Metadata-Version: 2.1
Name: kimmdy
Version: 5.1.11
Summary: Kinetic Monte Carlo Molecular Dynamics
Author: hits-mbm
Author-email: mbm@h-its.org
License: MIT
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Operating System :: OS Independent
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: dill
Requires-Dist: pyyaml
Requires-Dist: numpy
Requires-Dist: importlib-metadata
Requires-Dist: MDAnalysis
Provides-Extra: analysis
Requires-Dist: pandas ; extra == 'analysis'
Requires-Dist: matplotlib ; extra == 'analysis'
Requires-Dist: seaborn ; extra == 'analysis'
Provides-Extra: dev
Requires-Dist: pytest ; extra == 'dev'
Requires-Dist: tox ; extra == 'dev'
Requires-Dist: black ; extra == 'dev'
Requires-Dist: hypothesis ; extra == 'dev'
Requires-Dist: jupyter ; extra == 'dev'
Requires-Dist: quartodoc ; extra == 'dev'
Requires-Dist: pycallgraph2 ; extra == 'dev'
Requires-Dist: kimmdy-reactions ; extra == 'dev'
Requires-Dist: kimmdy-grappa ; extra == 'dev'
Requires-Dist: pandas ; extra == 'dev'
Requires-Dist: matplotlib ; extra == 'dev'
Requires-Dist: seaborn ; extra == 'dev'
Provides-Extra: grappa
Requires-Dist: kimmdy-grappa ; extra == 'grappa'
Provides-Extra: plugins
Requires-Dist: kimmdy-reactions ; extra == 'plugins'
Requires-Dist: kimmdy-grappa ; extra == 'plugins'
Provides-Extra: reactions
Requires-Dist: kimmdy-reactions ; extra == 'reactions'

# KIMMDY

[![tests on latest release](https://github.com/hits-mbm-dev/kimmdy/actions/workflows/test-release.yml/badge.svg)](https://github.com/hits-mbm-dev/kimmdy/actions/workflows/test-release.yml)

Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)

## Installation
**Note**: KIMMDY requires [GROMACS](https://www.gromacs.org/) to be installed.
Some reactions need a GROMACS version patched with [PLUMED](https://www.plumed.org/).
The gromacs version name should then contain `MODIFIED` or `plumed`.

```bash
pip install kimmdy
```

This installation includes only the most basic functionality as no plugins and analysis tools are installed.

To install the builtin reaction plugins, use

```bash
pip install kimmdy[reactions]
```

To install the builtin reactions and analysis tools use

```bash
pip install kimmdy[reactions,analysis]
```


## Documentation

The documentation is available [here](https://hits-mbm-dev.github.io/kimmdy/).

## Getting started

Head over to the [getting started](https://hits-mbm-dev.github.io/kimmdy/guide/tutorials/getting-started.html) tutorial.

## Development

### Development setup

Clone kimmdy and the default reaction and parameterization plugins and install requirements and kimmdy as editable via

```bash
git clone git@github.com:hits-mbm-dev/kimmdy.git
git clone git@github.com:hits-mbm-dev/kimmdy-reactions.git
git clone git@github.com:hits-mbm-dev/kimmdy-grappa.git
cd kimmdy
python -m venv .venv
source ./venv/bin/activate
pip install -r requirements.txt
```

Conventions:

* code style: black
* docstrings: numpy
* [Conventional commit](https://www.conventionalcommits.org/en/v1.0.0/) messages when possible for pretty release notes.


### Local testing

For developoment, we provide a docker image containing gromacs and multiple python versions to test against.  
To run the test locally, you must:

- install docker
- install [act](https://github.com/nektos/act), the easiest option is with github cli via `gh extension install https://github.com/nektos/gh-act`
- run tests with `gh extension exec act -j test --artifact-server-path ./artifacts`
- html coverage report is exported into `artifacts`

