Merge remote-tracking branch 'origin/main' into auto-update-10.5281/zenodo.7274275

Author: FynnBe

.github/workflows/validate_resources.yaml

@@ -97,7 +97,7 @@ jobs:
     - name: dynamic validation
       shell: bash -l {0}
       timeout-minutes: 30
-      run: python scripts/dynamic_validation.py dist/dynamic_validation_artifact ${{ matrix.resource_id }} ${{ matrix.version_id }} ${{ matrix.weight_format }} --create-env-outcome ${{ steps.create_env.outcome }}
+      run: python scripts/dynamic_validation.py dist/dynamic_validation_artifact ${{ matrix.resource_id }} ${{ matrix.version_id }} ${{ matrix.weight_format }} --create-env-outcome ${{ steps.create_env.outcome }} --${{ contains(inputs.deploy_to, 'gh-pages') && 'no-ignore' || 'ignore' }}-rdf-source-field-in-validation
     - name: Upload validation summary
       uses: actions/upload-artifact@v2
       with:

scripts/dynamic_validation.py

@@ -3,7 +3,9 @@
 from typing import List, Optional
 
 import typer
+from marshmallow import missing
 
+from bioimageio.spec import load_raw_resource_description
 from bioimageio.spec.shared import yaml
 
 
@@ -20,6 +22,8 @@ def main(
     weight_format: Optional[str] = typer.Argument(..., help="weight format to test model with."),
     rdf_dirs: List[Path] = (Path(__file__).parent / "../artifacts/static_validation_artifact",),
     create_env_outcome: str = "success",
+    # rdf_source might assume a resource has been deployed, if not (e.g. in a PR), rdf_source is expected to be invalid.
+    ignore_rdf_source_field_in_validation: bool = False,
 ):
     if weight_format is None:
         # no dynamic tests for non-model resources...
@@ -45,9 +49,14 @@ def main(
                 summary = test_summary_from_exception("check for test kwargs", e)
             else:
                 try:
-                    summary = test_resource(rdf_path, weight_format=weight_format, **test_kwargs)
+                    rd = load_raw_resource_description(rdf_path)
+                    if ignore_rdf_source_field_in_validation:
+                        rd.rdf_source = missing
+
+                    summary = test_resource(rd, weight_format=weight_format, **test_kwargs)
                 except Exception as e:
                     summary = test_summary_from_exception("call 'test_resource'", e)
+
     else:
         env_path = dist / "static_validation_artifact" / resource_id / version_id / f"conda_env_{weight_format}.yaml"
         if env_path.exists():