Merge pull request #149 from catalystneuro/restore_tools_on_documenta…

…tion_api

Re enable tools on the API documentation

.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:

docs/api/interfaces.icephys.rst

@@ -7,5 +7,5 @@ Base Interface
 
 
 Abf Interface
--------------------
+-------------
 .. automodule:: neuroconv.datainterfaces.icephys.abf.abfdatainterface

docs/api/interfaces.rst

@@ -1,10 +1,6 @@
 Interfaces
 ============
 
-.. automodule:: neuroconv
-    :members:
-    :no-undoc-members:
-
 .. toctree::
     :maxdepth: 4
 

docs/api/tools.neo.rst

@@ -0,0 +1,4 @@
+NEO
+---
+
+.. automodule:: neuroconv.tools.neo.neo

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

docs/api/tools.rst

@@ -7,3 +7,4 @@ Tools
     tools.spikeinterface
     tools.roiextractors
     tools.yaml_to_nwb_conversion
+    tools.neo

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)
 
 

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