Update apt sources in Dockerfile #80
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| name: Install test SINGE | |
| on: [push, pull_request] | |
| jobs: | |
| # Builds and tests the SINGE Docker image, tests SINGE in a Docker container | |
| docker: | |
| name: Install test Docker | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| # Pull from Docker Hub to use the cache | |
| # https://medium.com/mobileforgood/coding-tips-patterns-for-continuous-integration-with-docker-on-travis-ci-9cedb8348a62 | |
| # https://github.com/docker/build-push-action/issues/7 | |
| - name: Pull Docker image | |
| run: docker pull agitter/singe:tmp | |
| # Docker image build fails | |
| # The repository 'http://deb.debian.org/debian stretch Release' does no longer have a Release file. | |
| - name: Build Docker image | |
| uses: docker/build-push-action@v1 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| path: . | |
| dockerfile: docker/Dockerfile | |
| repository: agitter/singe | |
| tags: tmp | |
| cache_froms: agitter/singe:tmp | |
| add_git_labels: true | |
| # Only push when running on the master branch | |
| push: ${{ github.ref == 'refs/heads/master' }} | |
| - name: Test SINGE | |
| run: | | |
| # Store the md5sums of the tracked source files before running tests in the Docker image | |
| # The Docker image does not have git installed | |
| md5sum $(git ls-tree -r HEAD --name-only | grep '.*\.m$') > current_code.md5 | |
| # Run SINGE tests in the built Docker image | |
| # The conda environment should be activated before running the bash script | |
| # See https://github.com/conda/conda/issues/7980 | |
| docker run -v $(pwd):/SINGE -w /SINGE --entrypoint "/bin/bash" agitter/singe:tmp -c "source ~/.bashrc; conda activate singe-test; tests/docker_test.sh" | |
| # Proof-of-concept of running SINGE in a high-throughput style | |
| # Can be moved to run in a parallel job | |
| bash tests/high_throughput_test.sh | |
| # Test standalone SINGE run through Docker | |
| bash tests/standalone_test.sh | |
| # Test standalone SINGE on a branching dataset | |
| bash tests/standalone_branching_test.sh | |
| # Test standalone SINGE on a dataset with regulator indices | |
| bash tests/standalone_regix_test.sh | |
| # Confirm the hyperparameter generation script works | |
| cd scripts | |
| bash generate_hyperparameters.sh | |
| # Installs MATLAB runtime R2020a and tests compiled SINGE for macOS on test data | |
| macos: | |
| name: Install test macOS | |
| # See available macOS software https://github.com/actions/virtual-environments/blob/master/images/macos/macos-10.15-Readme.md | |
| runs-on: macos-latest | |
| env: | |
| SINGE_VERSION: v0.5.1 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Install conda environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: singe-test | |
| environment-file: tests/environment.yml | |
| auto-activate-base: false | |
| miniconda-version: 'latest' | |
| - name: Cache MATLAB runtime installer | |
| id: cache-installer | |
| uses: actions/cache@v1 | |
| with: | |
| path: installer | |
| key: ${{ runner.os }}-matlab-R2020a-installer | |
| - name: Download MATLAB runtime installer | |
| if: steps.cache-installer.outputs.cache-hit != 'true' | |
| run: wget --quiet --directory-prefix=installer http://ssd.mathworks.com/supportfiles/downloads/R2020a/Release/2/deployment_files/installer/complete/maci64/MATLAB_Runtime_R2020a_Update_2_maci64.dmg.zip | |
| - name: Install MATLAB runtime | |
| run: | | |
| unzip -d . -q installer/MATLAB_Runtime_R2020a_Update_2_maci64.dmg.zip | |
| hdiutil mount MATLAB_Runtime_R2020a_Update_2_maci64.dmg | |
| cp -R /Volumes/MATLAB_Runtime_R2020a_Update_2_maci64 . | |
| hdiutil unmount /Volumes/MATLAB_Runtime_R2020a_Update_2_maci64 | |
| sudo ./MATLAB_Runtime_R2020a_Update_2_maci64/InstallForMacOSX.app/Contents/MacOS/InstallForMacOSX -mode silent -agreeToLicense yes | |
| MATLAB_RUNTIME_PATH=/Applications/MATLAB/MATLAB_Runtime/v98 | |
| echo "MATLAB_RUNTIME_PATH=$MATLAB_RUNTIME_PATH" >> $GITHUB_ENV | |
| echo "DYLD_LIBRARY_PATH=$MATLAB_RUNTIME_PATH/runtime/maci64:$MATLAB_RUNTIME_PATH/sys/os/maci64:$MATLAB_RUNTIME_PATH/bin/maci64" >> $GITHUB_ENV | |
| echo "$MATLAB_RUNTIME_PATH/bin/maci64" >> $GITHUB_PATH | |
| - name: Download SINGE | |
| run: | | |
| wget --quiet https://github.com/gitter-lab/SINGE/releases/download/$SINGE_VERSION/SINGE_mac.tgz | |
| tar -xf SINGE_mac.tgz | |
| - name: Run and test SINGE | |
| shell: bash -l {0} | |
| run: | | |
| bash SINGE.sh $MATLAB_RUNTIME_PATH standalone data1/X_SCODE_data.mat data1/gene_list.mat Output tests/example_hyperparameters.txt | |
| ls -l Output | |
| bash tests/compare_example_output.sh Output tests/reference/latest 1e-02 1e-02 |