maintainers of this resource.\nIf not specified `authors` are maintainers and at least some of them should specify their `github_user` name",
      "items": {
        "$ref": "#/$defs/Maintainer"
      },
      "title": "Maintainers",
      "type": "array"
    },
    "rdf_source": {
      "anyOf": [
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "$ref": "#/$defs/RelativeFilePath"
        },
        {
          "format": "file-path",
          "title": "FilePath",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from.\nDo not set this field in a YAML file.",
      "title": "Rdf Source"
    },
    "tags": {
      "description": "Associated tags",
      "examples": [
        [
          "unet2d",
          "pytorch",
          "nucleus",
          "segmentation",
          "dsb2018"
        ]
      ],
      "items": {
        "type": "string"
      },
      "title": "Tags",
      "type": "array"
    },
    "version": {
      "anyOf": [
        {
          "$ref": "#/$defs/Version"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The version of the resource following SemVer 2.0."
    },
    "version_number": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "version number (n-th published version, not the semantic version)",
      "title": "Version Number"
    },
    "format_version": {
      "const": "0.2.4",
      "description": "The format version of this resource specification\n(not the `version` of the resource description)\nWhen creating a new resource always use the latest micro/patch version described here.\nThe `format_version` is important for any consumer software to understand how to parse the fields.",
      "title": "Format Version",
      "type": "string"
    },
    "badges": {
      "description": "badges associated with this resource",
      "items": {
        "$ref": "#/$defs/BadgeDescr"
      },
      "title": "Badges",
      "type": "array"
    },
    "documentation": {
      "anyOf": [
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "$ref": "#/$defs/RelativeFilePath"
        },
        {
          "format": "file-path",
          "title": "FilePath",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is `README.md`. An `.md` suffix is mandatory.",
      "examples": [
        "https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md",
        "README.md"
      ],
      "title": "Documentation"
    },
    "license": {
      "anyOf": [
        {
          "enum": [
            "0BSD",
            "AAL",
            "Abstyles",
            "AdaCore-doc",
            "Adobe-2006",
            "Adobe-Display-PostScript",
            "Adobe-Glyph",
            "Adobe-Utopia",
            "ADSL",
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            "AGPL-1.0-or-later",
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            "AMPAS",
            "ANTLR-PD",
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            "BSD-2-Clause-Views",
            "BSD-3-Clause",
            "BSD-3-Clause-acpica",
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            "copyleft-next-0.3.0",
            "copyleft-next-0.3.1",
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            "Cronyx",
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            "Cube",
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            "Eurosym",
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            "FreeBSD-DOC",
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            "FSFAP-no-warranty-disclaimer",
            "FSFUL",
            "FSFULLR",
            "FSFULLRWD",
            "FTL",
            "Furuseth",
            "fwlw",
            "GCR-docs",
            "GD",
            "GFDL-1.1-invariants-only",
            "GFDL-1.1-invariants-or-later",
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            "GFDL-1.1-no-invariants-or-later",
            "GFDL-1.1-only",
            "GFDL-1.1-or-later",
            "GFDL-1.2-invariants-only",
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            "GFDL-1.2-no-invariants-or-later",
            "GFDL-1.2-only",
            "GFDL-1.2-or-later",
            "GFDL-1.3-invariants-only",
            "GFDL-1.3-invariants-or-later",
            "GFDL-1.3-no-invariants-only",
            "GFDL-1.3-no-invariants-or-later",
            "GFDL-1.3-only",
            "GFDL-1.3-or-later",
            "Giftware",
            "GL2PS",
            "Glide",
            "Glulxe",
            "GLWTPL",
            "gnuplot",
            "GPL-1.0-only",
            "GPL-1.0-or-later",
            "GPL-2.0-only",
            "GPL-2.0-or-later",
            "GPL-3.0-only",
            "GPL-3.0-or-later",
            "Graphics-Gems",
            "gSOAP-1.3b",
            "gtkbook",
            "HaskellReport",
            "hdparm",
            "Hippocratic-2.1",
            "HP-1986",
            "HP-1989",
            "HPND",
            "HPND-DEC",
            "HPND-doc",
            "HPND-doc-sell",
            "HPND-export-US",
            "HPND-export-US-modify",
            "HPND-Fenneberg-Livingston",
            "HPND-INRIA-IMAG",
            "HPND-Kevlin-Henney",
            "HPND-Markus-Kuhn",
            "HPND-MIT-disclaimer",
            "HPND-Pbmplus",
            "HPND-sell-MIT-disclaimer-xserver",
            "HPND-sell-regexpr",
            "HPND-sell-variant",
            "HPND-sell-variant-MIT-disclaimer",
            "HPND-UC",
            "HTMLTIDY",
            "IBM-pibs",
            "ICU",
            "IEC-Code-Components-EULA",
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            "IJG-short",
            "ImageMagick",
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            "Imlib2",
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            "ISC-Veillard",
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            "Latex2e-translated-notice",
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            "LGPL-2.1-only",
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            "Linux-man-pages-1-para",
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            "Linux-man-pages-copyleft-2-para",
            "Linux-man-pages-copyleft-var",
            "Linux-OpenIB",
            "LOOP",
            "LPD-document",
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            "radvd",
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            "W3C",
            "W3C-19980720",
            "W3C-20150513",
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            "Watcom-1.0",
            "Widget-Workshop",
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            "Zeeff",
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            "Zimbra-1.3",
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            "Zlib",
            "zlib-acknowledgement",
            "ZPL-1.1",
            "ZPL-2.0",
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          ],
          "title": "LicenseId",
          "type": "string"
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        {
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            "bzip2-1.0.5",
            "eCos-2.0",
            "GFDL-1.1",
            "GFDL-1.2",
            "GFDL-1.3",
            "GPL-1.0",
            "GPL-1.0+",
            "GPL-2.0",
            "GPL-2.0+",
            "GPL-2.0-with-autoconf-exception",
            "GPL-2.0-with-bison-exception",
            "GPL-2.0-with-classpath-exception",
            "GPL-2.0-with-font-exception",
            "GPL-2.0-with-GCC-exception",
            "GPL-3.0",
            "GPL-3.0+",
            "GPL-3.0-with-autoconf-exception",
            "GPL-3.0-with-GCC-exception",
            "LGPL-2.0",
            "LGPL-2.0+",
            "LGPL-2.1",
            "LGPL-2.1+",
            "LGPL-3.0",
            "LGPL-3.0+",
            "Nunit",
            "StandardML-NJ",
            "wxWindows"
          ],
          "title": "DeprecatedLicenseId",
          "type": "string"
        },
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "A [SPDX license identifier](https://spdx.org/licenses/).\nWe do not support custom license beyond the SPDX license list, if you need that please\n[open a GitHub issue](https://github.com/bioimage-io/spec-bioimage-io/issues/new/choose\n) to discuss your intentions with the community.",
      "examples": [
        "CC0-1.0",
        "MIT",
        "BSD-2-Clause"
      ],
      "title": "License"
    }
  },
  "required": [
    "name",
    "description",
    "format_version"
  ],
  "title": "generic.v0_2.GenericDescrBase",
  "type": "object"
}

Fields:

attachments pydantic-field ¤

attachments: Optional[AttachmentsDescr] = None

file and other attachments

authors pydantic-field ¤

authors: List[Author]

The authors are the creators of the RDF and the primary points of contact.

badges pydantic-field ¤

badges: List[BadgeDescr]

badges associated with this resource

cite pydantic-field ¤

cite: List[CiteEntry]

citations

config pydantic-field ¤

config: Dict[str, YamlValue]

A field for custom configuration that can contain any keys not present in the RDF spec. This means you should not store, for example, a github repo URL in config since we already have the git_repo field defined in the spec. Keys in config may be very specific to a tool or consumer software. To avoid conflicting definitions, it is recommended to wrap added configuration into a sub-field named with the specific domain or tool name, for example: 

config:
    bioimageio:  # here is the domain name
        my_custom_key: 3837283
        another_key:
            nested: value
    imagej:       # config specific to ImageJ
        macro_dir: path/to/macro/file
If possible, please use snake_case for keys in config. You may want to list linked files additionally under attachments to include them when packaging a resource (packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains an altered rdf.yaml file with local references to the downloaded files)

covers pydantic-field ¤

covers: List[FileSource_cover]

Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.

description pydantic-field ¤

description: str

documentation pydantic-field ¤

documentation: Optional[FileSource] = None

URL or relative path to a markdown file with additional documentation. The recommended documentation file name is README.md. An .md suffix is mandatory.

download_url pydantic-field ¤

download_url: Optional[HttpUrl] = None

URL to download the resource from (deprecated)

file_name property ¤

file_name: Optional[FileName]

File name of the bioimageio.yaml file the description was loaded from.

format_version pydantic-field ¤

format_version: Literal['0.2.4'] = '0.2.4'

git_repo pydantic-field ¤

git_repo: Optional[str] = None

A URL to the Git repository where the resource is being developed.

icon pydantic-field ¤

icon: Union[str, FileSource, None] = None

An icon for illustration

id_emoji pydantic-field ¤

id_emoji: Optional[str] = None

UTF-8 emoji for display alongside the id.

implemented_format_version class-attribute ¤

implemented_format_version: Literal['0.2.4'] = '0.2.4'

implemented_format_version_tuple class-attribute ¤

implemented_format_version_tuple: Tuple[int, int, int]

license pydantic-field ¤

license: Union[
    LicenseId, DeprecatedLicenseId, str, None
] = None

A SPDX license identifier. We do not support custom license beyond the SPDX license list, if you need that please open a GitHub issue to discuss your intentions with the community.

links: List[str]

IDs of other bioimage.io resources

maintainers pydantic-field ¤

maintainers: List[Maintainer]

Maintainers of this resource. If not specified authors are maintainers and at least some of them should specify their github_user name

name pydantic-field ¤

name: NotEmpty[str]

A human-friendly name of the resource description

rdf_source pydantic-field ¤

rdf_source: Optional[FileSource] = None

Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from. Do not set this field in a YAML file.

root property ¤

root: Union[RootHttpUrl, DirectoryPath, ZipFile]

The URL/Path prefix to resolve any relative paths with.

tags pydantic-field ¤

tags: List[str]

Associated tags

uploader pydantic-field ¤

uploader: Optional[Uploader] = None

The person who uploaded the model (e.g. to bioimage.io)

validation_summary property ¤

validation_summary: ValidationSummary

version pydantic-field ¤

version: Optional[Version] = None

The version of the resource following SemVer 2.0.

version_number pydantic-field ¤

version_number: Optional[int] = None

version number (n-th published version, not the semantic version)

__pydantic_init_subclass__ classmethod ¤

__pydantic_init_subclass__(**kwargs: Any)
Source code in src/bioimageio/spec/_internal/common_nodes.py 
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@classmethod
def __pydantic_init_subclass__(cls, **kwargs: Any):
    super().__pydantic_init_subclass__(**kwargs)
    # set classvar implemented_format_version_tuple
    if "format_version" in cls.model_fields:
        if "." not in cls.implemented_format_version:
            cls.implemented_format_version_tuple = (0, 0, 0)
        else:
            fv_tuple = get_format_version_tuple(cls.implemented_format_version)
            assert fv_tuple is not None, (
                f"failed to cast '{cls.implemented_format_version}' to tuple"
            )
            cls.implemented_format_version_tuple = fv_tuple

accept_author_strings classmethod ¤

accept_author_strings(
    authors: Union[Any, Sequence[Any]],
) -> Any

we unofficially accept strings as author entries

Source code in src/bioimageio/spec/generic/v0_2.py 
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@field_validator("authors", mode="before")
@classmethod
def accept_author_strings(cls, authors: Union[Any, Sequence[Any]]) -> Any:
    """we unofficially accept strings as author entries"""
    if is_sequence(authors):
        authors = [{"name": a} if isinstance(a, str) else a for a in authors]

    if not authors:
        issue_warning("missing", value=authors, field="authors")

    return authors

deprecated_spdx_license classmethod ¤

deprecated_spdx_license(
    value: Optional[
        Union[LicenseId, DeprecatedLicenseId, str]
    ],
)
Source code in src/bioimageio/spec/generic/v0_2.py 
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@field_validator("license", mode="after")
@classmethod
def deprecated_spdx_license(
    cls, value: Optional[Union[LicenseId, DeprecatedLicenseId, str]]
):
    if isinstance(value, LicenseId):
        pass
    elif value is None:
        issue_warning("missing", value=value, field="license")
    elif isinstance(value, DeprecatedLicenseId):
        issue_warning(
            "'{value}' is a deprecated license identifier.",
            value=value,
            field="license",
        )
    elif isinstance(value, str):
        issue_warning(
            "'{value}' is an unknown license identifier.",
            value=value,
            field="license",
        )
    else:
        assert_never(value)

    return value

get_package_content ¤

get_package_content() -> Dict[
    FileName, Union[FileDescr, BioimageioYamlContent]
]

Returns package content without creating the package.

Source code in src/bioimageio/spec/_internal/common_nodes.py 
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def get_package_content(
    self,
) -> Dict[FileName, Union[FileDescr, BioimageioYamlContent]]:
    """Returns package content without creating the package."""
    content: Dict[FileName, FileDescr] = {}
    with PackagingContext(
        bioimageio_yaml_file_name=BIOIMAGEIO_YAML,
        file_sources=content,
    ):
        rdf_content: BioimageioYamlContent = self.model_dump(
            mode="json", exclude_unset=True
        )

    _ = rdf_content.pop("rdf_source", None)

    return {**content, BIOIMAGEIO_YAML: rdf_content}

load classmethod ¤

load(
    data: BioimageioYamlContentView,
    context: Optional[ValidationContext] = None,
) -> Union[Self, InvalidDescr]

factory method to create a resource description object

Source code in src/bioimageio/spec/_internal/common_nodes.py 
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@classmethod
def load(
    cls,
    data: BioimageioYamlContentView,
    context: Optional[ValidationContext] = None,
) -> Union[Self, InvalidDescr]:
    """factory method to create a resource description object"""
    context = context or get_validation_context()
    if context.perform_io_checks:
        file_descrs = extract_file_descrs({k: v for k, v in data.items()})
        populate_cache(file_descrs)  # TODO: add progress bar

    with context.replace(log_warnings=context.warning_level <= INFO):
        rd, errors, val_warnings = cls._load_impl(deepcopy_yaml_value(data))

    if context.warning_level > INFO:
        all_warnings_context = context.replace(
            warning_level=INFO, log_warnings=False, raise_errors=False
        )
        # raise all validation warnings by reloading
        with all_warnings_context:
            _, _, val_warnings = cls._load_impl(deepcopy_yaml_value(data))

    format_status = "failed" if errors else "passed"
    rd.validation_summary.add_detail(
        ValidationDetail(
            errors=errors,
            name=(
                "bioimageio.spec format validation"
                f" {rd.type} {cls.implemented_format_version}"
            ),
            status=format_status,
            warnings=val_warnings,
        ),
        update_status=False,  # avoid updating status from 'valid-format' to 'passed', but ...
    )
    if format_status == "failed":
        # ... update status in case of failure
        rd.validation_summary.status = "failed"

    return rd

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self

Validate a pydantic model instance.

PARAMETER DESCRIPTION

obj ¤

The object to validate.

TYPE: Union[Any, Mapping[str, Any]]

strict ¤

Whether to raise an exception on invalid fields.

TYPE: Optional[bool] DEFAULT: None

from_attributes ¤

Whether to extract data from object attributes.

TYPE: Optional[bool] DEFAULT: None

context ¤

Additional context to pass to the validator.

TYPE: Union[ValidationContext, Mapping[str, Any], None] DEFAULT: None

RAISES DESCRIPTION
ValidationError

If the object failed validation.
RETURNS DESCRIPTION
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self:
    """Validate a pydantic model instance.

    Args:
        obj: The object to validate.
        strict: Whether to raise an exception on invalid fields.
        from_attributes: Whether to extract data from object attributes.
        context: Additional context to pass to the validator.

    Raises:
        ValidationError: If the object failed validation.

    Returns:
        The validated description instance.
    """
    __tracebackhide__ = True

    if context is None:
        context = get_validation_context()
    elif isinstance(context, collections.abc.Mapping):
        context = ValidationContext(**context)

    assert not isinstance(obj, collections.abc.Mapping) or is_kwargs(obj), obj

    with context:
        # use validation context as context manager for equal behavior of __init__ and model_validate
        return super().model_validate(
            obj, strict=strict, from_attributes=from_attributes
        )

package ¤

package(
    dest: Optional[
        Union[ZipFile, IO[bytes], Path, str]
    ] = None,
) -> ZipFile

package the described resource as a zip archive

PARAMETER DESCRIPTION

dest ¤

(path/bytes stream of) destination zipfile

TYPE: Optional[Union[ZipFile, IO[bytes], Path, str]] DEFAULT: None

Source code in src/bioimageio/spec/_internal/common_nodes.py 
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def package(
    self, dest: Optional[Union[ZipFile, IO[bytes], Path, str]] = None, /
) -> ZipFile:
    """package the described resource as a zip archive

    Args:
        dest: (path/bytes stream of) destination zipfile
    """
    if dest is None:
        dest = BytesIO()

    if isinstance(dest, ZipFile):
        zip = dest
        if "r" in zip.mode:
            raise ValueError(
                f"zip file {dest} opened in '{zip.mode}' mode,"
                + " but write access is needed for packaging."
            )
    else:
        zip = ZipFile(dest, mode="w")

    if zip.filename is None:
        zip.filename = (
            str(getattr(self, "id", getattr(self, "name", "bioimageio"))) + ".zip"
        )

    content = self.get_package_content()
    write_content_to_zip(content, zip)
    return zip

warn_about_tag_categories classmethod ¤

warn_about_tag_categories(
    value: List[str], info: ValidationInfo
) -> List[str]
Source code in src/bioimageio/spec/generic/v0_2.py 
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@as_warning
@field_validator("tags")
@classmethod
def warn_about_tag_categories(
    cls, value: List[str], info: ValidationInfo
) -> List[str]:
    categories = TAG_CATEGORIES.get(info.data["type"], {})
    missing_categories: List[Mapping[str, Sequence[str]]] = []
    for cat, entries in categories.items():
        if not any(e in value for e in entries):
            missing_categories.append({cat: entries})

    if missing_categories:
        raise ValueError(
            "Missing tags from bioimage.io categories: {missing_categories}"
        )

    return value

GenericModelDescrBase pydantic-model ¤

Bases: ResourceDescrBase

Base for all resource descriptions including of model descriptions

Show JSON schema: 
{
  "$defs": {
    "AttachmentsDescr": {
      "additionalProperties": true,
      "properties": {
        "files": {
          "description": "File attachments",
          "items": {
            "anyOf": [
              {
                "description": "A URL with the HTTP or HTTPS scheme.",
                "format": "uri",
                "maxLength": 2083,
                "minLength": 1,
                "title": "HttpUrl",
                "type": "string"
              },
              {
                "$ref": "#/$defs/RelativeFilePath"
              },
              {
                "format": "file-path",
                "title": "FilePath",
                "type": "string"
              }
            ]
          },
          "title": "Files",
          "type": "array"
        }
      },
      "title": "generic.v0_2.AttachmentsDescr",
      "type": "object"
    },
    "Author": {
      "additionalProperties": false,
      "properties": {
        "affiliation": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Affiliation",
          "title": "Affiliation"
        },
        "email": {
          "anyOf": [
            {
              "format": "email",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Email",
          "title": "Email"
        },
        "orcid": {
          "anyOf": [
            {
              "description": "An ORCID identifier, see https://orcid.org/",
              "title": "OrcidId",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "An [ORCID iD](https://support.orcid.org/hc/en-us/sections/360001495313-What-is-ORCID\n) in hyphenated groups of 4 digits, (and [valid](\nhttps://support.orcid.org/hc/en-us/articles/360006897674-Structure-of-the-ORCID-Identifier\n) as per ISO 7064 11,2.)",
          "examples": [
            "0000-0001-2345-6789"
          ],
          "title": "Orcid"
        },
        "name": {
          "title": "Name",
          "type": "string"
        },
        "github_user": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Github User"
        }
      },
      "required": [
        "name"
      ],
      "title": "generic.v0_2.Author",
      "type": "object"
    },
    "CiteEntry": {
      "additionalProperties": false,
      "properties": {
        "text": {
          "description": "free text description",
          "title": "Text",
          "type": "string"
        },
        "doi": {
          "anyOf": [
            {
              "description": "A digital object identifier, see https://www.doi.org/",
              "pattern": "^10\\.[0-9]{4}.+$",
              "title": "Doi",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "A digital object identifier (DOI) is the prefered citation reference.\nSee https://www.doi.org/ for details. (alternatively specify `url`)",
          "title": "Doi"
        },
        "url": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "URL to cite (preferably specify a `doi` instead)",
          "title": "Url"
        }
      },
      "required": [
        "text"
      ],
      "title": "generic.v0_2.CiteEntry",
      "type": "object"
    },
    "Maintainer": {
      "additionalProperties": false,
      "properties": {
        "affiliation": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Affiliation",
          "title": "Affiliation"
        },
        "email": {
          "anyOf": [
            {
              "format": "email",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Email",
          "title": "Email"
        },
        "orcid": {
          "anyOf": [
            {
              "description": "An ORCID identifier, see https://orcid.org/",
              "title": "OrcidId",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "An [ORCID iD](https://support.orcid.org/hc/en-us/sections/360001495313-What-is-ORCID\n) in hyphenated groups of 4 digits, (and [valid](\nhttps://support.orcid.org/hc/en-us/articles/360006897674-Structure-of-the-ORCID-Identifier\n) as per ISO 7064 11,2.)",
          "examples": [
            "0000-0001-2345-6789"
          ],
          "title": "Orcid"
        },
        "name": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Name"
        },
        "github_user": {
          "title": "Github User",
          "type": "string"
        }
      },
      "required": [
        "github_user"
      ],
      "title": "generic.v0_2.Maintainer",
      "type": "object"
    },
    "RelativeFilePath": {
      "description": "A path relative to the `rdf.yaml` file (also if the RDF source is a URL).",
      "format": "path",
      "title": "RelativeFilePath",
      "type": "string"
    },
    "Uploader": {
      "additionalProperties": false,
      "properties": {
        "email": {
          "description": "Email",
          "format": "email",
          "title": "Email",
          "type": "string"
        },
        "name": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "name",
          "title": "Name"
        }
      },
      "required": [
        "email"
      ],
      "title": "generic.v0_2.Uploader",
      "type": "object"
    },
    "Version": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "integer"
        },
        {
          "type": "number"
        }
      ],
      "description": "wraps a packaging.version.Version instance for validation in pydantic models",
      "title": "Version"
    },
    "YamlValue": {
      "anyOf": [
        {
          "type": "boolean"
        },
        {
          "format": "date",
          "type": "string"
        },
        {
          "format": "date-time",
          "type": "string"
        },
        {
          "type": "integer"
        },
        {
          "type": "number"
        },
        {
          "type": "string"
        },
        {
          "items": {
            "$ref": "#/$defs/YamlValue"
          },
          "type": "array"
        },
        {
          "additionalProperties": {
            "$ref": "#/$defs/YamlValue"
          },
          "type": "object"
        },
        {
          "type": "null"
        }
      ]
    }
  },
  "additionalProperties": false,
  "description": "Base for all resource descriptions including of model descriptions",
  "properties": {
    "name": {
      "description": "A human-friendly name of the resource description",
      "minLength": 1,
      "title": "Name",
      "type": "string"
    },
    "description": {
      "title": "Description",
      "type": "string"
    },
    "covers": {
      "description": "Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')",
      "examples": [
        [
          "cover.png"
        ]
      ],
      "items": {
        "anyOf": [
          {
            "description": "A URL with the HTTP or HTTPS scheme.",
            "format": "uri",
            "maxLength": 2083,
            "minLength": 1,
            "title": "HttpUrl",
            "type": "string"
          },
          {
            "$ref": "#/$defs/RelativeFilePath"
          },
          {
            "format": "file-path",
            "title": "FilePath",
            "type": "string"
          }
        ]
      },
      "title": "Covers",
      "type": "array"
    },
    "id_emoji": {
      "anyOf": [
        {
          "examples": [
            "\ud83e\udd88",
            "\ud83e\udda5"
          ],
          "maxLength": 1,
          "minLength": 1,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "UTF-8 emoji for display alongside the `id`.",
      "title": "Id Emoji"
    },
    "authors": {
      "description": "The authors are the creators of the RDF and the primary points of contact.",
      "items": {
        "$ref": "#/$defs/Author"
      },
      "title": "Authors",
      "type": "array"
    },
    "attachments": {
      "anyOf": [
        {
          "$ref": "#/$defs/AttachmentsDescr"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "file and other attachments"
    },
    "cite": {
      "description": "citations",
      "items": {
        "$ref": "#/$defs/CiteEntry"
      },
      "title": "Cite",
      "type": "array"
    },
    "config": {
      "additionalProperties": {
        "$ref": "#/$defs/YamlValue"
      },
      "description": "A field for custom configuration that can contain any keys not present in the RDF spec.\nThis means you should not store, for example, a github repo URL in `config` since we already have the\n`git_repo` field defined in the spec.\nKeys in `config` may be very specific to a tool or consumer software. To avoid conflicting definitions,\nit is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,\nfor example:\n```yaml\nconfig:\n    bioimageio:  # here is the domain name\n        my_custom_key: 3837283\n        another_key:\n            nested: value\n    imagej:       # config specific to ImageJ\n        macro_dir: path/to/macro/file\n```\nIf possible, please use [`snake_case`](https://en.wikipedia.org/wiki/Snake_case) for keys in `config`.\nYou may want to list linked files additionally under `attachments` to include them when packaging a resource\n(packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains\nan altered rdf.yaml file with local references to the downloaded files)",
      "examples": [
        {
          "bioimageio": {
            "another_key": {
              "nested": "value"
            },
            "my_custom_key": 3837283
          },
          "imagej": {
            "macro_dir": "path/to/macro/file"
          }
        }
      ],
      "title": "Config",
      "type": "object"
    },
    "download_url": {
      "anyOf": [
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "URL to download the resource from (deprecated)",
      "title": "Download Url"
    },
    "git_repo": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "A URL to the Git repository where the resource is being developed.",
      "examples": [
        "https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad"
      ],
      "title": "Git Repo"
    },
    "icon": {
      "anyOf": [
        {
          "maxLength": 2,
          "minLength": 1,
          "type": "string"
        },
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "$ref": "#/$defs/RelativeFilePath"
        },
        {
          "format": "file-path",
          "title": "FilePath",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "An icon for illustration",
      "title": "Icon"
    },
    "links": {
      "description": "IDs of other bioimage.io resources",
      "examples": [
        [
          "ilastik/ilastik",
          "deepimagej/deepimagej",
          "zero/notebook_u-net_3d_zerocostdl4mic"
        ]
      ],
      "items": {
        "type": "string"
      },
      "title": "Links",
      "type": "array"
    },
    "uploader": {
      "anyOf": [
        {
          "$ref": "#/$defs/Uploader"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The person who uploaded the model (e.g. to bioimage.io)"
    },
    "maintainers": {
      "description": "Maintainers of this resource.\nIf not specified `authors` are maintainers and at least some of them should specify their `github_user` name",
      "items": {
        "$ref": "#/$defs/Maintainer"
      },
      "title": "Maintainers",
      "type": "array"
    },
    "rdf_source": {
      "anyOf": [
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "$ref": "#/$defs/RelativeFilePath"
        },
        {
          "format": "file-path",
          "title": "FilePath",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from.\nDo not set this field in a YAML file.",
      "title": "Rdf Source"
    },
    "tags": {
      "description": "Associated tags",
      "examples": [
        [
          "unet2d",
          "pytorch",
          "nucleus",
          "segmentation",
          "dsb2018"
        ]
      ],
      "items": {
        "type": "string"
      },
      "title": "Tags",
      "type": "array"
    },
    "version": {
      "anyOf": [
        {
          "$ref": "#/$defs/Version"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The version of the resource following SemVer 2.0."
    },
    "version_number": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "version number (n-th published version, not the semantic version)",
      "title": "Version Number"
    }
  },
  "required": [
    "name",
    "description"
  ],
  "title": "generic.v0_2.GenericModelDescrBase",
  "type": "object"
}

Fields:

attachments pydantic-field ¤

attachments: Optional[AttachmentsDescr] = None

file and other attachments

authors pydantic-field ¤

authors: List[Author]

The authors are the creators of the RDF and the primary points of contact.

cite pydantic-field ¤

cite: List[CiteEntry]

citations

config pydantic-field ¤

config: Dict[str, YamlValue]

A field for custom configuration that can contain any keys not present in the RDF spec. This means you should not store, for example, a github repo URL in config since we already have the git_repo field defined in the spec. Keys in config may be very specific to a tool or consumer software. To avoid conflicting definitions, it is recommended to wrap added configuration into a sub-field named with the specific domain or tool name, for example: 

config:
    bioimageio:  # here is the domain name
        my_custom_key: 3837283
        another_key:
            nested: value
    imagej:       # config specific to ImageJ
        macro_dir: path/to/macro/file
If possible, please use snake_case for keys in config. You may want to list linked files additionally under attachments to include them when packaging a resource (packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains an altered rdf.yaml file with local references to the downloaded files)

covers pydantic-field ¤

covers: List[FileSource_cover]

Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.

description pydantic-field ¤

description: str

download_url pydantic-field ¤

download_url: Optional[HttpUrl] = None

URL to download the resource from (deprecated)

file_name property ¤

file_name: Optional[FileName]

File name of the bioimageio.yaml file the description was loaded from.

git_repo pydantic-field ¤

git_repo: Optional[str] = None

A URL to the Git repository where the resource is being developed.

icon pydantic-field ¤

icon: Union[str, FileSource, None] = None

An icon for illustration

id_emoji pydantic-field ¤

id_emoji: Optional[str] = None

UTF-8 emoji for display alongside the id.

implemented_format_version_tuple class-attribute ¤

implemented_format_version_tuple: Tuple[int, int, int]

links: List[str]

IDs of other bioimage.io resources

maintainers pydantic-field ¤

maintainers: List[Maintainer]

Maintainers of this resource. If not specified authors are maintainers and at least some of them should specify their github_user name

name pydantic-field ¤

name: NotEmpty[str]

A human-friendly name of the resource description

rdf_source pydantic-field ¤

rdf_source: Optional[FileSource] = None

Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from. Do not set this field in a YAML file.

root property ¤

root: Union[RootHttpUrl, DirectoryPath, ZipFile]

The URL/Path prefix to resolve any relative paths with.

tags pydantic-field ¤

tags: List[str]

Associated tags

uploader pydantic-field ¤

uploader: Optional[Uploader] = None

The person who uploaded the model (e.g. to bioimage.io)

validation_summary property ¤

validation_summary: ValidationSummary

version pydantic-field ¤

version: Optional[Version] = None

The version of the resource following SemVer 2.0.

version_number pydantic-field ¤

version_number: Optional[int] = None

version number (n-th published version, not the semantic version)

__pydantic_init_subclass__ classmethod ¤

__pydantic_init_subclass__(**kwargs: Any)
Source code in src/bioimageio/spec/_internal/common_nodes.py 
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@classmethod
def __pydantic_init_subclass__(cls, **kwargs: Any):
    super().__pydantic_init_subclass__(**kwargs)
    # set classvar implemented_format_version_tuple
    if "format_version" in cls.model_fields:
        if "." not in cls.implemented_format_version:
            cls.implemented_format_version_tuple = (0, 0, 0)
        else:
            fv_tuple = get_format_version_tuple(cls.implemented_format_version)
            assert fv_tuple is not None, (
                f"failed to cast '{cls.implemented_format_version}' to tuple"
            )
            cls.implemented_format_version_tuple = fv_tuple

accept_author_strings classmethod ¤

accept_author_strings(
    authors: Union[Any, Sequence[Any]],
) -> Any

we unofficially accept strings as author entries

Source code in src/bioimageio/spec/generic/v0_2.py 
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@field_validator("authors", mode="before")
@classmethod
def accept_author_strings(cls, authors: Union[Any, Sequence[Any]]) -> Any:
    """we unofficially accept strings as author entries"""
    if is_sequence(authors):
        authors = [{"name": a} if isinstance(a, str) else a for a in authors]

    if not authors:
        issue_warning("missing", value=authors, field="authors")

    return authors

get_package_content ¤

get_package_content() -> Dict[
    FileName, Union[FileDescr, BioimageioYamlContent]
]

Returns package content without creating the package.

Source code in src/bioimageio/spec/_internal/common_nodes.py 
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def get_package_content(
    self,
) -> Dict[FileName, Union[FileDescr, BioimageioYamlContent]]:
    """Returns package content without creating the package."""
    content: Dict[FileName, FileDescr] = {}
    with PackagingContext(
        bioimageio_yaml_file_name=BIOIMAGEIO_YAML,
        file_sources=content,
    ):
        rdf_content: BioimageioYamlContent = self.model_dump(
            mode="json", exclude_unset=True
        )

    _ = rdf_content.pop("rdf_source", None)

    return {**content, BIOIMAGEIO_YAML: rdf_content}

load classmethod ¤

load(
    data: BioimageioYamlContentView,
    context: Optional[ValidationContext] = None,
) -> Union[Self, InvalidDescr]

factory method to create a resource description object

Source code in src/bioimageio/spec/_internal/common_nodes.py 
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@classmethod
def load(
    cls,
    data: BioimageioYamlContentView,
    context: Optional[ValidationContext] = None,
) -> Union[Self, InvalidDescr]:
    """factory method to create a resource description object"""
    context = context or get_validation_context()
    if context.perform_io_checks:
        file_descrs = extract_file_descrs({k: v for k, v in data.items()})
        populate_cache(file_descrs)  # TODO: add progress bar

    with context.replace(log_warnings=context.warning_level <= INFO):
        rd, errors, val_warnings = cls._load_impl(deepcopy_yaml_value(data))

    if context.warning_level > INFO:
        all_warnings_context = context.replace(
            warning_level=INFO, log_warnings=False, raise_errors=False
        )
        # raise all validation warnings by reloading
        with all_warnings_context:
            _, _, val_warnings = cls._load_impl(deepcopy_yaml_value(data))

    format_status = "failed" if errors else "passed"
    rd.validation_summary.add_detail(
        ValidationDetail(
            errors=errors,
            name=(
                "bioimageio.spec format validation"
                f" {rd.type} {cls.implemented_format_version}"
            ),
            status=format_status,
            warnings=val_warnings,
        ),
        update_status=False,  # avoid updating status from 'valid-format' to 'passed', but ...
    )
    if format_status == "failed":
        # ... update status in case of failure
        rd.validation_summary.status = "failed"

    return rd

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self

Validate a pydantic model instance.

PARAMETER DESCRIPTION

obj ¤

The object to validate.

TYPE: Union[Any, Mapping[str, Any]]

strict ¤

Whether to raise an exception on invalid fields.

TYPE: Optional[bool] DEFAULT: None

from_attributes ¤

Whether to extract data from object attributes.

TYPE: Optional[bool] DEFAULT: None

context ¤

Additional context to pass to the validator.

TYPE: Union[ValidationContext, Mapping[str, Any], None] DEFAULT: None

RAISES DESCRIPTION
ValidationError

If the object failed validation.
RETURNS DESCRIPTION
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self:
    """Validate a pydantic model instance.

    Args:
        obj: The object to validate.
        strict: Whether to raise an exception on invalid fields.
        from_attributes: Whether to extract data from object attributes.
        context: Additional context to pass to the validator.

    Raises:
        ValidationError: If the object failed validation.

    Returns:
        The validated description instance.
    """
    __tracebackhide__ = True

    if context is None:
        context = get_validation_context()
    elif isinstance(context, collections.abc.Mapping):
        context = ValidationContext(**context)

    assert not isinstance(obj, collections.abc.Mapping) or is_kwargs(obj), obj

    with context:
        # use validation context as context manager for equal behavior of __init__ and model_validate
        return super().model_validate(
            obj, strict=strict, from_attributes=from_attributes
        )

package ¤

package(
    dest: Optional[
        Union[ZipFile, IO[bytes], Path, str]
    ] = None,
) -> ZipFile

package the described resource as a zip archive

PARAMETER DESCRIPTION

dest ¤

(path/bytes stream of) destination zipfile

TYPE: Optional[Union[ZipFile, IO[bytes], Path, str]] DEFAULT: None

Source code in src/bioimageio/spec/_internal/common_nodes.py 
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def package(
    self, dest: Optional[Union[ZipFile, IO[bytes], Path, str]] = None, /
) -> ZipFile:
    """package the described resource as a zip archive

    Args:
        dest: (path/bytes stream of) destination zipfile
    """
    if dest is None:
        dest = BytesIO()

    if isinstance(dest, ZipFile):
        zip = dest
        if "r" in zip.mode:
            raise ValueError(
                f"zip file {dest} opened in '{zip.mode}' mode,"
                + " but write access is needed for packaging."
            )
    else:
        zip = ZipFile(dest, mode="w")

    if zip.filename is None:
        zip.filename = (
            str(getattr(self, "id", getattr(self, "name", "bioimageio"))) + ".zip"
        )

    content = self.get_package_content()
    write_content_to_zip(content, zip)
    return zip

warn_about_tag_categories classmethod ¤

warn_about_tag_categories(
    value: List[str], info: ValidationInfo
) -> List[str]
Source code in src/bioimageio/spec/generic/v0_2.py 
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@as_warning
@field_validator("tags")
@classmethod
def warn_about_tag_categories(
    cls, value: List[str], info: ValidationInfo
) -> List[str]:
    categories = TAG_CATEGORIES.get(info.data["type"], {})
    missing_categories: List[Mapping[str, Sequence[str]]] = []
    for cat, entries in categories.items():
        if not any(e in value for e in entries):
            missing_categories.append({cat: entries})

    if missing_categories:
        raise ValueError(
            "Missing tags from bioimage.io categories: {missing_categories}"
        )

    return value

HttpUrl ¤

Bases: RootHttpUrl


              flowchart TD
              bioimageio.spec.generic.v0_2.HttpUrl[HttpUrl]
              bioimageio.spec._internal.root_url.RootHttpUrl[RootHttpUrl]
              bioimageio.spec._internal.validated_string.ValidatedString[ValidatedString]

                              bioimageio.spec._internal.root_url.RootHttpUrl --> bioimageio.spec.generic.v0_2.HttpUrl
                                bioimageio.spec._internal.validated_string.ValidatedString --> bioimageio.spec._internal.root_url.RootHttpUrl
                



              click bioimageio.spec.generic.v0_2.HttpUrl href "" "bioimageio.spec.generic.v0_2.HttpUrl"
              click bioimageio.spec._internal.root_url.RootHttpUrl href "" "bioimageio.spec._internal.root_url.RootHttpUrl"
              click bioimageio.spec._internal.validated_string.ValidatedString href "" "bioimageio.spec._internal.validated_string.ValidatedString"

A URL with the HTTP or HTTPS scheme.

Returned by: Subclassed by: Used by:
METHOD DESCRIPTION
__get_pydantic_core_schema__
__get_pydantic_json_schema__
__new__
absolute

analog to absolute method of pathlib.
exists

True if URL is available
ATTRIBUTE DESCRIPTION
host

TYPE: Optional[str]

parent

TYPE: RootHttpUrl

parents

iterate over all URL parents (max 100)

TYPE: Iterable[RootHttpUrl]

path

TYPE: Optional[str]

root_model

TYPE: Type[RootModel[Any]]

scheme

TYPE: str

host property ¤

host: Optional[str]

parent property ¤

parent: RootHttpUrl

parents property ¤

parents: Iterable[RootHttpUrl]

iterate over all URL parents (max 100)

path property ¤

path: Optional[str]

root_model class-attribute ¤

root_model: Type[RootModel[Any]] = RootModel[
    pydantic.HttpUrl
]

scheme property ¤

scheme: str

__get_pydantic_core_schema__ classmethod ¤

__get_pydantic_core_schema__(
    source_type: Any, handler: GetCoreSchemaHandler
) -> CoreSchema
Source code in src/bioimageio/spec/_internal/validated_string.py 
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@classmethod
def __get_pydantic_core_schema__(
    cls, source_type: Any, handler: GetCoreSchemaHandler
) -> CoreSchema:
    return no_info_after_validator_function(cls, handler(str))

__get_pydantic_json_schema__ classmethod ¤

__get_pydantic_json_schema__(
    core_schema: CoreSchema, handler: GetJsonSchemaHandler
) -> JsonSchemaValue
Source code in src/bioimageio/spec/_internal/validated_string.py 
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@classmethod
def __get_pydantic_json_schema__(
    cls, core_schema: CoreSchema, handler: GetJsonSchemaHandler
) -> JsonSchemaValue:
    json_schema = cls.root_model.model_json_schema(mode=handler.mode)
    json_schema["title"] = cls.__name__.strip("_")
    if cls.__doc__:
        json_schema["description"] = cls.__doc__

    return json_schema

__new__ ¤

__new__(object: object)
Source code in src/bioimageio/spec/_internal/validated_string.py 
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def __new__(cls, object: object):
    _validated = cls.root_model.model_validate(object).root
    self = super().__new__(cls, _validated)
    self._validated = _validated
    return self._after_validator()

absolute ¤

absolute()

analog to absolute method of pathlib.

Source code in src/bioimageio/spec/_internal/root_url.py 
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def absolute(self):
    """analog to `absolute` method of pathlib."""
    return self

exists ¤

exists()

True if URL is available

Source code in src/bioimageio/spec/_internal/url.py 
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def exists(self):
    """True if URL is available"""
    if self._exists is None:
        ctxt = get_validation_context()
        try:
            with ctxt.replace(warning_level=warning_levels.WARNING):
                self._validated = _validate_url(self._validated)
        except Exception as e:
            if ctxt.log_warnings:
                logger.info(e)

            self._exists = False
        else:
            self._exists = True

    return self._exists

LicenseId ¤

Bases: ValidatedString


              flowchart TD
              bioimageio.spec.generic.v0_2.LicenseId[LicenseId]
              bioimageio.spec._internal.validated_string.ValidatedString[ValidatedString]

                              bioimageio.spec._internal.validated_string.ValidatedString --> bioimageio.spec.generic.v0_2.LicenseId
                


              click bioimageio.spec.generic.v0_2.LicenseId href "" "bioimageio.spec.generic.v0_2.LicenseId"
              click bioimageio.spec._internal.validated_string.ValidatedString href "" "bioimageio.spec._internal.validated_string.ValidatedString"
METHOD DESCRIPTION
__get_pydantic_core_schema__
__get_pydantic_json_schema__
__new__
ATTRIBUTE DESCRIPTION
root_model

TYPE: Type[RootModel[Any]]

root_model class-attribute ¤

root_model: Type[RootModel[Any]] = RootModel[
    LicenseIdLiteral
]

__get_pydantic_core_schema__ classmethod ¤

__get_pydantic_core_schema__(
    source_type: Any, handler: GetCoreSchemaHandler
) -> CoreSchema
Source code in src/bioimageio/spec/_internal/validated_string.py 
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@classmethod
def __get_pydantic_core_schema__(
    cls, source_type: Any, handler: GetCoreSchemaHandler
) -> CoreSchema:
    return no_info_after_validator_function(cls, handler(str))

__get_pydantic_json_schema__ classmethod ¤

__get_pydantic_json_schema__(
    core_schema: CoreSchema, handler: GetJsonSchemaHandler
) -> JsonSchemaValue
Source code in src/bioimageio/spec/_internal/validated_string.py 
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@classmethod
def __get_pydantic_json_schema__(
    cls, core_schema: CoreSchema, handler: GetJsonSchemaHandler
) -> JsonSchemaValue:
    json_schema = cls.root_model.model_json_schema(mode=handler.mode)
    json_schema["title"] = cls.__name__.strip("_")
    if cls.__doc__:
        json_schema["description"] = cls.__doc__

    return json_schema

__new__ ¤

__new__(object: object)
Source code in src/bioimageio/spec/_internal/validated_string.py 
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def __new__(cls, object: object):
    _validated = cls.root_model.model_validate(object).root
    self = super().__new__(cls, _validated)
    self._validated = _validated
    return self._after_validator()

LinkedResource pydantic-model ¤

Bases: Node

Reference to a bioimage.io resource

Show JSON schema: 
{
  "additionalProperties": false,
  "description": "Reference to a bioimage.io resource",
  "properties": {
    "id": {
      "description": "A valid resource `id` from the bioimage.io collection.",
      "minLength": 1,
      "title": "ResourceId",
      "type": "string"
    },
    "version_number": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "version number (n-th published version, not the semantic version) of linked resource",
      "title": "Version Number"
    }
  },
  "required": [
    "id"
  ],
  "title": "generic.v0_2.LinkedResource",
  "type": "object"
}

Fields:

id pydantic-field ¤

id: ResourceId

A valid resource id from the bioimage.io collection.

version_number pydantic-field ¤

version_number: Optional[int] = None

version number (n-th published version, not the semantic version) of linked resource

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self

Validate a pydantic model instance.

PARAMETER DESCRIPTION

obj ¤

The object to validate.

TYPE: Union[Any, Mapping[str, Any]]

strict ¤

Whether to raise an exception on invalid fields.

TYPE: Optional[bool] DEFAULT: None

from_attributes ¤

Whether to extract data from object attributes.

TYPE: Optional[bool] DEFAULT: None

context ¤

Additional context to pass to the validator.

TYPE: Union[ValidationContext, Mapping[str, Any], None] DEFAULT: None

RAISES DESCRIPTION
ValidationError

If the object failed validation.
RETURNS DESCRIPTION
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self:
    """Validate a pydantic model instance.

    Args:
        obj: The object to validate.
        strict: Whether to raise an exception on invalid fields.
        from_attributes: Whether to extract data from object attributes.
        context: Additional context to pass to the validator.

    Raises:
        ValidationError: If the object failed validation.

    Returns:
        The validated description instance.
    """
    __tracebackhide__ = True

    if context is None:
        context = get_validation_context()
    elif isinstance(context, collections.abc.Mapping):
        context = ValidationContext(**context)

    assert not isinstance(obj, collections.abc.Mapping) or is_kwargs(obj), obj

    with context:
        # use validation context as context manager for equal behavior of __init__ and model_validate
        return super().model_validate(
            obj, strict=strict, from_attributes=from_attributes
        )

Maintainer pydantic-model ¤

Bases: _Person

Show JSON schema: 
{
  "additionalProperties": false,
  "properties": {
    "affiliation": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Affiliation",
      "title": "Affiliation"
    },
    "email": {
      "anyOf": [
        {
          "format": "email",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Email",
      "title": "Email"
    },
    "orcid": {
      "anyOf": [
        {
          "description": "An ORCID identifier, see https://orcid.org/",
          "title": "OrcidId",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "An [ORCID iD](https://support.orcid.org/hc/en-us/sections/360001495313-What-is-ORCID\n) in hyphenated groups of 4 digits, (and [valid](\nhttps://support.orcid.org/hc/en-us/articles/360006897674-Structure-of-the-ORCID-Identifier\n) as per ISO 7064 11,2.)",
      "examples": [
        "0000-0001-2345-6789"
      ],
      "title": "Orcid"
    },
    "name": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Name"
    },
    "github_user": {
      "title": "Github User",
      "type": "string"
    }
  },
  "required": [
    "github_user"
  ],
  "title": "generic.v0_2.Maintainer",
  "type": "object"
}

Fields:

affiliation pydantic-field ¤

affiliation: Optional[str] = None

Affiliation

email pydantic-field ¤

email: Optional[EmailStr] = None

Email

github_user pydantic-field ¤

github_user: str

name pydantic-field ¤

name: Optional[str] = None

orcid pydantic-field ¤

orcid: Optional[OrcidId] = None

An ORCID iD in hyphenated groups of 4 digits, (and valid as per ISO 7064 11,2.)

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self

Validate a pydantic model instance.

PARAMETER DESCRIPTION

obj ¤

The object to validate.

TYPE: Union[Any, Mapping[str, Any]]

strict ¤

Whether to raise an exception on invalid fields.

TYPE: Optional[bool] DEFAULT: None

from_attributes ¤

Whether to extract data from object attributes.

TYPE: Optional[bool] DEFAULT: None

context ¤

Additional context to pass to the validator.

TYPE: Union[ValidationContext, Mapping[str, Any], None] DEFAULT: None

RAISES DESCRIPTION
ValidationError

If the object failed validation.
RETURNS DESCRIPTION
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self:
    """Validate a pydantic model instance.

    Args:
        obj: The object to validate.
        strict: Whether to raise an exception on invalid fields.
        from_attributes: Whether to extract data from object attributes.
        context: Additional context to pass to the validator.

    Raises:
        ValidationError: If the object failed validation.

    Returns:
        The validated description instance.
    """
    __tracebackhide__ = True

    if context is None:
        context = get_validation_context()
    elif isinstance(context, collections.abc.Mapping):
        context = ValidationContext(**context)

    assert not isinstance(obj, collections.abc.Mapping) or is_kwargs(obj), obj

    with context:
        # use validation context as context manager for equal behavior of __init__ and model_validate
        return super().model_validate(
            obj, strict=strict, from_attributes=from_attributes
        )

Node pydantic-model ¤

Bases: pydantic.BaseModel

Show JSON schema: 
{
  "additionalProperties": false,
  "properties": {},
  "title": "_internal.node.Node",
  "type": "object"
}

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self

Validate a pydantic model instance.

PARAMETER DESCRIPTION

obj ¤

The object to validate.

TYPE: Union[Any, Mapping[str, Any]]

strict ¤

Whether to raise an exception on invalid fields.

TYPE: Optional[bool] DEFAULT: None

from_attributes ¤

Whether to extract data from object attributes.

TYPE: Optional[bool] DEFAULT: None

context ¤

Additional context to pass to the validator.

TYPE: Union[ValidationContext, Mapping[str, Any], None] DEFAULT: None

RAISES DESCRIPTION
ValidationError

If the object failed validation.
RETURNS DESCRIPTION
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self:
    """Validate a pydantic model instance.

    Args:
        obj: The object to validate.
        strict: Whether to raise an exception on invalid fields.
        from_attributes: Whether to extract data from object attributes.
        context: Additional context to pass to the validator.

    Raises:
        ValidationError: If the object failed validation.

    Returns:
        The validated description instance.
    """
    __tracebackhide__ = True

    if context is None:
        context = get_validation_context()
    elif isinstance(context, collections.abc.Mapping):
        context = ValidationContext(**context)

    assert not isinstance(obj, collections.abc.Mapping) or is_kwargs(obj), obj

    with context:
        # use validation context as context manager for equal behavior of __init__ and model_validate
        return super().model_validate(
            obj, strict=strict, from_attributes=from_attributes
        )

OrcidId ¤

Bases: ValidatedString


              flowchart TD
              bioimageio.spec.generic.v0_2.OrcidId[OrcidId]
              bioimageio.spec._internal.validated_string.ValidatedString[ValidatedString]

                              bioimageio.spec._internal.validated_string.ValidatedString --> bioimageio.spec.generic.v0_2.OrcidId
                


              click bioimageio.spec.generic.v0_2.OrcidId href "" "bioimageio.spec.generic.v0_2.OrcidId"
              click bioimageio.spec._internal.validated_string.ValidatedString href "" "bioimageio.spec._internal.validated_string.ValidatedString"

An ORCID identifier, see https://orcid.org/

METHOD DESCRIPTION
__get_pydantic_core_schema__
__get_pydantic_json_schema__
__new__
ATTRIBUTE DESCRIPTION
root_model

TYPE: Type[RootModel[Any]]

root_model class-attribute ¤

root_model: Type[RootModel[Any]] = RootModel[str]

__get_pydantic_core_schema__ classmethod ¤

__get_pydantic_core_schema__(
    source_type: Any, handler: GetCoreSchemaHandler
) -> CoreSchema
Source code in src/bioimageio/spec/_internal/validated_string.py 
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@classmethod
def __get_pydantic_core_schema__(
    cls, source_type: Any, handler: GetCoreSchemaHandler
) -> CoreSchema:
    return no_info_after_validator_function(cls, handler(str))

__get_pydantic_json_schema__ classmethod ¤

__get_pydantic_json_schema__(
    core_schema: CoreSchema, handler: GetJsonSchemaHandler
) -> JsonSchemaValue
Source code in src/bioimageio/spec/_internal/validated_string.py 
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@classmethod
def __get_pydantic_json_schema__(
    cls, core_schema: CoreSchema, handler: GetJsonSchemaHandler
) -> JsonSchemaValue:
    json_schema = cls.root_model.model_json_schema(mode=handler.mode)
    json_schema["title"] = cls.__name__.strip("_")
    if cls.__doc__:
        json_schema["description"] = cls.__doc__

    return json_schema

__new__ ¤

__new__(object: object)
Source code in src/bioimageio/spec/_internal/validated_string.py 
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def __new__(cls, object: object):
    _validated = cls.root_model.model_validate(object).root
    self = super().__new__(cls, _validated)
    self._validated = _validated
    return self._after_validator()

RelativeFilePath ¤

Bases: RelativePathBase[Union[AbsoluteFilePath, HttpUrl, ZipPath]]


              flowchart TD
              bioimageio.spec.generic.v0_2.RelativeFilePath[RelativeFilePath]
              bioimageio.spec._internal.io.RelativePathBase[RelativePathBase]

                              bioimageio.spec._internal.io.RelativePathBase --> bioimageio.spec.generic.v0_2.RelativeFilePath
                


              click bioimageio.spec.generic.v0_2.RelativeFilePath href "" "bioimageio.spec.generic.v0_2.RelativeFilePath"
              click bioimageio.spec._internal.io.RelativePathBase href "" "bioimageio.spec._internal.io.RelativePathBase"

A path relative to the rdf.yaml file (also if the RDF source is a URL).

Used by:
METHOD DESCRIPTION
__repr__
__str__
absolute

get the absolute path/url
format
get_absolute
model_post_init

add validation @private
ATTRIBUTE DESCRIPTION
path

TYPE: PurePath

path property ¤

path: PurePath

__repr__ ¤

__repr__() -> str
Source code in src/bioimageio/spec/_internal/io.py 
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def __repr__(self) -> str:
    return f"RelativePath('{self}')"

__str__ ¤

__str__() -> str
Source code in src/bioimageio/spec/_internal/io.py 
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def __str__(self) -> str:
    return self.root.as_posix()

absolute ¤

absolute() -> AbsolutePathT

get the absolute path/url

(resolved at time of initialization with the root of the ValidationContext)

Source code in src/bioimageio/spec/_internal/io.py 
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def absolute(  # method not property analog to `pathlib.Path.absolute()`
    self,
) -> AbsolutePathT:
    """get the absolute path/url

    (resolved at time of initialization with the root of the ValidationContext)
    """
    return self._absolute

format ¤

format() -> str
Source code in src/bioimageio/spec/_internal/io.py 
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@model_serializer()
def format(self) -> str:
    return str(self)

get_absolute ¤

get_absolute(
    root: "RootHttpUrl | Path | AnyUrl | ZipFile",
) -> "AbsoluteFilePath | HttpUrl | ZipPath"
Source code in src/bioimageio/spec/_internal/io.py 
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def get_absolute(
    self, root: "RootHttpUrl | Path | AnyUrl | ZipFile"
) -> "AbsoluteFilePath | HttpUrl | ZipPath":
    absolute = self._get_absolute_impl(root)
    if (
        isinstance(absolute, Path)
        and (context := get_validation_context()).perform_io_checks
        and str(self.root) not in context.known_files
        and not absolute.is_file()
    ):
        raise ValueError(f"{absolute} does not point to an existing file")

    return absolute

model_post_init ¤

model_post_init(__context: Any) -> None

add validation @private

Source code in src/bioimageio/spec/_internal/io.py 
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def model_post_init(self, __context: Any) -> None:
    """add validation @private"""
    if not self.root.parts:  # an empty path can only be a directory
        raise ValueError(f"{self.root} is not a valid file path.")

    super().model_post_init(__context)

ResourceDescrBase pydantic-model ¤

Bases: NodeWithExplicitlySetFields, ABC, _ResourceDescrBaseAbstractFieldsProtocol

base class for all resource descriptions

Show JSON schema: 
{
  "additionalProperties": false,
  "description": "base class for all resource descriptions",
  "properties": {},
  "title": "_internal.common_nodes.ResourceDescrBase",
  "type": "object"
}

Fields:

file_name property ¤

file_name: Optional[FileName]

File name of the bioimageio.yaml file the description was loaded from.

implemented_format_version_tuple class-attribute ¤

implemented_format_version_tuple: Tuple[int, int, int]

root property ¤

root: Union[RootHttpUrl, DirectoryPath, ZipFile]

The URL/Path prefix to resolve any relative paths with.

validation_summary property ¤

validation_summary: ValidationSummary

__pydantic_init_subclass__ classmethod ¤

__pydantic_init_subclass__(**kwargs: Any)
Source code in src/bioimageio/spec/_internal/common_nodes.py 
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@classmethod
def __pydantic_init_subclass__(cls, **kwargs: Any):
    super().__pydantic_init_subclass__(**kwargs)
    # set classvar implemented_format_version_tuple
    if "format_version" in cls.model_fields:
        if "." not in cls.implemented_format_version:
            cls.implemented_format_version_tuple = (0, 0, 0)
        else:
            fv_tuple = get_format_version_tuple(cls.implemented_format_version)
            assert fv_tuple is not None, (
                f"failed to cast '{cls.implemented_format_version}' to tuple"
            )
            cls.implemented_format_version_tuple = fv_tuple

get_package_content ¤

get_package_content() -> Dict[
    FileName, Union[FileDescr, BioimageioYamlContent]
]

Returns package content without creating the package.

Source code in src/bioimageio/spec/_internal/common_nodes.py 
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def get_package_content(
    self,
) -> Dict[FileName, Union[FileDescr, BioimageioYamlContent]]:
    """Returns package content without creating the package."""
    content: Dict[FileName, FileDescr] = {}
    with PackagingContext(
        bioimageio_yaml_file_name=BIOIMAGEIO_YAML,
        file_sources=content,
    ):
        rdf_content: BioimageioYamlContent = self.model_dump(
            mode="json", exclude_unset=True
        )

    _ = rdf_content.pop("rdf_source", None)

    return {**content, BIOIMAGEIO_YAML: rdf_content}

load classmethod ¤

load(
    data: BioimageioYamlContentView,
    context: Optional[ValidationContext] = None,
) -> Union[Self, InvalidDescr]

factory method to create a resource description object

Source code in src/bioimageio/spec/_internal/common_nodes.py 
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@classmethod
def load(
    cls,
    data: BioimageioYamlContentView,
    context: Optional[ValidationContext] = None,
) -> Union[Self, InvalidDescr]:
    """factory method to create a resource description object"""
    context = context or get_validation_context()
    if context.perform_io_checks:
        file_descrs = extract_file_descrs({k: v for k, v in data.items()})
        populate_cache(file_descrs)  # TODO: add progress bar

    with context.replace(log_warnings=context.warning_level <= INFO):
        rd, errors, val_warnings = cls._load_impl(deepcopy_yaml_value(data))

    if context.warning_level > INFO:
        all_warnings_context = context.replace(
            warning_level=INFO, log_warnings=False, raise_errors=False
        )
        # raise all validation warnings by reloading
        with all_warnings_context:
            _, _, val_warnings = cls._load_impl(deepcopy_yaml_value(data))

    format_status = "failed" if errors else "passed"
    rd.validation_summary.add_detail(
        ValidationDetail(
            errors=errors,
            name=(
                "bioimageio.spec format validation"
                f" {rd.type} {cls.implemented_format_version}"
            ),
            status=format_status,
            warnings=val_warnings,
        ),
        update_status=False,  # avoid updating status from 'valid-format' to 'passed', but ...
    )
    if format_status == "failed":
        # ... update status in case of failure
        rd.validation_summary.status = "failed"

    return rd

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self

Validate a pydantic model instance.

PARAMETER DESCRIPTION

obj ¤

The object to validate.

TYPE: Union[Any, Mapping[str, Any]]

strict ¤

Whether to raise an exception on invalid fields.

TYPE: Optional[bool] DEFAULT: None

from_attributes ¤

Whether to extract data from object attributes.

TYPE: Optional[bool] DEFAULT: None

context ¤

Additional context to pass to the validator.

TYPE: Union[ValidationContext, Mapping[str, Any], None] DEFAULT: None

RAISES DESCRIPTION
ValidationError

If the object failed validation.
RETURNS DESCRIPTION
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self:
    """Validate a pydantic model instance.

    Args:
        obj: The object to validate.
        strict: Whether to raise an exception on invalid fields.
        from_attributes: Whether to extract data from object attributes.
        context: Additional context to pass to the validator.

    Raises:
        ValidationError: If the object failed validation.

    Returns:
        The validated description instance.
    """
    __tracebackhide__ = True

    if context is None:
        context = get_validation_context()
    elif isinstance(context, collections.abc.Mapping):
        context = ValidationContext(**context)

    assert not isinstance(obj, collections.abc.Mapping) or is_kwargs(obj), obj

    with context:
        # use validation context as context manager for equal behavior of __init__ and model_validate
        return super().model_validate(
            obj, strict=strict, from_attributes=from_attributes
        )

package ¤

package(
    dest: Optional[
        Union[ZipFile, IO[bytes], Path, str]
    ] = None,
) -> ZipFile

package the described resource as a zip archive

PARAMETER DESCRIPTION

dest ¤

(path/bytes stream of) destination zipfile

TYPE: Optional[Union[ZipFile, IO[bytes], Path, str]] DEFAULT: None

Source code in src/bioimageio/spec/_internal/common_nodes.py 
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def package(
    self, dest: Optional[Union[ZipFile, IO[bytes], Path, str]] = None, /
) -> ZipFile:
    """package the described resource as a zip archive

    Args:
        dest: (path/bytes stream of) destination zipfile
    """
    if dest is None:
        dest = BytesIO()

    if isinstance(dest, ZipFile):
        zip = dest
        if "r" in zip.mode:
            raise ValueError(
                f"zip file {dest} opened in '{zip.mode}' mode,"
                + " but write access is needed for packaging."
            )
    else:
        zip = ZipFile(dest, mode="w")

    if zip.filename is None:
        zip.filename = (
            str(getattr(self, "id", getattr(self, "name", "bioimageio"))) + ".zip"
        )

    content = self.get_package_content()
    write_content_to_zip(content, zip)
    return zip

ResourceId ¤

Bases: ValidatedString


              flowchart TD
              bioimageio.spec.generic.v0_2.ResourceId[ResourceId]
              bioimageio.spec._internal.validated_string.ValidatedString[ValidatedString]

                              bioimageio.spec._internal.validated_string.ValidatedString --> bioimageio.spec.generic.v0_2.ResourceId
                


              click bioimageio.spec.generic.v0_2.ResourceId href "" "bioimageio.spec.generic.v0_2.ResourceId"
              click bioimageio.spec._internal.validated_string.ValidatedString href "" "bioimageio.spec._internal.validated_string.ValidatedString"
Subclassed by:
METHOD DESCRIPTION
__get_pydantic_core_schema__
__get_pydantic_json_schema__
__new__
ATTRIBUTE DESCRIPTION
root_model

TYPE: Type[RootModel[Any]]

root_model class-attribute ¤

root_model: Type[RootModel[Any]] = RootModel[NotEmpty[str]]

__get_pydantic_core_schema__ classmethod ¤

__get_pydantic_core_schema__(
    source_type: Any, handler: GetCoreSchemaHandler
) -> CoreSchema
Source code in src/bioimageio/spec/_internal/validated_string.py 
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@classmethod
def __get_pydantic_core_schema__(
    cls, source_type: Any, handler: GetCoreSchemaHandler
) -> CoreSchema:
    return no_info_after_validator_function(cls, handler(str))

__get_pydantic_json_schema__ classmethod ¤

__get_pydantic_json_schema__(
    core_schema: CoreSchema, handler: GetJsonSchemaHandler
) -> JsonSchemaValue
Source code in src/bioimageio/spec/_internal/validated_string.py 
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@classmethod
def __get_pydantic_json_schema__(
    cls, core_schema: CoreSchema, handler: GetJsonSchemaHandler
) -> JsonSchemaValue:
    json_schema = cls.root_model.model_json_schema(mode=handler.mode)
    json_schema["title"] = cls.__name__.strip("_")
    if cls.__doc__:
        json_schema["description"] = cls.__doc__

    return json_schema

__new__ ¤

__new__(object: object)
Source code in src/bioimageio/spec/_internal/validated_string.py 
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def __new__(cls, object: object):
    _validated = cls.root_model.model_validate(object).root
    self = super().__new__(cls, _validated)
    self._validated = _validated
    return self._after_validator()

RestrictCharacters dataclass ¤

RestrictCharacters(alphabet: str)
METHOD DESCRIPTION
__get_pydantic_core_schema__
validate
ATTRIBUTE DESCRIPTION
alphabet

TYPE: str

alphabet instance-attribute ¤

alphabet: str

__get_pydantic_core_schema__ ¤

__get_pydantic_core_schema__(
    source: Type[Any], handler: GetCoreSchemaHandler
) -> CoreSchema
Source code in src/bioimageio/spec/_internal/validator_annotations.py 
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def __get_pydantic_core_schema__(
    self, source: Type[Any], handler: GetCoreSchemaHandler
) -> CoreSchema:
    if not self.alphabet:
        raise ValueError("Alphabet may not be empty")

    schema = handler(source)  # get the CoreSchema from the type / inner constraints
    if schema["type"] != "str" and not (
        schema["type"] == "function-after" and schema["schema"]["type"] == "str"
    ):
        raise TypeError("RestrictCharacters can only be applied to strings")

    return no_info_after_validator_function(
        self.validate,
        schema,
    )

validate ¤

validate(value: str) -> str
Source code in src/bioimageio/spec/_internal/validator_annotations.py 
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def validate(self, value: str) -> str:
    if any(c not in self.alphabet for c in value):
        raise ValueError(f"{value!r} is not restricted to {self.alphabet!r}")
    return value

Uploader pydantic-model ¤

Bases: Node

Show JSON schema: 
{
  "additionalProperties": false,
  "properties": {
    "email": {
      "description": "Email",
      "format": "email",
      "title": "Email",
      "type": "string"
    },
    "name": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "name",
      "title": "Name"
    }
  },
  "required": [
    "email"
  ],
  "title": "generic.v0_2.Uploader",
  "type": "object"
}

Fields:

email pydantic-field ¤

email: EmailStr

Email

name pydantic-field ¤

name: Optional[str] = None

name

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self

Validate a pydantic model instance.

PARAMETER DESCRIPTION

obj ¤

The object to validate.

TYPE: Union[Any, Mapping[str, Any]]

strict ¤

Whether to raise an exception on invalid fields.

TYPE: Optional[bool] DEFAULT: None

from_attributes ¤

Whether to extract data from object attributes.

TYPE: Optional[bool] DEFAULT: None

context ¤

Additional context to pass to the validator.

TYPE: Union[ValidationContext, Mapping[str, Any], None] DEFAULT: None

RAISES DESCRIPTION
ValidationError

If the object failed validation.
RETURNS DESCRIPTION
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self:
    """Validate a pydantic model instance.

    Args:
        obj: The object to validate.
        strict: Whether to raise an exception on invalid fields.
        from_attributes: Whether to extract data from object attributes.
        context: Additional context to pass to the validator.

    Raises:
        ValidationError: If the object failed validation.

    Returns:
        The validated description instance.
    """
    __tracebackhide__ = True

    if context is None:
        context = get_validation_context()
    elif isinstance(context, collections.abc.Mapping):
        context = ValidationContext(**context)

    assert not isinstance(obj, collections.abc.Mapping) or is_kwargs(obj), obj

    with context:
        # use validation context as context manager for equal behavior of __init__ and model_validate
        return super().model_validate(
            obj, strict=strict, from_attributes=from_attributes
        )

ValidatedString ¤

Bases: str


              flowchart TD
              bioimageio.spec.generic.v0_2.ValidatedString[ValidatedString]

              

              click bioimageio.spec.generic.v0_2.ValidatedString href "" "bioimageio.spec.generic.v0_2.ValidatedString"
Subclassed by:
METHOD DESCRIPTION
__get_pydantic_core_schema__
__get_pydantic_json_schema__
__new__
ATTRIBUTE DESCRIPTION
root_model

the pydantic root model to validate the string

TYPE: Type[RootModel[Any]]

root_model class-attribute ¤

root_model: Type[RootModel[Any]] = RootModel[str]

the pydantic root model to validate the string

__get_pydantic_core_schema__ classmethod ¤

__get_pydantic_core_schema__(
    source_type: Any, handler: GetCoreSchemaHandler
) -> CoreSchema
Source code in src/bioimageio/spec/_internal/validated_string.py 
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@classmethod
def __get_pydantic_core_schema__(
    cls, source_type: Any, handler: GetCoreSchemaHandler
) -> CoreSchema:
    return no_info_after_validator_function(cls, handler(str))

__get_pydantic_json_schema__ classmethod ¤

__get_pydantic_json_schema__(
    core_schema: CoreSchema, handler: GetJsonSchemaHandler
) -> JsonSchemaValue
Source code in src/bioimageio/spec/_internal/validated_string.py 
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@classmethod
def __get_pydantic_json_schema__(
    cls, core_schema: CoreSchema, handler: GetJsonSchemaHandler
) -> JsonSchemaValue:
    json_schema = cls.root_model.model_json_schema(mode=handler.mode)
    json_schema["title"] = cls.__name__.strip("_")
    if cls.__doc__:
        json_schema["description"] = cls.__doc__

    return json_schema

__new__ ¤

__new__(object: object)
Source code in src/bioimageio/spec/_internal/validated_string.py 
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def __new__(cls, object: object):
    _validated = cls.root_model.model_validate(object).root
    self = super().__new__(cls, _validated)
    self._validated = _validated
    return self._after_validator()

Version ¤

Bases: RootModel[Union[str, int, float]]


              flowchart TD
              bioimageio.spec.generic.v0_2.Version[Version]

              

              click bioimageio.spec.generic.v0_2.Version href "" "bioimageio.spec.generic.v0_2.Version"

wraps a packaging.version.Version instance for validation in pydantic models

METHOD DESCRIPTION
__eq__
__lt__
__str__
model_post_init

set _version attribute @private
ATTRIBUTE DESCRIPTION
base_version

The "base version" of the version.

TYPE: str

dev

The development number of the version.

TYPE: Optional[int]

epoch

The epoch of the version.

TYPE: int

is_devrelease

Whether this version is a development release.

TYPE: bool

is_postrelease

Whether this version is a post-release.

TYPE: bool

is_prerelease

Whether this version is a pre-release.

TYPE: bool

local

The local version segment of the version.

TYPE: Optional[str]

major

The first item of :attr:release or 0 if unavailable.

TYPE: int

micro

The third item of :attr:release or 0 if unavailable.

TYPE: int

minor

The second item of :attr:release or 0 if unavailable.

TYPE: int

post

The post-release number of the version.

TYPE: Optional[int]

pre

The pre-release segment of the version.

TYPE: Optional[Tuple[str, int]]

public

The public portion of the version.

TYPE: str

release

The components of the "release" segment of the version.

TYPE: Tuple[int, ...]

base_version property ¤

base_version: str

The "base version" of the version.

Version("1.2.3").base_version '1.2.3' Version("1.2.3+abc").base_version '1.2.3' Version("1!1.2.3+abc.dev1").base_version '1!1.2.3'

The "base version" is the public version of the project without any pre or post release markers.

dev property ¤

dev: Optional[int]

The development number of the version.

print(Version("1.2.3").dev) None Version("1.2.3.dev1").dev 1

epoch property ¤

epoch: int

The epoch of the version.

Version("2.0.0").epoch 0 Version("1!2.0.0").epoch 1

is_devrelease property ¤

is_devrelease: bool

Whether this version is a development release.

Version("1.2.3").is_devrelease False Version("1.2.3.dev1").is_devrelease True

is_postrelease property ¤

is_postrelease: bool

Whether this version is a post-release.

Version("1.2.3").is_postrelease False Version("1.2.3.post1").is_postrelease True

is_prerelease property ¤

is_prerelease: bool

Whether this version is a pre-release.

Version("1.2.3").is_prerelease False Version("1.2.3a1").is_prerelease True Version("1.2.3b1").is_prerelease True Version("1.2.3rc1").is_prerelease True Version("1.2.3dev1").is_prerelease True

local property ¤

local: Optional[str]

The local version segment of the version.

print(Version("1.2.3").local) None Version("1.2.3+abc").local 'abc'

major property ¤

major: int

The first item of :attr:release or 0 if unavailable.

Version("1.2.3").major 1

micro property ¤

micro: int

The third item of :attr:release or 0 if unavailable.

Version("1.2.3").micro 3 Version("1").micro 0

minor property ¤

minor: int

The second item of :attr:release or 0 if unavailable.

Version("1.2.3").minor 2 Version("1").minor 0

post property ¤

post: Optional[int]

The post-release number of the version.

print(Version("1.2.3").post) None Version("1.2.3.post1").post 1

pre property ¤

pre: Optional[Tuple[str, int]]

The pre-release segment of the version.

print(Version("1.2.3").pre) None Version("1.2.3a1").pre ('a', 1) Version("1.2.3b1").pre ('b', 1) Version("1.2.3rc1").pre ('rc', 1)

public property ¤

public: str

The public portion of the version.

Version("1.2.3").public '1.2.3' Version("1.2.3+abc").public '1.2.3' Version("1.2.3+abc.dev1").public '1.2.3'

release property ¤

release: Tuple[int, ...]

The components of the "release" segment of the version.

Version("1.2.3").release (1, 2, 3) Version("2.0.0").release (2, 0, 0) Version("1!2.0.0.post0").release (2, 0, 0)

Includes trailing zeroes but not the epoch or any pre-release / development / post-release suffixes.

__eq__ ¤

__eq__(other: Version)
Source code in src/bioimageio/spec/_internal/version_type.py 
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def __eq__(self, other: Version):
    return self._version == other._version

__lt__ ¤

__lt__(other: Version)
Source code in src/bioimageio/spec/_internal/version_type.py 
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def __lt__(self, other: Version):
    return self._version < other._version

__str__ ¤

__str__()
Source code in src/bioimageio/spec/_internal/version_type.py 
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def __str__(self):
    return str(self._version)

model_post_init ¤

model_post_init(__context: Any) -> None

set _version attribute @private

Source code in src/bioimageio/spec/_internal/version_type.py 
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def model_post_init(self, __context: Any) -> None:
    """set `_version` attribute @private"""
    self._version = packaging.version.Version(str(self.root))
    return super().model_post_init(__context)

WithSuffix dataclass ¤

WithSuffix(
    suffix: Union[LiteralString, Tuple[LiteralString, ...]],
    case_sensitive: bool,
)
Used by:
METHOD DESCRIPTION
__get_pydantic_core_schema__
validate
ATTRIBUTE DESCRIPTION
case_sensitive

TYPE: bool

suffix

TYPE: Union[LiteralString, Tuple[LiteralString, ...]]

case_sensitive instance-attribute ¤

case_sensitive: bool

suffix instance-attribute ¤

suffix: Union[LiteralString, Tuple[LiteralString, ...]]

__get_pydantic_core_schema__ ¤

__get_pydantic_core_schema__(
    source: Type[Any], handler: GetCoreSchemaHandler
)
Source code in src/bioimageio/spec/_internal/io.py 
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def __get_pydantic_core_schema__(
    self, source: Type[Any], handler: GetCoreSchemaHandler
):
    if not self.suffix:
        raise ValueError("suffix may not be empty")

    schema = handler(source)
    return core_schema.no_info_after_validator_function(
        self.validate,
        schema,
    )

validate ¤

validate(
    value: Union[FileSource, FileDescr],
) -> Union[FileSource, FileDescr]
Source code in src/bioimageio/spec/_internal/io.py 
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def validate(
    self, value: Union[FileSource, FileDescr]
) -> Union[FileSource, FileDescr]:
    return validate_suffix(value, self.suffix, case_sensitive=self.case_sensitive)

_Person pydantic-model ¤

Bases: Node

Show JSON schema: 
{
  "additionalProperties": false,
  "properties": {
    "affiliation": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Affiliation",
      "title": "Affiliation"
    },
    "email": {
      "anyOf": [
        {
          "format": "email",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Email",
      "title": "Email"
    },
    "orcid": {
      "anyOf": [
        {
          "description": "An ORCID identifier, see https://orcid.org/",
          "title": "OrcidId",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "An [ORCID iD](https://support.orcid.org/hc/en-us/sections/360001495313-What-is-ORCID\n) in hyphenated groups of 4 digits, (and [valid](\nhttps://support.orcid.org/hc/en-us/articles/360006897674-Structure-of-the-ORCID-Identifier\n) as per ISO 7064 11,2.)",
      "examples": [
        "0000-0001-2345-6789"
      ],
      "title": "Orcid"
    }
  },
  "title": "generic.v0_2._Person",
  "type": "object"
}

Fields:

affiliation pydantic-field ¤

affiliation: Optional[str] = None

Affiliation

email pydantic-field ¤

email: Optional[EmailStr] = None

Email

orcid pydantic-field ¤

orcid: Optional[OrcidId] = None

An ORCID iD in hyphenated groups of 4 digits, (and valid as per ISO 7064 11,2.)

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self

Validate a pydantic model instance.

PARAMETER DESCRIPTION

obj ¤

The object to validate.

TYPE: Union[Any, Mapping[str, Any]]

strict ¤

Whether to raise an exception on invalid fields.

TYPE: Optional[bool] DEFAULT: None

from_attributes ¤

Whether to extract data from object attributes.

TYPE: Optional[bool] DEFAULT: None

context ¤

Additional context to pass to the validator.

TYPE: Union[ValidationContext, Mapping[str, Any], None] DEFAULT: None

RAISES DESCRIPTION
ValidationError

If the object failed validation.
RETURNS DESCRIPTION
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: bool | None = None,
    by_name: bool | None = None,
) -> Self:
    """Validate a pydantic model instance.

    Args:
        obj: The object to validate.
        strict: Whether to raise an exception on invalid fields.
        from_attributes: Whether to extract data from object attributes.
        context: Additional context to pass to the validator.

    Raises:
        ValidationError: If the object failed validation.

    Returns:
        The validated description instance.
    """
    __tracebackhide__ = True

    if context is None:
        context = get_validation_context()
    elif isinstance(context, collections.abc.Mapping):
        context = ValidationContext(**context)

    assert not isinstance(obj, collections.abc.Mapping) or is_kwargs(obj), obj

    with context:
        # use validation context as context manager for equal behavior of __init__ and model_validate
        return super().model_validate(
            obj, strict=strict, from_attributes=from_attributes
        )

_convert_from_older_format ¤

_convert_from_older_format(
    data: BioimageioYamlContent,
) -> None

convert raw RDF data of an older format where possible

Source code in src/bioimageio/spec/generic/_v0_2_converter.py 
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def convert_from_older_format(data: BioimageioYamlContent) -> None:
    """convert raw RDF data of an older format where possible"""
    # check if we have future format version
    if "format_version" not in data:
        return

    fv = data["format_version"]
    if isinstance(fv, str) and tuple(map(int, fv.split(".")[:2])) > (0, 2):
        return

    # we unofficially accept strings as author entries
    authors = data.get("authors")
    if isinstance(authors, list):
        data["authors"] = [{"name": a} if isinstance(a, str) else a for a in authors]

    if data.get("format_version") in ("0.2.0", "0.2.1"):
        data["format_version"] = "0.2.2"

    if data.get("format_version") == "0.2.2":
        remove_slashes_from_names(data)
        data["format_version"] = "0.2.3"

    if data.get("format_version") == "0.2.3":
        if isinstance(config := data.get("config"), dict) and isinstance(
            bconfig := config.get("bioimageio"), dict
        ):
            if (nickname := bconfig.get("nickname")) is not None:
                data["id"] = nickname

            if (nickname_icon := bconfig.get("nickname_icon")) is not None:
                data["id_emoji"] = nickname_icon

        data["format_version"] = "0.2.4"

    remove_doi_prefix(data)
    remove_gh_prefix(data)

_remove_slashes ¤

_remove_slashes(s: str)
Source code in src/bioimageio/spec/generic/v0_2.py 
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def _remove_slashes(s: str):
    return s.replace("/", "").replace("\\", "")

as_warning ¤

as_warning(
    func: _V2Validator,
    *,
    mode: Literal[
        "after", "before", "plain", "wrap"
    ] = "after",
    severity: WarningSeverity = WARNING,
    msg: Optional[LiteralString] = None,
    msg_context: Optional[Dict[str, Any]] = None,
) -> ValidatorFunction

turn validation function into a no-op, based on warning level

Source code in src/bioimageio/spec/_internal/field_warning.py 
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def as_warning(
    func: "_V2Validator",
    *,
    mode: Literal["after", "before", "plain", "wrap"] = "after",
    severity: WarningSeverity = WARNING,
    msg: Optional[LiteralString] = None,
    msg_context: Optional[Dict[str, Any]] = None,
) -> ValidatorFunction:
    """turn validation function into a no-op, based on warning level"""

    def wrapper(value: Any, info: ValidationInfo) -> Any:
        try:
            call_validator_func(func, mode, value, info)
        except (AssertionError, ValueError) as e:
            issue_warning(
                msg or ",".join(e.args),
                field=info.field_name,
                log_depth=1,
                msg_context=msg_context,
                severity=severity,
                value=value,
            )

        return value

    return wrapper

is_sequence ¤

is_sequence(v: Any) -> TypeGuard[Sequence[Any]]

to avoid Sequence[Unknown]

Source code in src/bioimageio/spec/_internal/type_guards.py 
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def is_sequence(v: Any) -> TypeGuard[Sequence[Any]]:
    """to avoid Sequence[Unknown]"""
    return isinstance(v, collections.abc.Sequence)

issue_warning ¤

issue_warning(
    msg: LiteralString,
    *,
    value: Any,
    severity: WarningSeverity = WARNING,
    msg_context: Optional[Dict[str, Any]] = None,
    field: Optional[str] = None,
    log_depth: int = 1,
)
Source code in src/bioimageio/spec/_internal/field_warning.py 
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def issue_warning(
    msg: LiteralString,
    *,
    value: Any,
    severity: WarningSeverity = WARNING,
    msg_context: Optional[Dict[str, Any]] = None,
    field: Optional[str] = None,
    log_depth: int = 1,
):
    msg_context = {"value": value, "severity": severity, **(msg_context or {})}

    if severity >= (ctxt := get_validation_context()).warning_level:
        raise PydanticCustomError("warning", msg, msg_context)
    elif ctxt.log_warnings:
        log_msg = (field + ": " if field else "") + (msg.format(**msg_context))
        logger.opt(depth=log_depth).log(severity, log_msg)

warn ¤

warn(
    typ: Union[AnnotationMetaData, Any],
    msg: LiteralString,
    severity: WarningSeverity = WARNING,
)

treat a type or its annotation metadata as a warning condition

Source code in src/bioimageio/spec/_internal/field_warning.py 
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def warn(
    typ: Union[AnnotationMetaData, Any],
    msg: LiteralString,  # warning message, e.g. "'{value}' incompatible with {typ}
    severity: WarningSeverity = WARNING,
):
    """treat a type or its annotation metadata as a warning condition"""
    if isinstance(typ, get_args(AnnotationMetaData)):
        typ = Annotated[Any, typ]

    validator: TypeAdapter[Any] = TypeAdapter(typ)

    return AfterWarner(
        validator.validate_python, severity=severity, msg=msg, context={"typ": typ}
    )

wo_special_file_name ¤

wo_special_file_name(src: F) -> F
Source code in src/bioimageio/spec/_internal/io.py 
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def wo_special_file_name(src: F) -> F:
    if has_valid_bioimageio_yaml_name(src):
        raise ValueError(
            f"'{src}' not allowed here as its filename is reserved to identify"
            + f" '{BIOIMAGEIO_YAML}' (or equivalent) files."
        )

    return src