update docs and fix description in macs3 script #432
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: | |
| paths-ignore: | |
| - 'docs/**' | |
| 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 | |