add initial changelog.md and contributing.md

CHANGELOG.md

@@ -0,0 +1,37 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [1.0.1] - 2026
+### Added
+- Fixed atoms functionality
+- Ability to directly input stepsize
+### Changed
+- Moved ML-FSM repo from @jonmarks12 to @thegomeslab
+- Large documentation update, changed theme to furo, updated docstrings, added examples, various other improvements
+### Fixed
+- Minor bug fixes and stability improvements
+
+## [1.0.0] - 2025
+
+### Added
+- Initial public release of ML-FSM
+- Internal coordinates interpolation for the Freezing String Method
+- Support for ML-based potentials via ASE calculator interface
+- Support for AIMNet2, MACEOFF23, FAIR UMA, TensorNet, xTB, and QChem backends
+- Google Colab example notebook for Diels-Alder reaction with AIMNet2
+- Comprehensive example script (`examples/fsm_example.py`) covering most FSM functionality
+- Custom ASE calculator wrapper templates for NNPs without native ASE interfaces
+- Full test suite with pytest
+- Type annotations and mypy support
+- Sphinx documentation hosted on Read the Docs
+- Pixi-based development environment
+
+[Unreleased]: https://github.com/thegomeslab/ML-FSM/compare/v1.0.1...HEAD
+[1.0.1]: https://github.com/thegomeslab/ML-FSM/compare/v1.0.0...v1.0.1
+[1.0.0]: https://github.com/thegomeslab/ML-FSM/releases/tag/v1.0.0

CONTRIBUTING.md

@@ -0,0 +1,99 @@
+# Contributing to ML-FSM
+
+Thank you for your interest in contributing to ML-FSM! This document outlines the process for contributing and how to set up your development environment.
+
+## Project Maintainers
+
+ML-FSM is primarily developed and maintained at the [Gomes Lab](https://github.com/thegomeslab) at the University of Iowa. The package was co-created by Jonah Marks (now at AstraZeneca), who remains a maintainer, with additional contributions from Jonathon Vandezande.
+
+For questions, bug reports, or to discuss potential contributions, please contact:
+
+**Joe Gomes** — joe-gomes@uiowa.edu
+
+## Before You Open a Pull Request
+
+**Please open an issue or reach out before starting significant work.**
+
+If you have a bug report, feature request, or want to propose a change, start by [opening an issue](https://github.com/thegomeslab/ML-FSM/issues) on GitHub. For questions or to discuss a contribution before diving in, you can also contact Joe directly at the address above.
+
+This helps avoid duplicated effort and ensures your contribution aligns with the project's direction before you invest time in it.
+
+## Development Setup
+
+ML-FSM uses [Pixi](https://pixi.sh) to manage the development environment. Pixi handles dependencies, virtual environments, and task running — no manual conda/pip setup needed.
+
+### 1. Install Pixi
+
+```bash
+curl -fsSL https://pixi.sh/install.sh | bash
+```
+
+Or see the [Pixi installation docs](https://pixi.sh/latest/#installation) for other options.
+
+### 2. Clone the repository
+
+```bash
+git clone https://github.com/thegomeslab/ML-FSM.git
+cd ML-FSM
+```
+
+### 3. Set up the dev environment
+
+```bash
+pixi install -e dev
+```
+
+This creates an isolated environment with all development dependencies (pytest, ruff, mypy, sphinx, pre-commit, etc.) — no additional steps required.
+
+### 4. Install pre-commit hooks
+
+```bash
+pixi run -e dev pre-commit install
+```
+
+This registers the hooks so they run automatically on every commit.
+
+## Available Commands
+
+All development tasks are run via `pixi run` from the repository root. Make sure to use the `dev` environment (`-e dev`) or set it as your active environment.
+
+| Command | Description |
+|---|---|
+| `pixi run fmt` | Format code with ruff |
+| `pixi run lint` | Lint and auto-fix code with ruff |
+| `pixi run types` | Run static type checking with mypy |
+| `pixi run test` | Run the test suite with pytest |
+| `pixi run coverage` | Run tests with coverage report (generates `coverage.xml`) |
+| `pixi run docs` | Build the Sphinx documentation locally |
+| `pixi run all` | Run fmt, lint, types, test, and docs in sequence |
+
+For example:
+
+```bash
+pixi run test          # run tests
+pixi run fmt && pixi run lint  # format then lint
+pixi run all           # run everything
+```
+
+## Pre-commit Checks
+
+The pre-commit hooks run ruff format, ruff check, mypy, and pytest on every commit and push. Before opening a pull request, run the full pre-commit suite manually to make sure everything passes:
+
+```bash
+pixi run -e dev pre-commit run --all-files
+```
+
+Pull requests that fail any of these checks will not be merged.
+
+## Contribution Workflow
+
+1. [Open an issue](https://github.com/thegomeslab/ML-FSM/issues) or contact Joe to discuss your proposed change.
+2. Fork the repository and create a feature branch from `main`.
+3. Make your changes, adding tests for any new behavior.
+4. Run `pixi run all` to confirm everything passes.
+5. Run `pre-commit run --all-files` as a final check.
+6. Open a pull request against `main`, referencing the relevant issue.
+
+## Code Style
+
+This project uses [ruff](https://github.com/astral-sh/ruff) for formatting and linting, and [mypy](https://mypy-lang.org/) for static type checking. Docstrings follow the NumPy convention. The pre-commit hooks enforce these automatically — just run `pixi run fmt` and `pixi run lint` before committing.

README.md

@@ -7,8 +7,8 @@
 [![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/thegomeslab/ML-FSM/test.yml?branch=main&logo=github-actions)](https://github.com/jonmarks12/ML-FSM/actions/)
 [![Documentation Status](https://readthedocs.org/projects/ml-fsm/badge/?version=latest)](https://ml-fsm.readthedocs.io/en/latest/?badge=latest)
 [![codecov](https://codecov.io/gh/thegomeslab/ML-FSM/branch/main/graph/badge.svg)](https://codecov.io/gh/thegomeslab/ML-FSM)
-
-
+[![Contributing](https://img.shields.io/badge/contributions-welcome-brightgreen)](./CONTRIBUTING.md)
+[![Changelog](https://img.shields.io/badge/changelog-available-blue)](./CHANGELOG.md)
 
 
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/thegomeslab/ML-FSM/blob/dev/examples/FSM_Colab_AIMNet2.ipynb)
@@ -66,6 +66,12 @@ For projects using the FSM with ML-based potentials please cite:
 
 >Marks, J., & Gomes, J. (2025). Efficient Transition State Searches by Freezing String Method with Graph Neural Network Potentials. http://arxiv.org/abs/2501.06159
 
+## Contributing
+
+Contributions are welcome! Please read the [Contributing Guide](./CONTRIBUTING.md) before opening a pull request. We ask that you open an issue or reach out to the maintainer first to discuss proposed changes.
+
+See the [Changelog](./CHANGELOG.md) for a history of notable changes.
+
 ## License
 
 This project is licensed under the MIT License. See the [LICENSE](./LICENSE) file for details.