Ecoscope 197

.github/workflows/main.yml

@@ -37,4 +37,4 @@ jobs:
           pytest -v -r s --color=yes --cov=ecoscope --cov-append --cov-report=xml
 
       - name: Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v4

.github/workflows/nb_tests.yml

@@ -0,0 +1,35 @@
+name: Run notebook tests
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "*" ]
+env:
+  ER_USERNAME: ${{ secrets.ER_USERNAME }}
+  ER_PASSWORD: ${{ secrets.ER_PASSWORD }}
+  EE_ACCOUNT: ${{ secrets.EE_ACCOUNT }}
+  EE_PRIVATE_KEY_DATA: ${{ secrets.EE_PRIVATE_KEY_DATA }}
+
+
+jobs:
+  run_unit_tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout branch
+        uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10' 
+      - name: Install pip
+        run: python -m ensurepip --upgrade
+      - name: Install dependencies
+        run: pip install -r requirements-notebooks-test.txt
+      - name: Use the kernel
+        run: python -m ipykernel install --user --name=venv
+      - name: Run unit tests
+        run: pytest -n auto nb-tests/test_notebooks.py -s
+    env:
+      ER_USERNAME: ${{ secrets.ER_USERNAME }}
+      ER_PASSWORD: ${{ secrets.ER_PASSWORD }}
+      EE_ACCOUNT: ${{ secrets.EE_ACCOUNT }}
+      EE_PRIVATE_KEY_DATA: ${{ secrets.EE_PRIVATE_KEY_DATA }}

nb-tests/test_notebooks.py

@@ -0,0 +1,60 @@
+import os
+import re
+import pathlib
+from dataclasses import dataclass
+import ee
+import papermill
+import pytest
+
+try:
+    EE_ACCOUNT = os.getenv("EE_ACCOUNT")
+    EE_PRIVATE_KEY_DATA = os.getenv("EE_PRIVATE_KEY_DATA")
+    if EE_ACCOUNT and EE_PRIVATE_KEY_DATA:
+        ee.Initialize(credentials=ee.ServiceAccountCredentials(EE_ACCOUNT, key_data=EE_PRIVATE_KEY_DATA))
+except Exception:
+    raise ValueError("Earth Engine can not be initialized. Failing notebook tests")
+
+NB_DIR = pathlib.Path(__file__).parent.parent / "doc" / "source" / "notebooks"
+
+KNOWN_ERRORS_REGEXES = {  # This is basically a GitHub ticket queue
+    "EarthRanger_IO.ipynb": "Series found",
+    "Relocations_and_Trajectories.ipynb": "No module named 'branca'",
+    "EcoGraph.ipynb": "not a zip file",
+    "EcoPlot.ipynb": "not a zip file",
+    "Landscape Grid.ipynb": "No module named 'branca'",
+    "Seasonal Calculation.ipynb": "No module named 'branca'",
+    "Tracking Data Gantt Chart.ipynb": "Bad CRC-32 for file 'er_relocs.csv.zip'",
+    "Remote Sensing Time Series Anomaly.ipynb": "No module named 'branca'",
+    "Reduce Regions.ipynb": "No module named 'branca'",
+    "Landscape Dynamics Data.ipynb": "No module named 'branca'",
+}
+
+
+@dataclass
+class Notebook:
+    path: pathlib.Path
+    raises: bool = False
+    raises_match: str = None
+
+
+ALL_NOTEBOOKS = [
+    Notebook(
+        path=p,
+        raises=False if p.name not in KNOWN_ERRORS_REGEXES else True,
+        raises_match=KNOWN_ERRORS_REGEXES.get(p.name),
+    )
+    for p in NB_DIR.rglob("*.ipynb")
+]
+
+
+@pytest.mark.parametrize(
+    "notebook",
+    ALL_NOTEBOOKS,
+    ids=[nb.path.name for nb in ALL_NOTEBOOKS],
+)
+def test_notebooks(notebook: Notebook):
+    if notebook.raises:  # these are the ones we expect to raise errors
+        with pytest.raises(Exception, match=re.escape(notebook.raises_match)):
+            papermill.execute_notebook(str(notebook.path), "./output.ipynb", kernel_name="venv")
+        pytest.xfail(f"Notebook {notebook.path} is known to fail with error {notebook.raises_match}")
+    papermill.execute_notebook(str(notebook.path), "./output.ipynb", kernel_name="venv")

requirements-notebooks-test.txt

@@ -0,0 +1,6 @@
+pip-tools
+pytest
+papermill
+.[all]
+ipykernel
+pytest-xdist