Add and improve coverage

pyproject.toml

@@ -43,3 +43,23 @@ select = [
     "I", # isort
     "UP", # pyupgrade
 ]
+
+[tool.coverage.run]
+branch = true
+source = [
+    "src/clump_tracker",
+    "tests",
+    "src"
+]
+
+[tool.coverage.report]
+show_missing = true
+skip_covered = false
+
+# use exclude_also to *extend* the default exclude_lines,
+# and allow purely defensive code patterns
+exclude_also = [
+    "^\\s*raise NotImplementedError\\b",
+    "^\\s*raise RuntimeError\\b",
+    "^\\s*case _ as unreachable:",
+]

tests/test_basics.py

@@ -7,23 +7,31 @@
 from clump_tracker import gradient
 
 
-def test_tests():
-    assert True
+@pytest.fixture(params=[np.float32, np.float64, float])
+def dtype(request):
+    return request.param
 
 
-def _dtype():
-    return "dtype", [float, np.float32, np.float64]
+@pytest.fixture(params=[0, 1, 2])
+def axis(request):
+    return request.param
+
+
+@pytest.mark.xfail
+def test_gradient_unsupported_type():
+    field = np.arange(10, dtype=int) + 5
+    x = np.arange(10, dtype=int)
+    axis = 0
+    gradient(field, x, axis)
 
 
-@pytest.mark.parametrize(*_dtype())
 def test_gradient_1D_uniform(dtype):
     field = np.arange(10, dtype=dtype) + 5
     x = np.arange(10, dtype=dtype)
     axis = 0
     assert_array_equal(gradient(field, x, axis), np.gradient(field, x, axis=axis))
 
 
-@pytest.mark.parametrize(*_dtype())
 def test_gradient_1D_non_uniform(dtype):
     field = np.arange(10, dtype=float) + 5
     axis = 0
@@ -33,18 +41,12 @@ def test_gradient_1D_non_uniform(dtype):
     )
 
 
-def _dtype_and_axis():
-    return "axis,dtype", product(range(3), [float, np.float32, np.float64])
-
-
-@pytest.mark.parametrize(*_dtype_and_axis())
 def test_gradient_3D_uniform(axis, dtype):
     field = np.arange(9 * 10 * 11, dtype=dtype).reshape((9, 10, 11)) + 5
     x = np.arange(field.shape[axis], dtype=dtype)
     assert_array_equal(gradient(field, x, axis), np.gradient(field, x, axis=axis))
 
 
-@pytest.mark.parametrize(*_dtype_and_axis())
 def test_gradient_3D_non_uniform(axis, dtype):
     field = np.arange(9 * 10 * 11, dtype=dtype).reshape((9, 10, 11)) + 5
     x = np.geomspace(1, 10, field.shape[axis], dtype=dtype)

tests/test_cc.py

@@ -48,7 +48,7 @@ def _compute_cc_from_list_ref(indexes, x, y, z, max_distance):
     adj = _compute_adjacency_list_cartesian_ref(indexes, x, y, z, max_distance)
 
     # ajoute les voisins de p0 dans a_visiter
-    for i, _ in enumerate(indexes):
+    for i, _ in enumerate(indexes):  # pragma: no branch
         if not deja_vus[i]:
             composante_connexes.append([i])
         a_visiter = np.array([k in adj[i] for k in range(len(indexes))], dtype=bool)
@@ -172,6 +172,15 @@ def test_adjacency_list(indexes, dtype):
     ) == _compute_adjacency_list_cartesian_ref(indexes, x, y, z, 1.0)
 
 
+@pytest.mark.xfail
+def test_adjacency_list_unsupported_type(indexes):
+    x = np.linspace(0, 10, 50, dtype=int)
+    y = np.linspace(0, 5, 20, dtype=int)
+    z = np.linspace(0, 1, 5, dtype=int)
+
+    compute_adjacency_list_cartesian(indexes, x, y, z, 1.0)
+
+
 def test_cc_cartesian(cc_params, dtype):
     indexes = [[i, 0, 0] for i in range(3)]
     x = np.array([0, 1, 10], dtype=dtype)
@@ -181,3 +190,14 @@ def test_cc_cartesian(cc_params, dtype):
 
     actual = compute_cc(indexes, x, y, z, d, "cartesian")
     assert actual == expected
+
+
+@pytest.mark.xfail
+def test_cc_cartesian_unsupported_type(cc_params):
+    indexes = [[i, 0, 0] for i in range(3)]
+    x = np.array([0, 1, 10], dtype=int)
+    y = np.array([0], dtype=int)
+    z = np.array([0], dtype=int)
+    d, expected = cc_params
+
+    compute_cc(indexes, x, y, z, d, "cartesian")

tests/test_clump.py

@@ -0,0 +1,6 @@
+from clump_tracker.clumps import Clump
+
+
+def test_clump():
+    c = Clump(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7, 8.0, 9.0)
+    assert c.coords == (0.0, 1.0, 2.0)