add io functionality

Author: FynnBe

bioimageio/spec/_internal/types/__init__.py

@@ -9,8 +9,11 @@
 
 from bioimageio.spec._internal.constants import DOI_REGEX, SI_UNIT_REGEX
 from bioimageio.spec._internal.types._file_source import AbsoluteFilePath as AbsoluteFilePath
+from bioimageio.spec._internal.types._file_source import FileName as FileName
 from bioimageio.spec._internal.types._file_source import FileSource as FileSource
+from bioimageio.spec._internal.types._file_source import PermissiveFileSource as PermissiveFileSource
 from bioimageio.spec._internal.types._file_source import RelativeFilePath as RelativeFilePath
+from bioimageio.spec._internal.types._file_source import StrictFileSource as StrictFileSource
 from bioimageio.spec._internal.types._generated_spdx_license_type import DeprecatedLicenseId as DeprecatedLicenseId
 from bioimageio.spec._internal.types._generated_spdx_license_type import LicenseId as LicenseId
 from bioimageio.spec._internal.types._version import Version as Version
@@ -23,15 +26,15 @@
     validate_orcid_id,
 )
 
-T = TypeVar("T")
 S = TypeVar("S", bound=Sequence[Any])
-
 NotEmpty = Annotated[S, annotated_types.MinLen(1)]
 
 Datetime = Annotated[datetime, BeforeValidator(validate_datetime)]
 """Timestamp in [ISO 8601](#https://en.wikipedia.org/wiki/ISO_8601) format
 with a few restrictions listed [here](https://docs.python.org/3/library/datetime.html#datetime.datetime.fromisoformat)."""
 
+Doi = NewType("Doi", Annotated[str, StringConstraints(pattern=DOI_REGEX)])
+FormatVersionPlaceholder = Literal["latest", "discover"]
 IdentifierStr = Annotated[  # allows to init child NewTypes with str
     NotEmpty[str],
     AfterValidator(validate_identifier),
@@ -40,6 +43,7 @@
 Identifier = NewType("Identifier", IdentifierStr)
 LowerCaseIdentifierStr = Annotated[IdentifierStr, annotated_types.LowerCase]  # allows to init child NewTypes with str
 LowerCaseIdentifier = NewType("LowerCaseIdentifier", LowerCaseIdentifierStr)
+OrcidId = NewType("OrcidId", Annotated[str, AfterValidator(validate_orcid_id)])
 ResourceId = NewType(
     "ResourceId",
     Annotated[
@@ -48,11 +52,7 @@
         annotated_types.Predicate(lambda s: "\\" not in s and s[0] != "/" and s[-1] != "/"),
     ],
 )
-DatasetId = NewType("DatasetId", ResourceId)
-FileName = str
-OrcidId = NewType("OrcidId", Annotated[str, AfterValidator(validate_orcid_id)])
 Sha256 = NewType("Sha256", Annotated[str, annotated_types.Len(64, 64)])
-
 SiUnit = NewType(
     "SiUnit",
     Annotated[
@@ -62,8 +62,6 @@
     ],
 )
 Unit = Union[Literal["arbitrary unit", "px"], SiUnit]
-FormatVersionPlaceholder = Literal["latest", "discover"]
-
 
 # types as loaded from YAML 1.2 (with ruamel.yaml)
 YamlLeafValue = Union[bool, date, datetime, float, int, str, None]
@@ -76,5 +74,6 @@
 #   and don't open another issue a la https://github.com/pydantic/pydantic/issues/8021
 YamlValue = Union[YamlLeafValue, YamlArray, YamlMapping]
 
+# derived types
+DatasetId = NewType("DatasetId", ResourceId)
 RdfContent = Dict[str, YamlValue]
-Doi = NewType("Doi", Annotated[str, StringConstraints(pattern=DOI_REGEX)])

bioimageio/spec/_internal/types/_file_source.py

@@ -102,6 +102,8 @@ def _check_exists(self, root: Union[DirectoryPath, AnyUrl]) -> None:
             raise ValueError(f"{p} does not point to an existing directory")
 
 
+FileName = str
 AbsoluteFilePath = Annotated[FilePath, Predicate(Path.is_absolute)]
-
 FileSource = Union[HttpUrl, AbsoluteFilePath, RelativeFilePath]
+PermissiveFileSource = Union[FileSource, str]
+StrictFileSource = Union[HttpUrl, AbsoluteFilePath]

bioimageio/spec/_internal/utils.py

@@ -1,12 +1,15 @@
 from __future__ import annotations
 
 import sys
-from pathlib import Path
+from pathlib import Path, PurePath
 from typing import Any, Dict, Iterator, Tuple, Type, TypeVar, Union, get_args, get_origin
+from urllib.parse import urlparse
 
-from pydantic import BaseModel
+from pydantic import HttpUrl
 from typing_extensions import Annotated
 
+from bioimageio.spec.typing import RelativeFilePath
+
 K = TypeVar("K")
 V = TypeVar("V")
 NestedDict = Dict[K, "NestedDict[K, V] | V"]
@@ -94,4 +97,10 @@ def unindent(text: str, ignore_first_line: bool = False):
     return "\n".join(lines[:first] + [line[indent:] for line in lines[first:]])
 
 
-Model = TypeVar("Model", bound=BaseModel)
+def extract_file_name(src: Union[HttpUrl, PurePath, RelativeFilePath]) -> str:
+    if isinstance(src, RelativeFilePath):
+        return src.path.name
+    elif isinstance(src, PurePath):
+        return src.name
+    else:
+        return urlparse(str(src)).path.split("/")[-1]

bioimageio/spec/collection/v0_3.py

@@ -1,4 +1,4 @@
-from typing import ClassVar, List, Literal, Tuple, Union
+from typing import ClassVar, List, Literal, Union
 
 from pydantic import Field, TypeAdapter, field_validator
 from pydantic import HttpUrl as HttpUrl