test CI: final2 #25
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| # This is a basic workflow to help you get started with Actions | ||
| name: CI-Linux | ||
| # Controls when the action will run. Triggers the workflow on push or pull request | ||
| # events but only for the master branch | ||
| on: | ||
| push: | ||
| branches: [ master ] | ||
| pull_request: | ||
| branches: [ master ] | ||
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | ||
| jobs: | ||
| # This workflow contains a single job called "build" | ||
| build: | ||
| # The type of runner that the job will run on | ||
| runs-on: ubuntu-latest | ||
| # runs-on: ubuntu-22.04 | ||
| # Steps represent a sequence of tasks that will be executed as part of the job | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| # set up conda | ||
| - uses: s-weigand/[email protected] | ||
| - name: Install dependencies | ||
| # with: | ||
| # conda-channels: bioconda | ||
| # install dependencies | ||
| run: conda env create -f OrthoIndex.yaml | ||
| - name: Activate | ||
| run: | | ||
| conda init bash | ||
| conda init | ||
| source /home/runner/.bashrc | ||
| cat ~/.bashrc | ||
| conda env list | ||
| conda --version | ||
| # - run: export PATH=/usr/share/miniconda/envs/OrthoIndex/bin:$PATH | ||
| source /usr/share//miniconda/etc/profile.d/conda.sh | ||
| ls -al /usr/share/miniconda/envs/OrthoIndex/bin | ||
| which python | ||
| # - run: conda activate OrthoIndex | ||
| # - run: which python | ||
| - name: Install OrthoIndex | ||
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | ||
| run: export PATH=/usr/share/miniconda/envs/OrthoIndex/bin:$PATH && python setup.py install | ||
| # run: python setup.py install | ||
| - name: Test SOI | ||
| # run test | ||
| run: | | ||
| ls -al | ||
| pwd | ||
| cd example_data && export PATH=/usr/share/miniconda/envs/OrthoIndex/bin:$PATH && bash example.sh | ||
| # - run: cd example_data && bash example.sh | ||
