API docs (#337)

* initial setup of api docs * reformat * added testing * added testing * added imaging and segmentation extractors setup and numpy * added nwb extractors * added memmap extractors * added caiman * added hdf5 * added inscopix * added miniscope * added sbx * added cnmfe * added extract * added sima * added suite2p * added bruker * added micromanager * added scanimage * removed old api and renamed new api * fixed underlines * fixed caiman docstrings * updated changelog * removed redundant module docstrings * Revert "removed redundant module docstrings" This reverts commit 9b33075. * removed class section of module docstrings * Revert "removed class section of module docstrings" This reverts commit 4c96f57. * switched inscopix to full path * switched inscopix to automodule * private members = False * remove napoleon private check * pinned roiextractors dependency on api_docs branch * removed roiextractors from requirements-rtd * added local pip install to .readthedocs.yml
catalystneuro · May 24, 2024 · 3b670d7 · 3b670d7
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diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -8,6 +8,8 @@ build:
 python:
   install:
     - requirements: requirements-rtd.txt
+    - method: pip
+      path: .
 
 sphinx:
   configuration: docs/source/conf.py
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,7 @@
 
 * Add InscopixImagingExtractor: [#276](https://github.com/catalystneuro/roiextractors/pull/276)
 * Updated testing workflows to include python 3.12, m1/intel macos, and dev tests to check neuroconv: [PR #317](https://github.com/catalystneuro/roiextractors/pull/317)
+* Added API documentation: [#337](https://github.com/catalystneuro/roiextractors/pull/337)
 
 ### Fixes
 

diff --git a/docs/source/api.rst b/docs/source/api.rst
diff --git a/docs/source/api/base_imagingextractors.rst b/docs/source/api/base_imagingextractors.rst
@@ -0,0 +1,14 @@
+Base ImagingExtractors
+======================
+
+ImagingExtractor
+----------------
+.. automodule:: roiextractors.imagingextractor
+
+MultiImagingExtractor
+---------------------
+.. automodule:: roiextractors.multiimagingextractor
+
+VolumetricImagingExtractor
+--------------------------
+.. automodule:: roiextractors.volumetricimagingextractor
diff --git a/docs/source/api/base_segmentationextractors.rst b/docs/source/api/base_segmentationextractors.rst
@@ -0,0 +1,10 @@
+Base SegmentationExtractors
+===========================
+
+SegmentationExtractor
+---------------------
+.. automodule:: roiextractors.segmentationextractor
+
+MultiSegmentationExtractor
+--------------------------
+.. automodule:: roiextractors.multisegmentationextractor
diff --git a/docs/source/api/extraction_tools.rst b/docs/source/api/extraction_tools.rst
@@ -0,0 +1,3 @@
+Extraction Tools
+----------------
+.. automodule:: roiextractors.extraction_tools
diff --git a/docs/source/api/imaging_extractors/brukertiffimagingextractors.rst b/docs/source/api/imaging_extractors/brukertiffimagingextractors.rst
@@ -0,0 +1,3 @@
+BrukerTiffImagingExtractors
+---------------------------
+.. automodule:: roiextractors.extractors.tiffimagingextractors.brukertiffimagingextractor
diff --git a/docs/source/api/imaging_extractors/hdf5imagingextractor.rst b/docs/source/api/imaging_extractors/hdf5imagingextractor.rst
@@ -0,0 +1,3 @@
+Hdf5ImagingExtractor
+--------------------
+.. autoclass:: roiextractors.Hdf5ImagingExtractor
diff --git a/docs/source/api/imaging_extractors/index.rst b/docs/source/api/imaging_extractors/index.rst
@@ -0,0 +1,17 @@
+ImagingExtractors
+=================
+
+.. toctree::
+  :maxdepth: 1
+
+  numpyimagingextractor
+  nwbimagingextractor
+  memmapimagingextractors
+  hdf5imagingextractor
+  inscopiximagingextractor
+  miniscopeimagingextractor
+  sbximagingextractor
+  brukertiffimagingextractors
+  micromanagertiffimagingextractor
+  tiffimagingextractor
+  scanimagetiffimagingextractors
diff --git a/docs/source/api/imaging_extractors/inscopiximagingextractor.rst b/docs/source/api/imaging_extractors/inscopiximagingextractor.rst
@@ -0,0 +1,3 @@
+InscopixImagingExtractor
+------------------------
+.. automodule:: roiextractors.extractors.inscopixextractors.inscopiximagingextractor
diff --git a/docs/source/api/imaging_extractors/memmapimagingextractors.rst b/docs/source/api/imaging_extractors/memmapimagingextractors.rst
@@ -0,0 +1,10 @@
+MemmapImagingExtractors
+=======================
+
+MemmapImagingExtractor
+----------------------
+.. autoclass:: roiextractors.MemmapImagingExtractor
+
+NumpyMemmapImagingExtractor
+---------------------------
+.. autoclass:: roiextractors.NumpyMemmapImagingExtractor
diff --git a/docs/source/api/imaging_extractors/micromanagertiffimagingextractor.rst b/docs/source/api/imaging_extractors/micromanagertiffimagingextractor.rst
@@ -0,0 +1,3 @@
+MicroManagerTiffImagingExtractor
+--------------------------------
+.. autoclass:: roiextractors.MicroManagerTiffImagingExtractor
diff --git a/docs/source/api/imaging_extractors/miniscopeimagingextractor.rst b/docs/source/api/imaging_extractors/miniscopeimagingextractor.rst
@@ -0,0 +1,3 @@
+MiniscopeImagingExtractor
+-------------------------
+.. autoclass:: roiextractors.MiniscopeImagingExtractor
diff --git a/docs/source/api/imaging_extractors/numpyimagingextractor.rst b/docs/source/api/imaging_extractors/numpyimagingextractor.rst
@@ -0,0 +1,3 @@
+NumpyImagingExtractor
+---------------------
+.. autoclass:: roiextractors.NumpyImagingExtractor
diff --git a/docs/source/api/imaging_extractors/nwbimagingextractor.rst b/docs/source/api/imaging_extractors/nwbimagingextractor.rst
@@ -0,0 +1,3 @@
+NwbImagingExtractor
+-------------------
+.. autoclass:: roiextractors.NwbImagingExtractor
diff --git a/docs/source/api/imaging_extractors/sbximagingextractor.rst b/docs/source/api/imaging_extractors/sbximagingextractor.rst
@@ -0,0 +1,3 @@
+SbxImagingExtractor
+--------------------
+.. autoclass:: roiextractors.SbxImagingExtractor
diff --git a/docs/source/api/imaging_extractors/scanimagetiffimagingextractors.rst b/docs/source/api/imaging_extractors/scanimagetiffimagingextractors.rst
@@ -0,0 +1,10 @@
+ScanImageTiff
+=============
+
+ScanImageTiffImagingExtractors
+-------------------------------
+.. automodule:: roiextractors.extractors.tiffimagingextractors.scanimagetiffimagingextractor
+
+ScanImageTiffUtils
+------------------
+.. automodule:: roiextractors.extractors.tiffimagingextractors.scanimagetiff_utils
diff --git a/docs/source/api/imaging_extractors/tiffimagingextractor.rst b/docs/source/api/imaging_extractors/tiffimagingextractor.rst
@@ -0,0 +1,3 @@
+TiffImagingExtractor
+--------------------
+.. autoclass:: roiextractors.TiffImagingExtractor
diff --git a/docs/source/api/index.rst b/docs/source/api/index.rst
@@ -0,0 +1,12 @@
+API documentation
+=================
+
+.. toctree::
+  :maxdepth: 1
+
+  base_imagingextractors
+  base_segmentationextractors
+  extraction_tools
+  testing
+  imaging_extractors/index
+  segmentation_extractors/index
diff --git a/docs/source/api/segmentation_extractors/caimansegmentationextractor.rst b/docs/source/api/segmentation_extractors/caimansegmentationextractor.rst
@@ -0,0 +1,3 @@
+CaimanSegmentationExtractor
+---------------------------
+.. autoclass:: roiextractors.CaimanSegmentationExtractor
diff --git a/docs/source/api/segmentation_extractors/cnmfesegmentationextractor.rst b/docs/source/api/segmentation_extractors/cnmfesegmentationextractor.rst
@@ -0,0 +1,3 @@
+CnmfeSegmentationExtractor
+--------------------------
+.. autoclass:: roiextractors.CnmfeSegmentationExtractor
diff --git a/docs/source/api/segmentation_extractors/extractsegmentationextractors.rst b/docs/source/api/segmentation_extractors/extractsegmentationextractors.rst
@@ -0,0 +1,3 @@
+ExtractSegmentationExtractors
+=============================
+.. automodule:: roiextractors.extractors.schnitzerextractor.extractsegmentationextractor
diff --git a/docs/source/api/segmentation_extractors/index.rst b/docs/source/api/segmentation_extractors/index.rst
@@ -0,0 +1,13 @@
+SegmentationExtractors
+======================
+
+.. toctree::
+  :maxdepth: 1
+
+  numpysegmentationextractor
+  nwbsegmentationextractor
+  caimansegmentationextractor
+  cnmfesegmentationextractor
+  extractsegmentationextractors
+  simasegmentationextractor
+  suite2psegmentationextractor
diff --git a/docs/source/api/segmentation_extractors/numpysegmentationextractor.rst b/docs/source/api/segmentation_extractors/numpysegmentationextractor.rst
@@ -0,0 +1,3 @@
+NumpySegmentationExtractor
+--------------------------
+.. autoclass:: roiextractors.NumpySegmentationExtractor
diff --git a/docs/source/api/segmentation_extractors/nwbsegmentationextractor.rst b/docs/source/api/segmentation_extractors/nwbsegmentationextractor.rst
@@ -0,0 +1,3 @@
+NwbSegmentationExtractor
+------------------------
+.. autoclass:: roiextractors.NwbSegmentationExtractor
diff --git a/docs/source/api/segmentation_extractors/simasegmentationextractor.rst b/docs/source/api/segmentation_extractors/simasegmentationextractor.rst
@@ -0,0 +1,3 @@
+SimaSegmentationExtractor
+-------------------------
+.. autoclass:: roiextractors.SimaSegmentationExtractor
diff --git a/docs/source/api/segmentation_extractors/suite2psegmentationextractor.rst b/docs/source/api/segmentation_extractors/suite2psegmentationextractor.rst
@@ -0,0 +1,3 @@
+Suite2pSegmentationExtractor
+----------------------------
+.. autoclass:: roiextractors.Suite2pSegmentationExtractor
diff --git a/docs/source/api/testing.rst b/docs/source/api/testing.rst
@@ -0,0 +1,10 @@
+Testing
+=======
+
+Testing
+-------
+.. automodule:: roiextractors.testing
+
+Toy Examples
+------------
+.. automodule:: roiextractors.example_datasets.toy_example
diff --git a/docs/source/build_api/modules.rst b/docs/source/build_api/modules.rst
diff --git a/docs/source/build_api/roiextractors.example_datasets.rst b/docs/source/build_api/roiextractors.example_datasets.rst
diff --git a/docs/source/build_api/roiextractors.extractors.caiman.rst b/docs/source/build_api/roiextractors.extractors.caiman.rst
diff --git a/docs/source/build_api/roiextractors.extractors.hdf5imagingextractor.rst b/docs/source/build_api/roiextractors.extractors.hdf5imagingextractor.rst
diff --git a/docs/source/build_api/roiextractors.extractors.numpyextractors.rst b/docs/source/build_api/roiextractors.extractors.numpyextractors.rst
diff --git a/docs/source/build_api/roiextractors.extractors.nwbextractors.rst b/docs/source/build_api/roiextractors.extractors.nwbextractors.rst
diff --git a/docs/source/build_api/roiextractors.extractors.rst b/docs/source/build_api/roiextractors.extractors.rst
diff --git a/docs/source/build_api/roiextractors.extractors.schnitzerextractor.rst b/docs/source/build_api/roiextractors.extractors.schnitzerextractor.rst
diff --git a/docs/source/build_api/roiextractors.extractors.simaextractor.rst b/docs/source/build_api/roiextractors.extractors.simaextractor.rst