Add test for deprecated

pycrostates/segmentation/_base.py

@@ -119,7 +119,7 @@ def compute_parameters(self, norm_gfp: bool = True, return_dist: bool = False):
               durations of each segments assigned to a given state. Each value is
               expressed in seconds (s).
 
-        Warnings
+        warnings
         --------
         When working with `~mne.Epochs`, this method will put together segments of all
         epochs. This could lead to wrong interpretation especially on state durations.
@@ -222,7 +222,7 @@ def compute_transition_matrix(
         -------
         %(transition_matrix)s
 
-        Warnings
+        warnings
         --------
         When working with `~mne.Epochs`, this method will take into account transitions
         that occur between epochs. This could lead to wrong interpretation when working
@@ -239,9 +239,9 @@ def compute_transition_matrix(
         )
         _check_type(ignore_repetitions, (bool,), "ignore_repetitions")
         if ignore_self is not None:
-            logger.warn(
-                "The ignore_self parameter is deprecated and will be removed in \
-                future versions. Please use the ignore_repetitions parameter instead."
+            logger.warning(
+                "The 'ignore_self' parameter is deprecated and will be removed in \
+                future versions. Please use the 'ignore_repetitions' parameter instead."
             )
             ignore_repetitions = ignore_self
         return _compute_transition_matrix(
@@ -284,9 +284,9 @@ def compute_expected_transition_matrix(
         )
         _check_type(ignore_repetitions, (bool,), "ignore_repetitions")
         if ignore_self is not None:
-            logger.warn(
-                "The ignore_self parameter is deprecated and will be removed in \
-                future versions. Please use the ignore_repetitions parameter instead."
+            logger.warning(
+                "The 'ignore_self' parameter is deprecated and will be removed in \
+                future versions. Please use the 'ignore_repetitions' parameter instead."
             )
             ignore_repetitions = ignore_self
         return _compute_expected_transition_matrix(
@@ -389,7 +389,7 @@ def _check_predict_parameters(predict_parameters: dict):
             "reject_by_annotation",
         )
         # Let the door open for custom prediction with different keys, so log
-        # a warning instead of raising.
+        # a warninginstead of raising.
         for key in predict_parameters.keys():
             if key not in valid_keys:
                 logger.warning(

pycrostates/segmentation/tests/test_transitions.py

@@ -143,3 +143,20 @@ def test_check_labels_n_clusters():
         _check_labels_n_clusters(np.random.randint(0, 5, size=100).astype(float), 5)
     with pytest.raises(ValueError, match=re.escape("'[6 7]' are invalid")):
         _check_labels_n_clusters(np.random.randint(0, 8, size=100), 6)
+
+
+def test_deprecated_ignore_self(caplog):
+    labels = np.random.randint(0, 5, size=100)
+    log = "The 'ignore_self' parameter is deprecated"
+
+    caplog.clear()
+    M = compute_transition_matrix(labels, 5, ignore_self=True)
+    assert log in caplog.text
+    M_ = compute_transition_matrix(labels, 5, ignore_repetitions=True)
+    assert_allclose(M, M_)
+
+    caplog.clear()
+    M = compute_expected_transition_matrix(labels, 5, ignore_self=True)
+    assert log in caplog.text
+    M_ = compute_expected_transition_matrix(labels, 5, ignore_repetitions=True)
+    assert_allclose(M, M_)

pycrostates/segmentation/transitions.py

@@ -45,9 +45,9 @@ def compute_transition_matrix(
     )
     _check_type(ignore_repetitions, (bool,), "ignore_repetitions")
     if ignore_self is not None:
-        logger.warn(
-            "The ignore_self parameter is deprecated and will be removed in \
-            future versions. Please use the ignore_repetitions parameter instead."
+        logger.warning(
+            "The 'ignore_self' parameter is deprecated and will be removed in \
+            future versions. Please use the 'ignore_repetitions' parameter instead."
         )
         ignore_repetitions = ignore_self
     return _compute_transition_matrix(
@@ -132,9 +132,9 @@ def compute_expected_transition_matrix(
     )
     _check_type(ignore_repetitions, (bool,), "ignore_repetitions")
     if ignore_self is not None:
-        logger.warn(
-            "The ignore_self parameter is deprecated and will be removed in \
-            future versions. Please use the ignore_repetitions parameter instead."
+        logger.warning(
+            "The 'ignore_self' parameter is deprecated and will be removed in \
+            future versions. Please use the 'ignore_repetitions' parameter instead."
         )
         ignore_repetitions = ignore_self
     return _compute_expected_transition_matrix(