0.5.1

README.md

@@ -71,6 +71,10 @@ or
 pip install -U bioimageio.core
 ```
 
+## 🏞 Environment variables
+
+TODO: link to settings in dev docs
+
 ## 🤝 How to contribute
 
 ## ♥ Contributors
@@ -85,6 +89,10 @@ Made with [contrib.rocks](https://contrib.rocks).
 
 ### bioimageio.spec Python package
 
+#### bioimageio.spec 0.5.1
+
+* new patch version model 0.5.1
+
 #### bioimageio.spec 0.5.0post2
 
 * don't fail if CI env var is a string
@@ -228,11 +236,13 @@ Made with [contrib.rocks](https://contrib.rocks).
 
 ### Resource Description Format Versions
 
-#### model 0.5.1 (planned)
+#### model 0.5.1
 
 * Non-breaking changes
   * added `DataDependentSize` for `outputs.i.size` to specify an output shape that is not known before inference is run.
   * added optional `inputs.i.optional` field to indicate that a tensor may be `None`
+  * made data type assumptions in `preprocessing` and `postprocessing` explicit by adding `'ensure_dtype'` operations per default.
+  * allow to specify multiple thresholds (along an `axis`) in a 'binarize' processing step
 
 #### generic 0.3.0 / application 0.3.0 / collection 0.3.0 / dataset 0.3.0 / notebook 0.3.0
 

bioimageio/spec/VERSION

@@ -1,3 +1,3 @@
 {
-    "version": "0.5.0post2"
+    "version": "0.5.1"
 }

bioimageio/spec/__init__.py

@@ -13,6 +13,7 @@
 from ._description import build_description as build_description
 from ._description import dump_description as dump_description
 from ._description import validate_format as validate_format
+from ._internal import settings as settings
 from ._internal.common_nodes import InvalidDescr as InvalidDescr
 from ._internal.constants import VERSION
 from ._internal.validation_context import ValidationContext as ValidationContext

bioimageio/spec/_internal/_settings.py

@@ -1,5 +1,7 @@
+from pathlib import Path
 from typing import Optional, Union
 
+import pooch
 from pydantic import Field
 from pydantic_settings import BaseSettings, SettingsConfigDict
 from typing_extensions import Annotated
@@ -33,6 +35,9 @@ class Settings(BaseSettings, extra="ignore"):
     user_agent: Optional[str] = None
     """user agent for http requests"""
 
+    cache_path: Path = pooch.os_cache("bioimageio")
+    """bioimageio cache location"""
+
     @property
     def github_auth(self):
         if self.github_username is None or self.github_token is None:

bioimageio/spec/_internal/field_validation.py

@@ -12,10 +12,10 @@
 
 import requests
 
-from bioimageio.spec._internal._settings import settings
-from bioimageio.spec._internal.constants import KNOWN_GH_USERS, KNOWN_INVALID_GH_USERS
-from bioimageio.spec._internal.field_warning import issue_warning
-from bioimageio.spec._internal.validation_context import validation_context_var
+from ._settings import settings
+from .constants import KNOWN_GH_USERS, KNOWN_INVALID_GH_USERS
+from .field_warning import issue_warning
+from .validation_context import validation_context_var
 
 
 def is_valid_yaml_leaf_value(value: Any) -> bool:

bioimageio/spec/_internal/io.py

@@ -10,8 +10,10 @@
 from pathlib import Path, PurePath
 from typing import (
     Any,
+    ClassVar,
     Dict,
     Generic,
+    Iterable,
     List,
     Optional,
     Sequence,
@@ -22,6 +24,7 @@
     Union,
 )
 from urllib.parse import urlparse, urlsplit, urlunsplit
+from zipfile import ZipFile, is_zipfile
 
 import pooch
 import pydantic
@@ -52,6 +55,7 @@
 from .._internal._settings import settings
 from .._internal.io_basics import (
     ALL_BIOIMAGEIO_YAML_NAMES,
+    ALTERNATIVE_BIOIMAGEIO_YAML_NAMES,
     BIOIMAGEIO_YAML,
     AbsoluteDirectory,
     AbsoluteFilePath,
@@ -73,18 +77,17 @@
     SLOTS = {"slots": True}
 
 
-class Sha256(
-    ValidatedString[
+class Sha256(ValidatedString):
+    """SHA-256 hash value"""
+
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[
         Annotated[
             str,
             StringConstraints(
                 strip_whitespace=True, to_lower=True, min_length=64, max_length=64
             ),
         ]
-    ],
-    frozen=True,
-):
-    """SHA-256 hash value"""
+    ]
 
 
 AbsolutePathT = TypeVar(
@@ -303,7 +306,7 @@ def validate(self, value: FileSource) -> FileSource:
 
 
 def wo_special_file_name(src: FileSource) -> FileSource:
-    if has_valid_rdf_name(src):
+    if has_valid_bioimageio_yaml_name(src):
         raise ValueError(
             f"'{src}' not allowed here as its filename is reserved to identify"
             + f" '{BIOIMAGEIO_YAML}' (or equivalent) files."
@@ -323,7 +326,7 @@ def _package(value: FileSource, info: SerializationInfo) -> Union[str, Path, Fil
         if isinstance(value, Path):
             unpackaged = value
         elif isinstance(value, HttpUrl):
-            unpackaged = value.root
+            unpackaged = value
         elif isinstance(value, RelativeFilePath):
             unpackaged = Path(value.path)
         elif isinstance(value, AnyUrl):
@@ -395,22 +398,60 @@ def _package(value: FileSource, info: SerializationInfo) -> Union[str, Path, Fil
     AfterValidator(wo_special_file_name),
     include_in_package_serializer,
 ]
+InPackageIfLocalFileSource = Union[
+    Annotated[
+        Union[FilePath, RelativeFilePath],
+        AfterValidator(wo_special_file_name),
+        include_in_package_serializer,
+    ],
+    Union[HttpUrl, pydantic.HttpUrl],
+]
 
 
-def has_valid_rdf_name(src: FileSource) -> bool:
-    return is_valid_rdf_name(extract_file_name(src))
+def has_valid_bioimageio_yaml_name(src: FileSource) -> bool:
+    return is_valid_bioimageio_yaml_name(extract_file_name(src))
 
 
-def is_valid_rdf_name(file_name: FileName) -> bool:
-    for special in ALL_BIOIMAGEIO_YAML_NAMES:
-        if file_name.endswith(special):
+def is_valid_bioimageio_yaml_name(file_name: FileName) -> bool:
+    for bioimageio_name in ALL_BIOIMAGEIO_YAML_NAMES:
+        if file_name == bioimageio_name or file_name.endswith("." + bioimageio_name):
             return True
 
     return False
 
 
-def ensure_has_valid_rdf_name(src: FileSource) -> FileSource:
-    if not has_valid_rdf_name(src):
+def identify_bioimageio_yaml_file_name(file_names: Iterable[FileName]) -> FileName:
+    file_names = sorted(file_names)
+    for bioimageio_name in ALL_BIOIMAGEIO_YAML_NAMES:
+        for file_name in file_names:
+            if file_name == bioimageio_name or file_name.endswith(
+                "." + bioimageio_name
+            ):
+                return file_name
+
+    raise ValueError(
+        f"No {BIOIMAGEIO_YAML} found in {file_names}. (Looking for '{BIOIMAGEIO_YAML}'"
+        + " or or any of the alterntive file names:"
+        + f" {ALTERNATIVE_BIOIMAGEIO_YAML_NAMES}, or any file with an extension of"
+        + f"  those, e.g. 'anything.{BIOIMAGEIO_YAML}')."
+    )
+
+
+def find_bioimageio_yaml_file_name(path: Path) -> FileName:
+    if path.is_file():
+        if not is_zipfile(path):
+            return path.name
+
+        with ZipFile(path, "r") as f:
+            file_names = identify_bioimageio_yaml_file_name(f.namelist())
+    else:
+        file_names = [p.name for p in path.glob("*")]
+
+    return identify_bioimageio_yaml_file_name(file_names)
+
+
+def ensure_has_valid_bioimageio_yaml_name(src: FileSource) -> FileSource:
+    if not has_valid_bioimageio_yaml_name(src):
         raise ValueError(
             f"'{src}' does not have a valid filename to identify"
             + f" '{BIOIMAGEIO_YAML}' (or equivalent) files."
@@ -419,8 +460,8 @@ def ensure_has_valid_rdf_name(src: FileSource) -> FileSource:
     return src
 
 
-def ensure_is_valid_rdf_name(file_name: FileName) -> FileName:
-    if not is_valid_rdf_name(file_name):
+def ensure_is_valid_bioimageio_yaml_name(file_name: FileName) -> FileName:
+    if not is_valid_bioimageio_yaml_name(file_name):
         raise ValueError(
             f"'{file_name}' is not a valid filename to identify"
             + f" '{BIOIMAGEIO_YAML}' (or equivalent) files."
@@ -448,14 +489,14 @@ def ensure_is_valid_rdf_name(file_name: FileName) -> FileName:
 class OpenedBioimageioYaml:
     content: BioimageioYamlContent
     original_root: Union[AbsoluteDirectory, RootHttpUrl]
-    original_file_name: str
+    original_file_name: FileName
 
 
 @dataclass
 class DownloadedFile:
     path: FilePath
     original_root: Union[AbsoluteDirectory, RootHttpUrl]
-    original_file_name: str
+    original_file_name: FileName
 
 
 class HashKwargs(TypedDict):
@@ -502,6 +543,7 @@ def download(
     /,
     **kwargs: Unpack[HashKwargs],
 ) -> DownloadedFile:
+    """download `source` URL (or pass local file path)"""
     if isinstance(source, FileDescr):
         return source.download()
 
@@ -533,6 +575,7 @@ def download(
             known_hash=_get_known_hash(kwargs),
             downloader=downloader,
             fname=fname,
+            path=settings.cache_path,
         )
         local_source = Path(_ls).absolute()
         root = strict_source.parent

bioimageio/spec/_internal/io_basics.py

@@ -8,6 +8,6 @@
 AbsoluteDirectory = Annotated[DirectoryPath, Predicate(Path.is_absolute)]
 AbsoluteFilePath = Annotated[FilePath, Predicate(Path.is_absolute)]
 
-BIOIMAGEIO_YAML = "rdf.yaml"
-ALTERNATIVE_BIOIMAGEIO_YAML_NAMES = ("bioimageio.yaml", "model.yaml")
+BIOIMAGEIO_YAML = "bioimageio.yaml"
+ALTERNATIVE_BIOIMAGEIO_YAML_NAMES = ("rdf.yaml", "model.yaml")
 ALL_BIOIMAGEIO_YAML_NAMES = (BIOIMAGEIO_YAML,) + ALTERNATIVE_BIOIMAGEIO_YAML_NAMES

bioimageio/spec/_internal/io_utils.py

@@ -1,9 +1,8 @@
 import io
-import platform
 import warnings
 from contextlib import nullcontext
 from pathlib import Path
-from typing import IO, Any, Dict, Iterable, Mapping, Optional, TextIO, Union, cast
+from typing import IO, Any, Dict, Mapping, Optional, TextIO, Union, cast
 from zipfile import ZipFile, is_zipfile
 
 import numpy
@@ -13,24 +12,18 @@
 from typing_extensions import Unpack
 
 from .io import (
-    ALL_BIOIMAGEIO_YAML_NAMES,
     BIOIMAGEIO_YAML,
     BioimageioYamlContent,
     FileDescr,
     HashKwargs,
     OpenedBioimageioYaml,
     YamlValue,
     download,
+    find_bioimageio_yaml_file_name,
 )
-from .io_basics import ALTERNATIVE_BIOIMAGEIO_YAML_NAMES, FileName
+from .io_basics import FileName
 from .types import FileSource, PermissiveFileSource
 
-if platform.machine() == "wasm32":
-    import pyodide_http  # type: ignore
-
-    pyodide_http.patch_all()
-
-
 yaml = YAML(typ="safe")
 
 
@@ -91,34 +84,6 @@ def open_bioimageio_yaml(
     return OpenedBioimageioYaml(content, root, downloaded.original_file_name)
 
 
-def identify_bioimageio_yaml_file_name(file_names: Iterable[FileName]) -> FileName:
-    file_names = sorted(file_names)
-    for bioimageio_name in ALL_BIOIMAGEIO_YAML_NAMES:
-        for fname in file_names:
-            if fname == bioimageio_name or fname.endswith(f".{bioimageio_name}"):
-                return fname
-
-    raise ValueError(
-        f"No {BIOIMAGEIO_YAML} found in {file_names}. (Looking for '{BIOIMAGEIO_YAML}'"
-        + " or or any of the alterntive file names:"
-        + f" {ALTERNATIVE_BIOIMAGEIO_YAML_NAMES}, or any file with an extension of"
-        + f"  those, e.g. 'anything.{BIOIMAGEIO_YAML}')."
-    )
-
-
-def find_bioimageio_yaml_file_name(path: Path) -> FileName:
-    if path.is_file():
-        if not is_zipfile(path):
-            return path.name
-
-        with ZipFile(path, "r") as f:
-            file_names = identify_bioimageio_yaml_file_name(f.namelist())
-    else:
-        file_names = [p.name for p in path.glob("*")]
-
-    return identify_bioimageio_yaml_file_name(file_names)
-
-
 def unzip(
     zip_file: Union[FilePath, ZipFile],
     out_path: Optional[DirectoryPath] = None,

bioimageio/spec/_internal/license_id.py

@@ -1,24 +1,17 @@
-from typing import TypeVar
+from typing import Any, ClassVar, Type
+
+from pydantic import RootModel
 
 from ._generated_spdx_license_literals import (
     DeprecatedLicenseId as DeprecatedLicenseIdLiteral,
 )
 from ._generated_spdx_license_literals import LicenseId as LicenseIdLiteral
 from .validated_string import ValidatedString
 
-LicenceT = TypeVar("LicenceT", LicenseIdLiteral, DeprecatedLicenseIdLiteral)
-
-
-class _LicenseId(ValidatedString[LicenceT], frozen=True):
-    def __repr__(self):
-        # don't include full literal in class repr
-        name, *_ = self.__class__.__name__.split("[")
-        return f'{name}("{self.root}")'
-
 
-class DeprecatedLicenseId(_LicenseId[DeprecatedLicenseIdLiteral], frozen=True):
-    pass
+class LicenseId(ValidatedString):
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[LicenseIdLiteral]
 
 
-class LicenseId(_LicenseId[LicenseIdLiteral], frozen=True):
-    pass
+class DeprecatedLicenseId(ValidatedString):
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[DeprecatedLicenseIdLiteral]