normalize def, test, and add pylint to action

.github/workflows/main.yml

@@ -37,4 +37,8 @@ jobs:
 
     - name: Test with PyTest
       run: |
-        python -m pytest --cov=inflammation.models tests/test_models.py
+        python -m pytest --cov=inflammation.models tests/test_models.py
+
+    - name: Check style with Pylint
+      run: |
+        python3 -m pylint --fail-under=0 --reports=y inflammation

inflammation/models.py

@@ -59,3 +59,13 @@ def daily_min(data):
     """
 
     return np.min(data, axis=0)
+
+def patient_normalise(data):
+    """Normalise patient data from a 2D inflammation data array."""
+    max_val = np.nanmax(data, axis=1)
+    with np.errstate(invalid='ignore', divide='ignore'):
+        normalised = data / max_val[:, np.newaxis]
+    normalised[np.isnan(normalised)] = 0
+    normalised[normalised < 0] = 0
+
+    return normalised

tests/test_models.py

@@ -59,4 +59,17 @@ def test_daily_min_string():
     from inflammation.models import daily_min
 
     with pytest.raises(TypeError):
-        error_expected = daily_min([['Hello', 'there'], ['General', 'Kenobi']])
+        error_expected = daily_min([['Hello', 'there'], ['General', 'Kenobi']])
+
+@pytest.mark.parametrize(
+    "test, expected",
+    [
+        ([[0, 0, 0], [0, 0, 0], [0, 0, 0]], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]),
+        ([[1, 1, 1], [1, 1, 1], [1, 1, 1]], [[1, 1, 1], [1, 1, 1], [1, 1, 1]]),
+        ([[1, 2, 3], [4, 5, 6], [7, 8, 9]], [[0.33, 0.67, 1], [0.67, 0.83, 1], [0.78, 0.89, 1]]),
+    ])
+def test_patient_normalise(test, expected):
+    """Test normalisation works for arrays of one and positive integers.
+       Assumption that test accuracy of two decimal places is sufficient."""
+    from inflammation.models import patient_normalise
+    npt.assert_almost_equal(patient_normalise(np.array(test)), np.array(expected), decimal=2)