MAINT, DOC: some testing maintenance and doc updates

.gitignore

@@ -71,6 +71,7 @@ instance/
 # Sphinx documentation
 docs/_build/
 docs/build/
+docs/source/generated/auto_tutorials/
 
 # PyBuilder
 target/
@@ -131,6 +132,7 @@ dmypy.json
 
 # Demo thing to let people not pollute repos
 my_project_ll_config.yaml
+project_ll_config_face13_egi.yaml
 
 # VSCode ignore
 .vscode

docs/requirements_doc.txt

@@ -1,5 +1,5 @@
-sphinx!=4.1.0,<6
-pydata-sphinx-theme
+sphinx>=6
+shibuya
 sphinx-design
 sphinx-gallery
 sphinxemoji

docs/source/conf.py

@@ -67,22 +67,21 @@
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = "pydata_sphinx_theme"
+html_theme = "shibuya"
 html_static_path = ["_static"]
-html_theme_options = {
-    "logo": {
-        "image_light": "logo-lightmode_color.png",
-        "image_dark": "logo_white.png",
-    }
-}
+# TODO: add a svg file for the logo
+# html_theme_options = {
+#    "light_logo": "logo-lightmode_color.png",
+#    "dark_logo": "logo_white.png",
+# }
 
 # user made CSS to customize look
 html_css_files = [
     "css/custom.css",
 ]
 
 # Custom sidebar templates, maps document names to template names.
-html_sidebars = {"index": ["search-field.html", "sidebar-nav-bs", "globaltoc.html"]}
+# html_sidebars = {"index": ["search-field.html", "sidebar-nav-bs", "globaltoc.html"]}
 
 # NumPyDoc configuration -----------------------------------------------------
 

docs/source/contributing.rst

@@ -9,8 +9,8 @@ Building and Contributing to the Docs
 pyLossless uses `Sphinx <https://www.sphinx-doc.org/en/master/>`__ for building
 documentation. Specifically, we use the `PyData-sphinx-theme 
 <https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html>`__ as a
-design template for our page. We also use the `Napolean 
-<https://sphinxcontrib-napoleon.readthedocs.io/en/latest/index.html>`__
+design template for our page. We also use the `Numpydoc 
+<https://numpydoc.readthedocs.io/en/latest/index.html>`__
 and
 `autodoc <https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html>`__
 sphinx extensions to build API documentation directly from the pyLossless

docs/source/implementation.rst

@@ -147,7 +147,7 @@ Step 13: Run final ICA
 ----------------------
 
 A final ICA will be run, excluding the epochs that were identified to contain
-large deviations across ICs. These time periods are exlcuded to improve the
+large deviations across ICs. These time periods are excluded to improve the
 final ICA's decomposition.
 
 MNE-ICAlabel will be run on this decomposition to classify the ICs as brain,

pylossless/flagging.py

@@ -24,7 +24,8 @@ class FlaggedChs(dict):
     Attributes
     ----------
     ll : LosslessPipeline
-        the LosslessPipeline object that is flagging artifactual channels.
+        the :class:`~pylossless.pipeline.LosslessPipeline` object that is flagging
+        artifactual channels.
 
     Methods
     -------
@@ -86,10 +87,10 @@ def rereference(self, inst, **kwargs):
         Parameters
         ----------
         inst : mne.io.Raw
-            An instance of :class:`mne.io.Raw` that contains EEG channels.
+            An instance of :class:`~mne.io.Raw` that contains EEG channels.
         kwargs : dict
             dictionary of valid keyword arguments for the
-            :meth:`mne.io.Raw.set_eeg_reference` method.
+            :meth:`~mne.io.Raw.set_eeg_reference` method.
         """
         # Concatenate and remove duplicates
         bad_chs = list(

pylossless/pipeline.py

@@ -477,7 +477,37 @@ def warp_locs(self, raw):
 
 
 class LosslessPipeline:
-    """Class used to handle pipeline parameters."""
+    """Class used to handle pipeline parameters.
+
+    Parameters
+    ----------
+    config_fname : pathlib.Path
+        path to config file specifying the parameters to be used
+        in the pipeline.
+
+    Attributes
+    ----------
+    flags : dict
+        A dictionary of detailing the flagged channels, epochs, and ICs.
+        keys are ``'ch'``, ``'epoch'``, and ``'ic'``, and values are instances of
+        :class:`~pylossless.flagging.FlaggedChs`,
+        :class:`~pylossless.flagging.FlaggedEpochs`, and
+        :class:`~pylossless.flagging.FlaggedICs`, respectively.
+    config_fname : pathlib.Path
+        path to the config file specifying the parameters to be used in the
+        in the pipeline.
+    config : dict
+        A dictionary containing the pipeline parameters.
+    raw : mne.Raw
+        An instance of :class:`~mne.io.Raw` containing that will
+        be processed by the pipeline.
+    ica1 : mne.preprocessing.ICA
+        An instance of :class:`~mne.preprocessing.ICA`. The result of the initial ICA
+        run during the pipeline.
+    ica2 : mne.preprocessing.ICA
+        An instance of :class:`~mne.preprocessing.ICA`. The result of the final ICA run
+        during the pipeline.
+    """
 
     def __init__(self, config_fname=None):
         """Initialize class.
@@ -695,7 +725,7 @@ def _flag_volt_std(self, flag_dim, threshold=5e-5):
 
     def find_outlier_chs(self, inst):
         """Detect outlier Channels to leave out of rereference."""
-        # TODO: Re-use _detect_outliers here.
+        # TODO: Reuse _detect_outliers here.
         logger.info("🔍 Detecting channels to leave out of reference.")
         if isinstance(inst, mne.Epochs):
             epochs = inst

pylossless/tests/test_simulated.py

@@ -69,7 +69,7 @@ def data_fun(times):
 add_eog(raw_sim, random_state=rng)
 raw_sim.pick("eeg")
 
-# Save Info and Montage for later re-use
+# Save Info and Montage for later reuse
 montage = raw_sim.get_montage()
 info = mne.create_info(
     ch_names=raw_sim.ch_names,

pyproject.toml

@@ -1,5 +1,5 @@
 [tool.codespell]
-skip = "docs/source/generated"
+skip = "docs/source/generated,pylossless/assets"
 
 [tool.ruff]
 select = ["E", "F", "W", "D"] # pycodestle, pyflakes, Warning, Docstring