Update readme

CONTRIBUTING.md

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+# Contributing
+
+We welcome contributions to **grassp**! This guide will help you get started with contributing to the project.
+
+## Getting Started
+
+1. **Fork** the repository on GitHub.
+2. **Clone** your fork locally:
+
+   ```bash
+   git clone https://github.com/yourusername/grassp.git
+   cd grassp
+   ```
+
+3. **Create a development environment:**
+
+This installs the package with the `-e` option and development and documentation dependencies as well as pre-commit hooks.
+
+   ```bash
+   make setup-develop
+   ```
+
+## Testing
+
+1. Tests can be added to [grassp/tests](grassp/tests)
+2. Run the tests:
+
+   ```bash
+   pytest grassp/tests
+   ```
+
+## Code Style
+
+- Follow [PEP 8](https://peps.python.org/pep-0008/) style guidelines.
+- Use type hints where appropriate.
+- Add docstrings to all public functions.
+- Use [NumPy-style docstrings](https://numpydoc.readthedocs.io/en/latest/format.html).
+
+## Documentation
+
+- Update docstrings for any changed functions.
+- Update tutorials if adding new features.
+- Build docs locally to check formatting:
+
+   ```bash
+   cd docs
+   # Optional (if running into errors): make clean
+   make html
+   ```
+
+## Adding New public functions
+
+When adding support for new functionality:
+
+1. Add the code for the function in the most appropriate submodule
+   1. `preprocessing` is for data filtering, enrichment, qc
+   2. `tools` is for dimensionality reduction, classification, differential testing
+   3. `plotting` is for visualization
+   4. `io` is for reading from diffferent sources and writing outputs
+2. Make sure you follow the recommended [code style](#code-style) and describe the function and parameters accurately with a docstring
+3. Expose the function as public by importing it in the `__init__.py` file of the submodule
+4. Add the function to the documentation by adding it to the [api documentation](docs/source/api).
+5. [Build the documentation](#documentation) to check proper formatting.
+6. Add tests and [run them](#testing)
+7. Create a PR against `main`

README.md

@@ -1,8 +1,51 @@
-# grassp
-A python package for "GRaph-based Analysis of Subcellular/Spatial Proteomics"
+[![PyPI - Version](https://img.shields.io/pypi/v/grassp)](https://img.shields.io/pypi/v/grassp)
+[![CI](https://github.com/czbiohub-sf/grassp/actions/workflows/test.yml/badge.svg)](https://github.com/czbiohub-sf/grassp/actions/workflows/test.yml)
+[![docs online](https://img.shields.io/badge/docs-online-blue)](https://onsite.czbiohub.org/compbio/grassp/)
 
-## Installation 
+
+[anndata]: https://anndata.readthedocs.io
+[scanpy]: https://scanpy.readthedocs.io
+[protdata]: https://protdata.sf.czbiohub.org
+[documentation]: https://onsite.czbiohub.org/compbio/grassp/
+
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/czbiohub-sf/grassp/refs/heads/main/docs/source/_static/img/logo.svg" alt="grassp logo" width="300"/>
+</p>
+
+The **grassp** (**GR**aph-based **A**nalysis of **S**ubcellular/**S**patial **P**roteomics) python module enables fast, flexible and scalable analysis of subcellular proteomics datasets.
+
+It uses the [anndata][] format to store mass-spec data and analysis results and [scanpy][] for many of the dimensionality reduction and visualization functions.
+
+**grassp** enables
+
+- Reading the ouput format of most mass-spectrometry search engines (using [protdata][])
+- Calculating subcellular enrichment profiles of proteins for different experimental protocols
+- Annotating the subcellular location of proteins in an unsupervised and semi-supervised manner
+- Detecting proteins at the interface of organelles
+- Detecting multi-localizing proteins (work in progress)
+- Detecting re-localizing proteins between conditions (work in progress)
+- Combining multiple subcellular proteomics datasets
+- Assessing subcellular resolution
+- Finding the optimal experimental design for future experiments based on simulations
+- Integration of multiple modalities (e.g. Lipidomics) (work in progress)
+
+Please refer to the [documentation] for reference to individual functions and [tutorials](https://onsite.czbiohub.org/compbio/grassp/tutorials/index.html).
+
+## Installation
+
+grassp can be installed via [pip](https://pypi.org/project/pip/) from [PyPI](https://pypi.org/project/grassp/) with:
 ```
 pip install grassp
 ```
-## [Documentation](https://public.czbiohub.org/comp.bio/grassp/)
+For details on installation, please see the [install section of the documentation](https://onsite.czbiohub.org/compbio/grassp/installation.html)
+
+## Contributing
+
+If you'd like to contribute to **grassp** please feel free to look at our [contribution guide](https://onsite.czbiohub.org/compbio/grassp/contributing.html) and open a [Pull request](https://github.com/czbiohub-sf/grassp/pulls).
+
+## Authors
+
+**grassp** is created and maintained by the [Computational Biology Platform](https://www.czbiohub.org/comp-biology/) at the [Chan Zuckerberg Biohub San Francisco](https://www.czbiohub.org/sf/). For details, see the [Contributors page](https://onsite.czbiohub.org/compbio/grassp/contributors.html).
+
+To get in touch please use the [GihHub issues](https://github.com/czbiohub-sf/grassp/issues) page.