maint: upgrade ndarray crate #163
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| # The starting point of this script are the links provided on the maturing doc: | |
| # * https://github.com/nanoporetech/fast-ctc-decode/blob/b226ea0f2b2f4f474eff47349703d57d2ea4801b/.github/workflows/publish.yml | |
| # * https://github.com/konstin/complex-manylinux-maturin-docker/blob/main/.github/workflows/build.yml | |
| # Description of the usage of virtual env: | |
| # * https://packaging.python.org/guides/installing-using-pip-and-virtual-environments/ | |
| name: test-cdshealpix | |
| on: [push, workflow_dispatch] | |
| # Jobs run in parallel, see https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#jobs | |
| # Github hosted runner are: see https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners | |
| jobs: | |
| test-linux64-wheels: | |
| # Containers run in Linux | |
| runs-on: ubuntu-latest | |
| # Docker Hub image that 'build-linux-wheels' executes in. | |
| # See https://github.com/pypa/manylinux for this particular container: | |
| # * CPython 3.8, 3.9, ... installed in /opt/python/<python tag>-<abi tag> | |
| container: quay.io/pypa/manylinux2014_x86_64 | |
| env: {ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true} # Allow using Node16 actions required for CentOS7 | |
| # We are now in CentOS 7 64 bits | |
| steps: | |
| - name: "Checkout the full project" | |
| uses: actions/checkout@v3 | |
| # We need to install rust in the docker image (else, cargo is already available in github action) | |
| - name: "Install Rust" | |
| run: | | |
| curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y | |
| # Build wheels for all pre-installed python version (in /opt/python/, see docker image comment) | |
| # installing first maturin and using maturin: https://github.com/PyO3/maturin#pypy | |
| # For secrets, see https://docs.github.com/en/actions/reference/encrypted-secrets | |
| - name: "Build and run tests" | |
| shell: bash | |
| run: | | |
| source $HOME/.cargo/env | |
| for PYBIN in /opt/python/cp*-cp3{8,9,10,11,12,13}/bin; do | |
| "${PYBIN}/pip" install virtualenv | |
| "${PYBIN}/virtualenv" cdshealpixenv | |
| source cdshealpixenv/bin/activate | |
| pip install --upgrade pip | |
| pip install maturin | |
| maturin build --release --compatibility manylinux2014 | |
| maturin develop --release | |
| pip install -r requirements-dev.txt | |
| python -m pytest -v | |
| deactivate | |
| rm -r cdshealpixenv | |
| done | |
| ## So far desactivated because too long to build astropy wheels | |
| #test-aarch64-wheels: | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # img: quay.io/pypa/manylinux2014_aarch64 | |
| # steps: | |
| # - name: Checkout | |
| # uses: actions/checkout@v4 | |
| # - name: "Set up QEMU" | |
| # id: qemu | |
| # uses: docker/setup-qemu-action@v1 | |
| # - name: Install dependencies | |
| # run: | | |
| # docker run --rm -v ${{ github.workspace }}:/ws:rw --workdir=/ws \ | |
| # ${{ env.img }} \ | |
| # bash -exc 'curl --proto "=https" --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- --default-host aarch64-unknown-linux-gnu -y && \ | |
| # source $HOME/.cargo/env && \ | |
| # for PYBIN in /opt/python/cp3[78910]*/bin; do | |
| # echo "Loop on PYBIN: $PYBIN" | |
| # "${PYBIN}/pip" install virtualenv | |
| # "${PYBIN}/virtualenv" cdshealpixenv | |
| # source cdshealpixenv/bin/activate | |
| # pip install --upgrade pip | |
| # pip install maturin | |
| # cargo build --release --config "net.git-fetch-with-cli = true" | |
| # maturin build --release --compatibility manylinux2014 --target aarch64-unknown-linux-gnu --config "net.git-fetch-with-cli = true" | |
| # maturin develop --release --target aarch64-unknown-linux-gnu --config "net.git-fetch-with-cli = true" | |
| # pip install -r requirements-dev.txt | |
| # cd python | |
| # python -m pytest -v -s cdshealpix/tests/test_nested_healpix.py | |
| # python -m pytest -v -s cdshealpix/tests/test_ring_healpix.py | |
| # cd .. | |
| # pip freeze > requirements-uninstall.txt | |
| # pip uninstall -r requirements-uninstall.txt -y | |
| # deactivate | |
| # rm -r cdshealpixenv/ | |
| # done' | |
| test-macos-wheels: | |
| runs-on: macos-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13'] | |
| steps: | |
| # Checkout the project | |
| - name: "Checkout branch" | |
| uses: actions/checkout@v4 | |
| # Test Rust code | |
| #- name: Run rust wrapper tests | |
| # run: cargo test --verbose -- --nocapture | |
| # Set up python, see https://docs.github.com/en/actions/guides/building-and-testing-python | |
| - name: "Set up Python ${{ matrix.python-version }} on MacOS" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| # Test python code | |
| - name: "Build and test wheel for Python ${{ matrix.python-version }} on MacOS" | |
| run: | | |
| # Install, create and activate a python virtualenv | |
| rustup target add x86_64-apple-darwin | |
| pip install virtualenv | |
| virtualenv cdshealpixenv | |
| source cdshealpixenv/bin/activate | |
| # Install and use maturin | |
| pip install --upgrade pip | |
| pip install maturin | |
| maturin -V | |
| maturin build --release --target universal2-apple-darwin | |
| maturin develop --release | |
| # Install dependencies | |
| pip install -r requirements-dev.txt | |
| # Run tests | |
| python -m pytest -v | |
| # Clean | |
| #pip freeze > requirements-uninstall.txt | |
| #pip uninstall -r requirements-uninstall.txt -y | |
| deactivate | |
| #rm -r cdshealpixenv/ | |
| test-windows-wheels: | |
| runs-on: windows-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13'] | |
| steps: | |
| # Checkout the project | |
| - name: "Checkout branch" | |
| uses: actions/checkout@v4 | |
| # Test Rust code | |
| #- name: Run rust wrapper tests | |
| # run: cargo test --verbose -- --nocapture | |
| # Set up python, see https://docs.github.com/en/actions/guides/building-and-testing-python | |
| - name: "Set up Python ${{ matrix.python-version }} on Windows" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| # Test python code | |
| - name: "Build and test wheel for Python ${{ matrix.python-version }} on Windows" | |
| run: | | |
| # Install, create and activate a python virtualenv | |
| # See: https://mothergeo-py.readthedocs.io/en/latest/development/how-to/venv-win.html | |
| pip install virtualenv | |
| virtualenv cdshealpixenv | |
| .\cdshealpixenv\Scripts\activate | |
| pip install --upgrade pip | |
| # Install and use maturin | |
| pip install maturin | |
| maturin -V | |
| maturin develop --release | |
| # Install dependencies | |
| pip install -r requirements-dev.txt | |
| # Run tests | |
| python -m pytest -v | |
| deactivate | |
| # Build the doc and run the tests in the doc (only for python 3.12 on ubuntu) | |
| test-doc: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: "Checkout branch" | |
| uses: actions/checkout@v4 | |
| - name: "Set up Python 3.12 on Ubuntu" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.12' | |
| - name: "Build and test doc" | |
| run: | | |
| # Install virtualenv | |
| pip install virtualenv | |
| # Create and activate a new virtualenv | |
| virtualenv cdshealpixenv | |
| source cdshealpixenv/bin/activate | |
| # Install maturin | |
| pip install --upgrade pip | |
| pip install maturin | |
| sudo apt-get install pandoc | |
| maturin -V | |
| # Build and install cdshealpix | |
| maturin develop --release | |
| # Install dependencies needed to build the docs | |
| pip install -r requirements-doc.txt | |
| # Compile the docs and run the test examples | |
| cd ./docs | |
| # * Generate the HTML files | |
| make html | |
| # * Run the API test examples | |
| make doctest | |
| cd .. | |
| # Switch of the virtualenv | |
| deactivate | |