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Implement run/test/workflow_edit/autoupdate from non default tool sheds #1445

Merged
merged 14 commits into from
May 7, 2024
Merged

Implement run/test/workflow_edit/autoupdate from non default tool sheds #1445

merged 14 commits into from
May 7, 2024

Commits on Apr 11, 2024

  1. Implement autoupdate with alternative shed tools

    @mvdbeek
    mvdbeek committed Apr 11, 2024
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  2. Fix for new toolshed ?

    @mvdbeek
    mvdbeek committed Apr 11, 2024
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  3. Make find_repos_from_tool_id fit for new toolshed

    @mvdbeek
    mvdbeek committed Apr 11, 2024
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  4. Fix tool shed selection

    @mvdbeek
    mvdbeek committed Apr 11, 2024
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  5. Add test for workflow update from mixed tool sheds

    @mvdbeek
    mvdbeek committed Apr 11, 2024
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  6. Type fixes

    @mvdbeek
    mvdbeek committed Apr 11, 2024
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  7. Drop outdated comment

    @mvdbeek
    mvdbeek committed Apr 11, 2024
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  8. Fix tool lint check for correct tool version

    @mvdbeek
    mvdbeek committed Apr 11, 2024
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  9. Use tox-managed virtualenv in make lint-docs

    @mvdbeek
    mvdbeek committed Apr 11, 2024
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  10. Don't fail linting on local tools

    @mvdbeek
    mvdbeek committed Apr 11, 2024
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  11. Ignore toil cwltool warning in lint_sphinx_output.py

    @mvdbeek
    mvdbeek committed Apr 11, 2024
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Commits on May 7, 2024

  1. Generalize finding tool sheds from runnable 

    Should now work for workflow_edit, test, run etc if targeting a local or
docker instance.
    @mvdbeek
    mvdbeek committed May 7, 2024
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  2. Use MAIN_TOOLSHED_URL instead of literal url

    @mvdbeek
    mvdbeek committed May 7, 2024
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  3. Simplify local_galaxy_config

    @mvdbeek
    mvdbeek committed May 7, 2024
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