update io functions

bioimageio/spec/__init__.py

@@ -12,7 +12,7 @@
 from bioimageio.spec._description import validate_format as validate_format
 from bioimageio.spec._internal.constants import VERSION
 from bioimageio.spec._io import load_description as load_description
-from bioimageio.spec._io import save_description as save_description
+from bioimageio.spec._io import save_bioimageio_yaml_only as save_bioimageio_yaml_only
 from bioimageio.spec.application import AnyApplication as AnyApplication
 from bioimageio.spec.application import Application as Application
 from bioimageio.spec.collection import AnyCollection as AnyCollection

bioimageio/spec/_internal/io_utils.py

@@ -10,7 +10,7 @@
 from zipfile import ZipFile, is_zipfile
 
 import pooch
-from pydantic import AnyUrl, DirectoryPath, FilePath, HttpUrl, TypeAdapter
+from pydantic import AnyUrl, DirectoryPath, FilePath, HttpUrl, NewPath, TypeAdapter
 from ruamel.yaml import YAML
 from typing_extensions import NotRequired, Unpack
 
@@ -87,7 +87,7 @@ def read_yaml(file: Union[FilePath, TextIO]) -> YamlValue:
         yaml.load(f)
 
 
-def write_yaml(content: YamlValue, /, file: Union[FilePath, TextIO]):
+def write_yaml(content: YamlValue, /, file: Union[NewPath, FilePath, TextIO]):
     if isinstance(file, Path):
         cm = file.open("w", encoding="utf-8")
     else:

bioimageio/spec/_internal/types/__init__.py

@@ -65,7 +65,6 @@
         BeforeValidator(lambda s: s.replace("×", "·").replace("*", "·").replace(" ", "·") if isinstance(s, str) else s),
     ],
 )
-Unit = Union[Literal["arbitrary unit", "px"], SiUnit]
 
 # types as loaded from YAML 1.2 (with ruamel.yaml)
 YamlLeafValue = Union[bool, date, datetime, float, int, str, None]
@@ -81,3 +80,4 @@
 # derived types
 DatasetId = NewType("DatasetId", ResourceId)
 BioimageioYamlContent = Dict[str, YamlValue]
+BioimageioYamlSource = Union[PermissiveFileSource, BioimageioYamlContent]

bioimageio/spec/_io.py

@@ -1,6 +1,6 @@
 from typing import Literal, TextIO, Union, cast
 
-from pydantic import FilePath
+from pydantic import FilePath, NewPath
 
 from bioimageio.spec import ResourceDescription
 from bioimageio.spec._description import InvalidDescription, build_description, dump_description
@@ -30,7 +30,9 @@ def load_description(
     )
 
 
-def save_description(rd: Union[ResourceDescription, BioimageioYamlContent], /, file: Union[FilePath, TextIO]):
+def save_bioimageio_yaml_only(
+    rd: Union[ResourceDescription, BioimageioYamlContent], /, file: Union[NewPath, FilePath, TextIO]
+):
     if isinstance(rd, ResourceDescriptionBase):
         content = dump_description(rd)
     else:

bioimageio/spec/_package.py

@@ -6,29 +6,32 @@
 from typing import Any, Dict, Literal, Optional, Sequence, Tuple, Union, cast
 from zipfile import ZIP_DEFLATED
 
-from pydantic import AnyUrl, DirectoryPath, FilePath, HttpUrl
+from pydantic import AnyUrl, DirectoryPath, FilePath, HttpUrl, NewPath
 
 from bioimageio.spec import model
 from bioimageio.spec._description import InvalidDescription, ResourceDescription, build_description, dump_description
 from bioimageio.spec._internal.base_nodes import Node, ResourceDescriptionBase
 from bioimageio.spec._internal.constants import IN_PACKAGE_MESSAGE
 from bioimageio.spec._internal.io_utils import (
     BIOIMAGEIO_YAML,
-    PermissiveFileSource,
     download,
     open_bioimageio_yaml,
     write_yaml,
     write_zip,
 )
-from bioimageio.spec._internal.types import BioimageioYamlContent, FileName, RelativeFilePath, YamlValue
+from bioimageio.spec._internal.types import (
+    BioimageioYamlContent,
+    BioimageioYamlSource,
+    FileName,
+    RelativeFilePath,
+    YamlValue,
+)
 from bioimageio.spec._internal.types._file_source import extract_file_name
 from bioimageio.spec._internal.utils import nest_dict_with_narrow_first_key
 from bioimageio.spec._internal.validation_context import ValidationContext
 from bioimageio.spec.model.v0_4 import WeightsFormat
 from bioimageio.spec.summary import Loc
 
-BioimageioYamlSource = Union[PermissiveFileSource, ResourceDescription, BioimageioYamlContent]
-
 
 def fill_resource_package_content(
     package_content: Dict[Loc, Union[HttpUrl, RelativeFilePath]],
@@ -131,7 +134,7 @@ def get_resource_package_content(
 
 
 def _prepare_resource_package(
-    rdf_source: BioimageioYamlSource,
+    source: Union[BioimageioYamlSource, ResourceDescription],
     /,
     *,
     weights_priority_order: Optional[Sequence[WeightsFormat]] = None,
@@ -144,26 +147,26 @@ def _prepare_resource_package(
         weights_priority_order: If given only the first weights format present in the model is included.
                                 If none of the prioritized weights formats is found all are included.
     """
-    if isinstance(rdf_source, ResourceDescriptionBase):
-        rd = rdf_source
+    if isinstance(source, ResourceDescriptionBase):
+        rd = source
         _ctxt = rd._internal_validation_context  # pyright: ignore[reportPrivateUsage]
         context = ValidationContext(root=_ctxt["root"], file_name=_ctxt["file_name"])
-    elif isinstance(rdf_source, dict):
+    elif isinstance(source, dict):
         context = ValidationContext()
         rd = build_description(
-            rdf_source,
+            source,
             context=context,
         )
     else:
-        rdf = open_bioimageio_yaml(rdf_source)
+        rdf = open_bioimageio_yaml(source)
         context = ValidationContext(root=rdf.original_root, file_name=rdf.original_file_name)
         rd = build_description(
             rdf.content,
             context=context,
         )
 
     if isinstance(rd, InvalidDescription):
-        raise ValueError(f"{rdf_source} is invalid: {rd.validation_summaries[0]}")
+        raise ValueError(f"{source} is invalid: {rd.validation_summaries[0]}")
 
     package_content = get_resource_package_content(rd, weights_priority_order=weights_priority_order)
 
@@ -177,11 +180,11 @@ def _prepare_resource_package(
     return local_package_content
 
 
-def write_package_as_folder(
-    rdf_source: BioimageioYamlSource,
+def save_bioimageio_package_as_folder(
+    source: Union[BioimageioYamlSource, ResourceDescription],
     /,
     *,
-    output_path: Optional[DirectoryPath] = None,
+    output_path: Union[NewPath, DirectoryPath, None] = None,
     weights_priority_order: Optional[  # model only
         Sequence[
             Literal[
@@ -198,16 +201,16 @@ def write_package_as_folder(
     """Write the content of a bioimage.io resource package to a folder.
 
     Args:
-        rd: bioimage.io resource description
+        source: bioimageio resource description
         output_path: file path to write package to
         weights_priority_order: If given only the first weights format present in the model is included.
                                 If none of the prioritized weights formats is found all are included.
 
     Returns:
-        path to zipped bioimage.io package in BIOIMAGEIO_CACHE_PATH or 'output_path'
+        directory path to bioimageio package folder
     """
     package_content = _prepare_resource_package(
-        rdf_source,
+        source,
         weights_priority_order=weights_priority_order,
     )
     if output_path is None:
@@ -224,13 +227,13 @@ def write_package_as_folder(
     return output_path
 
 
-def write_package(
-    rdf_source: BioimageioYamlSource,
+def save_bioimageio_package(
+    source: Union[BioimageioYamlSource, ResourceDescription],
     /,
     *,
     compression: int = ZIP_DEFLATED,
     compression_level: int = 1,
-    output_path: Optional[Path] = None,
+    output_path: Union[NewPath, FilePath, None] = None,
     weights_priority_order: Optional[  # model only
         Sequence[
             Literal[
@@ -244,10 +247,10 @@ def write_package(
         ]
     ] = None,
 ) -> FilePath:
-    """Package a bioimage.io resource as a zip file.
+    """Package a bioimageio resource as a zip file.
 
     Args:
-        rd: bioimage.io resource description
+        rd: bioimageio resource description
         compression: The numeric constant of compression method.
         compression_level: Compression level to use when writing files to the archive.
                            See https://docs.python.org/3/library/zipfile.html#zipfile.ZipFile
@@ -256,10 +259,10 @@ def write_package(
                                 If none of the prioritized weights formats is found all are included.
 
     Returns:
-        path to zipped bioimage.io package in BIOIMAGEIO_CACHE_PATH or 'output_path'
+        path to zipped bioimageio package
     """
     package_content = _prepare_resource_package(
-        rdf_source,
+        source,
         weights_priority_order=weights_priority_order,
     )
     if output_path is None:

bioimageio/spec/utils.py

@@ -0,0 +1 @@
+from bioimageio.spec._internal.io_utils import download as download