Merge pull request #225 from bobleesj/warnings

1) Capture no wavelength `UserWarning` for `test_q_to_thh` method 2) discuss passing variables to `@pytest.mark.parametrize`

Author: sbillinge

src/diffpy/utils/transforms.py

@@ -4,12 +4,10 @@
 import numpy as np
 
 wavelength_warning_emsg = (
-    "INFO: no wavelength has been specified. You can continue "
-    "to use the DiffractionObject but some of its powerful features "
-    "will not be available. To specify a wavelength, set "
-    "diffraction_object.wavelength = [number], "
-    "where diffraction_object is the variable name of you Diffraction Object, "
-    "and number is the wavelength in angstroms."
+    "No wavelength has been specified. You can continue to use the DiffractionObject, but "
+    "some of its powerful features will not be available. "
+    "To specify a wavelength, if you have do = DiffractionObject(xarray, yarray, 'tth'), "
+    "you may set do.wavelength = 1.54 for a wavelength of 1.54 angstroms."
 )
 invalid_tth_emsg = "Two theta exceeds 180 degrees. Please check the input values for errors."
 invalid_q_or_d_or_wavelength_emsg = (

tests/test_diffraction_objects.py

@@ -164,11 +164,11 @@ def test_diffraction_objects_equality(inputs1, inputs2, expected):
 
 
 def test_on_xtype():
-    test = DiffractionObject(wavelength=2 * np.pi, xarray=np.array([30, 60]), yarray=np.array([1, 2]), xtype="tth")
-    assert np.allclose(test.on_xtype("tth"), [np.array([30, 60]), np.array([1, 2])])
-    assert np.allclose(test.on_xtype("2theta"), [np.array([30, 60]), np.array([1, 2])])
-    assert np.allclose(test.on_xtype("q"), [np.array([0.51764, 1]), np.array([1, 2])])
-    assert np.allclose(test.on_xtype("d"), [np.array([12.13818, 6.28319]), np.array([1, 2])])
+    do = DiffractionObject(wavelength=2 * np.pi, xarray=np.array([30, 60]), yarray=np.array([1, 2]), xtype="tth")
+    assert np.allclose(do.on_xtype("tth"), [np.array([30, 60]), np.array([1, 2])])
+    assert np.allclose(do.on_xtype("2theta"), [np.array([30, 60]), np.array([1, 2])])
+    assert np.allclose(do.on_xtype("q"), [np.array([0.51764, 1]), np.array([1, 2])])
+    assert np.allclose(do.on_xtype("d"), [np.array([12.13818, 6.28319]), np.array([1, 2])])
 
 
 def test_init_invalid_xtype():
@@ -184,34 +184,34 @@ def test_init_invalid_xtype():
 
 params_index = [
     # UC1: exact match
-    ([4 * np.pi, np.array([30.005, 60]), np.array([1, 2]), "tth", "tth", 30.005], [0]),
+    (4 * np.pi, np.array([30.005, 60]), np.array([1, 2]), "tth", "tth", 30.005, [0]),
     # UC2: target value lies in the array, returns the (first) closest index
-    ([4 * np.pi, np.array([30, 60]), np.array([1, 2]), "tth", "tth", 45], [0]),
-    ([4 * np.pi, np.array([30, 60]), np.array([1, 2]), "tth", "q", 0.25], [0]),
+    (4 * np.pi, np.array([30, 60]), np.array([1, 2]), "tth", "tth", 45, [0]),
+    (4 * np.pi, np.array([30, 60]), np.array([1, 2]), "tth", "q", 0.25, [0]),
     # UC3: target value out of the range, returns the closest index
-    ([4 * np.pi, np.array([0.25, 0.5, 0.71]), np.array([1, 2, 3]), "q", "q", 0.1], [0]),
-    ([4 * np.pi, np.array([30, 60]), np.array([1, 2]), "tth", "tth", 63], [1]),
+    (4 * np.pi, np.array([0.25, 0.5, 0.71]), np.array([1, 2, 3]), "q", "q", 0.1, [0]),
+    (4 * np.pi, np.array([30, 60]), np.array([1, 2]), "tth", "tth", 63, [1]),
 ]
 
 
-@pytest.mark.parametrize("inputs, expected", params_index)
-def test_get_array_index(inputs, expected):
-    test = DiffractionObject(wavelength=inputs[0], xarray=inputs[1], yarray=inputs[2], xtype=inputs[3])
-    actual = test.get_array_index(value=inputs[5], xtype=inputs[4])
-    assert actual == expected[0]
+@pytest.mark.parametrize("wavelength, xarray, yarray, xtype_1, xtype_2, value, expected_index", params_index)
+def test_get_array_index(wavelength, xarray, yarray, xtype_1, xtype_2, value, expected_index):
+    do = DiffractionObject(wavelength=wavelength, xarray=xarray, yarray=yarray, xtype=xtype_1)
+    actual_index = do.get_array_index(value=value, xtype=xtype_2)
+    assert actual_index == expected_index
 
 
 def test_get_array_index_bad():
-    test = DiffractionObject(wavelength=2 * np.pi, xarray=np.array([]), yarray=np.array([]), xtype="tth")
+    do = DiffractionObject(wavelength=2 * np.pi, xarray=np.array([]), yarray=np.array([]), xtype="tth")
     with pytest.raises(ValueError, match=re.escape("The 'tth' array is empty. Please ensure it is initialized.")):
-        test.get_array_index(value=30)
+        do.get_array_index(value=30)
 
 
 def test_dump(tmp_path, mocker):
     x, y = np.linspace(0, 5, 6), np.linspace(0, 5, 6)
     directory = Path(tmp_path)
     file = directory / "testfile"
-    test = DiffractionObject(
+    do = DiffractionObject(
         wavelength=1.54,
         name="test",
         scat_quantity="x-ray",
@@ -222,7 +222,7 @@ def test_dump(tmp_path, mocker):
     )
     mocker.patch("importlib.metadata.version", return_value="3.3.0")
     with freeze_time("2012-01-14"):
-        test.dump(file, "q")
+        do.dump(file, "q")
     with open(file, "r") as f:
         actual = f.read()
     expected = (
@@ -360,15 +360,15 @@ def test_all_array_getter():
 
 
 def test_all_array_setter():
-    actual_do = DiffractionObject()
+    do = DiffractionObject()
 
     # Attempt to directly modify the property
     with pytest.raises(
         AttributeError,
         match="Direct modification of attribute 'all_arrays' is not allowed. "
         "Please use 'input_data' to modify 'all_arrays'.",
     ):
-        actual_do.all_arrays = np.empty((4, 4))
+        do.all_arrays = np.empty((4, 4))
 
 
 def test_id_getter():

tests/test_transforms.py

@@ -1,81 +1,96 @@
+import re
+
 import numpy as np
 import pytest
 
 from diffpy.utils.transforms import d_to_q, d_to_tth, q_to_d, q_to_tth, tth_to_d, tth_to_q
 
 params_q_to_tth = [
     # UC1: Empty q values, no wavelength, return empty arrays
-    ([None, np.empty((0))], np.empty((0))),
+    (None, np.empty((0)), np.empty((0))),
     # UC2: Empty q values, wavelength specified, return empty arrays
-    ([4 * np.pi, np.empty((0))], np.empty(0)),
+    (4 * np.pi, np.empty((0)), np.empty(0)),
     # UC3: User specified valid q values, no wavelength, return empty arrays
     (
-        [None, np.array([0, 0.2, 0.4, 0.6, 0.8, 1])],
+        None,
+        np.array([0, 0.2, 0.4, 0.6, 0.8, 1]),
         np.array([0, 1, 2, 3, 4, 5]),
     ),
     # UC4: User specified valid q values (with wavelength)
     # expected tth values are 2*arcsin(q) in degrees
-    ([4 * np.pi, np.array([0, 1 / np.sqrt(2), 1.0])], np.array([0, 90.0, 180.0])),
+    (4 * np.pi, np.array([0, 1 / np.sqrt(2), 1.0]), np.array([0, 90.0, 180.0])),
 ]
 
 
-@pytest.mark.parametrize("inputs, expected", params_q_to_tth)
-def test_q_to_tth(inputs, expected):
-    actual = q_to_tth(inputs[1], inputs[0])
-    assert np.allclose(expected, actual)
+@pytest.mark.parametrize("wavelength, q, expected_tth", params_q_to_tth)
+def test_q_to_tth(wavelength, q, expected_tth):
+
+    wavelength_warning_emsg = (
+        "No wavelength has been specified. You can continue to use the DiffractionObject, but "
+        "some of its powerful features will not be available. "
+        "To specify a wavelength, if you have do = DiffractionObject(xarray, yarray, 'tth'), "
+        "you may set do.wavelength = 1.54 for a wavelength of 1.54 angstroms."
+    )
+    if wavelength is None:
+        with pytest.warns(UserWarning, match=re.escape(wavelength_warning_emsg)):
+            actual_tth = q_to_tth(q, wavelength)
+    else:
+        actual_tth = q_to_tth(q, wavelength)
+
+    assert np.allclose(expected_tth, actual_tth)
 
 
 params_q_to_tth_bad = [
     # UC1: user specified invalid q values that result in tth > 180 degrees
     (
-        [4 * np.pi, np.array([0.2, 0.4, 0.6, 0.8, 1, 1.2])],
-        [
-            ValueError,
-            "The supplied input array and wavelength will result in an impossible two-theta. "
-            "Please check these values and re-instantiate the DiffractionObject with correct values.",
-        ],
+        4 * np.pi,
+        np.array([0.2, 0.4, 0.6, 0.8, 1, 1.2]),
+        ValueError,
+        "The supplied input array and wavelength will result in an impossible two-theta. "
+        "Please check these values and re-instantiate the DiffractionObject with correct values.",
     ),
     # UC2: user specified a wrong wavelength that result in tth > 180 degrees
     (
-        [100, np.array([0, 0.2, 0.4, 0.6, 0.8, 1])],
-        [
-            ValueError,
-            "The supplied input array and wavelength will result in an impossible two-theta. "
-            "Please check these values and re-instantiate the DiffractionObject with correct values.",
-        ],
+        100,
+        np.array([0, 0.2, 0.4, 0.6, 0.8, 1]),
+        ValueError,
+        "The supplied input array and wavelength will result in an impossible two-theta. "
+        "Please check these values and re-instantiate the DiffractionObject with correct values.",
     ),
 ]
 
 
-@pytest.mark.parametrize("inputs, expected", params_q_to_tth_bad)
-def test_q_to_tth_bad(inputs, expected):
-    with pytest.raises(expected[0], match=expected[1]):
-        q_to_tth(inputs[1], inputs[0])
+@pytest.mark.parametrize("q, wavelength, expected_error_type, expected_error_msg", params_q_to_tth_bad)
+def test_q_to_tth_bad(q, wavelength, expected_error_type, expected_error_msg):
+    with pytest.raises(expected_error_type, match=expected_error_msg):
+        q_to_tth(wavelength, q)
 
 
 params_tth_to_q = [
     # UC0: User specified empty tth values (without wavelength)
-    ([None, np.array([])], np.array([])),
+    (None, np.array([]), np.array([])),
     # UC1: User specified empty tth values (with wavelength)
-    ([4 * np.pi, np.array([])], np.array([])),
+    (4 * np.pi, np.array([]), np.array([])),
     # UC2: User specified valid tth values between 0-180 degrees (without wavelength)
     (
-        [None, np.array([0, 30, 60, 90, 120, 180])],
+        None,
+        np.array([0, 30, 60, 90, 120, 180]),
         np.array([0, 1, 2, 3, 4, 5]),
     ),
     # UC3: User specified valid tth values between 0-180 degrees (with wavelength)
     # expected q values are sin15, sin30, sin45, sin60, sin90
     (
-        [4 * np.pi, np.array([0, 30.0, 60.0, 90.0, 120.0, 180.0])],
+        4 * np.pi,
+        np.array([0, 30.0, 60.0, 90.0, 120.0, 180.0]),
         np.array([0, 0.258819, 0.5, 0.707107, 0.866025, 1]),
     ),
 ]
 
 
-@pytest.mark.parametrize("inputs, expected", params_tth_to_q)
-def test_tth_to_q(inputs, expected):
-    actual = tth_to_q(inputs[1], inputs[0])
-    assert np.allclose(actual, expected)
+@pytest.mark.parametrize("wavelength, tth, expected_q", params_tth_to_q)
+def test_tth_to_q(wavelength, tth, expected_q):
+    actual_q = tth_to_q(tth, wavelength)
+    assert np.allclose(actual_q, expected_q)
 
 
 params_tth_to_q_bad = [