fix: Override error on filterwarnings to pass notebook tests (#1841)

* Use 'scrapbook' as it is the new name of 'nteract-scrapbook', which is no longer
maintained or developed.
* Restrict 'papermill' and 'scrapbook' to compatible releases at the patch level
for API stability.
* Override error on filterwarnings for the 'notebooks' GHA workflow as it is testing
for the notebooks to run with the latest pyhf API, not if the Jupyter infrastructure
is warning free.
* Use the papermill.execute_notebook 'cwd' optional argument to change the execution
directory safely.
* Use a concurrency group to limit the notebook testing workflow to only one run
at a time.
   - c.f. https://docs.github.com/en/actions/using-jobs/using-concurrency

.github/workflows/notebooks.yml

@@ -6,6 +6,10 @@ on:
   - cron:  '1 0 * * *'
   workflow_dispatch:
 
+concurrency:
+  group: notebooks-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   test:
 
@@ -16,15 +20,23 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.10
+
+    - name: Set up Python
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip --quiet install --upgrade .[complete]
-        python -m pip list
+        python -m pip install --upgrade .[test]
+
+    - name: List installed Python packages
+      run: python -m pip list
+
     - name: Test example notebooks
       run: |
-        pytest tests/test_notebooks.py
+        # Override the ini option for filterwarnings with an empty list to disable error
+        # on filterwarnings as testing for notebooks to run with the latest API, not if
+        # Jupyter infrastructure is warning free.
+        pytest --override-ini filterwarnings= tests/test_notebooks.py

setup.py

@@ -38,8 +38,8 @@
             'pytest-console-scripts',
             'pytest-mpl',
             'pydocstyle',
-            'papermill~=2.0',
-            'nteract-scrapbook~=0.2',
+            'papermill~=2.3.4',
+            'scrapbook~=0.5.0',
             'jupyter',
             'graphviz',
         ]

tests/test_notebooks.py

@@ -1,8 +1,9 @@
 import sys
-import os
+from pathlib import Path
+
 import papermill as pm
-import scrapbook as sb
 import pytest
+import scrapbook as sb
 
 
 @pytest.fixture()
@@ -11,6 +12,7 @@ def common_kwargs(tmpdir):
     return {
         'output_path': str(outputnb),
         'kernel_name': f'python{sys.version_info.major}',
+        'progress_bar': False,
     }
 
 
@@ -19,17 +21,19 @@ def test_hello_world(common_kwargs):
 
 
 def test_xml_importexport(common_kwargs):
+    # Change directories to make users not have to worry about paths to follow example
+    execution_dir = Path.cwd() / "docs" / "examples" / "notebooks"
     pm.execute_notebook(
-        'docs/examples/notebooks/XML_ImportExport.ipynb', **common_kwargs
+        execution_dir / "XML_ImportExport.ipynb", cwd=execution_dir, **common_kwargs
     )
 
 
 def test_statisticalanalysis(common_kwargs):
     # The Binder example uses specific relative paths
-    cwd = os.getcwd()
-    os.chdir(os.path.join(cwd, 'docs/examples/notebooks/binderexample'))
-    pm.execute_notebook('StatisticalAnalysis.ipynb', **common_kwargs)
-    os.chdir(cwd)
+    execution_dir = Path.cwd() / "docs" / "examples" / "notebooks" / "binderexample"
+    pm.execute_notebook(
+        execution_dir / "StatisticalAnalysis.ipynb", cwd=execution_dir, **common_kwargs
+    )
 
 
 def test_shapefactor(common_kwargs):
@@ -39,35 +43,33 @@ def test_shapefactor(common_kwargs):
 def test_multichannel_coupled_histos(common_kwargs):
     pm.execute_notebook(
         'docs/examples/notebooks/multichannel-coupled-histo.ipynb',
-        parameters={'validation_datadir': 'validation/data'},
+        parameters={"validation_datadir": str(Path.cwd() / "validation" / "data")},
         **common_kwargs,
     )
 
 
 def test_multibinpois(common_kwargs):
     pm.execute_notebook(
         'docs/examples/notebooks/multiBinPois.ipynb',
-        parameters={'validation_datadir': 'validation/data'},
+        parameters={"validation_datadir": str(Path.cwd() / "validation" / "data")},
         **common_kwargs,
     )
     nb = sb.read_notebook(common_kwargs['output_path'])
     assert nb.scraps['number_2d_successpoints'].data > 200
 
 
 def test_pullplot(common_kwargs):
-    # Change directories to make users not have to worry about paths to follow example
-    cwd = os.getcwd()
-    os.chdir(os.path.join(cwd, "docs/examples/notebooks"))
-    pm.execute_notebook("pullplot.ipynb", **common_kwargs)
-    os.chdir(cwd)
+    execution_dir = Path.cwd() / "docs" / "examples" / "notebooks"
+    pm.execute_notebook(
+        execution_dir / "pullplot.ipynb", cwd=execution_dir, **common_kwargs
+    )
 
 
 def test_impactplot(common_kwargs):
-    # Change directories to make users not have to worry about paths to follow example
-    cwd = os.getcwd()
-    os.chdir(os.path.join(cwd, "docs/examples/notebooks"))
-    pm.execute_notebook("ImpactPlot.ipynb", **common_kwargs)
-    os.chdir(cwd)
+    execution_dir = Path.cwd() / "docs" / "examples" / "notebooks"
+    pm.execute_notebook(
+        execution_dir / "ImpactPlot.ipynb", cwd=execution_dir, **common_kwargs
+    )
 
 
 def test_toys(common_kwargs):