Update conf.py

Author: ainaadekunle

docs/source/conf.py

@@ -9,6 +9,11 @@
 if PROJECT_ROOT not in sys.path:
     sys.path.insert(0, PROJECT_ROOT)
 
+# Add src to path for autodoc
+SRC_DIR = os.path.join(PROJECT_ROOT, "src")
+if SRC_DIR not in sys.path:
+    sys.path.insert(0, SRC_DIR)
+
 project = "FastMDAnalysis"
 copyright = f"{datetime.now():%Y}, Adekunle Aina"
 author = "Adekunle Aina"
@@ -18,7 +23,7 @@
 
 extensions = [
     "sphinx.ext.autodoc",
-    "sphinx.ext.autosummary",
+    "sphinx.ext.autosummary", 
     "sphinx.ext.napoleon",
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
@@ -29,11 +34,12 @@
     "members": True,
     "undoc-members": False,
     "show-inheritance": True,
+    "special-members": "__init__",
 }
 
 autodoc_mock_imports = [
     "mdtraj",
-    "numpy",
+    "numpy", 
     "matplotlib",
     "matplotlib.pyplot",
     "sklearn",
@@ -42,6 +48,8 @@
 
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", {}),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None),
 }
 
 templates_path = ["_templates"]
@@ -54,3 +62,24 @@
     "navigation_depth": 4,
 }
 primary_domain = "py"
+
+# Auto-generate API documentation on build
+def setup(app):
+    from sphinx.ext import apidoc
+    
+    def run_apidoc(_):
+        apidoc_main = getattr(apidoc, 'main', None)
+        if apidoc_main is None:
+            # Fallback for older Sphinx versions
+            from sphinx.ext.apidoc import main as apidoc_main
+        
+        apidoc_main([
+            '-f',  # Force overwrite
+            '-e',  # Put each module/class on its own page
+            '-M',  # Put module documentation before submodule
+            '-o', 
+            os.path.join(os.path.dirname(__file__)),  # Output to source/
+            os.path.join(PROJECT_ROOT, 'src', 'fastmdanalysis')  # Package path
+        ])
+    
+    app.connect('builder-inited', run_apidoc)