Merge branch 'main' into update_reupload_script

.github/workflows/backup.yaml

@@ -1,9 +1,10 @@
 name: backup
-run-name: backup ${{vars.S3_BUCKET}}/${{vars.S3_FOLDER}} to ${{ inputs.ZENODO_URL }}
+run-name: backup ${{vars.S3_BUCKET}}/${{vars.S3_FOLDER}} to ${{ vars.ZENODO_URL }}
 
 on:
   schedule:
-    - cron: "0 0 * * 0" # every sunday at midnight
+    - cron: "0 8 * * *" # every day at 8am
+  workflow_dispatch:
 
 concurrency: ${{vars.ZENODO_URL}}
 

bioimageio_collection_backoffice/generate_collection_json.py

@@ -29,6 +29,7 @@ def generate_collection_json(
     with collection_template.open() as f:
         collection = json.load(f)
 
+    collection["config"]["url_root"] = client.get_file_url("").strip("/")
     for p in remote_collection.get_all_published_versions():
         collection["collection"].append(create_entry(p))
 
@@ -79,7 +80,10 @@ def maybe_swap_with_thumbnail(
 
         if isinstance(src, str):
             clean_name = Path(src).name  # remove any leading './'
-            return thumbnails.get(clean_name, src)
+            if clean_name in thumbnails:
+                return p.get_file_url(thumbnails[clean_name])
+            else:
+                return src
 
         return src
 

bioimageio_collection_backoffice/remote_resource.py

@@ -255,6 +255,9 @@ def get_uploader(self):
 
         return Uploader(email=email, name=name)
 
+    def get_file_url(self, path: str):
+        return self.client.get_file_url(f"{self.folder}files/{path}")
+
     def get_file_urls(self):
         return self.client.get_file_urls(f"{self.folder}files/")
 

bioimageio_collection_backoffice/validate_format.py

@@ -9,7 +9,7 @@
 from bioimageio.spec.model.v0_5 import Version, WeightsFormat
 from bioimageio.spec.summary import ErrorEntry, ValidationDetail
 from ruyaml import YAML
-from typing_extensions import assert_never
+from typing_extensions import assert_never, get_args
 
 from .db_structure.log import BioimageioLogWithDefaults, LogWithDefaults
 from .remote_resource import PublishedVersion, StagedVersion
@@ -204,7 +204,7 @@ def prepare_dynamic_test_cases(
         for wf, entry in rd.weights:
             # we skip the keras validation for now, see
             # https://github.com/bioimage-io/collection-bioimage-io/issues/16
-            if not isinstance(entry, SupportedWeightsEntry):
+            if not isinstance(entry, get_args(SupportedWeightsEntry)):
                 warnings.warn(f"{wf} weights are currently not validated")
                 continue
 

collection_template.json

@@ -37,7 +37,6 @@
             "dataset"
         ],
         "default_type": "model",
-        "url_root": "https://raw.githubusercontent.com/bioimage-io/collection-bioimage-io/gh-pages",
         "partners": [
             {
                 "id": "bioimageio",

setup.py

@@ -32,8 +32,8 @@
     ],
     packages=find_packages(exclude=["tests"]),
     install_requires=[
-        "bioimageio.core @ git+https://github.com/bioimage-io/core-bioimage-io-python@f0f0a94022ea4ad570c9124c647e3027d9c94b43",  # TODO: change to released version
-        "bioimageio.spec @ git+https://github.com/bioimage-io/spec-bioimage-io@4c1e18d6e6382a5b06d90107defb2f15e9319421",
+        "bioimageio.core @ git+https://github.com/bioimage-io/core-bioimage-io-python@b84d33b321b1f4e755aebe900f0bd74ed74eb012",  # TODO: change to released version
+        "bioimageio.spec @ git+https://github.com/bioimage-io/spec-bioimage-io@68479898acdb4a7e4b53a04d86ad6fc014c69ed9",
         "fire",
         "loguru",
         "minio==7.2.4",