From 576c0227f5b4d0a496e00675b1c3f098f1b2b328 Mon Sep 17 00:00:00 2001
From: CodyCBakerPhD <codycbakerphd@gmail.com>
Date: Tue, 13 Aug 2024 12:30:20 -0400
Subject: [PATCH] mirror API docs

---
 docs/api/nwbinspector.rst        |  2 +-
 docs/api/register_check.rst      |  4 +++-
 docs/api/tools.rst               |  9 +++++---
 docs/conf.py                     | 38 ++++++++++++++++++++++++++++++--
 docs/gen_checks_by_importance.py | 35 -----------------------------
 5 files changed, 46 insertions(+), 42 deletions(-)
 delete mode 100644 docs/gen_checks_by_importance.py

diff --git a/docs/api/nwbinspector.rst b/docs/api/nwbinspector.rst
index 1fb49417c..d1d5bfad8 100644
--- a/docs/api/nwbinspector.rst
+++ b/docs/api/nwbinspector.rst
@@ -1,4 +1,4 @@
 Core Library
 ============
 
-.. automodule:: nwbinspector.nwbinspector
+.. automodule:: nwbinspector._nwbinspector
diff --git a/docs/api/register_check.rst b/docs/api/register_check.rst
index ca3fa6271..213f503fa 100644
--- a/docs/api/register_check.rst
+++ b/docs/api/register_check.rst
@@ -3,4 +3,6 @@ Data Classes and Check Registration
 
 All common data class used across the package, as well as the decorator for adding a check function to the registry.
 
-.. automodule:: nwbinspector.register_checks
+.. automodule:: nwbinspector._types
+
+.. automodule:: nwbinspector._registration
diff --git a/docs/api/tools.rst b/docs/api/tools.rst
index 48028764e..60384deb3 100644
--- a/docs/api/tools.rst
+++ b/docs/api/tools.rst
@@ -1,5 +1,5 @@
-Tools for Organizating and Displaying Reports
-=============================================
+Tools for Organizing and Displaying Reports
+===========================================
 
 .. automodule:: nwbinspector
     :members:
@@ -9,5 +9,8 @@ Tools for Organizating and Displaying Reports
 .. toctree::
     :maxdepth: 4
 
-.. automodule:: nwbinspector.inspector_tools
+.. automodule:: nwbinspector._organization
+    :noindex:
+
+.. automodule:: nwbinspector._formatting
     :noindex:
diff --git a/docs/conf.py b/docs/conf.py
index f1605ca2d..998c66e8d 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,9 +1,12 @@
+import os
 import sys
 from pathlib import Path
 
+from nwbinspector import available_checks
+from collections import defaultdict
+
 sys.path.append(str(Path(__file__).parent))
 from conf_extlinks import extlinks, intersphinx_mapping
-from gen_checks_by_importance import gen_checks_by_importance
 
 sys.path.insert(0, Path(__file__).resolve().parents[1])
 
@@ -73,4 +76,35 @@ def setup(app):
     app.connect("autodoc-process-docstring", add_refs_to_docstrings)
 
 
-gen_checks_by_importance()
+def _gen_checks_by_importance():
+    dd = defaultdict(list)
+
+    for x in available_checks:
+        dd[x.importance.name.replace("_", " ")].append(x)
+
+    generate_checks_rst_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), "checks_by_importance.rst")
+    with open(generate_checks_rst_file, "w") as f:
+        f.write(
+            """Checks by Importance
+======================
+
+This section lists the available checks organized by their importance level.
+
+"""
+        )
+
+        for importance_level, checks in dd.items():
+            f.write(
+                f"""{importance_level}
+{'-' * (len(f'{importance_level}') + 1)}
+
+"""
+            )
+
+            for check in checks:
+                f.write(f"*  :py:func:`~{check.__module__}.{check.__name__}`\n")
+
+            f.write("\n")
+
+
+_gen_checks_by_importance()
diff --git a/docs/gen_checks_by_importance.py b/docs/gen_checks_by_importance.py
deleted file mode 100644
index d65614999..000000000
--- a/docs/gen_checks_by_importance.py
+++ /dev/null
@@ -1,35 +0,0 @@
-import os
-from nwbinspector import available_checks
-
-from collections import defaultdict
-
-
-def gen_checks_by_importance():
-    dd = defaultdict(list)
-
-    for x in available_checks:
-        dd[x.importance.name.replace("_", " ")].append(x)
-
-    generate_checks_rst_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), "checks_by_importance.rst")
-    with open(generate_checks_rst_file, "w") as f:
-        f.write(
-            """Checks by Importance
-======================
-
-This section lists the available checks organized by their importance level.
-
-"""
-        )
-
-        for importance_level, checks in dd.items():
-            f.write(
-                f"""{importance_level}
-{'-' * (len(f'{importance_level}') + 1)}
-
-"""
-            )
-
-            for check in checks:
-                f.write(f"*  :py:func:`~{check.__module__}.{check.__name__}`\n")
-
-            f.write("\n")