Initial implementation of bwapy (#1)

* feat: initial implementation of python bindings for `bwa aln`, `bwa mem`, and `bwa index`

.github/CODEOWNERS

@@ -0,0 +1 @@
+*  @nh13

.github/workflows/ci.yml

@@ -0,0 +1,89 @@
+name: CI
+
+on: push
+env:
+  POETRY_VERSION: 1.8
+
+jobs:
+  testing:
+    runs-on: ubuntu-24.04
+    strategy:
+      matrix:
+        PYTHON_VERSION: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: 'true'
+    - name: Set up Python ${{matrix.PYTHON_VERSION}}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{matrix.PYTHON_VERSION}}
+
+    - name: Get full Python version
+      id: full-python-version
+      shell: bash
+      run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+
+    - name: Install poetry
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        pip install poetry==${{env.POETRY_VERSION}}
+
+    - name: Configure poetry
+      shell: bash
+      run: poetry config virtualenvs.in-project true
+
+    - name: Set up cache
+      uses: actions/cache@v2
+      id: cache
+      with:
+        path: .venv
+        key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}
+
+    - name: Ensure cache is healthy
+      if: steps.cache.outputs.cache-hit == 'true'
+      shell: bash
+      run: poetry run pip --version >/dev/null 2>&1 || rm -rf .venv
+
+    - name: Check that the lock file is up to date
+      shell: bash
+      run: |
+        poetry lock --check
+
+    - name: Install deps
+      shell: bash
+      run: |
+        poetry install
+
+    - name: Style checking
+      shell: bash
+      run: |
+        poetry run ruff format --check pybwa tests
+
+    - name: Run lint
+      shell: bash
+      run: |
+        poetry run ruff check pybwa tests
+
+    - name: Run mypy
+      shell: bash
+      run: |
+        poetry run mypy pybwa tests --config=pyproject.toml
+
+    - name: Run pytest
+      shell: bash
+      run: |
+        poetry run python -m pytest --cov=pybwa --cov-report=xml --cov-branch 
+
+    - name: Run docs
+      shell: bash
+      run: |
+        set -euo pipefail
+        cd docs
+        poetry run make html
+
+    - name: Upload code coverage
+      uses: codecov/[email protected]
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/publish_pybwa.yml

@@ -0,0 +1,129 @@
+name: publish pybwa
+
+on:
+  push:
+    tags: '\d+.\d+.\d+'
+
+env:
+  POETRY_VERSION: 1.8.2
+
+jobs:
+  on-main-branch-check:
+    runs-on: ubuntu-24.04
+    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: ${{ needs.on-main-branch-check.outputs.on_main == 'true' }}
+    uses: "./.github/workflows/tests.yml"
+
+  build-wheels:
+    name: build wheels
+    needs: tests
+    uses: "./.github/workflows/wheels.yml"
+
+  build-sdist:
+    name: build source distribution
+    needs: tests
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: true
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Install poetry
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install poetry==${{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: pybwa-sdist
+          path: dist/*.tar.gz
+
+  publish-to-pypi:
+    runs-on: ubuntu-24.04
+    needs: [build-wheels, build-sdist]
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: packages
+          pattern: 'pybwa-*'
+          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-24.04
+    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-24.04
+    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.make-changelog.outputs.release_body }}
+          draft: false
+          prerelease: false

.github/workflows/readthedocs.yaml

@@ -0,0 +1,16 @@
+name: readthedocs/actions
+on:
+  pull_request_target:
+    types:
+      - opened
+
+permissions:
+  pull-requests: write
+
+jobs:
+  documentation-links:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: readthedocs/actions/preview@v1
+        with:
+          project-slug: "pybwa"

.github/workflows/wheels.yml

@@ -0,0 +1,34 @@
+name: build wheels
+
+on:
+  pull_request:
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  build-wheels:
+    name: Build wheels for ${{ matrix.python }}
+    runs-on: ubuntu-24.04
+    strategy:
+      matrix:
+        python: ["3.9", "3.10", "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: ${{ matrix.python }}
+
+      - name: Build wheels
+        run: pip wheel --no-deps -w wheelhouse .
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: pybwa-wheels-${{ matrix.python }}
+          path: ./wheelhouse/pybwa*.whl
+          if-no-files-found: error

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "bwa"]
+	path = bwa
+	url = https://github.com/lh3/bwa.git

.readthedocs.yml

@@ -0,0 +1,20 @@
+version: 2
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.9"
+  jobs:
+    pre_install:
+      - pip install poetry==1.8.3
+      - poetry config virtualenvs.create false
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install
+submodules:
+  include: all
+sphinx:
+  configuration: docs/conf.py
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

README.md

@@ -1 +1,29 @@
-# bwapy
+[![Language][language-badge]][language-link]
+[![Code Style][code-style-badge]][code-style-link]
+[![Type Checked][type-checking-badge]][type-checking-link]
+[![PEP8][pep-8-badge]][pep-8-link]
+[![Code Coverage][code-coverage-badge]][code-coverage-link]
+[![License][license-badge]][license-link]
+
+
+[language-badge]:       http://img.shields.io/badge/language-python-brightgreen.svg
+[language-link]:        http://www.python.org/
+[code-style-badge]:     https://img.shields.io/badge/code%20style-black-000000.svg
+[code-style-link]:      https://black.readthedocs.io/en/stable/
+[type-checking-badge]:  http://www.mypy-lang.org/static/mypy_badge.svg
+[type-checking-link]:   http://mypy-lang.org/
+[pep-8-badge]:          https://img.shields.io/badge/code%20style-pep8-brightgreen.svg
+[pep-8-link]:           https://www.python.org/dev/peps/pep-0008/
+[code-coverage-badge]:  https://codecov.io/gh/fulcrumgenomics/pybwa/branch/main/graph/badge.svg
+[code-coverage-link]:   https://codecov.io/gh/fulcrumgenomics/pybwa
+[license-badge]:        http://img.shields.io/badge/license-MIT-blue.svg
+[license-link]:         https://github.com/fulcrumgenomics/pybwa/blob/main/LICENSE
+
+# pybwa
+
+Python language bindings for [bwa][bwa-link].
+
+See documentation on [pybwa.readthedocs.org][rtd-link].
+
+[rtd-link]: http://pybwa.readthedocs.org/en/stable
+[bwa-link]: https://github.com/lh3/bwa