Merge pull request #725 from bioimage-io/dev

Fix `ValidationSummary.add_detail()`

Author: FynnBe

.github/workflows/build.yml

@@ -188,7 +188,7 @@ jobs:
 
   pip-build:
     name: Build and publish to PyPI
-    needs: [test, conda-build]
+    needs: [deploy, conda-build]
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repository

changelog.md

@@ -10,6 +10,10 @@ In this file we log both:
 
 This changelog includes implementation details and my reference the [changes to the Resource Description Format](#changes-to-the-resource-description-format), e.g. in entry [bioimageio.spec 0.5.2](#bioimageiospec-052).
 
+#### bioimageio.spec 0.5.5.7
+
+- Fix `ValidationSummary.add_detail()` (respect 'valid-format' status)
+
 #### bioimageio.spec 0.5.5.6
 
 - Add BIOIMAGEIO_HTTP_TIMEOUT environment variable to adjust timeout for http requests.

src/bioimageio/spec/_internal/common_nodes.py

@@ -233,18 +233,22 @@ def load(
             with all_warnings_context:
                 _, _, val_warnings = cls._load_impl(deepcopy_yaml_value(data))
 
+        format_status = "failed" if errors else "passed"
         rd.validation_summary.add_detail(
             ValidationDetail(
                 errors=errors,
                 name=(
                     "bioimageio.spec format validation"
                     f" {rd.type} {cls.implemented_format_version}"
                 ),
-                status="failed" if errors else "passed",
+                status=format_status,
                 warnings=val_warnings,
-                context=context.summary,  # context for format validation detail is identical
-            )
+            ),
+            update_status=False,  # avoid updating status from 'valid-format' to 'passed', but ...
         )
+        if format_status == "failed":
+            # ... update status in case of failure
+            rd.validation_summary.status = "failed"
 
         return rd
 

src/bioimageio/spec/_package.py

@@ -235,7 +235,7 @@ def save_bioimageio_package(
     """Package a bioimageio resource as a zip file.
 
     Args:
-        rd: bioimageio resource description
+        source: 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
@@ -298,7 +298,7 @@ def save_bioimageio_package_to_stream(
     """Package a bioimageio resource into a stream.
 
     Args:
-        rd: bioimageio resource description
+        source: 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

src/bioimageio/spec/_version.py

@@ -1 +1 @@
-VERSION = "0.5.5.6"
+VERSION = "0.5.5.7"

src/bioimageio/spec/summary.py

@@ -245,16 +245,22 @@ class ValidationSummary(BaseModel, extra="allow"):
 
     name: str
     """Name of the validation"""
+
     source_name: str
     """Source of the validated bioimageio description"""
+
     id: Optional[str] = None
     """ID of the resource being validated"""
+
     type: str
     """Type of the resource being validated"""
+
     format_version: str
     """Format version of the resource being validated"""
+
     status: Literal["passed", "valid-format", "failed"]
-    """overall status of the bioimageio validation"""
+    """Overall status of the bioimageio validation"""
+
     metadata_completeness: Annotated[float, annotated_types.Interval(ge=0, le=1)] = 0.0
     """Estimate of completeness of the metadata in the resource description.
 
@@ -375,11 +381,15 @@ def display(
             include_conda_list=include_conda_list,
         )
 
-    def add_detail(self, detail: ValidationDetail):
-        if detail.status == "failed":
-            self.status = "failed"
-        elif detail.status != "passed":
-            assert_never(detail.status)
+    def add_detail(self, detail: ValidationDetail, update_status: bool = True):
+        if update_status:
+            if self.status == "valid-format" and detail.status == "passed":
+                # once status is 'valid-format' we can only improve to 'passed'
+                self.status = "passed"
+            elif self.status == "passed" and detail.status == "failed":
+                # once status is 'passed' it can only degrade to 'valid-format'
+                self.status = "valid-format"
+            # once format is 'failed' it cannot improve
 
         self.details.append(detail)
 

tests/test_description.py

@@ -43,6 +43,6 @@ def test_no_forward_compatibility(unet2d_data: BioimageioYamlContent):
 
 
 def test_update_format(unet2d_path_old: str):
-    updated = update_format(unet2d_path_old)
+    updated = update_format(unet2d_path_old, perform_io_checks=False)
     assert updated.type == "model"
     assert updated.format_version == ModelDescr.implemented_format_version

tests/test_example_specs.py

@@ -58,6 +58,7 @@ def test_example_descr_paths(
         as_latest=False,
         exclude_fields_from_roundtrip=EXCLUDE_FIELDS_FROM_ROUNDTRIP.get(key, set()),
         bioimageio_json_schema=bioimageio_json_schema,
+        perform_io_checks=False,
     )