Feat/doctests

docs/source/api_reference.rst

@@ -157,4 +157,43 @@ When rate limits are exceeded, the API returns HTTP 429 with:
        "message": "Rate limit exceeded. Please try again later.",
        "retry_after": 60
      }
-   } 
+   }
+
+
+API Python Reference
+====================
+
+.. automodule:: src.api
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. automodule:: src.cache
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. automodule:: src.main
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. automodule:: src.metadata
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. automodule:: src.prithvi
+    :members:
+    :undoc-members:
+    :show-inheritance: 
+
+.. automodule:: src.protecting_group
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. automodule:: src.variables
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/conf.py

@@ -32,6 +32,8 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.napoleon',
     'sphinx.ext.viewcode',
     'sphinx.ext.intersphinx',
     'sphinx.ext.todo',
@@ -44,6 +46,10 @@
     'myst_parser',
 ]
 
+autodoc_mock_imports = [
+    "flask", "flask_cors", "rdkit", "rootutils", "structlog", "dotenv", "aizynthfinder"
+]
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 

docs/source/index.rst

@@ -78,6 +78,8 @@ Why DeepRetro?
      - Developer setup, contribution guidelines, and code structure.
    * - :doc:`contributing`
      - How to contribute to the project.
+   * - :doc:`tutorial`
+     - Step-by-step tutorial for using the DeepRetro GUI.
 
 .. toctree::
    :maxdepth: 2
@@ -88,4 +90,5 @@ Why DeepRetro?
    user_guide
    api_reference
    development
-   contributing
+   contributing
+   tutorial