Testing the new versions #265
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| name: Unit Tests | |
| on: | |
| push: | |
| branches-ignore: | |
| - 'test_deploy' | |
| pull_request: | |
| branches: | |
| - '*' | |
| concurrency: | |
| group: ci-tests-${{ github.ref }}-1 | |
| # main should run through entire queue of commits for debugging | |
| cancel-in-progress: ${{ github.ref_name != 'main'}} | |
| jobs: | |
| run_tester: | |
| runs-on: ${{ matrix.config.os }} | |
| if: "!contains(github.event.head_commit.message, 'ci skip')" | |
| env: | |
| RENV_PATHS_ROOT: ~/.local/share/renv | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {name: '3.13', os: ubuntu-latest, python: '3.13', r: 'release'} | |
| - {name: '3.12', os: ubuntu-latest, python: '3.12', r: 'release'} | |
| - {name: '3.11', os: ubuntu-latest, python: '3.11', r: 'release'} | |
| - {name: '3.10', os: ubuntu-latest, python: '3.10', r: 'release'} | |
| - {name: '3.9', os: ubuntu-latest, python: '3.9', r: 'release'} | |
| steps: | |
| - name: Get current date | |
| id: date | |
| run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update -qq | |
| sudo apt-get install -y pandoc gfortran libblas-dev liblapack-dev libedit-dev llvm-dev libcurl4-openssl-dev ffmpeg libhdf5-dev libfribidi-dev libharfbuzz-dev | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.config.python }} | |
| - name: Set up R | |
| id: setup-r | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - name: Cache Python packages | |
| uses: pat-s/always-upload-cache@v2 | |
| with: | |
| path: ${{ env.pythonLocation }} | |
| key: ${{runner.os}}-pip-${{ env.pythonLocation }}-${{ hashFiles('setup.py') }} | |
| restore-keys: ${{runner.os}}-pip-${{ env.pythonLocation }}- | |
| - name: Cache R packages | |
| uses: pat-s/always-upload-cache@v2 | |
| if: startsWith(runner.os, 'Linux') | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-R-${{ steps.setup-r.outputs.installed-r-version }}-${{ hashFiles('DESCRIPTION') }} | |
| restore-keys: | | |
| ${{ runner.os }}-R-${{ steps.setup-r.outputs.installed-r-version }}- | |
| - name: Install python tools | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install --upgrade wheel setuptools | |
| - name: Set up rpy2 | |
| run: | | |
| pip install rpy2 | |
| echo "LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}" >> $GITHUB_ENV | |
| - name: Install scprep | |
| id: install-python-packages | |
| run: | | |
| pip install --upgrade .[test] | |
| python -c "import scprep" | |
| - name: Install R packages | |
| id: install-r-packages | |
| run: | | |
| install.packages(c("BiocManager", "devtools")) | |
| BiocManager::install(c("splatter", "slingshot")) | |
| devtools::install_github("dynverse/dyngen") | |
| devtools::install_github("dynverse/dynwrap") | |
| shell: Rscript {0} | |
| - name: Run tests | |
| run: nose2 -vvv | |
| - name: Coveralls | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| COVERALLS_SERVICE_NAME: github | |
| run: | | |
| coveralls | |
| - name: Upload check results on fail | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ matrix.config.name }}_results | |
| path: check |