feat : reduce htslib dependency #491
Workflow file for this run
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - master | |
| paths: | |
| - "**.py" | |
| - "**/Dockerfile" | |
| - ".github/workflows/*.yml" | |
| - poetry.lock | |
| - pyproject.toml | |
| pull_request: | |
| branches: | |
| - main | |
| - master | |
| paths: | |
| - "**.py" | |
| - "**/Dockerfile" | |
| - ".github/workflows/*.yml" | |
| - poetry.lock | |
| - pyproject.toml | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| tests: | |
| name: ${{ matrix.session }} ${{ matrix.python }} / ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - { python: "3.10", os: "ubuntu-latest", session: "pre-commit" } | |
| - { python: "3.10", os: "ubuntu-latest", session: "safety" } | |
| - { python: "3.10", os: "ubuntu-latest", session: "mypy" } | |
| - { python: "3.9", os: "ubuntu-latest", session: "mypy" } | |
| - { python: "3.10", os: "ubuntu-latest", session: "docs-build" } | |
| - { python: "3.11", os: "ubuntu-latest", session: "tests" } | |
| - { python: "3.10", os: "ubuntu-latest", session: "tests" } | |
| - { python: "3.9", os: "ubuntu-latest", session: "tests" } | |
| - { python: "3.11", os: "macos-latest", session: "tests" } | |
| - { python: "3.10", os: "macos-latest", session: "tests" } | |
| - { python: "3.9", os: "macos-latest", session: "tests" } | |
| env: | |
| NOXSESSION: ${{ matrix.session }} | |
| FORCE_COLOR: "1" | |
| PRE_COMMIT_COLOR: "always" | |
| steps: | |
| - name: Check out the repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: Cache pip packages | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ matrix.python }}-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip-${{ matrix.python }}- | |
| ${{ runner.os }}-pip- | |
| - name: Cache Poetry virtual environment | |
| uses: actions/cache@v3 | |
| with: | |
| path: .venv | |
| key: ${{ runner.os }}-poetry-${{ matrix.python }}-${{ hashFiles('pyproject.toml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-poetry-${{ matrix.python }}- | |
| ${{ runner.os }}-poetry- | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Upgrade pip | |
| run: | | |
| pip install --constraint=.github/workflows/constraints.txt pip | |
| pip --version | |
| - name: Upgrade pip in virtual environments | |
| shell: python | |
| run: | | |
| import os | |
| import pip | |
| with open(os.environ["GITHUB_ENV"], mode="a") as io: | |
| print(f"VIRTUALENV_PIP={pip.__version__}", file=io) | |
| - name: Install Dependencies | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -q --no-install-recommends --no-install-suggests libhts-dev libssl-dev | |
| - name: Cache macOS dependencies | |
| if: matrix.os == 'macos-latest' | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/brew-cache | |
| key: macos-brew-${{ hashFiles('**/Dockerfile') }} | |
| restore-keys: | | |
| macos-brew- | |
| - name: Configure Homebrew | |
| if: matrix.os == 'macos-latest' | |
| uses: Homebrew/actions/setup-homebrew@master | |
| - name: Install Dependencies | |
| if: matrix.os == 'macos-latest' | |
| env: | |
| HOMEBREW_NO_AUTO_UPDATE: 1 | |
| HOMEBREW_NO_INSTALL_CLEANUP: 1 # Do not run brew cleanup automatically. | |
| HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: 1 # Do not automatically update packages. | |
| run: | | |
| brew install htslib | |
| brew install openssl@3 | |
| ln -sf $(brew --prefix openssl)/include/openssl /usr/local/include/openssl | |
| ln -sf $(brew --prefix openssl)/lib/*a /usr/local/lib/ | |
| ln -sf $(brew --prefix openssl)/lib/*dylib /usr/local/lib/ | |
| - name: Install Poetry | |
| run: | | |
| pipx install --pip-args=--constraint=.github/workflows/constraints.txt poetry | |
| poetry --version | |
| - name: debug | |
| if: matrix.os == 'macos-latest' | |
| run: | | |
| which python | |
| - name: Install Nox | |
| run: | | |
| pipx install --pip-args=--constraint=.github/workflows/constraints.txt nox | |
| pipx inject --pip-args=--constraint=.github/workflows/constraints.txt nox nox-poetry | |
| nox --version | |
| - name: Compute pre-commit cache key | |
| if: matrix.session == 'pre-commit' | |
| id: pre-commit-cache | |
| shell: python | |
| run: | | |
| import hashlib | |
| import sys | |
| python = "py{}.{}".format(*sys.version_info[:2]) | |
| payload = sys.version.encode() + sys.executable.encode() | |
| digest = hashlib.sha256(payload).hexdigest() | |
| result = "${{ runner.os }}-{}-{}-pre-commit".format(python, digest[:8]) | |
| print("::set-output name=result::{}".format(result)) | |
| - name: Restore pre-commit cache | |
| uses: actions/cache@v3 | |
| if: matrix.session == 'pre-commit' | |
| with: | |
| path: ~/.cache/pre-commit | |
| key: ${{ steps.pre-commit-cache.outputs.result }}-${{ hashFiles('.pre-commit-config.yaml') }} | |
| restore-keys: | | |
| ${{ steps.pre-commit-cache.outputs.result }}- | |
| - name: Run Nox | |
| run: | | |
| nox --force-color --python=${{ matrix.python }} | |
| - name: Upload coverage data | |
| if: always() && matrix.session == 'tests' | |
| uses: "actions/upload-artifact@v3" | |
| with: | |
| name: coverage-data | |
| path: ".coverage.*" | |
| - name: Upload documentation | |
| if: matrix.session == 'docs-build' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: docs | |
| path: docs/_build | |
| coverage: | |
| runs-on: ubuntu-latest | |
| needs: tests | |
| steps: | |
| - name: Check out the repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Upgrade pip | |
| run: | | |
| pip install --constraint=.github/workflows/constraints.txt pip | |
| pip --version | |
| - name: Install Poetry | |
| run: | | |
| pipx install --pip-args=--constraint=.github/workflows/constraints.txt poetry | |
| poetry --version | |
| - name: Install Nox | |
| run: | | |
| pipx install --pip-args=--constraint=.github/workflows/constraints.txt nox | |
| pipx inject --pip-args=--constraint=.github/workflows/constraints.txt nox nox-poetry | |
| nox --version | |
| - name: Download coverage data | |
| uses: actions/download-artifact@v3.0.2 | |
| with: | |
| name: coverage-data | |
| - name: Combine coverage data and display human readable report | |
| run: | | |
| nox --force-color --session=coverage -v | |
| - name: Create coverage report | |
| run: | | |
| nox --force-color --session=coverage -- xml | |
| - name: Upload coverage report | |
| uses: codecov/codecov-action@v3 |