From 29d0dc43a975048ed2d4758fd1da18f6148cb9e8 Mon Sep 17 00:00:00 2001
From: Roberto Rossini <71787608+robomics@users.noreply.github.com>
Date: Fri, 20 Dec 2024 14:16:26 +0100
Subject: [PATCH 1/3] Update installation instructions

---
 README.md | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/README.md b/README.md
index 581edf81..2df70dbf 100644
--- a/README.md
+++ b/README.md
@@ -25,6 +25,24 @@ StripePy is developed on Linux and macOS and is also tested on Windows.
 
 ## Installing StripePy
 
+### Installing with pip
+
+```bash
+pip install stripepy-hic
+```
+
+<!--
+
+### Installing with conda
+
+```bash
+conda create -n stripepy -c conda-forge -c bioconda stripepy-hic
+```
+
+-->
+
+### Installing from source
+
 Instructions for Linux and macOS:
 
 ```bash
@@ -35,6 +53,9 @@ python3 -m venv venv
 # get StripePy source code
 git clone https://github.com/paulsengroup/StripePy.git
 
+# optional, checkout a specific version
+# git checkout v0.0.2
+
 # install StripePy
 cd StripePy
 pip install .
@@ -54,6 +75,9 @@ venv\Scripts\activate
 # get StripePy source code
 git clone https://github.com/paulsengroup/StripePy.git
 
+# optional, checkout a specific version
+# git checkout v0.0.2
+
 # install StripePy
 cd StripePy
 pip install .

From a6014d5f220fd3cce07bd0a03abfd7d557898de0 Mon Sep 17 00:00:00 2001
From: Roberto Rossini <71787608+robomics@users.noreply.github.com>
Date: Fri, 20 Dec 2024 14:16:35 +0100
Subject: [PATCH 2/3] Update badges

---
 README.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 2df70dbf..525fcdf5 100644
--- a/README.md
+++ b/README.md
@@ -6,14 +6,15 @@ SPDX-License-Identifier: MIT
 
 # StripePy
 
-[![License](https://img.shields.io/badge/license-MIT-green)](./LICENSE)
+[![License](https://img.shields.io/badge/license-MIT-green)](https://github.com/paulsengroup/StripePy/blob/main/LICENCE)
 [![CI](https://github.com/paulsengroup/StripePy/actions/workflows/ci.yml/badge.svg)](https://github.com/paulsengroup/StripePy/actions/workflows/ci.yml)
 [![Build Dockerfile](https://github.com/paulsengroup/StripePy/actions/workflows/build-dockerfile.yml/badge.svg)](https://github.com/paulsengroup/StripePy/actions/workflows/build-dockerfile.yml)
+[![Zenodo DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14394042.svg)](https://doi.org/10.5281/zenodo.14394041)
 
 <!--
 [![Download from Bioconda](https://img.shields.io/conda/vn/bioconda/StripePy?label=bioconda&logo=Anaconda)](https://anaconda.org/bioconda/StripePy)
 [![docs](https://readthedocs.org/projects/stripepy/badge/?version=stable)](https://stripepy.readthedocs.io/en/latest/?badge=stable)
-[![Zenodo DOI](https://zenodo.org/badge/DOI/TODO/zenodo.TODO.svg)](https://doi.org/TODO/zenodo.TODO)
+
 -->
 
 ---

From f6a807154cc132ad219bcf61303bb8e4dfe5687c Mon Sep 17 00:00:00 2001
From: Roberto Rossini <71787608+robomics@users.noreply.github.com>
Date: Fri, 20 Dec 2024 14:20:20 +0100
Subject: [PATCH 3/3] Update image in the README such that it is correctly
 rendered on PyPI

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 525fcdf5..9f43771b 100644
--- a/README.md
+++ b/README.md
@@ -1132,7 +1132,7 @@ Now you are ready to run all cells.
 
 Running the last cell will display a HiGlass window embedded in the Jupyter notebook (note that the interface may take a while to load).
 
-![HiGlass window](docs/assets/4DNFI9GMP2J8_chr2_156mbp_higlass_view.png)
+![HiGlass window](https://github.com/paulsengroup/StripePy/blob/main/docs/assets/4DNFI9GMP2J8_chr2_156mbp_higlass_view.png?raw=true)
 
 ## Generating plots