Update README.rst (#374) #2050
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| name: tests | |
| on: | |
| pull_request: | |
| branches: | |
| - "*" | |
| push: | |
| branches: | |
| - "master" | |
| env: | |
| cache-version: "cache-v1" | |
| jobs: | |
| changes: | |
| name: Checking changed files | |
| runs-on: ubuntu-latest | |
| outputs: | |
| keepgoing: ${{ steps.changed-files.outputs.any_changed }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v41 | |
| with: | |
| files: | | |
| *.{yml,yaml,py} | |
| **/*.{yml,yaml,py} | |
| requirements.txt | |
| container/database | |
| container/tests | |
| container/scripts/*.py | |
| tests | |
| - name: List all changed files | |
| run: | | |
| for file in ${{ steps.changed-files.outputs.all_changed_files }}; do | |
| echo "$file was changed" | |
| done | |
| echo ${{ steps.changed-files.outputs.any_changed }} | |
| tests: | |
| needs: | |
| - changes | |
| if: needs.changes.outputs.keepgoing == 'true' | |
| timeout-minutes: 720 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| max-parallel: 10 | |
| matrix: | |
| config: | |
| - { python-version: 3.9, os: ubuntu-latest } | |
| - { python-version: "3.10", os: ubuntu-latest } | |
| - { python-version: "3.11", os: ubuntu-latest } | |
| - { python-version: 3.9, os: macos-latest } | |
| - { python-version: "3.10", os: macos-latest } | |
| - { python-version: "3.11", os: macos-latest } | |
| # disabled until it's fixed. | |
| runs-on: ${{ matrix.config.os }} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| NOT_CRAN: true | |
| TZ: UTC | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-node@v3 | |
| - name: Install ubuntu system dependencies | |
| if: matrix.config.os == 'ubuntu-latest' | |
| run: | | |
| sudo apt-get install libcurl4-openssl-dev | |
| sudo apt-get update -y && sudo apt-get install -y zlib1g-dev libglpk-dev libgmp3-dev libxml2-dev libicu-dev libhdf5-serial-dev libcurl4-gnutls-dev | |
| - name: Install macOS system dependencies | |
| if: matrix.config.os == 'macos-latest' | |
| run: | | |
| brew install cairo pkg-config autoconf automake libtool | |
| - name: Cache conda | |
| uses: actions/cache@v3 | |
| env: | |
| # Increase this value to reset cache if etc/example-environment.yml has not changed | |
| CACHE_NUMBER: 2 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ | |
| hashFiles('environment.yml') }} | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-activate-base: true | |
| auto-update-conda: true | |
| activate-environment: dandelion | |
| channels: conda-forge, bioconda, anaconda, defaults | |
| channel-priority: true | |
| python-version: ${{ matrix.config.python-version }} | |
| environment-file: environment.yml | |
| use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! | |
| - name: Display Python version | |
| run: | | |
| python --version | |
| which python | |
| - name: Setup blast and igblast | |
| # just in case this happens again in the future | |
| # conda install -c bioconda igblast blast ncbi-vdb=2.11.0 | |
| # https://github.com/bioconda/bioconda-recipes/issues/33479 | |
| run: | | |
| conda install -c bioconda "igblast>=1.17.0" blast | |
| - name: Test if blast works | |
| run: | | |
| blastn -h | |
| - name: Test if igblast works | |
| run: | | |
| igblastn -h | |
| - id: R | |
| name: Check R version | |
| run: | | |
| R --version > VERSION | |
| echo "version=$(head -1 VERSION | awk '{print $3}')" >> $GITHUB_OUTPUT | |
| echo "mainbiocversion=$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')" >> $GITHUB_OUTPUT | |
| echo "subbiocversion=$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $2}')" >> $GITHUB_OUTPUT | |
| echo "biocversion=$(Rscript -e 'cat(as.character(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')" >> $GITHUB_OUTPUT | |
| shell: bash -l {0} | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ steps.R.outputs.version}} | |
| - name: Cache ubuntu R packages | |
| if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os == 'ubuntu-latest'" | |
| uses: actions/cache@v3 | |
| with: | |
| path: /home/runner/work/_temp/Library | |
| key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}- | |
| - name: Cache macOS R packages | |
| if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os != 'ubuntu-latest'" | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}- | |
| - name: Setup r-lib/remotes | |
| run: | | |
| options(install.packages.compile.from.source = "never") | |
| install.packages(c('remotes', 'optparse', 'RCurl', 'XML','matrixStats', 'stringi')) | |
| shell: Rscript {0} | |
| - name: Install Dandelion | |
| run: | | |
| python -m pip install ".[scirpy]" | |
| python -m pip install palantir | |
| python -m pip install git+https://github.com/emdann/milopy.git | |
| - name: Install ubuntu R dependencies | |
| if: matrix.config.os == 'ubuntu-latest' | |
| run: | | |
| options(install.packages.compile.from.source = "never") | |
| remotes::install_cran("BiocManager") | |
| BiocManager::install(c('Biostrings', 'GenomicAlignments', 'IRanges')) | |
| install.packages(c('shazam', 'alakazam', 'tigger', 'optparse')) | |
| shell: Rscript {0} | |
| - name: Install macOS R dependencies | |
| if: matrix.config.os != 'ubuntu-latest' | |
| run: | | |
| options(install.packages.compile.from.source = "never") | |
| remotes::install_cran("BiocManager") | |
| BiocManager::install(c('Biostrings', 'GenomicAlignments', 'IRanges')) | |
| install.packages(c('shazam', 'alakazam', 'tigger', 'optparse')) | |
| shell: Rscript {0} | |
| - name: Test if R dependencies are installed properly | |
| run: | | |
| Rscript tests/r_dependencies.R | |
| shell: bash -l {0} | |
| - name: Test with pytest | |
| run: | | |
| python -m pytest --cov=dandelion --cov-report=xml --ignore=container -rP -W ignore::DeprecationWarning -W ignore::PendingDeprecationWarning -W ignore::FutureWarning | |
| - name: Show coverage | |
| run: | | |
| coverage report | |
| - name: Upload coverage to Codecov | |
| if: matrix.config.os == 'ubuntu-latest' && matrix.config.python-version == '3.10' && github.actor == 'zktuong' && github.repository == 'zktuong/dandelion' | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: ./coverage.xml | |
| directory: ./coverage/reports/ | |
| env_vars: ${{ format('OS={0},PYTHON={1}', matrix.config.os, matrix.config.python-version) }} | |
| flags: unittests | |
| name: codecov-umbrella | |
| fail_ci_if_error: true | |
| path_to_write_report: ./coverage/codecov_report.txt | |
| verbose: true |