diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..bb699e1b --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,36 @@ +# Contributing to flowerMD + +Thank you for considering contributing to flowerMD! We welcome all contributions +in the form of bug reports, feature requests, code contributions, suggestions, etc. + +The default branch for this repository is `main`. Please submit all pull requests +to the `main` branch. + +## Bug reports and feature requests +For bug reports and feature requests, please open an issue on the +[GitHub issue tracker](https://github.com/cmelab/flowerMD/issues). + +If you are reporting a bug, please include the following information: +- A short description of the bug +- A minimal working example that reproduces the bug +- The expected behavior +- The actual behavior +- The version of flowerMD you are using + +For feature requests, please include a short description of the feature you would +like to see added to flowerMD. + +## Code contributions +We welcome all code contributions in the form of pull requests. If you are +interested in contributing code, please follow the steps below: +- Fork the repository (default branch is `main`) +- Create a new branch for your feature/bug fix +- Create the `flowermd` conda environment using the `environment-cpu.yml` or `environment-gpu.yml` file +- Make your changes +- Install the latest version of pre-commit using `conda install -c conda-forge pre-commit` and run `pre-commit install` in the root directory of the repository +- Commit your changes and make sure all the pre-commit hooks pass +- Push your changes to your fork and create a pull request +- Assign the pull request to a reviewer and wait for the reviewers feedback + +New functionalities should be covered by unit tests. If you are adding a new +function/feature/class please follow the existing style for docstrings. diff --git a/README.md b/README.md index 371fd6da..d2cff320 100644 --- a/README.md +++ b/README.md @@ -39,6 +39,12 @@ how to use flowerMD and what functionalities it provides. ## Documentation Documentation is available at [https://flowermd.readthedocs.io](https://flowermd.readthedocs.io) +## Contributing +We welcome all contributions to flowerMD. Please see +[contributing guidelines](CONTRIBUTING.md) for more information. + + + [//]: # (#### Using the built in molecules, systems and forcefields:) [//]: # (README, documentation and tutorials are a work in progress.) diff --git a/paper/paper.bib b/paper/paper.bib index 0b6c435b..83eddf3c 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -80,19 +80,15 @@ @article{chodera_2007 langid = {english}, } -@misc{hoomd_2019, - title = {{HOOMD}-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations}, - url = {http://arxiv.org/abs/1308.5587}, - shorttitle = {{HOOMD}-blue}, - number = {{arXiv}:1308.5587}, - publisher = {{arXiv}}, - author = {Anderson, Joshua A. and Glaser, Jens and Glotzer, Sharon C.}, - urldate = {2023-10-03}, - date = {2019-10-18}, - langid = {english}, - eprinttype = {arxiv}, - eprint = {1308.5587 [physics]}, - keywords = {Physics - Computational Physics}, +@article{anderson2020hoomd, + title={HOOMD-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations}, + author={Anderson, Joshua A and Glaser, Jens and Glotzer, Sharon C}, + journal={Computational Materials Science}, + volume={173}, + pages={109363}, + year={2020}, + publisher={Elsevier}, + doi={10.1016/j.commatsci.2019.109363} } @article{polyply_2022, @@ -144,7 +140,8 @@ @article{martin2018pyprism number={8}, pages={2906--2922}, year={2018}, - publisher={ACS Publications} + publisher={ACS Publications}, + doi={10.1021/acs.macromol.8b00011} } @Inbook{Klein2016mBuild, diff --git a/paper/paper.md b/paper/paper.md index 7c81751d..85abc4a7 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -24,7 +24,7 @@ authors: corresponding: true affiliation: 1 affiliations: - - name: Boise State University, Boise, ID, USA + - name: Boise State University, Boise, ID, United States of America index: 1 date: 16 October 2023 bibliography: paper.bib