From ccfe60b1a909251ff842b829675059dafe175f8a Mon Sep 17 00:00:00 2001
From: Sricharan Reddy Varra <sricharanvarra@gmail.com>
Date: Fri, 19 Jul 2024 14:31:09 -0700
Subject: [PATCH] =?UTF-8?q?=F0=9F=93=9D=20Updated=20README?=
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updated README
---
 README.md | 47 +++++++++++++++++++++++++----------------------
 1 file changed, 25 insertions(+), 22 deletions(-)

diff --git a/README.md b/README.md
index 3532711..60f4adf 100644
--- a/README.md
+++ b/README.md
@@ -1,39 +1,40 @@
 # tonic-vitessce
 
-[![Tests][badge-tests]][link-tests]
-[![Documentation][badge-docs]][link-docs]
+[![Website][badge-ghpages]][link-ghpages]
+
+<!-- [![Tests][badge-tests]][link-tests]
+[![Documentation][badge-docs]][link-docs] -->
 
 [badge-tests]: https://img.shields.io/github/actions/workflow/status/srivarra/tonic-vitessce/test.yaml?branch=main
 [link-tests]: https://github.com/angelolab/tonic-vitessce/actions/workflows/test.yml
 [badge-docs]: https://img.shields.io/readthedocs/tonic-vitessce
+[badge-ghpages]: https://img.shields.io/website?url=https%3A%2F%2Fangelolab.github.io%2Ftonic-vitessce%2F&up_message=GitHub%20Pages
 
 Vitessce Configs and Data Conversion for the TONIC Publication.
 
-## Getting started
-
-Please refer to the [documentation][link-docs]. In particular, the
+## Development
 
--   [API documentation][link-api].
+### Getting started
 
-## Installation
+<!-- Please refer to the [documentation][link-docs]. In particular, the
 
-You need to have Python 3.10 or newer installed on your system. If you don't have
-Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge) or [Rye](https://github.com/astral-sh/rye) if you prefer `.venvs`.
+-   [API documentation][link-api]. -->
 
-There are several alternative options to install tonic-vitessce:
+-   `src/` contains the package which to convert the data from `.csv`, and `.tiff` into `AnnData` `.zarr` and `OME-ZARR` `ome.zarr` files
+-   `ghpages-site` contains the source for the GitHub Pages website.
+    -   The site uses Astro JS for the build system, and TypeScript + React for the functionality.
+    -   You can find the Vitessce Config for the TONIC data [here](ghpages-site/src/components/vitessce/configs/tonic.ts)
 
-<!--
-1) Install the latest release of `tonic-vitessce` from [PyPI][link-pypi]:
+### Installation
 
-```bash
-pip install tonic-vitessce
-```
--->
+You need to have Python 3.10 or newer installed on your system. If you don't have
+Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge) or [Rye](https://github.com/astral-sh/rye) if you prefer to use a `.venv`.
 
-1. Install the latest development version:
+1. Install the latest development version by cloning the repo
 
-```bash
-pip install git+https://github.com/angelolab/tonic-vitessce.git@main
+```zsh
+git clone https://github.com/angelolab/tonic-vitessce.git
+pip install tonic-vitessce/tonic-vitessce
 ```
 
 ## Release notes
@@ -42,16 +43,18 @@ See the [changelog][changelog].
 
 ## Contact
 
-For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
 If you found a bug, please use the [issue tracker][issue-tracker].
 
 ## Citation
 
 > t.b.a
 
-[scverse-discourse]: https://discourse.scverse.org/
+<!-- [scverse-discourse]: https://discourse.scverse.org/ -->
+
 [issue-tracker]: https://github.com/srivarra/tonic-vitessce/issues
 [changelog]: https://tonic-vitessce.readthedocs.io/latest/changelog.html
 [link-docs]: https://tonic-vitessce.readthedocs.io
 [link-api]: https://tonic-vitessce.readthedocs.io/latest/api.html
-[link-pypi]: https://pypi.org/project/tonic-vitessce
+[link-ghpages]: https://angelolab.github.io/tonic-vitessce
+
+<!-- [link-pypi]: https://pypi.org/project/tonic-vitessce -->