Merge branch 'master' into pr-57

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,12 +1,26 @@
 ## Description
+
 Provide a brief description of the PR's purpose here.
 
+### Type of Change
+
+- [ ] Bug fix
+- [ ] New feature
+- [ ] Documentation update
+- [ ] Unit test and CI update
+- [ ] Other
+
 ## Todos
 Notable points that this PR has either accomplished or will accomplish.
   - [ ] TODO 1
+  - [ ] TODO 2
 
-## Questions
-- [ ] Question1
+### Checklist
+Starting from PR #62, external PRs must keep the following checklist in the PR. 
 
-## Status
-- [ ] Ready to go
+- [ ] I have read the [contributing guidelines](CONTRIBUTING.md).
+- [ ] My code follows the project’s coding style and is free from linting errors examined by `flake8`.
+- [ ] My code comes with docstrings that follow the [NumPy docstrings standard](https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard).
+- [ ] I have updated the documentation in the `docs` directory if my changes affect the project's functionality or usage.
+- [ ] I have added new tests for new features or changes to existing features. The code coverage is at least 90%.
+- [ ] My code passes all unit tests and CI tests on CircleCI.

CONTRIBUTING.md

@@ -0,0 +1,73 @@
+# Contributing to `ensemble_md`
+
+Thank you for your interest in contributing to `ensemble_md`! We welcome contributions from the community and appreciate your efforts to improve the project. Please follow these guidelines to help us manage contributions effectively.
+
+## General workflow
+We use a "Pull request, Review, and Merge" workflow for contributions to this project: codes can only be added to the master branch through pull requests (PRs). To contribute to the project, please follow these steps:
+
+1. **Fork the Repository**: Click the "Fork" button at the top right of this repository to create your own copy of the project.
+2. **Clone Your Fork**: Clone your fork to your local machine:
+   ```bash
+   git clone https://github.com/{your-username}/ensemble_md.git
+   ```
+3. ***Create a Branch***: Create a new branch for your changes:
+    ```bash
+    git checkout -b {your-feature-branch}
+    ```
+4. **Make Changes**: Make your changes to the project, and commit them to your branch using Git:
+    ```bash
+    git add .
+    git commit -m "Your commit message"
+    ```
+5. **Push Changes**: Push your changes to your fork on GitHub:
+    ```bash
+    git push origin {your-feature-branch}
+    ```
+6. **Create a Pull Request**: Go to the GitHub page of your fork and create a new pull request. Make sure to provide a clear description of your changes in the PR. Check the [pull request template](.github/PULL_REQUEST_TEMPLATE.md) for more information on what to include in your PR.
+
+## Contribution Guidelines
+
+### Coding Style
+We use [PEP8 coding style](https://peps.python.org/pep-0008/) for this project. Please follow the guidelines to maintain consistency in code style. Before you submit a pull request, run the following command in the root directory of the project to check your code for PEP8 compliance:
+  ```bash
+  flake8 ensemble_md
+  ``` 
+  Any errors or warnings should be fixed before submitting your pull request. (We accept PRs with `E501` and `E741` errors, but the errors should be suppressed by appending `# noqa: E501` or `#noqa: E741` at the end of the line.)
+
+### Docstrings and documentation
+Whenever there is a new function or class added, please include a docstring that describes the purpose of the function or class. For this project, we follow the [NumPy docstrings standard](https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard). Please visit the docstrings of existing functions or classes for reference.
+
+If your changes affect any part of the project's functionality or usage, or add new features or algorithms to the project, please update the documentation in the `docs` directory accordingly. We use [Sphinx](https://www.sphinx-doc.org/en/master/) to generate documentation. Please ensure that your changes do not break the documentation build. You can build the documentation locally by running the following command in the `docs` directory:
+```bash
+make html
+```
+and then opening the `docs/build/html/index.html` file in your browser to view the documentation. If you implement a new simulation method in `ensemble_md`, we encourage you to include a tutorial in the documentation by including a `.ipynb` file in the `docs/example` folder. Ideally, the tutorial should be able to be run on [Binder](https://mybinder.org/), for which additional dependencies (if any) should be added to `environment.yml` in the root directory of the project.
+
+### Unit tests and continuous integration
+To maintain the quality of the project, we require that the merging code be covered by unit tests to at least 90% coverage. We use [pytest](https://docs.pytest.org/en/stable/) for unit testing. Please add new tests for new features or changes to existing features. You can run the tests locally by running the following command in the root directory of the project:
+```bash
+pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/
+```
+This will generate a coverage report in the `coverage.xml` file in the root directory of the project. To view the coverage report, you can run the following command:
+```bash
+coverage report
+```
+For tests that require the use of MPI, you might want to use a command like the following to run the tests:
+```bash
+mpirun -np 4 pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/{tests_that_use_mpi.py} --with-mpi
+```
+For continuous integration (CI), we use [CircleCI](https://circleci.com/) to run tests on every pull request and push to the repository. Make any necessary changes to the CI configuration file (`.circleci/config.yml`) to ensure that your changes pass the CI tests before submitting a pull request.
+
+## Reporting issues
+If you encounter any issues with the project, please report them by opening an issue on the GitHub repository. When reporting an issue, please provide a clear description of the problem, including the steps to reproduce the issue, the expected behavior, and the actual behavior. If possible, include any error messages or stack traces that you encountered. Please refer to the [issue template](.github/ISSUE_TEMPLATE.md) for more information on what to include in your issue report.
+
+## Code of Conduct
+By participating in this project, you agree to abide by the [Code of Conduct](CODE_OF_CONDUCT.md). We are committed to providing a welcoming and inclusive environment for everyone.
+
+## Contact
+For any questions or further assistance, please don't hesitate to contact us as wehs7661@colorado.edu.
+
+---
+Thank you for your contributions to `ensemble_md`! We appreciate your help in making this project better for everyone.
+
+**`ensemble_md` Development Team**

README.md

@@ -28,6 +28,10 @@ https://doi.org/10.48550/arXiv.2408.11038)
 - Wei-Tse Hsu, University of Colorado, Boulder (weitse.hsu@colorado.edu)
 - Anika Friedman, University of Colorado, Boulder (anika.friedman@colorado.edu)
 
+### Contributing
+
+We welcome contributions to this project! Please see our [contributing guidelines](CONTRIBUTING.md) for more information on how to get started.
+
 
 ### Acknowledgements