v0_3

Used by:

•  spec  GenericDescr
• API Reference The bioimage.io Format Specifications  generic
  •  GenericDescr
  •  GenericDescr_v0_3

CLASS	DESCRIPTION
Author
BadgeDescr	A custom badge
BioimageioConfig	bioimage.io internal metadata.
CiteEntry	A citation that should be referenced in work using this resource.
Config	A place to store additional metadata (often tool specific).
Converter
DeprecatedLicenseId
Doi	A digital object identifier, see https://www.doi.org/
FileDescr	A file description
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
LinkedResourceBase
Maintainer
Node
OrcidId	An ORCID identifier, see https://orcid.org/
Predicate
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
Sha256	A SHA-256 hash value
Uploader
ValidatedString
Version	wraps a packaging.version.Version instance for validation in pydantic models
WithSuffix
_AuthorConv
_Author_v0_2
_MaintainerConv
_Maintainer_v0_2

FUNCTION	DESCRIPTION
_has_no_slash
as_warning	turn validation function into a no-op, based on warning level
convert_from_older_format	convert raw RDF data of an older format where possible
is_dict	to avoid Dict[Unknown, Unknown]
is_yaml_value
issue_warning
validate_github_user
warn	treat a type or its annotation metadata as a warning condition

ATTRIBUTE	DESCRIPTION
BioimageioYamlContent
FAIR
FileDescr_	A FileDescr whose source is included when packaging the resource.
FileSource_	A file source that is included when packaging the resource.
FileSource_cover
FileSource_documentation
KNOWN_SPECIFIC_RESOURCE_TYPES
NotEmpty
ResourceDescrType
TAG_CATEGORIES	TYPE: Mapping[str, Mapping[str, Sequence[str]]]
VALID_COVER_IMAGE_EXTENSIONS
__all__
_author_conv
_maintainer_conv

BioimageioYamlContent module-attribute

BioimageioYamlContent = Dict[str, YamlValue]

Returned by:

•  spec
  •  dump_description
  •  get_resource_package_content

Used by:

•  spec
  •  save_bioimageio_yaml_only
  •  update_format
  •  update_hashes
  •  upload
  •  validate_format
• API Reference The bioimage.io Format Specifications
  • Generic
    •  v0_2  _convert_from_older_format
    •  v0_3  convert_from_older_format
  • Model  v0_4  convert_from_older_format

FAIR module-attribute

FAIR = A

FileDescr_ module-attribute

FileDescr_ = FileDescr

A FileDescr whose source is included when packaging the resource.

Used by:

• API Reference The bioimage.io Format Specifications Model  v0_5
  •  FileDescr_dependencies
  •  FileDescr_external_data

FileSource_ module-attribute

FileSource_ = FileSource

A file source that is included when packaging the resource.

Subclassed by:

• API Reference The bioimage.io Format Specifications Model  v0_5
  •  _InputTensorConv
  •  _OutputTensorConv

Used by:

• API Reference The bioimage.io Format Specifications
  • Generic
    •  v0_2  FileSource_cover
    •  v0_3
      •  FileSource_cover
      •  FileSource_documentation
  • Model  v0_5  FileSource_documentation

FileSource_cover module-attribute

FileSource_cover = FileSource_

FileSource_documentation module-attribute

FileSource_documentation = FileSource_

KNOWN_SPECIFIC_RESOURCE_TYPES module-attribute

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

NotEmpty module-attribute

NotEmpty = S

Used by:

• API Reference The bioimage.io Format Specifications Model  v0_5  TVs

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",
)

__all__ module-attribute

__all__ = [
    "Author",
    "BadgeDescr",
    "CiteEntry",
    "DeprecatedLicenseId",
    "Doi",
    "FileDescr",
    "GenericDescr",
    "HttpUrl",
    "KNOWN_SPECIFIC_RESOURCE_TYPES",
    "LicenseId",
    "LinkedResource",
    "Maintainer",
    "OrcidId",
    "RelativeFilePath",
    "ResourceId",
    "Sha256",
    "Uploader",
    "VALID_COVER_IMAGE_EXTENSIONS",
    "Version",
]

_author_conv module-attribute

_author_conv = _AuthorConv(_Author_v0_2, Author)

_maintainer_conv module-attribute

_maintainer_conv = _MaintainerConv(
    _Maintainer_v0_2, Maintainer
)

Author pydantic-model

Bases: _Author_v0_2

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_3.Author",
  "type": "object"
}

Fields:

• affiliation (Optional[str])
• email (Optional[EmailStr])
• orcid (Optional[OrcidId])
• name (str)
• github_user (Optional[str])

Validators:

• _validate_github_user → github_user

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

@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:

• label (str)
• icon (Optional[Union[Union[FilePath, RelativeFilePath], Union[HttpUrl, pydantic.HttpUrl]]])
• url (HttpUrl)

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

@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
        )

BioimageioConfig pydantic-model

Bases: Node

bioimage.io internal metadata.

Show JSON schema:

{
  "additionalProperties": true,
  "description": "bioimage.io internal metadata.",
  "properties": {},
  "title": "generic.v0_3.BioimageioConfig",
  "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

@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

A citation that should be referenced in work using this resource.

Show JSON schema:

{
  "additionalProperties": false,
  "description": "A citation that should be referenced in work using this resource.",
  "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.\nNote:\n    Either **doi** or **url** have to be specified.",
      "title": "Doi"
    },
    "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 cite (preferably specify a **doi** instead/also).\nNote:\n    Either **doi** or **url** have to be specified.",
      "title": "Url"
    }
  },
  "required": [
    "text"
  ],
  "title": "generic.v0_3.CiteEntry",
  "type": "object"
}

Fields:

• text (str)
• doi (Optional[Doi])
• url (Optional[HttpUrl])

Validators:

• _check_doi_or_url

doi pydantic-field

doi: Optional[Doi] = None

A digital object identifier (DOI) is the prefered citation reference. See https://www.doi.org/ for details. Note: Either doi or url have to be specified.

text pydantic-field

text: str

free text description

url pydantic-field

url: Optional[HttpUrl] = None

URL to cite (preferably specify a doi instead/also). Note: Either doi or url have to be specified.

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

@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
        )

Config pydantic-model

Bases: Node

A place to store additional metadata (often tool specific).

Such additional metadata is typically set programmatically by the respective tool or by people with specific insights into the tool. If you want to store additional metadata that does not match any of the other fields, think of a key unlikely to collide with anyone elses use-case/tool and save it here.

Please consider creating an issue in the bioimageio.spec repository if you are not sure if an existing field could cover your use case or if you think such a field should exist.

Show JSON schema:

{
  "$defs": {
    "BioimageioConfig": {
      "additionalProperties": true,
      "description": "bioimage.io internal metadata.",
      "properties": {},
      "title": "generic.v0_3.BioimageioConfig",
      "type": "object"
    }
  },
  "additionalProperties": true,
  "description": "A place to store additional metadata (often tool specific).\n\nSuch additional metadata is typically set programmatically by the respective tool\nor by people with specific insights into the tool.\nIf you want to store additional metadata that does not match any of the other\nfields, think of a key unlikely to collide with anyone elses use-case/tool and save\nit here.\n\nPlease consider creating [an issue in the bioimageio.spec repository](https://github.com/bioimage-io/spec-bioimage-io/issues/new?template=Blank+issue)\nif you are not sure if an existing field could cover your use case\nor if you think such a field should exist.",
  "properties": {
    "bioimageio": {
      "$ref": "#/$defs/BioimageioConfig"
    }
  },
  "title": "generic.v0_3.Config",
  "type": "object"
}

Fields:

• bioimageio (BioimageioConfig)

Validators:

• _validate_extra_fields

bioimageio pydantic-field

bioimageio: BioimageioConfig

bioimage.io internal metadata.

__getitem__

__getitem__(key: str) -> Any

Allows to access the config as a dictionary.

Source code in src/bioimageio/spec/generic/v0_3.py

def __getitem__(self, key: str) -> Any:
    """Allows to access the config as a dictionary."""
    return getattr(self, key)

__setitem__

__setitem__(key: str, value: Any) -> None

Allows to set the config as a dictionary.

Source code in src/bioimageio/spec/generic/v0_3.py

def __setitem__(self, key: str, value: Any) -> None:
    """Allows to set the config as a dictionary."""
    setattr(self, key, value)

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

@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
        )

Converter

Converter(src: Type[SRC], tgt: Type[TGT])

Bases: Generic[SRC, TGT, Unpack[CArgs]], ABC

              flowchart TD
              bioimageio.spec.generic.v0_3.Converter[Converter]

              

              click bioimageio.spec.generic.v0_3.Converter href "" "bioimageio.spec.generic.v0_3.Converter"
            

Subclassed by:

• API Reference The bioimage.io Format Specifications
  • Generic  v0_3
    •  _AuthorConv
    •  _MaintainerConv
  • Model  v0_5
    •  _ArchFileConv
    •  _ArchLibConv
    •  _InputTensorConv
    •  _ModelConv
    •  _OutputTensorConv

METHOD	DESCRIPTION
convert	convert source node
convert_as_dict

ATTRIBUTE	DESCRIPTION
src	TYPE: Final[Type[SRC]]
tgt	TYPE: Final[Type[TGT]]

Source code in src/bioimageio/spec/_internal/node_converter.py

def __init__(self, src: Type[SRC], tgt: Type[TGT], /):
    super().__init__()
    self.src: Final[Type[SRC]] = src
    self.tgt: Final[Type[TGT]] = tgt

src instance-attribute

src: Final[Type[SRC]] = src

tgt instance-attribute

tgt: Final[Type[TGT]] = tgt

convert

convert(source: SRC, /, *args: Unpack[CArgs]) -> TGT

convert source node

PARAMETER	DESCRIPTION
source	A bioimageio description node TYPE: SRC

RAISES	DESCRIPTION
ValidationError	conversion failed

Source code in src/bioimageio/spec/_internal/node_converter.py

def convert(self, source: SRC, /, *args: Unpack[CArgs]) -> TGT:
    """convert `source` node

    Args:
        source: A bioimageio description node

    Raises:
        ValidationError: conversion failed
    """
    data = self.convert_as_dict(source, *args)
    return assert_all_params_set_explicitly(self.tgt)(**data)

convert_as_dict

convert_as_dict(
    source: SRC, /, *args: Unpack[CArgs]
) -> Dict[str, Any]

Source code in src/bioimageio/spec/_internal/node_converter.py

def convert_as_dict(self, source: SRC, /, *args: Unpack[CArgs]) -> Dict[str, Any]:
    return cast(Dict[str, Any], self._convert(source, dict, *args))

DeprecatedLicenseId

Bases: ValidatedString

              flowchart TD
              bioimageio.spec.generic.v0_3.DeprecatedLicenseId[DeprecatedLicenseId]
              bioimageio.spec._internal.validated_string.ValidatedString[ValidatedString]

                              bioimageio.spec._internal.validated_string.ValidatedString --> bioimageio.spec.generic.v0_3.DeprecatedLicenseId
                


              click bioimageio.spec.generic.v0_3.DeprecatedLicenseId href "" "bioimageio.spec.generic.v0_3.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

@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

@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

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_3.Doi[Doi]
              bioimageio.spec._internal.validated_string.ValidatedString[ValidatedString]

                              bioimageio.spec._internal.validated_string.ValidatedString --> bioimageio.spec.generic.v0_3.Doi
                


              click bioimageio.spec.generic.v0_3.Doi href "" "bioimageio.spec.generic.v0_3.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

@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

@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

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()

FileDescr pydantic-model

Bases: Node

A file description

Show JSON schema:

{
  "$defs": {
    "RelativeFilePath": {
      "description": "A path relative to the `rdf.yaml` file (also if the RDF source is a URL).",
      "format": "path",
      "title": "RelativeFilePath",
      "type": "string"
    }
  },
  "additionalProperties": false,
  "description": "A file description",
  "properties": {
    "source": {
      "anyOf": [
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "$ref": "#/$defs/RelativeFilePath"
        },
        {
          "format": "file-path",
          "title": "FilePath",
          "type": "string"
        }
      ],
      "description": "File source",
      "title": "Source"
    },
    "sha256": {
      "anyOf": [
        {
          "description": "A SHA-256 hash value",
          "maxLength": 64,
          "minLength": 64,
          "title": "Sha256",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "SHA256 hash value of the **source** file.",
      "title": "Sha256"
    }
  },
  "required": [
    "source"
  ],
  "title": "_internal.io.FileDescr",
  "type": "object"
}

Fields:

• source (FileSource)
• sha256 (Optional[Sha256])

sha256 pydantic-field

sha256: Optional[Sha256] = None

SHA256 hash value of the source file.

source pydantic-field

source: FileSource

File source

download

download(
    *,
    progressbar: Union[
        Progressbar, Callable[[], Progressbar], bool, None
    ] = None,
)

alias for .get_reader

Source code in src/bioimageio/spec/_internal/io.py

def download(
    self,
    *,
    progressbar: Union[Progressbar, Callable[[], Progressbar], bool, None] = None,
):
    """alias for `.get_reader`"""
    return get_reader(self.source, progressbar=progressbar, sha256=self.sha256)

get_reader

get_reader(
    *,
    progressbar: Union[
        Progressbar, Callable[[], Progressbar], bool, None
    ] = None,
)

open the file source (download if needed)

Source code in src/bioimageio/spec/_internal/io.py

def get_reader(
    self,
    *,
    progressbar: Union[Progressbar, Callable[[], Progressbar], bool, None] = None,
):
    """open the file source (download if needed)"""
    return get_reader(self.source, progressbar=progressbar, sha256=self.sha256)

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

@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
        )

validate_sha256

validate_sha256(force_recompute: bool = False) -> None

validate the sha256 hash value of the source file

Source code in src/bioimageio/spec/_internal/io.py

def validate_sha256(self, force_recompute: bool = False) -> None:
    """validate the sha256 hash value of the **source** file"""
    context = get_validation_context()
    src_str = str(self.source)
    if not force_recompute and src_str in context.known_files:
        actual_sha = context.known_files[src_str]
    else:
        reader = get_reader(self.source, sha256=self.sha256)
        if force_recompute:
            actual_sha = get_sha256(reader)
        else:
            actual_sha = reader.sha256

        context.known_files[src_str] = actual_sha

    if actual_sha is None:
        return
    elif self.sha256 == actual_sha:
        pass
    elif self.sha256 is None or context.update_hashes:
        self.sha256 = actual_sha
    elif self.sha256 != actual_sha:
        raise ValueError(
            f"Sha256 mismatch for {self.source}. Expected {self.sha256}, got "
            + f"{actual_sha}. Update expected `sha256` or point to the matching "
            + "file."
        )

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": {
    "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_3.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"
    },
    "BioimageioConfig": {
      "additionalProperties": true,
      "description": "bioimage.io internal metadata.",
      "properties": {},
      "title": "generic.v0_3.BioimageioConfig",
      "type": "object"
    },
    "CiteEntry": {
      "additionalProperties": false,
      "description": "A citation that should be referenced in work using this resource.",
      "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.\nNote:\n    Either **doi** or **url** have to be specified.",
          "title": "Doi"
        },
        "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 cite (preferably specify a **doi** instead/also).\nNote:\n    Either **doi** or **url** have to be specified.",
          "title": "Url"
        }
      },
      "required": [
        "text"
      ],
      "title": "generic.v0_3.CiteEntry",
      "type": "object"
    },
    "Config": {
      "additionalProperties": true,
      "description": "A place to store additional metadata (often tool specific).\n\nSuch additional metadata is typically set programmatically by the respective tool\nor by people with specific insights into the tool.\nIf you want to store additional metadata that does not match any of the other\nfields, think of a key unlikely to collide with anyone elses use-case/tool and save\nit here.\n\nPlease consider creating [an issue in the bioimageio.spec repository](https://github.com/bioimage-io/spec-bioimage-io/issues/new?template=Blank+issue)\nif you are not sure if an existing field could cover your use case\nor if you think such a field should exist.",
      "properties": {
        "bioimageio": {
          "$ref": "#/$defs/BioimageioConfig"
        }
      },
      "title": "generic.v0_3.Config",
      "type": "object"
    },
    "FileDescr": {
      "additionalProperties": false,
      "description": "A file description",
      "properties": {
        "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"
            }
          ],
          "description": "File source",
          "title": "Source"
        },
        "sha256": {
          "anyOf": [
            {
              "description": "A SHA-256 hash value",
              "maxLength": 64,
              "minLength": 64,
              "title": "Sha256",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "SHA256 hash value of the **source** file.",
          "title": "Sha256"
        }
      },
      "required": [
        "source"
      ],
      "title": "_internal.io.FileDescr",
      "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_3.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"
    }
  },
  "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.\nMay only contains letters, digits, underscore, minus, parentheses and spaces.",
      "maxLength": 128,
      "minLength": 5,
      "title": "Name",
      "type": "string"
    },
    "description": {
      "default": "",
      "description": "A string containing a brief description.",
      "maxLength": 1024,
      "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 or 1:1.\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg')",
      "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": 2,
          "minLength": 1,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "UTF-8 emoji for display alongside the `id`.",
      "title": "Id Emoji"
    },
    "authors": {
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          ],
          "title": "DeprecatedLicenseId",
          "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)\nto discuss your intentions with the community.",
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        "BSD-2-Clause"
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        },
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          "type": "null"
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      ],
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          "minLength": 1,
          "type": "string"
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        {
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      "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 has to specify their `github_user` name",
      "items": {
        "$ref": "#/$defs/Maintainer"
      },
      "title": "Maintainers",
      "type": "array"
    },
    "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_comment": {
      "anyOf": [
        {
          "maxLength": 512,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "A comment on the version of the resource.",
      "title": "Version Comment"
    },
    "format_version": {
      "const": "0.3.0",
      "description": "The **format** version of this resource specification",
      "title": "Format Version",
      "type": "string"
    },
    "documentation": {
      "anyOf": [
        {
          "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"
            }
          ],
          "examples": [
            "https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md",
            "README.md"
          ]
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "URL or relative path to a markdown file encoded in UTF-8 with additional documentation.\nThe recommended documentation file name is `README.md`. An `.md` suffix is mandatory.",
      "title": "Documentation"
    },
    "badges": {
      "description": "badges associated with this resource",
      "items": {
        "$ref": "#/$defs/BadgeDescr"
      },
      "title": "Badges",
      "type": "array"
    },
    "config": {
      "$ref": "#/$defs/Config",
      "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 there is a `git_repo` field.\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    giraffe_neckometer:  # here is the domain name\n        length: 3837283\n        address:\n            home: zoo\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.)"
    },
    "type": {
      "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"
    },
    "parent": {
      "anyOf": [
        {
          "minLength": 1,
          "title": "ResourceId",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The description from which this one is derived",
      "title": "Parent"
    },
    "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",
    "format_version",
    "type"
  ],
  "title": "generic 0.3.0",
  "type": "object"
}

Fields:

• _validation_summary (Optional[ValidationSummary])
• _root (Union[RootHttpUrl, DirectoryPath, ZipFile])
• _file_name (Optional[FileName])
• name (str)
• description (FAIR[str])
• covers (List[FileSource_cover])
• id_emoji (Optional[str])
• authors (FAIR[List[Author]])
• attachments (List[FileDescr_])
• cite (FAIR[List[CiteEntry]])
• license (FAIR[Union[LicenseId, DeprecatedLicenseId, None]])
• git_repo (Optional[HttpUrl])
• icon (Union[str, FileSource_, None])
• links (List[str])
• uploader (Optional[Uploader])
• maintainers (List[Maintainer])
• tags (FAIR[List[str]])
• version (Optional[Version])
• version_comment (Optional[str])
• format_version (Literal['0.3.0'])
• documentation (FAIR[Optional[FileSource_documentation]])
• badges (List[BadgeDescr])
• config (Config)
• type (str)
• id (Optional[ResourceId])
• parent (Optional[ResourceId])
• source (Optional[HttpUrl])

Validators:

• check_specific_types → type

attachments pydantic-field

attachments: List[FileDescr_]

file attachments

authors pydantic-field

authors: FAIR[List[Author]]

The authors are the creators of this resource description and the primary points of contact.

badges pydantic-field

badges: List[BadgeDescr]

badges associated with this resource

cite pydantic-field

cite: FAIR[List[CiteEntry]]

citations

config pydantic-field

config: Config

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 there is a git_repo field. 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:
    giraffe_neckometer:  # here is the domain name
        length: 3837283
        address:
            home: zoo
    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.

description pydantic-field

description: FAIR[str] = ''

A string containing a brief description.

documentation pydantic-field

documentation: FAIR[Optional[FileSource_documentation]] = (
    None
)

URL or relative path to a markdown file encoded in UTF-8 with additional documentation. The recommended documentation file name is README.md. An .md suffix is mandatory.

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['0.3.0'] = '0.3.0'

git_repo pydantic-field

git_repo: Optional[HttpUrl] = 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, e.g. on bioimage.io

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['0.3.0'] = '0.3.0'

implemented_format_version_tuple class-attribute

implemented_format_version_tuple: Tuple[int, int, int]

implemented_type class-attribute

implemented_type: Literal['generic'] = 'generic'

license pydantic-field

license: FAIR[
    Union[LicenseId, DeprecatedLicenseId, 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 pydantic-field

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 has to specify their github_user name

name pydantic-field

name: str

A human-friendly name of the resource description. May only contains letters, digits, underscore, minus, parentheses and spaces.

parent pydantic-field

parent: Optional[ResourceId] = None

The description from which this one is derived

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: FAIR[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_comment pydantic-field

version_comment: Optional[str] = None

A comment on the version of the resource.

__pydantic_init_subclass__ classmethod

__pydantic_init_subclass__(**kwargs: Any)

Source code in src/bioimageio/spec/_internal/common_nodes.py

@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

check_specific_types pydantic-validator

check_specific_types(value: str) -> str

Source code in src/bioimageio/spec/generic/v0_3.py

@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

convert_from_old_format_wo_validation classmethod

convert_from_old_format_wo_validation(
    data: BioimageioYamlContent,
) -> None

Convert metadata following an older format version to this classes' format without validating the result.

Source code in src/bioimageio/spec/generic/v0_3.py

@classmethod
def convert_from_old_format_wo_validation(cls, data: BioimageioYamlContent) -> None:
    """Convert metadata following an older format version to this classes' format
    without validating the result.
    """
    convert_from_older_format(data)

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

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

@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

@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

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_3.py

@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[Dict[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(
            f"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": {
    "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_3.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"
    },
    "BioimageioConfig": {
      "additionalProperties": true,
      "description": "bioimage.io internal metadata.",
      "properties": {},
      "title": "generic.v0_3.BioimageioConfig",
      "type": "object"
    },
    "CiteEntry": {
      "additionalProperties": false,
      "description": "A citation that should be referenced in work using this resource.",
      "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.\nNote:\n    Either **doi** or **url** have to be specified.",
          "title": "Doi"
        },
        "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 cite (preferably specify a **doi** instead/also).\nNote:\n    Either **doi** or **url** have to be specified.",
          "title": "Url"
        }
      },
      "required": [
        "text"
      ],
      "title": "generic.v0_3.CiteEntry",
      "type": "object"
    },
    "Config": {
      "additionalProperties": true,
      "description": "A place to store additional metadata (often tool specific).\n\nSuch additional metadata is typically set programmatically by the respective tool\nor by people with specific insights into the tool.\nIf you want to store additional metadata that does not match any of the other\nfields, think of a key unlikely to collide with anyone elses use-case/tool and save\nit here.\n\nPlease consider creating [an issue in the bioimageio.spec repository](https://github.com/bioimage-io/spec-bioimage-io/issues/new?template=Blank+issue)\nif you are not sure if an existing field could cover your use case\nor if you think such a field should exist.",
      "properties": {
        "bioimageio": {
          "$ref": "#/$defs/BioimageioConfig"
        }
      },
      "title": "generic.v0_3.Config",
      "type": "object"
    },
    "FileDescr": {
      "additionalProperties": false,
      "description": "A file description",
      "properties": {
        "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"
            }
          ],
          "description": "File source",
          "title": "Source"
        },
        "sha256": {
          "anyOf": [
            {
              "description": "A SHA-256 hash value",
              "maxLength": 64,
              "minLength": 64,
              "title": "Sha256",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "SHA256 hash value of the **source** file.",
          "title": "Sha256"
        }
      },
      "required": [
        "source"
      ],
      "title": "_internal.io.FileDescr",
      "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_3.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"
    }
  },
  "additionalProperties": false,
  "description": "Base for all resource descriptions except for the model descriptions",
  "properties": {
    "name": {
      "description": "A human-friendly name of the resource description.\nMay only contains letters, digits, underscore, minus, parentheses and spaces.",
      "maxLength": 128,
      "minLength": 5,
      "title": "Name",
      "type": "string"
    },
    "description": {
      "default": "",
      "description": "A string containing a brief description.",
      "maxLength": 1024,
      "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 or 1:1.\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg')",
      "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": 2,
          "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 this resource description and the primary points of contact.",
      "items": {
        "$ref": "#/$defs/Author"
      },
      "title": "Authors",
      "type": "array"
    },
    "attachments": {
      "description": "file attachments",
      "items": {
        "$ref": "#/$defs/FileDescr"
      },
      "title": "Attachments",
      "type": "array"
    },
    "cite": {
      "description": "citations",
      "items": {
        "$ref": "#/$defs/CiteEntry"
      },
      "title": "Cite",
      "type": "array"
    },
    "license": {
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        {
          "enum": [
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            "Adobe-2006",
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            "gnuplot",
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            "Latex2e-translated-notice",
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            "MIT-advertising",
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            "MIT-testregex",
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            "NAIST-2003",
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            "NetCDF",
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            "PDDL-1.0",
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            "PHP-3.01",
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            "Python-2.0.1",
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            "QPL-1.0-INRIA-2004",
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            "RSA-MD",
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            "Spencer-99",
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            "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": "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)\nto discuss your intentions with the community.",
      "examples": [
        "CC0-1.0",
        "MIT",
        "BSD-2-Clause"
      ],
      "title": "License"
    },
    "git_repo": {
      "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": "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, e.g. on bioimage.io",
      "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 has to specify their `github_user` name",
      "items": {
        "$ref": "#/$defs/Maintainer"
      },
      "title": "Maintainers",
      "type": "array"
    },
    "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_comment": {
      "anyOf": [
        {
          "maxLength": 512,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "A comment on the version of the resource.",
      "title": "Version Comment"
    },
    "format_version": {
      "const": "0.3.0",
      "description": "The **format** version of this resource specification",
      "title": "Format Version",
      "type": "string"
    },
    "documentation": {
      "anyOf": [
        {
          "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"
            }
          ],
          "examples": [
            "https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md",
            "README.md"
          ]
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "URL or relative path to a markdown file encoded in UTF-8 with additional documentation.\nThe recommended documentation file name is `README.md`. An `.md` suffix is mandatory.",
      "title": "Documentation"
    },
    "badges": {
      "description": "badges associated with this resource",
      "items": {
        "$ref": "#/$defs/BadgeDescr"
      },
      "title": "Badges",
      "type": "array"
    },
    "config": {
      "$ref": "#/$defs/Config",
      "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 there is a `git_repo` field.\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    giraffe_neckometer:  # here is the domain name\n        length: 3837283\n        address:\n            home: zoo\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.)"
    }
  },
  "required": [
    "name",
    "format_version"
  ],
  "title": "generic.v0_3.GenericDescrBase",
  "type": "object"
}

Fields:

• _validation_summary (Optional[ValidationSummary])
• _root (Union[RootHttpUrl, DirectoryPath, ZipFile])
• _file_name (Optional[FileName])
• name (str)
• description (FAIR[str])
• covers (List[FileSource_cover])
• id_emoji (Optional[str])
• authors (FAIR[List[Author]])
• attachments (List[FileDescr_])
• cite (FAIR[List[CiteEntry]])
• license (FAIR[Union[LicenseId, DeprecatedLicenseId, None]])
• git_repo (Optional[HttpUrl])
• icon (Union[str, FileSource_, None])
• links (List[str])
• uploader (Optional[Uploader])
• maintainers (List[Maintainer])
• tags (FAIR[List[str]])
• version (Optional[Version])
• version_comment (Optional[str])
• format_version (Literal['0.3.0'])
• documentation (FAIR[Optional[FileSource_documentation]])
• badges (List[BadgeDescr])
• config (Config)

attachments pydantic-field

attachments: List[FileDescr_]

file attachments

authors pydantic-field

authors: FAIR[List[Author]]

The authors are the creators of this resource description and the primary points of contact.

badges pydantic-field

badges: List[BadgeDescr]

badges associated with this resource

cite pydantic-field

cite: FAIR[List[CiteEntry]]

citations

config pydantic-field

config: Config

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 there is a git_repo field. 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:
    giraffe_neckometer:  # here is the domain name
        length: 3837283
        address:
            home: zoo
    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.

description pydantic-field

description: FAIR[str] = ''

A string containing a brief description.

documentation pydantic-field

documentation: FAIR[Optional[FileSource_documentation]] = (
    None
)

URL or relative path to a markdown file encoded in UTF-8 with additional documentation. The recommended documentation file name is README.md. An .md suffix is mandatory.

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['0.3.0'] = '0.3.0'

git_repo pydantic-field

git_repo: Optional[HttpUrl] = 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, e.g. on bioimage.io

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['0.3.0'] = '0.3.0'

implemented_format_version_tuple class-attribute

implemented_format_version_tuple: Tuple[int, int, int]

license pydantic-field

license: FAIR[
    Union[LicenseId, DeprecatedLicenseId, 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 pydantic-field

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 has to specify their github_user name

name pydantic-field

name: str

A human-friendly name of the resource description. May only contains letters, digits, underscore, minus, parentheses and spaces.

root property

root: Union[RootHttpUrl, DirectoryPath, ZipFile]

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

tags pydantic-field

tags: FAIR[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_comment pydantic-field

version_comment: Optional[str] = None

A comment on the version of the resource.

__pydantic_init_subclass__ classmethod

__pydantic_init_subclass__(**kwargs: Any)

Source code in src/bioimageio/spec/_internal/common_nodes.py

@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

convert_from_old_format_wo_validation classmethod

convert_from_old_format_wo_validation(
    data: BioimageioYamlContent,
) -> None

Convert metadata following an older format version to this classes' format without validating the result.

Source code in src/bioimageio/spec/generic/v0_3.py

@classmethod
def convert_from_old_format_wo_validation(cls, data: BioimageioYamlContent) -> None:
    """Convert metadata following an older format version to this classes' format
    without validating the result.
    """
    convert_from_older_format(data)

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

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

@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

@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

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_3.py

@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[Dict[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(
            f"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": {
    "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_3.Author",
      "type": "object"
    },
    "CiteEntry": {
      "additionalProperties": false,
      "description": "A citation that should be referenced in work using this resource.",
      "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.\nNote:\n    Either **doi** or **url** have to be specified.",
          "title": "Doi"
        },
        "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 cite (preferably specify a **doi** instead/also).\nNote:\n    Either **doi** or **url** have to be specified.",
          "title": "Url"
        }
      },
      "required": [
        "text"
      ],
      "title": "generic.v0_3.CiteEntry",
      "type": "object"
    },
    "FileDescr": {
      "additionalProperties": false,
      "description": "A file description",
      "properties": {
        "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"
            }
          ],
          "description": "File source",
          "title": "Source"
        },
        "sha256": {
          "anyOf": [
            {
              "description": "A SHA-256 hash value",
              "maxLength": 64,
              "minLength": 64,
              "title": "Sha256",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "SHA256 hash value of the **source** file.",
          "title": "Sha256"
        }
      },
      "required": [
        "source"
      ],
      "title": "_internal.io.FileDescr",
      "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_3.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"
    }
  },
  "additionalProperties": false,
  "description": "Base for all resource descriptions including of model descriptions",
  "properties": {
    "name": {
      "description": "A human-friendly name of the resource description.\nMay only contains letters, digits, underscore, minus, parentheses and spaces.",
      "maxLength": 128,
      "minLength": 5,
      "title": "Name",
      "type": "string"
    },
    "description": {
      "default": "",
      "description": "A string containing a brief description.",
      "maxLength": 1024,
      "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 or 1:1.\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg')",
      "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": 2,
          "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 this resource description and the primary points of contact.",
      "items": {
        "$ref": "#/$defs/Author"
      },
      "title": "Authors",
      "type": "array"
    },
    "attachments": {
      "description": "file attachments",
      "items": {
        "$ref": "#/$defs/FileDescr"
      },
      "title": "Attachments",
      "type": "array"
    },
    "cite": {
      "description": "citations",
      "items": {
        "$ref": "#/$defs/CiteEntry"
      },
      "title": "Cite",
      "type": "array"
    },
    "license": {
      "anyOf": [
        {
          "enum": [
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            "Adobe-2006",
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            "gnuplot",
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            "GPL-2.0-only",
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            "GPL-3.0-or-later",
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            "HP-1989",
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            "HPND-export-US",
            "HPND-export-US-modify",
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            "HPND-sell-variant",
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            "Latex2e-translated-notice",
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            "Mackerras-3-Clause-acknowledgment",
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            "mailprio",
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            "Martin-Birgmeier",
            "McPhee-slideshow",
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            "MirOS",
            "MIT",
            "MIT-0",
            "MIT-advertising",
            "MIT-CMU",
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            "MIT-Festival",
            "MIT-Modern-Variant",
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            "MIT-testregex",
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            "mpi-permissive",
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            "MPL-2.0-no-copyleft-exception",
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            "MulanPSL-2.0",
            "Multics",
            "Mup",
            "NAIST-2003",
            "NASA-1.3",
            "Naumen",
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            "NCSA",
            "Net-SNMP",
            "NetCDF",
            "Newsletr",
            "NGPL",
            "NICTA-1.0",
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            "NIST-PD-fallback",
            "NIST-Software",
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            "PDDL-1.0",
            "PHP-3.0",
            "PHP-3.01",
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            "psutils",
            "Python-2.0",
            "Python-2.0.1",
            "python-ldap",
            "Qhull",
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            "QPL-1.0-INRIA-2004",
            "radvd",
            "Rdisc",
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            "RPL-1.5",
            "RPSL-1.0",
            "RSA-MD",
            "RSCPL",
            "Ruby",
            "SAX-PD",
            "SAX-PD-2.0",
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            "SGI-B-1.0",
            "SGI-B-1.1",
            "SGI-B-2.0",
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            "Sleepycat",
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            "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": "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)\nto discuss your intentions with the community.",
      "examples": [
        "CC0-1.0",
        "MIT",
        "BSD-2-Clause"
      ],
      "title": "License"
    },
    "git_repo": {
      "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": "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, e.g. on bioimage.io",
      "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 has to specify their `github_user` name",
      "items": {
        "$ref": "#/$defs/Maintainer"
      },
      "title": "Maintainers",
      "type": "array"
    },
    "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_comment": {
      "anyOf": [
        {
          "maxLength": 512,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "A comment on the version of the resource.",
      "title": "Version Comment"
    }
  },
  "required": [
    "name"
  ],
  "title": "generic.v0_3.GenericModelDescrBase",
  "type": "object"
}

Fields:

• _validation_summary (Optional[ValidationSummary])
• _root (Union[RootHttpUrl, DirectoryPath, ZipFile])
• _file_name (Optional[FileName])
• name (str)
• description (FAIR[str])
• covers (List[FileSource_cover])
• id_emoji (Optional[str])
• authors (FAIR[List[Author]])
• attachments (List[FileDescr_])
• cite (FAIR[List[CiteEntry]])
• license (FAIR[Union[LicenseId, DeprecatedLicenseId, None]])
• git_repo (Optional[HttpUrl])
• icon (Union[str, FileSource_, None])
• links (List[str])
• uploader (Optional[Uploader])
• maintainers (List[Maintainer])
• tags (FAIR[List[str]])
• version (Optional[Version])
• version_comment (Optional[str])

attachments pydantic-field

attachments: List[FileDescr_]

file attachments

authors pydantic-field

authors: FAIR[List[Author]]

The authors are the creators of this resource description and the primary points of contact.

cite pydantic-field

cite: FAIR[List[CiteEntry]]

citations

covers pydantic-field

covers: List[FileSource_cover]

Cover images.

description pydantic-field

description: FAIR[str] = ''

A string containing a brief description.

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[HttpUrl] = 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, e.g. on bioimage.io

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]

license pydantic-field

license: FAIR[
    Union[LicenseId, DeprecatedLicenseId, 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 pydantic-field

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 has to specify their github_user name

name pydantic-field

name: str

A human-friendly name of the resource description. May only contains letters, digits, underscore, minus, parentheses and spaces.

root property

root: Union[RootHttpUrl, DirectoryPath, ZipFile]

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

tags pydantic-field

tags: FAIR[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_comment pydantic-field

version_comment: Optional[str] = None

A comment on the version of the resource.

__pydantic_init_subclass__ classmethod

__pydantic_init_subclass__(**kwargs: Any)

Source code in src/bioimageio/spec/_internal/common_nodes.py

@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

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

@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

@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

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_3.py

@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[Dict[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(
            f"Missing tags from bioimage.io categories: {missing_categories}"
        )

    return value

HttpUrl

Bases: RootHttpUrl

              flowchart TD
              bioimageio.spec.generic.v0_3.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_3.HttpUrl
                                bioimageio.spec._internal.validated_string.ValidatedString --> bioimageio.spec._internal.root_url.RootHttpUrl
                



              click bioimageio.spec.generic.v0_3.HttpUrl href "" "bioimageio.spec.generic.v0_3.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:

•  spec
  •  get_resource_package_content
  •  upload

Subclassed by:

• API Reference The bioimage.io Format Specifications
  • Application
    •  v0_2  RelativeFilePath
    •  v0_3  RelativeFilePath
  • Dataset
    •  v0_2  RelativeFilePath
    •  v0_3  RelativeFilePath
  • Generic
    •  v0_2  RelativeFilePath
    •  v0_3  RelativeFilePath
  • Model
    •  v0_4  RelativeFilePath
    •  v0_5  RelativeFilePath
  • Notebook
    •  v0_2  RelativeFilePath
    •  v0_3  RelativeFilePath

Used by:

• API Reference The bioimage.io Format Specifications
  • Generic  v0_2  FileSource
  • Model  v0_5  FileSource
  • Notebook
    •  v0_2  NotebookSource
    •  v0_3  NotebookSource

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

@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

@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

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

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

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_3.LicenseId[LicenseId]
              bioimageio.spec._internal.validated_string.ValidatedString[ValidatedString]

                              bioimageio.spec._internal.validated_string.ValidatedString --> bioimageio.spec.generic.v0_3.LicenseId
                


              click bioimageio.spec.generic.v0_3.LicenseId href "" "bioimageio.spec.generic.v0_3.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

@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

@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

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: LinkedResourceBase

Reference to a bioimage.io resource

Show JSON schema:

{
  "$defs": {
    "Version": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "integer"
        },
        {
          "type": "number"
        }
      ],
      "description": "wraps a packaging.version.Version instance for validation in pydantic models",
      "title": "Version"
    }
  },
  "additionalProperties": false,
  "description": "Reference to a bioimage.io resource",
  "properties": {
    "version": {
      "anyOf": [
        {
          "$ref": "#/$defs/Version"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The version of the linked resource following SemVer 2.0."
    },
    "id": {
      "description": "A valid resource `id` from the official bioimage.io collection.",
      "minLength": 1,
      "title": "ResourceId",
      "type": "string"
    }
  },
  "required": [
    "id"
  ],
  "title": "generic.v0_3.LinkedResource",
  "type": "object"
}

Fields:

• version (Optional[Version])
• id (ResourceId)

id pydantic-field

id: ResourceId

A valid resource id from the official bioimage.io collection.

version pydantic-field

version: Optional[Version] = None

The version of the linked resource following SemVer 2.0.

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

@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
        )

LinkedResourceBase pydantic-model

Bases: Node

Show JSON schema:

{
  "$defs": {
    "Version": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "integer"
        },
        {
          "type": "number"
        }
      ],
      "description": "wraps a packaging.version.Version instance for validation in pydantic models",
      "title": "Version"
    }
  },
  "additionalProperties": false,
  "properties": {
    "version": {
      "anyOf": [
        {
          "$ref": "#/$defs/Version"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The version of the linked resource following SemVer 2.0."
    }
  },
  "title": "generic.v0_3.LinkedResourceBase",
  "type": "object"
}

Fields:

• version (Optional[Version])

version pydantic-field

version: Optional[Version] = None

The version of the linked resource following SemVer 2.0.

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

@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: _Maintainer_v0_2

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_3.Maintainer",
  "type": "object"
}

Fields:

• affiliation (Optional[str])
• email (Optional[EmailStr])
• orcid (Optional[OrcidId])
• name (Optional[str])
• github_user (str)

Validators:

• validate_github_user → github_user

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

@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
        )

validate_github_user pydantic-validator

validate_github_user(value: str)

Source code in src/bioimageio/spec/generic/v0_3.py

@field_validator("github_user", mode="after")
def validate_github_user(cls, value: str):
    return validate_github_user(value)

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

@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_3.OrcidId[OrcidId]
              bioimageio.spec._internal.validated_string.ValidatedString[ValidatedString]

                              bioimageio.spec._internal.validated_string.ValidatedString --> bioimageio.spec.generic.v0_3.OrcidId
                


              click bioimageio.spec.generic.v0_3.OrcidId href "" "bioimageio.spec.generic.v0_3.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

@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

@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

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()

Predicate dataclass

Predicate()

Bases: annotated_types.Predicate

              flowchart TD
              bioimageio.spec.generic.v0_3.Predicate[Predicate]

              

              click bioimageio.spec.generic.v0_3.Predicate href "" "bioimageio.spec.generic.v0_3.Predicate"
            

METHOD	DESCRIPTION
__str__

__str__

__str__()

Source code in src/bioimageio/spec/_internal/validator_annotations.py

def __str__(self):
    return f"Predicate({self.func.__name__})"

RelativeFilePath

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

              flowchart TD
              bioimageio.spec.generic.v0_3.RelativeFilePath[RelativeFilePath]
              bioimageio.spec._internal.io.RelativePathBase[RelativePathBase]

                              bioimageio.spec._internal.io.RelativePathBase --> bioimageio.spec.generic.v0_3.RelativeFilePath
                


              click bioimageio.spec.generic.v0_3.RelativeFilePath href "" "bioimageio.spec.generic.v0_3.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:

• API Reference The bioimage.io Format Specifications
  • Generic  v0_2  FileSource
  • Model  v0_5
    •  FileSource
    •  extract_file_name
  • Notebook
    •  v0_2  NotebookSource
    •  v0_3  NotebookSource

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

def __repr__(self) -> str:
    return f"RelativePath('{self}')"

__str__

__str__() -> str

Source code in src/bioimageio/spec/_internal/io.py

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

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

@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

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

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:

• _validation_summary (Optional[ValidationSummary])
• _root (Union[RootHttpUrl, DirectoryPath, ZipFile])
• _file_name (Optional[FileName])

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

@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

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

@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

@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

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_3.ResourceId[ResourceId]
              bioimageio.spec._internal.validated_string.ValidatedString[ValidatedString]

                              bioimageio.spec._internal.validated_string.ValidatedString --> bioimageio.spec.generic.v0_3.ResourceId
                


              click bioimageio.spec.generic.v0_3.ResourceId href "" "bioimageio.spec.generic.v0_3.ResourceId"
              click bioimageio.spec._internal.validated_string.ValidatedString href "" "bioimageio.spec._internal.validated_string.ValidatedString"
            

Subclassed by:

• API Reference The bioimage.io Format Specifications
  • Application  v0_3  ApplicationId
  • Dataset  v0_3  DatasetId
  • Model  v0_5
    •  DatasetId
    •  ModelId
  • Notebook  v0_3  NotebookId

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

@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

@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

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

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

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

Sha256

Bases: ValidatedString

              flowchart TD
              bioimageio.spec.generic.v0_3.Sha256[Sha256]
              bioimageio.spec._internal.validated_string.ValidatedString[ValidatedString]

                              bioimageio.spec._internal.validated_string.ValidatedString --> bioimageio.spec.generic.v0_3.Sha256
                


              click bioimageio.spec.generic.v0_3.Sha256 href "" "bioimageio.spec.generic.v0_3.Sha256"
              click bioimageio.spec._internal.validated_string.ValidatedString href "" "bioimageio.spec._internal.validated_string.ValidatedString"
            

A SHA-256 hash value

Subclassed by:

• API Reference The bioimage.io Format Specifications Model  v0_5  _ArchFileConv

Used by:

•  spec
  •  ValidationContext
  •  load_dataset_description
  •  load_description
  •  load_description_and_validate_format_only
  •  load_model_description
• API Reference  summary  ValidationContextSummary

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

@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

@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

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()

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 (EmailStr)
• name (Optional[str])

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

@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_3.ValidatedString[ValidatedString]

              

              click bioimageio.spec.generic.v0_3.ValidatedString href "" "bioimageio.spec.generic.v0_3.ValidatedString"
            

Subclassed by:

• API Reference The bioimage.io Format Specifications
  • Application
    •  v0_2
      •  Doi
      •  OrcidId
      •  ResourceId
    •  v0_3
      •  DeprecatedLicenseId
      •  Doi
      •  LicenseId
      •  OrcidId
      •  ResourceId
      •  Sha256
  • Dataset
    •  v0_2
      •  Doi
      •  OrcidId
      •  ResourceId
    •  v0_3
      •  DeprecatedLicenseId
      •  Doi
      •  LicenseId
      •  OrcidId
      •  ResourceId
      •  Sha256
  • Generic
    •  v0_2
      •  DeprecatedLicenseId
      •  Doi
      •  LicenseId
      •  OrcidId
      •  ResourceId
    •  v0_3
      •  DeprecatedLicenseId
      •  Doi
      •  LicenseId
      •  OrcidId
      •  ResourceId
      •  Sha256
  • Model
    •  v0_4
      •  Doi
      •  Identifier
      •  LicenseId
      •  LowerCaseIdentifier
      •  OrcidId
      •  ResourceId
      •  Sha256
      •  ValidatedStringWithInnerNode
    •  v0_5
      •  DeprecatedLicenseId
      •  Doi
      •  Identifier
      •  LicenseId
      •  LowerCaseIdentifier
      •  OrcidId
      •  ResourceId
      •  Sha256
      •  SiUnit
  • Notebook
    •  v0_2
      •  Doi
      •  OrcidId
      •  ResourceId
    •  v0_3
      •  DeprecatedLicenseId
      •  Doi
      •  LicenseId
      •  OrcidId
      •  ResourceId
      •  Sha256

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

@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

@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

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_3.Version[Version]

              

              click bioimageio.spec.generic.v0_3.Version href "" "bioimageio.spec.generic.v0_3.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

def __eq__(self, other: Version):
    return self._version == other._version

__lt__

__lt__(other: Version)

Source code in src/bioimageio/spec/_internal/version_type.py

def __lt__(self, other: Version):
    return self._version < other._version

__str__

__str__()

Source code in src/bioimageio/spec/_internal/version_type.py

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

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:

• API Reference The bioimage.io Format Specifications Notebook  v0_2  _WithNotebookSuffix

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

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

def validate(
    self, value: Union[FileSource, FileDescr]
) -> Union[FileSource, FileDescr]:
    return validate_suffix(value, self.suffix, case_sensitive=self.case_sensitive)

_AuthorConv

_AuthorConv(src: Type[SRC], tgt: Type[TGT])

Bases: Converter[_Author_v0_2, Author]

              flowchart TD
              bioimageio.spec.generic.v0_3._AuthorConv[_AuthorConv]
              bioimageio.spec._internal.node_converter.Converter[Converter]

                              bioimageio.spec._internal.node_converter.Converter --> bioimageio.spec.generic.v0_3._AuthorConv
                


              click bioimageio.spec.generic.v0_3._AuthorConv href "" "bioimageio.spec.generic.v0_3._AuthorConv"
              click bioimageio.spec._internal.node_converter.Converter href "" "bioimageio.spec._internal.node_converter.Converter"
            

Used by:

• API Reference The bioimage.io Format Specifications
  • Dataset  v0_3  _author_conv
  • Generic  v0_3  _author_conv
  • Model  v0_5  _author_conv

METHOD	DESCRIPTION
convert	convert source node
convert_as_dict

ATTRIBUTE	DESCRIPTION
src	TYPE: Final[Type[SRC]]
tgt	TYPE: Final[Type[TGT]]

Source code in src/bioimageio/spec/_internal/node_converter.py

def __init__(self, src: Type[SRC], tgt: Type[TGT], /):
    super().__init__()
    self.src: Final[Type[SRC]] = src
    self.tgt: Final[Type[TGT]] = tgt

src instance-attribute

src: Final[Type[SRC]] = src

tgt instance-attribute

tgt: Final[Type[TGT]] = tgt

convert

convert(source: SRC, /, *args: Unpack[CArgs]) -> TGT

convert source node

PARAMETER	DESCRIPTION
source	A bioimageio description node TYPE: SRC

RAISES	DESCRIPTION
ValidationError	conversion failed

Source code in src/bioimageio/spec/_internal/node_converter.py

def convert(self, source: SRC, /, *args: Unpack[CArgs]) -> TGT:
    """convert `source` node

    Args:
        source: A bioimageio description node

    Raises:
        ValidationError: conversion failed
    """
    data = self.convert_as_dict(source, *args)
    return assert_all_params_set_explicitly(self.tgt)(**data)

convert_as_dict

convert_as_dict(
    source: SRC, /, *args: Unpack[CArgs]
) -> Dict[str, Any]

Source code in src/bioimageio/spec/_internal/node_converter.py

def convert_as_dict(self, source: SRC, /, *args: Unpack[CArgs]) -> Dict[str, Any]:
    return cast(Dict[str, Any], self._convert(source, dict, *args))

_Author_v0_2 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 (Optional[str])
• email (Optional[EmailStr])
• orcid (Optional[OrcidId])
• name (str)
• github_user (Optional[str])

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

@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
        )

_MaintainerConv

_MaintainerConv(src: Type[SRC], tgt: Type[TGT])

Bases: Converter[_Maintainer_v0_2, Maintainer]

              flowchart TD
              bioimageio.spec.generic.v0_3._MaintainerConv[_MaintainerConv]
              bioimageio.spec._internal.node_converter.Converter[Converter]

                              bioimageio.spec._internal.node_converter.Converter --> bioimageio.spec.generic.v0_3._MaintainerConv
                


              click bioimageio.spec.generic.v0_3._MaintainerConv href "" "bioimageio.spec.generic.v0_3._MaintainerConv"
              click bioimageio.spec._internal.node_converter.Converter href "" "bioimageio.spec._internal.node_converter.Converter"
            

Used by:

• API Reference The bioimage.io Format Specifications
  • Dataset  v0_3  _maintainer_conv
  • Generic  v0_3  _maintainer_conv
  • Model  v0_5  _maintainer_conv

METHOD	DESCRIPTION
convert	convert source node
convert_as_dict

ATTRIBUTE	DESCRIPTION
src	TYPE: Final[Type[SRC]]
tgt	TYPE: Final[Type[TGT]]

Source code in src/bioimageio/spec/_internal/node_converter.py

def __init__(self, src: Type[SRC], tgt: Type[TGT], /):
    super().__init__()
    self.src: Final[Type[SRC]] = src
    self.tgt: Final[Type[TGT]] = tgt

src instance-attribute

src: Final[Type[SRC]] = src

tgt instance-attribute

tgt: Final[Type[TGT]] = tgt

convert

convert(source: SRC, /, *args: Unpack[CArgs]) -> TGT

convert source node

PARAMETER	DESCRIPTION
source	A bioimageio description node TYPE: SRC

RAISES	DESCRIPTION
ValidationError	conversion failed

Source code in src/bioimageio/spec/_internal/node_converter.py

def convert(self, source: SRC, /, *args: Unpack[CArgs]) -> TGT:
    """convert `source` node

    Args:
        source: A bioimageio description node

    Raises:
        ValidationError: conversion failed
    """
    data = self.convert_as_dict(source, *args)
    return assert_all_params_set_explicitly(self.tgt)(**data)

convert_as_dict

convert_as_dict(
    source: SRC, /, *args: Unpack[CArgs]
) -> Dict[str, Any]

Source code in src/bioimageio/spec/_internal/node_converter.py

def convert_as_dict(self, source: SRC, /, *args: Unpack[CArgs]) -> Dict[str, Any]:
    return cast(Dict[str, Any], self._convert(source, dict, *args))

_Maintainer_v0_2 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 (Optional[str])
• email (Optional[EmailStr])
• orcid (Optional[OrcidId])
• name (Optional[str])
• github_user (str)

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

@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
        )

_has_no_slash

_has_no_slash(s: str) -> bool

Source code in src/bioimageio/spec/generic/v0_3.py

def _has_no_slash(s: str) -> bool:
    return "/" not in s and "\\" not in s

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

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

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_3_converter.py

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
    fv = data.get("format_version", "0.2.0")
    if (
        not isinstance(fv, str)
        or fv.count(".") != 2
        or tuple(map(int, fv.split(".")[:2])) > (0, 3)
    ):
        return

    convert_from_older_format_v0_2(data)

    convert_attachments(data)
    convert_cover_images(data)

    _ = data.pop("download_url", None)
    _ = data.pop("rdf_source", None)

    if "name" in data and isinstance(data["name"], str):
        data["name"] = "".join(
            c if c in string.ascii_letters + string.digits + "_+- ()" else " "
            for c in data["name"]
        )[:128]

    data["format_version"] = "0.3.0"

is_dict

is_dict(v: Any) -> TypeGuard[Dict[Any, Any]]

to avoid Dict[Unknown, Unknown]

Source code in src/bioimageio/spec/_internal/type_guards.py

def is_dict(v: Any) -> TypeGuard[Dict[Any, Any]]:
    """to avoid Dict[Unknown, Unknown]"""
    return isinstance(v, dict)

is_yaml_value

is_yaml_value(value: Any) -> TypeGuard[YamlValue]

Source code in src/bioimageio/spec/_internal/io.py

def is_yaml_value(value: Any) -> TypeGuard[YamlValue]:
    return is_yaml_leaf_value(value) or is_yaml_list(value) or is_yaml_dict(value)

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

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)

validate_github_user

validate_github_user(
    username: str,
    hotfix_known_errorenous_names: bool = True,
) -> str

Source code in src/bioimageio/spec/_internal/field_validation.py

def validate_github_user(
    username: str, hotfix_known_errorenous_names: bool = True
) -> str:
    if hotfix_known_errorenous_names:
        if username == "Constantin Pape":
            return "constantinpape"

    if (
        username.lower() in KNOWN_GITHUB_USERS
        or not get_validation_context().perform_io_checks
    ):
        return username

    if username.lower() in KNOWN_INVALID_GITHUB_USERS:
        raise ValueError(f"Known invalid GitHub user '{username}'")

    try:
        r = httpx.get(
            f"https://api.github.com/users/{username}",
            auth=settings.github_auth,
            timeout=settings.http_timeout,
        )
    except httpx.TimeoutException:
        issue_warning(
            "Could not verify GitHub user '{value}' due to connection timeout",
            value=username,
        )
    else:
        if r.status_code == 403 and r.reason_phrase == "rate limit exceeded":
            issue_warning(
                "Could not verify GitHub user '{value}' due to GitHub API rate limit",
                value=username,
            )
        elif r.status_code != 200:
            KNOWN_INVALID_GITHUB_USERS.add(username.lower())
            raise ValueError(f"Could not find GitHub user '{username}'")

        KNOWN_GITHUB_USERS.add(username.lower())

    return username

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

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}
    )