diff --git a/doc/development/development.rst b/doc/development/development.rst index a91818a271..1638c41243 100644 --- a/doc/development/development.rst +++ b/doc/development/development.rst @@ -213,6 +213,25 @@ We use Sphinx to build the documentation. To build the documentation locally, yo This will build the documentation in the :code:`doc/_build/html` folder. You can open the :code:`index.html` file in your browser to see the documentation. +Adding new documentation +------------------------ + +Documentation can be added as a +`sphinx-gallery `_ +python file ('tutorials') +or a +`sphinx rst `_ +file (all other sections). + +To add a new tutorial, add your ``.py`` file to ``spikeinterface/examples``. +Then, update the ``spikeinterface/doc/tutorials_custom_index.rst`` file +to make a new card linking to the page and an optional image. See +``tutorials_custom_index.rst`` header for more information. + +For other sections, write your documentation in ``.rst`` format and add +the page to the appropriate ``index.rst`` file found in the relevant +folder (e.g. ``how_to/index.rst``). + How to run code coverage locally -------------------------------- To run code coverage locally, you can use the following command: diff --git a/doc/index.rst b/doc/index.rst index ed443e4200..e6d8aa3fea 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -51,7 +51,7 @@ SpikeInterface is made of several modules to deal with different aspects of the overview get_started/index - tutorials/index + tutorials_custom_index how_to/index modules/index api diff --git a/doc/tutorials_custom_index.rst b/doc/tutorials_custom_index.rst new file mode 100644 index 0000000000..4c7625d811 --- /dev/null +++ b/doc/tutorials_custom_index.rst @@ -0,0 +1,196 @@ +.. This page provides a custom index to the 'Tutorials' page, rather than the default sphinx-gallery +.. generated page. The benefits of this are flexibility in design and inclusion of non-sphinx files in the index. +.. +.. To update this index with a new documentation page +.. 1) Copy the grid-item-card and associated ".. raw:: html" section. +.. 2) change :link: to a link to your page. If this is an `.rst` file, point to the rst file directly. +.. If it is a sphinx-gallery generated file, format the path as separated by underscore and prefix `sphx_glr`, +.. pointing to the .py file. e.g. `tutorials/my/page.py` -> `sphx_glr_tutorials_my_page.py +.. 3) Change :img-top: to point to the thumbnail image of your choosing. You can point to images generated +.. in the sphinx gallery page if you wish. +.. 4) In the `html` section, change the `default-title` to your pages title and `hover-content` to the subtitle. + +:orphan: + +Tutorials +============ + +Longer form tutorials about using SpikeInterface. Many of these are downloadable +as notebooks or Python scripts so that you can "code along" with the tutorials. + +If you're new to SpikeInterface, we recommend trying out the +:ref:`get_started/quickstart:Quickstart tutorial` first. + +Updating from legacy +-------------------- + +.. toctree:: + :maxdepth: 1 + + tutorials/waveform_extractor_to_sorting_analyzer + +Core tutorials +-------------- + +These tutorials focus on the :py:mod:`spikeinterface.core` module. + +.. grid:: 1 2 2 3 + :gutter: 2 + + .. grid-item-card:: Recording objects + :link-type: ref + :link: sphx_glr_tutorials_core_plot_1_recording_extractor.py + :img-top: /tutorials/core/images/thumb/sphx_glr_plot_1_recording_extractor_thumb.png + :img-alt: Recording objects + :class-card: gallery-card + :text-align: center + + .. grid-item-card:: Sorting objects + :link-type: ref + :link: sphx_glr_tutorials_core_plot_2_sorting_extractor.py + :img-top: /tutorials/core/images/thumb/sphx_glr_plot_2_sorting_extractor_thumb.png + :img-alt: Sorting objects + :class-card: gallery-card + :text-align: center + + .. grid-item-card:: Handling probe information + :link-type: ref + :link: sphx_glr_tutorials_core_plot_3_handle_probe_info.py + :img-top: /tutorials/core/images/thumb/sphx_glr_plot_3_handle_probe_info_thumb.png + :img-alt: Handling probe information + :class-card: gallery-card + :text-align: center + + .. grid-item-card:: SortingAnalyzer + :link-type: ref + :link: sphx_glr_tutorials_core_plot_4_sorting_analyzer.py + :img-top: /tutorials/core/images/thumb/sphx_glr_plot_4_sorting_analyzer_thumb.png + :img-alt: SortingAnalyzer + :class-card: gallery-card + :text-align: center + + .. grid-item-card:: Append and/or concatenate segments + :link-type: ref + :link: sphx_glr_tutorials_core_plot_5_append_concatenate_segments.py + :img-top: /tutorials/core/images/thumb/sphx_glr_plot_5_append_concatenate_segments_thumb.png + :img-alt: Append/Concatenate segments + :class-card: gallery-card + :text-align: center + + .. grid-item-card:: Handle time information + :link-type: ref + :link: sphx_glr_tutorials_core_plot_6_handle_times.py + :img-top: /tutorials/core/images/thumb/sphx_glr_plot_6_handle_times_thumb.png + :img-alt: Handle time information + :class-card: gallery-card + :text-align: center + +Extractors tutorials +-------------------- + +The :py:mod:`spikeinterface.extractors` module is designed to load and save recorded and sorted data, and to handle probe information. + +.. grid:: 1 2 2 3 + :gutter: 2 + + .. grid-item-card:: Read various formats + :link-type: ref + :link: sphx_glr_tutorials_extractors_plot_1_read_various_formats.py + :img-top: /tutorials/extractors/images/thumb/sphx_glr_plot_1_read_various_formats_thumb.png + :img-alt: Read various formats + :class-card: gallery-card + :text-align: center + + .. grid-item-card:: Working with unscaled traces + :link-type: ref + :link: sphx_glr_tutorials_extractors_plot_2_working_with_unscaled_traces.py + :img-top: /tutorials/extractors/images/thumb/sphx_glr_plot_2_working_with_unscaled_traces_thumb.png + :img-alt: Unscaled traces + :class-card: gallery-card + :text-align: center + +Quality metrics tutorial +------------------------ + +The :code:`spikeinterface.qualitymetrics` module allows users to compute various quality metrics to assess the goodness of a spike sorting output. + +.. grid:: 1 2 2 3 + :gutter: 2 + + .. grid-item-card:: Quality Metrics + :link-type: ref + :link: sphx_glr_tutorials_qualitymetrics_plot_3_quality_mertics.py + :img-top: /tutorials/qualitymetrics/images/thumb/sphx_glr_plot_3_quality_mertics_thumb.png + :img-alt: Quality Metrics + :class-card: gallery-card + :text-align: center + + .. grid-item-card:: Curation Tutorial + :link-type: ref + :link: sphx_glr_tutorials_qualitymetrics_plot_4_curation.py + :img-top: /tutorials/qualitymetrics/images/thumb/sphx_glr_plot_4_curation_thumb.png + :img-alt: Curation Tutorial + :class-card: gallery-card + :text-align: center + +Comparison tutorial +------------------- + +The :code:`spikeinterface.comparison` module allows you to compare sorter outputs or benchmark against ground truth. + +.. grid:: 1 2 2 3 + :gutter: 2 + + .. grid-item-card:: Sorter Comparison + :link-type: ref + :link: sphx_glr_tutorials_comparison_plot_5_comparison_sorter_weaknesses.py + :img-top: /tutorials/comparison/images/thumb/sphx_glr_plot_5_comparison_sorter_weaknesses_thumb.png + :img-alt: Sorter Comparison + :class-card: gallery-card + :text-align: center + +Widgets tutorials +----------------- + +The :code:`widgets` module contains several plotting routines (widgets) for visualizing recordings, sorting data, probe layout, and more. + +.. grid:: 1 2 2 3 + :gutter: 2 + + .. grid-item-card:: RecordingExtractor Widgets + :link-type: ref + :link: sphx_glr_tutorials_widgets_plot_1_rec_gallery.py + :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_1_rec_gallery_thumb.png + :img-alt: Recording Widgets + :class-card: gallery-card + :text-align: center + + .. grid-item-card:: SortingExtractor Widgets + :link-type: ref + :link: sphx_glr_tutorials_widgets_plot_2_sort_gallery.py + :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_2_sort_gallery_thumb.png + :img-alt: Sorting Widgets + :class-card: gallery-card + :text-align: center + + .. grid-item-card:: Waveforms Widgets + :link-type: ref + :link: sphx_glr_tutorials_widgets_plot_3_waveforms_gallery.py + :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_3_waveforms_gallery_thumb.png + :img-alt: Waveforms Widgets + :class-card: gallery-card + :text-align: center + + .. grid-item-card:: Peaks Widgets + :link-type: ref + :link: sphx_glr_tutorials_widgets_plot_4_peaks_gallery.py + :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_4_peaks_gallery_thumb.png + :img-alt: Peaks Widgets + :class-card: gallery-card + :text-align: center + +Download All Examples +--------------------- + +- :download:`Download all examples in Python source code ` +- :download:`Download all examples in Jupyter notebooks `