Merge 0e6e1d9 into 6888034

.github/workflows/continuous-integration.yml

@@ -52,9 +52,12 @@ jobs:
         flag-name: run-${{ matrix.os }}-${{matrix.python-version}}
         parallel: true
         github-token : ${{ secrets.GITHUB_TOKEN}}
+
   finish:
     needs: test
     runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 2
     steps:
     - name: Coveralls Finished
       env:
@@ -63,4 +66,12 @@ jobs:
       with:
         parallel-finished: true
         github-token : ${{ secrets.GITHUB_TOKEN }}
+    - name: Set up Python 3.8 for notebook
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Test with notebook
+      run: |
+        pip install -r requirements-test.txt
+        pytest test_notebooks/notebook_tests.py
         

.github/workflows/release-drafter.yml

@@ -5,6 +5,7 @@ on:
     # branches to consider in the event; optional, defaults to all
     branches:
       - mainline
+      - WHY-2304_notebook_tests
 
 jobs:
   update_release_draft:
@@ -13,4 +14,4 @@ jobs:
       # Drafts your next Release notes as Pull Requests are merged into "mainline"
       - uses: release-drafter/release-drafter@v5
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

requirements-test.txt

@@ -31,3 +31,4 @@ xlrd==2.0.1
 openpyxl==3.0.6
 smart-open==4.1.2
 tqdm==4.54.0
+nbconvert==6.0.7

test_notebooks/conftest.py

@@ -0,0 +1,13 @@
+import os
+import sys
+import pytest
+_MY_DIR = os.path.realpath(os.path.dirname(__file__))
+# Allow import of the test utilities packages
+
+
+@pytest.fixture(scope="session")
+def notebooks_path():
+
+    notebook_path = os.path.join(
+        _MY_DIR, os.pardir, os.pardir, "notebooks")
+    return os.path.abs(notebook_path)

test_notebooks/notebook_tests.py

@@ -0,0 +1,51 @@
+from nbconvert.preprocessors import CellExecutionError
+from nbconvert.preprocessors import ExecutePreprocessor
+import nbformat
+import subprocess
+import os
+import pytest
+
+TEST_DIR = os.path.dirname(os.path.abspath(__file__))
+PARENT_DIR = os.path.join(TEST_DIR, os.pardir, "..")
+
+
+def process_notebook(notebook_filename, html_directory="notebook-html"):
+    """Checks if an IPython notebook runs without error from start to finish. If so, writes the notebook to HTML (with outputs) and overwrites the .ipynb file (without outputs)."""
+
+    with open(notebook_filename) as f:
+        nb = nbformat.read(f, as_version=4)
+
+    ep = ExecutePreprocessor(timeout=600, kernel_name="python3", allow_errors=True)
+
+    try:
+        # Check that the notebook runs
+        ep.preprocess(nb, {"metadata": {"path": ""}})
+    except CellExecutionError:
+        raise
+
+    print(f"Successfully executed {notebook_filename}")
+    return
+
+
+def test_all_notebooks(remove_fail_test=True):
+    """
+    Runs `process_notebook` on all notebooks in the git repository.
+    """
+
+    # Get all files included in the git repository
+    git_files = subprocess.check_output("git ls-tree --full-tree --name-only -r HEAD", shell=True).decode("utf-8").splitlines()
+
+    # Get just the notebooks from the git files
+    notebooks = [fn for fn in git_files if fn.endswith(".ipynb")]
+    print(notebooks)
+
+    # Test each notebook
+    for notebook in notebooks:
+        print("Testing", notebook)
+        process_notebook(os.path.join(PARENT_DIR, notebook))
+
+    return
+
+
+if __name__ == "__main__":
+    test_all_notebooks()