diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 11662e251..60ea831e7 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,9 +6,9 @@ version: 2 # Set the version of Python and other tools you might need build: - os: ubuntu-20.04 + os: ubuntu-22.04 tools: - python: "3.8" + python: "3.9" # Build documentation in the docs/ directory with Sphinx sphinx: diff --git a/docs/api/interfaces.icephys.rst b/docs/api/interfaces.icephys.rst index 57386ccdb..7ca3e6aa7 100644 --- a/docs/api/interfaces.icephys.rst +++ b/docs/api/interfaces.icephys.rst @@ -7,5 +7,5 @@ Base Interface Abf Interface -------------------- +------------- .. automodule:: neuroconv.datainterfaces.icephys.abf.abfdatainterface diff --git a/docs/api/interfaces.rst b/docs/api/interfaces.rst index 809a2c7d4..c46a25588 100644 --- a/docs/api/interfaces.rst +++ b/docs/api/interfaces.rst @@ -1,10 +1,6 @@ Interfaces ============ -.. automodule:: neuroconv - :members: - :no-undoc-members: - .. toctree:: :maxdepth: 4 diff --git a/docs/api/tools.neo.rst b/docs/api/tools.neo.rst new file mode 100644 index 000000000..3c482467a --- /dev/null +++ b/docs/api/tools.neo.rst @@ -0,0 +1,4 @@ +NEO +--- + +.. automodule:: neuroconv.tools.neo.neo diff --git a/docs/api/tools.roiextractors.rst b/docs/api/tools.roiextractors.rst index c585eab72..02f3a0a83 100644 --- a/docs/api/tools.roiextractors.rst +++ b/docs/api/tools.roiextractors.rst @@ -1,3 +1,11 @@ ROI extractors ============== + +Interface with roiextractors +---------------------------- .. automodule:: neuroconv.tools.roiextractors.roiextractors + + +Imaging extractor iterator +-------------------------- +.. automodule:: neuroconv.tools.roiextractors.imagingextractordatachunkiterator diff --git a/docs/api/tools.rst b/docs/api/tools.rst index d5caa212a..5b261df1f 100644 --- a/docs/api/tools.rst +++ b/docs/api/tools.rst @@ -7,3 +7,4 @@ Tools tools.spikeinterface tools.roiextractors tools.yaml_to_nwb_conversion + tools.neo diff --git a/docs/conf.py b/docs/conf.py index 20ea8e5a6..dd434495d 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -11,9 +11,9 @@ extensions = [ "sphinx.ext.napoleon", # Support for NumPy and Google style docstrings "sphinx.ext.autodoc", # Includes documentation from docstrings in docs/api - "sphinx.ext.autosummary", # To-add + "sphinx.ext.autosummary", # Not clear. Please add if you know "sphinx_toggleprompt", # Used to control >>> behavior in the conversion gallery example doctests - "sphinx_copybutton", # Used to control the copy button behavior in the conversion gallery doctsts + "sphinx_copybutton", # Used to control the copy button behavior in the conversion gallery doctests "sphinx.ext.intersphinx", # Allows links to other sphinx project documentation sites "sphinx_search.extension", # Allows for auto search function the documentation "sphinx.ext.viewcode", # Shows source code in the documentation @@ -26,13 +26,11 @@ html_theme = "sphinx_rtd_theme" html_static_path = ["_static"] -# These paths are either relative to html_static_path -# or fully qualified paths (eg. https://...) +# These paths are either relative to html_static_path or fully qualified paths (eg. https://...) html_css_files = [ "css/custom.css", ] - html_theme_options = { "collapse_navigation": False, } @@ -51,8 +49,8 @@ napoleon_include_special_with_doc = True # Autodoc -autoclass_content = "both" -autodoc_member_order = "bysource" +autoclass_content = "both" # Concatenates docstring of the class with that of its __init__ +autodoc_member_order = "bysource" # Displays classes and methods by their order in source code autodata_content = "both" autodoc_default_options = { "members": True, @@ -70,7 +68,7 @@ def _correct_signatures(app, what, name, obj, options, signature, return_annotat return (signature, return_annotation) -def setup(app): +def setup(app): # This makes the data-interfaces signatures display on the docs/api, they don't otherwise app.connect("autodoc-process-signature", _correct_signatures) diff --git a/requirements-rtd.txt b/requirements-rtd.txt index 81e08ed2e..9d9dcc9e0 100644 --- a/requirements-rtd.txt +++ b/requirements-rtd.txt @@ -1,7 +1,9 @@ -myst_parser==0.18.0 Jinja2<3.1 Sphinx==5.1.1 sphinx_rtd_theme==1.0.0 readthedocs-sphinx-search==0.1.2 sphinx-toggleprompt==0.2.0 sphinx-copybutton==0.5.0 +spikeinterface>=0.95.1 # Necessary to display tools.spikeinterface +spikeextractors>=0.9.10 # Necessary to display tools.spikeinterface +roiextractors>=0.5.0 # Necessary to displays tools.roiextractors