From 9853a2c96e00efb7423577df5c62dd529f64f4ee Mon Sep 17 00:00:00 2001
From: Mihaela Duta <mihaela.duta@dtc.ox.ac.uk>
Date: Wed, 13 Nov 2024 16:15:01 +0000
Subject: [PATCH] Simplified sphinx source code.

---
 .gitignore            |  1 +
 docs/source/code.rst  | 68 ++++---------------------------------------
 docs/source/conf.py   | 23 ++++++++++++++-
 docs/source/index.rst |  2 +-
 4 files changed, 30 insertions(+), 64 deletions(-)

diff --git a/.gitignore b/.gitignore
index edb2d91..99717a5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
 .DS_Store
 __pycache__/
 .venv/
+docs/source/_autosummary/
 docs/build/
\ No newline at end of file
diff --git a/docs/source/code.rst b/docs/source/code.rst
index c72f2b1..a4b517d 100644
--- a/docs/source/code.rst
+++ b/docs/source/code.rst
@@ -1,65 +1,9 @@
-Code documentation
-==================
 
-Anomaly detection
------------------
+Code Reference
+==============
 
-.. automodule:: l2gv2.anomaly_detection
-   :members:
-   :undoc-members:
-   :show-inheritance:
+.. autosummary::
+   :toctree: _autosummary
+   :recursive:
 
-Induced subgraph
-----------------
-
-.. automodule:: l2gv2.induced_subgraph
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Manopt optimization
--------------------
-
-.. automodule:: l2gv2.manopt_optimization
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Models
-------
-
-.. automodule:: l2gv2.models
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Embeddings
-----------
-
-.. automodule:: l2gv2.embedding.embeddings
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Patch
------
-
-.. automodule:: l2gv2.patch.lazy
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-.. automodule:: l2gv2.patch.patch
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-.. automodule:: l2gv2.patch.patches
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-.. automodule:: l2gv2.patch.utils
-    :members:
-    :undoc-members:
-    :show-inheritance:
\ No newline at end of file
+   l2gv2
\ No newline at end of file
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 39a8032..656875a 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -18,7 +18,28 @@
 templates_path = ["_templates"]
 exclude_patterns = []
 
-autodoc_mock_imports = ["optuna", "autograd", "pymanopt", "tqdm", "torch", "numba", "numpy", "pandas", "sklearn", "scipy", "community", "torch_geometric", "torch_scatter", "local2global", "raphtory", "local2global_embedding", "networkx", "matplotlib", "nfts", "polars"]
+autodoc_mock_imports = [
+    "optuna",
+    "autograd",
+    "pymanopt",
+    "tqdm",
+    "torch",
+    "numba",
+    "numpy",
+    "pandas",
+    "sklearn",
+    "scipy",
+    "community",
+    "torch_geometric",
+    "torch_scatter",
+    "local2global",
+    "raphtory",
+    "local2global_embedding",
+    "networkx",
+    "matplotlib",
+    "nfts",
+    "polars",
+]
 
 
 # -- Options for HTML output -------------------------------------------------
diff --git a/docs/source/index.rst b/docs/source/index.rst
index ff3dd9f..5c6decd 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -7,7 +7,7 @@ l2gv2 documentation
 ====================
 
 .. toctree::
-   :maxdepth: 4
+   :maxdepth: 5
 
    intro
    code