Merge pull request #668 from macs3-project/feat/macs3/fragmentfile #709
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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/ |