Merge support iwyu and clang-tidy

Add support for clang-tidy [1] and iwyu [2] tools.

### Overview
These tools allow to statically find potential programming issues and include
issues, respectively. They are able to find a lot of potential issues (both bugs
or style problems), so they are a useful addition for contributors. For now, no
specific configuration is included but it is possible to give a style file which
would control what we consider to be errors and what are not.

The use of the tools is controlled through the respective `GINKGO_WITH_CLANG_TIDY`
and `GINKGO_WITH_IWYU` variables. They are turned off by default, but their
availability is highlighted in the main `README.md`

[1]: https://clang.llvm.org/extra/clang-tidy/
[2]: https://include-what-you-use.org/

### Details
+ Fix some unrelated link problems in the main `README.md`.
+ The two programs are found through CMake `find_program`. This means that the path can be directly given for `iwyu` and `clang-tidy` through the variables `GINKGO_IWYU_PATH=/path/to/iwyu` and `GINKGO_CLANG_TIDY_PATH=/path/to/clang-tidy`, respectively.
+ Adapt containers to bundle a correct version of `iwyu` and `clang-tidy`. There are often problems with standard C headers for these tools and this can be fixed either through adding symlinks or through correct compilation. See [this link for more information](include-what-you-use/include-what-you-use#679).
+ Add CI steps which gather the full `iwyu` and `clang-tidy` output


### Related PR: #298

.gitlab-ci.yml

@@ -348,6 +348,30 @@ no-circular-deps:
   dependencies: []
   allow_failure: no
 
+# Run clang-tidy and iwyu
+clang-tidy:
+  <<: *default_build
+  stage: code_quality
+  image: localhost:5000/gko-cuda100-gnu7-llvm60
+  variables:
+    <<: *default_variables
+    BUILD_OMP: "ON"
+    BUILD_CUDA: "ON"
+    EXTRA_CMAKE_FLAGS: '-DGINKGO_WITH_CLANG_TIDY=ON'
+  dependencies: []
+  allow_failure: yes
+
+iwyu:
+  <<: *default_build
+  stage: code_quality
+  image: localhost:5000/gko-cuda100-gnu7-llvm60
+  variables:
+    <<: *default_variables
+    BUILD_OMP: "ON"
+    BUILD_CUDA: "ON"
+    EXTRA_CMAKE_FLAGS: '-DGINKGO_WITH_IWYU=ON'
+  dependencies: []
+  allow_failure: yes
 
 # Deploy documentation to github-pages
 gh-pages:

CMakeLists.txt

@@ -10,8 +10,6 @@ include(cmake/create_test.cmake)
 include(cmake/install_helpers.cmake)
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
 
-include(cmake/build_type_helpers.cmake)
-
 # Ginkgo configuration options
 option(GINKGO_DEVEL_TOOLS "Add development tools to the build system" ON)
 option(GINKGO_BUILD_TESTS "Generate build files for unit tests" ON)
@@ -26,6 +24,8 @@ option(GINKGO_SKIP_DEPENDENCY_UPDATE
 option(GINKGO_EXPORT_BUILD_DIR
     "Make Ginkgo export its build directory to the CMake package registry."
     OFF)
+option(GINKGO_WITH_CLANG_TIDY "Make Ginkgo call `clang-tidy` to find programming issues." OFF)
+option(GINKGO_WITH_IWYU "Make Ginkgo call `iwyu` (Include What You Use) to find include issues." OFF)
 set(GINKGO_VERBOSE_LEVEL "1" CACHE STRING
   "Verbosity level. Put 0 to turn off. 1 activates a few important messages.")
 set(GINKGO_COMPILER_FLAGS "-Wpedantic" CACHE STRING
@@ -49,7 +49,7 @@ endif()
 
 # Ensure we have a debug postfix
 if(NOT DEFINED CMAKE_DEBUG_POSTFIX)
-  set(CMAKE_DEBUG_POSTFIX "d")
+    set(CMAKE_DEBUG_POSTFIX "d")
 endif()
 
 if(GINKGO_BUILD_TESTS)
@@ -62,6 +62,17 @@ if(GINKGO_BUILD_TESTS)
     include(CTest)
 endif()
 
+if (GINKGO_WITH_CLANG_TIDY)
+  find_program(GINKGO_CLANG_TIDY_PATH clang-tidy)
+endif()
+
+if (GINKGO_WITH_IWYU)
+  find_program(GINKGO_IWYU_PATH iwyu)
+endif()
+
+
+include(cmake/build_type_helpers.cmake)
+
 
 # Find important header files, store the definitions in include/ginkgo/config.h.in
 # For details, see https://gitlab.kitware.com/cmake/community/wikis/doc/tutorials/How-To-Write-Platform-Checks

INSTALL.md

@@ -36,6 +36,12 @@ Ginkgo adds the following additional switches to control what is being built:
     Ginkgo's documentation. The default is `OFF`.
 *   `-DGINKGO_EXPORT_BUILD_DIR={ON, OFF}` adds the Ginkgo build directory to the
     CMake package registry. The default is `OFF`.
+*   `-DGINKGO_WITH_CLANG_TIDY={ON, OFF}` makes Ginkgo call `clang-tidy` to find
+    programming issues. The path can be manually controlled with the CMake
+    variable `-DGINKGO_CLANG_TIDY_PATH=<path>`.
+*   `-DGINKGO_WITH_IWYU={ON, OFF}` makes Ginkgo call `iwyu` to find include
+    issues. The path can be manually controlled with the CMake variable
+    `-DGINKGO_IWYU_PATH=<path>`. 
 *   `-DGINKGO_VERBOSE_LEVEL=integer` sets the verbosity of Ginkgo.
     * `0` disables all output in the main libraries,
     * `1` enables a few important messages related to unexpected behavior (default).

README.md

@@ -4,7 +4,7 @@
 [![Coverage](https://codecov.io/gh/ginkgo-project/ginkgo/branch/develop/graph/badge.svg)](https://codecov.io/gh/ginkgo-project/ginkgo)
 [![CDash dashboard](https://img.shields.io/badge/CDash-Access-blue.svg)](http://my.cdash.org/index.php?project=Ginkgo+Project)
 [![Documentation](https://img.shields.io/badge/Documentation-latest-blue.svg)](https://ginkgo-project.github.io/ginkgo/doc/develop/)
-[![License](https://img.shields.io/github/license/ginkgo-project/ginkgo.svg)](LICENSE)
+[![License](https://img.shields.io/github/license/ginkgo-project/ginkgo.svg)](./LICENSE)
 [![c++ standard](https://img.shields.io/badge/c%2B%2B-11-blue.svg)](https://en.wikipedia.org/wiki/C%2B%2B#Standardization)
 
 Ginkgo is a high-performance linear algebra library for manycore systems, with a
@@ -48,6 +48,8 @@ In addition, if you want to contribute code to Ginkgo, you will also need the
 following:
 
 *   _clang-format 5.0.1+_ (ships as part of _clang_)
+*   _clang-tidy_ (optional, when setting the flag `-DGINKGO_WITH_CLANG_TIDY=ON`)
+*   _iwyu_ (Include What You Use, optional, when setting the flag `-DGINKGO_WITH_IWYU=ON`)
 
 ### Windows
 
@@ -91,7 +93,7 @@ Ginkgo does comprehensive unit tests using Google Tests. These tests are enabled
 A unique feature of Ginkgo is the ability to run benchmarks and view your results
 with the help of the [Ginkgo Performance Explorer (GPE)](https://ginkgo-project.github.io/gpe/). 
 
-More details about this can be found in the [documentation](https://ginkgo-project.github.io/ginkgo/doc/master/)
+More details about this can be found in the [BENCHMARKING.md page](./BENCHMARKING.md)
 
 Contributing to Ginkgo
 ---------------------------
@@ -103,7 +105,7 @@ external contributors like in the example below.
 
 #### Contributors
 I hereby place all my contributions in this codebase under a BSD-3-Clause
-license, as specified in the repository's [LICENSE](LICENSE) file.
+license, as specified in the repository's [LICENSE](./LICENSE) file.
 
 Name Surname <email@domain> Institution(s)
 

cmake/GinkgoConfig.cmake.in

@@ -51,6 +51,11 @@ set(GINKGO_SKIP_DEPENDENCY_UPDATE @GINKGO_SKIP_DEPENDENCY_UPDATE@)
 set(GINKGO_EXPORT_BUILD_DIR @GINKGO_EXPORT_BUILD_DIR@)
 set(GINKGO_VERBOSE_LEVEL @GINKGO_VERBOSE_LEVEL@)
 
+set(GINKGO_WITH_CLANG_TIDY @GINKGO_WITH_CLANG_TIDY@)
+set(GINKGO_WITH_IWYU @GINKGO_WITH_IWYU@)
+set(GINKGO_CLANG_TIDY_PATH @GINKGO_CLANG_TIDY_PATH@)
+set(GINKGO_IWYU_PATH @GINKGO_IWYU_PATH@)
+
 set(GINKGO_JACOBI_FULL_OPTIMIZATIONS @GINKGO_JACOBI_FULL_OPTIMIZATIONS@)
 
 set(GINKGO_CUDA_ARCHITECTURES @GINKGO_CUDA_ARCHITECTURES@)

cmake/build_helpers.cmake

@@ -11,4 +11,10 @@ endfunction()
 
 function(ginkgo_compile_features name)
     target_compile_features("${name}" PUBLIC cxx_std_11)
+    if(GINKGO_WITH_CLANG_TIDY AND GINKGO_CLANG_TIDY_PATH)
+        set_property(TARGET "${name}" PROPERTY CXX_CLANG_TIDY "${GINKGO_CLANG_TIDY_PATH};-checks=*")
+    endif()
+    if(GINKGO_WITH_IWYU AND GINKGO_IWYU_PATH)
+        set_property(TARGET "${name}" PROPERTY CXX_INCLUDE_WHAT_YOU_USE ${GINKGO_IWYU_PATH})
+    endif()
 endfunction()

dev_tools/containers/ginkgo-cuda-base.py

@@ -3,14 +3,17 @@
 Contents:
 	CUDA version set by the user
 	GNU compilers version set by the user
-	LLVM/Clang version set by the user
+	LLVM/Clang clang-tidy version set by the user
 	OpenMP latest apt version for Clang+OpenMP
 	Python 2 and 3 (upstream)
 	cmake (upstream)
 	git, openssh, doxygen, curl, valgrind, graphviz latest apt version
+	iwyu precompiled version 6.0
 """
 # pylint: disable=invalid-name, undefined-variable, used-before-assignment
 
+import os
+
 cuda_version = USERARG.get('cuda', '10.0')
 
 image = 'nvidia/cuda:{}-devel-ubuntu16.04'.format(cuda_version)
@@ -21,6 +24,7 @@
 Stage0 += python()
 Stage0 += cmake(eula=True)
 Stage0 += apt_get(ospackages=['git', 'openssh-client', 'doxygen', 'curl', 'valgrind', 'graphviz'])
+Stage0 += apt_get(ospackages=['iwyu'])
 
 # GNU compilers
 gnu_version = USERARG.get('gnu', '7')
@@ -31,6 +35,17 @@
 Stage0 += llvm(version=llvm_version, extra_repository=True)
 Stage0 += apt_get(ospackages=['libomp-dev']) #required for openmp+clang
 
+# clang-tidy
+clangtidy = ['clang-tidy-{}'.format(llvm_version)]
+Stage0 += packages(apt_ppas=['ppa:xorg-edgers/ppa'], apt=clangtidy)
+clangtidyln = ['ln -s /usr/bin/clang-tidy-{} /usr/bin/clang-tidy'.format(llvm_version)]
+Stage0 += shell(commands=clangtidyln)
+
+# IWYU
+if os.path.isdir('bin/'):
+        Stage0 += copy(src='bin/*', dest='/usr/bin/')
+
+
 # Correctly set the LIBRARY_PATH
 Stage0 += environment(variables={'LIBRARY_PATH': '/usr/local/cuda/lib64/stubs'})
 Stage0 += environment(variables={'LD_LIBRARY_PATH': '/usr/local/cuda/lib64/stubs'})

dev_tools/containers/ginkgo-nocuda-base.py

@@ -9,6 +9,7 @@
 	build-essential, git, openssh, doxygen, curl, valgrind latest apt version
 	graphviz, ghostscript, texlive, texlive-latex-extra, latest apt version
 	texlive-science, texlive-fonts-extra, texlive-publishers latest apt version
+	clang-tidy, iwyu: latest apt version
 	papi: adds package libpfm4, and copy precompiled papi headers and files
             from a directory called 'papi'
 """
@@ -25,6 +26,7 @@
 Stage0 += apt_get(ospackages=['build-essential', 'git', 'openssh-client', 'doxygen', 'curl', 'valgrind'])
 Stage0 += apt_get(ospackages=['graphviz', 'ghostscript', 'texlive', 'texlive-latex-extra'])
 Stage0 += apt_get(ospackages=['texlive-science', 'texlive-fonts-extra', 'texlive-publishers'])
+Stage0 += apt_get(ospackages=['clang-tidy', 'iwyu'])
 
 # GNU compilers
 gnu_version = USERARG.get('gnu', '8')

dev_tools/containers/gko-cuda100-gnu7-llvm60.baseimage

@@ -26,6 +26,11 @@ RUN apt-get update -y && \
         graphviz && \
     rm -rf /var/lib/apt/lists/*
 
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+        iwyu && \
+    rm -rf /var/lib/apt/lists/*
+
 # GNU compiler
 RUN apt-get update -y && \
     apt-get install -y --no-install-recommends software-properties-common && \
@@ -53,6 +58,18 @@ RUN apt-get update -y && \
         libomp-dev && \
     rm -rf /var/lib/apt/lists/*
 
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends software-properties-common && \
+    apt-add-repository ppa:xorg-edgers/ppa -y && \
+    apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+        clang-tidy-6.0 && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN ln -s /usr/bin/clang-tidy-6.0 /usr/bin/clang-tidy
+
+COPY bin/* /usr/bin/
+
 ENV LIBRARY_PATH=/usr/local/cuda/lib64/stubs
 
 ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64/stubs

dev_tools/containers/gko-cuda90-gnu5-llvm39.baseimage

@@ -26,6 +26,11 @@ RUN apt-get update -y && \
         graphviz && \
     rm -rf /var/lib/apt/lists/*
 
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+        iwyu && \
+    rm -rf /var/lib/apt/lists/*
+
 # GNU compiler
 RUN apt-get update -y && \
     apt-get install -y --no-install-recommends software-properties-common && \
@@ -53,6 +58,18 @@ RUN apt-get update -y && \
         libomp-dev && \
     rm -rf /var/lib/apt/lists/*
 
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends software-properties-common && \
+    apt-add-repository ppa:xorg-edgers/ppa -y && \
+    apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+        clang-tidy-3.9 && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN ln -s /usr/bin/clang-tidy-3.9 /usr/bin/clang-tidy
+
+COPY bin/* /usr/bin/
+
 ENV LIBRARY_PATH=/usr/local/cuda/lib64/stubs
 
 ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64/stubs

dev_tools/containers/gko-cuda91-gnu6-llvm40.baseimage

@@ -26,6 +26,11 @@ RUN apt-get update -y && \
         graphviz && \
     rm -rf /var/lib/apt/lists/*
 
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+        iwyu && \
+    rm -rf /var/lib/apt/lists/*
+
 # GNU compiler
 RUN apt-get update -y && \
     apt-get install -y --no-install-recommends software-properties-common && \
@@ -53,6 +58,18 @@ RUN apt-get update -y && \
         libomp-dev && \
     rm -rf /var/lib/apt/lists/*
 
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends software-properties-common && \
+    apt-add-repository ppa:xorg-edgers/ppa -y && \
+    apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+        clang-tidy-4.0 && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN ln -s /usr/bin/clang-tidy-4.0 /usr/bin/clang-tidy
+
+COPY bin/* /usr/bin/
+
 ENV LIBRARY_PATH=/usr/local/cuda/lib64/stubs
 
 ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64/stubs

dev_tools/containers/gko-cuda92-gnu7-llvm50.baseimage

@@ -26,6 +26,11 @@ RUN apt-get update -y && \
         graphviz && \
     rm -rf /var/lib/apt/lists/*
 
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+        iwyu && \
+    rm -rf /var/lib/apt/lists/*
+
 # GNU compiler
 RUN apt-get update -y && \
     apt-get install -y --no-install-recommends software-properties-common && \
@@ -53,6 +58,18 @@ RUN apt-get update -y && \
         libomp-dev && \
     rm -rf /var/lib/apt/lists/*
 
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends software-properties-common && \
+    apt-add-repository ppa:xorg-edgers/ppa -y && \
+    apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+        clang-tidy-5.0 && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN ln -s /usr/bin/clang-tidy-5.0 /usr/bin/clang-tidy
+
+COPY bin/* /usr/bin/
+
 ENV LIBRARY_PATH=/usr/local/cuda/lib64/stubs
 
 ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64/stubs

dev_tools/containers/gko-nocuda-gnu8-llvm70.baseimage

@@ -43,11 +43,8 @@ RUN apt-get update -y && \
 
 RUN apt-get update -y && \
     apt-get install -y --no-install-recommends \
-        texlive \
-        texlive-latex-extra \
-        texlive-science \
-        texlive-fonts-extra \
-        texlive-publishers && \
+        clang-tidy \
+        iwyu && \
     rm -rf /var/lib/apt/lists/*
 
 # GNU compiler