build_and_test.yml

name: Build and test

on:
  push:
    branches:
      - "main"
      - "staging"
      - "dev"

  pull_request:
    branches:
      - "*"

env:
  PROGRAM_NAME: InteinFinder

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

      - run: brew install tree
        if: matrix.os == 'macos-11'

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

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

      - name: Setup just
        run: |
          \curl \
            --proto '=https' \
            --tlsv1.2 \
            -sSf \
            https://just.systems/install.sh \
          | bash -s -- \
            --to "$LOCAL_PATH" \
            --tag 1.13.0

      - name: Download MAFFT
        run: |
          \curl -L \
          https://mafft.cbrc.jp/alignment/software/mafft-7.490-without-extensions-src.tgz \
          | tar xz \
          && cd mafft-*/core/ && make clean && make && sudo make install

      - name: Download & Install MMseqs2 (ubuntu)
        run: |
          \curl -L \
          https://github.com/soedinglab/MMseqs2/releases/download/13-45111/mmseqs-linux-sse2.tar.gz \
          | tar xz \
          && mv mmseqs/bin/mmseqs "$LOCAL_PATH"
        if: matrix.os == 'ubuntu-20.04'

      - name: Download & Install MMseqs2 (macOS)
        run: |
          \curl -L \
          https://github.com/soedinglab/MMseqs2/releases/download/13-45111/mmseqs-osx-universal.tar.gz \
          | tar xz \
          && mv mmseqs/bin/mmseqs "$LOCAL_PATH"
        if: matrix.os == 'macos-11'

      - name: Download & Install NCBI BLAST+ (ubuntu)
        run: |
          \curl -L \
          https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-x64-linux.tar.gz \
          | tar xz \
          && mv ncbi-blast-2.12.0+/bin/rpsblast "${LOCAL_PATH}/rpsblast+" \
          && mv ncbi-blast-2.12.0+/bin/makeprofiledb "${LOCAL_PATH}/makeprofiledb"
        if: matrix.os == 'ubuntu-20.04'

      - name: Download & Install NCBI BLAST+ (macOS)
        run: |
          \curl -L \
          https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-x64-macosx.tar.gz \
          | tar xz \
          && mv ncbi-blast-2.12.0+/bin/rpsblast "${LOCAL_PATH}/rpsblast+" \
          && mv ncbi-blast-2.12.0+/bin/makeprofiledb "${LOCAL_PATH}/makeprofiledb"
        if: matrix.os == 'macos-11'

      - name: Use OCaml ${{ matrix.ocaml-compiler }} (ubuntu)
        uses: ocaml/setup-ocaml@v2
        with:
          ocaml-compiler: ${{ matrix.ocaml-compiler }}
          dune-cache: true
          cache-prefix: v1-${{ matrix.os }}
          opam-pin: false
          opam-depext: false
        if: matrix.os == 'ubuntu-20.04'

      - name: Use OCaml ${{ matrix.ocaml-compiler }} (macOS)
        uses: ocaml/setup-ocaml@v2
        with:
          ocaml-compiler: ${{ matrix.ocaml-compiler }}
          dune-cache: false
          cache-prefix: v1-${{ matrix.os }}
          opam-pin: false
          opam-depext: false
        if: matrix.os == 'macos-11'

      - name: Install tiny_config
        run: |
          git clone https://github.com/mooreryan/tiny_config.git
          cd tiny_config
          opam install base otoml yaml
          opam pin add tiny_config .
          opam pin add tiny_toml .
          opam install tiny_config
          opam install tiny_toml

      - run: opam install --locked . --deps-only --with-doc --with-test

      - name: Check dev profile
        run: |
          opam exec -- just clean
          opam exec -- just build_dev
          opam exec -- just test_dev
          opam exec -- just install_dev
        if: matrix.ocaml-compiler == '4.14.1'

      # Send the coverage.
      - name: Send coverage
        run: |
          opam install bisect_ppx
          opam exec -- just send_coverage
        if: matrix.ocaml-compiler == '4.14.1' && matrix.os == 'ubuntu-20.04'
        env:
          COVERALLS_REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}

      - name: Check release profile
        run: |
          opam exec -- just clean
          opam exec -- just build_release
          opam exec -- just test_release
          opam exec -- just install_release
        if: matrix.ocaml-compiler == '4.14.1'

      - name: Upload InteinFinder artifact
        uses: actions/upload-artifact@v2
        with:
          name: ${{ env.PROGRAM_NAME }}-${{ matrix.os }}
          path: _build/install/default/bin/${{ env.PROGRAM_NAME }}
        if: matrix.ocaml-compiler == '4.14.1'

      - name: Upload RemoveInteins artifact
        uses: actions/upload-artifact@v2
        with:
          name: RemoveInteins-${{ matrix.os }}
          path: _build/install/default/bin/RemoveInteins
        if: matrix.ocaml-compiler == '4.14.1'