From 3b670d7c23b4f5b26bc2062ddb7f394bb9cc9df6 Mon Sep 17 00:00:00 2001 From: Paul Adkisson Date: Fri, 24 May 2024 14:10:46 -0400 Subject: [PATCH] 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 9b330757369cb8b8966a9d78bc13c84012eb2671. * removed class section of module docstrings * Revert "removed class section of module docstrings" This reverts commit 4c96f570e65e7e51f6bc8e109f3b4d91c822bae2. * 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 --- .readthedocs.yml | 2 + CHANGELOG.md | 1 + docs/source/api.rst | 8 -- docs/source/api/base_imagingextractors.rst | 14 +++ .../api/base_segmentationextractors.rst | 10 +++ docs/source/api/extraction_tools.rst | 3 + .../brukertiffimagingextractors.rst | 3 + .../hdf5imagingextractor.rst | 3 + docs/source/api/imaging_extractors/index.rst | 17 ++++ .../inscopiximagingextractor.rst | 3 + .../memmapimagingextractors.rst | 10 +++ .../micromanagertiffimagingextractor.rst | 3 + .../miniscopeimagingextractor.rst | 3 + .../numpyimagingextractor.rst | 3 + .../nwbimagingextractor.rst | 3 + .../sbximagingextractor.rst | 3 + .../scanimagetiffimagingextractors.rst | 10 +++ .../tiffimagingextractor.rst | 3 + docs/source/api/index.rst | 12 +++ .../caimansegmentationextractor.rst | 3 + .../cnmfesegmentationextractor.rst | 3 + .../extractsegmentationextractors.rst | 3 + .../api/segmentation_extractors/index.rst | 13 +++ .../numpysegmentationextractor.rst | 3 + .../nwbsegmentationextractor.rst | 3 + .../simasegmentationextractor.rst | 3 + .../suite2psegmentationextractor.rst | 3 + docs/source/api/testing.rst | 10 +++ docs/source/build_api/modules.rst | 8 -- .../roiextractors.example_datasets.rst | 21 ----- .../roiextractors.extractors.caiman.rst | 21 ----- ...actors.extractors.hdf5imagingextractor.rst | 21 ----- ...iextractors.extractors.numpyextractors.rst | 21 ----- ...roiextractors.extractors.nwbextractors.rst | 21 ----- .../build_api/roiextractors.extractors.rst | 25 ------ ...tractors.extractors.schnitzerextractor.rst | 29 ------- ...roiextractors.extractors.simaextractor.rst | 21 ----- .../roiextractors.extractors.suite2p.rst | 21 ----- ...actors.extractors.tiffimagingextractor.rst | 21 ----- docs/source/build_api/roiextractors.rst | 86 ------------------- docs/source/build_api/setup.rst | 7 -- docs/source/conf.py | 3 +- docs/source/index.rst | 1 + requirements-rtd.txt | 1 - .../caiman/caimansegmentationextractor.py | 4 +- 45 files changed, 154 insertions(+), 336 deletions(-) delete mode 100644 docs/source/api.rst create mode 100644 docs/source/api/base_imagingextractors.rst create mode 100644 docs/source/api/base_segmentationextractors.rst create mode 100644 docs/source/api/extraction_tools.rst create mode 100644 docs/source/api/imaging_extractors/brukertiffimagingextractors.rst create mode 100644 docs/source/api/imaging_extractors/hdf5imagingextractor.rst create mode 100644 docs/source/api/imaging_extractors/index.rst create mode 100644 docs/source/api/imaging_extractors/inscopiximagingextractor.rst create mode 100644 docs/source/api/imaging_extractors/memmapimagingextractors.rst create mode 100644 docs/source/api/imaging_extractors/micromanagertiffimagingextractor.rst create mode 100644 docs/source/api/imaging_extractors/miniscopeimagingextractor.rst create mode 100644 docs/source/api/imaging_extractors/numpyimagingextractor.rst create mode 100644 docs/source/api/imaging_extractors/nwbimagingextractor.rst create mode 100644 docs/source/api/imaging_extractors/sbximagingextractor.rst create mode 100644 docs/source/api/imaging_extractors/scanimagetiffimagingextractors.rst create mode 100644 docs/source/api/imaging_extractors/tiffimagingextractor.rst create mode 100644 docs/source/api/index.rst create mode 100644 docs/source/api/segmentation_extractors/caimansegmentationextractor.rst create mode 100644 docs/source/api/segmentation_extractors/cnmfesegmentationextractor.rst create mode 100644 docs/source/api/segmentation_extractors/extractsegmentationextractors.rst create mode 100644 docs/source/api/segmentation_extractors/index.rst create mode 100644 docs/source/api/segmentation_extractors/numpysegmentationextractor.rst create mode 100644 docs/source/api/segmentation_extractors/nwbsegmentationextractor.rst create mode 100644 docs/source/api/segmentation_extractors/simasegmentationextractor.rst create mode 100644 docs/source/api/segmentation_extractors/suite2psegmentationextractor.rst create mode 100644 docs/source/api/testing.rst delete mode 100644 docs/source/build_api/modules.rst delete mode 100644 docs/source/build_api/roiextractors.example_datasets.rst delete mode 100644 docs/source/build_api/roiextractors.extractors.caiman.rst delete mode 100644 docs/source/build_api/roiextractors.extractors.hdf5imagingextractor.rst delete mode 100644 docs/source/build_api/roiextractors.extractors.numpyextractors.rst delete mode 100644 docs/source/build_api/roiextractors.extractors.nwbextractors.rst delete mode 100644 docs/source/build_api/roiextractors.extractors.rst delete mode 100644 docs/source/build_api/roiextractors.extractors.schnitzerextractor.rst delete mode 100644 docs/source/build_api/roiextractors.extractors.simaextractor.rst delete mode 100644 docs/source/build_api/roiextractors.extractors.suite2p.rst delete mode 100644 docs/source/build_api/roiextractors.extractors.tiffimagingextractor.rst delete mode 100644 docs/source/build_api/roiextractors.rst delete mode 100644 docs/source/build_api/setup.rst diff --git a/.readthedocs.yml b/.readthedocs.yml index 50688d3a..e4fdd9c3 100644 --- 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 index 89756ebc..2287c6ae 100644 --- 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 deleted file mode 100644 index c6358dab..00000000 --- a/docs/source/api.rst +++ /dev/null @@ -1,8 +0,0 @@ -API documentation -================= - -.. toctree:: - :maxdepth: 0 - :glob: - - build_api/* diff --git a/docs/source/api/base_imagingextractors.rst b/docs/source/api/base_imagingextractors.rst new file mode 100644 index 00000000..a06c2de4 --- /dev/null +++ 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 new file mode 100644 index 00000000..919993d1 --- /dev/null +++ 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 new file mode 100644 index 00000000..f12d12c1 --- /dev/null +++ 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 new file mode 100644 index 00000000..64f889fc --- /dev/null +++ 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 new file mode 100644 index 00000000..471243d0 --- /dev/null +++ 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 new file mode 100644 index 00000000..72cd6fdb --- /dev/null +++ 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 new file mode 100644 index 00000000..25861375 --- /dev/null +++ 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 new file mode 100644 index 00000000..34349f2d --- /dev/null +++ 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 new file mode 100644 index 00000000..0edcdc24 --- /dev/null +++ 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 new file mode 100644 index 00000000..d47bf977 --- /dev/null +++ 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 new file mode 100644 index 00000000..9fbc391f --- /dev/null +++ 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 new file mode 100644 index 00000000..db9ac58c --- /dev/null +++ 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 new file mode 100644 index 00000000..04761387 --- /dev/null +++ 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 new file mode 100644 index 00000000..1cedf421 --- /dev/null +++ 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 new file mode 100644 index 00000000..c0a28d2a --- /dev/null +++ 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 new file mode 100644 index 00000000..80b88075 --- /dev/null +++ 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 new file mode 100644 index 00000000..f63284f2 --- /dev/null +++ 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 new file mode 100644 index 00000000..16c4f663 --- /dev/null +++ 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 new file mode 100644 index 00000000..20cd1f39 --- /dev/null +++ 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 new file mode 100644 index 00000000..a6fb782d --- /dev/null +++ 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 new file mode 100644 index 00000000..2a8aaa2e --- /dev/null +++ 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 new file mode 100644 index 00000000..f7e74bab --- /dev/null +++ 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 new file mode 100644 index 00000000..deb099d0 --- /dev/null +++ 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 new file mode 100644 index 00000000..1e89b70c --- /dev/null +++ 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 new file mode 100644 index 00000000..00f93e04 --- /dev/null +++ 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 deleted file mode 100644 index 9bf59166..00000000 --- a/docs/source/build_api/modules.rst +++ /dev/null @@ -1,8 +0,0 @@ -roiextractors -============= - -.. toctree:: - :maxdepth: 4 - - roiextractors - setup diff --git a/docs/source/build_api/roiextractors.example_datasets.rst b/docs/source/build_api/roiextractors.example_datasets.rst deleted file mode 100644 index 70a95a97..00000000 --- a/docs/source/build_api/roiextractors.example_datasets.rst +++ /dev/null @@ -1,21 +0,0 @@ -roiextractors.example\_datasets package -======================================= - -Submodules ----------- - -roiextractors.example\_datasets.toy\_example module ---------------------------------------------------- - -.. automodule:: roiextractors.example_datasets.toy_example - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: roiextractors.example_datasets - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/build_api/roiextractors.extractors.caiman.rst b/docs/source/build_api/roiextractors.extractors.caiman.rst deleted file mode 100644 index 0858b470..00000000 --- a/docs/source/build_api/roiextractors.extractors.caiman.rst +++ /dev/null @@ -1,21 +0,0 @@ -roiextractors.extractors.caiman package -======================================= - -Submodules ----------- - -roiextractors.extractors.caiman.caimansegmentationextractor module ------------------------------------------------------------------- - -.. automodule:: roiextractors.extractors.caiman.caimansegmentationextractor - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: roiextractors.extractors.caiman - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/build_api/roiextractors.extractors.hdf5imagingextractor.rst b/docs/source/build_api/roiextractors.extractors.hdf5imagingextractor.rst deleted file mode 100644 index 58979657..00000000 --- a/docs/source/build_api/roiextractors.extractors.hdf5imagingextractor.rst +++ /dev/null @@ -1,21 +0,0 @@ -roiextractors.extractors.hdf5imagingextractor package -===================================================== - -Submodules ----------- - -roiextractors.extractors.hdf5imagingextractor.hdf5imagingextractor module -------------------------------------------------------------------------- - -.. automodule:: roiextractors.extractors.hdf5imagingextractor.hdf5imagingextractor - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: roiextractors.extractors.hdf5imagingextractor - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/build_api/roiextractors.extractors.numpyextractors.rst b/docs/source/build_api/roiextractors.extractors.numpyextractors.rst deleted file mode 100644 index fd2f56c0..00000000 --- a/docs/source/build_api/roiextractors.extractors.numpyextractors.rst +++ /dev/null @@ -1,21 +0,0 @@ -roiextractors.extractors.numpyextractors package -================================================ - -Submodules ----------- - -roiextractors.extractors.numpyextractors.numpyextractors module ---------------------------------------------------------------- - -.. automodule:: roiextractors.extractors.numpyextractors.numpyextractors - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: roiextractors.extractors.numpyextractors - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/build_api/roiextractors.extractors.nwbextractors.rst b/docs/source/build_api/roiextractors.extractors.nwbextractors.rst deleted file mode 100644 index ccc8a29a..00000000 --- a/docs/source/build_api/roiextractors.extractors.nwbextractors.rst +++ /dev/null @@ -1,21 +0,0 @@ -roiextractors.extractors.nwbextractors package -============================================== - -Submodules ----------- - -roiextractors.extractors.nwbextractors.nwbextractors module ------------------------------------------------------------ - -.. automodule:: roiextractors.extractors.nwbextractors.nwbextractors - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: roiextractors.extractors.nwbextractors - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/build_api/roiextractors.extractors.rst b/docs/source/build_api/roiextractors.extractors.rst deleted file mode 100644 index 9c7550cd..00000000 --- a/docs/source/build_api/roiextractors.extractors.rst +++ /dev/null @@ -1,25 +0,0 @@ -roiextractors.extractors package -================================ - -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - roiextractors.extractors.caiman - roiextractors.extractors.hdf5imagingextractor - roiextractors.extractors.numpyextractors - roiextractors.extractors.nwbextractors - roiextractors.extractors.schnitzerextractor - roiextractors.extractors.simaextractor - roiextractors.extractors.suite2p - roiextractors.extractors.tiffimagingextractor - -Module contents ---------------- - -.. automodule:: roiextractors.extractors - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/build_api/roiextractors.extractors.schnitzerextractor.rst b/docs/source/build_api/roiextractors.extractors.schnitzerextractor.rst deleted file mode 100644 index 4e222e62..00000000 --- a/docs/source/build_api/roiextractors.extractors.schnitzerextractor.rst +++ /dev/null @@ -1,29 +0,0 @@ -roiextractors.extractors.schnitzerextractor package -=================================================== - -Submodules ----------- - -roiextractors.extractors.schnitzerextractor.cnmfesegmentationextractor module ------------------------------------------------------------------------------ - -.. automodule:: roiextractors.extractors.schnitzerextractor.cnmfesegmentationextractor - :members: - :undoc-members: - :show-inheritance: - -roiextractors.extractors.schnitzerextractor.extractsegmentationextractor module -------------------------------------------------------------------------------- - -.. automodule:: roiextractors.extractors.schnitzerextractor.extractsegmentationextractor - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: roiextractors.extractors.schnitzerextractor - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/build_api/roiextractors.extractors.simaextractor.rst b/docs/source/build_api/roiextractors.extractors.simaextractor.rst deleted file mode 100644 index 2eae05cc..00000000 --- a/docs/source/build_api/roiextractors.extractors.simaextractor.rst +++ /dev/null @@ -1,21 +0,0 @@ -roiextractors.extractors.simaextractor package -============================================== - -Submodules ----------- - -roiextractors.extractors.simaextractor.simasegmentationextractor module ------------------------------------------------------------------------ - -.. automodule:: roiextractors.extractors.simaextractor.simasegmentationextractor - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: roiextractors.extractors.simaextractor - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/build_api/roiextractors.extractors.suite2p.rst b/docs/source/build_api/roiextractors.extractors.suite2p.rst deleted file mode 100644 index 24857a1b..00000000 --- a/docs/source/build_api/roiextractors.extractors.suite2p.rst +++ /dev/null @@ -1,21 +0,0 @@ -roiextractors.extractors.suite2p package -======================================== - -Submodules ----------- - -roiextractors.extractors.suite2p.suite2psegmentationextractor module --------------------------------------------------------------------- - -.. automodule:: roiextractors.extractors.suite2p.suite2psegmentationextractor - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: roiextractors.extractors.suite2p - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/build_api/roiextractors.extractors.tiffimagingextractor.rst b/docs/source/build_api/roiextractors.extractors.tiffimagingextractor.rst deleted file mode 100644 index cfa24c41..00000000 --- a/docs/source/build_api/roiextractors.extractors.tiffimagingextractor.rst +++ /dev/null @@ -1,21 +0,0 @@ -roiextractors.extractors.tiffimagingextractor package -===================================================== - -Submodules ----------- - -roiextractors.extractors.tiffimagingextractor.tiffimagingextractor module -------------------------------------------------------------------------- - -.. automodule:: roiextractors.extractors.tiffimagingextractor.tiffimagingextractor - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: roiextractors.extractors.tiffimagingextractor - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/build_api/roiextractors.rst b/docs/source/build_api/roiextractors.rst deleted file mode 100644 index fc3e3afb..00000000 --- a/docs/source/build_api/roiextractors.rst +++ /dev/null @@ -1,86 +0,0 @@ -roiextractors package -===================== - -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - roiextractors.example_datasets - roiextractors.extractors - -Submodules ----------- - -roiextractors.extraction\_tools module --------------------------------------- - -.. automodule:: roiextractors.extraction_tools - :members: - :undoc-members: - :show-inheritance: - -roiextractors.extractorlist module ----------------------------------- - -.. automodule:: roiextractors.extractorlist - :members: - :undoc-members: - :show-inheritance: - -roiextractors.imagingextractor module -------------------------------------- - -.. automodule:: roiextractors.imagingextractor - :members: - :undoc-members: - :show-inheritance: - -roiextractors.memmapextractors module -------------------------------------- - -.. automodule:: roiextractors.memmapextractors - :members: - :undoc-members: - :show-inheritance: - -roiextractors.multisegmentationextractor module ------------------------------------------------ - -.. automodule:: roiextractors.multisegmentationextractor - :members: - :undoc-members: - :show-inheritance: - -roiextractors.segmentationextractor module ------------------------------------------- - -.. automodule:: roiextractors.segmentationextractor - :members: - :undoc-members: - :show-inheritance: - -roiextractors.testing module ----------------------------- - -.. automodule:: roiextractors.testing - :members: - :undoc-members: - :show-inheritance: - -roiextractors.version module ----------------------------- - -.. automodule:: roiextractors.version - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: roiextractors - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/build_api/setup.rst b/docs/source/build_api/setup.rst deleted file mode 100644 index 552eb49d..00000000 --- a/docs/source/build_api/setup.rst +++ /dev/null @@ -1,7 +0,0 @@ -setup module -============ - -.. automodule:: setup - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/conf.py b/docs/source/conf.py index a26ddd1e..2519b9f4 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -43,7 +43,6 @@ napoleon_use_param = False napoleon_use_ivar = True napoleon_include_init_with_doc = False -napoleon_include_private_with_doc = True napoleon_include_special_with_doc = True # Autodoc @@ -53,7 +52,7 @@ autodoc_default_options = { "members": True, "member-order": "bysource", - "private-members": True, + "private-members": False, "show-inheritance": False, "toctree": True, } diff --git a/docs/source/index.rst b/docs/source/index.rst index 50e9b7eb..116a4268 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -31,5 +31,6 @@ With this package, a user can: usage usecase contribute + api/index licence contact diff --git a/requirements-rtd.txt b/requirements-rtd.txt index 9fdd2959..403fb912 100644 --- a/requirements-rtd.txt +++ b/requirements-rtd.txt @@ -4,5 +4,4 @@ sphinx_rtd_theme readthedocs-sphinx-search sphinx-toggleprompt sphinx-copybutton -roiextractors pydata_sphinx_theme diff --git a/src/roiextractors/extractors/caiman/caimansegmentationextractor.py b/src/roiextractors/extractors/caiman/caimansegmentationextractor.py index 686210c8..d88dabd4 100644 --- a/src/roiextractors/extractors/caiman/caimansegmentationextractor.py +++ b/src/roiextractors/extractors/caiman/caimansegmentationextractor.py @@ -50,7 +50,7 @@ def __init__(self, file_path: PathType): Parameters ---------- file_path: str - The location of the folder containing caiman *.hdf5 output file. + The location of the folder containing caiman .hdf5 output file. """ SegmentationExtractor.__init__(self) self.file_path = file_path @@ -170,7 +170,7 @@ def get_rejected_list(self): @staticmethod def write_segmentation(segmentation_object: SegmentationExtractor, save_path: PathType, overwrite: bool = True): - """Write a segmentation object to a *.hdf5 or *.h5 file specified by save_path. + """Write a segmentation object to a .hdf5 or .h5 file specified by save_path. Parameters ----------