MAINT: Test on macOS arm64

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/release.yml

@@ -0,0 +1,5 @@
+changelog:
+  exclude:
+    authors:
+      - dependabot
+      - pre-commit-ci

.github/workflows/unit_tests.yml

@@ -25,13 +25,16 @@ jobs:
             python-version: "3.9"
             mne-version: mne-main
           - os: ubuntu-latest
-            python-version: "3.11"
+            python-version: "3.12"
             mne-version: mne-main
-          - os: macos-latest
-            python-version: "3.11"
+          - os: macos-13  # Intel
+            python-version: "3.12"
+            mne-version: mne-main
+          - os: macos-14  # arm64
+            python-version: "3.12"
             mne-version: mne-main
           - os: windows-latest
-            python-version: "3.11"
+            python-version: "3.12"
             mne-version: mne-main
     env:
       TZ: Europe/Berlin

.pre-commit-config.yaml

@@ -1,16 +1,10 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.11.0
-    hooks:
-      - id: black
-        args: [--quiet]
-
   # Ruff mne_connectivity
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.6
+    rev: v0.4.4
     hooks:
       - id: ruff
-        name: ruff mne_connectivity
+        name: ruff lint mne_connectivity
         args: ["--fix"]
         files: ^mne_connectivity/
 
@@ -19,7 +13,7 @@ repos:
     rev: v0.1.6
     hooks:
       - id: ruff
-        name: ruff tutorials and examples
+        name: ruff lint tutorials and examples
         # D103: missing docstring in public function
         # D400: docstring first line must end with period
         args: ["--ignore=D103,D400", "--fix"]
@@ -51,5 +45,11 @@ repos:
           - tomli
         files: ^doc/.*\.(rst|inc)$
 
+  # toml-sort
+  - repo: https://github.com/pappasam/toml-sort.git
+    rev: v0.23.1
+    hooks:
+      - id: toml-sort-fix
+
 ci:
   autofix_prs: false

Makefile

@@ -85,24 +85,7 @@ upload-pipy:
 	python setup.py sdist bdist_egg register upload
 
 flake:
-	@if command -v flake8 > /dev/null; then \
-		echo "Running flake8"; \
-		flake8 --count mne_connectivity examples; \
-	else \
-		echo "flake8 not found, please install it!"; \
-		exit 1; \
-	fi;
-	@echo "flake8 passed"
-
-black:
-	@if command -v black > /dev/null; then \
-		echo "Running black"; \
-		black mne_connectivity examples; \
-	else \
-		echo "black not found, please install it!"; \
-		exit 1; \
-	fi;
-	@echo "black passed"
+	ruff check .
 
 isort:
 	@if command -v isort > /dev/null; then \
@@ -140,13 +123,3 @@ build-doc:
 	make -C doc/ clean
 	make -C doc/ html-noplot
 	cd doc/ && make view
-
-run-checks:
-	isort --check .
-	black --check mne_connectivity examples
-	flake8 .
-	@$(MAKE) pydocstyle
-	@$(MAKE) codespell-error
-	ruff .
-	toml-sort ./pyproject.toml --check
-	yamllint . -c .yamllint.yml --strict

examples/compare_coherency_methods.py

@@ -420,10 +420,10 @@ def plot_connectivity_circle():
 )
 axis.set_xlabel("Frequency (Hz)")
 axis.set_ylabel("Connectivity (A.U.)")
-axis.annotate("$\pm$45°\ninteraction", xy=(12.5, 0.9))
-axis.annotate("$\pm$90°\ninteraction", xy=(26.5, 0.9))
+axis.annotate("$\\pm$45°\ninteraction", xy=(12.5, 0.9))
+axis.annotate("$\\pm$90°\ninteraction", xy=(26.5, 0.9))
 axis.legend(loc="upper left")
-fig.suptitle("CaCoh vs. MIC\n$\pm$45° & $\pm$90° interactions")
+fig.suptitle("CaCoh vs. MIC\n$\\pm$45° & $\\pm$90° interactions")
 
 ###############################################################################
 # In situations where non-physiological zero time-lag interactions are present,
@@ -455,10 +455,10 @@ def plot_connectivity_circle():
 axis.plot(imcoh.freqs, imcoh_mean_subbed, linewidth=2, label="ImCoh", linestyle="--")
 axis.set_xlabel("Frequency (Hz)")
 axis.set_ylabel("Mean-corrected connectivity (A.U.)")
-axis.annotate("$\pm$45°\ninteraction", xy=(13, 0.25))
-axis.annotate("$\pm$90°\ninteraction", xy=(26.5, 0.25))
+axis.annotate("$\\pm$45°\ninteraction", xy=(13, 0.25))
+axis.annotate("$\\pm$90°\ninteraction", xy=(26.5, 0.25))
 axis.legend(loc="upper left")
-fig.suptitle("Coh vs. ImCoh\n$\pm$45° & $\pm$90° interactions")
+fig.suptitle("Coh vs. ImCoh\n$\\pm$45° & $\\pm$90° interactions")
 
 ###############################################################################
 # Bivariate vs. multivariate coherency methods

examples/compare_connectivity_over_time_over_trial.py

@@ -74,13 +74,13 @@
 #
 # License: BSD (3-clause)
 
-import numpy as np
 import matplotlib.pyplot as plt
 import mne
+import numpy as np
+from mne.datasets import sample
 
 from mne_connectivity import spectral_connectivity_epochs, spectral_connectivity_time
 from mne_connectivity.viz import plot_sensors_connectivity
-from mne.datasets import sample
 
 rng = np.random.default_rng(1234)  # set seed for reproducibility
 

examples/connectivity_classes.py

@@ -17,12 +17,13 @@
 # License: BSD (3-clause)
 
 import os.path as op
-import numpy as np
 
 import mne
-from mne_connectivity import spectral_connectivity_epochs
+import numpy as np
 from mne.datasets import sample
 
+from mne_connectivity import spectral_connectivity_epochs
+
 # %%
 # Set parameters
 data_path = sample.data_path()

examples/cwt_sensor_connectivity.py

@@ -13,14 +13,15 @@
 # License: BSD (3-clause)
 
 import os.path as op
-import numpy as np
 
 import mne
+import numpy as np
 from mne import io
-from mne_connectivity import spectral_connectivity_epochs, seed_target_indices
 from mne.datasets import sample
 from mne.time_frequency import AverageTFR
 
+from mne_connectivity import seed_target_indices, spectral_connectivity_epochs
+
 print(__doc__)
 
 ###############################################################################

examples/dpli_wpli_pli.py

@@ -16,12 +16,12 @@
 # License: BSD (3-clause)
 
 
+import matplotlib.pyplot as plt
 import mne
 import numpy as np
-import matplotlib.pyplot as plt
+from mne.datasets import sample
 
 from mne_connectivity import spectral_connectivity_epochs
-from mne.datasets import sample
 
 ###############################################################################
 # Background

examples/dynamic/mne_var_connectivity.py

@@ -16,14 +16,12 @@
 # Authors: Adam Li <[email protected]>
 #
 # License: BSD (3-clause)
-import numpy as np
-
+import matplotlib.pyplot as plt
 import mne
+import numpy as np
 from mne import make_fixed_length_epochs
 from mne_bids import BIDSPath, read_raw_bids
 
-import matplotlib.pyplot as plt
-
 from mne_connectivity import vector_auto_regression
 
 # %%

examples/granger_causality.py

@@ -15,11 +15,11 @@
 
 # %%
 
+import mne
 import numpy as np
 from matplotlib import pyplot as plt
-
-import mne
 from mne.datasets.fieldtrip_cmc import data_path
+
 from mne_connectivity import spectral_connectivity_epochs
 
 ###############################################################################

examples/mic_mim.py

@@ -18,13 +18,13 @@
 
 # %%
 
+import mne
 import numpy as np
-from matplotlib import pyplot as plt
 from matplotlib import patheffects as pe
-
-import mne
+from matplotlib import pyplot as plt
 from mne import EvokedArray, make_fixed_length_epochs
 from mne.datasets.fieldtrip_cmc import data_path
+
 from mne_connectivity import seed_target_indices, spectral_connectivity_epochs
 
 ###############################################################################

examples/mixed_source_space_connectivity.py

@@ -13,16 +13,16 @@
 # License: BSD (3-clause)
 
 import os.path as op
-import numpy as np
-import matplotlib.pyplot as plt
 
+import matplotlib.pyplot as plt
 import mne
+import numpy as np
+from mne import make_forward_solution, setup_source_space, setup_volume_source_space
 from mne.datasets import sample
-from mne import setup_volume_source_space, setup_source_space
-from mne import make_forward_solution
 from mne.io import read_raw_fif
-from mne.minimum_norm import make_inverse_operator, apply_inverse_epochs
+from mne.minimum_norm import apply_inverse_epochs, make_inverse_operator
 from mne.viz import circular_layout
+
 from mne_connectivity import spectral_connectivity_epochs
 from mne_connectivity.viz import plot_connectivity_circle
 

examples/mne_inverse_coherence_epochs.py

@@ -11,11 +11,11 @@
 #
 # License: BSD (3-clause)
 
-import numpy as np
-
 import mne
+import numpy as np
 from mne.datasets import sample
 from mne.minimum_norm import apply_inverse, apply_inverse_epochs, read_inverse_operator
+
 from mne_connectivity import seed_target_indices, spectral_connectivity_epochs
 
 print(__doc__)

examples/mne_inverse_connectivity_spectrum.py

@@ -12,10 +12,10 @@
 # License: BSD (3-clause)
 
 import matplotlib.pyplot as plt
-
 import mne
 from mne.datasets import sample
 from mne.minimum_norm import apply_inverse_epochs, read_inverse_operator
+
 from mne_connectivity import spectral_connectivity_epochs
 
 print(__doc__)

examples/mne_inverse_envelope_correlation.py

@@ -40,14 +40,14 @@
 
 import os.path as op
 
-import numpy as np
 import matplotlib.pyplot as plt
-
 import mne
+import numpy as np
+from mne.minimum_norm import apply_inverse_epochs, make_inverse_operator
+from mne.preprocessing import compute_proj_ecg, compute_proj_eog
+
 import mne_connectivity
 from mne_connectivity import envelope_correlation
-from mne.minimum_norm import make_inverse_operator, apply_inverse_epochs
-from mne.preprocessing import compute_proj_ecg, compute_proj_eog
 
 data_path = mne.datasets.brainstorm.bst_resting.data_path()
 subjects_dir = op.join(data_path, "subjects")