Use assert_allclose instead of np.allclose and np.isclose(...).all() (#…

…115)

* use assert_allclose instead of assert np.allclose

* replace assert np.isclose(...).all() with assert_allclose and use sane rtol=1e-7, atol=0 in remaining np.allclose tests

* fix warning about gradient_kwargs

* fix missing f-string

* update style configuration

* run ruff, isort, black

* bump MNE req. to 1.1.0 and above

* fix missed black

* remove test on pick_channels

* clean-up following black

* run black again..

* trigger cis

* trigger cis with MNE 1.5

* shorten strings through 88 character length

* fix style

* fix documentation build

.github/workflows/code-style.yml

@@ -1,7 +1,4 @@
 name: style
-# https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#concurrency
-# https://docs.github.com/en/developers/webhooks-and-events/events/github-event-types#pullrequestevent
-# workflow name, PR number (empty on push), push ref (empty on PR)
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
   cancel-in-progress: true
@@ -27,10 +24,8 @@ jobs:
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools wheel
           python -m pip install --progress-bar off .[style]
-      - name: Run flake8
-        uses: py-actions/flake8@v2
-        with:
-          path: "pycrostates"
+      - name: Run Ruff
+        run: ruff check pycrostates
       - name: Run isort
         uses: isort/isort-action@master
       - name: Run black
@@ -43,6 +38,7 @@ jobs:
           check_filenames: true
           check_hidden: true
           skip: ./.git,./build,./.github,*.bib
+          ignore_words_file: ./.codespellignore
       - name: Run pydocstyle
         run: pydocstyle .
       - name: Run bibclean

docs/source/conf.py

@@ -156,6 +156,7 @@
     "bool": ":class:`python:bool`",
     "Path": "pathlib.Path",
     # MNE
+    "ConductorModel": "mne.bem.ConductorModel",
     "DigMontage": "mne.channels.DigMontage",
     "Epochs": "mne.Epochs",
     "Evoked": "mne.Evoked",
@@ -169,6 +170,7 @@
     "EpochsSegmentation": "pycrostates.segmentation.EpochsSegmentation",
     # Matplotlib
     "Axes": "matplotlib.axes.Axes",
+    "Axes3D": "mpl_toolkits.mplot3d.axes3d.Axes3D",
     "colormap": ":doc:`colormap <matplotlib:tutorials/colors/colormaps>`",
     "Figure": "matplotlib.figure.Figure",
     # Scipy
@@ -178,9 +180,11 @@
     "instance",
     "of",
     "shape",
+    "n_ch_groups",
     "n_channels",
     "n_clusters",
     "n_epochs",
+    "n_picks",
     "n_samples",
 }