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Guide to contributing to the BioSimulations and BioSimulators platforms

We enthusiastically welcome contributions to BioSimulations and BioSimulators! This document describes how developers can contribute the BioSimulations and BioSimulators platforms (e.g., web applications, REST APIs, databases, and simulation services). Information for investigators about contributing simulation projects to BioSimulations is available here. Information for simulation software tool developers about contributing simulation tools to BioSimulators is available at here.

Code of Conduct

All developer and contributors are expected to follow the BioSimulations and BioSimulators Code of Conduct.

Providing Feedback

Please provide any Feedback through GitHub Issues or our Discussion Forum.

Coordinating contributions

Before getting started, please use GitHub issues to announce your plans to the community so that other developers can provide input into your plans and coordinate their own work. If you plan to include significant contribution or changes, please also contact the lead developers at info@biosimulations.org to coordinate your planned contributions with other ongoing efforts. As the development community grows, we will institute additional infrastructure as needed, such as a leadership committee and regular online meetings.

Development

Please see the Getting Started guide for information on how to start working with the codebase and develop locally.

Coding convention

BioSimulations and BioSimulators follow standard TypeScript style conventions:

  • Module names: lower-dash-case
  • Class names: UpperCamelCase
  • Function names: lowerCamelCase
  • Variable names: lowerCamelCase

Further information about style conventions can be found in the lint rules definition.

Linting

We strive to create high-quality code. BioSimulations and BioSimulators use ESLint to identify potential errors. ESLint can be executed by running nx affected:lint to lint all applications and libraries or nx run {app-or-lib}:lint to lint an individual application or library.

See the README for the COMBINE API for more information about linting the COMBINE API.

Testing

We strive to have complete test coverage of BioSimulations and BioSimulators. As such, all contributions to BioSimulations and BioSimulators should be tested. In particular, each module should be accompanied by a specification test in the same directory with the extension .spec.ts. All applications and libraries can be tested by running nx affected:test. Individual applications or libraries can be tested by running nx run {app-or-lib}:test.

Upon each push and pull request to GitHub, GitHub will trigger actions to execute all of the tests.

See the README for the COMBINE API for more information about testing the COMBINE API.

Submitting changes

Please use GitHub pull requests to submit changes. Each request should include a brief description of the new and/or modified features. Upon each pull request, GitHub will trigger actions to lint and test all of the applications and libraries. Pull requests will be approved once all tests are passing and the pull request is reviewed by one of the lead developers.

Commit convention

BioSimulations and BioSimulators uses conventional commits to enable changelog generation and versioning. Developers are encouraged to use Commitizen to easily create compliant commit messages. To use Commitizen, simply run npm run commit instead of git commit to commit changes.

Releasing and deploying new versions

Contact info@biosimulations.org to request release and deployment of changes.


Last update: 2022-07-03