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📝 Updated README
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srivarra committed Jul 19, 2024
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# 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
Expand All @@ -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 -->

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