CI: switch to testing example .py files instead of notebooks

.github/workflows/notebooktest-package.yml → .github/workflows/test-tutorials.yml

@@ -1,4 +1,4 @@
-name: Notebooks
+name: Tutorials
 
 on: [push]
 
@@ -30,13 +30,13 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install pathos pygraphviz neuron cloud-volume k3d scikit-image open3d
         python -m pip install -e .[test-notebook,all]
-    - name: Run notebooks
+    - name: Run tutorials
       uses: coactions/setup-xvfb@v1
       env:
         NEUPRINT_APPLICATION_CREDENTIALS: ${{ secrets.neuprint }}
         INSECT_BRAIN_DB_USER: ${{ secrets.insect_brain_db_user }}
         INSECT_BRAIN_DB_PASSWORD: ${{ secrets.insect_brain_db_password }}
       with:
         run: |
-          export NAVIS_HEADLESS=TRUE
-          python tests/test_notebooks.py
+          NAVIS_PLOT3D_BACKEND="plotly"
+          python tests/test_tutorials.py

tests/test_tutorials.py

@@ -0,0 +1,48 @@
+"""
+Code to execute code examples notebooks in /docs/examples.
+
+This will not be run through pytest but is meant to be run in a separate CI job.
+"""
+
+import subprocess
+from pathlib import Path
+
+# If Jupyter is not installed, this will fail.
+# We will belay the import error in case the
+# user wants to run only the other parts of the
+# test suite.
+try:
+    import nbformat
+    from nbconvert.preprocessors import ExecutePreprocessor
+except ImportError:
+    nbformat = None
+    pass
+except BaseException:
+    raise
+
+SKIP = [
+
+]
+
+if __name__ == "__main__":
+    # Recursively search for notebooks
+    path = Path(__file__).parent.parent / "docs/examples"
+
+    files = list(path.rglob("*.py"))
+    for i, file in enumerate(files):
+        if not file.is_file():
+            continue
+        if file.name in SKIP:
+            continue
+
+        print(f"Executing {file.name} [{i+1}/{len(files)}]... ", end="", flush=True)
+        try:
+            p = subprocess.run(["python", str(file)], check=True, capture_output=True, timeout=600)
+        except subprocess.CalledProcessError as e:
+            print("Failed.")
+            print(e.stdout.decode())
+            print(e.stderr.decode())
+            raise
+        print("Done.", flush=True)
+
+    print("All done.")