migrate from osx-11 to osx-12 #1059
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| 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 master 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 | |
| - name: update cabal | |
| run: cabal update | |
| - name: add random Haskell lib | |
| run: cabal install --lib random | |
| - name: Checkout truth | |
| run: git clone --branch master 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 = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf | |
| - name: make | |
| run: make -j 3 | |
| - name: make install | |
| run: sudo make install | |
| - name: debug0 | |
| run: find / -name "*librna*" 2> /dev/null | |
| - name: debug0 | |
| run: which -a gapc | |
| - name: debug1 | |
| run: ls /Users | |
| - name: debug2 | |
| run: ls /Users/runner && True; | |
| - name: debug3 | |
| run: ls /Users/runner/work && True; | |
| - name: debug4 | |
| run: ls /Users/runner/work/gapc && True; | |
| - name: debug5 | |
| run: ls /Users/runner/work/gapc/lib && True; | |
| - name: debug6 | |
| run: ls -latr /Users/runner/work/gapc/gapc/lib/rtlib && True; | |
| - name: test-mod | |
| run: make test-mod TRUTH_DIR=$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/* |