From b975d4a7388d6781d5265e93314447f190e7eec1 Mon Sep 17 00:00:00 2001
From: jules-samaran <samaran.jules@gmail.com>
Date: Thu, 29 Feb 2024 18:18:06 +0100
Subject: [PATCH] Fix codeblocks in docs

---
 docs/source/index.rst | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/docs/source/index.rst b/docs/source/index.rst
index 5cd08cc..82b4790 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -7,15 +7,25 @@ Welcome to scConfluence's documentation!
 ========================================
 
 .. toctree::
+   :hidden:
    :maxdepth: 1
+   :glob:
    :caption: Tutorials
 
    tutorials/*.ipynb
+
 .. toctree::
    :hidden:
    :maxdepth: 3
    :caption: API
 
+   model
+   unimodal
+   base_module
+   nn
+   distributions
+   dataset_utils
+
 scConfluence is a novel method for the integration of unpaired multiomics data combining
 uncoupled autoencoders and Inverse Optimal Transport to learn low-dimensional cell
 embeddings. These embeddings can then be used for visualization and clustering, useful
@@ -41,6 +51,7 @@ Installation should typically take a minute and is continuously tested with Pyth
 on an Ubuntu virtual machine.
 
 .. code-block:: bash
+
    pip install scconfluence
 
 
@@ -48,6 +59,7 @@ via GitHub (development version)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. code-block:: bash
+
    git clone git@github.com:cantinilab/scconfluence.git
    cd scconfluence
    pip install .
@@ -57,6 +69,7 @@ Test your development installation (optional)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. code-block:: bash
+
    pip install pytest
    pytest .
 
@@ -71,6 +84,7 @@ You may download a preprocessed 10X Multiome demo dataset `here <https://figshar
 A GPU is not required for the method to run, but is strongly recommended.
 
 .. code-block:: python
+
    import scconfluence
    import mudata as md
    import scanpy as sc