add links to developer docs to readme #93
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| --- # yamllint disable-line rule:new-lines | |
| name: SACCHARIS Conda Test Suite | |
| on: # yamllint disable-line rule:truthy | |
| push: | |
| branches: | |
| - main | |
| - test | |
| pull_request: | |
| branches: | |
| - main | |
| - test | |
| workflow_dispatch: | |
| jobs: | |
| build-test-linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.3.1' | |
| - name: Install rsaccharis and dependencies | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| run: > | |
| Rscript -e 'install.packages("BiocManager", repos = "http://cran.us.r-project.org")' | |
| -e 'if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager");BiocManager::install()' | |
| -e 'BiocManager::install(c("remotes", "saccharis/rsaccharis"), dependencies=TRUE)' | |
| - name: Set up Python 3.11 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.11' | |
| - name: Set up conda/mamba | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| mamba-version: "*" | |
| channel-priority: true | |
| channels: conda-forge,bioconda,defaults | |
| environment-file: environment.yml | |
| - name: Add conda to system path | |
| run: | | |
| # $CONDA is an environment variable pointing to the root of the miniconda directory | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| # - name: Install conda dependencies | |
| # run: conda env update --file environment.yml --name base | |
| - name: Build and install SACCHARIS | |
| run: | | |
| conda install conda-build | |
| conda build . | |
| conda install --use-local saccharis | |
| - name: Lint with flake8 | |
| run: | | |
| conda install flake8 | |
| # 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 | |
| - name: Test with pytest | |
| run: | | |
| conda install pytest | |
| pytest tests_package | |
| - name: Zip build artifact | |
| if: ${{ failure() }} | |
| run: zip -r artifact.zip /home/runner/work/ | |
| - name: Upload build artifact | |
| uses: actions/upload-artifact@v3 | |
| if: ${{ failure() }} | |
| with: | |
| name: artifact-all | |
| path: artifact.zip | |
| retention-days: 5 |