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CONTRIBUTING.md

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Contributing Guide

Thank you for investing your time in contributing to our project!

Read our Code of Conduct to keep our community approachable and respectable.

Issues and Support

If you find a problem or have a question about the content in this repository and how to use it, please create an issue in the Issues Tracker. Make sure you describe the problem as clearly as possible.

Workflow to Make Contributions

We are very happy about contributions!

It is recommended to use an ontology editor such as Protégé. If you want to contribute changes, please do so by:

  1. Clone this repository (fork for external contributors).

  2. Creating a new feature branch.

  3. Apply your changes.

    Edit the ontology files using a suitable ontology editor or text editor. Adhere to the GFO's existing coding style and conventions. Ensure your changes are well-documented and understandable. You can run the following command with docker to check your changes locally (in this case modules/gfo-core.owl is checked):

    docker run -it -v .:/gfo -w /gfo obolibrary/odklite robot report --input modules/gfo-core.owl --profile qc_report/profile.txt

  4. Commit and push all changes.

  5. Create a pull request.

    On GitHub, create a pull request from your branch to the main branch of the official GFO repository. Provide a clear description of your changes and the rationale behind them.

  6. Review and Feedback.

    Be prepared to address feedback and suggestions from the GFO community and maintainers. Work collaboratively with other contributors to refine your changes.

Development Hints

Editing Ontology Files

We recommend Protégé as a user-friendly ontology editor. Please make sure that you use the same version that was used to create the file. Otherwise, unnecessary formatting changes may be added, making it difficult to review changes.

Building GFO Artifacts

GFO artifacts are built with Widoco and published via GitHub Pages in the gh-pages branch.

You can run Widoco manually using docker and the following command:

docker run -it --rm \
  -v .:/usr/local/widoco/gfo ghcr.io/dgarijo/widoco \
  -ontFile gfo/gfo.owl \
  -outFolder gfo/release/latest \
  -rewriteAll \
  -includeAnnotationProperties \
  -uniteSections \
  -noPlaceHolderText \
  -includeImportedOntologies