Initial commit

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]>

.github/CODEOWNERS

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

.github/workflows/publish.yml

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

.github/workflows/tests.yml

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+name: tests
+
+on:
+  push:
+    branches:
+      - "**"
+    tags:
+      - "!**"
+  workflow_call:
+
+env:
+  POETRY_VERSION: 1.8.2
+
+jobs:
+  Tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        PYTHON_VERSION: ["3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Checkout fulcrumgenomics/bwa
+        uses: actions/checkout@v4
+        with:
+          repository: fulcrumgenomics/bwa
+          ref: interactive_aln
+          path: bwa
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.PYTHON_VERSION }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.PYTHON_VERSION }}
+
+      - name: Set up miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          channels: conda-forge,bioconda
+          activate-environment: prymer
+          environment-file: prymer.yml
+          channel-priority: true
+          auto-update-conda: true
+          auto-activate-base: false
+          python-version: ${{ matrix.PYTHON_VERSION }}
+
+      - name: Install fulcrumgenomics/bwa
+        shell: bash -l {0}
+        run: |
+          conda activate prymer
+          pushd bwa
+          make -j $(nproc)
+          cp bwa ${CONDA_PREFIX}/bin
+          popd
+
+      - name: Configure poetry and check lock file
+        shell: bash -l {0}
+        run: |
+          conda activate prymer
+          poetry config virtualenvs.in-project false
+          poetry check --lock
+
+      - name: Poetry install
+        shell: bash -l {0}
+        run: |
+          conda activate prymer
+          poetry lock --no-update
+          poetry install --with dev
+
+      - name: Unit tests (with doctest and coverage)
+        shell: bash -l {0}
+        run: |
+          conda activate prymer
+          poetry run pytest --cov=prymer --cov-report=xml --cov-branch --doctest-plus --doctest-modules prymer tests
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Style checking
+        shell: bash -l {0}
+        run: |
+          conda activate prymer
+          poetry run ruff format --check
+
+      - name: Run lint
+        shell: bash -l {0}
+        run: |
+          conda activate prymer
+          poetry run ruff check
+
+      - name: Run mypy
+        shell: bash -l {0}
+        run: |
+          conda activate prymer
+          poetry run mypy
+
+      - name: Run docs
+        shell: bash -l {0}
+        run: |
+          conda activate prymer
+          set -euo pipefail
+          poetry run mkdocs build --strict

.github/workflows/wheels.yml

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+name: build wheels
+
+on:
+  pull_request:
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  build-wheels:
+    name: Build wheels for ${{ matrix.python }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: ["3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: "true"
+
+      - name: Set up Python ${{ matrix.PYTHON_VERSION }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Build wheels
+        run: pip wheel -w wheelhouse .
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: prymer-wheels-${{ matrix.python }}
+          path: ./wheelhouse/*.whl
+          if-no-files-found: error