Merge pull request #80 from cmelab/joss-prereview

Address JOSS prereview comments

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.

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.)

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,

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