change structure of initiating conda bash and sourcing bash in workfl… #73
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| # This workflow will install Python dependencies, run tests with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python package build | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| workflow_dispatch: | |
| branches: [ main ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.7, 3.8, 3.9] | |
| # steps: | |
| # - uses: actions/checkout@v2 | |
| # - uses: conda-incubator/setup-miniconda@v2 | |
| # with: | |
| # python-version: 3.9 | |
| # - name: Set up Python ${{ matrix.python-version }} | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: ${{ matrix.python-version }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: s-weigand/setup-conda@v1 | |
| with: | |
| activate-conda: false | |
| - run: conda create -n myenv python=3.9 | |
| - run: conda --version | |
| - run: which python | |
| - name: Show working dir | |
| shell: bash | |
| run: ls | |
| - name: Add reademption bin to PATH | |
| shell: bash | |
| run: echo "bin" >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest | |
| python -m pip install matplotlib | |
| python -m pip install biopython | |
| python -m pip install pysam | |
| python -m pip install pandas | |
| python -m pip install seaborn | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Update | |
| shell: bash | |
| run: sudo apt-get update | |
| - name: init bash | |
| shell: bash | |
| run: conda init bash | |
| - name: source bash | |
| shell: bash | |
| run: source /home/runner/.bashrc | |
| - name: activate conda env | |
| shell: bash | |
| run: conda activate myenv | |
| - name: Install packages | |
| shell: bash | |
| run: sudo apt-get install -y python3 python3-setuptools python3-pip cython3 zlib1g-dev make libncurses5-dev libxml2-dev libcurl4-openssl-dev r-base | |
| - name: Conda info | |
| shell: bash | |
| run: conda info | |
| - name: Conda install segemehl | |
| shell: bash | |
| run: conda install -c bioconda segemehl=0.3.4 | |
| - name: Conda list | |
| shell: bash | |
| run: conda list | |
| - name: List conda bin | |
| run: ls $CONDA/bin | |
| - name: Add conda bin (segemehl.x) to PATH | |
| shell: bash | |
| run: echo "$CONDA/bin" >> $GITHUB_PATH | |
| - name: Install DESEQ2 | |
| shell: bash | |
| run: sudo echo "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager') ; BiocManager::install('DESeq2'); install.packages('gplots')" | sudo R --no-save | |
| - name: Test with pytest | |
| run: | | |
| pytest |