added normalise func and testing func

inflammation/models.py

@@ -32,3 +32,12 @@ def daily_min(data):
     """Calculate the daily min of a 2D inflammation data array."""
     return np.min(data, axis=0)
 
+def patient_normalise(data):
+    """Normalise patient data from a 2D inflammation data array."""
+    maximum = np.max(data, axis=1)
+    assert (maximum !=0).all()
+    with np.errstate(invalid='ignore', divide='ignore'):
+        normalised = data / maximum[:, np.newaxis]
+    normalised[np.isnan(normalised)] = 0
+    normalised[normalised < 0] = 0
+    return normalised

tests/test_models.py

@@ -67,4 +67,37 @@ def test_daily_min_string(test):
     from inflammation.models import daily_min
 
     with pytest.raises(TypeError):
-        error_expected = daily_min(test)
+        _ = daily_min(test)
+
+@pytest.mark.parametrize(
+    "test, expected, expect_raises",
+    [
+        ([[0, 0, 0], [0, 0, 0], [0, 0, 0]],
+         [[0, 0, 0], [0, 0, 0], [0, 0, 0]],
+         AssertionError),
+         (
+            "hello",
+            None,
+            ValueError,
+        ),
+        ([[1, 1, 1], [1, 1, 1], [1, 1, 1]],
+         [[1, 1, 1], [1, 1, 1], [1, 1, 1]],
+         None),
+        ([[-1, -1, 1], [-1, -1, 1], [-1, -1, 1]],
+         [[0, 0, 1], [0, 0, 1], [0, 0, 1]],
+         None),
+        ([[1, 2, 3], [4, 5, 6], [7, 8, 9]],
+         [[0.33, 0.67, 1], [0.67, 0.83, 1], [0.78, 0.89, 1]],
+         None),
+    ])
+def test_patient_normalise(test, expected,expect_raises):
+    """Test normalisation works for arrays of one and positive integers.
+       Test with a relative and absolute tolerance of 0.01."""
+    from inflammation.models import patient_normalise
+    if expect_raises is not None:
+        with pytest.raises(expect_raises):
+            result = patient_normalise(np.array(test))
+            npt.assert_allclose(result, np.array(expected), rtol=1e-2, atol=1e-2)
+    else:
+        result = patient_normalise(np.array(test))
+        npt.assert_allclose(result, np.array(expected), rtol=1e-2, atol=1e-2)