CI #790
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| name: CI | |
| on: | |
| push: | |
| branches: ['**'] | |
| schedule: | |
| # Triggers the workflow 9:00 PM every sunday | |
| - cron: "0 21 * * 0" | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: psf/black@stable | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 | |
| pip install -e . | |
| - 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: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| model: ["Basset,HAL", "DeepSEA/variantEffects,Optimus_5Prime", "labranchor,SiSp", | |
| "MaxEntScan/5prime,pwm_HOCOMOCO/human/AHR", "FactorNet/FOXA2/onePeak_Unique35_DGF,Basenji", | |
| "CleTimer/customBP,DeepBind/Arabidopsis_thaliana/RBP/D00283.001_RNAcompete_At_0284", | |
| "lsgkm-SVM/Chip/OpenChrom/Cmyc/K562,rbp_eclip/AARS", "CpGenie/A549_ENCSR000DDI,Divergent421,DeepCpG_DNA/Hou2016_HepG2_dna", | |
| "MPRA-DragoNN/DeepFactorizedModel", "extended_coda", "MMSplice/deltaLogitPSI", | |
| "MMSplice/mtsplice", "DeepMEL/DeepMEL", "Framepool", "KipoiSplice/4", "deepTarget", | |
| "AttentiveChrome/E003", "BPNet-OSKN", "SeqVec/embedding", "Xpresso/human_GM12878", | |
| "epidermal_basset/encode-roadmap.basset.clf.testfold-0", "DeepFlyBrain", | |
| "APARENT/site_probabilities", "APARENT/veff", "DeepSTARR", "scbasset", "TREDNet/phase_one", | |
| "a2z-chromatin/a2z-accessibility"] | |
| runs-on: ubuntu-latest | |
| env: | |
| SINGULARITY_PULL_FOLDER: "/home/runner/singularity/" | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.10' | |
| - name: Setup Go | |
| uses: actions/setup-go@v3 | |
| - name: Fetch system level dependencies | |
| run: sudo apt-get -q update && sudo apt-get install -y build-essential squashfs-tools | |
| libseccomp-dev cryptsetup libhdf5-serial-dev pkg-config | |
| - name: Build and install Apptainer | |
| run: | | |
| export VERSION=1.0.2 && \ | |
| wget https://github.com/apptainer/apptainer/releases/download/v${VERSION}/apptainer-${VERSION}.tar.gz && \ | |
| tar -xzf apptainer-${VERSION}.tar.gz && \ | |
| cd apptainer-${VERSION} | |
| ./mconfig -v -p /usr/local | |
| make -C ./builddir all && sudo make -C ./builddir install | |
| cd ../ && rm apptainer-${VERSION}.tar.gz && rm -rf apptainer-${VERSION} | |
| - name: Install kipoi_containers | |
| run: | | |
| mkdir -p /home/runner/singularity/ | |
| python -m pip install --upgrade pip | |
| pip install -e . | |
| - name: Test with pytest | |
| run: | | |
| pytest -s test-containers/test_models_from_command_line.py --model=${{ matrix.model }} | |
| docker system prune -a -f | |
| testdockerandsingularity: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| ZENODO_ACCESS_TOKEN: ${{ secrets.ZENODOACCESSTOKEN }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.10' | |
| - name: Build and install Apptainer | |
| run: | | |
| export VERSION=1.0.2 && \ | |
| wget https://github.com/apptainer/apptainer/releases/download/v${VERSION}/apptainer-${VERSION}.tar.gz && \ | |
| tar -xzf apptainer-${VERSION}.tar.gz && \ | |
| cd apptainer-${VERSION} | |
| ./mconfig -v -p /usr/local | |
| make -C ./builddir all && sudo make -C ./builddir install | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config | |
| python -m pip install --upgrade pip | |
| pip install -e . | |
| - name: Test kipoi_containers and send coverage report to coveralls.io | |
| run: |- | |
| pip install coveralls | |
| docker pull kipoi/kipoi-docker:mmsplice | |
| docker pull kipoi/kipoi-docker:mmsplice-slim | |
| coverage run -m pytest -s test-docker/test_docker_handler.py test-singularity test-containers/test_update_all_singularity_images.py | |
| coveralls --service=github |