summary

Utilities for summarizing and formatting BioImage.IO validation results.

This module defines data structures to capture validation errors, warnings, and summaries for BioImage.IO resource descriptions, along with helpers to format these results as plain text, Markdown, or HTML for reporting and diagnostics.

Used by:

• API Reference  spec  ValidationSummary

Classes:

Name	Description
ErrorEntry	An error in a ValidationDetail
InstalledPackage
ValidationDetail	a detail in a validation summary
ValidationEntry	Base of ErrorEntry and WarningEntry
ValidationSummary	Summarizes output of all bioimageio validations and tests
WarningEntry	A warning in a ValidationDetail

Functions:

Name	Description
format_loc	helper to format a location tuple loc

Attributes:

Name	Type	Description
CONDA_CMD
Loc		location of error/warning in a nested data structure
WARNING_LEVEL_TO_NAME	Mapping[WarningLevel, WarningLevelName]
WARNING_NAME_TO_LEVEL	Mapping[WarningLevelName, WarningLevel]
WARNING_SEVERITY_TO_NAME	Mapping[WarningSeverity, WarningSeverityName]
WarningLevelName
WarningSeverityName

CONDA_CMD module-attribute

CONDA_CMD = (
    "conda.bat"
    if platform.system() == "Windows"
    else "conda"
)

Loc module-attribute

Loc = Tuple[Union[int, str], ...]

location of error/warning in a nested data structure

Used by:

• API Reference  summary  format_loc

WARNING_LEVEL_TO_NAME module-attribute

WARNING_LEVEL_TO_NAME: Mapping[
    WarningLevel, WarningLevelName
] = MappingProxyType(
    {
        INFO: INFO_NAME,
        WARNING: WARNING_NAME,
        ALERT: ALERT_NAME,
        ERROR: ERROR_NAME,
    }
)

Used by:

• API Reference  summary  WARNING_NAME_TO_LEVEL

WARNING_NAME_TO_LEVEL module-attribute

WARNING_NAME_TO_LEVEL: Mapping[
    WarningLevelName, WarningLevel
] = MappingProxyType(
    {v: k for k, v in (WARNING_LEVEL_TO_NAME.items())}
)

WARNING_SEVERITY_TO_NAME module-attribute

WARNING_SEVERITY_TO_NAME: Mapping[
    WarningSeverity, WarningSeverityName
] = MappingProxyType(
    {
        INFO: INFO_NAME,
        WARNING: WARNING_NAME,
        ALERT: ALERT_NAME,
    }
)

WarningLevelName module-attribute

WarningLevelName = Literal[WarningSeverityName, 'error']

Returned by:

• API Reference  summary
  •  WARNING_LEVEL_TO_NAME
  •  WARNING_NAME_TO_LEVEL

WarningSeverityName module-attribute

WarningSeverityName = Literal['info', 'warning', 'alert']

Returned by:

• API Reference  summary  WARNING_SEVERITY_TO_NAME

Used by:

• API Reference  summary  WarningLevelName

ErrorEntry pydantic-model

Bases: ValidationEntry

An error in a ValidationDetail

Show JSON schema:

{
  "description": "An error in a `ValidationDetail`",
  "properties": {
    "loc": {
      "items": {
        "anyOf": [
          {
            "type": "integer"
          },
          {
            "type": "string"
          }
        ]
      },
      "title": "Loc",
      "type": "array"
    },
    "msg": {
      "title": "Msg",
      "type": "string"
    },
    "type": {
      "anyOf": [
        {
          "enum": [
            "no_such_attribute",
            "json_invalid",
            "json_type",
            "needs_python_object",
            "recursion_loop",
            "missing",
            "frozen_field",
            "frozen_instance",
            "extra_forbidden",
            "invalid_key",
            "get_attribute_error",
            "model_type",
            "model_attributes_type",
            "dataclass_type",
            "dataclass_exact_type",
            "default_factory_not_called",
            "none_required",
            "greater_than",
            "greater_than_equal",
            "less_than",
            "less_than_equal",
            "multiple_of",
            "finite_number",
            "too_short",
            "too_long",
            "iterable_type",
            "iteration_error",
            "string_type",
            "string_sub_type",
            "string_unicode",
            "string_too_short",
            "string_too_long",
            "string_pattern_mismatch",
            "enum",
            "dict_type",
            "mapping_type",
            "list_type",
            "tuple_type",
            "set_type",
            "set_item_not_hashable",
            "bool_type",
            "bool_parsing",
            "int_type",
            "int_parsing",
            "int_parsing_size",
            "int_from_float",
            "float_type",
            "float_parsing",
            "bytes_type",
            "bytes_too_short",
            "bytes_too_long",
            "bytes_invalid_encoding",
            "value_error",
            "assertion_error",
            "literal_error",
            "missing_sentinel_error",
            "date_type",
            "date_parsing",
            "date_from_datetime_parsing",
            "date_from_datetime_inexact",
            "date_past",
            "date_future",
            "time_type",
            "time_parsing",
            "datetime_type",
            "datetime_parsing",
            "datetime_object_invalid",
            "datetime_from_date_parsing",
            "datetime_past",
            "datetime_future",
            "timezone_naive",
            "timezone_aware",
            "timezone_offset",
            "time_delta_type",
            "time_delta_parsing",
            "frozen_set_type",
            "is_instance_of",
            "is_subclass_of",
            "callable_type",
            "union_tag_invalid",
            "union_tag_not_found",
            "arguments_type",
            "missing_argument",
            "unexpected_keyword_argument",
            "missing_keyword_only_argument",
            "unexpected_positional_argument",
            "missing_positional_only_argument",
            "multiple_argument_values",
            "url_type",
            "url_parsing",
            "url_syntax_violation",
            "url_too_long",
            "url_scheme",
            "uuid_type",
            "uuid_parsing",
            "uuid_version",
            "decimal_type",
            "decimal_parsing",
            "decimal_max_digits",
            "decimal_max_places",
            "decimal_whole_digits",
            "complex_type",
            "complex_str_parsing"
          ],
          "type": "string"
        },
        {
          "type": "string"
        }
      ],
      "title": "Type"
    },
    "with_traceback": {
      "default": false,
      "title": "With Traceback",
      "type": "boolean"
    },
    "traceback_md": {
      "default": "",
      "title": "Traceback Md",
      "type": "string"
    },
    "traceback_html": {
      "default": "",
      "title": "Traceback Html",
      "type": "string"
    }
  },
  "required": [
    "loc",
    "msg",
    "type"
  ],
  "title": "ErrorEntry",
  "type": "object"
}

Fields:

• loc (Loc)
• msg (str)
• type (Union[ErrorType, str])
• with_traceback (bool)
• traceback_md (str)
• traceback_html (str)
• _traceback_rich (Optional[rich.traceback.Traceback])

loc pydantic-field

loc: Loc

msg pydantic-field

msg: str

traceback_html pydantic-field

traceback_html: str = ''

traceback_md pydantic-field

traceback_md: str = ''

traceback_rich property

traceback_rich: Optional[rich.traceback.Traceback]

type pydantic-field

type: Union[ErrorType, str]

with_traceback pydantic-field

with_traceback: bool = False

model_post_init

model_post_init(__context: Any)

Source code in src/bioimageio/spec/summary.py

def model_post_init(self, __context: Any):
    if self.with_traceback and not (self.traceback_md or self.traceback_html):
        self._traceback_rich = rich.traceback.Traceback()
        console = rich.console.Console(
            record=True,
            file=open(os.devnull, "wt", encoding="utf-8"),
            color_system="truecolor",
            width=120,
            tab_size=4,
            soft_wrap=True,
        )
        console.print(self._traceback_rich)
        if not self.traceback_md:
            self.traceback_md = console.export_text(clear=False)

        if not self.traceback_html:
            self.traceback_html = console.export_html(clear=False)

InstalledPackage

Bases: NamedTuple

              flowchart TD
              bioimageio.spec.summary.InstalledPackage[InstalledPackage]

              

              click bioimageio.spec.summary.InstalledPackage href "" "bioimageio.spec.summary.InstalledPackage"
            

Attributes:

Name	Type	Description
build	str
channel	str
name	str
version	str

build class-attribute instance-attribute

build: str = ''

channel class-attribute instance-attribute

channel: str = ''

name instance-attribute

name: str

version instance-attribute

version: str

ValidationDetail pydantic-model

Bases: BaseModel

a detail in a validation summary

Show JSON schema:

{
  "$defs": {
    "CondaEnv": {
      "description": "Represenation of the content of a conda environment.yaml file",
      "properties": {
        "name": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Name"
        },
        "channels": {
          "items": {
            "type": "string"
          },
          "title": "Channels",
          "type": "array"
        },
        "dependencies": {
          "items": {
            "anyOf": [
              {
                "type": "string"
              },
              {
                "$ref": "#/$defs/PipDeps"
              }
            ]
          },
          "title": "Dependencies",
          "type": "array"
        }
      },
      "title": "CondaEnv",
      "type": "object"
    },
    "ErrorEntry": {
      "description": "An error in a `ValidationDetail`",
      "properties": {
        "loc": {
          "items": {
            "anyOf": [
              {
                "type": "integer"
              },
              {
                "type": "string"
              }
            ]
          },
          "title": "Loc",
          "type": "array"
        },
        "msg": {
          "title": "Msg",
          "type": "string"
        },
        "type": {
          "anyOf": [
            {
              "enum": [
                "no_such_attribute",
                "json_invalid",
                "json_type",
                "needs_python_object",
                "recursion_loop",
                "missing",
                "frozen_field",
                "frozen_instance",
                "extra_forbidden",
                "invalid_key",
                "get_attribute_error",
                "model_type",
                "model_attributes_type",
                "dataclass_type",
                "dataclass_exact_type",
                "default_factory_not_called",
                "none_required",
                "greater_than",
                "greater_than_equal",
                "less_than",
                "less_than_equal",
                "multiple_of",
                "finite_number",
                "too_short",
                "too_long",
                "iterable_type",
                "iteration_error",
                "string_type",
                "string_sub_type",
                "string_unicode",
                "string_too_short",
                "string_too_long",
                "string_pattern_mismatch",
                "enum",
                "dict_type",
                "mapping_type",
                "list_type",
                "tuple_type",
                "set_type",
                "set_item_not_hashable",
                "bool_type",
                "bool_parsing",
                "int_type",
                "int_parsing",
                "int_parsing_size",
                "int_from_float",
                "float_type",
                "float_parsing",
                "bytes_type",
                "bytes_too_short",
                "bytes_too_long",
                "bytes_invalid_encoding",
                "value_error",
                "assertion_error",
                "literal_error",
                "missing_sentinel_error",
                "date_type",
                "date_parsing",
                "date_from_datetime_parsing",
                "date_from_datetime_inexact",
                "date_past",
                "date_future",
                "time_type",
                "time_parsing",
                "datetime_type",
                "datetime_parsing",
                "datetime_object_invalid",
                "datetime_from_date_parsing",
                "datetime_past",
                "datetime_future",
                "timezone_naive",
                "timezone_aware",
                "timezone_offset",
                "time_delta_type",
                "time_delta_parsing",
                "frozen_set_type",
                "is_instance_of",
                "is_subclass_of",
                "callable_type",
                "union_tag_invalid",
                "union_tag_not_found",
                "arguments_type",
                "missing_argument",
                "unexpected_keyword_argument",
                "missing_keyword_only_argument",
                "unexpected_positional_argument",
                "missing_positional_only_argument",
                "multiple_argument_values",
                "url_type",
                "url_parsing",
                "url_syntax_violation",
                "url_too_long",
                "url_scheme",
                "uuid_type",
                "uuid_parsing",
                "uuid_version",
                "decimal_type",
                "decimal_parsing",
                "decimal_max_digits",
                "decimal_max_places",
                "decimal_whole_digits",
                "complex_type",
                "complex_str_parsing"
              ],
              "type": "string"
            },
            {
              "type": "string"
            }
          ],
          "title": "Type"
        },
        "with_traceback": {
          "default": false,
          "title": "With Traceback",
          "type": "boolean"
        },
        "traceback_md": {
          "default": "",
          "title": "Traceback Md",
          "type": "string"
        },
        "traceback_html": {
          "default": "",
          "title": "Traceback Html",
          "type": "string"
        }
      },
      "required": [
        "loc",
        "msg",
        "type"
      ],
      "title": "ErrorEntry",
      "type": "object"
    },
    "PipDeps": {
      "description": "Pip dependencies to include in conda dependecies",
      "properties": {
        "pip": {
          "items": {
            "type": "string"
          },
          "title": "Pip",
          "type": "array"
        }
      },
      "title": "PipDeps",
      "type": "object"
    },
    "ValidationContextSummary": {
      "additionalProperties": false,
      "properties": {
        "file_name": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "File Name"
        },
        "original_source_name": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Original Source Name"
        },
        "perform_io_checks": {
          "default": true,
          "title": "Perform Io Checks",
          "type": "boolean"
        },
        "known_files": {
          "additionalProperties": {
            "anyOf": [
              {
                "description": "A SHA-256 hash value",
                "maxLength": 64,
                "minLength": 64,
                "title": "Sha256",
                "type": "string"
              },
              {
                "type": "null"
              }
            ]
          },
          "title": "Known Files",
          "type": "object"
        },
        "update_hashes": {
          "default": false,
          "title": "Update Hashes",
          "type": "boolean"
        },
        "root": {
          "anyOf": [
            {
              "description": "An untested HTTP URL, possibly a 'URL folder' or an invalid HTTP URL",
              "format": "uri",
              "maxLength": 2083,
              "minLength": 1,
              "title": "RootHttpUrl",
              "type": "string"
            },
            {
              "format": "path",
              "type": "string"
            },
            {
              "const": "in-memory",
              "type": "string"
            }
          ],
          "default": ".",
          "title": "Root"
        }
      },
      "title": "ValidationContextSummary",
      "type": "object"
    },
    "WarningEntry": {
      "description": "A warning in a `ValidationDetail`",
      "properties": {
        "loc": {
          "items": {
            "anyOf": [
              {
                "type": "integer"
              },
              {
                "type": "string"
              }
            ]
          },
          "title": "Loc",
          "type": "array"
        },
        "msg": {
          "title": "Msg",
          "type": "string"
        },
        "type": {
          "anyOf": [
            {
              "enum": [
                "no_such_attribute",
                "json_invalid",
                "json_type",
                "needs_python_object",
                "recursion_loop",
                "missing",
                "frozen_field",
                "frozen_instance",
                "extra_forbidden",
                "invalid_key",
                "get_attribute_error",
                "model_type",
                "model_attributes_type",
                "dataclass_type",
                "dataclass_exact_type",
                "default_factory_not_called",
                "none_required",
                "greater_than",
                "greater_than_equal",
                "less_than",
                "less_than_equal",
                "multiple_of",
                "finite_number",
                "too_short",
                "too_long",
                "iterable_type",
                "iteration_error",
                "string_type",
                "string_sub_type",
                "string_unicode",
                "string_too_short",
                "string_too_long",
                "string_pattern_mismatch",
                "enum",
                "dict_type",
                "mapping_type",
                "list_type",
                "tuple_type",
                "set_type",
                "set_item_not_hashable",
                "bool_type",
                "bool_parsing",
                "int_type",
                "int_parsing",
                "int_parsing_size",
                "int_from_float",
                "float_type",
                "float_parsing",
                "bytes_type",
                "bytes_too_short",
                "bytes_too_long",
                "bytes_invalid_encoding",
                "value_error",
                "assertion_error",
                "literal_error",
                "missing_sentinel_error",
                "date_type",
                "date_parsing",
                "date_from_datetime_parsing",
                "date_from_datetime_inexact",
                "date_past",
                "date_future",
                "time_type",
                "time_parsing",
                "datetime_type",
                "datetime_parsing",
                "datetime_object_invalid",
                "datetime_from_date_parsing",
                "datetime_past",
                "datetime_future",
                "timezone_naive",
                "timezone_aware",
                "timezone_offset",
                "time_delta_type",
                "time_delta_parsing",
                "frozen_set_type",
                "is_instance_of",
                "is_subclass_of",
                "callable_type",
                "union_tag_invalid",
                "union_tag_not_found",
                "arguments_type",
                "missing_argument",
                "unexpected_keyword_argument",
                "missing_keyword_only_argument",
                "unexpected_positional_argument",
                "missing_positional_only_argument",
                "multiple_argument_values",
                "url_type",
                "url_parsing",
                "url_syntax_violation",
                "url_too_long",
                "url_scheme",
                "uuid_type",
                "uuid_parsing",
                "uuid_version",
                "decimal_type",
                "decimal_parsing",
                "decimal_max_digits",
                "decimal_max_places",
                "decimal_whole_digits",
                "complex_type",
                "complex_str_parsing"
              ],
              "type": "string"
            },
            {
              "type": "string"
            }
          ],
          "title": "Type"
        },
        "severity": {
          "default": 30,
          "enum": [
            20,
            30,
            35
          ],
          "title": "Severity",
          "type": "integer"
        }
      },
      "required": [
        "loc",
        "msg",
        "type"
      ],
      "title": "WarningEntry",
      "type": "object"
    }
  },
  "additionalProperties": true,
  "description": "a detail in a validation summary",
  "properties": {
    "name": {
      "title": "Name",
      "type": "string"
    },
    "status": {
      "enum": [
        "passed",
        "failed"
      ],
      "title": "Status",
      "type": "string"
    },
    "loc": {
      "default": [],
      "items": {
        "anyOf": [
          {
            "type": "integer"
          },
          {
            "type": "string"
          }
        ]
      },
      "title": "Loc",
      "type": "array"
    },
    "errors": {
      "items": {
        "$ref": "#/$defs/ErrorEntry"
      },
      "title": "Errors",
      "type": "array"
    },
    "warnings": {
      "items": {
        "$ref": "#/$defs/WarningEntry"
      },
      "title": "Warnings",
      "type": "array"
    },
    "context": {
      "anyOf": [
        {
          "$ref": "#/$defs/ValidationContextSummary"
        },
        {
          "type": "null"
        }
      ],
      "default": null
    },
    "recommended_env": {
      "anyOf": [
        {
          "$ref": "#/$defs/CondaEnv"
        },
        {
          "type": "null"
        }
      ],
      "default": null
    },
    "saved_conda_compare": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Saved Conda Compare"
    }
  },
  "required": [
    "name",
    "status"
  ],
  "title": "ValidationDetail",
  "type": "object"
}

Fields:

• name (str)
• status (Literal['passed', 'failed'])
• loc (Loc)
• errors (List[ErrorEntry])
• warnings (List[WarningEntry])
• context (Optional[ValidationContextSummary])
• recommended_env (Optional[CondaEnv])
• saved_conda_compare (Optional[str])

Validators:

• _load_legacy

conda_compare property

conda_compare: Optional[str]

context pydantic-field

context: Optional[ValidationContextSummary] = None

errors pydantic-field

errors: List[ErrorEntry]

loc pydantic-field

loc: Loc = ()

location in the RDF that this detail applies to

name pydantic-field

name: str

recommended_env pydantic-field

recommended_env: Optional[CondaEnv] = None

recommended conda environemnt for this validation detail

saved_conda_compare pydantic-field

saved_conda_compare: Optional[str] = None

output of conda compare <recommended env>

status pydantic-field

status: Literal['passed', 'failed']

status_icon property

status_icon: str

warnings pydantic-field

warnings: List[WarningEntry]

ValidationEntry pydantic-model

Bases: BaseModel

Base of ErrorEntry and WarningEntry

Show JSON schema:

{
  "description": "Base of `ErrorEntry` and `WarningEntry`",
  "properties": {
    "loc": {
      "items": {
        "anyOf": [
          {
            "type": "integer"
          },
          {
            "type": "string"
          }
        ]
      },
      "title": "Loc",
      "type": "array"
    },
    "msg": {
      "title": "Msg",
      "type": "string"
    },
    "type": {
      "anyOf": [
        {
          "enum": [
            "no_such_attribute",
            "json_invalid",
            "json_type",
            "needs_python_object",
            "recursion_loop",
            "missing",
            "frozen_field",
            "frozen_instance",
            "extra_forbidden",
            "invalid_key",
            "get_attribute_error",
            "model_type",
            "model_attributes_type",
            "dataclass_type",
            "dataclass_exact_type",
            "default_factory_not_called",
            "none_required",
            "greater_than",
            "greater_than_equal",
            "less_than",
            "less_than_equal",
            "multiple_of",
            "finite_number",
            "too_short",
            "too_long",
            "iterable_type",
            "iteration_error",
            "string_type",
            "string_sub_type",
            "string_unicode",
            "string_too_short",
            "string_too_long",
            "string_pattern_mismatch",
            "enum",
            "dict_type",
            "mapping_type",
            "list_type",
            "tuple_type",
            "set_type",
            "set_item_not_hashable",
            "bool_type",
            "bool_parsing",
            "int_type",
            "int_parsing",
            "int_parsing_size",
            "int_from_float",
            "float_type",
            "float_parsing",
            "bytes_type",
            "bytes_too_short",
            "bytes_too_long",
            "bytes_invalid_encoding",
            "value_error",
            "assertion_error",
            "literal_error",
            "missing_sentinel_error",
            "date_type",
            "date_parsing",
            "date_from_datetime_parsing",
            "date_from_datetime_inexact",
            "date_past",
            "date_future",
            "time_type",
            "time_parsing",
            "datetime_type",
            "datetime_parsing",
            "datetime_object_invalid",
            "datetime_from_date_parsing",
            "datetime_past",
            "datetime_future",
            "timezone_naive",
            "timezone_aware",
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            "time_delta_type",
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            "frozen_set_type",
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            "callable_type",
            "union_tag_invalid",
            "union_tag_not_found",
            "arguments_type",
            "missing_argument",
            "unexpected_keyword_argument",
            "missing_keyword_only_argument",
            "unexpected_positional_argument",
            "missing_positional_only_argument",
            "multiple_argument_values",
            "url_type",
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            "url_syntax_violation",
            "url_too_long",
            "url_scheme",
            "uuid_type",
            "uuid_parsing",
            "uuid_version",
            "decimal_type",
            "decimal_parsing",
            "decimal_max_digits",
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            "decimal_whole_digits",
            "complex_type",
            "complex_str_parsing"
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        {
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      ],
      "title": "Type"
    }
  },
  "required": [
    "loc",
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    "type"
  ],
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  "type": "object"
}

Fields:

• loc (Loc)
• msg (str)
• type (Union[ErrorType, str])

loc pydantic-field

loc: Loc

msg pydantic-field

msg: str

type pydantic-field

type: Union[ErrorType, str]

ValidationSummary pydantic-model

Bases: BaseModel

Summarizes output of all bioimageio validations and tests for one specific ResourceDescr instance.

Show JSON schema:

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      "description": "A warning in a `ValidationDetail`",
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  },
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  "description": "Summarizes output of all bioimageio validations and tests\nfor one specific `ResourceDescr` instance.",
  "properties": {
    "name": {
      "title": "Name",
      "type": "string"
    },
    "source_name": {
      "title": "Source Name",
      "type": "string"
    },
    "id": {
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        {
          "type": "string"
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        {
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      ],
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      ],
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      "maximum": 1,
      "minimum": 0,
      "title": "Metadata Completeness",
      "type": "number"
    },
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      },
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      "type": "array"
    },
    "env": {
      "items": {
        "$ref": "#/$defs/InstalledPackage"
      },
      "title": "Env",
      "type": "array",
      "uniqueItems": true
    },
    "saved_conda_list": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
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    }
  },
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    "name",
    "source_name",
    "type",
    "format_version",
    "status",
    "details"
  ],
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  "type": "object"
}

Fields:

• name (str)
• source_name (str)
• id (Optional[str])
• version (Optional[Version])
• type (str)
• format_version (str)
• status (Literal['passed', 'valid-format', 'failed'])
• metadata_completeness (Annotated[float, annotated_types.Interval(ge=0, le=1)])
• details (List[ValidationDetail])
• env (Set[InstalledPackage])
• saved_conda_list (Optional[str])

Validators:

• _convert_old_env → env

conda_list property

conda_list: str

details pydantic-field

details: List[ValidationDetail]

List of validation details

env pydantic-field

env: Set[InstalledPackage]

List of selected, relevant package versions

errors property

errors: List[ErrorEntry]

format_version pydantic-field

format_version: str

Format version of the validated resource

id pydantic-field

id: Optional[str] = None

ID of the validated resource

metadata_completeness pydantic-field

metadata_completeness: Annotated[
    float, annotated_types.Interval(ge=0, le=1)
] = 0.0

Estimate of completeness of the metadata in the resource description.

This completeness estimate may change with subsequent releases

and should be considered bioimageio.spec version specific.

name pydantic-field

name: str

Name of the validation

saved_conda_list pydantic-field

saved_conda_list: Optional[str] = None

source_name pydantic-field

source_name: str

Source of the validated bioimageio description

status pydantic-field

status: Literal['passed', 'valid-format', 'failed']

Overall status of the bioimageio validation

status_icon property

status_icon: str

type pydantic-field

type: str

Type of the validated resource

version pydantic-field

version: Optional[Version] = None

Version of the validated resource

warnings property

warnings: List[WarningEntry]

add_detail

add_detail(
    detail: ValidationDetail, update_status: bool = True
) -> None

Source code in src/bioimageio/spec/summary.py

def add_detail(self, detail: ValidationDetail, update_status: bool = True) -> None:
    if update_status:
        if self.status == "valid-format" and detail.status == "passed":
            # once status is 'valid-format' we can only improve to 'passed'
            self.status = "passed"
        elif self.status == "passed" and detail.status == "failed":
            # once status is 'passed' it can only degrade to 'valid-format'
            self.status = "valid-format"
        # once format is 'failed' it cannot improve

    self.details.append(detail)

display

display(
    *,
    width: Optional[int] = None,
    include_conda_list: bool = False,
    tab_size: int = 4,
    soft_wrap: bool = True,
) -> None

Source code in src/bioimageio/spec/summary.py

def display(
    self,
    *,
    width: Optional[int] = None,
    include_conda_list: bool = False,
    tab_size: int = 4,
    soft_wrap: bool = True,
) -> None:
    try:  # render as HTML in Jupyter notebook
        from IPython.core.getipython import get_ipython
        from IPython.display import (
            display_html,  # pyright: ignore[reportUnknownVariableType]
        )
    except ImportError:
        pass
    else:
        if get_ipython() is not None:
            _ = display_html(
                self.format_html(
                    width=width, include_conda_list=include_conda_list
                ),
                raw=True,
            )
            return

    # render with rich
    _ = self._format(
        target=rich.console.Console(
            width=width,
            tab_size=tab_size,
            soft_wrap=soft_wrap,
        ),
        width=width,
        include_conda_list=include_conda_list,
    )

format

format(
    *,
    width: Optional[int] = None,
    include_conda_list: bool = False,
) -> str

Format summary as Markdown string (alias to format_md)

Source code in src/bioimageio/spec/summary.py

def format(
    self,
    *,
    width: Optional[int] = None,
    include_conda_list: bool = False,
) -> str:
    """Format summary as Markdown string (alias to `format_md`)"""
    return self.format_md(width=width, include_conda_list=include_conda_list)

format_html

format_html(
    *,
    width: Optional[int] = None,
    include_conda_list: bool = False,
) -> str

Source code in src/bioimageio/spec/summary.py

def format_html(
    self,
    *,
    width: Optional[int] = None,
    include_conda_list: bool = False,
) -> str:
    md_with_html = self._format(
        target="html", width=width, include_conda_list=include_conda_list
    )
    return markdown.markdown(
        md_with_html, extensions=["tables", "fenced_code", "nl2br"]
    )

format_md

format_md(
    *,
    width: Optional[int] = None,
    include_conda_list: bool = False,
) -> str

Format summary as Markdown string

Source code in src/bioimageio/spec/summary.py

def format_md(
    self,
    *,
    width: Optional[int] = None,
    include_conda_list: bool = False,
) -> str:
    """Format summary as Markdown string"""
    return self._format(
        width=width, target="md", include_conda_list=include_conda_list
    )

load_json classmethod

load_json(path: Path) -> Self

Load validation/test summary from a suitable JSON file

Source code in src/bioimageio/spec/summary.py

@classmethod
def load_json(cls, path: Path) -> Self:
    """Load validation/test summary from a suitable JSON file"""
    json_str = Path(path).read_text(encoding="utf-8")
    return cls.model_validate_json(json_str)

log

log(
    to: Union[
        Literal["display"],
        Path,
        Sequence[Union[Literal["display"], Path]],
    ],
) -> List[Path]

Convenience method to display the validation summary in the terminal and/or save it to disk. See save for details.

Source code in src/bioimageio/spec/summary.py

def log(
    self,
    to: Union[Literal["display"], Path, Sequence[Union[Literal["display"], Path]]],
) -> List[Path]:
    """Convenience method to display the validation summary in the terminal and/or
    save it to disk. See `save` for details."""
    if to == "display":
        display = True
        save_to = []
    elif isinstance(to, Path):
        display = False
        save_to = [to]
    else:
        display = "display" in to
        save_to = [p for p in to if p != "display"]

    if display:
        self.display()

    return self.save(save_to)

save

save(
    path: Union[Path, Sequence[Path]] = Path(
        "{id}_summary_{now}"
    ),
) -> List[Path]

Save the validation/test summary in JSON, Markdown or HTML format.

Returns:

Type	Description
List[Path]	List of file paths the summary was saved to.

Notes: - Format is chosen based on the suffix: .json, .md, .html. - If path has no suffix it is assumed to be a direcotry to which a summary.json, summary.md and summary.html are saved to.

Source code in src/bioimageio/spec/summary.py

def save(
    self, path: Union[Path, Sequence[Path]] = Path("{id}_summary_{now}")
) -> List[Path]:
    """Save the validation/test summary in JSON, Markdown or HTML format.

    Returns:
        List of file paths the summary was saved to.

    Notes:
    - Format is chosen based on the suffix: `.json`, `.md`, `.html`.
    - If **path** has no suffix it is assumed to be a direcotry to which a
      `summary.json`, `summary.md` and `summary.html` are saved to.
    """
    if isinstance(path, (str, Path)):
        path = [Path(path)]

    # folder to file paths
    file_paths: List[Path] = []
    for p in path:
        if p.suffix:
            file_paths.append(p)
        else:
            file_paths.extend(
                [
                    p / "summary.json",
                    p / "summary.md",
                    p / "summary.html",
                ]
            )

    now = datetime.now(timezone.utc).strftime("%Y%m%dT%H%M%SZ")
    for p in file_paths:
        p = Path(str(p).format(id=self.id or "bioimageio", now=now))
        if p.suffix == ".json":
            self.save_json(p)
        elif p.suffix == ".md":
            self.save_markdown(p)
        elif p.suffix == ".html":
            self.save_html(p)
        else:
            raise ValueError(f"Unknown summary path suffix '{p.suffix}'")

    return file_paths

save_html

save_html(path: Path = Path('summary.html')) -> None

Save rendered validation/test summary as HTML file.

Source code in src/bioimageio/spec/summary.py

def save_html(self, path: Path = Path("summary.html")) -> None:
    """Save rendered validation/test summary as HTML file."""
    path.parent.mkdir(exist_ok=True, parents=True)

    html = self.format_html()
    _ = path.write_text(html, encoding="utf-8")
    logger.info("Saved HTML formatted summary to {}", path.absolute())

save_json

save_json(
    path: Path = Path("summary.json"),
    *,
    indent: Optional[int] = 2,
) -> None

Save validation/test summary as JSON file.

Source code in src/bioimageio/spec/summary.py

def save_json(
    self, path: Path = Path("summary.json"), *, indent: Optional[int] = 2
) -> None:
    """Save validation/test summary as JSON file."""
    json_str = self.model_dump_json(indent=indent)
    path.parent.mkdir(exist_ok=True, parents=True)
    _ = path.write_text(json_str, encoding="utf-8")
    logger.info("Saved summary to {}", path.absolute())

save_markdown

save_markdown(path: Path = Path('summary.md')) -> None

Save rendered validation/test summary as Markdown file.

Source code in src/bioimageio/spec/summary.py

def save_markdown(self, path: Path = Path("summary.md")) -> None:
    """Save rendered validation/test summary as Markdown file."""
    formatted = self.format_md()
    path.parent.mkdir(exist_ok=True, parents=True)
    _ = path.write_text(formatted, encoding="utf-8")
    logger.info("Saved Markdown formatted summary to {}", path.absolute())

WarningEntry pydantic-model

Bases: ValidationEntry

A warning in a ValidationDetail

Show JSON schema:

{
  "description": "A warning in a `ValidationDetail`",
  "properties": {
    "loc": {
      "items": {
        "anyOf": [
          {
            "type": "integer"
          },
          {
            "type": "string"
          }
        ]
      },
      "title": "Loc",
      "type": "array"
    },
    "msg": {
      "title": "Msg",
      "type": "string"
    },
    "type": {
      "anyOf": [
        {
          "enum": [
            "no_such_attribute",
            "json_invalid",
            "json_type",
            "needs_python_object",
            "recursion_loop",
            "missing",
            "frozen_field",
            "frozen_instance",
            "extra_forbidden",
            "invalid_key",
            "get_attribute_error",
            "model_type",
            "model_attributes_type",
            "dataclass_type",
            "dataclass_exact_type",
            "default_factory_not_called",
            "none_required",
            "greater_than",
            "greater_than_equal",
            "less_than",
            "less_than_equal",
            "multiple_of",
            "finite_number",
            "too_short",
            "too_long",
            "iterable_type",
            "iteration_error",
            "string_type",
            "string_sub_type",
            "string_unicode",
            "string_too_short",
            "string_too_long",
            "string_pattern_mismatch",
            "enum",
            "dict_type",
            "mapping_type",
            "list_type",
            "tuple_type",
            "set_type",
            "set_item_not_hashable",
            "bool_type",
            "bool_parsing",
            "int_type",
            "int_parsing",
            "int_parsing_size",
            "int_from_float",
            "float_type",
            "float_parsing",
            "bytes_type",
            "bytes_too_short",
            "bytes_too_long",
            "bytes_invalid_encoding",
            "value_error",
            "assertion_error",
            "literal_error",
            "missing_sentinel_error",
            "date_type",
            "date_parsing",
            "date_from_datetime_parsing",
            "date_from_datetime_inexact",
            "date_past",
            "date_future",
            "time_type",
            "time_parsing",
            "datetime_type",
            "datetime_parsing",
            "datetime_object_invalid",
            "datetime_from_date_parsing",
            "datetime_past",
            "datetime_future",
            "timezone_naive",
            "timezone_aware",
            "timezone_offset",
            "time_delta_type",
            "time_delta_parsing",
            "frozen_set_type",
            "is_instance_of",
            "is_subclass_of",
            "callable_type",
            "union_tag_invalid",
            "union_tag_not_found",
            "arguments_type",
            "missing_argument",
            "unexpected_keyword_argument",
            "missing_keyword_only_argument",
            "unexpected_positional_argument",
            "missing_positional_only_argument",
            "multiple_argument_values",
            "url_type",
            "url_parsing",
            "url_syntax_violation",
            "url_too_long",
            "url_scheme",
            "uuid_type",
            "uuid_parsing",
            "uuid_version",
            "decimal_type",
            "decimal_parsing",
            "decimal_max_digits",
            "decimal_max_places",
            "decimal_whole_digits",
            "complex_type",
            "complex_str_parsing"
          ],
          "type": "string"
        },
        {
          "type": "string"
        }
      ],
      "title": "Type"
    },
    "severity": {
      "default": 30,
      "enum": [
        20,
        30,
        35
      ],
      "title": "Severity",
      "type": "integer"
    }
  },
  "required": [
    "loc",
    "msg",
    "type"
  ],
  "title": "WarningEntry",
  "type": "object"
}

Fields:

• loc (Loc)
• msg (str)
• type (Union[ErrorType, str])
• severity (WarningSeverity)

loc pydantic-field

loc: Loc

msg pydantic-field

msg: str

severity pydantic-field

severity: WarningSeverity = WARNING

severity_name property

severity_name: WarningSeverityName

type pydantic-field

type: Union[ErrorType, str]

format_loc

format_loc(
    loc: Loc,
    target: Union[
        Literal["md", "html", "plain"], rich.console.Console
    ],
) -> str

helper to format a location tuple loc

Source code in src/bioimageio/spec/summary.py

def format_loc(
    loc: Loc, target: Union[Literal["md", "html", "plain"], rich.console.Console]
) -> str:
    """helper to format a location tuple **loc**"""
    loc_str = ".".join(f"({x})" if x[0].isupper() else x for x in map(str, loc))

    # additional field validation can make the location information quite convoluted, e.g.
    # `weights.pytorch_state_dict.dependencies.source.function-after[validate_url_ok(), url['http','https']]` Input should be a valid URL, relative URL without a base
    # therefore we remove the `.function-after[validate_url_ok(), url['http','https']]` here
    loc_str, *_ = loc_str.split(".function-after")
    if loc_str:
        if target == "md" or isinstance(target, rich.console.Console):
            start = "`"
            end = "`"
        elif target == "html":
            start = "<code>"
            end = "</code>"
        elif target == "plain":
            start = ""
            end = ""
        else:
            assert_never(target)

        return f"{start}{loc_str}{end}"
    else:
        return ""