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Contributing Guidelines

Thank you for considering contributing to our database repository. Your contributions are valuable and help improve the quality of our work.

Our repository follows the FAIR (Findable, Accessible, Interoperable, and Reusable) principles, which promote the usability and long-term value of data and resources. As a contributor, it is important to adhere to these principles and pay attention to metadata and data quality.

Thus when you add the simulation to the database be sure to specify the arguments subset_name, task, user. Additionally, when updating metadata, use the update_metadata function to ensure that the information accurately reflects the latest changes and additions.

Data submission process

  1. Fork the repository on GitHub by clicking the "Fork" button.

  2. Clone your forked repository locally using the following command:

    git clone https://github.com/<your-github-username>/Enhancing_ReaxFF_DFT_database.git

  3. Make the necessary changes to your local repository.

  4. (Optional) Install the pre-commit hook to perform code checks before committing your changes.

  5. Pull and rebase any changes made by others to the main branch since you started working on your changes:

    git pull --rebase

  6. If you have committed multiple changes locally, squash them into a single commit before submitting a pull request (PR). You can do this by following these steps:

    • Run git log to find the commit ID of your first local commit.

    • Use the commit ID to rebase and squash the commits by running:

      git rebase <FIRST-COMMIT-ID> -i

    • Mark all of the commits except the first as "squash" in the interactive rebase window.

    Note: We prefer a single commit as the first revision of a PR for easier review.

  7. Push your changes to your forked repository:

git push -f fork master

Note: Use the -f option if you have used your fork for previous PRs.

  1. Go to your forked repository on GitHub and click the "New pull request" button to create a new pull request.

  2. If your reviewers provide feedback, make the necessary changes locally, rerun the tests, and update your forked repository:

    git push fork main

    Note: Do not squash commits after the PR has been sent, as it resets the state held by GitHub about what files each reviewer has seen.

  3. If additional changes have been made to the main branch and you need to update your fork, pull the changes as a merge (not a rebase):

    git pull
git push fork main

    Note: Using merges instead of rebases allows GitHub to hide the content of merge commits, reducing noise in the commit history.

  4. Once the reviewer approves your change with LGTM, it's time to submit. Use the "Squash and merge" option when merging to the main branch. We use squash merging to maintain a clean commit history in the master branch.

  5. For a step-by-step tutorial on contributing to GitHub, check out How to Contribute on GitHub.

How pre-commit

What it is pre-commit?

pre-commit is a mechanism provided by the version control system Git that allows to execute code checks right before committing your changes. It helps ensure code quality by catching potential issues such as typos or style mistakes.

Besicaly force lazy developers to control his code to avoid stupid typos or style mistakes.

Lazy developers

Why I should use pre-commit?

When coding, it's easy to follow your own style and logic, which can sometimes result in chaotic and hard-to-read code. pre-commit helps mitigate this by enforcing code checks, preventing situations like the infamous "Spaghetti Code."

Thus, with pre-commit we are trying to basically avoid the situation below:

Spaghetti Code

How to use pre-commit

Our repository includes a configuration file (.pre-commit-config.yaml) for pre-commit hooks. Follow these steps to set it up:

  1. Install pre-commit using pip:

    pip install pre-commit

  2. Activate pre-commit to run before every git commit:

    pre-commit install

  3. Test it by running:

    pre-commit run

Note

To commit without running pre-commit, you can use the git commit --no-verify command. However, this will fail in the remote repository due to the "Continous Integration" workflow that checks all changes on every push and pull.

Hooks list

Hook auto-fix
pre-commit-hooks ✅
isort ✅
pyupgrade ✅
black ✅
blacken-docs ✅
nbQA ✅ and ❌
flake8 ❌
mypy ❌

Note

Note that many of these hooks can automatically fix code issues. If the checks fail, try running git commit again, and the hook will pass successfully.