Merge branch 'main' into cacoh

.github/workflows/unit_tests.yml

@@ -51,7 +51,7 @@ jobs:
           pyvista: false
       - name: Install dependencies
         run: |
-          pip install --upgrade pip setuptools wheel
+          python -m pip install --upgrade pip setuptools wheel
           pip install --upgrade --upgrade-strategy eager .[test]
       - if: matrix.mne-version == 'mne-stable'
         run: pip install --upgrade mne

benchmarks/bench_var.py

@@ -7,6 +7,7 @@
 against that of statsmodels to prevent us from creating
 a dependency on statsmodels.
 """
+
 import numpy as np
 from memory_profiler import profile
 from statsmodels.tsa.vector_ar.var_model import VAR

benchmarks/single_epoch_conn.py

@@ -3,10 +3,11 @@
 Generate Test Dataset for Spectral Connectivity Over Time With Frites
 =====================================================================
 
-As of v0.3, mne-connectivity ported over an implementation for 
+As of v0.3, mne-connectivity ported over an implementation for
 spectral connectivity over epochs. This file will generate the test
 dataset used with Frites v0.4.1.
 """
+
 import mne
 import numpy as np
 from frites.conn import conn_spec

mne_connectivity/spectral/epochs.py

@@ -645,9 +645,27 @@ def spectral_connectivity_epochs(
     method : str | list of str
         Connectivity measure(s) to compute. These can be ``['coh', 'cohy',
         'imcoh', 'cacoh', 'mic', 'mim', 'plv', 'ciplv', 'ppc', 'pli', 'dpli',
-        'wpli', 'wpli2_debiased', 'gc', 'gc_tr']``. Multivariate methods
-        (``['cacoh', 'mic', 'mim', 'gc', 'gc_tr]``) cannot be called with the
-        other methods.
+        'wpli', 'wpli2_debiased', 'gc', 'gc_tr']``. These are:
+
+        * %(coh)s
+        * %(cohy)s
+        * %(imcoh)s
+        * %(cacoh)s
+        * %(mic)s
+        * %(mim)s
+        * %(plv)s
+        * %(ciplv)s
+        * %(ppc)s
+        * %(pli)s
+        * %(pli2_unbiased)s
+        * %(dpli)s
+        * %(wpli)s
+        * %(wpli2_debiased)s
+        * %(gc)s
+        * %(gc_tr)s
+
+        Multivariate methods (``['cacoh', 'mic', 'mim', 'gc', 'gc_tr]``) cannot
+        be called with the other methods.
     indices : tuple of array | None
         Two arrays with indices of connections for which to compute
         connectivity. If a bivariate method is called, each array for the seeds

mne_connectivity/spectral/time.py

@@ -69,19 +69,21 @@ def spectral_connectivity_time(
         Only the frequencies within the range specified by ``fmin`` and
         ``fmax`` are used.
     method : str | list of str
-        Connectivity measure(s) to compute. These can be
-        ``['coh', 'cacoh', 'mic', 'mim', 'plv', 'ciplv', 'pli', 'wpli', 'gc',
-        'gc_tr']``. These are:
-        * 'coh'   : Coherence
-        * 'cacoh' : Canonical Coherency (CaCoh)
-        * 'mic'   : Maximised Imaginary part of Coherency (MIC)
-        * 'mim'   : Multivariate Interaction Measure (MIM)
-        * 'plv'   : Phase-Locking Value (PLV)
-        * 'ciplv' : Corrected imaginary Phase-Locking Value
-        * 'pli'   : Phase-Lag Index
-        * 'wpli'  : Weighted Phase-Lag Index
-        * 'gc'    : State-space Granger Causality (GC)
-        * 'gc_tr' : State-space GC on time-reversed signals
+        Connectivity measure(s) to compute. These can be ``['coh', 'cacoh',
+        'mic', 'mim', 'plv', 'ciplv', 'pli', 'wpli', 'gc', 'gc_tr']``. These
+        are:
+
+        * %(coh)s
+        * %(cacoh)s
+        * %(mic)s
+        * %(mim)s
+        * %(plv)s
+        * %(ciplv)s
+        * %(pli)s
+        * %(wpli)s
+        * %(gc)s
+        * %(gc_tr)s
+
         Multivariate methods (``['cacoh', 'mic', 'mim', 'gc', 'gc_tr]``) cannot
         be called with the other methods.
     average : bool

mne_connectivity/utils/docs.py

@@ -68,6 +68,23 @@
         as xarray ``attrs``.
 """
 
+docdict["coh"] = "'coh' : Coherence"
+docdict["cohy"] = "'cohy' : Coherency"
+docdict["imcoh"] = "'imcoh' : Imaginary part of coherency"
+docdict["cacoh"] = "'cacoh' : Canonical Coherency (CaCoh)"
+docdict["mic"] = "'mic' : Maximised Imaginary part of Coherency (MIC)"
+docdict["mim"] = "'mim' : Multivariate Interaction Measure (MIM)"
+docdict["plv"] = "'plv' : Phase-Locking Value (PLV)"
+docdict["ciplv"] = "'ciplv' : Corrected Imaginary PLV (ciPLV)"
+docdict["ppc"] = "'ppc' : Pairwise Phase Consistency (PPC)"
+docdict["pli"] = "'pli' : Phase Lag Index (PLI)"
+docdict["pli2_unbiased"] = "'pli2_unbiased' : Unbiased estimator of squared PLI"
+docdict["dpli"] = "'dpli' : Directed PLI (DPLI)"
+docdict["wpli"] = "'wpli' : Weighted PLI (WPLI)"
+docdict["wpli2_debiased"] = "'wpli2_debiased' : Debiased estimator of squared WPLI"
+docdict["gc"] = "'gc' : State-space Granger Causality (GC)"
+docdict["gc_tr"] = "'gc_tr' : State-space GC on time-reversed signals"
+
 # Downstream container variables
 docdict[
     "freqs"

pyproject.toml

@@ -110,8 +110,8 @@ test = [
   'pandas',
   'pymatreader',
   'PyQt6',
-  'pytest',
   'pytest-cov',
+  'pytest<8.0.0',
   'statsmodels',
 ]