Update Docs (#43)

* Update Docs

* Add overview

* Update Links in Readme

README.md

@@ -1,12 +1,25 @@
+# atomID
+
 [![Continuous Integration](https://github.com/Materials-Data-Science-and-Informatics/atomID/actions/workflows/ci.yml/badge.svg)](https://github.com/Materials-Data-Science-and-Informatics/atomID/actions/workflows/ci.yml)
-[![Docs](https://github.com/Materials-Data-Science-and-Informatics/atomID/actions/workflows/docs.yml/badge.svg)](https://github.com/Materials-Data-Science-and-Informatics/atomID/actions/workflows/docs.yml)
+[![Docs](https://github.com/Materials-Data-Science-and-Informatics/atomID/actions/workflows/docs.yml/badge.svg)](https://materials-data-science-and-informatics.github.io/atomID/)
 [![PyPI - Version](https://img.shields.io/pypi/v/atomid)](https://pypi.org/project/atomID/)
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/atomid)](https://img.shields.io/pypi/v/atomid)
 
-# atomID
-
 Welcome to the `atomID` package! This README will guide you through the initial steps required to start using the `AnnotateCrystal` class for annotating crystal structures and defects. Follow the steps outlined below to get started.
 
+## Overview
+
+"AtomID" is an open-source Python package designed to annotate crystal structure data, enhancing data standardisation and interoperability in the field of computational materials science.
+
+
+## Key Features
+
+- **Multi-format Data Input**: Supports data import from multiple commonly used formats, such as CIF, POSCAR, and LAMMPS, ensuring compatibility across various modelling tools and workflows.
+- **Crystal Structure Identification**: Utilises Common Neighbour Analysis to accurately identify crystal structures within different lattices.
+- **Defect Detection and Characterisation**: Applies Wigner-Seitz analysis to detect and categorise various types of lattice defects.
+- **Defect Concentration Calculation**: Computes the concentration of different point defects.
+- **Knowledge Graph Creation**: Generates a knowledge graph for crystal structures using the Computational Material Sample Ontology (CMSO), which can be exported and stored in Turtle (TTL) format, enabling sharing and complex querying on the data.
+
 ## Installation
 
 To begin, you need to install the `atomID` package. This can be done using pip:
@@ -90,14 +103,14 @@ crystal.annotate_defects("path/to/your/reference_file.poscar", "vasp")
 crystal.write_to_file("Al_inter.ttl", "ttl")
 ```
 
-# Documentation
+## Documentation
 
-Detailed documentation for the `atomID` package can be found in [docs](https://github.com/Materials-Data-Science-and-Informatics/atomID/tree/main/docs) folder.
+Detailed documentation for the `atomID` package can be found in the [docs](https://github.com/Materials-Data-Science-and-Informatics/atomID/tree/main/docs) folder.
 
-# Contributing
+## Contributing
 
-Please refer to the [CONTRIBUTING GUIDE](https://github.com/Materials-Data-Science-and-Informatics/atomID/blob/main/docs/contributing.md) on contributing to the `atomID` package.
+Please refer to the [CONTRIBUTING GUIDE](https://materials-data-science-and-informatics.github.io/atomID/contributing/) on contributing to the `atomID` package.
 
-# Contact
+## Contact
 
-For any queries or feedback, kindly create an issue on the [GitHub repository](https://github.com/Materials-Data-Science-and-Informatics/atomID)
+For any queries or feedback, kindly create an issue on the [GitHub repository](https://github.com/Materials-Data-Science-and-Informatics/atomID).

docs/quickstart.md

@@ -2,6 +2,14 @@
 
 Welcome to the atomID package quickstart guide! This guide will help you get started with using the `AnnotateCrystal` class for annotating crystal structures and defects. Follow the steps below to begin.
 
+## Key Features
+
+- **Multi-format Data Input**: Supports data import from multiple commonly used formats, such as CIF, POSCAR, and LAMMPS, ensuring compatibility across various modelling tools and workflows.
+- **Crystal Structure Identification**: Utilises Common Neighbour Analysis to accurately identify crystal structures within different lattices.
+- **Defect Detection and Characterisation**: Applies Wigner-Seitz analysis to detect and categorise various types of lattice defects.
+- **Defect Concentration Calculation**: Computes the concentration of different point defects.
+- **Knowledge Graph Creation**: Generates a knowledge graph for crystal structures using the Computational Material Sample Ontology (CMSO), which can be exported and stored in Turtle (TTL) format, enabling sharing and complex querying on the data.
+
 ## Installation
 
 First, ensure you have the `atomID` package installed. You can install it via pip:
@@ -85,4 +93,4 @@ crystal.annotate_defects("path/to/your/reference_file.poscar", "vasp")
 crystal.write_to_file("Al_inter.ttl", "ttl")
 ```
 
-With these steps, you should be able to start annotating your crystal structures and defects using the atomID package. For more detailed information and advanced usage, please refer to the official documentation.
+With these steps, you should be able to start annotating your crystal structures and defects using the atomID package. For more detailed information and advanced usage, please refer to the official documentation.