update tests, clean up

Author: FynnBe

bioimageio/spec/_description.py

@@ -214,7 +214,7 @@ def _get_rd_class(type_: str, /, format_version: str = LATEST) -> Union[Type[Res
 
         ma, mi, _pa = rd_class.implemented_format_version_tuple
         key = f"{ma}.{mi}"
-        assert key not in per_fv
+        assert key not in per_fv, (key, per_fv)
         per_fv[key] = rd_class
 
     for typ, rd_class in _iterate_over_latest_rd_classes():
@@ -245,7 +245,7 @@ def _iterate_over_rd_classes() -> Iterable[Tuple[str, Type[ResourceDescription]]
         if typ is PydanticUndefined:
             typ = "generic"
 
-        assert isinstance(typ, str)
+        assert isinstance(typ, str), typ
         yield typ, rd_class
 
 
@@ -255,5 +255,5 @@ def _iterate_over_latest_rd_classes() -> Iterable[Tuple[str, Type[ResourceDescri
         if typ is PydanticUndefined:
             typ = "generic"
 
-        assert isinstance(typ, str)
+        assert isinstance(typ, str), typ
         yield typ, rd_class

bioimageio/spec/_internal/base_nodes.py

@@ -88,9 +88,9 @@ def _set_undefined_field_descriptions_from_var_docstrings_impl(cls, klass: Type[
 
         unindented_source = unindent(source)
         module = ast.parse(unindented_source)
-        assert isinstance(module, ast.Module)
+        assert isinstance(module, ast.Module), module
         class_def = module.body[0]
-        assert isinstance(class_def, ast.ClassDef)
+        assert isinstance(class_def, ast.ClassDef), class_def
         if len(class_def.body) < 2:
             return
 
@@ -163,8 +163,8 @@ def validation_summaries(self) -> List[ValidationSummary]:
     def root(self) -> Union[AnyUrl, DirectoryPath]:
         return self._internal_validation_context["root"]
 
-    @abstractmethod
     @classmethod
+    @abstractmethod
     def convert_from_older_format(cls, data: BioimageioYamlContent, context: InternalValidationContext) -> None:
         ...
 
@@ -191,7 +191,7 @@ def __pydantic_init_subclass__(cls, **kwargs: Any):
                 cls.implemented_format_version_tuple = cast(
                     Tuple[int, int, int], tuple(int(x) for x in cls.implemented_format_version.split("."))
                 )
-            assert len(cls.implemented_format_version_tuple) == 3
+            assert len(cls.implemented_format_version_tuple) == 3, cls.implemented_format_version_tuple
 
     @classmethod
     def _update_context(cls, context: InternalValidationContext, data: BioimageioYamlContent) -> None:
@@ -228,7 +228,7 @@ def model_validate(
 
         context = get_internal_validation_context(context)
         if isinstance(obj, dict):
-            assert all(isinstance(k, str) for k in obj)
+            assert all(isinstance(k, str) for k in obj), obj
             cls._update_context(context, obj)
 
         return super().model_validate(
@@ -349,7 +349,7 @@ def __getattr__(self, name: str):
 
     @classmethod
     def __get_pydantic_core_schema__(cls, source: Type[Any], handler: GetCoreSchemaHandler) -> core_schema.CoreSchema:
-        assert issubclass(source, StringNode)
+        assert issubclass(source, StringNode), source
         return core_schema.with_info_after_validator_function(
             cls._validate,
             core_schema.str_schema(pattern=cls._pattern),

bioimageio/spec/_internal/constants.py

@@ -21,7 +21,7 @@
 
 with files("bioimageio.spec").joinpath("VERSION").open("r", encoding="utf-8") as f:
     VERSION: str = json.load(f)["version"]
-    assert isinstance(VERSION, str)
+    assert isinstance(VERSION, str), VERSION
 
 DOI_REGEX = r"^10\.[0-9]{4}.+$"  # lax DOI regex validating the first 7 DOI characters only
 

bioimageio/spec/_internal/types/_file_source.py

@@ -1,9 +1,9 @@
 from __future__ import annotations
 
 import pathlib
-from pathlib import Path, PurePosixPath
+from pathlib import Path, PurePath, PurePosixPath
 from typing import Any, Union
-from urllib.parse import urlsplit, urlunsplit
+from urllib.parse import urlparse, urlsplit, urlunsplit
 
 from annotated_types import Predicate
 from pydantic import (
@@ -119,3 +119,12 @@ def _check_exists(self, root: Union[DirectoryPath, HttpUrl]) -> None:
 FileSource = Union[HttpUrl, AbsoluteFilePath, RelativeFilePath]
 PermissiveFileSource = Union[FileSource, str]
 StrictFileSource = Union[HttpUrl, AbsoluteFilePath]
+
+
+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/_internal/utils.py

@@ -1,15 +1,13 @@
 from __future__ import annotations
 
 import sys
-from pathlib import Path, PurePath
+from pathlib import Path
 from typing import Any, Dict, Iterator, Tuple, Type, TypeVar, Union, get_args, get_origin
-from urllib.parse import urlparse, urlsplit, urlunsplit
+from urllib.parse import urlsplit, urlunsplit
 
 from pydantic import AnyUrl, HttpUrl
 from typing_extensions import Annotated
 
-from bioimageio.spec._internal.types._file_source import RelativeFilePath
-
 K = TypeVar("K")
 V = TypeVar("V")
 NestedDict = Dict[K, "NestedDict[K, V] | V"]
@@ -18,7 +16,7 @@
 if sys.version_info < (3, 9):
 
     def files(package_name: str):
-        assert package_name == "bioimageio.spec"
+        assert package_name == "bioimageio.spec", package_name
         return Path(__file__).parent.parent
 
 else:
@@ -106,12 +104,3 @@ def unindent(text: str, ignore_first_line: bool = False):
 
     indent = min(len(line) - len(line.lstrip(" ")) for line in filled_lines)
     return "\n".join(lines[:first] + [line[indent:] for line in lines[first:]])
-
-
-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/_io.py

@@ -28,7 +28,8 @@
     StrictFileSource,
     YamlValue,
 )
-from bioimageio.spec._internal.utils import extract_file_name, get_parent_url
+from bioimageio.spec._internal.types._file_source import extract_file_name
+from bioimageio.spec._internal.utils import get_parent_url
 from bioimageio.spec._internal.validation_context import ValidationContext
 
 if platform.machine() == "wasm32":

bioimageio/spec/_package.py

@@ -13,7 +13,8 @@
 from bioimageio.spec._internal.base_nodes import Node, ResourceDescriptionBase
 from bioimageio.spec._internal.constants import IN_PACKAGE_MESSAGE
 from bioimageio.spec._internal.types import BioimageioYamlContent, FileName, RelativeFilePath, YamlValue
-from bioimageio.spec._internal.utils import extract_file_name, nest_dict_with_narrow_first_key
+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._io import (
     BIOIMAGEIO_YAML,

bioimageio/spec/application/v0_2.py

@@ -4,15 +4,16 @@
 from pydantic import HttpUrl as HttpUrl
 from typing_extensions import Annotated
 
-from bioimageio.spec._internal.types import FileSource as FileSource
-from bioimageio.spec._internal.types import RelativeFilePath as RelativeFilePath
+from bioimageio.spec.generic.v0_2 import AbsoluteFilePath as AbsoluteFilePath
 from bioimageio.spec.generic.v0_2 import Attachments as Attachments
 from bioimageio.spec.generic.v0_2 import Author as Author
 from bioimageio.spec.generic.v0_2 import Badge as Badge
 from bioimageio.spec.generic.v0_2 import CiteEntry as CiteEntry
+from bioimageio.spec.generic.v0_2 import FileSource as FileSource
 from bioimageio.spec.generic.v0_2 import GenericBase
 from bioimageio.spec.generic.v0_2 import LinkedResource as LinkedResource
 from bioimageio.spec.generic.v0_2 import Maintainer as Maintainer
+from bioimageio.spec.generic.v0_2 import RelativeFilePath as RelativeFilePath
 
 
 class Application(GenericBase, title="bioimage.io application specification"):

bioimageio/spec/application/v0_3.py

@@ -4,15 +4,16 @@
 from pydantic import HttpUrl as HttpUrl
 from typing_extensions import Annotated
 
-from bioimageio.spec._internal.types import FileSource as FileSource
-from bioimageio.spec._internal.types import RelativeFilePath as RelativeFilePath
+from bioimageio.spec.generic.v0_3 import AbsoluteFilePath as AbsoluteFilePath
 from bioimageio.spec.generic.v0_3 import Attachment as Attachment
 from bioimageio.spec.generic.v0_3 import Author as Author
 from bioimageio.spec.generic.v0_3 import Badge as Badge
 from bioimageio.spec.generic.v0_3 import CiteEntry as CiteEntry
+from bioimageio.spec.generic.v0_3 import FileSource as FileSource
 from bioimageio.spec.generic.v0_3 import GenericBase
 from bioimageio.spec.generic.v0_3 import LinkedResource as LinkedResource
 from bioimageio.spec.generic.v0_3 import Maintainer as Maintainer
+from bioimageio.spec.generic.v0_3 import RelativeFilePath as RelativeFilePath
 
 
 class Application(GenericBase, title="bioimage.io application specification"):

bioimageio/spec/collection/v0_2.py

@@ -18,18 +18,22 @@
 from bioimageio.spec._internal.base_nodes import Node
 from bioimageio.spec._internal.constants import ALERT
 from bioimageio.spec._internal.field_warning import warn
-from bioimageio.spec._internal.types import BioimageioYamlContent, NotEmpty, RelativeFilePath, ResourceId, YamlValue
+from bioimageio.spec._internal.types import BioimageioYamlContent, NotEmpty, YamlValue
 from bioimageio.spec._internal.validation_context import InternalValidationContext
 from bioimageio.spec.application.v0_2 import Application as Application
 from bioimageio.spec.dataset.v0_2 import Dataset as Dataset
+from bioimageio.spec.generic.v0_2 import AbsoluteFilePath as AbsoluteFilePath
 from bioimageio.spec.generic.v0_2 import Attachments as Attachments
 from bioimageio.spec.generic.v0_2 import Author as Author
 from bioimageio.spec.generic.v0_2 import Badge as Badge
 from bioimageio.spec.generic.v0_2 import CiteEntry as CiteEntry
+from bioimageio.spec.generic.v0_2 import FileSource as FileSource
 from bioimageio.spec.generic.v0_2 import Generic as Generic
 from bioimageio.spec.generic.v0_2 import GenericBase
 from bioimageio.spec.generic.v0_2 import LinkedResource as LinkedResource
 from bioimageio.spec.generic.v0_2 import Maintainer as Maintainer
+from bioimageio.spec.generic.v0_2 import RelativeFilePath as RelativeFilePath
+from bioimageio.spec.generic.v0_2 import ResourceId as ResourceId
 from bioimageio.spec.model.v0_4 import Model as Model
 from bioimageio.spec.notebook.v0_2 import Notebook as Notebook
 
@@ -161,7 +165,9 @@ def check_unique_ids_impl(value: NotEmpty[Sequence[CollectionEntryBase]]):
     def _update_context(cls, context: InternalValidationContext, data: BioimageioYamlContent) -> None:
         super()._update_context(context, data)
         collection_base_content = {k: v for k, v in data.items() if k != "collection"}
-        assert "collection_base_content" not in context or context["collection_base_content"] == collection_base_content
+        assert (
+            "collection_base_content" not in context or context["collection_base_content"] == collection_base_content
+        ), context
         context["collection_base_content"] = collection_base_content
 
     @staticmethod