build_and_test.yml

name: Build and Test

on:
  push:
    branches:
      - "main"
      - "staging"
  pull_request:
    branches:
      - "*"

env:
  PROGRAM_NAME: pasv

jobs:
  build:
    strategy:
      fail-fast: false
      matrix:
        os:
          - macos-11
          - ubuntu-20.04
        ocaml-compiler:
          - 4.14.1

    runs-on: ${{ matrix.os }}

    steps:
      - name: Checkout code
        uses: actions/checkout@v2
        with:
          submodules: recursive

      - run: echo "LOCAL_PATH=$HOME/.local/bin" >> $GITHUB_ENV
      - run: echo "CLUSTALO_EXE=$LOCAL_PATH/clustalo" >> $GITHUB_ENV

      - name: Setup path
        run: |
          mkdir -p "$LOCAL_PATH"
          echo "$LOCAL_PATH" >> $GITHUB_PATH

      - name: Download Clustal Omega (Linux)
        run: |
          \curl -L http://www.clustal.org/omega/clustalo-1.2.4-Ubuntu-x86_64 > "$CLUSTALO_EXE"
        if: matrix.os == 'ubuntu-20.04'

      - name: Download Clustal Omega (MacOS)
        # 1.2.4 isn't available for MacOS
        run: |
          \curl -L http://www.clustal.org/omega/clustal-omega-1.2.3-macosx > "$CLUSTALO_EXE"
        if: matrix.os == 'macos-11'

      - name: Setup and check Clustal Omega
        run: |
          chmod 755 "$CLUSTALO_EXE"
          clustalo --version

      - name: Download MAFFT
        run: |
          \curl -L https://mafft.cbrc.jp/alignment/software/mafft-7.481-without-extensions-src.tgz \
          | tar xz

      - name: Install MAFFT
        run: cd mafft-*/core/ && make clean && make && sudo make install

      - name: Download HMMER
        run: \curl -L http://eddylab.org/software/hmmer/hmmer-3.3.2.tar.gz | tar xz

      - name: Install HMMER
        run: cd hmmer-3.3.2 && ./configure && make && sudo make install

      - name: Use OCaml ${{ matrix.ocaml-compiler }}
        uses: ocaml/setup-ocaml@v2
        with:
          ocaml-compiler: ${{ matrix.ocaml-compiler }}
          dune-cache: ${{ matrix.os != 'macos-11' }}
          cache-prefix: v1-${{ matrix.os }}

      - name: Install OCaml deps (Ubuntu)
        run: opam update && opam install --locked . --deps-only --with-doc --with-test
        if: matrix.os == 'ubuntu-20.04'

      - name: Install OCaml deps (MacOS)
        run: opam update && opam install --locked . --jobs 1 --deps-only --with-doc --with-test
        if: matrix.os == 'macos-11'

      - name: Test (Ubuntu)
        run: opam exec -- make test
        if: matrix.os == 'ubuntu-20.04'

      - name: Test (MacOS)
        run: opam exec -- make test_mac
        if: matrix.os == 'macos-11'

      - run: opam exec -- make send_coverage
        if: matrix.ocaml-compiler == '4.12.0'
        env:
          COVERALLS_REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}

      - name: Build (Ubuntu)
        run: opam exec -- make build_release
        if: matrix.os == 'ubuntu-20.04'

      - name: Build (MacOS)
        run: opam exec -- make build_release_mac
        if: matrix.os == 'macos-11'

      - name: Upload the build artifact
        uses: actions/upload-artifact@v2
        with:
          name: ${{ matrix.os }}-${{ matrix.ocaml-compiler }}-${{ env.PROGRAM_NAME }}
          path: _build/install/default/bin/${{ env.PROGRAM_NAME }}