33class ApplicationDescr(GenericDescrBase):
34    """Bioimage.io description of an application."""
35
36    implemented_type: ClassVar[Literal["application"]] = "application"
37    if TYPE_CHECKING:
38        type: Literal["application"] = "application"
39    else:
40        type: Literal["application"]
41
42    id: Optional[ApplicationId] = None
43    """bioimage.io-wide unique resource identifier
44    assigned by bioimage.io; version **un**specific."""
45
46    parent: Optional[ApplicationId] = None
47    """The description from which this one is derived"""
48
49    source: Annotated[
50        FAIR[Optional[FileSource_]],
51        Field(description="URL or path to the source of the application"),
52    ] = None
53    """The primary source of the application"""

 80class BioimageioCondaEnv(CondaEnv):
 81    """A special `CondaEnv` that
 82    - automatically adds bioimageio specific dependencies
 83    - sorts dependencies
 84    """
 85
 86    @model_validator(mode="after")
 87    def _normalize_bioimageio_conda_env(self):
 88        """update a conda env such that we have bioimageio.core and sorted dependencies"""
 89        for req_channel in ("conda-forge", "nodefaults"):
 90            if req_channel not in self.channels:
 91                self.channels.append(req_channel)
 92
 93        if "defaults" in self.channels:
 94            warnings.warn("removing 'defaults' from conda-channels")
 95            self.channels.remove("defaults")
 96
 97        if "pip" not in self.dependencies:
 98            self.dependencies.append("pip")
 99
100        for dep in self.dependencies:
101            if isinstance(dep, PipDeps):
102                pip_section = dep
103                pip_section.pip.sort()
104                break
105        else:
106            pip_section = None
107
108        if (
109            pip_section is None
110            or not any(pd.startswith("bioimageio.core") for pd in pip_section.pip)
111        ) and not any(
112            d.startswith("bioimageio.core")
113            or d.startswith("conda-forge::bioimageio.core")
114            for d in self.dependencies
115            if not isinstance(d, PipDeps)
116        ):
117            self.dependencies.append("conda-forge::bioimageio.core")
118
119        self.dependencies.sort()
120        return self

173def build_description(
174    content: BioimageioYamlContentView,
175    /,
176    *,
177    context: Optional[ValidationContext] = None,
178    format_version: Union[FormatVersionPlaceholder, str] = DISCOVER,
179) -> Union[ResourceDescr, InvalidDescr]:
180    """build a bioimage.io resource description from an RDF's content.
181
182    Use `load_description` if you want to build a resource description from an rdf.yaml
183    or bioimage.io zip-package.
184
185    Args:
186        content: loaded rdf.yaml file (loaded with YAML, not bioimageio.spec)
187        context: validation context to use during validation
188        format_version: (optional) use this argument to load the resource and
189                        convert its metadata to a higher format_version
190
191    Returns:
192        An object holding all metadata of the bioimage.io resource
193
194    """
195
196    return build_description_impl(
197        content,
198        context=context,
199        format_version=format_version,
200        get_rd_class=_get_rd_class,
201    )

 40class DatasetDescr(GenericDescrBase):
 41    """A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage
 42    processing.
 43    """
 44
 45    implemented_type: ClassVar[Literal["dataset"]] = "dataset"
 46    if TYPE_CHECKING:
 47        type: Literal["dataset"] = "dataset"
 48    else:
 49        type: Literal["dataset"]
 50
 51    id: Optional[DatasetId] = None
 52    """bioimage.io-wide unique resource identifier
 53    assigned by bioimage.io; version **un**specific."""
 54
 55    parent: Optional[DatasetId] = None
 56    """The description from which this one is derived"""
 57
 58    source: FAIR[Optional[HttpUrl]] = None
 59    """"URL to the source of the dataset."""
 60
 61    @model_validator(mode="before")
 62    @classmethod
 63    def _convert(cls, data: Dict[str, Any], /) -> Dict[str, Any]:
 64        if (
 65            data.get("type") == "dataset"
 66            and isinstance(fv := data.get("format_version"), str)
 67            and fv.startswith("0.2.")
 68        ):
 69            old = DatasetDescr02.load(data)
 70            if isinstance(old, InvalidDescr):
 71                return data
 72
 73            return cast(
 74                Dict[str, Any],
 75                (cls if TYPE_CHECKING else dict)(
 76                    attachments=(
 77                        []
 78                        if old.attachments is None
 79                        else [FileDescr(source=f) for f in old.attachments.files]
 80                    ),
 81                    authors=[
 82                        _author_conv.convert_as_dict(a) for a in old.authors
 83                    ],  # pyright: ignore[reportArgumentType]
 84                    badges=old.badges,
 85                    cite=[
 86                        {"text": c.text, "doi": c.doi, "url": c.url} for c in old.cite
 87                    ],  # pyright: ignore[reportArgumentType]
 88                    config=old.config,  # pyright: ignore[reportArgumentType]
 89                    covers=old.covers,
 90                    description=old.description,
 91                    documentation=old.documentation,
 92                    format_version="0.3.0",
 93                    git_repo=old.git_repo,  # pyright: ignore[reportArgumentType]
 94                    icon=old.icon,
 95                    id=None if old.id is None else DatasetId(old.id),
 96                    license=old.license,  # type: ignore
 97                    links=old.links,
 98                    maintainers=[
 99                        _maintainer_conv.convert_as_dict(m) for m in old.maintainers
100                    ],  # pyright: ignore[reportArgumentType]
101                    name=old.name,
102                    source=old.source,
103                    tags=old.tags,
104                    type=old.type,
105                    uploader=old.uploader,
106                    version=old.version,
107                    **(old.model_extra or {}),
108                ),
109            )
110
111        return data

66def dump_description(
67    rd: Union[ResourceDescr, InvalidDescr],
68    /,
69    *,
70    exclude_unset: bool = True,
71    exclude_defaults: bool = False,
72) -> BioimageioYamlContent:
73    """Converts a resource to a dictionary containing only simple types that can directly be serialzed to YAML.
74
75    Args:
76        rd: bioimageio resource description
77        exclude_unset: Exclude fields that have not explicitly be set.
78        exclude_defaults: Exclude fields that have the default value (even if set explicitly).
79    """
80    return rd.model_dump(
81        mode="json", exclude_unset=exclude_unset, exclude_defaults=exclude_defaults
82    )

92def enable_pretty_validation_errors_in_ipynb():
93    """DEPRECATED; this is enabled by default at import time."""
94    warnings.warn(
95        "deprecated, this is enabled by default at import time.",
96        DeprecationWarning,
97        stacklevel=2,
98    )

491class GenericDescr(GenericDescrBase, extra="ignore"):
492    """Specification of the fields used in a generic bioimage.io-compliant resource description file (RDF).
493
494    An RDF is a YAML file that describes a resource such as a model, a dataset, or a notebook.
495    Note that those resources are described with a type-specific RDF.
496    Use this generic resource description, if none of the known specific types matches your resource.
497    """
498
499    implemented_type: ClassVar[Literal["generic"]] = "generic"
500    if TYPE_CHECKING:
501        type: Annotated[str, LowerCase] = "generic"
502        """The resource type assigns a broad category to the resource."""
503    else:
504        type: Annotated[str, LowerCase]
505        """The resource type assigns a broad category to the resource."""
506
507    id: Optional[
508        Annotated[ResourceId, Field(examples=["affable-shark", "ambitious-sloth"])]
509    ] = None
510    """bioimage.io-wide unique resource identifier
511    assigned by bioimage.io; version **un**specific."""
512
513    parent: Optional[ResourceId] = None
514    """The description from which this one is derived"""
515
516    source: Optional[HttpUrl] = None
517    """The primary source of the resource"""
518
519    @field_validator("type", mode="after")
520    @classmethod
521    def check_specific_types(cls, value: str) -> str:
522        if value in KNOWN_SPECIFIC_RESOURCE_TYPES:
523            raise ValueError(
524                f"Use the {value} description instead of this generic description for"
525                + f" your '{value}' resource."
526            )
527
528        return value

27def get_conda_env(
28    *,
29    entry: SupportedWeightsEntry,
30    env_name: Optional[Union[Literal["DROP"], str]] = None,
31) -> BioimageioCondaEnv:
32    """get the recommended Conda environment for a given weights entry description"""
33    if isinstance(entry, (v0_4.OnnxWeightsDescr, v0_5.OnnxWeightsDescr)):
34        conda_env = _get_default_onnx_env(opset_version=entry.opset_version)
35    elif isinstance(
36        entry,
37        (
38            v0_4.PytorchStateDictWeightsDescr,
39            v0_5.PytorchStateDictWeightsDescr,
40            v0_4.TorchscriptWeightsDescr,
41            v0_5.TorchscriptWeightsDescr,
42        ),
43    ):
44        if (
45            isinstance(entry, v0_5.TorchscriptWeightsDescr)
46            or entry.dependencies is None
47        ):
48            conda_env = _get_default_pytorch_env(pytorch_version=entry.pytorch_version)
49        else:
50            conda_env = _get_env_from_deps(entry.dependencies)
51
52    elif isinstance(
53        entry,
54        (
55            v0_4.TensorflowSavedModelBundleWeightsDescr,
56            v0_5.TensorflowSavedModelBundleWeightsDescr,
57        ),
58    ):
59        if entry.dependencies is None:
60            conda_env = _get_default_tf_env(tensorflow_version=entry.tensorflow_version)
61        else:
62            conda_env = _get_env_from_deps(entry.dependencies)
63    elif isinstance(
64        entry,
65        (v0_4.KerasHdf5WeightsDescr, v0_5.KerasHdf5WeightsDescr),
66    ):
67        conda_env = _get_default_tf_env(tensorflow_version=entry.tensorflow_version)
68    else:
69        assert_never(entry)
70
71    if env_name == "DROP":
72        conda_env.name = None
73    elif env_name is not None:
74        conda_env.name = env_name
75
76    return conda_env

40def get_resource_package_content(
41    rd: ResourceDescr,
42    /,
43    *,
44    bioimageio_yaml_file_name: FileName = BIOIMAGEIO_YAML,
45    weights_priority_order: Optional[Sequence[WeightsFormat]] = None,  # model only
46) -> Dict[FileName, Union[HttpUrl, AbsoluteFilePath, BioimageioYamlContent, ZipPath]]:
47    ret: Dict[
48        FileName, Union[HttpUrl, AbsoluteFilePath, BioimageioYamlContent, ZipPath]
49    ] = {}
50    for k, v in get_package_content(
51        rd,
52        bioimageio_yaml_file_name=bioimageio_yaml_file_name,
53        weights_priority_order=weights_priority_order,
54    ).items():
55        if isinstance(v, FileDescr):
56            if isinstance(v.source, (Path, RelativeFilePath)):
57                ret[k] = v.source.absolute()
58            else:
59                ret[k] = v.source
60
61        else:
62            ret[k] = v
63
64    return ret

192def get_validation_context(
193    default: Optional[ValidationContext] = None,
194) -> ValidationContext:
195    """Get the currently active validation context (or a default)"""
196    return _validation_context_var.get() or default or ValidationContext()

392class InvalidDescr(
393    ResourceDescrBase,
394    extra="allow",
395    title="An invalid resource description",
396):
397    """A representation of an invalid resource description"""
398
399    implemented_type: ClassVar[Literal["unknown"]] = "unknown"
400    if TYPE_CHECKING:  # see NodeWithExplicitlySetFields
401        type: Any = "unknown"
402    else:
403        type: Any
404
405    implemented_format_version: ClassVar[Literal["unknown"]] = "unknown"
406    if TYPE_CHECKING:  # see NodeWithExplicitlySetFields
407        format_version: Any = "unknown"
408    else:
409        format_version: Any

180def load_dataset_description(
181    source: Union[PermissiveFileSource, ZipFile],
182    /,
183    *,
184    format_version: Union[FormatVersionPlaceholder, str] = DISCOVER,
185    perform_io_checks: Optional[bool] = None,
186    known_files: Optional[Dict[str, Optional[Sha256]]] = None,
187    sha256: Optional[Sha256] = None,
188) -> AnyDatasetDescr:
189    """same as `load_description`, but addtionally ensures that the loaded
190    description is valid and of type 'dataset'.
191    """
192    rd = load_description(
193        source,
194        format_version=format_version,
195        perform_io_checks=perform_io_checks,
196        known_files=known_files,
197        sha256=sha256,
198    )
199    return ensure_description_is_dataset(rd)

232def load_description_and_validate_format_only(
233    source: Union[PermissiveFileSource, ZipFile],
234    /,
235    *,
236    format_version: Union[FormatVersionPlaceholder, str] = DISCOVER,
237    perform_io_checks: Optional[bool] = None,
238    known_files: Optional[Dict[str, Optional[Sha256]]] = None,
239    sha256: Optional[Sha256] = None,
240) -> ValidationSummary:
241    """same as `load_description`, but only return the validation summary.
242
243    Returns:
244        Validation summary of the bioimage.io resource found at `source`.
245
246    """
247    rd = load_description(
248        source,
249        format_version=format_version,
250        perform_io_checks=perform_io_checks,
251        known_files=known_files,
252        sha256=sha256,
253    )
254    assert rd.validation_summary is not None
255    return rd.validation_summary

 57def load_description(
 58    source: Union[PermissiveFileSource, ZipFile],
 59    /,
 60    *,
 61    format_version: Union[FormatVersionPlaceholder, str] = DISCOVER,
 62    perform_io_checks: Optional[bool] = None,
 63    known_files: Optional[Dict[str, Optional[Sha256]]] = None,
 64    sha256: Optional[Sha256] = None,
 65) -> Union[ResourceDescr, InvalidDescr]:
 66    """load a bioimage.io resource description
 67
 68    Args:
 69        source: Path or URL to an rdf.yaml or a bioimage.io package
 70                (zip-file with rdf.yaml in it).
 71        format_version: (optional) Use this argument to load the resource and
 72                        convert its metadata to a higher format_version.
 73        perform_io_checks: Wether or not to perform validation that requires file io,
 74                           e.g. downloading a remote files. The existence of local
 75                           absolute file paths is still being checked.
 76        known_files: Allows to bypass download and hashing of referenced files
 77                     (even if perform_io_checks is True).
 78                     Checked files will be added to this dictionary
 79                     with their SHA-256 value.
 80        sha256: Optional SHA-256 value of **source**
 81
 82    Returns:
 83        An object holding all metadata of the bioimage.io resource
 84
 85    """
 86    if isinstance(source, ResourceDescrBase):
 87        name = getattr(source, "name", f"{str(source)[:10]}...")
 88        logger.warning("returning already loaded description '{}' as is", name)
 89        return source  # pyright: ignore[reportReturnType]
 90
 91    opened = open_bioimageio_yaml(source, sha256=sha256)
 92
 93    context = get_validation_context().replace(
 94        root=opened.original_root,
 95        file_name=opened.original_file_name,
 96        perform_io_checks=perform_io_checks,
 97        known_files=known_files,
 98    )
 99
100    return build_description(
101        opened.content,
102        context=context,
103        format_version=format_version,
104    )

131def load_model_description(
132    source: Union[PermissiveFileSource, ZipFile],
133    /,
134    *,
135    format_version: Union[FormatVersionPlaceholder, str] = DISCOVER,
136    perform_io_checks: Optional[bool] = None,
137    known_files: Optional[Dict[str, Optional[Sha256]]] = None,
138    sha256: Optional[Sha256] = None,
139) -> AnyModelDescr:
140    """same as `load_description`, but addtionally ensures that the loaded
141    description is valid and of type 'model'.
142
143    Raises:
144        ValueError: for invalid or non-model resources
145    """
146    rd = load_description(
147        source,
148        format_version=format_version,
149        perform_io_checks=perform_io_checks,
150        known_files=known_files,
151        sha256=sha256,
152    )
153    return ensure_description_is_model(rd)