ci+scripts: address review nits from #170

.github/workflows/check-notebooks.yml

@@ -0,0 +1,19 @@
+name: Check notebooks
+on:
+  pull_request:
+    paths:
+      - 'src/tutorials/**/*.ipynb'
+      - 'src/how-to/**/*.ipynb'
+      - 'mkdocs.yaml'
+      - 'scripts/check_notebook_versions.py'
+      - '.github/workflows/check-notebooks.yml'
+jobs:
+  check-versions:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Verify notebook DataJoint connection banners are current
+        run: python scripts/check_notebook_versions.py

scripts/check_notebook_versions.py

@@ -80,22 +80,22 @@ def main() -> int:
             notebooks.extend(p for p in d.rglob("*.ipynb") if ".ipynb_checkpoints" not in str(p))
     notebooks.sort()
 
-    stale: list[tuple[Path, tuple[int, int, int]]] = []
+    stale: dict[Path, set[tuple[int, int, int]]] = {}
     checked = 0
     for nb in notebooks:
         had_banner = False
         for ver in iter_banner_versions(nb):
             had_banner = True
             if ver[0] != target_major or ver[1] != target_minor:
-                stale.append((nb.relative_to(repo), ver))
-                break
+                stale.setdefault(nb.relative_to(repo), set()).add(ver)
         if had_banner:
             checked += 1
 
     if stale:
         print(f"Stale DataJoint connection banner(s) (target: {target_major}.{target_minor}.x):")
-        for path, ver in stale:
-            print(f"  {path}: found {ver[0]}.{ver[1]}.{ver[2]}")
+        for path, vers in sorted(stale.items()):
+            for ver in sorted(vers):
+                print(f"  {path}: found {ver[0]}.{ver[1]}.{ver[2]}")
         print(f"\nRe-execute notebooks with MODE=EXECUTE or MODE=EXECUTE_PG.")
         return 1
 

scripts/execute_notebooks.py

@@ -174,15 +174,21 @@ def main():
     print(f"  DJ_USER: {env.get('DJ_USER')}")
 
     # Pre-cache scikit-image datasets so the one-time "Downloading file ..."
-    # message doesn't leak into committed notebook outputs.
+    # message doesn't leak into committed notebook outputs. Warnings go to
+    # stderr so a transient gitlab.com hiccup is visible in CI logs without
+    # silently re-introducing the download chatter on the next refresh.
     print("\nPre-caching scikit-image datasets...")
-    import skimage.data as _sk_data
-    for _loader in (_sk_data.hubble_deep_field, _sk_data.human_mitosis):
-        try:
-            _loader()
-            print(f"  cached: {_loader.__name__}")
-        except Exception as _e:
-            print(f"  pre-cache warn: {_loader.__name__}: {_e}")
+    try:
+        import skimage.data as _sk_data
+    except ImportError as _e:
+        print(f"  skipping pre-cache (scikit-image not installed): {_e}", file=sys.stderr)
+    else:
+        for _loader in (_sk_data.hubble_deep_field, _sk_data.human_mitosis):
+            try:
+                _loader()
+                print(f"  cached: {_loader.__name__}")
+            except Exception as _e:
+                print(f"  pre-cache warn: {_loader.__name__}: {_e}", file=sys.stderr)
 
     # Find notebooks
     notebooks = find_notebooks(args.base_path)