From 3f4c5b5278962aa60b9b043033bd85d7749890a5 Mon Sep 17 00:00:00 2001
From: jykr <jayoung_ryu@g.harvard.edu>
Date: Mon, 1 Apr 2024 13:22:23 -0500
Subject: [PATCH] add sheilds

---
 README.md      |  4 +++-
 docs/conf.py   |  1 -
 docs/index.rst | 42 ++++++++++++++++++++++++++++++++----------
 3 files changed, 35 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index e41abc9..e9d5665 100755
--- a/README.md
+++ b/README.md
@@ -2,7 +2,9 @@
 
 [![PyPI pyversions](https://img.shields.io/pypi/pyversions/crispr-bean)](https://pypi.org/project/crispr-bean/)
 [![PyPI version](https://img.shields.io/pypi/v/crispr-bean)](https://pypi.org/project/crispr-bean/)
-[![Code style](https://img.shields.io/badge/code%20style-black-black)](https://github.com/psf/black)
+[![Test](https://github.com/pinellolab/crispr-bean/actions/workflows/CI.yml/badge.svg)](https://github.com/pinellolab/crispr-bean/actions/workflows/CI.yml)
+[![Documentation](https://github.com/pinellolab/crispr-bean/actions/workflows/documentation.yml/badge.svg)](https://github.com/pinellolab/crispr-bean/actions/workflows/documentation.yml)
+[![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0)
 
 `bean` improves CRISPR pooled screen analysis by 1) unconfounding variable per-guide editing outcome by considering genotypic outcome from *reporter* sequence and 2) through accurate modeling of screen procedure.
 
diff --git a/docs/conf.py b/docs/conf.py
index 57b4e26..e5ba831 100755
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -35,7 +35,6 @@
 source_suffix = [".rst", ".md"]
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
-
 html_theme = "alabaster"
 html_static_path = ["_static"]
 html_logo = "assets/beans.svg"
diff --git a/docs/index.rst b/docs/index.rst
index d785cc7..7aaedda 100755
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -2,42 +2,64 @@
    sphinx-quickstart on Fri Mar 29 19:10:46 2024.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
+====================================
+Welcome to `bean` documentation!
+====================================
+
+.. image:: https://img.shields.io/pypi/pyversions/crispr-bean
+   :target: https://pypi.org/project/crispr-bean/
+   :alt: PyPI pyversions
+
+.. image:: https://img.shields.io/pypi/v/crispr-bean
+   :target: https://pypi.org/project/crispr-bean/
+   :alt: PyPI version
+
+.. image:: https://github.com/pinellolab/crispr-bean/actions/workflows/CI.yml/badge.svg
+   :target: https://github.com/pinellolab/crispr-bean/actions/workflows/CI.yml
+   :alt: Test
+
+.. image:: https://github.com/pinellolab/crispr-bean/actions/workflows/documentation.yml/badge.svg
+   :target: https://github.com/pinellolab/crispr-bean/actions/workflows/documentation.yml
+   :alt: Documentation
+
+.. image:: https://img.shields.io/badge/License-AGPL%20v3-blue.svg
+   :target: https://www.gnu.org/licenses/agpl-3.0
+   :alt: License: AGPL v3
+
 
-Welcome to `bean`'s documentation!
-================================================================
 `bean` improves CRISPR pooled screen analysis by 1) unconfounding variable per-guide editing outcome by considering genotypic outcome from *reporter* sequence and 2) through accurate modeling of screen procedure.
 
 .. image:: assets/summary.png
   :width: 700
   :alt: BEAN schematic
 
-===================
+
 Workflows
-===================
+--------------------------
 .. toctree::
     :maxdepth: 2
 
     tutorials
 
-===================
+
 API references
-===================
+--------------------------
 .. toctree::
     :maxdepth: 3
 
     input
     subcommands
 
-===========================
+
 Screen data structure
-===========================
+--------------------------
 .. toctree::
 
     reporterscreen
 
-=========================
+
 Indices and tables
-=========================
+--------------------------
 
 * :ref:`genindex`
 * :ref:`modindex`