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annotate README.md @ 0:209b663a4f62 draft

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author goeckslab
date Wed, 18 Jun 2025 15:38:19 +0000
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1 # Galaxy-Pycaret
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2 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.
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3
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4 # Install Galaxy-Pycaret into Galaxy
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6 * Update `tool_conf.xml` to include Galaxy-Pycaret tools. See [documentation](https://docs.galaxyproject.org/en/master/admin/tool_panel.html) for more details. This is an example:
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7 ```
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8 <section id="pycaret" name="Pycaret Applications">
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9 <tool file="galaxy-pycaret/tools/pycaret_train.xml" />
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10 </section>
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11 ```
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13 * 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:
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14 ```
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15 execution:
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16 default: local
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17 environments:
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18 local:
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19 runner: local
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20 docker_enabled: true
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21 ```
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22 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.
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23 See [documentation](https://docs.galaxyproject.org/en/master/admin/jobs.html#running-jobs-in-containers) for job_conf configuration.
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24 * If you haven’t set `sanitize_all_html: false` in `galaxy.yml`, please set it to False to enable our HTML report functionality.
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25 * Should be good to go.
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27 # Make contributions
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29 ## Getting Started
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31 To get started, you’ll need to fork the repository, clone it locally, and create a new branch for your contributions.
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32
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33 1. **Fork the Repository**: Click the "Fork" button at the top right of this page.
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34 2. **Clone the Fork**:
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35 ```bash
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36 git clone https://github.com/<your-username>/Galaxy-Pycaret.git
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37 cd <your-repo>
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38 ```
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39 3. **Create a Feature/hotfix/bugfix Branch**:
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40 ```bash
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41 git checkout -b feature/<feature-branch-name>
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42 ```
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43 or
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44 ```bash
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45 git checkout -b hotfix/<hoxfix-branch-name>
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46 ```
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47 or
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48 ```bash
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49 git checkout -b bugfix/<bugfix-branch-name>
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50 ```
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51
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52 ## How We Manage the Repo
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53
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54 We follow a structured branching and merging strategy to ensure code quality and stability.
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55
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56 1. **Main Branches**:
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57 - **`main`**: Contains production-ready code.
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58 - **`dev`**: Contains code that is ready for the next release.
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59
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60 2. **Supporting Branches**:
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61 - **Feature Branches**: Created from `dev` for new features.
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62 - **Bugfix Branches**: Created from `dev` for bug fixes.
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63 - **Release Branches**: Created from `dev` when preparing a new release.
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64 - **Hotfix Branches**: Created from `main` for critical fixes in production.
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65
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66 ### Workflow
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67
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68 - **Feature Development**:
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69 - Branch from `dev`.
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70 - Work on your feature.
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71 - Submit a Pull Request (PR) to `dev`.
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72 - **Hotfixes**:
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73 - Branch from `main`.
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74 - Fix the issue.
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75 - Merge back into both `main` and `dev`.
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77 ## Contribution Guidelines
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79 We welcome contributions of all kinds. To make contributions easy and effective, please follow these guidelines:
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80
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81 1. **Create an Issue**: Before starting work on a major change, create an issue to discuss it.
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82 2. **Fork and Branch**: Fork the repo and create a feature branch.
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83 3. **Write Tests**: Ensure your changes are well-tested if applicable.
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84 4. **Code Style**: Follow the project’s coding conventions.
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85 5. **Commit Messages**: Write clear and concise commit messages.
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86 6. **Pull Request**: Submit a PR to the `dev` branch. Ensure your PR description is clear and includes the issue number.
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87
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88 ### Submitting a Pull Request
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89
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90 1. **Push your Branch**:
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91 ```bash
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92 git push origin feature/<feature-branch-name>
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93 ```
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94 2. **Open a Pull Request**:
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95 - Navigate to the original repository where you created your fork.
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96 - Click on the "New Pull Request" button.
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97 - Select `dev` as the base branch and your feature branch as the compare branch.
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98 - Fill in the PR template with details about your changes.
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99
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100 3. **Rebase or Merge `dev` into Your Feature Branch**:
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101 - 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:
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102
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103 4. **Resolve Conflicts**:
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104 - If there are any conflicts during the rebase or merge, Git will pause and allow you to resolve the conflicts.
209b663a4f62 planemo upload for repository https://github.com/goeckslab/gleam commit 5dd048419fcbd285a327f88267e93996cd279ee6
goeckslab
parents:
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105
209b663a4f62 planemo upload for repository https://github.com/goeckslab/gleam commit 5dd048419fcbd285a327f88267e93996cd279ee6
goeckslab
parents:
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106 5. **Review Process**: Your PR will be reviewed by a team member. Please address any feedback and update your PR as needed.