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Galaxy-Pycaret

A library of Galaxy machine learning tools based on PyCaret — part of the Galaxy ML2 tools, aiming to provide simple, powerful, and robust machine learning capabilities for Galaxy users.

Install Galaxy-Pycaret into Galaxy

  • Update tool_conf.xml to include Galaxy-Pycaret tools. See documentation for more details. This is an example:
<section id="pycaret" name="Pycaret Applications">
  <tool file="galaxy-pycaret/tools/pycaret_train.xml" />
</section>
  • Configure the job_conf.yml under lib/galaxy/config/sample to enable the docker for the environment you want the Ludwig related job running in. This is an example:
execution:
 default: local
 environments:
   local:
     runner: local
     docker_enabled: true

If you are using an older version of Galaxy, then job_conf.xml would be something you want to configure instead of job_conf.yml. Then you would want to configure destination instead of execution and environment. See documentation for job_conf configuration.

  • If you haven’t set sanitize_all_html: false in galaxy.yml, please set it to False to enable our HTML report functionality.
  • Should be good to go.

Make contributions

Getting Started

To get started, you’ll need to fork the repository, clone it locally, and create a new branch for your contributions.

  1. Fork the Repository: Click the "Fork" button at the top right of this page.
  2. Clone the Fork:
  git clone https://github.com/<your-username>/Galaxy-Pycaret.git
  cd <your-repo>
  1. Create a Feature/hotfix/bugfix Branch:
  git checkout -b feature/<feature-branch-name>

or

  git checkout -b hotfix/<hoxfix-branch-name>

or

  git checkout -b bugfix/<bugfix-branch-name>

How We Manage the Repo

We follow a structured branching and merging strategy to ensure code quality and stability.

  1. Main Branches:

    • main: Contains production-ready code.
    • dev: Contains code that is ready for the next release.

  2. Supporting Branches:

    • Feature Branches: Created from dev for new features.
    • Bugfix Branches: Created from dev for bug fixes.
    • Release Branches: Created from dev when preparing a new release.
    • Hotfix Branches: Created from main for critical fixes in production.

Workflow

  • Feature Development:
    • Branch from dev.
    • Work on your feature.
    • Submit a Pull Request (PR) to dev.
  • Hotfixes:
    • Branch from main.
    • Fix the issue.
    • Merge back into both main and dev.

Contribution Guidelines

We welcome contributions of all kinds. To make contributions easy and effective, please follow these guidelines:

  1. Create an Issue: Before starting work on a major change, create an issue to discuss it.
  2. Fork and Branch: Fork the repo and create a feature branch.
  3. Write Tests: Ensure your changes are well-tested if applicable.
  4. Code Style: Follow the project’s coding conventions.
  5. Commit Messages: Write clear and concise commit messages.
  6. Pull Request: Submit a PR to the dev branch. Ensure your PR description is clear and includes the issue number.

Submitting a Pull Request

  1. Push your Branch:

    git push origin feature/<feature-branch-name>

  2. Open a Pull Request:

    • Navigate to the original repository where you created your fork.
    • Click on the "New Pull Request" button.
    • Select dev as the base branch and your feature branch as the compare branch.
    • Fill in the PR template with details about your changes.

  3. Rebase or Merge dev into Your Feature Branch:

    • Before submitting your PR or when dev has been updated, rebase or merge dev into your feature branch to ensure your branch is up to date:

  4. Resolve Conflicts:

    • If there are any conflicts during the rebase or merge, Git will pause and allow you to resolve the conflicts.

  5. Review Process: Your PR will be reviewed by a team member. Please address any feedback and update your PR as needed.