tests.yml

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@v35
        with:
          files: |
            *.{yml,yaml,py}
            **/*.{yml,yaml,py}
            container/database
            container/tests
            container/*.{yml,yaml,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: 3.7, os: ubuntu-latest }
          - { python-version: 3.8, os: ubuntu-latest }
          - { python-version: 3.9, os: ubuntu-latest }
          - { python-version: "3.10", os: ubuntu-latest }
          - { python-version: 3.7, os: macos-latest }
          - { python-version: 3.8, os: macos-latest }
          - { python-version: 3.9, os: macos-latest }
          - { python-version: "3.10", 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: 0
        with:
          path: ~/conda_pkgs_dir
          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
            hashFiles('environment.yml') }}

      - name: Setup Miniconda
        uses: conda-incubator/setup-miniconda@v2.1.1
        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 .
          python -m pip install palantir==1.0.1
          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
        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