Merge pull request #690 from bioimage-io/dev

FynnBe · web-flow · commit 93146f976a00 · 2025-03-27T00:28:40.000+01:00
fix default validation context
diff --git a/bioimageio/spec/VERSION b/bioimageio/spec/VERSION
@@ -1,3 +1,3 @@
 {
-    "version": "0.5.4.0"
+    "version": "0.5.4.1"
 }
diff --git a/bioimageio/spec/_description.py b/bioimageio/spec/_description.py
@@ -10,7 +10,7 @@
 from ._internal.common_nodes import InvalidDescr
 from ._internal.io import BioimageioYamlContent
 from ._internal.types import FormatVersionPlaceholder
-from ._internal.validation_context import validation_context_var
+from ._internal.validation_context import get_validation_context
 from .application import (
     AnyApplicationDescr,
     ApplicationDescr,
@@ -224,7 +224,7 @@ def validate_format(
         Alternatively you can use `bioimagieo.spec.load_description` and access the
         `validation_summary` attribute of the returned object.
     """
-    with context or validation_context_var.get():
+    with context or get_validation_context():
         rd = build_description(data, format_version=format_version)
 
     assert rd.validation_summary is not None
diff --git a/bioimageio/spec/_description_impl.py b/bioimageio/spec/_description_impl.py
@@ -5,7 +5,7 @@
 from ._internal.common_nodes import InvalidDescr, ResourceDescrBase
 from ._internal.io import BioimageioYamlContent
 from ._internal.types import FormatVersionPlaceholder
-from ._internal.validation_context import ValidationContext, validation_context_var
+from ._internal.validation_context import ValidationContext, get_validation_context
 from .summary import (
     ErrorEntry,
     ValidationDetail,
@@ -55,7 +55,7 @@ def build_description_impl(
     format_version: Union[FormatVersionPlaceholder, str] = DISCOVER,
     get_rd_class: Callable[[Any, Any], Type[ResourceDescrT]],
 ) -> Union[ResourceDescrT, InvalidDescr]:
-    context = context or validation_context_var.get()
+    context = context or get_validation_context()
     errors: List[ErrorEntry] = []
     if isinstance(content, dict):
         for minimum in ("type", "format_version"):
diff --git a/bioimageio/spec/_internal/common_nodes.py b/bioimageio/spec/_internal/common_nodes.py
@@ -41,13 +41,8 @@
 from .packaging_context import PackagingContext
 from .root_url import RootHttpUrl
 from .url import HttpUrl
-from .utils import (
-    get_format_version_tuple,
-)
-from .validation_context import (
-    ValidationContext,
-    validation_context_var,
-)
+from .utils import get_format_version_tuple
+from .validation_context import ValidationContext, get_validation_context
 from .warning_levels import ALERT, ERROR, INFO
 
 
@@ -148,7 +143,10 @@ def _ignore_future_patch(cls, data: Union[Dict[Any, Any], Any], /) -> Any:
 
     @model_validator(mode="after")
     def _set_init_validation_summary(self) -> Self:
-        context = validation_context_var.get()
+        context = get_validation_context()
+        detail_name = (
+            "Created" if isinstance(self, InvalidDescr) else "Successfully created"
+        ) + f" `{self.__class__.__name__}` object."
         self._validation_summary = ValidationSummary(
             name="bioimageio format validation",
             source_name=context.source_name,
@@ -158,11 +156,8 @@ def _set_init_validation_summary(self) -> Self:
             status="failed" if isinstance(self, InvalidDescr) else "valid-format",
             details=[
                 ValidationDetail(
-                    name=(
-                        f"Sucessfully created `{self.__class__.__name__}` object."
-                        + " Further validation is pending."
-                    ),
-                    status="passed",
+                    name=detail_name,
+                    status="failed" if isinstance(self, InvalidDescr) else "passed",
                     context=context.summary,
                 )
             ],
@@ -175,11 +170,11 @@ def validation_summary(self) -> ValidationSummary:
         return self._validation_summary
 
     _root: Union[RootHttpUrl, DirectoryPath, ZipFile] = PrivateAttr(
-        default_factory=lambda: validation_context_var.get().root
+        default_factory=lambda: get_validation_context().root
     )
 
     _file_name: Optional[FileName] = PrivateAttr(
-        default_factory=lambda: validation_context_var.get().file_name
+        default_factory=lambda: get_validation_context().file_name
     )
 
     @property
@@ -211,7 +206,7 @@ def load(
         cls, data: BioimageioYamlContent, context: Optional[ValidationContext] = None
     ) -> Union[Self, InvalidDescr]:
         """factory method to create a resource description object"""
-        context = context or validation_context_var.get()
+        context = context or get_validation_context()
         assert isinstance(data, dict)
         with context:
             rd, errors, val_warnings = cls._load_impl(deepcopy(data))
@@ -247,7 +242,7 @@ def _load_impl(
         val_errors: List[ErrorEntry] = []
         val_warnings: List[WarningEntry] = []
 
-        context = validation_context_var.get()
+        context = get_validation_context()
         try:
             rd = cls.model_validate(data)
         except pydantic.ValidationError as e:
@@ -275,7 +270,7 @@ def _load_impl(
                         msg=(
                             f"Encountered {len(val_warnings)} more severe than warning"
                             " level "
-                            f"'{WARNING_LEVEL_TO_NAME[validation_context_var.get().warning_level]}'"
+                            f"'{WARNING_LEVEL_TO_NAME[context.warning_level]}'"
                         ),
                         type="severe_warnings",
                     )
diff --git a/bioimageio/spec/_internal/field_validation.py b/bioimageio/spec/_internal/field_validation.py
@@ -15,7 +15,7 @@
 from .constants import KNOWN_GH_USERS, KNOWN_INVALID_GH_USERS
 from .field_warning import issue_warning
 from .type_guards import is_mapping, is_sequence, is_tuple
-from .validation_context import validation_context_var
+from .validation_context import get_validation_context
 
 
 def is_valid_yaml_leaf_value(value: Any) -> bool:
@@ -64,7 +64,7 @@ def validate_gh_user(username: str, hotfix_known_errorenous_names: bool = True)
 
     if (
         username.lower() in KNOWN_GH_USERS
-        or not validation_context_var.get().perform_io_checks
+        or not get_validation_context().perform_io_checks
     ):
         return username
 
diff --git a/bioimageio/spec/_internal/field_warning.py b/bioimageio/spec/_internal/field_warning.py
@@ -15,7 +15,7 @@
 )
 from typing_extensions import Annotated, LiteralString
 
-from .validation_context import validation_context_var
+from .validation_context import get_validation_context
 from .warning_levels import WARNING, WarningSeverity
 
 if TYPE_CHECKING:
@@ -142,8 +142,8 @@ def issue_warning(
     field: Optional[str] = None,
 ):
     msg_context = {"value": value, "severity": severity, **(msg_context or {})}
-    if severity >= validation_context_var.get().warning_level:
+    if severity >= (ctxt := get_validation_context()).warning_level:
         raise PydanticCustomError("warning", msg, msg_context)
-    elif validation_context_var.get().log_warnings:
+    elif ctxt.log_warnings:
         log_msg = (field + ": " if field else "") + (msg.format(**msg_context))
         logger.opt(depth=1).log(severity, log_msg)
diff --git a/bioimageio/spec/_internal/node.py b/bioimageio/spec/_internal/node.py
@@ -12,7 +12,7 @@
 from typing_extensions import Self
 
 from .type_guards import is_kwargs
-from .validation_context import ValidationContext, validation_context_var
+from .validation_context import ValidationContext, get_validation_context
 
 
 def _node_title_generator(node: Type[Node]) -> str:
@@ -64,7 +64,7 @@ def model_validate(
         __tracebackhide__ = True
 
         if context is None:
-            context = validation_context_var.get()
+            context = get_validation_context()
         elif isinstance(context, dict):
             context = ValidationContext(**context)
 
diff --git a/bioimageio/spec/_internal/url.py b/bioimageio/spec/_internal/url.py
@@ -9,7 +9,7 @@
 
 from .field_warning import issue_warning
 from .root_url import RootHttpUrl
-from .validation_context import validation_context_var
+from .validation_context import get_validation_context
 
 
 def _validate_url(url: Union[str, pydantic.HttpUrl]) -> pydantic.HttpUrl:
@@ -127,7 +127,7 @@ class HttpUrl(RootHttpUrl):
 
     def _after_validator(self):
         self = super()._after_validator()
-        context = validation_context_var.get()
+        context = get_validation_context()
         if (
             context.perform_io_checks
             and str(self._validated) not in context.known_files
diff --git a/bioimageio/spec/_internal/validation_context.py b/bioimageio/spec/_internal/validation_context.py
@@ -54,7 +54,7 @@ class ValidationContext(ValidationContextBase):
     if it matches its expected SHA256 hash value.
     """
 
-    _context_tokens: "List[Token[ValidationContext]]" = field(
+    _context_tokens: "List[Token[Optional[ValidationContext]]]" = field(
         init=False, default_factory=list
     )
 
@@ -94,11 +94,11 @@ def summary(self):
         )
 
     def __enter__(self):
-        self._context_tokens.append(validation_context_var.set(self))
+        self._context_tokens.append(_validation_context_var.set(self))
         return self
 
     def __exit__(self, type, value, traceback):  # type: ignore
-        validation_context_var.reset(self._context_tokens.pop(-1))
+        _validation_context_var.reset(self._context_tokens.pop(-1))
 
     def replace(  # TODO: probably use __replace__ when py>=3.13
         self,
@@ -160,11 +160,13 @@ def source_name(self) -> str:
                 return str(source)
 
 
-validation_context_var: ContextVar[ValidationContext] = ContextVar(
-    "validation_context_var", default=ValidationContext()
+_validation_context_var: ContextVar[Optional[ValidationContext]] = ContextVar(
+    "validation_context_var", default=None
 )
 
 
-def get_validation_context():
-    """Get the currently active validation context"""
-    return validation_context_var.get()
+def get_validation_context(
+    default: Optional[ValidationContext] = None,
+) -> ValidationContext:
+    """Get the currently active validation context (or a default)"""
+    return _validation_context_var.get() or default or ValidationContext()
diff --git a/bioimageio/spec/_io.py b/bioimageio/spec/_io.py
@@ -21,7 +21,7 @@
 from ._internal.io_basics import Sha256
 from ._internal.io_utils import open_bioimageio_yaml, write_yaml
 from ._internal.types import FormatVersionPlaceholder
-from ._internal.validation_context import validation_context_var
+from ._internal.validation_context import get_validation_context
 from .common import PermissiveFileSource
 from .dataset import AnyDatasetDescr, DatasetDescr
 from .model import AnyModelDescr, ModelDescr
@@ -86,7 +86,7 @@ def load_description(
 
     opened = open_bioimageio_yaml(source, sha256=sha256)
 
-    context = validation_context_var.get().replace(
+    context = get_validation_context().replace(
         root=opened.original_root,
         file_name=opened.original_file_name,
         perform_io_checks=perform_io_checks,
@@ -281,7 +281,7 @@ def update_format(
     if isinstance(source, dict):
         descr = build_description(
             source,
-            context=validation_context_var.get().replace(
+            context=get_validation_context().replace(
                 root=root, perform_io_checks=perform_io_checks
             ),
             format_version=LATEST,
@@ -311,7 +311,7 @@ def update_hashes(
     else:
         root = None
 
-    context = validation_context_var.get().replace(
+    context = get_validation_context().replace(
         update_hashes=True, root=root, perform_io_checks=True
     )
     with context:
diff --git a/bioimageio/spec/_package.py b/bioimageio/spec/_package.py
@@ -21,7 +21,7 @@
 from ._internal.packaging_context import PackagingContext
 from ._internal.url import HttpUrl
 from ._internal.utils import get_os_friendly_file_name
-from ._internal.validation_context import validation_context_var
+from ._internal.validation_context import get_validation_context
 from ._internal.warning_levels import ERROR
 from ._io import load_description
 from .model.v0_4 import WeightsFormat
@@ -79,7 +79,7 @@ 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.
     """
-    context = validation_context_var.get()
+    context = get_validation_context()
     bioimageio_yaml_file_name = context.file_name
     if isinstance(source, ResourceDescrBase):
         descr = source
@@ -229,7 +229,7 @@ def save_bioimageio_package(
         compression=compression,
         compression_level=compression_level,
     )
-    with validation_context_var.get().replace(warning_level=ERROR):
+    with get_validation_context().replace(warning_level=ERROR):
         if isinstance((exported := load_description(output_path)), InvalidDescr):
             raise ValueError(
                 f"Exported package '{output_path}' is invalid:"
diff --git a/bioimageio/spec/model/v0_4.py b/bioimageio/spec/model/v0_4.py
@@ -957,13 +957,10 @@ def zero_batch_step_and_one_batch_size(self) -> Self:
     @model_validator(mode="after")
     def validate_preprocessing_kwargs(self) -> Self:
         for p in self.preprocessing:
-            kwargs_axes = p.kwargs.get("axes", "")
-            if not isinstance(kwargs_axes, str):
-                raise ValueError(
-                    f"Expected an `axes` string, but got {type(kwargs_axes)}"
-                )
-
-            if any(a not in self.axes for a in kwargs_axes):
+            kwargs_axes = p.kwargs.get("axes")
+            if isinstance(kwargs_axes, str) and any(
+                a not in self.axes for a in kwargs_axes
+            ):
                 raise ValueError("`kwargs.axes` needs to be subset of `axes`")
 
         return self
diff --git a/bioimageio/spec/model/v0_5.py b/bioimageio/spec/model/v0_5.py
@@ -75,7 +75,7 @@
 from .._internal.types import Identifier as Identifier
 from .._internal.types import NotEmpty as NotEmpty
 from .._internal.url import HttpUrl as HttpUrl
-from .._internal.validation_context import validation_context_var
+from .._internal.validation_context import get_validation_context
 from .._internal.validator_annotations import RestrictCharacters
 from .._internal.version_type import Version as Version
 from .._internal.warning_levels import INFO
@@ -217,7 +217,12 @@ class TensorId(LowerCaseIdentifier):
 
 def _normalize_axis_id(a: str):
     a = str(a)
-    return _AXIS_ID_MAP.get(a, a)
+    normalized = _AXIS_ID_MAP.get(a, a)
+    if a != normalized:
+        logger.opt(depth=3).warning(
+            "Normalized axis id from '{}' to '{}'.", a, normalized
+        )
+    return normalized
 
 
 class AxisId(LowerCaseIdentifier):
@@ -1493,10 +1498,7 @@ def _validate_axes(cls, axes: Sequence[AnyAxis]) -> Sequence[AnyAxis]:
 
     @model_validator(mode="after")
     def _validate_sample_tensor(self) -> Self:
-        if (
-            self.sample_tensor is None
-            or not validation_context_var.get().perform_io_checks
-        ):
+        if self.sample_tensor is None or not get_validation_context().perform_io_checks:
             return self
 
         local = download(self.sample_tensor.source, sha256=self.sample_tensor.sha256)
@@ -2552,7 +2554,7 @@ class ModelDescr(GenericModelDescrBase):
     @field_validator("documentation", mode="after")
     @classmethod
     def _validate_documentation(cls, value: DocumentationSource) -> DocumentationSource:
-        if not validation_context_var.get().perform_io_checks:
+        if not get_validation_context().perform_io_checks:
             return value
 
         doc_path = download(value).path
@@ -2682,7 +2684,7 @@ def _validate_axis(
 
     @model_validator(mode="after")
     def _validate_test_tensors(self) -> Self:
-        if not validation_context_var.get().perform_io_checks:
+        if not get_validation_context().perform_io_checks:
             return self
 
         test_output_arrays = [
@@ -2897,7 +2899,7 @@ def _validate_parent_is_not_self(self) -> Self:
 
     @model_validator(mode="after")
     def _add_default_cover(self) -> Self:
-        if not validation_context_var.get().perform_io_checks or self.covers:
+        if not get_validation_context().perform_io_checks or self.covers:
             return self
 
         try:
diff --git a/bioimageio/spec/summary.py b/bioimageio/spec/summary.py
@@ -495,6 +495,9 @@ def format_code(
         cell_width_limit: int = 120,
     ):
 
+        if not code.strip():
+            return ""
+
         if target == "html":
             html_lang = f' lang="{lang}"' if lang else ""
             code = f"<pre{html_lang}>{code}</pre>"
diff --git a/changelog.md b/changelog.md
diff --git a/tests/test_io.py b/tests/test_io.py
diff --git a/tests/test_specific_reexports_generics.py b/tests/test_specific_reexports_generics.py

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,3 @@`
`1`	`1`	`{`
`2`		`- "version": "0.5.4.0"`
	`2`	`+ "version": "0.5.4.1"`
`3`	`3`	`}`