Reproducible Research #156
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| name: Reproducible Research | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| schedule: | |
| - cron: 42 8 */21 * * | |
| jobs: | |
| tcpdbench-ubuntu: | |
| name: Check TCPDBench (direct) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Install dependencies | |
| run: sudo apt-get update && sudo apt-get install build-essential latexmk texlive-latex-extra | |
| shell: bash | |
| - name: Install Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.8' | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@v2-branch | |
| with: | |
| r-version: 'release' | |
| - name: Install R dependencies | |
| run: | | |
| install.packages(c('argparse', 'exactRankTests')) | |
| shell: Rscript {0} | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: true | |
| - name: Install Python dependencies | |
| run: pip install -r ./analysis/requirements.txt | |
| shell: bash | |
| - name: Clone TCPD | |
| run: git clone https://github.com/alan-turing-institute/TCPD ../TCPD | |
| shell: bash | |
| - name: Build TCPD | |
| run: cd ../TCPD && make export | |
| shell: bash | |
| - name: Copy datasets | |
| run: mkdir -p ./datasets && cp ../TCPD/export/*.json ./datasets/ && pwd && ls -1 . | |
| shell: bash | |
| - name: Skip annotation simulation p-values | |
| run: touch ./analysis/output/tables/annotation_simulation_pvalues.tex | |
| shell: bash | |
| - name: Make results | |
| run: make results | |
| shell: bash | |
| - name: Check results | |
| run: git checkout ./analysis/output/cd_diagrams/*.pdf && git checkout ./analysis/output/figures/anno_hist/histogram*.pdf && git diff --exit-code | |
| shell: bash | |
| tcpdbench-docker: | |
| name: Check TCPDBench (docker) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: TCPDBench docker check | |
| run: ./.github/scripts/test_docker.sh | |
| shell: bash |