Merge pull request #678 from kaizhang/master #712
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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/**' | |
| - '**.md' | |
| - 'ChangeLog' | |
| - '.github/workflows/**' | |
| - '!.github/workflows/build-and-test-MACS3-non-x64.yml' | |
| pull_request: | |
| paths-ignore: | |
| - 'docs/**' | |
| - '**.md' | |
| - 'ChangeLog' | |
| - '.github/workflows/**' | |
| - '!.github/workflows/build-and-test-MACS3-non-x64.yml' | |
| jobs: | |
| build_job: | |
| runs-on: ubuntu-22.04 | |
| name: Build on ${{ matrix.arch }} with Python 3.10 | |
| strategy: | |
| matrix: | |
| include: | |
| - arch: aarch64 | |
| steps: | |
| - name: Checkout MACS | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: 'true' | |
| - name: Set up arch and run | |
| uses: uraimo/run-on-arch-action@v2 | |
| id: build | |
| with: | |
| arch: ${{ matrix.arch }} | |
| distro: ubuntu22.04 | |
| githubToken: ${{ github.token }} | |
| # The shell to run commands with in the container | |
| shell: /bin/bash | |
| # Create an artifacts directory | |
| setup: | | |
| chmod a+rw ${PWD} | |
| # Mount the current working directory (with checked-out codes) as /MACS3 in the container | |
| dockerRunArgs: | | |
| -v "${PWD}:/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: | | |
| # install dependencies | |
| apt-get update -qq -y | |
| # We install the dependencies for compiling and installing | |
| # the python libraries that MACS3 depends on. | |
| apt-get install -yq apt-utils bc libblas3 liblapack3 libblas-dev liblapack-dev libopenblas-dev pkg-config python3 python3-pip python3-venv python3-wheel meson ninja-build cmake procps zlib1g zlib1g-dev gfortran | |
| run: | | |
| echo `uname -a` | |
| cd ~ | |
| # let's create virtualenv | |
| python3 -m venv macsenv | |
| # activate macsenv | |
| source macsenv/bin/activate | |
| # cd to source code directory | |
| cd /MACS3 | |
| # pip will be upgraded | |
| python3 -m pip install --upgrade pip | |
| # install dependencies | |
| if [ -f requirements.txt ]; then | |
| python3 -m pip install -r requirements.txt; | |
| fi | |
| # install MACS3 | |
| python3 -m pip install . | |
| # output versions of installed libraries | |
| python3 -m pip freeze | |
| # run test | |
| pytest --runxfail && cd test && ./cmdlinetest macs3 | |
| - name: Archive cmdlinetest results | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: cmdlinetest-hmmratac-results-${{ matrix.arch }} | |
| path: temp/macs3_run_hmmratac/ |