Merge remote-tracking branch 'upstream/main' into bugfix_bads_included

Author: tsbinns

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne_connectivity
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.12
+    rev: v0.13.0
     hooks:
       - id: ruff
         name: ruff lint mne_connectivity
@@ -10,7 +10,7 @@ repos:
 
   # Ruff tutorials and examples
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.12
+    rev: v0.13.0
     hooks:
       - id: ruff
         name: ruff lint tutorials and examples
@@ -47,7 +47,7 @@ repos:
 
   # toml-sort
   - repo: https://github.com/pappasam/toml-sort.git
-    rev: v0.24.2
+    rev: v0.24.3
     hooks:
       - id: toml-sort-fix
 

mne_connectivity/vector_ar/tests/test_var.py

@@ -281,6 +281,10 @@ def test_vector_auto_regression():
         conn.get_data().mean(axis=0), single_conn.get_data(), decimal=1
     )
 
+    # compute single var with multiple lags
+    single_conn_plags = vector_auto_regression(data, model="avg-epochs", lags=2)
+    single_conn_plags.get_data("dense")  # just check data can be reshaped properly
+
     # compute residuals
     residuals = data - parr_conn.predict(data)
     assert residuals.shape == data.shape

mne_connectivity/vector_ar/var.py

@@ -36,7 +36,7 @@ def vector_auto_regression(
     ----------
     data : array_like, shape (n_epochs, n_signals, n_times) | Epochs | generator
         The data from which to compute connectivity. The epochs dimension is interpreted
-        differently, depending on ``'output'`` argument.
+        differently, depending on the ``'model'`` argument.
     times : array_like | None
         The time points used to construct the epoched ``data``. If ``None``, then
         ``times_used`` in the returned ``conn`` will not be available.
@@ -58,7 +58,7 @@ def vector_auto_regression(
 
     Returns
     -------
-    conn : Connectivity | EpochConnectivity | TemporalConnectivity | EpochTemporalConnectivity
+    conn : Connectivity | TemporalConnectivity | EpochConnectivity | EpochTemporalConnectivity
         The connectivity data estimated.
 
     See Also