From 4f04fa3bd6464384e95ef5829e494d080a5fc321 Mon Sep 17 00:00:00 2001
From: "William F. Broderick" <billbrod@gmail.com>
Date: Mon, 2 Jun 2025 11:53:34 -0400
Subject: [PATCH 1/2] fix API doc

---
 docs/conf.py   | 2 +-
 docs/index.rst | 6 +++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index eb082db..f079465 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -37,7 +37,7 @@
     'numpydoc',
     'nbsphinx',
     'nbsphinx_link',
-    'sphinxcontrib.apidoc',
+    "sphinx.ext.autodoc",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
diff --git a/docs/index.rst b/docs/index.rst
index 7246c3e..84d5871 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -80,7 +80,6 @@ for image processing, here are some resources to get you started:
 
    installation
    developerguide
-   api/modules
 
 .. toctree::
    :maxdepth: 2
@@ -89,3 +88,8 @@ for image processing, here are some resources to get you started:
    :numbered:
 
    tutorials/*
+
+.. toctree::
+   :caption: API Documentation
+
+   api/modules

From 84ad4522c0dbab10f6941c6589cbabd95270659f Mon Sep 17 00:00:00 2001
From: "William F. Broderick" <billbrod@gmail.com>
Date: Mon, 2 Jun 2025 12:16:42 -0400
Subject: [PATCH 2/2] actually correct apidoc

---
 docs/conf.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index f079465..ebac45b 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -37,7 +37,7 @@
     'numpydoc',
     'nbsphinx',
     'nbsphinx_link',
-    "sphinx.ext.autodoc",
+    'sphinxcontrib.apidoc',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -205,4 +205,4 @@
 
 
 # -- Extension configuration -------------------------------------------------
-apidoc_module_dir = "../pyrtools"
+apidoc_module_dir = "../src/pyrtools"