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Co-authored-by: Yossi Farjoun <[email protected]> Co-authored-by: Jeff Gentry <[email protected]> Co-authored-by: Tim Fennell <[email protected]> Co-authored-by: Nils Homer <[email protected]> Co-authored-by: Erin McAuley <[email protected]> Co-authored-by: Matt Stone <[email protected]>
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‎.github/CODEOWNERS

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# Default owners: Nils and Tim
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* @nh13 @tfenne

‎.github/workflows/publish.yml

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name: publish
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on:
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push:
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tags: '\d+.\d+.\d+'
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env:
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POETRY_VERSION: 1.8.2
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jobs:
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on-main-branch-check:
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runs-on: ubuntu-latest
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outputs:
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on_main: ${{ steps.contains_tag.outputs.retval }}
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- uses: rickstaa/action-contains-tag@v1
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id: contains_tag
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with:
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reference: "main"
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tag: "${{ github.ref_name }}"
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tests:
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name: tests
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needs: on-main-branch-check
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if: ${{ needs.on-main-branch-check.outputs.on_main == 'true' }}
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uses: "./.github/workflows/tests.yml"
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build-wheels:
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name: build wheels
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needs: tests
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uses: "./.github/workflows/wheels.yml"
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build-sdist:
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name: build source distribution
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needs: tests
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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submodules: true
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- uses: actions/setup-python@v5
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with:
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python-version: 3.12
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- name: Install poetry
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run: |
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python -m pip install --upgrade pip
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python -m pip install poetry==${{env.POETRY_VERSION}}
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- name: Configure poetry
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shell: bash
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run: poetry config virtualenvs.in-project true
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- name: Install dependencies
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run: poetry install --no-interaction --no-root --without=dev
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- name: Install project
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run: poetry install --no-interaction --without=dev
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- name: Build package
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run: poetry build --format=sdist
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- uses: actions/upload-artifact@v4
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with:
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name: prymer-sdist
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path: dist/*.tar.gz
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publish-to-pypi:
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runs-on: ubuntu-latest
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needs: [build-wheels, build-sdist]
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environment: pypi
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permissions:
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id-token: write
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steps:
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- uses: actions/download-artifact@v4
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with:
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path: packages
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pattern: 'prymer-*'
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merge-multiple: true
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- uses: pypa/gh-action-pypi-publish@release/v1
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with:
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packages-dir: packages/
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skip-existing: true
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verbose: true
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make-changelog:
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runs-on: ubuntu-latest
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needs: publish-to-pypi
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outputs:
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release_body: ${{ steps.git-cliff.outputs.content }}
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steps:
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- name: Checkout the Repository at the Tagged Commit
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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ref: ${{ github.ref_name }}
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- name: Generate a Changelog
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uses: orhun/git-cliff-action@v3
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id: git-cliff
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with:
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config: pyproject.toml
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args: --latest --verbose
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env:
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GITHUB_REPO: ${{ github.repository }}
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make-github-release:
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runs-on: ubuntu-latest
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environment: github
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permissions:
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contents: write
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pull-requests: read
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needs: make-changelog
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steps:
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- name: Create Draft Release
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id: create_release
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uses: softprops/action-gh-release@v2
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with:
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name: ${{ github.ref_name }}
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body: |
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${{ needs.draft-changelog.outputs.release_body }}
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draft: false
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prerelease: false

‎.github/workflows/tests.yml

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name: tests
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on:
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push:
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branches:
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- "**"
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tags:
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- "!**"
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workflow_call:
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env:
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POETRY_VERSION: 1.8.2
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jobs:
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Tests:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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PYTHON_VERSION: ["3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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- name: Checkout fulcrumgenomics/bwa
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uses: actions/checkout@v4
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with:
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repository: fulcrumgenomics/bwa
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ref: interactive_aln
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path: bwa
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fetch-depth: 0
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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: Set up miniconda
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniforge-variant: Mambaforge
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miniforge-version: latest
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channels: conda-forge,bioconda
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activate-environment: prymer
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environment-file: prymer.yml
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channel-priority: true
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auto-update-conda: true
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auto-activate-base: false
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python-version: ${{ matrix.PYTHON_VERSION }}
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- name: Install fulcrumgenomics/bwa
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shell: bash -l {0}
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run: |
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conda activate prymer
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pushd bwa
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make -j $(nproc)
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cp bwa ${CONDA_PREFIX}/bin
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popd
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- name: Configure poetry and check lock file
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shell: bash -l {0}
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run: |
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conda activate prymer
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poetry config virtualenvs.in-project false
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poetry check --lock
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- name: Poetry install
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shell: bash -l {0}
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run: |
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conda activate prymer
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poetry lock --no-update
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poetry install --with dev
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- name: Unit tests (with doctest and coverage)
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shell: bash -l {0}
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run: |
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conda activate prymer
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poetry run pytest --cov=prymer --cov-report=xml --cov-branch --doctest-plus --doctest-modules prymer tests
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- name: Upload coverage reports to Codecov
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uses: codecov/[email protected]
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Style checking
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shell: bash -l {0}
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run: |
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conda activate prymer
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poetry run ruff format --check
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- name: Run lint
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shell: bash -l {0}
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run: |
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conda activate prymer
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poetry run ruff check
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- name: Run mypy
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shell: bash -l {0}
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run: |
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conda activate prymer
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poetry run mypy
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- name: Run docs
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shell: bash -l {0}
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run: |
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conda activate prymer
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set -euo pipefail
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poetry run mkdocs build --strict

‎.github/workflows/wheels.yml

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name: build wheels
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on:
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pull_request:
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workflow_call:
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workflow_dispatch:
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jobs:
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build-wheels:
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name: Build wheels for ${{ matrix.python }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python: ["3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: "true"
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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: ${{ matrix.python }}
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- name: Build wheels
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run: pip wheel -w wheelhouse .
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- name: Upload wheels
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uses: actions/upload-artifact@v4
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with:
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name: prymer-wheels-${{ matrix.python }}
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path: ./wheelhouse/*.whl
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if-no-files-found: error

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