Merge branch 'development/experimental-migration' into 'master'

Merge 0.1 head

See merge request !97

.clang-format

@@ -25,9 +25,25 @@ BraceWrapping:
 NamespaceIndentation: All
 FixNamespaceComments: true
 
-IndentWrappedFunctionNames: true
+IndentWrappedFunctionNames: false # Do not indent after function def break
 AllowShortFunctionsOnASingleLine: Inline
 AlwaysBreakTemplateDeclarations: true
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: true
+AlignEscapedNewlines: Right
+AlignOperands: true
+AlignTrailingComments: true
+BreakConstructorInitializers: BeforeComma
+BreakStringLiterals: true
+CompactNamespaces: true
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 2
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+MaxEmptyLinesToKeep: 2
 
 # For loop
-ForEachMacros: ['mln_forall', 'mln_foreach']
+ForEachMacros: ['mln_forall', 'mln_foreach', 'mln_foreach_new', 'mln_reverse_foreach']

.gitignore

 /build*
 /cmake-build-*
-/doc/build
-/doc/html
-/doc/doxyxml
 /doc/source/images/*.png
-.vscode
+/test_package/build
+/doc/source/_build
 .vs
 .idea
 *.pyc
-compile_commands.json
\ No newline at end of file
+compile_commands.json
+/venv_*/
+/**/.DS_Store
+.nfs*
\ No newline at end of file

.gitlab-ci.yml

 stages:
     - build
     - test
+    - bench
     - deploy
 
-image: carlinet/buildimage
+cache:
+    paths:
+        - .cache/conan/data
 
+variables:
+    FEDORA_RAWHIDE: "${CI_REGISTRY}/olena/pylene-dockers/fedora-rawhide"
+    FEDORA_31: "${CI_REGISTRY}/olena/pylene-dockers/fedora-31"
+    PACKAGE_NAME: "pylene"                                                      # Conan package name
+    PACKAGE_TAG: "stable"                                                       # Conan tag
+    PACKAGE_VERSION: "head"                                                     # Version to build
+    CMAKE_BUILD_PARALLEL_LEVEL: 6
+    CONAN_USER: "lrde"
+
+before_script:
+        - conan config set storage.path="${CI_PROJECT_DIR}/.cache/conan/data"
+
+########
+# Test #
+########
+
+windows-debug:
+    before_script:
+        - conan config set storage.path="${env:CI_PROJECT_DIR}\.cache\conan\data"
+        - Invoke-BatchFile -Path "${env:VCVAR2019}" -Parameters "${env:ARCH}"
+    stage: build
+    script:
+        - mkdir build; cd build
+        - conan install .. -s build_type=Debug --build missing
+        - cmake .. -G Ninja -DCMAKE_BUILD_TYPE=debug -D CMAKE_TOOLCHAIN_FILE="C:\vcpkg\scripts\buildsystems\vcpkg.cmake"
+        - cmake --build . --target build-tests
+        - ctest -L UnitTests --schedule-random --output-on-failure
+    dependencies: []
+    artifacts:
+        reports:
+            junit: [build/tests/UT*.xml, build/bench/tests/UT*.xml]
+        expire_in: 1 week
+    tags: [ windows ]
+    rules:
+        - if: $CI_MERGE_REQUEST_ID
+        - if: $CI_COMMIT_BRANCH == "master"
+        - when: manual
+    variables:
+        VCVAR2019: 'C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Auxiliary\Build\vcvarsall.bat'
+        ARCH: x64
 
 .job-build-linux-base: &distcheck-linux-base
-    stage: test
+    stage: build
     script:
         - mkdir build && cd build
-        - cmake .. -DCMAKE_BUILD_TYPE=$PYLENE_CONFIGURATION -DPYLENE_BUILD_BENCHMARKS=OFF
-        - cmake --build . --target check
+        - conan install .. -pr gcc-9 --build missing -e CXX=g++ -e CC=gcc
+        - cmake -G Ninja .. -DCMAKE_BUILD_TYPE=$PYLENE_CONFIGURATION -DSANITIZE_ADDRESS=$ASAN -DSANITIZE_MEMORY=$MSAN -DSANITIZE_UNDEFINED=$UBSAN
+        - cmake --build . --target Pylene
+        - cmake --build . --target build-tests
+        - ctest -L UnitTests --schedule-random --output-on-failure
+    dependencies: []
+    artifacts:
+        reports:
+            junit: [build/tests/UT*.xml, build/bench/tests/UT*.xml]
+        expire_in: 1 week
 
+# Msan not available for gcc. It requires instrumented libstdc++ and instrumented thirdparties so it is disabled for now.
+# No tsan because no multithreaded code for now
+# Asan, memsan and tsan are incompatible with each other within the same binary
+# Asan and ubsan can work together
 
-distcheck-linux-gcc-release:
+
+distcheck-linux-gcc9-release:
     <<: *distcheck-linux-base
+    image: ${FEDORA_31}
     variables:
         PYLENE_CONFIGURATION: "Release"
         CXX: "g++"
         CC: "gcc"
+        ASAN: "OFF"
+        MSAN: "OFF"
+        UBSAN: "OFF"
 
-distcheck-linux-clang-release:
-    <<: *distcheck-linux-base
-    variables:
-        PYLENE_CONFIGURATION: "Release"
-        CXX: "clang++"
-        CC: "clang"
-
-distcheck-linux-gcc-debug:
+distcheck-linux-gcc9-debug-asan-ubsan:
     <<: *distcheck-linux-base
+    image: ${FEDORA_31}
     variables:
         PYLENE_CONFIGURATION: "Debug"
         CXX: "g++"
         CC: "gcc"
+        ASAN: "ON"
+        MSAN: "OFF"
+        UBSAN: "ON"
+
 
-distcheck-linux-clang-debug:
+distcheck-linux-coverage:
     <<: *distcheck-linux-base
+    image: ${FEDORA_31}
+    after_script:
+        - mkdir coverage
+        - gcovr --root pylene build -s --xml cobertura --html-details coverage/index.html
     variables:
         PYLENE_CONFIGURATION: "Debug"
-        CXX: "clang++"
-        CC: "clang"
+        CXX: "g++"
+        CC: "gcc"
+        CXXFLAGS: "-fprofile-arcs -ftest-coverage"
+        CFLAGS: "-fprofile-arcs -ftest-coverage"
+    artifacts:
+        paths:
+            - coverage/
+        reports:
+            cobertura: cobertura
+        expire_in: 1 week
+    coverage: '/lines: \d+\.\d+\%/'
+    rules:
+        - if: $CI_MERGE_REQUEST_ID
+        - if: $CI_COMMIT_BRANCH == "master"
+        - when: manual
 
-build-doc-images:
-    stage: build
+#########
+# Bench #
+#########
+
+.job-bench-linux-base: &distbench-linux-base
+    stage: bench
     script:
         - mkdir build && cd build
-        - cmake .. -DCMAKE_BUILD_TYPE=Release -DPYLENE_BUILD_BENCHMARKS=OFF
-        - cmake --build . --target build-images
+        - conan install .. -pr gcc-9 --build missing -e CXX=g++ -e CC=gcc
+        - cmake -G Ninja .. -DCMAKE_BUILD_TYPE=Release
+        - cmake --build . --target fetch-external-data
+        - cmake --build . --target build-bench
+        - cmake --build . --target run-all-benchmarks
+        - ctest -L SpeedTests -V
+    tags: [ "pylene-benchmarks" ]
+    when: manual
+    dependencies: []
     artifacts:
+        name: "benchmark-results"
         paths:
-            - doc/source/images
-        expire_in: 2 days
+            - build/bench/*.json
+        expire_in: 1 week
+
+distbench-linux-gcc9-release:
+    <<: *distbench-linux-base
+    image: ${FEDORA_31}
+    variables:
+        CXX: "g++"
+        CC: "gcc"
+
 
 
 #################
@@ -59,14 +154,17 @@ build-doc-images:
 #################
 
 .documentation-base:  &documentation-base
-    stage: test
+    image: ${FEDORA_31}
+    stage: build
     script:
-        - cd doc
-        - doxygen
-        - sphinx-build -b html source ../public
+        - mkdir build && cd build
+        - conan install -u .. -pr gcc-9 --build missing -e CXX=g++ -e CC=gcc
+        - cmake -G Ninja .. -DCMAKE_BUILD_TYPE=Release
+        - cmake --build . --target build-doc
+        - mkdir ../public && mv doc/sphinx/* ../public/
     artifacts:
         name: "documentation"
-        expire_in: 2 days
+        expire_in: 1 week
         paths:
             - public/
 
@@ -74,10 +172,26 @@ build-doc-images:
 documentation:
     <<: *documentation-base
     except:
-    - dev
+        - dev
+
+
+##########
+# Deploy #
+##########
 
-# Deploy
 pages:
     <<: *documentation-base
     only:
-    - dev
+        - dev
+
+package:
+    image: ${FEDORA_31}
+    stage: deploy
+    dependencies: []
+    script:
+        - mkdir build && cd build
+        - conan user carlinet -r lrde-public -p $CONAN_LRDE_API_KEY
+        - conan create .. $CONAN_USER/$PACKAGE_TAG -pr gcc-9 --build missing -e CXX=g++ -e CC=gcc
+        - conan upload -r lrde-public --all $PACKAGE_NAME/$PACKAGE_VERSION@$CONAN_USER/$PACKAGE_TAG
+    rules:
+        - if: $CI_COMMIT_BRANCH == "master" || $CI_COMMIT_BRANCH == "development/cpp20"

.vscode/.cmaketools.json

+{
+  "variant": null,
+  "activeEnvironments": [],
+  "codeModel": null
+}
\ No newline at end of file

.vscode/c_cpp_properties.json

+{
+    "configurations": [
+        {
+            "name": "Mac",
+            "includePath": [
+                "/usr/include",
+                "/usr/local/include",
+                "${workspaceRoot}"
+            ],
+            "defines": [],
+            "intelliSenseMode": "clang-x64",
+            "browse": {
+                "path": [
+                    "/usr/include",
+                    "/usr/local/include",
+                    "${workspaceRoot}"
+                ],
+                "limitSymbolsToIncludedHeaders": true,
+                "databaseFilename": ""
+            },
+            "macFrameworkPath": [
+                "/System/Library/Frameworks",
+                "/Library/Frameworks"
+            ]
+        },
+        {
+            "name": "Linux",
+            "includePath": [
+                "/usr/include/c++/6",
+                "/usr/include/x86_64-linux-gnu/c++/6",
+                "/usr/include/c++/6/backward",
+                "/usr/lib/gcc/x86_64-linux-gnu/6/include",
+                "/usr/local/include",
+                "/usr/lib/gcc/x86_64-linux-gnu/6/include-fixed",
+                "/usr/include/x86_64-linux-gnu",
+                "/usr/include",
+                "${workspaceRoot}",
+                "${workspaceFolder}/pylene/include"
+            ],
+            "defines": [],
+            "intelliSenseMode": "clang-x64",
+            "browse": {
+                "path": [
+                    "/usr/include/c++/6",
+                    "/usr/include/x86_64-linux-gnu/c++/6",
+                    "/usr/include/c++/6/backward",
+                    "/usr/lib/gcc/x86_64-linux-gnu/6/include",
+                    "/usr/local/include",
+                    "/usr/lib/gcc/x86_64-linux-gnu/6/include-fixed",
+                    "/usr/include/x86_64-linux-gnu",
+                    "/usr/include",
+                    "${workspaceRoot}"
+                ],
+                "limitSymbolsToIncludedHeaders": true,
+                "databaseFilename": ""
+            },
+            "compilerPath": "/usr/local/bin/clang",
+            "cStandard": "c11",
+            "cppStandard": "c++17",
+            "configurationProvider": "vector-of-bool.cmake-tools"
+        },
+        {
+            "name": "Win32",
+            "includePath": [
+                "C:/Program Files (x86)/Microsoft Visual Studio 14.0/VC/include",
+                "${workspaceRoot}"
+            ],
+            "defines": [
+                "_DEBUG",
+                "UNICODE"
+            ],
+            "intelliSenseMode": "msvc-x64",
+            "browse": {
+                "path": [
+                    "C:/Program Files (x86)/Microsoft Visual Studio 14.0/VC/include/*",
+                    "${workspaceRoot}"
+                ],
+                "limitSymbolsToIncludedHeaders": true,
+                "databaseFilename": ""
+            }
+        }
+    ],
+    "version": 4
+}
\ No newline at end of file

.vscode/launch.json

+{
+  // Use IntelliSense to learn about possible attributes.
+  // Hover to view descriptions of existing attributes.
+  // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "name": "(lldb) Launch",
+      "type": "lldb",
+      "request": "launch",
+      "program": "enter program name, for example ${workspaceFolder}/a.out",
+      "args": [],
+      "stopOnEntry": false,
+      "cwd": "${workspaceFolder}",
+      "linux": {
+        "args": [],
+        "terminal": "external",
+        "initCommands": [
+          {
+            "description": "Enable pretty-printing for gdb",
+            "text": "-enable-pretty-printing",
+            "ignoreFailures": true
+          }
+        ]
+      }
+    },
+    {
+      "name": "(gdb) Launch",
+      "type": "cppdbg",
+      "request": "launch",
+      "program": "enter program name, for example ${workspaceFolder}/a.out",
+      "args": [],
+      "stopAtEntry": false,
+      "cwd": "${workspaceFolder}",
+      "environment": [],
+      "externalConsole": true,
+      "MIMode": "gdb",
+      "setupCommands": [
+        {
+          "description": "Enable pretty-printing for gdb",
+          "text": "-enable-pretty-printing",
+          "ignoreFailures": true
+        }
+      ]
+    }
+  ]
+}
\ No newline at end of file

.vscode/settings.json

+{
+}
\ No newline at end of file

.vscode/tasks.json

+{
+    // See https://go.microsoft.com/fwlink/?LinkId=733558
+    // for the documentation about the tasks.json format
+    "version": "2.0.0",
+    "tasks": [
+        {
+            "label": "mkdir-remote",
+            "type": "shell",
+            "command": "ssh node7 'mkdir -p /work/mroynard/lrde/pylene/build-remote'",
+            "group": "build"
+        },
+        {
+            "label": "mkdir-remote-release",
+            "type": "shell",
+            "command": "ssh node7 'mkdir -p /work/mroynard/lrde/pylene/build-remote-release'",
+            "group": "build"
+        },
+        {
+            "label": "conan-remote",
+            "dependsOn": "mkdir-remote",
+            "type": "shell",
+            "command": "ssh node7 'cd /work/mroynard/lrde/pylene/build-remote && source ../venv_python371/bin/activate && ../venv_python371/bin/conan install --build missing -o benchmark=True -o gtest=True -o freeimage=True ..'",
+            "group": "build"
+        },
+        {
+            "label": "conan-remote-release",
+            "dependsOn": "mkdir-remote-release",
+            "type": "shell",
+            "command": "ssh node7 'cd /work/mroynard/lrde/pylene/build-remote-release && source ../venv_python371/bin/activate && ../venv_python371/bin/conan install --build missing -o benchmark=True -o gtest=True -o freeimage=True ..'",
+            "group": "build"
+        },
+        {
+            "label": "configure-remote",
+            "dependsOn": "conan-remote",
+            "type": "shell",
+            "command": "ssh node7 'cd /work/mroynard/lrde/pylene/build-remote && cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug -DCMAKE_EXPORT_COMPILE_COMMANDS=ON ..'",
+            "group": "build"
+        },
+        {
+            "label": "configure-remote-release",
+            "dependsOn": "conan-remote-release",
+            "type": "shell",
+            "command": "ssh node7 'cd /work/mroynard/lrde/pylene/build-remote-release && cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DCMAKE_EXPORT_COMPILE_COMMANDS=ON ..'",
+            "group": "build"
+        },
+        {
+            "label": "build-check-remote",
+            "dependsOn": "configure-remote",
+            "type": "shell",
+            "command": "ssh node7 'cd /work/mroynard/lrde/pylene/build-remote && cmake --build . --target check --config Debug -- -j12 | tee check.log.txt'",
+            "group": "build",
+            "problemMatcher": "$gcc"
+        },
+        {
+            "label": "only-build-check-remote",
+            "type": "shell",
+            "command": "ssh node7 'cd /work/mroynard/lrde/pylene/build-remote && cmake --build . --target check --config Debug -- -j12 | tee check.log.txt'",
+            "group": "build",
+            "problemMatcher": "$gcc"
+        },
+        {
+            "label": "build-benchmarks-remote-release",
+            "dependsOn": "configure-remote-release",
+            "type": "shell",
+            "command": "ssh node7 'cd /work/mroynard/lrde/pylene/build-remote-release && cmake --build . --target benchmarks --config Release -- -j12 | tee bench.log.txt'",
+            "group": "build",
+            "problemMatcher": "$gcc"
+        },
+        {
+            "label": "only-build-benchmarks-remote-release",
+            "type": "shell",
+            "command": "ssh node7 'cd /work/mroynard/lrde/pylene/build-remote-release && cmake --build . --target benchmarks --config Release -- -j12 | tee bench.log.txt'",
+            "group": "build",
+            "problemMatcher": "$gcc"
+        },
+        {
+            "label": "run-benchmarks-remote-release",
+            "dependsOn": "build-benchmarks-remote-release",
+            "type": "shell",
+            "command": "ssh node7 'cd /work/mroynard/lrde/pylene/build-remote-release && cmake --build . --target benchmarks-run --config Release -- -j1'",
+            "group": "build",
+            "problemMatcher": "$gcc"
+        },
+        {
+            "label": "build-doc-remote",
+            "dependsOn": "configure-remote",
+            "type": "shell",
+            "command": "ssh node7 'cd /work/mroynard/lrde/pylene/build-remote && source ../venv_python371/bin/activate && cmake --build . --target doc -- -j12 | tee doc.log.txt'",
+            "group": "build",
+            "problemMatcher": "$gcc"
+        },
+        {
+            "label": "only-build-doc-remote",
+            "type": "shell",
+            "command": "ssh node7 'cd /work/mroynard/lrde/pylene/build-remote && source ../venv_python371/bin/activate && cmake --build . --target doc -- -j12 | tee doc.log.txt'",
+            "group": "build",
+            "problemMatcher": "$gcc"
+        },
+        {
+            "label": "clean-remote",
+            "type": "shell",
+            "command": "ssh node7 'cd /work/mroynard/lrde/pylene/build-remote && rm -rf CMakeCache.txt CMakeFiles'",
+            "group": "build",
+        },
+        {
+            "label": "clean-remote-release",
+            "type": "shell",
+            "command": "ssh node7 'cd /work/mroynard/lrde/pylene/build-remote-release && rm -rf CMakeCache.txt CMakeFiles'",
+            "group": "build",
+        },
+        {
+            "label": "clang-format-current",
+            "type": "shell",
+            "command": "clang-format -i ${file} ",
+            "group": "none"
+        }
+    ]
+}
\ No newline at end of file

CMakeLists.txt

 cmake_minimum_required(VERSION 3.8.2)
-project(MILENA)
+project(Pylene)
 
 # Add FindTBB directory to CMake's module path
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/cmake/")
 
-find_package(Boost 1.42 COMPONENTS program_options REQUIRED)
+
+if (EXISTS "${CMAKE_BINARY_DIR}/conanbuildinfo.cmake")
+  include("${CMAKE_BINARY_DIR}/conanbuildinfo.cmake")
+  conan_set_rpath()
+  conan_set_std()
+  conan_set_fpic()
+  conan_check_compiler()
+  conan_set_libcxx()
+  conan_set_vs_runtime()
+endif()
+
+
+if (EXISTS "${CMAKE_CURRENT_BINARY_DIR}/conan_paths.cmake")
+  include("${CMAKE_CURRENT_BINARY_DIR}/conan_paths.cmake")
+endif ()
+
+find_package(Boost 1.58 COMPONENTS program_options REQUIRED)
 find_package(FreeImage REQUIRED)
 find_package(TBB)
 find_package(Qt4)
 
-# CONFIGURATION OPTIONS
-set(MLN_USE_TBB YES CACHE BOOL "Set to NO to disable use of TBB and parallelization")
-option(PYLENE_BUILD_BENCHMARKS "Require Google Benchmark library. Set to YES to enable the compilation of benchmarks." YES)
 
-# Proper project creation
-set(MLN_INCLUDE_DIR "${PROJECT_SOURCE_DIR}")
-if(MSVC OR APPLE)
-  #dummy static project not linked anywere needed so that a vcxproj is generated with the sources in the solution
-  set_property(GLOBAL PROPERTY USE_FOLDERS ON)
-  file(GLOB_RECURSE MLN_SOURCES  "${MLN_INCLUDE_DIR}/*.hpp")
-  add_library(Mln_srcs EXCLUDE_FROM_ALL STATIC ${MLN_SOURCES})
-  set_target_properties(Mln_srcs PROPERTIES LINKER_LANGUAGE CXX)
-  # target_compile_features(Mln_srcs PUBLIC cxx_std_14)
-  target_include_directories(Mln_srcs PUBLIC ${MLN_INCLUDE_DIR})
-  source_group(TREE ${MLN_INCLUDE_DIR} FILES ${MLN_SOURCES})
-endif()
 
-add_library(Mln INTERFACE)
-target_include_directories(Mln INTERFACE ${MLN_INCLUDE_DIR})
+# CONFIGURE COMPILER LAUNCHERS
 
+option(USE_CCACHE "Use ccache as compiler launcher" ON)
+option(USE_DISTCC "Use ccache as compiler launcher" OFF)
 
-include_directories(SYSTEM ${Boost_INCLUDE_DIR})
-include_directories(${FreeImage_INCLUDE_DIRS})
-link_directories(${FreeImage_LIBRARY_DIR})
-link_directories(${Boost_LIBRARY_DIRS})
+if (USE_CCACHE AND USE_DISTCC)
+  message(FATAL_ERROR "You can't use both distcc and ccache at the same time. Please choose either one.")
+endif (USE_CCACHE AND USE_DISTCC)
 
-if (TBB_FOUND AND MLN_USE_TBB)
-  include_directories(${TBB_INCLUDE_DIRS})
-  link_directories(${TBB_LIBRARY_DIRS})
-  link_libraries(${TBB_LIBRARIES})
-else()
-  set(MLN_USE_TBB OFF)
-  add_definitions(-DMLN_NO_TBB)
-endif()
+# ccache
+if (USE_CCACHE)
+  find_program(CCACHE_FOUND ccache)
+  if (CCACHE_FOUND)
+    message(STATUS "ccache found")
+    set_property(GLOBAL PROPERTY RULE_LAUNCH_COMPILE ccache)
+    set_property(GLOBAL PROPERTY RULE_LAUNCH_LINK ccache)
+  endif (CCACHE_FOUND)
+endif (USE_CCACHE)
 
-if (UNIX AND NOT APPLE)
-   link_libraries(rt)
-endif()
+# distcc
+if (USE_DISTCC)
+  find_program(DISTCC_FOUND distcc)
+  if (DISTCC_FOUND)