Merge branch 'master' into cvc_description #1136
Workflow file for this run
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| name: "Library" | |
| on: [push, pull_request] | |
| jobs: | |
| basicchecks: | |
| name: Basic checks | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository | |
| outputs: | |
| hassecrets: ${{ steps.checksecrets.outputs.hassecrets }} | |
| steps: | |
| - name: Checkout Colvars | |
| uses: actions/checkout@v3 | |
| - name: Load compiler cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.ccache | |
| key: ${{ runner.os }}-build-basic-${{ github.sha }} | |
| restore-keys: ${{ runner.os }}-build-basic- | |
| - name: Get small downloadable packages | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: 'Colvars/build-tools-packages' | |
| ref: 'master' | |
| path: 'devel-tools/packages' | |
| - name: Install build dependencies for library | |
| run: | | |
| sudo apt -y install ccache tcl8.6-dev clang | |
| - name: Test build recipes | |
| run: bash devel-tools/check_build_recipes | |
| - name: Convert BibTeX references to code | |
| shell: bash | |
| working-directory: doc | |
| run: | | |
| make update-code-refs | |
| if [ -n "$(git status --porcelain ../src/colvarmodule_refs.h)" ] ; then | |
| echo "Code citations out of date; please run make update-code-refs in the doc folder" >& 2 | |
| exit 1 | |
| fi | |
| - name: Build and test library (GCC) | |
| env: | |
| CCACHE: ccache | |
| run: cmake -P devel-tools/build_test_library.cmake | |
| - name: Check documentation of command-line scripting interface | |
| shell: bash | |
| working-directory: doc | |
| run: | | |
| make update-cvscript-cmdline-doc | |
| if [ -n "$(git status --porcelain cvscript-tcl.tex)" ] ; then | |
| echo "Command-line scripting doc out of date; please run make update-cvscript-cmdline-doc and commit changes" >& 2 | |
| exit 1 | |
| fi | |
| - name: Build and test library (Clang) | |
| env: | |
| CMAKE_BUILD_DIR: build-clang | |
| CCACHE: ccache | |
| CXX: clang++ | |
| CC: clang | |
| run: cmake -P devel-tools/build_test_library.cmake | |
| - name: Build library with debug flags enabled | |
| env: | |
| CCACHE: ccache | |
| run: cmake -D COLVARS_DEBUG=ON -P devel-tools/build_test_library.cmake | |
| - name: Check whether secrets are available | |
| id: checksecrets | |
| env: | |
| PULL_ORACLE_DEVELOPER_STUDIO: ${{ secrets.PULL_ORACLE_DEVELOPER_STUDIO }} | |
| run: | | |
| echo "hassecrets=${{ env.PULL_ORACLE_DEVELOPER_STUDIO != '' }}" >> $GITHUB_OUTPUT | |
| build-doc: | |
| name: Build documentation | |
| runs-on: ubuntu-latest | |
| needs: basicchecks | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Load containers cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.apptainer | |
| key: Linux-x86_64-containers-build-doc-2023-07-19 | |
| - name: Install Apptainer | |
| shell: bash | |
| run: | | |
| wget https://github.com/apptainer/apptainer/releases/download/v1.0.3/apptainer_1.0.3_amd64.deb | |
| sudo apt-get -y install ./apptainer_1.0.3_amd64.deb | |
| - name: Get container image | |
| shell: bash | |
| working-directory: devel-tools | |
| run: | | |
| apptainer remote status SylabsCloud || apptainer remote add --no-login SylabsCloud cloud.sylabs.io | |
| apptainer remote use SylabsCloud | |
| apptainer pull texlive.sif library://giacomofiorin/default/colvars_development:texlive | |
| - name: Checkout website repository | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: 'Colvars/colvars.github.io' | |
| path: 'website' | |
| - name: Build doc | |
| working-directory: website | |
| env: | |
| COLVARSDIR: ${{ github.workspace }} | |
| FORCE: 1 # Ignore error if branch isn't master | |
| run: apptainer exec ${COLVARSDIR}/devel-tools/texlive.sif make | |
| codeql: | |
| name: CodeQL analysis | |
| runs-on: ubuntu-latest | |
| needs: basicchecks | |
| if: ${{ ! github.event.repository.private }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install build dependencies for library | |
| run: | | |
| sudo apt-get -y install tcl8.6-dev | |
| - name: Checkout OpenMM (for Lepton library) | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: 'openmm/openmm' | |
| ref: 'master' | |
| path: 'openmm-source' | |
| - name: Initialize CodeQL | |
| uses: github/codeql-action/init@v2 | |
| with: | |
| languages: cpp | |
| - name: Build Colvars library with CMake | |
| run: cmake -P devel-tools/build_test_library.cmake | |
| - name: Perform CodeQL Analysis | |
| uses: github/codeql-action/analyze@v2 | |
| build-linux-x86_64-many: | |
| name: Linux x86_64 (many compilers) | |
| runs-on: ubuntu-latest | |
| needs: basicchecks | |
| if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository | |
| env: | |
| CCACHE: ccache | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Load compiler ccache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.ccache | |
| key: ${{ runner.os }}-build-multiple-${{ github.sha }} | |
| restore-keys: ${{ runner.os }}-build-multiple- | |
| # Using an exact key to forgo saving it in case of a match (tarring up | |
| # is expensive); also including a date to allow a force-update. | |
| - name: Load containers cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.apptainer | |
| key: Linux-x86_64-containers-build-2023-07-20 | |
| - name: Get small downloadable packages | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: 'Colvars/build-tools-packages' | |
| ref: 'master' | |
| path: 'devel-tools/packages' | |
| - name: Install Apptainer | |
| shell: bash | |
| run: | | |
| wget https://github.com/apptainer/apptainer/releases/download/v1.0.3/apptainer_1.0.3_amd64.deb | |
| sudo apt-get -y install ./apptainer_1.0.3_amd64.deb | |
| - name: Get container image | |
| shell: bash | |
| working-directory: devel-tools | |
| run: | | |
| apptainer remote status SylabsCloud || apptainer remote add --no-login SylabsCloud cloud.sylabs.io | |
| apptainer remote use SylabsCloud | |
| apptainer pull CentOS7-devel.sif library://giacomofiorin/default/colvars_development:centos7 | |
| apptainer pull CentOS9-devel.sif library://giacomofiorin/default/colvars_development:centos9 | |
| - name: GCC 4.8, C++11 (CentOS 7) | |
| env: | |
| CXX_STANDARD: 11 | |
| CXX: g++ | |
| CXX_VERSION: 4.8 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \ | |
| cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: Clang 3.4, C++11 (CentOS 7) | |
| env: | |
| CXX_STANDARD: 11 | |
| CXX: clang++ | |
| CXX_VERSION: 11 | |
| CC: clang | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \ | |
| cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: Clang 7, C++17 (CentOS 7) | |
| env: | |
| CXX_STANDARD: 17 | |
| CXX: clang++ | |
| CXX_VERSION: 7 | |
| CC: clang | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \ | |
| scl enable llvm-toolset-${CXX_VERSION} -- \ | |
| cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 8, C++14 (CentOS 7) | |
| env: | |
| CXX_STANDARD: 14 | |
| CXX: g++ | |
| CXX_VERSION: 8 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \ | |
| scl enable devtoolset-${CXX_VERSION} -- \ | |
| cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 8, C++17 (CentOS 7) | |
| env: | |
| CXX_STANDARD: 17 | |
| CXX: g++ | |
| CXX_VERSION: 8 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \ | |
| scl enable devtoolset-${CXX_VERSION} -- \ | |
| cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 9, C++14 (CentOS 7) | |
| env: | |
| CXX_STANDARD: 14 | |
| CXX: g++ | |
| CXX_VERSION: 9 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \ | |
| scl enable devtoolset-${CXX_VERSION} -- \ | |
| cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 10, C++17 (CentOS 7) | |
| env: | |
| CXX_STANDARD: 17 | |
| CXX: g++ | |
| CXX_VERSION: 10 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \ | |
| scl enable devtoolset-${CXX_VERSION} -- \ | |
| cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 11, C++11 (CentOS 9) | |
| env: | |
| CXX_STANDARD: 11 | |
| CXX: g++ | |
| CXX_VERSION: 11 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 11, C++14 (CentOS 9) | |
| env: | |
| CXX_STANDARD: 14 | |
| CXX: g++ | |
| CXX_VERSION: 11 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 11, C++17 (CentOS 9) | |
| env: | |
| CXX_STANDARD: 17 | |
| CXX: g++ | |
| CXX_VERSION: 11 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 11, C++20 (CentOS 9) | |
| env: | |
| CXX_STANDARD: 20 | |
| CXX: g++ | |
| CXX_VERSION: 11 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 12, C++11 (CentOS 9) | |
| env: | |
| CXX_STANDARD: 11 | |
| CXX: g++ | |
| CXX_VERSION: 12 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| scl enable gcc-toolset-12 -- \ | |
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 12, C++20 (CentOS 9) | |
| env: | |
| CXX_STANDARD: 20 | |
| CXX: g++ | |
| CXX_VERSION: 12 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| scl enable gcc-toolset-12 -- \ | |
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: Clang 16, C++11 (CentOS 9) | |
| env: | |
| CXX_STANDARD: 11 | |
| CXX: clang++ | |
| CXX_VERSION: 16 | |
| CC: clang | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: Clang 16, C++17 (CentOS 9) | |
| env: | |
| CXX_STANDARD: 17 | |
| CXX: clang++ | |
| CXX_VERSION: 16 | |
| CC: clang | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: Clang 16, C++20 (CentOS 9) | |
| env: | |
| CXX_STANDARD: 20 | |
| CXX: clang++ | |
| CXX_VERSION: 16 | |
| CC: clang | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| build-linux-x86_64-sun: | |
| name: Linux x86_64 (Sun compiler) | |
| runs-on: ubuntu-latest | |
| needs: basicchecks | |
| if: needs.basicchecks.outputs.hassecrets == 'true' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Load containers cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.apptainer | |
| key: Linux-x86_64-containers-build-2023-07-20 | |
| - name: Checkout Sun compiler (Oracle Developer Studio) | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: 'Colvars/oracle' | |
| ssh-key: ${{ secrets.PULL_ORACLE_DEVELOPER_STUDIO }} | |
| ref: 'master' | |
| path: ${{github.workspace}}/oracle | |
| - name: Get small downloadable packages | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: 'Colvars/build-tools-packages' | |
| ref: 'master' | |
| path: 'devel-tools/packages' | |
| - name: Install Apptainer | |
| shell: bash | |
| run: | | |
| wget https://github.com/apptainer/apptainer/releases/download/v1.0.3/apptainer_1.0.3_amd64.deb | |
| sudo apt-get -y install ./apptainer_1.0.3_amd64.deb | |
| - name: Get container image | |
| shell: bash | |
| working-directory: devel-tools | |
| run: | | |
| apptainer remote status SylabsCloud || apptainer remote add --no-login SylabsCloud cloud.sylabs.io | |
| apptainer remote use SylabsCloud | |
| apptainer pull CentOS7-devel.sif library://giacomofiorin/default/colvars_development:centos7 | |
| apptainer pull CentOS9-devel.sif library://giacomofiorin/default/colvars_development:centos9 | |
| - name: Build library with Sun compiler (Oracle Developer Studio) | |
| shell: bash | |
| env: | |
| CC: ${{github.workspace}}/oracle/developerstudio12.6/bin/cc | |
| CXX: ${{github.workspace}}/oracle/developerstudio12.6/bin/CC | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \ | |
| cmake3 -D CMAKE_CXX_STANDARD=11 -P devel-tools/build_test_library.cmake | |
| build-windows-x86_64-msvc: | |
| name: Windows x86_64 (MSVC) | |
| runs-on: windows-latest | |
| needs: basicchecks | |
| if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Get small downloadable packages | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: 'Colvars/build-tools-packages' | |
| ref: 'master' | |
| path: 'devel-tools/packages' | |
| - name: Build and test library with CMake | |
| # We need to set CMAKE_SYSTEM_NAME manually in script mode | |
| run: cmake -D CMAKE_SYSTEM_NAME=Windows -P devel-tools/build_test_library.cmake | |
| build-macos-x86_64-clang: | |
| name: macOS x86_64 (AppleClang) | |
| runs-on: macos-latest | |
| needs: basicchecks | |
| if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Get small downloadable packages | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: 'Colvars/build-tools-packages' | |
| ref: 'master' | |
| path: 'devel-tools/packages' | |
| - name: Build and test library with CMake | |
| # We need to set CMAKE_SYSTEM_NAME manually in script mode | |
| run: cmake -D CMAKE_SYSTEM_NAME=Darwin -P devel-tools/build_test_library.cmake |