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Merge pull request #88 from skoudoro/project-update
RF: large packaging update
2 parents 30dd0f4 + 79966be commit 43edfbb

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‎.flake8‎

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[flake8]
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max-line-length = 88
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max-complexity = 10
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exclude =
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.git,
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__pycache__,
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.tox,
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.eggs,
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*.egg,
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build,
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dist

‎.github/workflows/codeformat.yml‎

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name: Code Format
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on:
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push:
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branches: [master]
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pull_request:
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branches: [master]
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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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name: Pre-commit checks
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runs-on: ubuntu-latest
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steps:
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- name: Check out repository
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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: "3.12"
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- name: Install and run pre-commit hooks
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uses: pre-commit/action@v3.0.1

‎.github/workflows/coverage.yml‎

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name: Coverage
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on:
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push:
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branches: [master]
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pull_request:
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branches: [master]
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permissions:
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contents: read
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jobs:
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coverage:
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name: Code Coverage
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runs-on: ubuntu-latest
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steps:
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- name: Check out repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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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: "3.12"
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cache: pip
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cache-dependency-path: pyproject.toml
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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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python -m pip install -e .[test]
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- name: Run tests with coverage
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run: |
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pytest trx/tests --cov=trx --cov-report=xml --cov-report=term-missing
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v4
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with:
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files: ./coverage.xml
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flags: unittests
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name: codecov-trx
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fail_ci_if_error: false
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verbose: true
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

‎.github/workflows/docbuild.yml‎

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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.9"]
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python-version: ["3.13"]
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0 # Fetch all history and tags for setuptools_scm
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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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
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cd docs
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make html
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- name: Upload docs
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uses: actions/upload-artifact@v1
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uses: actions/upload-artifact@v4
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with:
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name: docs
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path: docs/_build/html
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deploy-dev:
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needs: build
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runs-on: ubuntu-latest
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if: github.event_name == 'push' && github.ref == 'refs/heads/master' && github.repository == 'tee-ar-ex/trx-python'
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steps:
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- uses: actions/checkout@v4
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- uses: actions/download-artifact@v4
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with:
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name: docs
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path: docs/_build/html
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- name: Publish dev docs to Github Pages
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uses: JamesIves/github-pages-deploy-action@v4
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with:
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branch: gh-pages
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folder: docs/_build/html
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target-folder: dev
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deploy-release:
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needs: build
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runs-on: ubuntu-latest
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if: startsWith(github.ref, 'refs/tags/') && github.repository == 'tee-ar-ex/trx-python'
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steps:
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- uses: actions/checkout@v4
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- uses: actions/download-artifact@v4
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with:
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name: docs
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path: docs/_build/html
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- name: Publish docs to Github Pages
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if: startsWith(github.event.ref, 'refs/tags')
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- name: Get version from tag
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id: get_version
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run: echo "VERSION=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT
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- name: Fetch existing switcher.json from gh-pages
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run: |
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curl -sSL https://tee-ar-ex.github.io/trx-python/switcher.json -o switcher.json || echo '[]' > switcher.json
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- name: Update switcher.json with new version
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run: python tools/update_switcher.py switcher.json --version ${{ steps.get_version.outputs.VERSION }}
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- name: Create root files (redirect + switcher.json)
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run: |
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mkdir -p root_files
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cp switcher.json root_files/
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cat > root_files/index.html << 'EOF'
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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<title>trx-python - TRX File Format for Tractography</title>
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<meta name="description" content="trx-python is a Python implementation of the TRX file format for tractography data, designed for efficient handling of brain fiber tract streamlines.">
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<meta name="robots" content="index, follow">
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<link rel="canonical" href="https://tee-ar-ex.github.io/trx-python/stable/">
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<meta http-equiv="refresh" content="0; URL=https://tee-ar-ex.github.io/trx-python/stable/">
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<script>window.location.replace("https://tee-ar-ex.github.io/trx-python/stable/");</script>
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</head>
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<body>
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<h1>trx-python Documentation</h1>
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<p>Python implementation of the TRX file format for tractography data.</p>
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<p>If you are not redirected automatically, visit the <a href="https://tee-ar-ex.github.io/trx-python/stable/">stable documentation</a>.</p>
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</body>
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</html>
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EOF
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- name: Publish root files (redirect + switcher.json)
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uses: JamesIves/github-pages-deploy-action@v4
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with:
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branch: gh-pages
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folder: root_files
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target-folder: .
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clean: false
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- name: Publish release docs to Github Pages
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uses: JamesIves/github-pages-deploy-action@v4
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with:
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branch: gh-pages
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folder: docs/_build/html
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target-folder: ${{ steps.get_version.outputs.VERSION }}
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- name: Publish stable docs to Github Pages
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uses: JamesIves/github-pages-deploy-action@v4
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with:
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branch: gh-pages
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folder: docs/_build/html
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target-folder: stable

‎.github/workflows/publish-to-test-pypi.yml‎

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name: Publish Python 🐍 distributions 📦 to PyPI and TestPyPI
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on: push
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on:
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push:
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branches:
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- master
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tags:
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- '*'
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jobs:
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build-n-publish:
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name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
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build:
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name: Build distribution 📦
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runs-on: ubuntu-latest
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if: github.repository == 'tee-ar-ex/trx-python'
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steps:
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- uses: actions/checkout@master
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- name: Set up Python 3.9
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uses: actions/setup-python@v1
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0 # Fetch all history and tags for setuptools_scm
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- name: Set up Python 3.11
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uses: actions/setup-python@v5
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with:
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python-version: 3.9
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python-version: "3.11"
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- name: Install pypa/build
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run: >-
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python -m
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pip install
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build
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--user
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run: python -m pip install build --user
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- name: Build a binary wheel and a source tarball
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run: >-
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python -m
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build
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--sdist
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--wheel
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--outdir dist/
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.
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run: python -m build --sdist --wheel --outdir dist/ .
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- name: Upload distribution artifacts
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uses: actions/upload-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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publish-to-testpypi:
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name: Publish to TestPyPI
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needs: build
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runs-on: ubuntu-latest
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environment:
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name: testpypi
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url: https://test.pypi.org/p/trx-python
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permissions:
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id-token: write
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steps:
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- name: Download distribution artifacts
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uses: actions/download-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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- name: Publish distribution 📦 to Test PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.test_pypi_password }}
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repository_url: https://test.pypi.org/legacy/
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repository-url: https://test.pypi.org/legacy/
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publish-to-pypi:
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name: Publish to PyPI
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needs: build
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runs-on: ubuntu-latest
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if: startsWith(github.ref, 'refs/tags/')
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environment:
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name: pypi
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url: https://pypi.org/p/trx-python
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permissions:
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id-token: write
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steps:
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- name: Download distribution artifacts
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uses: actions/download-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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- name: Publish distribution 📦 to PyPI
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if: startsWith(github.event.ref, 'refs/tags')
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uses: pypa/gh-action-pypi-publish@release/v1
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github-release:
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name: Create GitHub Release
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needs: publish-to-pypi
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v4
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- name: Download distribution artifacts
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uses: actions/download-artifact@v4
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with:
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user: __token__
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password: ${{ secrets.pypi_password }}
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name: python-package-distributions
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path: dist/
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- name: Get version from tag
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id: get_version
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run: echo "VERSION=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT
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- name: Create GitHub Release
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env:
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GH_TOKEN: ${{ github.token }}
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run: |
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gh release create "${{ steps.get_version.outputs.VERSION }}" \
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--title "Release ${{ steps.get_version.outputs.VERSION }}" \
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--generate-notes \
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dist/*

‎.github/workflows/python-package.yml‎

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‎.github/workflows/test.yml‎

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name: Tests
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on:
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push:
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branches: [master]
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pull_request:
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branches: [master]
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permissions:
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contents: read
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jobs:
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test:
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name: Python ${{ matrix.python-version }} • ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.11", "3.12", "3.13"]
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os: [ubuntu-latest, windows-latest, macos-latest]
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0 # needed for setuptools_scm version detection
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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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cache: pip
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cache-dependency-path: pyproject.toml
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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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python -m pip install -e .[dev,test]
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- name: Test
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run: spin test

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