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Merge pull request #122 from loli/Release_0.5.0
Release 0.5.0
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‎.bettercodehub.yml

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‎.github/workflows/README.md

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# MedPy's CI/CD workflows
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## Build & release
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Upon creating a release or a pre-release on GitHub, the package is *build* and *published* to [test.pypi.org](https://test.pypi.org).
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Install from test PyPi with `python -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple medpy==x.y.z.`. This ensures that the dependencies are installed from the proper PyPI.
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After making sure that the package published there is installable and passes all tests, the final *publish* to [pypi.org](https://pypi.org) can be triggered manually from the GitHub UI.
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Note that publishing only works for releases created directly from the `master` branch. Releasees published from other branches should always be pre-releases and never published to [pypi.org](https://pypi.org), but only [test.pypi.org](https://test.pypi.org).
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## pre-commit.yml
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Makes sure that all PRs and all releases adhere to the pre-commit rules.
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## run-test*.yml
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Makes sure that all PRs and all releases pass the tests.

‎.github/workflows/build-publish-test.yml

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# Build package & publish a release to PyPI (test)
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# Given a tag, downloads the associated code, builds the package, and uploads the source tarball as artifact
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# This version releases to https://test.pypi.org/ for testing purposes
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# Triggers on: all published releases (incl pre-releases)
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name: Build package & release to PyPI (test)
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on:
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release:
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types: [published]
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permissions:
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contents: read
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: 3.x
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build
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- name: Build a source tarball
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run: python -m build --sdist
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- name: Store the distribution packages
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uses: actions/[email protected]
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with:
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name: python-package-distributions-${{ github.ref_name }}
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path: dist/
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publish-test:
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needs:
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- build
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runs-on: ubuntu-latest
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environment:
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name: pypi-publish-test
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url: https://test.pypi.org/p/medpy
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permissions:
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id-token: write # IMPORTANT: mandatory for trusted publishing
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steps:
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- name: Download dists
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uses: actions/[email protected] # make sure that same major version as actions/upload-artifact
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with:
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name: python-package-distributions-${{ github.ref_name }}
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path: dist/
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- name: Publish package
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uses: pypa/[email protected]
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with:
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repository-url: https://test.pypi.org/legacy/ # test publish platform

‎.github/workflows/pre-commit.yml

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# Runs the pre-commit hooks to make sure that all changes are properly formatted and such
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# Triggers on: All PRs that are mergable, but not for draft PRs
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# Triggers on: all published releases (incl draft releases)
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name: Pre-commit hooks
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on:
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pull_request:
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types: [opened, synchronize, reopened, ready_for_review]
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release:
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types: [published]
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permissions:
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contents: read
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jobs:
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pre-commit:
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if: github.event.pull_request.draft == false
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: 3.x
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- uses: pre-commit/[email protected]
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- uses: pre-commit-ci/[email protected]
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if: always()

‎.github/workflows/publish.yml

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# Publish a release to PyPI
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# Requires build package workflow to run first
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# This version releases to https://pypi.org/, only trigger if the release has been thorough tested
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name: Build package & release to PyPI
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on:
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workflow_dispatch:
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inputs:
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tag:
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description: "Select release to publish"
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required: true
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permissions:
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contents: read
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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ref: ${{ inputs.tag }}
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: 3.x
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build
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- name: Build a source tarball
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run: python -m build --sdist
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- name: Store the distribution packages
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uses: actions/[email protected]
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with:
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name: python-package-distributions-${{ inputs.tag }}
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path: dist/
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publish:
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needs:
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- build
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runs-on: ubuntu-latest
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environment:
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name: pypi-publish
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url: https://pypi.org/p/medpy
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permissions:
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id-token: write # IMPORTANT: mandatory for trusted publishing
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steps:
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- name: Download dists
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uses: actions/[email protected] # make sure that same major version as actions/upload-artifact
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with:
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name: python-package-distributions-${{ inputs.tag }}
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path: dist/
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- name: Publish package
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uses: pypa/[email protected]

‎.github/workflows/run-tests-gc.yml

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# Install the package and run the graph-cut tests
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# This test is kept separate, as the graphcut functionality is optional and unstable
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# Triggers on: All PRs that are mergable, but not for draft PRs
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# Triggers on: all published releases (incl pre-releases)
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# Note: the dependency libboost_python will always be installed against the OS's main python version,
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# independent of the python version set-up. They are 22.04 = 3.10 and 20.04 = 3.8.
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name: Run tests (graphcut only)
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on:
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pull_request:
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types: [opened, synchronize, reopened, ready_for_review]
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release:
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types: [published]
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permissions:
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contents: read
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jobs:
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run-tests-gc-ubuntu-22_04:
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if: github.event.pull_request.draft == false
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runs-on: ubuntu-22.04
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python 3.10
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uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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- name: Install system dependencies for graphcut functionality
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run: sudo apt-get install -y libboost-python-dev build-essential
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- name: Install with test dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install -v .[test]
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- name: Test with pytest (graphcut test only)
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run: cd tests && pytest graphcut_/*
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run-tests-gc-test-ubuntu-20_04:
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if: github.event.pull_request.draft == false
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runs-on: ubuntu-20.04
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python 3.8
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uses: actions/setup-python@v5
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with:
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python-version: "3.8"
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- name: Install system dependencies for graphcut functionality
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run: sudo apt-get install -y libboost-python-dev build-essential
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- name: Install with test dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install -v .[test]
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- name: Test with pytest (graphcut test only)
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run: cd tests && pytest graphcut_/*

‎.github/workflows/run-tests.yml

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# Install the package and run all tests except the graph-cut ones
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# Triggers on: All PRs that are mergable, but not for draft PRs
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# Triggers on: all published releases (incl pre-releases)
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name: Run tests (wo graphcut)
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on:
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pull_request:
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types: [opened, synchronize, reopened, ready_for_review]
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release:
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types: [published]
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permissions:
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contents: read
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jobs:
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run-tests:
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if: github.event.pull_request.draft == false
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.8", "3.9", "3.10", "3.11"]
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os: [ubuntu-latest, macos-latest]
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install with test dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install .[test]
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- name: Test with pytest
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run: |
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pytest tests/features_/*
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pytest tests/filter_/*
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pytest tests/io_/*
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pytest tests/metric_/*

‎.gitignore

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TODO.txt
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# Images #
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##########
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# Images
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*.nii
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*.mhd
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*.raw
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# DOC dirs #
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############
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# Local virtual envs
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.venv/
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# DOC dirs
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doc/build/
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doc/generated/
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doc/source/generated/
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# Notebooks dirs #
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##################
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# Notebooks dirs
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.ipynb_checkpoints
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# BUILD dirs #
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##############
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# BUILD dirs
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build/
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dist/
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MedPy.egg-info/
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# Only locally used, temporary .py scripts. #
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#############################################
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# Only locally used, temporary .py scripts.
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_*.py
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!__init__.py
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# Backup files #
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################
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# Backup files
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*.bak
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# Compiled source #
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###################
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# Compiled source
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*.com
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*.class
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*.dll
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*.pyc
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*.pyo
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# Packages #
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############
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# Packages
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# it's better to unpack these files and commit the raw source
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# git has its own built in compression methods
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*.7z
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*.tar
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*.zip
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# Logs and databases #
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######################
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# Logs and databases
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*.log
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*.sql
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*.sqlite
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# OS generated files #
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######################
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# OS generated files
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.DS_Store*
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ehthumbs.db
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Icon?
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Thumbs.db
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*~
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# Eclipse and PyDev project files #
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###################################
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# Eclipse and PyDev project files
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.project
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.pydevproject
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.settings/
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.metadata/
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# Suggestions by GitHub for Python projects #
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#############################################
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# Suggestions by GitHub for Python projects
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# Packages
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*.egg
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*.egg-info
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# Unit test / coverage reports
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.coverage
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.tox
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.hypothesis
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#Translations
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*.mo

‎.gitmodules

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