add retest_all workflow

.github/workflows/retest_all.yaml

@@ -0,0 +1,41 @@
+name: retest all bioimageio resources adding to their logs
+
+on: workflow_dispatch
+concurrency: retest
+
+jobs:
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{steps.get_matrix.outputs.matrix}}
+
+    steps:
+      - run: wget ${{vars.S3_HOST}}/${{vars.S3_BUCKET}}/${{vars.S3_FOLDER}}/collection.json
+      - shell: python
+        id: get_matrix
+        run: |
+          import json, os
+
+          with open("collection.json") as f:
+            collection = json.load(f)
+
+          published = [{"id": entry["id"], "v": entry["version"]} for entry in collection["collection"]]
+          matrix = {"include": published}
+          with open(os.environ["GITHUB_OUTPUT"], "a") as f:
+            print(f"matrix={matrix}", file=f)
+
+  test:
+    needs: setup
+    strategy:
+      matrix: ${{fromJson(needs.setup.outputs.matrix)}}
+    uses: bioimage-io/collection/.github/workflows/test_call.yaml@main
+    with:
+      resource_id: ${{matrix.id}}
+      version: ${{matrix.v}}
+      conclude: 'no'
+      S3_HOST: ${{vars.S3_HOST}}
+      S3_BUCKET: ${{vars.S3_BUCKET}}
+      S3_FOLDER: ${{vars.S3_FOLDER}}
+    secrets: inherit
+
+# TODO: call emailer

.github/workflows/test_call.yaml

@@ -11,6 +11,11 @@ on:
         description: "Version number prefixed with 'staged/', e.g. 'staged/1' (testing published versions again is not (yet) implemented)"
         required: true
         type: string
+      conclude:
+        description: "Wether or not to trigger a status update based on test results"
+        required: false
+        default: 'yes'
+        type: string
       S3_HOST:
         required: true
         type: string
@@ -91,7 +96,7 @@ jobs:
 
   conclude:
     needs: [validate_format, test]
-    if: always() # run even if test job fails
+    if: (inputs.conclude == 'yes') && always()  # run even if test job fails
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

bioimageio_collection_backoffice/_backoffice.py

@@ -53,10 +53,6 @@ def stage(self, resource_id: str, package_url: str):
     def validate_format(self, resource_id: str, version: str):
         """validate a (staged) resource version's bioimageio.yaml"""
         rv = get_remote_resource_version(self.client, resource_id, version)
-        if isinstance(rv, PublishedVersion):
-            logger.error("Revalidation of published resources is not implemented")
-            return
-
         dynamic_test_cases, conda_envs = validate_format(rv)
         set_gh_actions_outputs(
             has_dynamic_test_cases=bool(dynamic_test_cases),

bioimageio_collection_backoffice/generate_collection_json.py

@@ -109,6 +109,7 @@ def maybe_swap_with_thumbnail(
         entry["nickname_icon"] = entry["id_emoji"]
         entry["entry_source"] = client.get_file_url(rdf_s3_path)
         entry["rdf_source"] = entry["entry_source"]
+        entry["version"] = v
         entry["versions"] = versions
         return entry
 

bioimageio_collection_backoffice/validate_format.py

@@ -11,7 +11,7 @@
 from ruyaml import YAML
 from typing_extensions import assert_never
 
-from .remote_resource import StagedVersion
+from .remote_resource import PublishedVersion, StagedVersion
 from .s3_structure.log import BioimageioLog, Logs
 
 yaml = YAML(typ="safe")
@@ -218,12 +218,14 @@ def prepare_dynamic_test_cases(
     return validation_cases, conda_envs
 
 
-def validate_format(staged: StagedVersion):
-    if not staged.exists():
-        raise ValueError(f"{staged} not found")
+def validate_format(rv: Union[StagedVersion, PublishedVersion]):
+    if not rv.exists():
+        raise ValueError(f"{rv} not found")
 
-    staged.set_testing_status("Validating RDF format")
-    rdf_source = staged.rdf_url
+    if isinstance(rv, StagedVersion):
+        rv.set_testing_status("Validating RDF format")
+
+    rdf_source = rv.rdf_url
     rd = load_description(rdf_source, format_version="discover")
     if not isinstance(rd, InvalidDescr):
         rd.validation_summary.add_detail(
@@ -251,15 +253,15 @@ def validate_format(staged: StagedVersion):
         rd = rd_latest
         rd.validation_summary.status = "passed"  # passed in 'discover' mode
         if not isinstance(rd, InvalidDescr) and rd.version is not None:
-            published = staged.get_versions().published
-            if str(rd.version) in {v.sem_ver for v in published.values()}:
-                error = ErrorEntry(
-                    loc=("version",),
-                    msg=f"Trying to publish version {rd.version} again!",
-                    type="error",
-                )
-            else:
-                error = None
+            error = None
+            if isinstance(rv, StagedVersion):
+                published = rv.get_versions().published
+                if str(rd.version) in {v.sem_ver for v in published.values()}:
+                    error = ErrorEntry(
+                        loc=("version",),
+                        msg=f"Trying to publish version {rd.version} again!",
+                        type="error",
+                    )
 
             rd.validation_summary.add_detail(
                 ValidationDetail(
@@ -270,5 +272,5 @@ def validate_format(staged: StagedVersion):
             )
 
     summary = rd.validation_summary
-    staged.extend_log(Logs(bioimageio_spec=[BioimageioLog(log=summary)]))
+    rv.extend_log(Logs(bioimageio_spec=[BioimageioLog(log=summary)]))
     return dynamic_test_cases, conda_envs