use sphinx-apidoc rather than manual list of modules

this avoids missing modules in the documentation

for each release, re-build the rst files by first deleting contents of /docs/source then running `sphinx-apidoc -o docs/source opensoundscape -T` from the root dir, and deleting the "opensoundscape packe" heading in /docs/source/opensoundscape.rst

docs/index.rst

@@ -103,6 +103,7 @@ Suggested citation:
    tutorials/train_cnn
    tutorials/transfer_learning
    tutorials/training_birdnet_and_perch
+   tutorials/training_with_lightning
    tutorials/customize_cnn_training
    tutorials/preprocess_audio_dataset
    tutorials/acoustic_localization
@@ -122,11 +123,11 @@ Suggested citation:
    classifier_guide/retrain_cnn
 
 .. toctree::
-   :maxdepth: 1
-   :hidden:
-   :caption: Codebase Documentation
+   :maxdepth: 4
+   :caption: API Documentation
+
+   source/opensoundscape
 
-   api/modules
 
 
 .. toctree::

docs/requirements.txt

@@ -1,8 +1,8 @@
 sphinx>=7.2.6
 ipykernel
 nbsphinx
-docutils>=0.18.1,<0.19
-mistune<2.0.0
+docutils
+mistune
 sphinx-copybutton>=0.5.2
 sphinx-rtd-theme>=1.3.0
 sphinx-mdinclude

docs/source/opensoundscape.localization.rst

@@ -0,0 +1,61 @@
+opensoundscape.localization package
+===================================
+
+Submodules
+----------
+
+opensoundscape.localization.audiomoth\_sync module
+--------------------------------------------------
+
+.. automodule:: opensoundscape.localization.audiomoth_sync
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.localization.localization\_algorithms module
+-----------------------------------------------------------
+
+.. automodule:: opensoundscape.localization.localization_algorithms
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.localization.position\_estimate module
+-----------------------------------------------------
+
+.. automodule:: opensoundscape.localization.position_estimate
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.localization.spatial\_event module
+-------------------------------------------------
+
+.. automodule:: opensoundscape.localization.spatial_event
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.localization.synchronized\_recorder\_array module
+----------------------------------------------------------------
+
+.. automodule:: opensoundscape.localization.synchronized_recorder_array
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.localization.utils module
+----------------------------------------
+
+.. automodule:: opensoundscape.localization.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: opensoundscape.localization
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/opensoundscape.ml.rst

@@ -0,0 +1,109 @@
+opensoundscape.ml package
+=========================
+
+Submodules
+----------
+
+opensoundscape.ml.bioacoustics\_model\_zoo module
+-------------------------------------------------
+
+.. automodule:: opensoundscape.ml.bioacoustics_model_zoo
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.ml.cam module
+----------------------------
+
+.. automodule:: opensoundscape.ml.cam
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.ml.cnn module
+----------------------------
+
+.. automodule:: opensoundscape.ml.cnn
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.ml.cnn\_architectures module
+-------------------------------------------
+
+.. automodule:: opensoundscape.ml.cnn_architectures
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.ml.dataloaders module
+------------------------------------
+
+.. automodule:: opensoundscape.ml.dataloaders
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.ml.datasets module
+---------------------------------
+
+.. automodule:: opensoundscape.ml.datasets
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.ml.lightning module
+----------------------------------
+
+.. automodule:: opensoundscape.ml.lightning
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.ml.loss module
+-----------------------------
+
+.. automodule:: opensoundscape.ml.loss
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.ml.safe\_dataset module
+--------------------------------------
+
+.. automodule:: opensoundscape.ml.safe_dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.ml.sampling module
+---------------------------------
+
+.. automodule:: opensoundscape.ml.sampling
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.ml.shallow\_classifier module
+--------------------------------------------
+
+.. automodule:: opensoundscape.ml.shallow_classifier
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+opensoundscape.ml.utils module
+------------------------------
+
+.. automodule:: opensoundscape.ml.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: opensoundscape.ml
+   :members:
+   :undoc-members:
+   :show-inheritance: