try paths-ignore #420
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | ||
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | ||
| name: MACS3 CI non x64 | ||
| on: [push, pull_request] | ||
| paths-ignore: | ||
| - 'docs/**' | ||
| jobs: | ||
| build_job: | ||
| runs-on: ubuntu-20.04 | ||
| name: Build on ${{ matrix.arch }} | ||
| strategy: | ||
| matrix: | ||
| include: | ||
| - arch: aarch64 | ||
| distro: bullseye | ||
| - arch: armv7 | ||
| distro: bullseye | ||
| - arch: ppc64le | ||
| distro: bullseye | ||
| - arch: s390x | ||
| distro: bullseye | ||
| steps: | ||
| - name: Checkout MACS | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| submodules: 'true' | ||
| - name: Set up arch and run (bullseye Python 3.9) | ||
| uses: uraimo/run-on-arch-action@v2 | ||
| id: build | ||
| with: | ||
| arch: ${{ matrix.arch }} | ||
| distro: ${{ matrix.distro }} | ||
| githubToken: ${{ github.token }} | ||
| # The shell to run commands with in the container | ||
| shell: /bin/bash | ||
| # Mount the current working directory (with checked-out codes) as /MACS3 in the container | ||
| dockerRunArgs: | | ||
| -v "${PWD}:/MACS3" -u macs3 | ||
| # Create an artifacts directory on runner | ||
| # Install some dependencies in the container. This speeds up builds if | ||
| # you are also using githubToken. Any dependencies installed here will | ||
| # be part of the container image that gets cached, so subsequent | ||
| # builds don't have to re-install them. The image layer is cached | ||
| # publicly in your project's package repository, so it is vital that | ||
| # no secrets are present in the container state or logs. | ||
| install: | | ||
| useradd -m macs3 | ||
| mkdir -p /MACS3 | ||
| chown -R macs3:macs3 /MACS3 | ||
| # install dependencies | ||
| apt-get update -qq -y | ||
| apt-get install apt-utils | ||
| apt-get install -yq libblas3 liblapack3 libblas-dev liblapack-dev | ||
| # we rely on Debian/Linux python packages for numpy/scipy/sklearn | ||
| apt-get install -yq python3 python3-pip python3-virtualenv python3-wheel python3-numpy python3-scipy python3-sklearn cython3 | ||
| apt-get install -yq procps zlib1g zlib1g-dev gfortran | ||
| run: | | ||
| echo `uname -a` | ||
| cd /home/macs3/ | ||
| # let's create virtualenv | ||
| virtualenv --system-site-packages macsenv | ||
| source macsenv/bin/activate | ||
| # copy source code over | ||
| cp -r /MACS3 . | ||
| cd MACS3 | ||
| # let's make sure this file is gone... | ||
| rm -f no-global-site-packages.txt | ||
| # upgrade pip | ||
| pip install --progress-bar off --upgrade pip | ||
| # install dependencies that are not in Debian/Linux | ||
| pip install --upgrade-strategy only-if-needed --progress-bar off Cython | ||
| pip install --upgrade-strategy only-if-needed --progress-bar off hmmlearn | ||
| pip install --upgrade-strategy only-if-needed --progress-bar off cykhash | ||
| pip install --upgrade --progress-bar off pytest | ||
| # install MACS3; only-if-needed won't try to upgrade Debian/Linux python3 libs | ||
| pip install --upgrade-strategy only-if-needed --no-build-isolation --progress-bar off . | ||
| # run test | ||
| pytest --runxfail && cd test && ./cmdlinetest-nohmmratac macs3 | ||
