adapt docs for refactor

neuromodulation · Nov 12, 2024 · 0b17e3f · 0b17e3f
1 parent 647a0a1
commit 0b17e3f
Show file tree

Hide file tree

Showing 66 changed files with 252 additions and 191 deletions.
diff --git a/.github/workflows/docs_pages.yml b/.github/workflows/docs_pages.yml
@@ -30,7 +30,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-          uv pip install .[docs]
+          pip install .[docs]
 
       - name: make the sphinx docs
         run: |

diff --git a/docs/source/RMAP.rst b/docs/source/RMAP.rst
@@ -0,0 +1,8 @@
+RMAP
+====
+
+.. autoclass:: analysis.RMAP.ConnectivityChannelSelector
+      :members:
+
+.. autoclass:: analysis.RMAP.RMAPCross_Val_ChannelSelector
+      :members:
diff --git a/docs/source/api_documentation.rst b/docs/source/api_documentation.rst
@@ -1,51 +1,84 @@
 API Documentation
 =================
 
-Parametrization
+
+Analysis
+--------
+
+.. toctree::
+   :maxdepth: 4
+
+   decode
+   feature_reader
+   plots
+   RMAP
+   stats
+
+
+Feature Classes
 ---------------
 
 .. toctree::
    :maxdepth: 4
 
-   nm_stream_abc
-   nm_stream
-   nm_settings
-   nm_define_nmchannels
-   nm_generator
-   nm_run_analysis
-   nm_resample
-   nm_normalization
-   nm_rereference
-   nm_projection
-   nm_IO
-
-Feature Estimation
-------------------
+   bispectra
+   bursts
+   coherence
+   fooof
+   hjorth
+   linelength
+   mne_connectivity
+   nolds
+   oscillatory
+   sharpwaves
+   bandpower
+
+
+Filter
+------
 
 .. toctree::
    :maxdepth: 4
 
-   nm_features
-   nm_filter
-   nm_oscillatory
-   nm_fooof
-   nm_kalmanfilter 
-   nm_hjorth
-   nm_sharpwaves
-   nm_bursts
-   nm_coherence
-   nm_nolds
-   nm_mne_connectivity
-   nm_linelength
+   mne_filter
+   notch_filter
 
-Analysis
---------
+
+Processing
+----------
 
 .. toctree::
    :maxdepth: 4
 
-   nm_analysis
-   nm_decode
-   nm_plots
-   nm_RMAP
-   nm_stats
+   artifacts
+   normalization
+   projection
+   rereference
+   resample
+
+
+stream
+------
+
+.. toctree::
+   :maxdepth: 4
+
+   generator
+   mnelsl_player
+   mnelsl_stream
+   settings
+   stream
+
+
+utils
+-----
+
+.. toctree::
+   :maxdepth: 4
+
+   channels
+   database
+   io
+   logging
+   types
+
diff --git a/docs/source/artifacts.rst b/docs/source/artifacts.rst
@@ -0,0 +1,5 @@
+artifacts
+=========
+
+.. autoclass:: processing.artifacts.PARRMArtifactRejection
+      :members:
diff --git a/docs/source/bandpower.rst b/docs/source/bandpower.rst
@@ -0,0 +1,5 @@
+bandpower
+=========
+
+.. autoclass:: features.bandpower.BandPower
+      :members:
diff --git a/docs/source/bispectra.rst b/docs/source/bispectra.rst
@@ -0,0 +1,5 @@
+bispectra
+=========
+
+.. autoclass:: features.bispectra.Bispectra
+      :members:
diff --git a/docs/source/bursts.rst b/docs/source/bursts.rst
@@ -0,0 +1,5 @@
+bursts
+======
+
+.. autoclass:: features.bursts.Bursts
+      :members:
diff --git a/docs/source/channels.rst b/docs/source/channels.rst
@@ -0,0 +1,5 @@
+channels
+========
+
+.. automodule:: utils.channels
+      :members:
diff --git a/docs/source/coherence.rst b/docs/source/coherence.rst
@@ -0,0 +1,5 @@
+coherence
+=========
+
+.. autoclass:: features.coherence.Coherence
+      :members:
diff --git a/docs/source/database.rst b/docs/source/database.rst
@@ -0,0 +1,5 @@
+database
+========
+
+.. autoclass:: utils.database.NMDatabase
+      :members:
diff --git a/docs/source/decode.rst b/docs/source/decode.rst
@@ -0,0 +1,5 @@
+decode
+======
+
+.. autoclass:: analysis.decode.Decoder
+      :members:
diff --git a/docs/source/feature_reader.rst b/docs/source/feature_reader.rst
@@ -0,0 +1,5 @@
+feature_reader
+==============
+
+.. autoclass:: analysis.feature_reader.FeatureReader
+      :members:
diff --git a/docs/source/fooof.rst b/docs/source/fooof.rst
@@ -0,0 +1,5 @@
+fooof
+=====
+
+.. autoclass:: features.fooof.FooofAnalyzer
+      :members:
diff --git a/docs/source/generator.rst b/docs/source/generator.rst
@@ -0,0 +1,5 @@
+generator
+=========
+
+.. autoclass:: stream.generator.RawDataGenerator
+      :members:
diff --git a/docs/source/hjorth.rst b/docs/source/hjorth.rst
@@ -0,0 +1,5 @@
+hjorth
+======
+
+.. autoclass:: features.hjorth_raw.Hjorth
+      :members:
diff --git a/docs/source/io.rst b/docs/source/io.rst
@@ -0,0 +1,5 @@
+io
+==
+
+.. automodule:: utils.io
+      :members:
diff --git a/docs/source/linelength.rst b/docs/source/linelength.rst
@@ -0,0 +1,5 @@
+linelength
+==========
+
+.. autoclass:: features.linelength.LineLength
+      :members:
diff --git a/docs/source/logging.rst b/docs/source/logging.rst
@@ -0,0 +1,5 @@
+logging
+=======
+
+.. autoclass:: utils.logging.NMLogger
+      :members:
diff --git a/docs/source/mne_connectivity.rst b/docs/source/mne_connectivity.rst
@@ -0,0 +1,5 @@
+mne_connectivity
+================
+
+.. autoclass:: features.mne_connectivity.MNEConnectivity
+      :members:
diff --git a/docs/source/mne_filter.rst b/docs/source/mne_filter.rst
@@ -0,0 +1,5 @@
+mne_filter
+==========
+
+.. autoclass:: filter.mne_filter.MNEFilter
+      :members:
diff --git a/docs/source/mnelsl_player.rst b/docs/source/mnelsl_player.rst
@@ -0,0 +1,5 @@
+mnelsl_player
+==============
+
+.. autoclass:: stream.mnelsl_player.LSLOfflinePlayer
+      :members:
diff --git a/docs/source/mnelsl_stream.rst b/docs/source/mnelsl_stream.rst
@@ -0,0 +1,5 @@
+mnelsl_stream
+=============
+
+.. autoclass:: stream.mnelsl_stream.LSLStream
+      :members:
diff --git a/docs/source/nm_IO.rst b/docs/source/nm_IO.rst
diff --git a/docs/source/nm_RMAP.rst b/docs/source/nm_RMAP.rst
diff --git a/docs/source/nm_analysis.rst b/docs/source/nm_analysis.rst
diff --git a/docs/source/nm_bursts.rst b/docs/source/nm_bursts.rst
diff --git a/docs/source/nm_coherence.rst b/docs/source/nm_coherence.rst
diff --git a/docs/source/nm_decode.rst b/docs/source/nm_decode.rst
diff --git a/docs/source/nm_define_nmchannels.rst b/docs/source/nm_define_nmchannels.rst
diff --git a/docs/source/nm_features.rst b/docs/source/nm_features.rst
diff --git a/docs/source/nm_filter.rst b/docs/source/nm_filter.rst
diff --git a/docs/source/nm_fooof.rst b/docs/source/nm_fooof.rst
diff --git a/docs/source/nm_generator.rst b/docs/source/nm_generator.rst
diff --git a/docs/source/nm_hjorth.rst b/docs/source/nm_hjorth.rst
diff --git a/docs/source/nm_kalmanfilter.rst b/docs/source/nm_kalmanfilter.rst
diff --git a/docs/source/nm_linelength.rst b/docs/source/nm_linelength.rst
diff --git a/docs/source/nm_mne_connectivity.rst b/docs/source/nm_mne_connectivity.rst
diff --git a/docs/source/nm_nolds.rst b/docs/source/nm_nolds.rst
diff --git a/docs/source/nm_normalization.rst b/docs/source/nm_normalization.rst
diff --git a/docs/source/nm_oscillatory.rst b/docs/source/nm_oscillatory.rst