Merge branch 'main' into auto-update-10.5281/zenodo.6559474

Author: FynnBe

.github/workflows/auto_update_main.yaml

@@ -72,9 +72,6 @@ jobs:
         mv tmp_download_counts.json dist/download_counts.json
     - name: update partner resources
       run: python scripts/update_partner_resources.py
-    - name: add documentation files to preview
-      if: github.event_name == 'pull_request'
-      run: python scripts/download_documentation.py
     - name: Upload preview of updated partner resources
       if: github.event_name == 'pull_request'
       uses: actions/upload-artifact@v2

.github/workflows/validate_resources.yaml

@@ -132,17 +132,20 @@ jobs:
       run: python scripts/download_partner_test_summaries.py
     - name: prepare to deploy
       run: python scripts/prepare_to_deploy.py --branch ${{ github.head_ref || github.ref }}
-    - name: Upload preview
-      if: contains(inputs.deploy_to, 'preview')
-      uses: actions/upload-artifact@v2
-      with:
-        name: preview
-        path: dist/gh_pages_update
-        retention-days: 90
     - name: Deploy to gh-pages 🚀
       if: contains(inputs.deploy_to, 'gh-pages')
       uses: JamesIves/[email protected]
       with:
         branch: gh-pages
         clean: false  # Keeping the old files
         folder: dist/gh_pages_update
+    - name: add documentation files to preview
+      if: contains(inputs.deploy_to, 'preview')  # only download documentation for preview to ease review
+      run: python scripts/download_documentation.py --folder dist/gh_pages_update
+    - name: Upload preview
+      if: contains(inputs.deploy_to, 'preview')
+      uses: actions/upload-artifact@v2
+      with:
+        name: preview
+        path: dist/gh_pages_update
+        retention-days: 90

scripts/static_validation.py

@@ -83,12 +83,15 @@ def get_default_env(
     if tensorflow_version is not None:
         # tensorflow 1 is not available on conda, so we need to inject this as a pip dependency
         if tensorflow_version.major == 1:
+            tensorflow_version = max(tensorflow_version, Version("1.13"))  # tf <1.13 not available anymore
             assert opset_version is None
             assert pytorch_version is None
             conda_env["dependencies"] = ["pip", "python >=3.7,<3.8"]  # tf 1.15 not available for py>=3.8
             # get bioimageio.core (and its dependencies) via pip as well to avoid conda/pip mix
+            # protobuf pin: tf 1 does not pin an upper limit for protobuf,
+            #               but fails to load models saved with protobuf 3 when installing protobuf 4.
             conda_env["dependencies"].append(
-                {"pip": [f"bioimageio.core", f"tensorflow {get_version_range(tensorflow_version)}"]}
+                {"pip": [f"bioimageio.core", f"tensorflow {get_version_range(tensorflow_version)}", "protobuf <4.0"]}
             )
         else:  # use conda otherwise
             conda_env["dependencies"].append(f"tensorflow {get_version_range(tensorflow_version)}")