Update Dockerfile #114
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| name: tests | |
| on: | |
| push: | |
| branches: [ master, dev ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| lint: | |
| name: Lint Python code with flake8 | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| test: | |
| name: Run unit and integrative tests | |
| needs: [lint] | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ ubuntu-latest, macos-latest ] | |
| python-version: [3.6, 3.7, 3.8] | |
| exclude: | |
| - os: macos-latest | |
| python-version: 3.8 | |
| env: | |
| PY_COV_VERSION: "3.7" | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install pytest codecov tox | |
| if [ -f requirements.txt ]; then python -m pip install -r requirements.txt; fi | |
| - name: Install system dependencies | |
| if: ${{ matrix.os != 'macos-latest' }} | |
| run: | | |
| sudo apt update; | |
| sudo apt -y install gcc dpkg-dev zip git libz-dev default-jdk time time libssl-dev libsqlite3-dev \ | |
| autotools-dev libtool flex bison cmake automake autoconf \ | |
| python3-distutils python3-dev; | |
| sudo apt install python-six -y; | |
| - name: Setup Miniconda | |
| if: ${{ matrix.os != 'macos-latest' }} | |
| uses: conda-incubator/[email protected] | |
| with: | |
| auto-update-conda: true | |
| miniconda-version: 'latest' | |
| activate-environment: ts-test | |
| auto-activate-base: false | |
| python-version: ${{ matrix.python-version }} | |
| allow-softlinks: true | |
| environment-file: ci/environment-test.yml | |
| - name: Install dependencies not on conda | |
| shell: bash -l {0} | |
| if: ${{ matrix.os != 'macos-latest' }} | |
| run: | | |
| wget https://github.com/hallamlab/TreeSAPP/raw/master/treesapp/sub_binaries/BMGE.jar; | |
| sudo mv BMGE.jar /usr/local/bin/; | |
| wget -O od-seq.tar.gz http://www.bioinf.ucd.ie/download/od-seq.tar.gz; tar -xzf od-seq.tar.gz; | |
| ODSEQ_SOURCES="OD-Seq/AliReader.cpp OD-Seq/Bootstrap.cpp OD-Seq/DistCalc.cpp OD-Seq/DistMatReader.cpp | |
| OD-Seq/DistWriter.cpp OD-Seq/FastaWriter.cpp OD-Seq/IQR.cpp OD-Seq/ODseq.cpp OD-Seq/PairwiseAl.cpp | |
| OD-Seq/Protein.cpp OD-Seq/ResultWriter.cpp OD-Seq/runtimeargs.cpp OD-Seq/util.cpp"; | |
| sudo g++ -fopenmp -o /usr/local/bin/OD-seq $ODSEQ_SOURCES; | |
| rm od-seq.tar.gz; | |
| - name: Run tox | |
| if: ${{ matrix.os != 'macos-latest' }} | |
| shell: bash -l {0} | |
| run: | | |
| echo $PATH | |
| PYTHON_VERSION=$( echo ${{ matrix.python-version }} | sed 's/\.//g') | |
| tox -e coverage-py${PYTHON_VERSION}-ts | |
| if [ ${{ matrix.python-version }} == $PY_COV_VERSION ]; then tox -e coverage_report; fi | |
| - name: Upload coverage to Codecov | |
| if: ${{ matrix.python-version == env.PY_COV_VERSION }} && ${{ matrix.os == 'ubuntu-latest' }} | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| files: ./coverage.xml | |
| name: codecov-umbrella | |
| fail_ci_if_error: false | |
| path_to_write_report: ./codecov_report.txt | |
| verbose: true |