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v0_2 ¤

Used by:

Classes:

Name Description
ApplicationDescr

Bioimage.io description of an application.
ApplicationId
AttachmentsDescr
Author
BadgeDescr

A custom badge
CiteEntry
Doi

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

A URL with the HTTP or HTTPS scheme.
LinkedApplication

Reference to a bioimage.io application.
LinkedResource

Reference to a bioimage.io resource
Maintainer
OrcidId

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

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

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

Attributes:

Name Type Description
FileSource_

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

FileSource_ module-attribute ¤

FileSource_ = Annotated[
    FileSource,
    AfterValidator(wo_special_file_name),
    include_in_package,
]

A file source that is included when packaging the resource.

Used by:

VALID_COVER_IMAGE_EXTENSIONS module-attribute ¤

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

ApplicationDescr pydantic-model ¤

Bases: GenericDescrBase

Bioimage.io description of an application.

Show JSON schema: 
{
  "$defs": {
    "AttachmentsDescr": {
      "additionalProperties": true,
      "properties": {
        "files": {
          "description": "File attachments",
          "items": {
            "anyOf": [
              {
                "description": "A URL with the HTTP or HTTPS scheme.",
                "format": "uri",
                "maxLength": 2083,
                "minLength": 1,
                "title": "HttpUrl",
                "type": "string"
              },
              {
                "$ref": "#/$defs/RelativeFilePath"
              },
              {
                "format": "file-path",
                "title": "FilePath",
                "type": "string"
              }
            ]
          },
          "title": "Files",
          "type": "array"
        }
      },
      "title": "generic.v0_2.AttachmentsDescr",
      "type": "object"
    },
    "Author": {
      "additionalProperties": false,
      "properties": {
        "affiliation": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Affiliation",
          "title": "Affiliation"
        },
        "email": {
          "anyOf": [
            {
              "format": "email",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Email",
          "title": "Email"
        },
        "orcid": {
          "anyOf": [
            {
              "description": "An ORCID identifier, see https://orcid.org/",
              "title": "OrcidId",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "An [ORCID iD](https://support.orcid.org/hc/en-us/sections/360001495313-What-is-ORCID\n) in hyphenated groups of 4 digits, (and [valid](\nhttps://support.orcid.org/hc/en-us/articles/360006897674-Structure-of-the-ORCID-Identifier\n) as per ISO 7064 11,2.)",
          "examples": [
            "0000-0001-2345-6789"
          ],
          "title": "Orcid"
        },
        "name": {
          "title": "Name",
          "type": "string"
        },
        "github_user": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Github User"
        }
      },
      "required": [
        "name"
      ],
      "title": "generic.v0_2.Author",
      "type": "object"
    },
    "BadgeDescr": {
      "additionalProperties": false,
      "description": "A custom badge",
      "properties": {
        "label": {
          "description": "badge label to display on hover",
          "examples": [
            "Open in Colab"
          ],
          "title": "Label",
          "type": "string"
        },
        "icon": {
          "anyOf": [
            {
              "format": "file-path",
              "title": "FilePath",
              "type": "string"
            },
            {
              "$ref": "#/$defs/RelativeFilePath"
            },
            {
              "description": "A URL with the HTTP or HTTPS scheme.",
              "format": "uri",
              "maxLength": 2083,
              "minLength": 1,
              "title": "HttpUrl",
              "type": "string"
            },
            {
              "format": "uri",
              "maxLength": 2083,
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "badge icon (included in bioimage.io package if not a URL)",
          "examples": [
            "https://colab.research.google.com/assets/colab-badge.svg"
          ],
          "title": "Icon"
        },
        "url": {
          "description": "target URL",
          "examples": [
            "https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb"
          ],
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        }
      },
      "required": [
        "label",
        "url"
      ],
      "title": "generic.v0_2.BadgeDescr",
      "type": "object"
    },
    "CiteEntry": {
      "additionalProperties": false,
      "properties": {
        "text": {
          "description": "free text description",
          "title": "Text",
          "type": "string"
        },
        "doi": {
          "anyOf": [
            {
              "description": "A digital object identifier, see https://www.doi.org/",
              "pattern": "^10\\.[0-9]{4}.+$",
              "title": "Doi",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "A digital object identifier (DOI) is the prefered citation reference.\nSee https://www.doi.org/ for details. (alternatively specify `url`)",
          "title": "Doi"
        },
        "url": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "URL to cite (preferably specify a `doi` instead)",
          "title": "Url"
        }
      },
      "required": [
        "text"
      ],
      "title": "generic.v0_2.CiteEntry",
      "type": "object"
    },
    "Maintainer": {
      "additionalProperties": false,
      "properties": {
        "affiliation": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Affiliation",
          "title": "Affiliation"
        },
        "email": {
          "anyOf": [
            {
              "format": "email",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Email",
          "title": "Email"
        },
        "orcid": {
          "anyOf": [
            {
              "description": "An ORCID identifier, see https://orcid.org/",
              "title": "OrcidId",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "An [ORCID iD](https://support.orcid.org/hc/en-us/sections/360001495313-What-is-ORCID\n) in hyphenated groups of 4 digits, (and [valid](\nhttps://support.orcid.org/hc/en-us/articles/360006897674-Structure-of-the-ORCID-Identifier\n) as per ISO 7064 11,2.)",
          "examples": [
            "0000-0001-2345-6789"
          ],
          "title": "Orcid"
        },
        "name": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Name"
        },
        "github_user": {
          "title": "Github User",
          "type": "string"
        }
      },
      "required": [
        "github_user"
      ],
      "title": "generic.v0_2.Maintainer",
      "type": "object"
    },
    "RelativeFilePath": {
      "description": "A path relative to the `rdf.yaml` file (also if the RDF source is a URL).",
      "format": "path",
      "title": "RelativeFilePath",
      "type": "string"
    },
    "Uploader": {
      "additionalProperties": false,
      "properties": {
        "email": {
          "description": "Email",
          "format": "email",
          "title": "Email",
          "type": "string"
        },
        "name": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "name",
          "title": "Name"
        }
      },
      "required": [
        "email"
      ],
      "title": "generic.v0_2.Uploader",
      "type": "object"
    },
    "Version": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "integer"
        },
        {
          "type": "number"
        }
      ],
      "description": "wraps a packaging.version.Version instance for validation in pydantic models",
      "title": "Version"
    },
    "YamlValue": {
      "anyOf": [
        {
          "type": "boolean"
        },
        {
          "format": "date",
          "type": "string"
        },
        {
          "format": "date-time",
          "type": "string"
        },
        {
          "type": "integer"
        },
        {
          "type": "number"
        },
        {
          "type": "string"
        },
        {
          "items": {
            "$ref": "#/$defs/YamlValue"
          },
          "type": "array"
        },
        {
          "additionalProperties": {
            "$ref": "#/$defs/YamlValue"
          },
          "type": "object"
        },
        {
          "type": "null"
        }
      ]
    }
  },
  "additionalProperties": false,
  "description": "Bioimage.io description of an application.",
  "properties": {
    "name": {
      "description": "A human-friendly name of the resource description",
      "minLength": 1,
      "title": "Name",
      "type": "string"
    },
    "description": {
      "title": "Description",
      "type": "string"
    },
    "covers": {
      "description": "Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')",
      "examples": [
        [
          "cover.png"
        ]
      ],
      "items": {
        "anyOf": [
          {
            "description": "A URL with the HTTP or HTTPS scheme.",
            "format": "uri",
            "maxLength": 2083,
            "minLength": 1,
            "title": "HttpUrl",
            "type": "string"
          },
          {
            "$ref": "#/$defs/RelativeFilePath"
          },
          {
            "format": "file-path",
            "title": "FilePath",
            "type": "string"
          }
        ]
      },
      "title": "Covers",
      "type": "array"
    },
    "id_emoji": {
      "anyOf": [
        {
          "examples": [
            "\ud83e\udd88",
            "\ud83e\udda5"
          ],
          "maxLength": 1,
          "minLength": 1,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "UTF-8 emoji for display alongside the `id`.",
      "title": "Id Emoji"
    },
    "authors": {
      "description": "The authors are the creators of the RDF and the primary points of contact.",
      "items": {
        "$ref": "#/$defs/Author"
      },
      "title": "Authors",
      "type": "array"
    },
    "attachments": {
      "anyOf": [
        {
          "$ref": "#/$defs/AttachmentsDescr"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "file and other attachments"
    },
    "cite": {
      "description": "citations",
      "items": {
        "$ref": "#/$defs/CiteEntry"
      },
      "title": "Cite",
      "type": "array"
    },
    "config": {
      "additionalProperties": {
        "$ref": "#/$defs/YamlValue"
      },
      "description": "A field for custom configuration that can contain any keys not present in the RDF spec.\nThis means you should not store, for example, a github repo URL in `config` since we already have the\n`git_repo` field defined in the spec.\nKeys in `config` may be very specific to a tool or consumer software. To avoid conflicting definitions,\nit is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,\nfor example:\n```yaml\nconfig:\n    bioimageio:  # here is the domain name\n        my_custom_key: 3837283\n        another_key:\n            nested: value\n    imagej:       # config specific to ImageJ\n        macro_dir: path/to/macro/file\n```\nIf possible, please use [`snake_case`](https://en.wikipedia.org/wiki/Snake_case) for keys in `config`.\nYou may want to list linked files additionally under `attachments` to include them when packaging a resource\n(packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains\nan altered rdf.yaml file with local references to the downloaded files)",
      "examples": [
        {
          "bioimageio": {
            "another_key": {
              "nested": "value"
            },
            "my_custom_key": 3837283
          },
          "imagej": {
            "macro_dir": "path/to/macro/file"
          }
        }
      ],
      "title": "Config",
      "type": "object"
    },
    "download_url": {
      "anyOf": [
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "URL to download the resource from (deprecated)",
      "title": "Download Url"
    },
    "git_repo": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "A URL to the Git repository where the resource is being developed.",
      "examples": [
        "https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad"
      ],
      "title": "Git Repo"
    },
    "icon": {
      "anyOf": [
        {
          "maxLength": 2,
          "minLength": 1,
          "type": "string"
        },
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "$ref": "#/$defs/RelativeFilePath"
        },
        {
          "format": "file-path",
          "title": "FilePath",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "An icon for illustration",
      "title": "Icon"
    },
    "links": {
      "description": "IDs of other bioimage.io resources",
      "examples": [
        [
          "ilastik/ilastik",
          "deepimagej/deepimagej",
          "zero/notebook_u-net_3d_zerocostdl4mic"
        ]
      ],
      "items": {
        "type": "string"
      },
      "title": "Links",
      "type": "array"
    },
    "uploader": {
      "anyOf": [
        {
          "$ref": "#/$defs/Uploader"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The person who uploaded the model (e.g. to bioimage.io)"
    },
    "maintainers": {
      "description": "Maintainers of this resource.\nIf not specified `authors` are maintainers and at least some of them should specify their `github_user` name",
      "items": {
        "$ref": "#/$defs/Maintainer"
      },
      "title": "Maintainers",
      "type": "array"
    },
    "rdf_source": {
      "anyOf": [
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "$ref": "#/$defs/RelativeFilePath"
        },
        {
          "format": "file-path",
          "title": "FilePath",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from.\nDo not set this field in a YAML file.",
      "title": "Rdf Source"
    },
    "tags": {
      "description": "Associated tags",
      "examples": [
        [
          "unet2d",
          "pytorch",
          "nucleus",
          "segmentation",
          "dsb2018"
        ]
      ],
      "items": {
        "type": "string"
      },
      "title": "Tags",
      "type": "array"
    },
    "version": {
      "anyOf": [
        {
          "$ref": "#/$defs/Version"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The version of the resource following SemVer 2.0."
    },
    "version_number": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "version number (n-th published version, not the semantic version)",
      "title": "Version Number"
    },
    "format_version": {
      "const": "0.2.4",
      "description": "The format version of this resource specification\n(not the `version` of the resource description)\nWhen creating a new resource always use the latest micro/patch version described here.\nThe `format_version` is important for any consumer software to understand how to parse the fields.",
      "title": "Format Version",
      "type": "string"
    },
    "badges": {
      "description": "badges associated with this resource",
      "items": {
        "$ref": "#/$defs/BadgeDescr"
      },
      "title": "Badges",
      "type": "array"
    },
    "documentation": {
      "anyOf": [
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "$ref": "#/$defs/RelativeFilePath"
        },
        {
          "format": "file-path",
          "title": "FilePath",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is `README.md`. An `.md` suffix is mandatory.",
      "examples": [
        "https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md",
        "README.md"
      ],
      "title": "Documentation"
    },
    "license": {
      "anyOf": [
        {
          "enum": [
            "0BSD",
            "3D-Slicer-1.0",
            "AAL",
            "Abstyles",
            "AdaCore-doc",
            "Adobe-2006",
            "Adobe-Display-PostScript",
            "Adobe-Glyph",
            "Adobe-Utopia",
            "ADSL",
            "AFL-1.1",
            "AFL-1.2",
            "AFL-2.0",
            "AFL-2.1",
            "AFL-3.0",
            "Afmparse",
            "AGPL-1.0-only",
            "AGPL-1.0-or-later",
            "AGPL-3.0-only",
            "AGPL-3.0-or-later",
            "Aladdin",
            "AMD-newlib",
            "AMDPLPA",
            "AML",
            "AML-glslang",
            "AMPAS",
            "ANTLR-PD",
            "ANTLR-PD-fallback",
            "any-OSI",
            "any-OSI-perl-modules",
            "Apache-1.0",
            "Apache-1.1",
            "Apache-2.0",
            "APAFML",
            "APL-1.0",
            "App-s2p",
            "APSL-1.0",
            "APSL-1.1",
            "APSL-1.2",
            "APSL-2.0",
            "Arphic-1999",
            "Artistic-1.0",
            "Artistic-1.0-cl8",
            "Artistic-1.0-Perl",
            "Artistic-2.0",
            "Artistic-dist",
            "Aspell-RU",
            "ASWF-Digital-Assets-1.0",
            "ASWF-Digital-Assets-1.1",
            "Baekmuk",
            "Bahyph",
            "Barr",
            "bcrypt-Solar-Designer",
            "Beerware",
            "Bitstream-Charter",
            "Bitstream-Vera",
            "BitTorrent-1.0",
            "BitTorrent-1.1",
            "blessing",
            "BlueOak-1.0.0",
            "Boehm-GC",
            "Boehm-GC-without-fee",
            "Borceux",
            "Brian-Gladman-2-Clause",
            "Brian-Gladman-3-Clause",
            "BSD-1-Clause",
            "BSD-2-Clause",
            "BSD-2-Clause-Darwin",
            "BSD-2-Clause-first-lines",
            "BSD-2-Clause-Patent",
            "BSD-2-Clause-pkgconf-disclaimer",
            "BSD-2-Clause-Views",
            "BSD-3-Clause",
            "BSD-3-Clause-acpica",
            "BSD-3-Clause-Attribution",
            "BSD-3-Clause-Clear",
            "BSD-3-Clause-flex",
            "BSD-3-Clause-HP",
            "BSD-3-Clause-LBNL",
            "BSD-3-Clause-Modification",
            "BSD-3-Clause-No-Military-License",
            "BSD-3-Clause-No-Nuclear-License",
            "BSD-3-Clause-No-Nuclear-License-2014",
            "BSD-3-Clause-No-Nuclear-Warranty",
            "BSD-3-Clause-Open-MPI",
            "BSD-3-Clause-Sun",
            "BSD-4-Clause",
            "BSD-4-Clause-Shortened",
            "BSD-4-Clause-UC",
            "BSD-4.3RENO",
            "BSD-4.3TAHOE",
            "BSD-Advertising-Acknowledgement",
            "BSD-Attribution-HPND-disclaimer",
            "BSD-Inferno-Nettverk",
            "BSD-Protection",
            "BSD-Source-beginning-file",
            "BSD-Source-Code",
            "BSD-Systemics",
            "BSD-Systemics-W3Works",
            "BSL-1.0",
            "BUSL-1.1",
            "bzip2-1.0.6",
            "C-UDA-1.0",
            "CAL-1.0",
            "CAL-1.0-Combined-Work-Exception",
            "Caldera",
            "Caldera-no-preamble",
            "Catharon",
            "CATOSL-1.1",
            "CC-BY-1.0",
            "CC-BY-2.0",
            "CC-BY-2.5",
            "CC-BY-2.5-AU",
            "CC-BY-3.0",
            "CC-BY-3.0-AT",
            "CC-BY-3.0-AU",
            "CC-BY-3.0-DE",
            "CC-BY-3.0-IGO",
            "CC-BY-3.0-NL",
            "CC-BY-3.0-US",
            "CC-BY-4.0",
            "CC-BY-NC-1.0",
            "CC-BY-NC-2.0",
            "CC-BY-NC-2.5",
            "CC-BY-NC-3.0",
            "CC-BY-NC-3.0-DE",
            "CC-BY-NC-4.0",
            "CC-BY-NC-ND-1.0",
            "CC-BY-NC-ND-2.0",
            "CC-BY-NC-ND-2.5",
            "CC-BY-NC-ND-3.0",
            "CC-BY-NC-ND-3.0-DE",
            "CC-BY-NC-ND-3.0-IGO",
            "CC-BY-NC-ND-4.0",
            "CC-BY-NC-SA-1.0",
            "CC-BY-NC-SA-2.0",
            "CC-BY-NC-SA-2.0-DE",
            "CC-BY-NC-SA-2.0-FR",
            "CC-BY-NC-SA-2.0-UK",
            "CC-BY-NC-SA-2.5",
            "CC-BY-NC-SA-3.0",
            "CC-BY-NC-SA-3.0-DE",
            "CC-BY-NC-SA-3.0-IGO",
            "CC-BY-NC-SA-4.0",
            "CC-BY-ND-1.0",
            "CC-BY-ND-2.0",
            "CC-BY-ND-2.5",
            "CC-BY-ND-3.0",
            "CC-BY-ND-3.0-DE",
            "CC-BY-ND-4.0",
            "CC-BY-SA-1.0",
            "CC-BY-SA-2.0",
            "CC-BY-SA-2.0-UK",
            "CC-BY-SA-2.1-JP",
            "CC-BY-SA-2.5",
            "CC-BY-SA-3.0",
            "CC-BY-SA-3.0-AT",
            "CC-BY-SA-3.0-DE",
            "CC-BY-SA-3.0-IGO",
            "CC-BY-SA-4.0",
            "CC-PDDC",
            "CC-PDM-1.0",
            "CC-SA-1.0",
            "CC0-1.0",
            "CDDL-1.0",
            "CDDL-1.1",
            "CDL-1.0",
            "CDLA-Permissive-1.0",
            "CDLA-Permissive-2.0",
            "CDLA-Sharing-1.0",
            "CECILL-1.0",
            "CECILL-1.1",
            "CECILL-2.0",
            "CECILL-2.1",
            "CECILL-B",
            "CECILL-C",
            "CERN-OHL-1.1",
            "CERN-OHL-1.2",
            "CERN-OHL-P-2.0",
            "CERN-OHL-S-2.0",
            "CERN-OHL-W-2.0",
            "CFITSIO",
            "check-cvs",
            "checkmk",
            "ClArtistic",
            "Clips",
            "CMU-Mach",
            "CMU-Mach-nodoc",
            "CNRI-Jython",
            "CNRI-Python",
            "CNRI-Python-GPL-Compatible",
            "COIL-1.0",
            "Community-Spec-1.0",
            "Condor-1.1",
            "copyleft-next-0.3.0",
            "copyleft-next-0.3.1",
            "Cornell-Lossless-JPEG",
            "CPAL-1.0",
            "CPL-1.0",
            "CPOL-1.02",
            "Cronyx",
            "Crossword",
            "CryptoSwift",
            "CrystalStacker",
            "CUA-OPL-1.0",
            "Cube",
            "curl",
            "cve-tou",
            "D-FSL-1.0",
            "DEC-3-Clause",
            "diffmark",
            "DL-DE-BY-2.0",
            "DL-DE-ZERO-2.0",
            "DOC",
            "DocBook-DTD",
            "DocBook-Schema",
            "DocBook-Stylesheet",
            "DocBook-XML",
            "Dotseqn",
            "DRL-1.0",
            "DRL-1.1",
            "DSDP",
            "dtoa",
            "dvipdfm",
            "ECL-1.0",
            "ECL-2.0",
            "EFL-1.0",
            "EFL-2.0",
            "eGenix",
            "Elastic-2.0",
            "Entessa",
            "EPICS",
            "EPL-1.0",
            "EPL-2.0",
            "ErlPL-1.1",
            "etalab-2.0",
            "EUDatagrid",
            "EUPL-1.0",
            "EUPL-1.1",
            "EUPL-1.2",
            "Eurosym",
            "Fair",
            "FBM",
            "FDK-AAC",
            "Ferguson-Twofish",
            "Frameworx-1.0",
            "FreeBSD-DOC",
            "FreeImage",
            "FSFAP",
            "FSFAP-no-warranty-disclaimer",
            "FSFUL",
            "FSFULLR",
            "FSFULLRSD",
            "FSFULLRWD",
            "FSL-1.1-ALv2",
            "FSL-1.1-MIT",
            "FTL",
            "Furuseth",
            "fwlw",
            "Game-Programming-Gems",
            "GCR-docs",
            "GD",
            "generic-xts",
            "GFDL-1.1-invariants-only",
            "GFDL-1.1-invariants-or-later",
            "GFDL-1.1-no-invariants-only",
            "GFDL-1.1-no-invariants-or-later",
            "GFDL-1.1-only",
            "GFDL-1.1-or-later",
            "GFDL-1.2-invariants-only",
            "GFDL-1.2-invariants-or-later",
            "GFDL-1.2-no-invariants-only",
            "GFDL-1.2-no-invariants-or-later",
            "GFDL-1.2-only",
            "GFDL-1.2-or-later",
            "GFDL-1.3-invariants-only",
            "GFDL-1.3-invariants-or-later",
            "GFDL-1.3-no-invariants-only",
            "GFDL-1.3-no-invariants-or-later",
            "GFDL-1.3-only",
            "GFDL-1.3-or-later",
            "Giftware",
            "GL2PS",
            "Glide",
            "Glulxe",
            "GLWTPL",
            "gnuplot",
            "GPL-1.0-only",
            "GPL-1.0-or-later",
            "GPL-2.0-only",
            "GPL-2.0-or-later",
            "GPL-3.0-only",
            "GPL-3.0-or-later",
            "Graphics-Gems",
            "gSOAP-1.3b",
            "gtkbook",
            "Gutmann",
            "HaskellReport",
            "HDF5",
            "hdparm",
            "HIDAPI",
            "Hippocratic-2.1",
            "HP-1986",
            "HP-1989",
            "HPND",
            "HPND-DEC",
            "HPND-doc",
            "HPND-doc-sell",
            "HPND-export-US",
            "HPND-export-US-acknowledgement",
            "HPND-export-US-modify",
            "HPND-export2-US",
            "HPND-Fenneberg-Livingston",
            "HPND-INRIA-IMAG",
            "HPND-Intel",
            "HPND-Kevlin-Henney",
            "HPND-Markus-Kuhn",
            "HPND-merchantability-variant",
            "HPND-MIT-disclaimer",
            "HPND-Netrek",
            "HPND-Pbmplus",
            "HPND-sell-MIT-disclaimer-xserver",
            "HPND-sell-regexpr",
            "HPND-sell-variant",
            "HPND-sell-variant-MIT-disclaimer",
            "HPND-sell-variant-MIT-disclaimer-rev",
            "HPND-UC",
            "HPND-UC-export-US",
            "HTMLTIDY",
            "IBM-pibs",
            "ICU",
            "IEC-Code-Components-EULA",
            "IJG",
            "IJG-short",
            "ImageMagick",
            "iMatix",
            "Imlib2",
            "Info-ZIP",
            "Inner-Net-2.0",
            "InnoSetup",
            "Intel",
            "Intel-ACPI",
            "Interbase-1.0",
            "IPA",
            "IPL-1.0",
            "ISC",
            "ISC-Veillard",
            "Jam",
            "JasPer-2.0",
            "jove",
            "JPL-image",
            "JPNIC",
            "JSON",
            "Kastrup",
            "Kazlib",
            "Knuth-CTAN",
            "LAL-1.2",
            "LAL-1.3",
            "Latex2e",
            "Latex2e-translated-notice",
            "Leptonica",
            "LGPL-2.0-only",
            "LGPL-2.0-or-later",
            "LGPL-2.1-only",
            "LGPL-2.1-or-later",
            "LGPL-3.0-only",
            "LGPL-3.0-or-later",
            "LGPLLR",
            "Libpng",
            "libpng-1.6.35",
            "libpng-2.0",
            "libselinux-1.0",
            "libtiff",
            "libutil-David-Nugent",
            "LiLiQ-P-1.1",
            "LiLiQ-R-1.1",
            "LiLiQ-Rplus-1.1",
            "Linux-man-pages-1-para",
            "Linux-man-pages-copyleft",
            "Linux-man-pages-copyleft-2-para",
            "Linux-man-pages-copyleft-var",
            "Linux-OpenIB",
            "LOOP",
            "LPD-document",
            "LPL-1.0",
            "LPL-1.02",
            "LPPL-1.0",
            "LPPL-1.1",
            "LPPL-1.2",
            "LPPL-1.3a",
            "LPPL-1.3c",
            "lsof",
            "Lucida-Bitmap-Fonts",
            "LZMA-SDK-9.11-to-9.20",
            "LZMA-SDK-9.22",
            "Mackerras-3-Clause",
            "Mackerras-3-Clause-acknowledgment",
            "magaz",
            "mailprio",
            "MakeIndex",
            "man2html",
            "Martin-Birgmeier",
            "McPhee-slideshow",
            "metamail",
            "Minpack",
            "MIPS",
            "MirOS",
            "MIT",
            "MIT-0",
            "MIT-advertising",
            "MIT-Click",
            "MIT-CMU",
            "MIT-enna",
            "MIT-feh",
            "MIT-Festival",
            "MIT-Khronos-old",
            "MIT-Modern-Variant",
            "MIT-open-group",
            "MIT-testregex",
            "MIT-Wu",
            "MITNFA",
            "MMIXware",
            "Motosoto",
            "MPEG-SSG",
            "mpi-permissive",
            "mpich2",
            "MPL-1.0",
            "MPL-1.1",
            "MPL-2.0",
            "MPL-2.0-no-copyleft-exception",
            "mplus",
            "MS-LPL",
            "MS-PL",
            "MS-RL",
            "MTLL",
            "MulanPSL-1.0",
            "MulanPSL-2.0",
            "Multics",
            "Mup",
            "NAIST-2003",
            "NASA-1.3",
            "Naumen",
            "NBPL-1.0",
            "NCBI-PD",
            "NCGL-UK-2.0",
            "NCL",
            "NCSA",
            "NetCDF",
            "Newsletr",
            "NGPL",
            "ngrep",
            "NICTA-1.0",
            "NIST-PD",
            "NIST-PD-fallback",
            "NIST-Software",
            "NLOD-1.0",
            "NLOD-2.0",
            "NLPL",
            "Nokia",
            "NOSL",
            "Noweb",
            "NPL-1.0",
            "NPL-1.1",
            "NPOSL-3.0",
            "NRL",
            "NTIA-PD",
            "NTP",
            "NTP-0",
            "O-UDA-1.0",
            "OAR",
            "OCCT-PL",
            "OCLC-2.0",
            "ODbL-1.0",
            "ODC-By-1.0",
            "OFFIS",
            "OFL-1.0",
            "OFL-1.0-no-RFN",
            "OFL-1.0-RFN",
            "OFL-1.1",
            "OFL-1.1-no-RFN",
            "OFL-1.1-RFN",
            "OGC-1.0",
            "OGDL-Taiwan-1.0",
            "OGL-Canada-2.0",
            "OGL-UK-1.0",
            "OGL-UK-2.0",
            "OGL-UK-3.0",
            "OGTSL",
            "OLDAP-1.1",
            "OLDAP-1.2",
            "OLDAP-1.3",
            "OLDAP-1.4",
            "OLDAP-2.0",
            "OLDAP-2.0.1",
            "OLDAP-2.1",
            "OLDAP-2.2",
            "OLDAP-2.2.1",
            "OLDAP-2.2.2",
            "OLDAP-2.3",
            "OLDAP-2.4",
            "OLDAP-2.5",
            "OLDAP-2.6",
            "OLDAP-2.7",
            "OLDAP-2.8",
            "OLFL-1.3",
            "OML",
            "OpenPBS-2.3",
            "OpenSSL",
            "OpenSSL-standalone",
            "OpenVision",
            "OPL-1.0",
            "OPL-UK-3.0",
            "OPUBL-1.0",
            "OSET-PL-2.1",
            "OSL-1.0",
            "OSL-1.1",
            "OSL-2.0",
            "OSL-2.1",
            "OSL-3.0",
            "PADL",
            "Parity-6.0.0",
            "Parity-7.0.0",
            "PDDL-1.0",
            "PHP-3.0",
            "PHP-3.01",
            "Pixar",
            "pkgconf",
            "Plexus",
            "pnmstitch",
            "PolyForm-Noncommercial-1.0.0",
            "PolyForm-Small-Business-1.0.0",
            "PostgreSQL",
            "PPL",
            "PSF-2.0",
            "psfrag",
            "psutils",
            "Python-2.0",
            "Python-2.0.1",
            "python-ldap",
            "Qhull",
            "QPL-1.0",
            "QPL-1.0-INRIA-2004",
            "radvd",
            "Rdisc",
            "RHeCos-1.1",
            "RPL-1.1",
            "RPL-1.5",
            "RPSL-1.0",
            "RSA-MD",
            "RSCPL",
            "Ruby",
            "Ruby-pty",
            "SAX-PD",
            "SAX-PD-2.0",
            "Saxpath",
            "SCEA",
            "SchemeReport",
            "Sendmail",
            "Sendmail-8.23",
            "Sendmail-Open-Source-1.1",
            "SGI-B-1.0",
            "SGI-B-1.1",
            "SGI-B-2.0",
            "SGI-OpenGL",
            "SGP4",
            "SHL-0.5",
            "SHL-0.51",
            "SimPL-2.0",
            "SISSL",
            "SISSL-1.2",
            "SL",
            "Sleepycat",
            "SMAIL-GPL",
            "SMLNJ",
            "SMPPL",
            "SNIA",
            "snprintf",
            "SOFA",
            "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",
            "SUL-1.0",
            "Sun-PPP",
            "Sun-PPP-2000",
            "SunPro",
            "SWL",
            "swrule",
            "Symlinks",
            "TAPR-OHL-1.0",
            "TCL",
            "TCP-wrappers",
            "TermReadKey",
            "TGPPL-1.0",
            "ThirdEye",
            "threeparttable",
            "TMate",
            "TORQUE-1.1",
            "TOSL",
            "TPDL",
            "TPL-1.0",
            "TrustedQSL",
            "TTWL",
            "TTYP0",
            "TU-Berlin-1.0",
            "TU-Berlin-2.0",
            "Ubuntu-font-1.0",
            "UCAR",
            "UCL-1.0",
            "ulem",
            "UMich-Merit",
            "Unicode-3.0",
            "Unicode-DFS-2015",
            "Unicode-DFS-2016",
            "Unicode-TOU",
            "UnixCrypt",
            "Unlicense",
            "Unlicense-libtelnet",
            "Unlicense-libwhirlpool",
            "UPL-1.0",
            "URT-RLE",
            "Vim",
            "VOSTROM",
            "VSL-1.0",
            "W3C",
            "W3C-19980720",
            "W3C-20150513",
            "w3m",
            "Watcom-1.0",
            "Widget-Workshop",
            "Wsuipa",
            "WTFPL",
            "wwl",
            "X11",
            "X11-distribute-modifications-variant",
            "X11-swapped",
            "Xdebug-1.03",
            "Xerox",
            "Xfig",
            "XFree86-1.1",
            "xinetd",
            "xkeyboard-config-Zinoviev",
            "xlock",
            "Xnet",
            "xpp",
            "XSkat",
            "xzoom",
            "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+",
            "Net-SNMP",
            "Nunit",
            "StandardML-NJ",
            "wxWindows"
          ],
          "title": "DeprecatedLicenseId",
          "type": "string"
        },
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "A [SPDX license identifier](https://spdx.org/licenses/).\nWe do not support custom license beyond the SPDX license list, if you need that please\n[open a GitHub issue](https://github.com/bioimage-io/spec-bioimage-io/issues/new/choose\n) to discuss your intentions with the community.",
      "examples": [
        "CC0-1.0",
        "MIT",
        "BSD-2-Clause"
      ],
      "title": "License"
    },
    "type": {
      "const": "application",
      "title": "Type",
      "type": "string"
    },
    "id": {
      "anyOf": [
        {
          "minLength": 1,
          "title": "ApplicationId",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version **un**specific.",
      "title": "Id"
    },
    "source": {
      "anyOf": [
        {
          "description": "A URL with the HTTP or HTTPS scheme.",
          "format": "uri",
          "maxLength": 2083,
          "minLength": 1,
          "title": "HttpUrl",
          "type": "string"
        },
        {
          "$ref": "#/$defs/RelativeFilePath"
        },
        {
          "format": "file-path",
          "title": "FilePath",
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "URL or path to the source of the application",
      "title": "Source"
    }
  },
  "required": [
    "name",
    "description",
    "format_version",
    "type"
  ],
  "title": "application 0.2.4",
  "type": "object"
}

Fields:

Validators:

attachments pydantic-field ¤

attachments: Optional[AttachmentsDescr] = None

file and other attachments

authors pydantic-field ¤

authors: List[Author]

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

badges pydantic-field ¤

badges: List[BadgeDescr]

badges associated with this resource

cite pydantic-field ¤

cite: List[CiteEntry]

citations

config pydantic-field ¤

config: Annotated[
    Dict[str, YamlValue],
    Field(
        examples=[
            dict(
                bioimageio={
                    my_custom_key: 3837283,
                    another_key: {nested: value},
                },
                imagej={
                    macro_dir: path / to / macro / file
                },
            )
        ]
    ),
]

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

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

covers pydantic-field ¤

covers: List[FileSource_cover]

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

description pydantic-field ¤

description: str

documentation pydantic-field ¤

documentation: Annotated[
    Optional[FileSource],
    Field(
        examples=[
            "https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md",
            README.md,
        ]
    ),
] = None

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

download_url pydantic-field ¤

download_url: Optional[HttpUrl] = None

URL to download the resource from (deprecated)

file_name property ¤

file_name: Optional[FileName]

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

format_version pydantic-field ¤

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

git_repo pydantic-field ¤

git_repo: Annotated[
    Optional[str],
    Field(
        examples=[
            "https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad"
        ]
    ),
] = None

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

icon pydantic-field ¤

icon: Union[
    Annotated[str, Len(min_length=1, max_length=2)],
    FileSource,
    None,
] = None

An icon for illustration

id pydantic-field ¤

id: Optional[ApplicationId] = None

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

id_emoji pydantic-field ¤

id_emoji: Optional[
    Annotated[
        str,
        Len(min_length=1, max_length=1),
        Field(examples=["🦈", "🦥"]),
    ]
] = None

UTF-8 emoji for display alongside the id.

implemented_format_version class-attribute ¤

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

implemented_format_version_tuple class-attribute ¤

implemented_format_version_tuple: Tuple[int, int, int]

implemented_type class-attribute ¤

implemented_type: Literal['application'] = 'application'

license pydantic-field ¤

license: Annotated[
    Union[LicenseId, DeprecatedLicenseId, str, None],
    Field(
        union_mode=left_to_right,
        examples=[CC0 - 1.0, MIT, BSD - 2 - Clause],
    ),
] = 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: Annotated[
    List[str],
    Field(
        examples=[
            (
                ilastik / ilastik,
                deepimagej / deepimagej,
                zero / notebook_u - net_3d_zerocostdl4mic,
            )
        ]
    ),
]

IDs of other bioimage.io resources

maintainers pydantic-field ¤

maintainers: List[Maintainer]

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

name pydantic-field ¤

name: Annotated[
    NotEmpty[str],
    warn(MaxLen(128), "Longer than 128 characters."),
]

A human-friendly name of the resource description

rdf_source pydantic-field ¤

rdf_source: Optional[FileSource] = None

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

root property ¤

root: Union[RootHttpUrl, DirectoryPath, ZipFile]

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

source pydantic-field ¤

source: Annotated[
    Optional[FileSource_],
    Field(
        description="URL or path to the source of the application"
    ),
] = None

The primary source of the application

tags pydantic-field ¤

tags: Annotated[
    List[str],
    Field(
        examples=[
            (
                unet2d,
                pytorch,
                nucleus,
                segmentation,
                dsb2018,
            )
        ]
    ),
]

Associated tags

type pydantic-field ¤

type: Literal['application'] = 'application'

uploader pydantic-field ¤

uploader: Optional[Uploader] = None

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

validation_summary property ¤

validation_summary: ValidationSummary

version pydantic-field ¤

version: Optional[Version] = None

The version of the resource following SemVer 2.0.

version_number pydantic-field ¤

version_number: Optional[int] = None

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

__pydantic_init_subclass__ classmethod ¤

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

accept_author_strings pydantic-validator ¤

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

we unofficially accept strings as author entries

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

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

    return authors

deprecated_spdx_license pydantic-validator ¤

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

    return value

get_package_content ¤

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

Returns package content without creating the package.

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

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

    return {**content, BIOIMAGEIO_YAML: rdf_content}

load classmethod ¤

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

factory method to create a resource description object

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

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

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

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

    return rd

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[
        Literal["allow", "ignore", "forbid"]
    ] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = None,
) -> Self

Validate a pydantic model instance.

Parameters:

Name Type Description Default

obj ¤

 Union[Any, Mapping[str, Any]]

The object to validate.

 required

strict ¤

 Optional[bool]

Whether to raise an exception on invalid fields.

 None

from_attributes ¤

 Optional[bool]

Whether to extract data from object attributes.

 None

context ¤

 Union[ValidationContext, Mapping[str, Any], None]

Additional context to pass to the validator.

 None

Raises:

Type Description
ValidationError

If the object failed validation.

Returns:

Type Description
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[Literal["allow", "ignore", "forbid"]] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = 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

    # TODO: pass on extra with pydantic >=2.12
    if extra is not None:
        warnings.warn("`extra` argument is currently ignored")

    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

Parameters:

Name Type Description Default

dest ¤

 Optional[Union[ZipFile, IO[bytes], Path, str]]

(path/bytes stream of) destination zipfile

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

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

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

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

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

warn_about_tag_categories pydantic-validator ¤

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

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

    return value

ApplicationId ¤

Bases: ResourceId


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

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



              click bioimageio.spec.application.v0_2.ApplicationId href "" "bioimageio.spec.application.v0_2.ApplicationId"
              click bioimageio.spec.generic.v0_2.ResourceId href "" "bioimageio.spec.generic.v0_2.ResourceId"
              click bioimageio.spec._internal.validated_string.ValidatedString href "" "bioimageio.spec._internal.validated_string.ValidatedString"

Methods:

Name Description
__get_pydantic_core_schema__
__get_pydantic_json_schema__
__new__

Attributes:

Name Type Description
root_model Type[RootModel[Any]]

the pydantic root model to validate the string

root_model class-attribute ¤

root_model: Type[RootModel[Any]] = RootModel[
    Annotated[
        NotEmpty[str],
        AfterValidator(str.lower),
        RestrictCharacters(
            string.ascii_lowercase + string.digits + "_-/."
        ),
        annotated_types.Predicate(
            lambda s: (
                not (s.startswith("/") or s.endswith("/"))
            )
        ),
    ]
]

the pydantic root model to validate the string

__get_pydantic_core_schema__ classmethod ¤

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

__get_pydantic_json_schema__ classmethod ¤

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

    return json_schema

__new__ ¤

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

AttachmentsDescr pydantic-model ¤

Bases: Node

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

Config:

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

Fields:

files pydantic-field ¤

files: List[FileSource_]

File attachments

model_config class-attribute instance-attribute ¤

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

update pydantic model config to allow additional unknown keys

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[
        Literal["allow", "ignore", "forbid"]
    ] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = None,
) -> Self

Validate a pydantic model instance.

Parameters:

Name Type Description Default

obj ¤

 Union[Any, Mapping[str, Any]]

The object to validate.

 required

strict ¤

 Optional[bool]

Whether to raise an exception on invalid fields.

 None

from_attributes ¤

 Optional[bool]

Whether to extract data from object attributes.

 None

context ¤

 Union[ValidationContext, Mapping[str, Any], None]

Additional context to pass to the validator.

 None

Raises:

Type Description
ValidationError

If the object failed validation.

Returns:

Type Description
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[Literal["allow", "ignore", "forbid"]] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = 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

    # TODO: pass on extra with pydantic >=2.12
    if extra is not None:
        warnings.warn("`extra` argument is currently ignored")

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

Author pydantic-model ¤

Bases: _Person

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

Fields:

affiliation pydantic-field ¤

affiliation: Optional[str] = None

Affiliation

email pydantic-field ¤

email: Optional[EmailStr] = None

Email

github_user pydantic-field ¤

github_user: Optional[str] = None

name pydantic-field ¤

name: Annotated[str, AfterValidator(_remove_slashes)]

orcid pydantic-field ¤

orcid: Annotated[
    Optional[OrcidId],
    Field(examples=["0000-0001-2345-6789"]),
] = 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,
    extra: Optional[
        Literal["allow", "ignore", "forbid"]
    ] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = None,
) -> Self

Validate a pydantic model instance.

Parameters:

Name Type Description Default

obj ¤

 Union[Any, Mapping[str, Any]]

The object to validate.

 required

strict ¤

 Optional[bool]

Whether to raise an exception on invalid fields.

 None

from_attributes ¤

 Optional[bool]

Whether to extract data from object attributes.

 None

context ¤

 Union[ValidationContext, Mapping[str, Any], None]

Additional context to pass to the validator.

 None

Raises:

Type Description
ValidationError

If the object failed validation.

Returns:

Type Description
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[Literal["allow", "ignore", "forbid"]] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = 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

    # TODO: pass on extra with pydantic >=2.12
    if extra is not None:
        warnings.warn("`extra` argument is currently ignored")

    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 (Annotated[str, Field(examples=[Open in Colab])])
  • icon (Annotated[Optional[Union[Annotated[Union[FilePath, RelativeFilePath], AfterValidator(wo_special_file_name), include_in_package], Union[HttpUrl, pydantic.HttpUrl]]], Field(examples=['https://colab.research.google.com/assets/colab-badge.svg'])])
  • url (Annotated[HttpUrl, Field(examples=['https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb'])])

icon pydantic-field ¤

icon: Annotated[
    Optional[
        Union[
            Annotated[
                Union[FilePath, RelativeFilePath],
                AfterValidator(wo_special_file_name),
                include_in_package,
            ],
            Union[HttpUrl, pydantic.HttpUrl],
        ]
    ],
    Field(
        examples=[
            "https://colab.research.google.com/assets/colab-badge.svg"
        ]
    ),
] = None

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

label pydantic-field ¤

label: Annotated[str, Field(examples=[Open in Colab])]

badge label to display on hover

url pydantic-field ¤

url: Annotated[
    HttpUrl,
    Field(
        examples=[
            "https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb"
        ]
    ),
]

target URL

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[
        Literal["allow", "ignore", "forbid"]
    ] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = None,
) -> Self

Validate a pydantic model instance.

Parameters:

Name Type Description Default

obj ¤

 Union[Any, Mapping[str, Any]]

The object to validate.

 required

strict ¤

 Optional[bool]

Whether to raise an exception on invalid fields.

 None

from_attributes ¤

 Optional[bool]

Whether to extract data from object attributes.

 None

context ¤

 Union[ValidationContext, Mapping[str, Any], None]

Additional context to pass to the validator.

 None

Raises:

Type Description
ValidationError

If the object failed validation.

Returns:

Type Description
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[Literal["allow", "ignore", "forbid"]] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = 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

    # TODO: pass on extra with pydantic >=2.12
    if extra is not None:
        warnings.warn("`extra` argument is currently ignored")

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

CiteEntry pydantic-model ¤

Bases: Node

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

Fields:

Validators:

doi pydantic-field ¤

doi: Optional[Doi] = None

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

text pydantic-field ¤

text: str

free text description

url pydantic-field ¤

url: Optional[str] = None

URL to cite (preferably specify a doi instead)

accept_prefixed_doi pydantic-validator ¤

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

    return doi

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[
        Literal["allow", "ignore", "forbid"]
    ] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = None,
) -> Self

Validate a pydantic model instance.

Parameters:

Name Type Description Default

obj ¤

 Union[Any, Mapping[str, Any]]

The object to validate.

 required

strict ¤

 Optional[bool]

Whether to raise an exception on invalid fields.

 None

from_attributes ¤

 Optional[bool]

Whether to extract data from object attributes.

 None

context ¤

 Union[ValidationContext, Mapping[str, Any], None]

Additional context to pass to the validator.

 None

Raises:

Type Description
ValidationError

If the object failed validation.

Returns:

Type Description
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[Literal["allow", "ignore", "forbid"]] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = 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

    # TODO: pass on extra with pydantic >=2.12
    if extra is not None:
        warnings.warn("`extra` argument is currently ignored")

    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
        )

Doi ¤

Bases: ValidatedString


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

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


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

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

Methods:

Name Description
__get_pydantic_core_schema__
__get_pydantic_json_schema__
__new__

Attributes:

Name Type Description
root_model Type[RootModel[Any]]

the pydantic root model to validate the string

root_model class-attribute ¤

root_model: Type[RootModel[Any]] = RootModel[
    Annotated[str, StringConstraints(pattern=DOI_REGEX)]
]

the pydantic root model to validate the string

__get_pydantic_core_schema__ classmethod ¤

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

__get_pydantic_json_schema__ classmethod ¤

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

    return json_schema

__new__ ¤

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

HttpUrl ¤

Bases: RootHttpUrl


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

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



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

A URL with the HTTP or HTTPS scheme.

Returned by: Subclassed by: Used by:

Methods:

Name Description
__get_pydantic_core_schema__
__get_pydantic_json_schema__
__new__
absolute

analog to absolute method of pathlib.
exists

True if URL is available

Attributes:

Name Type Description
host Optional[str]
parent RootHttpUrl
parents Iterable[RootHttpUrl]

iterate over all URL parents (max 100)
path Optional[str]
root_model Type[RootModel[Any]]

the pydantic root model to validate the string
scheme str
suffix 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
]

the pydantic root model to validate the string

scheme property ¤

scheme: str

suffix property ¤

suffix: str

__get_pydantic_core_schema__ classmethod ¤

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

__get_pydantic_json_schema__ classmethod ¤

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

    return json_schema

__new__ ¤

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

absolute ¤

absolute()

analog to absolute method of pathlib.

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

exists ¤

exists()

True if URL is available

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

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

    return self._exists

LinkedApplication pydantic-model ¤

Bases: Node

Reference to a bioimage.io application.

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

Fields:

id pydantic-field ¤

id: ApplicationId

A valid application id from the bioimage.io collection.

version_number pydantic-field ¤

version_number: Optional[int] = None

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

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[
        Literal["allow", "ignore", "forbid"]
    ] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = None,
) -> Self

Validate a pydantic model instance.

Parameters:

Name Type Description Default

obj ¤

 Union[Any, Mapping[str, Any]]

The object to validate.

 required

strict ¤

 Optional[bool]

Whether to raise an exception on invalid fields.

 None

from_attributes ¤

 Optional[bool]

Whether to extract data from object attributes.

 None

context ¤

 Union[ValidationContext, Mapping[str, Any], None]

Additional context to pass to the validator.

 None

Raises:

Type Description
ValidationError

If the object failed validation.

Returns:

Type Description
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[Literal["allow", "ignore", "forbid"]] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = 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

    # TODO: pass on extra with pydantic >=2.12
    if extra is not None:
        warnings.warn("`extra` argument is currently ignored")

    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
        )

LinkedResource pydantic-model ¤

Bases: Node

Reference to a bioimage.io resource

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

Fields:

id pydantic-field ¤

id: ResourceId

A valid resource id from the bioimage.io collection.

version_number pydantic-field ¤

version_number: Optional[int] = None

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

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[
        Literal["allow", "ignore", "forbid"]
    ] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = None,
) -> Self

Validate a pydantic model instance.

Parameters:

Name Type Description Default

obj ¤

 Union[Any, Mapping[str, Any]]

The object to validate.

 required

strict ¤

 Optional[bool]

Whether to raise an exception on invalid fields.

 None

from_attributes ¤

 Optional[bool]

Whether to extract data from object attributes.

 None

context ¤

 Union[ValidationContext, Mapping[str, Any], None]

Additional context to pass to the validator.

 None

Raises:

Type Description
ValidationError

If the object failed validation.

Returns:

Type Description
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[Literal["allow", "ignore", "forbid"]] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = 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

    # TODO: pass on extra with pydantic >=2.12
    if extra is not None:
        warnings.warn("`extra` argument is currently ignored")

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

Maintainer pydantic-model ¤

Bases: _Person

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

Fields:

affiliation pydantic-field ¤

affiliation: Optional[str] = None

Affiliation

email pydantic-field ¤

email: Optional[EmailStr] = None

Email

github_user pydantic-field ¤

github_user: str

name pydantic-field ¤

name: Optional[
    Annotated[str, AfterValidator(_remove_slashes)]
] = None

orcid pydantic-field ¤

orcid: Annotated[
    Optional[OrcidId],
    Field(examples=["0000-0001-2345-6789"]),
] = 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,
    extra: Optional[
        Literal["allow", "ignore", "forbid"]
    ] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = None,
) -> Self

Validate a pydantic model instance.

Parameters:

Name Type Description Default

obj ¤

 Union[Any, Mapping[str, Any]]

The object to validate.

 required

strict ¤

 Optional[bool]

Whether to raise an exception on invalid fields.

 None

from_attributes ¤

 Optional[bool]

Whether to extract data from object attributes.

 None

context ¤

 Union[ValidationContext, Mapping[str, Any], None]

Additional context to pass to the validator.

 None

Raises:

Type Description
ValidationError

If the object failed validation.

Returns:

Type Description
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[Literal["allow", "ignore", "forbid"]] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = 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

    # TODO: pass on extra with pydantic >=2.12
    if extra is not None:
        warnings.warn("`extra` argument is currently ignored")

    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.application.v0_2.OrcidId[OrcidId]
              bioimageio.spec._internal.validated_string.ValidatedString[ValidatedString]

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


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

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

Methods:

Name Description
__get_pydantic_core_schema__
__get_pydantic_json_schema__
__new__

Attributes:

Name Type Description
root_model Type[RootModel[Any]]

the pydantic root model to validate the string

root_model class-attribute ¤

root_model: Type[RootModel[Any]] = RootModel[
    Annotated[str, AfterValidator(_validate_orcid_id)]
]

the pydantic root model to validate the string

__get_pydantic_core_schema__ classmethod ¤

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

__get_pydantic_json_schema__ classmethod ¤

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

    return json_schema

__new__ ¤

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

RelativeFilePath ¤

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


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

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


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

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

Used by:

Methods:

Name Description
__repr__
__str__
absolute

get the absolute path/url
format
get_absolute
model_post_init

add validation @private

Attributes:

Name Type Description
path PurePath
suffix

path property ¤

path: PurePath

suffix property ¤

suffix

__repr__ ¤

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

__str__ ¤

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

absolute ¤

absolute() -> AbsolutePathT

get the absolute path/url

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

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

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

format ¤

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

get_absolute ¤

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

    return absolute

model_post_init ¤

model_post_init(__context: Any) -> None

add validation @private

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

    super().model_post_init(__context)

ResourceId ¤

Bases: ValidatedString


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

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


              click bioimageio.spec.application.v0_2.ResourceId href "" "bioimageio.spec.application.v0_2.ResourceId"
              click bioimageio.spec._internal.validated_string.ValidatedString href "" "bioimageio.spec._internal.validated_string.ValidatedString"
Subclassed by:

Methods:

Name Description
__get_pydantic_core_schema__
__get_pydantic_json_schema__
__new__

Attributes:

Name Type Description
root_model Type[RootModel[Any]]

the pydantic root model to validate the string

root_model class-attribute ¤

root_model: Type[RootModel[Any]] = RootModel[
    Annotated[
        NotEmpty[str],
        AfterValidator(str.lower),
        RestrictCharacters(
            string.ascii_lowercase + string.digits + "_-/."
        ),
        annotated_types.Predicate(
            lambda s: (
                not (s.startswith("/") or s.endswith("/"))
            )
        ),
    ]
]

the pydantic root model to validate the string

__get_pydantic_core_schema__ classmethod ¤

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

__get_pydantic_json_schema__ classmethod ¤

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

    return json_schema

__new__ ¤

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

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[Annotated[str, AfterValidator(_remove_slashes)]])

email pydantic-field ¤

email: EmailStr

Email

name pydantic-field ¤

name: Optional[
    Annotated[str, AfterValidator(_remove_slashes)]
] = None

name

model_validate classmethod ¤

model_validate(
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[
        Literal["allow", "ignore", "forbid"]
    ] = None,
    from_attributes: Optional[bool] = None,
    context: Union[
        ValidationContext, Mapping[str, Any], None
    ] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = None,
) -> Self

Validate a pydantic model instance.

Parameters:

Name Type Description Default

obj ¤

 Union[Any, Mapping[str, Any]]

The object to validate.

 required

strict ¤

 Optional[bool]

Whether to raise an exception on invalid fields.

 None

from_attributes ¤

 Optional[bool]

Whether to extract data from object attributes.

 None

context ¤

 Union[ValidationContext, Mapping[str, Any], None]

Additional context to pass to the validator.

 None

Raises:

Type Description
ValidationError

If the object failed validation.

Returns:

Type Description
Self

The validated description instance.
Source code in src/bioimageio/spec/_internal/node.py 
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@classmethod
def model_validate(
    cls,
    obj: Union[Any, Mapping[str, Any]],
    *,
    strict: Optional[bool] = None,
    extra: Optional[Literal["allow", "ignore", "forbid"]] = None,
    from_attributes: Optional[bool] = None,
    context: Union[ValidationContext, Mapping[str, Any], None] = None,
    by_alias: Optional[bool] = None,
    by_name: Optional[bool] = 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

    # TODO: pass on extra with pydantic >=2.12
    if extra is not None:
        warnings.warn("`extra` argument is currently ignored")

    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
        )

Version ¤

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


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

              

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

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

Methods:

Name Description
__eq__
__lt__
__str__
model_post_init

set _version attribute @private

Attributes:

Name Type Description
base_version str

The "base version" of the version.
dev Optional[int]

The development number of the version.
epoch int

The epoch of the version.
is_devrelease bool

Whether this version is a development release.
is_postrelease bool

Whether this version is a post-release.
is_prerelease bool

Whether this version is a pre-release.
local Optional[str]

The local version segment of the version.
major int

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

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

The second item of :attr:release or 0 if unavailable.
post Optional[int]

The post-release number of the version.
pre Optional[Tuple[str, int]]

The pre-release segment of the version.
public str

The public portion of the version.
release Tuple[int, ...]

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

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: Any)
Source code in src/bioimageio/spec/_internal/version_type.py 
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def __eq__(self, other: Any):
    if not isinstance(other, Version):
        return NotImplemented
    return self._version == other._version

__lt__ ¤

__lt__(other: Any)
Source code in src/bioimageio/spec/_internal/version_type.py 
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def __lt__(self, other: Any):
    if not isinstance(other, Version):
        return NotImplemented

    return self._version < other._version

__str__ ¤

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

model_post_init ¤

model_post_init(__context: Any) -> None

set _version attribute @private

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