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Silence Clang static analyzer warnings #1262

Silence Clang static analyzer warnings

Silence Clang static analyzer warnings #1262

Workflow file for this run

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echo "Code citations out of date; please run make update-code-refs in the doc folder" 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echo "Command-line scripting doc out of date; please run make update-cvscript-cmdline-doc and commit changes" 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: |
sudo add-apt-repository -y ppa:apptainer/ppa
sudo apt update
sudo apt install -y apptainer-suid
- 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: ${{ ! github.event.repository.private }}
steps:
- uses: actions/checkout@v3
- name: Install build dependencies for library
run: |
sudo apt-get -y install tcl8.6-dev
- name: Checkout OpenMM (for Lepton library)
uses: actions/checkout@v3
with:
repository: 'openmm/openmm'
ref: 'master'
path: 'openmm-source'
- name: Initialize CodeQL
uses: github/codeql-action/init@v2
with:
languages: cpp
- name: Build Colvars library with CMake
run: cmake -P devel-tools/build_test_library.cmake
- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v2
static-analyser:
name: Clang Static Analyser
runs-on: ubuntu-latest
needs: basicchecks
steps:
- uses: actions/checkout@v3
- name: Install build dependencies for library
run: |
sudo apt -y install tcl8.6-dev clang
- name: Checkout OpenMM (for Lepton library)
uses: actions/checkout@v3
with:
repository: 'openmm/openmm'
ref: 'master'
path: 'openmm-source'
- name: Perform Clang Static Analyser
env:
CCACHE: ccache
CXX: clang++
CC: clang
run: | # Retrieve warnings generated but not the ones of OpenMM
scan-build-11 --use-cc=clang --use-c++=clang++ cmake -P devel-tools/build_test_library.cmake 2>&1 | tee build_analyser.log \
awk '/warning/,/warning.*generated|^$/' build_analyser.log | awk '!/openmm.*warning/,/warning.*generated|^$/' | tee warnings_analyser.log \
if [ -s warnings_analyser.log ] ; then echo "Found compiler warning during build"; cat warnings_analyser.log; exit 1; fi
- name: Archive warnings artifacts
uses: actions/upload-artifact@v3
with:
name: warnings_analyser
path: warnings_analyser.log
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
CMAKE_GENERATOR: Ninja
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-2023-09-05
- 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: |
sudo add-apt-repository -y ppa:apptainer/ppa
sudo apt update
sudo apt install -y apptainer-suid
- 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-2023-09-05
- 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: |
sudo add-apt-repository -y ppa:apptainer/ppa
sudo apt update
sudo apt install -y apptainer-suid
- 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