add more CI checks (#13)

* adding doxygen and cppcheck and clang-tidy

* reorg docker naming

* try to throw error when cmake fails

* fix doxyfile.in to have dynamic include...and exclude tpls

* install updated doxygen manually

.github/workflows/continuousIntegration.yml

@@ -28,22 +28,42 @@ jobs:
   #       BUILD_AND_TEST_ARGS: --test-code-style
   #     run: ./scripts/ci_build_and_test.sh
 
-  # documentation:
-  #   needs: [check_pull_request_is_not_a_draft]
-  #   runs-on: ubuntu-22.04
-  #   steps:
-  #   - name: Checkout Repository
-  #     uses: actions/checkout@v3
-  #     with:
-  #       submodules: true
-  #       lfs: false
-  #   - name: Check documentation
-  #     env:
-  #       DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc9
-  #       CMAKE_BUILD_TYPE: Release
-  #       BUILD_AND_TEST_ARGS: --test-documentation
-  #     run: ./scripts/ci_build_and_test.sh
+  doxygen_check:
+    runs-on: ubuntu-22.04
+    steps:
+    - name: Checkout Repository
+      uses: actions/checkout@v3
+      with:
+        submodules: true
+        lfs: false
+    - name: Check doxygen
+      env:
+        DOCKER_REPOSITORY: geosx/ubuntu:22.04
+        HOST_CONFIG: hostconfigs/environment.cmake
+        CMAKE_CXX_COMPILER: /usr/bin/clang++
+        CMAKE_C_COMPILER: /usr/bin/clang
+        CMAKE_BUILD_TYPE: Release
+        BUILD_AND_TEST_ARGS: --test-doxygen
+      run: ./scripts/ci_build_and_test.sh
+
 
+  code_checks:
+        runs-on: ubuntu-22.04
+        steps:
+        - name: Checkout Repository
+          uses: actions/checkout@v3
+          with:
+            submodules: true
+            lfs: false
+        - name: code_checks
+          env:
+            DOCKER_REPOSITORY: geosx/ubuntu:22.04
+            HOST_CONFIG: hostconfigs/environment.cmake
+            CMAKE_CXX_COMPILER: /usr/bin/clang++
+            CMAKE_C_COMPILER: /usr/bin/clang
+            CMAKE_BUILD_TYPE: Release
+            BUILD_AND_TEST_ARGS: --code_checks
+          run: ./scripts/ci_build_and_test.sh
 
   linux_builds:
     name: ${{matrix.name}}
@@ -54,63 +74,94 @@ jobs:
       matrix:
         include:
           - name: RHEL8.8-clang15-dbg (ubi8.8, clang-15.0.7, Debug)
-            DOCKER_REPOSITORY: geosx/ubi8:ubi8.8-854
+            DOCKER_REPOSITORY: geosx/ubi:8.8-854
             OS: ubuntu-22.04
             CMAKE_CXX_COMPILER: clang++
             CMAKE_C_COMPILER: clang
             CMAKE_BUILD_TYPE: Debug
 
           - name: RHEL8.8-clang15-rel (ubi8.8, clang-15.0.7, Release)
-            DOCKER_REPOSITORY: geosx/ubi8:ubi8.8-854
+            DOCKER_REPOSITORY: geosx/ubi:8.8-854
             OS: ubuntu-22.04
             CMAKE_CXX_COMPILER: clang++
             CMAKE_C_COMPILER: clang
             CMAKE_BUILD_TYPE: Release
-            CLANGTIDY_EXECUTABLE: clang-tidy
 
           - name: RHEL8.8-gcc12-dbg (ubi8.8, gcc 12.2.1, Debug)
-            DOCKER_REPOSITORY: geosx/ubi8:ubi8.8-854
+            DOCKER_REPOSITORY: geosx/ubi:8.8-854
             OS: ubuntu-22.04
             CMAKE_CXX_COMPILER: /opt/rh/gcc-toolset-12/root/bin/g++
             CMAKE_C_COMPILER: /opt/rh/gcc-toolset-12/root/bin/gcc
             CMAKE_BUILD_TYPE: Debug
 
           - name: RHEL8.8-gcc12-rel (ubi8.8, gcc 12.2.1, Release)
-            DOCKER_REPOSITORY: geosx/ubi8:ubi8.8-854
+            DOCKER_REPOSITORY: geosx/ubi:8.8-854
             OS: ubuntu-22.04
             CMAKE_CXX_COMPILER: /opt/rh/gcc-toolset-12/root/bin/g++
             CMAKE_C_COMPILER: /opt/rh/gcc-toolset-12/root/bin/gcc
             CMAKE_BUILD_TYPE: Release
 
-          - name: ubuntu22-gcc11-cuda11-rel (ubi8.8, gcc 11.4.0, cuda-12.2.2, Release)
-            DOCKER_REPOSITORY: geosx/ubuntu22:ubuntu22.04-cuda11.8.0
+          - name: ubuntu22-gcc11-rel (ubi8.8, gcc 11.4.0, Release)
+            DOCKER_REPOSITORY: geosx/ubuntu:22.04
+            OS: ubuntu-22.04
+            CMAKE_CXX_COMPILER: /usr/bin/g++
+            CMAKE_C_COMPILER: /usr/bin/gcc
+            CMAKE_BUILD_TYPE: Release
+            BUILD_AND_TEST_ARGS: "--disable-unit-tests"
+
+          - name: ubuntu22-clang14-rel (ubi8.8, clang-14.0.0, Release)
+            DOCKER_REPOSITORY: geosx/ubuntu:22.04
+            OS: ubuntu-22.04
+            CMAKE_CXX_COMPILER: /usr/bin/clang++
+            CMAKE_C_COMPILER: /usr/bin/clang
+            CMAKE_BUILD_TYPE: Release
+            BUILD_AND_TEST_ARGS: "--disable-unit-tests"
+
+          - name: ubuntu22-clang14-dbg (ubi8.8, clang-14.0.0, Debug)
+            DOCKER_REPOSITORY: geosx/ubuntu:22.04
+            OS: ubuntu-22.04
+            CMAKE_CXX_COMPILER: /usr/bin/clang++
+            CMAKE_C_COMPILER: /usr/bin/clang
+            CMAKE_BUILD_TYPE: Debug
+            BUILD_AND_TEST_ARGS: "--disable-unit-tests"
+
+          - name: ubuntu22-gcc11-dbg (ubi8.8, gcc 11.4.0, Release)
+            DOCKER_REPOSITORY: geosx/ubuntu:22.04
+            OS: ubuntu-22.04
+            CMAKE_CXX_COMPILER: /usr/bin/g++
+            CMAKE_C_COMPILER: /usr/bin/gcc
+            CMAKE_BUILD_TYPE: Debug
+            BUILD_AND_TEST_ARGS: "--disable-unit-tests"
+
+          - name: ubuntu22-gcc11-cuda11-rel (ubi8.8, gcc 11.4.0, cuda-11.8.0, Release)
+            DOCKER_REPOSITORY: geosx/ubuntu:22.04-cuda11.8.0
             OS: ubuntu-22.04
             CMAKE_CXX_COMPILER: /usr/bin/g++
             CMAKE_C_COMPILER: /usr/bin/gcc
             CMAKE_BUILD_TYPE: Release
             ENABLE_CUDA: ON
             BUILD_AND_TEST_ARGS: "--disable-unit-tests"
 
-          - name: ubuntu22-gcc11-cuda11-dbg (ubi8.8, gcc 11.4.0, cuda-12.2.2, Debug)
-            DOCKER_REPOSITORY: geosx/ubuntu22:ubuntu22.04-cuda11.8.0
+          - name: ubuntu22-gcc11-cuda11-dbg (ubi8.8, gcc 11.4.0, cuda-11.8.0, Debug)
+            DOCKER_REPOSITORY: geosx/ubuntu:22.04-cuda11.8.0
             OS: ubuntu-22.04
             CMAKE_CXX_COMPILER: /usr/bin/g++
             CMAKE_C_COMPILER: /usr/bin/gcc
             CMAKE_BUILD_TYPE: Debug
             ENABLE_CUDA: ON
             BUILD_AND_TEST_ARGS: "--disable-unit-tests"
 
-          - name: ubuntu22-clang14-cuda11-rel (ubi8.8, clang-14.0.0, cuda-12.2.2, Release)
-            DOCKER_REPOSITORY: geosx/ubuntu22:ubuntu22.04-cuda11.8.0
+          - name: ubuntu22-clang14-cuda11-rel (ubi8.8, clang-14.0.0, cuda-11.8.0, Release)
+            DOCKER_REPOSITORY: geosx/ubuntu:22.04-cuda11.8.0
             OS: ubuntu-22.04
             CMAKE_CXX_COMPILER: /usr/bin/clang++
             CMAKE_C_COMPILER: /usr/bin/clang
             CMAKE_BUILD_TYPE: Release
             ENABLE_CUDA: ON
             BUILD_AND_TEST_ARGS: "--disable-unit-tests"
 
-          - name: ubuntu22-clang14-cuda11-dbg (ubi8.8, clang-14.0.0, cuda-12.2.2, Debug)
-            DOCKER_REPOSITORY: geosx/ubuntu22:ubuntu22.04-cuda11.8.0
+          - name: ubuntu22-clang14-cuda11-dbg (ubi8.8, clang-14.0.0, cuda-11.8.0, Debug)
+            DOCKER_REPOSITORY: geosx/ubuntu:22.04-cuda11.8.0
             OS: ubuntu-22.04
             CMAKE_CXX_COMPILER: /usr/bin/clang++
             CMAKE_C_COMPILER: /usr/bin/clang
@@ -119,7 +170,7 @@ jobs:
             BUILD_AND_TEST_ARGS: "--disable-unit-tests"
 
           - name: RHEL8.8-clang15-cuda12-rel (ubi8.8, clang-15.0.7, cuda-12.2.2, Release)
-            DOCKER_REPOSITORY: geosx/ubi8:ubi8.8-cuda12.2.2
+            DOCKER_REPOSITORY: geosx/ubi:8.8-cuda12.2.2
             OS: ubuntu-22.04
             CMAKE_CXX_COMPILER: clang++
             CMAKE_C_COMPILER: clang
@@ -128,7 +179,7 @@ jobs:
             BUILD_AND_TEST_ARGS: "--disable-unit-tests"
 
           - name: RHEL8.8-gcc12-cuda12-rel (ubi8.8, gcc 12.2.1, cuda-12.2.2, Release)
-            DOCKER_REPOSITORY: geosx/ubi8:ubi8.8-cuda12.2.2
+            DOCKER_REPOSITORY: geosx/ubi:8.8-cuda12.2.2
             OS: ubuntu-22.04
             CMAKE_CXX_COMPILER: /opt/rh/gcc-toolset-12/root/bin/g++
             CMAKE_C_COMPILER: /opt/rh/gcc-toolset-12/root/bin/gcc
@@ -153,6 +204,28 @@ jobs:
         CMAKE_C_COMPILER: ${{ matrix.CMAKE_C_COMPILER }}
         CMAKE_BUILD_TYPE: ${{ matrix.CMAKE_BUILD_TYPE }}
         ENABLE_CUDA: ${{ matrix.ENABLE_CUDA }}
-        BUILD_AND_TEST_ARGS: ${{ matrix.BUILD_AND_TEST_ARGS }}
+        BUILD_AND_TEST_ARGS: ${{ matrix.BUILD_AND_TEST_ARGS }} --build-exe
         HOST_CONFIG: hostconfigs/environment.cmake
       run: ./scripts/ci_build_and_test.sh
+
+  check_that_all_jobs_succeeded:
+    runs-on: ubuntu-22.04
+    needs:
+    - linux_builds
+    - doxygen_check
+    - code_checks
+    if: ${{ always() }}
+    env:
+      RETURN_VAL: |
+        ${{
+        needs.linux_builds.result == 'success' &&
+        needs.doxygen_check.result == 'success' &&
+        needs.code_checks.result == 'success'
+        }}
+    steps:
+    - name: PR Success
+      if: ${{ contains(env.RETURN_VAL, 'true') }}
+      run: "true"
+    - name: PR Failure
+      if: ${{ contains(env.RETURN_VAL, 'false') }}
+      run: "false"

cmake/CMakeBasics.cmake

@@ -25,16 +25,4 @@ blt_append_custom_compiler_flag( FLAGS_VAR CMAKE_CXX_FLAGS_DEBUG
                                  CLANG "-fstandalone-debug"
                                 )
 
-blt_append_custom_compiler_flag( FLAGS_VAR GEOSX_NINJA_FLAGS
-                  DEFAULT     " "
-                  GNU         "-fdiagnostics-color=always"
-                  CLANG       "-fcolor-diagnostics"
-                  )
-
-
-if( ${CMAKE_MAKE_PROGRAM} STREQUAL "ninja" OR ${CMAKE_MAKE_PROGRAM} MATCHES ".*/ninja$" )
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${GEOSX_NINJA_FLAGS}")
-endif()
-
-
 set( CAMP_ENABLE_TESTS OFF CACHE BOOL "")

cmake/Macros.cmake

@@ -45,8 +45,19 @@ macro(shiva_add_code_checks)
                          SOURCES   ${_sources}
                          UNCRUSTIFY_CFG_FILE ${PROJECT_SOURCE_DIR}/src/uncrustify.cfg
                          CPPCHECK_FLAGS ${CPPCHECK_FLAGS}
-                         D
                          )
 
+    if( CPPCHECK_FOUND )
+        add_test( NAME testCppCheck
+                COMMAND bash -c "make cppcheck_check 2> >(tee cppcheck.err) >/dev/null && exit $(cat cppcheck.err | wc -l)"
+                WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+                )
+    endif()
 
+    if( CLANGTIDY_FOUND )
+        add_test( NAME testClangTidy
+                COMMAND bash -c "make clang_tidy_check 2> >(tee tidyCheck.err) >/dev/null && exit $(cat tidyCheck.err | wc -l)"
+                WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+                )
+    endif()
 endmacro(shiva_add_code_checks)

docker/buildAndPush.bash

@@ -2,8 +2,7 @@
 
 
 
-images="ubuntu22-cuda11:ubuntu22.04-cuda11.8.0"
-# ubi8:ubi8.8-854 ubi8-cuda11:ubi8.8-cuda11.8.0  ubi8-cuda12:ubi8.8-cuda12.2.2
+images="ubuntu:22.04 ubuntu-cuda11:22.04-cuda11.8.0 ubi:8.8-854 ubi-cuda11:8.8-cuda11.8.0  ubi-cuda12:8.8-cuda12.2.2"
 
 for image in $images; do
   imagePart=(${image//:/ })
@@ -15,10 +14,12 @@ for image in $images; do
 
   repo=geosx/${dirRoot}:${tag}
 
+  echo 
   echo dir=${dir}
   echo repo=${repo}
+  echo 
 
 
-docker build ${dir} -t ${repo}
-docker push ${repo}
+  docker build ${dir} -t ${repo}
+  docker push ${repo}
 done

docker/ubuntu22-cuda11/Dockerfile → docker/ubuntu-cuda11/Dockerfile

@@ -8,7 +8,9 @@ RUN ln -fs /usr/share/zoneinfo/America/Los_Angeles /etc/localtime && \
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
         curl \
         python3 \
-        clang
+        clang \
+        cppcheck \
+        clang-tidy
 
 ARG CMAKE_VERSION=3.23.5
 RUN curl -fsSL -k  https://cmake.org/files/v${CMAKE_VERSION%.[0-9]*}/cmake-${CMAKE_VERSION}-linux-x86_64.tar.gz | tar --directory=/usr/local --strip-components=1 -xzf -

docker/ubuntu/Dockerfile

@@ -0,0 +1,20 @@
+FROM ubuntu:22.04 AS ubuntu22
+
+# install required packages 
+RUN ln -fs /usr/share/zoneinfo/America/Los_Angeles /etc/localtime && \
+    apt-get update && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+        curl \
+        python3 \
+        make \
+	gcc \
+	g++ \
+        clang \
+        cppcheck \
+        clang-tidy
+
+ARG CMAKE_VERSION=3.23.5
+RUN curl -fsSL -k  https://cmake.org/files/v${CMAKE_VERSION%.[0-9]*}/cmake-${CMAKE_VERSION}-linux-x86_64.tar.gz | tar --directory=/usr/local --strip-components=1 -xzf -
+
+ARG DOXYGEN_VERSION=1.9.8
+RUN curl -fsSL -k  https://www.doxygen.nl/files/doxygen-${DOXYGEN_VERSION}.linux.bin.tar.gz | tar --directory=/usr/local --strip-components=1 -xzf -

docs/CMakeLists.txt

@@ -1,3 +1,8 @@
 if(DOXYGEN_FOUND)
     blt_add_doxygen_target( shiva_doxygen )
+
+    add_test( NAME testDoxygenCheck
+          COMMAND bash -c "${mkdir_cmd} ${DOXYGEN_EXECUTABLE} Doxyfile 2> >(tee doxygen.err) && exit $(cat doxygen.err | wc -l)"
+          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+          )
 endif()

docs/Doxyfile.in

@@ -943,7 +943,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ../../src
+INPUT                  = @PROJECT_SOURCE_DIR@/src
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1000,7 +1000,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = 
+EXCLUDE                = @PROJECT_SOURCE_DIR@/tpl/*
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded

scripts/ci_build_and_test_in_container.sh

@@ -12,7 +12,7 @@ free -m
 function or_die () {
     "$@"
     local status=$?
-
+    echo status = $status
     if [[ $status != 0 ]] ; then
         echo ERROR $status command: $@
         exit $status
@@ -49,16 +49,26 @@ if [[ "$*" == *--test-code-style* ]]; then
 fi
 
 # Documentation check
-if [[ "$*" == *--test-documentation* ]]; then
+if [[ "$*" == *--test-doxygen* ]]; then
   or_die ctest --output-on-failure -R "testDoxygenCheck"
   exit 0
 fi
 
-or_die make
+# code checks
+if [[ "$*" == *----code_checks* ]]; then
+  or_die ctest --output-on-failure -R "testCppCheck|testClangTidy"
+  exit 0
+fi
+
+if [[ "$*" == *--build-exe* ]]; then
+  or_die make -j $(nproc)
 
-if [[ "$*" != *--disable-unit-tests* ]]; then
-  or_die ctest --output-on-failure -E "testUncrustifyCheck|testDoxygenCheck"
+  if [[ "$*" != *--disable-unit-tests* ]]; then
+    or_die ctest --output-on-failure -E "testUncrustifyCheck|testDoxygenCheck|testCppCheck|testClangTidy"
+  fi
 fi
 
 
-exit 0
+
+
+exit 0

scripts/config-build.py

@@ -166,5 +166,10 @@ def extract_cmake_location(file_path):
 print("Changing to build directory...")
 os.chdir(buildpath)
 print("Executing cmake line: '%s'\n" % cmakeline)
-subprocess.call(cmakeline,shell=True)
+
+try:
+    subprocess.call(cmakeline,shell=True)
+except:
+    print("CMake failed.  See above output for details.")
+    sys.exit(1)