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Update Python support docs
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CONTRIBUTING.rst

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@@ -106,35 +106,35 @@ Before you submit a pull request, check that it meets these guidelines:
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1. If the pull request adds functionality, the docs should be updated. Put
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your new functionality into a function with a docstring.
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2. The pull request should work for Python >=3.7. Check
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https://travis-ci.org/galaxyproject/planemo/pull_requests
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2. The pull request should work for Python >=3.10. Check
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https://github.com/galaxyproject/planemo/actions
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and make sure that the tests pass for all supported Python versions.
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Tips
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----
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To run a subset of tests::
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% make tox ENV=py37-unit ARGS='--tests tests/test_shed_upload.py'
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% make tox ENV=py310-unit ARGS='--tests tests/test_shed_upload.py'
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This will use Tox_ to run the specified tests using Python 3.7. ``ENV`` here
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can be used to specify different Python version (e.g. ``py36`` or
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``py37``).
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This will use Tox_ to run the specified tests using Python 3.10. ``ENV`` here
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can be used to specify a different supported Python version (e.g. ``py311`` or
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``py312``).
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Even more granularity is also possible by specifying specific test methods.::
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make tox ENV=py37-unit ARGS='--tests tests/test_shed_upload.py:ShedUploadTestCase.test_tar_from_git'
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make tox ENV=py310-unit ARGS='--tests tests/test_shed_upload.py:ShedUploadTestCase.test_tar_from_git'
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``tox`` can be used to run tests directly also (use ``. .venv/bin/activate``
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to ensure it is on your ``PATH``).
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::
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tox -e py37-unit -- --tests tests/test_shed_upload.py
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tox -e py310-unit -- --tests tests/test_shed_upload.py
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Tox_ itself is configured to wrap nose_. One can skip Tox_ and run
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``nosetests`` directly.
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Tox_ itself is configured to wrap pytest_. One can skip Tox_ and run
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``pytest`` directly.
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::
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``tox`` executable can be supplied with a ``-e`` argument to specify a
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testing environment. Planemo defines the following environments:
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``py37-lint``
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Lint the planemo code using Python 3.7.
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``py310-lint``
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Lint the planemo code using Python 3.10.
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``py37-lint_docs``
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``py310-lint_docs``
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Lint the docs reStructuredText.
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``py37-lint_docstrings``
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``py310-lint_docstrings``
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Lint the project Python docstrings (doesn't pass currently).
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``py37-unit-quick``
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Run the fastest unit tests (with least external dependencies) on Python 3.7.
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``py310-unit-quick``
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Run the fastest unit tests (with least external dependencies) on Python 3.10.
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``py37-unit-nonredundant-noclientbuild-gx-2005``
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Run tests that are marked as targeting a Galaxy branch and test against Galaxy 20.05.
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``py310-unit-nonredundant-noclientbuild-gx-250``
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Run tests that are marked as targeting a Galaxy branch and test against Galaxy 25.0.
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Skip tests that are marked as redundant or that require a Galaxy client build.
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``py37-unit-gx-dev``
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``py310-unit-gx-dev``
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Run tests that are marked as targeting a Galaxy branch and test against Galaxy's dev branch.
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Pre-commit Hooks
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~~~~~~~~~~~~~~~~~~~~~
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Planemo pull requests are automatically linted and tested using `TravisCI
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<https://travis-ci.org/galaxyproject/planemo>`__. A git pre-commit `hook
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Planemo pull requests are automatically linted and tested using `GitHub Actions
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<https://github.com/galaxyproject/planemo/actions>`__. A git pre-commit `hook
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<http://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks>`__ can be setup
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to lint and/or test Planemo before committing to catch problems that would
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be detected by TravisCI as early as possible.
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be detected by GitHub Actions as early as possible.
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The following command will install a pre-commit hook that lints the Planemo
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code::
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make setup-git-hook-lint-and-test
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.. _Tox: https://tox.readthedocs.org/en/latest/
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.. _nose: https://nose.readthedocs.org/en/latest/
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.. _pytest: https://docs.pytest.org/en/latest/

README.rst

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For a traditional Python installation of Planemo, first set up a virtualenv
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for ``planemo`` (this example creates a new one in ``.venv``) containing
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Python 3.8 or newer and then install with ``pip``. Planemo must be installed
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Python 3.10 or newer and then install with ``pip``. Planemo must be installed
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with pip 7.0 or newer.
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::
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.. _Conda: http://conda.pydata.org/
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.. _Docker: https://www.docker.com/
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.. _Vagrant: https://www.vagrantup.com/
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.. _Travis CI: http://travis-ci.org/
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.. _`tools-devteam`: https://github.com/galaxyproject/tools-devteam
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.. _`tools-iuc`: https://github.com/galaxyproject/tools-iuc
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.. _Building Galaxy Tools Using Planemo: http://planemo.readthedocs.io/en/latest/writing_standalone.html

docs/installation.rst

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If your ``PATH`` contains a Python installed through Conda it should likely not be used to run Planemo,
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please consider using a tool such uv_ to manage native Python installations and environments.
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Planemo runs on Python 3.8 or newer. Planemo can be used to run multiple versions of Galaxy,
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Planemo runs on Python 3.10 or newer. Planemo can be used to run multiple versions of Galaxy,
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but please note that the last Galaxy release that fully supports Python 2.7 is 19.09.
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Conda_ (Experimental)

tox.ini

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[tox]
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envlist = py{37}-lint, py37-mypy, py37-unit-quick, py37-lint_docstrings, py37-lint_docs, py{37}-unit, py37-gxwf_test_test
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envlist = py{310}-lint, py310-mypy, py310-unit-quick, py310-lint_docstrings, py310-lint_docs, py{310}-unit, py310-gxwf_test_test
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source_dir = planemo
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test_dir = tests
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