c-cpp.yml

name: github action build & CI

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]
  workflow_dispatch:
    inputs:
      logLevel:
        description: 'Log level'
        required: true
        default: 'warning'
      tags:
        description: 'Test scenario tags'

jobs:
  gapc_ubuntu:
    needs: cpplint
    strategy:
      matrix:
        # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners
        # as of 21st Sep 2021, ubuntu-16.04 is no longer supported by github actions: https://github.blog/changelog/2021-04-29-github-actions-ubuntu-16-04-lts-virtual-environment-will-be-removed-on-september-20-2021/
        # 18.04 burnout: https://github.com/actions/runner-images/issues/6002
        os: [ubuntu-20.04, ubuntu-22.04]
    runs-on: ${{ matrix.os }}
    steps:
    - name: Update apt
      run: sudo apt-get update
    - name: Install dependencies
      run: sudo apt-get install flex bison make libboost-all-dev libgsl-dev python3 python3-pip

    - name: Checkout truth
      run: git clone --branch tikz3 https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite

    - uses: actions/checkout@v3
    - name: configure
      run: ./configure --prefix $GITHUB_WORKSPACE
    - name: make
      run: make -j 2
    - name: make install
      run: sudo make install

    - name: test-mod
      run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_ubuntu
    - name: test-mod_outside
      run: make -j 2 test-mod_outside TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_ubuntu
    - name: test-regress
      run: make test-regress TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth
    - name: test-ambiguity
      run: make test-ambiguity TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth
    - name: test-unit
      run: make test-unit
    # we need to install Haskell (especially the System.Random lib) for paralell tests, since we compare Haskell ADP with gapc
    - uses: haskell-actions/setup@v2
      with:
        cabal-version: '3.6.2.0'  # pin version on 2023-02-09 to enable proper cabal installtion
      id: haskell
    - name: cabal
      run: |
        ${{ steps.haskell.outputs.cabal-exe }} v2-update
        ${{ steps.haskell.outputs.cabal-exe }} v2-install --lib random

    - name: test-paral
      run: |
        package_path=$HOME/.cabal/store/ghc-`${{ steps.haskell.outputs.ghc-exe }} --version | rev | cut -d " " -f 1 | rev`/package.db
        GHC="ghc -package-db $package_path" make test-paral

  gapc_osx:
    needs: cpplint
    strategy:
      matrix:
        # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners
        os: [macos-12]
    runs-on: ${{ matrix.os }}
    steps:
    - name: Install dependencies
      run: brew install bison@2.7 cmake boost gsl gnu-sed libomp gmp cabal-install ghc
    - name: update cabal
      run: cabal update
    - name: add random Haskell lib
      run: cabal install --lib random
    - name: add base Haskell lib containers (prelude, Data.Map, Data.Map.Strict)
      run: cabal install --lib base
    - name: Checkout truth
      run: git clone --branch tikz3 https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite

    - uses: actions/checkout@v3
    - name: configure
      run: ./configure --prefix $GITHUB_WORKSPACE
    - name: patch configuration for OSX
      run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@2.7/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf
    - name: make
      run: make -j 3
    - name: make install
      run: sudo make install

    - name: test-mod
      run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx
    - name: test-mod_outside
      run: make -j 2 test-mod_outside TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx
    - name: test-regress
      run: make test-regress TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth
    - name: test-ambiguity
      run: make test-ambiguity TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth
    - name: test-unit
      run: make test-unit
    - name: test-paral
      run: make test-paral

  fold-grammars:
    needs: cpplint
    strategy:
      matrix:
        task: [default, shapes, pkiss, alishapes, palikiss, knotinframe]
    runs-on: ubuntu-latest
    steps:
    # install gapcs
    - name: Update apt
      run: sudo apt-get update
    - name: Install dependencies
      run: sudo apt-get install flex bison make libboost-all-dev libgsl-dev python3 python3-pip python3-biopython
    - uses: actions/checkout@v3
    - name: configure
      run: ./configure
    - name: make
      run: make -j 2
    - name: make install
      run: sudo make install

    - name: clone fold-grammars
      run: git clone --branch master https://github.com/jlab/fold-grammars.git $GITHUB_WORKSPACE/../fold-grammars
    - name: configure fold-grammars
      run: |
        cd $GITHUB_WORKSPACE/../fold-grammars
        sed -i "s#bgapDir = '/vol/gapc/'#bgapDir = '/usr/local/'#" Misc/Applications/lib/foldGrammars/Settings.pm
        sed -i "s#rootDir = '/vol/fold-grammars/src/'#rootDir = '`pwd`/'#" Misc/Applications/lib/foldGrammars/Settings.pm
    - name: execute tests
      run: |
        cd $GITHUB_WORKSPACE/../fold-grammars
        if [[ "${{ matrix.task }}" == "default" ]]; then pushd .; cd Misc/Test-Suite/GeorgStyle/; bash run.sh ../Truth; cd ../StefanStyle/; python test_cofold.py; popd; fi
        pushd .
        cd Misc/Test-Suite/StefanStyle/
        perl runTests.pl 2 ${{ matrix.task }}
        popd

  cpplint:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v3
    - uses: actions/setup-python@v4
    - run: pip install cpplint
    - run: cpplint --recursive --counting 'detailed' --filter="-runtime/references,-build/include_subdir" --extensions=cc,hh src/ rtlib/
    - run: cpplint --counting 'detailed' --filter="-build/include_subdir,-readability/casting,-runtime/arrays" --extensions=c,h librna/rnalib.{c,h}
    - run: cpplint --recursive --counting 'detailed' --filter="-runtime/references,-build/include_subdir" testdata/unittest/*