https://github.com/mdanalysis/waterdynamics
Analysis of water dynamics in molecular dynamics trajectories and water interactions with other molecules.
https://github.com/mdanalysis/waterdynamics
Last synced: about 1 year ago
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Analysis of water dynamics in molecular dynamics trajectories and water interactions with other molecules.
- Host: GitHub
- URL: https://github.com/mdanalysis/waterdynamics
- Owner: MDAnalysis
- License: gpl-2.0
- Created: 2023-10-05T22:44:13.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-07-22T04:10:16.000Z (almost 2 years ago)
- Last Synced: 2024-10-29T17:33:22.889Z (over 1 year ago)
- Language: Python
- Homepage: https://mdanalysis.org/waterdynamics
- Size: 8.37 MB
- Stars: 5
- Watchers: 7
- Forks: 4
- Open Issues: 10
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Authors: AUTHORS.md
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README
waterdynamics
==============================
[//]: # (Badges)
| **Latest release** | [![Last release tag][badge_release]][url_latest_release] ![GitHub commits since latest release (by date) for a branch][badge_commits_since] |
| :----------------- | :------- |
| **Status** | [![GH Actions Status][badge_actions]][url_actions] [![codecov][badge_codecov]][url_codecov] [![Docs][badge_docs]][docs_workflow] |
| **Community** | [![Powered by MDAnalysis][badge_mda]][url_mda]|
[badge_actions]: https://github.com/MDAnalysis/waterdynamics/actions/workflows/gh-ci.yaml/badge.svg
[badge_codecov]: https://codecov.io/gh/MDAnalysis/waterdynamics/branch/main/graph/badge.svg
[badge_commits_since]: https://img.shields.io/github/commits-since/MDAnalysis/waterdynamics/latest
[badge_docs]: https://github.com/MDAnalysis/waterdynamics/actions/workflows/docs.yaml/badge.svg
[docs_workflow]: https://github.com/MDAnalysis/waterdynamics/actions/workflows/docs.yaml
[badge_license]: https://img.shields.io/badge/License-GPLv2-blue.svg
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[badge_release]: https://img.shields.io/github/release-pre/MDAnalysis/waterdynamics.svg
[url_actions]: https://github.com/MDAnalysis/waterdynamics/actions?query=branch%3Amain+workflow%3Agh-ci
[url_codecov]: https://codecov.io/gh/MDAnalysis/waterdynamics/branch/main
[url_docs]: https://waterdynamics.readthedocs.io/en/latest/?badge=latest
[url_latest_release]: https://github.com/MDAnalysis/waterdynamics/releases
[url_mda]: https://www.mdanalysis.org
Analysis of water dynamics in molecular dynamics trajectories and water interactions with other molecules.
Documentation for waterdynamics can be found at .
waterdynamics is bound by a [Code of Conduct](https://github.com/MDAnalysis/waterdynamics/blob/main/CODE_OF_CONDUCT.md).
### Installation
To build waterdynamics from source,
we highly recommend using virtual environments.
If possible, we strongly recommend that you use
[Anaconda](https://docs.conda.io/en/latest/) as your package manager.
Below we provide instructions both for `conda` and
for `pip`.
#### With conda
Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) installed.
Create a virtual environment and activate it:
```
conda create --name waterdynamics
conda activate waterdynamics
```
Install the development and documentation dependencies:
```
conda env update --name waterdynamics --file devtools/conda-envs/test_env.yaml
conda env update --name waterdynamics --file docs/requirements.yaml
```
Build this package from source:
```
pip install -e .
```
If you want to update your dependencies (which can be risky!), run:
```
conda update --all
```
And when you are finished, you can exit the virtual environment with:
```
conda deactivate
```
#### With pip
##### Install from PyPI
The latest release of waterdynamics is available on [PyPI](https://pypi.org/project/waterdynamics/) and can be installed with:
```
pip install waterdynamics
```
##### Install from source
To build the package from source, run:
```
pip install .
```
If you want to create a development environment, install
the dependencies required for tests and docs with:
```
pip install ".[test,doc]"
```
### Copyright
The waterdynamics source code is hosted at https://github.com/MDAnalysis/waterdynamics
and is available under the Lesser GNU General Public License, version 2.1 or later (see the file [LICENSE](https://github.com/MDAnalysis/waterdynamics/blob/main/LICENSE)).
Copyright (c) 2023, MDAnalysis
#### Acknowledgements
Project based on the
[MDAnalysis Cookiecutter](https://github.com/MDAnalysis/cookiecutter-mda) version 0.1.
Please cite [MDAnalysis](https://github.com/MDAnalysis/mdanalysis#citation) when using waterdynamics in published work.