Merge pull request #99 from IOHprofiler/dev

Dev

.github/workflows/macos.yml

@@ -73,6 +73,7 @@ jobs:
       run: |
         brew install ninja
         python -m pip install --upgrade pip
-        python setup.py develop
+        pip install mypy
+        pip install -e . -v
     - name: Run unit tests
       run: python -m unittest -v

.github/workflows/python-publish.yml

@@ -81,7 +81,7 @@ jobs:
             sudo apt update -y
             sudo apt install ninja-build -y
             python -m pip install --upgrade pip
-            pip install setuptools wheel twine
+            pip install setuptools wheel twine mypy
         - name: Build and publish
           env:
             TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}

.github/workflows/ubuntu.yml

@@ -84,6 +84,7 @@ jobs:
         sudo apt update -y
         sudo apt install ninja-build -y
         python -m pip install --upgrade pip
-        python setup.py develop
+        pip install mypy
+        pip install -e . -v
     - name: Run unit tests
       run: python -m unittest -v

.github/workflows/windows.yml

@@ -61,6 +61,7 @@ jobs:
     - name: Install library
       run: |
         python -m pip install --upgrade pip
-        python setup.py develop
+        pip install mypy
+        pip install -e . -v
     - name: Run unit tests
       run: python -m unittest -v

.gitignore

@@ -178,5 +178,10 @@ cython_debug/
 
 data/
 
-test.py
 CMakeSettings.json
+.clangd
+compile_commands.json
+debug
+release
+ioh_data
+run.py

.gitmodules

@@ -1,11 +1,15 @@
-[submodule "external/pybind11"]
-	path = external/pybind11
-	url = ../../pybind/pybind11
-	branch = stable
-[submodule "external/googletest"]
-	path = external/googletest
-	url = ../../google/googletest/
-	branch = v1.10.x
+[submodule "external/pybind11"]
+	path = external/pybind11
+	url = https://github.com/pybind/pybind11
+	branch = stable
+[submodule "external/googletest"]
+	path = external/googletest
+	url = https://github.com/google/googletest
+	branch = v1.10.x
 [submodule "external/fmt"]
 	path = external/fmt
-	url = [email protected]:fmtlib/fmt
+	url = https://github.com/fmtlib/fmt
+[submodule "external/clutchlog"]
+	path = external/clutchlog
+	url = https://github.com/jacobdenobel/clutchlog.git
+

CMakeLists.txt

@@ -1,6 +1,6 @@
 ## Build the ioh library.
 ##
-cmake_minimum_required(VERSION 3.12)
+cmake_minimum_required(VERSION 3.12) 
 
 project(ioh   
     VERSION 0.0.0.1
@@ -23,14 +23,14 @@ if(MSVC)
     set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} /MTd ")
 endif()  
 
-if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU") 
+if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")  
     SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -pedantic -std=c++17 -lstdc++fs")
     set(CMAKE_CXX_FLAGS_RELEASE "-O3 -ffast-math")
     if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 6.0 AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.0)
         link_libraries(stdc++fs)
         add_compile_definitions(FSEXPERIMENTAL)
     endif()
-endif() 
+endif()   
 
 # Define project targets.
 file(GLOB_RECURSE HEADERS include/ioh *.hpp) 
@@ -48,7 +48,8 @@ add_library(ioh::ioh ALIAS ioh)
 add_subdirectory(${EXTERNAL_DIR}/fmt)
 target_link_libraries(ioh INTERFACE fmt::fmt-header-only)
 
-
+# Include external clutchlog lib
+include_directories(${EXTERNAL_DIR}/clutchlog)
 
 # Add Python Library
 if(ENABLE_PYTHON_PROBLEMS)

README.md

@@ -1,4 +1,6 @@
-# IOHprofiler: IOHexperimenter
+IOHprofiler: IOHexperimenter {#mainpage}
+=========
+
 ![Ubuntu g++-{10, 9, 8}](https://github.com/IOHprofiler/IOHexperimenter/workflows/Ubuntu/badge.svg)
 ![MacOS clang++, g++-{9, 8}](https://github.com/IOHprofiler/IOHexperimenter/workflows/MacOS/badge.svg)
 ![Windows MVSC-2019](https://github.com/IOHprofiler/IOHexperimenter/workflows/Windows/badge.svg)

containers/issue94.dockdef

@@ -0,0 +1,42 @@
+
+FROM ubuntu
+
+# Dependencies
+RUN apt -y update
+RUN apt -y install software-properties-common
+RUN add-apt-repository universe
+RUN apt -y update
+RUN apt -y dist-upgrade
+RUN apt -y install git g++-8 cmake make
+RUN apt clean
+RUN update-alternatives --install /usr/bin/c++ c++ /usr/bin/g++-8 80
+RUN update-alternatives --set c++ /usr/bin/g++-8
+
+# Temporary directory where we are going to build everything.
+RUN tmpdir=$(mktemp -d)
+RUN mkdir -p ${tmpdir}/ioh/
+WORKDIR ${tmpdir}/ioh/
+
+# Build IOH
+RUN git clone --branch analyzer-logger --single-branch --recurse-submodules https://github.com/jdreo/IOHexperimenter.git
+WORKDIR ${tmpdir}/ioh/IOHexperimenter
+RUN mkdir -p debug
+WORKDIR ${tmpdir}/ioh/IOHexperimenter/debug
+RUN cmake -D CMAKE_BUILD_TYPE=Debug -D BUILD_TESTS=ON -D BUILD_EXAMPLE=ON -D BUILD_GMOCK=ON ..
+RUN make
+
+# Install
+RUN mkdir -p /usr/local/opt/ioh
+RUN cp tests/test_* /usr/local/opt/ioh/
+
+# Clean-up
+RUN rm -rf ${tmpdir}
+
+# keep cmake to run ctest
+RUN apt -y purge software-properties-common git g++-8 make
+RUN apt -y --purge autoremove
+RUN apt -y autoclean
+RUN apt clean
+
+WORKDIR /usr/local/opt/ioh/
+CMD ['/usr/local/opt/ioh/test_store']

containers/issue94.sh

@@ -0,0 +1,2 @@
+docker build -f issue94.dockdef -t ioh/issue94 .
+docker run -t ioh/issue94 /usr/local/opt/ioh/test_store --gtest_filter=BaseTest.store_properties XDebug

doc/CmakeLists.txt → doc/CMakeLists.txt

@@ -3,8 +3,8 @@ find_package(Sphinx REQUIRED)
 
 #This will be the main output of our command
 set(DOXYGEN_INPUT_DIR ${PROJECT_SOURCE_DIR}/include)
-set(DOXYGEN_OUTPUT_DIR ${CMAKE_CURRENT_BINARY_DIR}/doxygen)
-set(DOXYGEN_INDEX_FILE ${DOXYGEN_OUTPUT_DIR}/html/index.html)
+set(DOXYGEN_OUTPUT_DIR ${PROJECT_SOURCE_DIR}/docs)
+set(DOXYGEN_INDEX_FILE ${DOXYGEN_OUTPUT_DIR}/index.html)
 set(DOXYFILE_IN ${CMAKE_CURRENT_SOURCE_DIR}/doxygen/Doxyfile.in)
 set(DOXYFILE_OUT ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile)
 
@@ -20,7 +20,7 @@ add_custom_command(OUTPUT ${DOXYGEN_INDEX_FILE}
                    VERBATIM
                    )
 
-add_custom_target(Doxygen ALL DEPENDS ${DOXYGEN_INDEX_FILE}) 
+add_custom_target(doc ALL DEPENDS ${DOXYGEN_INDEX_FILE}) 
 
 ## Sphinx
 set(SPHINX_SOURCE ${CMAKE_CURRENT_SOURCE_DIR}/sphinx)

doc/doxygen/Doxyfile.in

@@ -32,7 +32,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "ioh"
+PROJECT_NAME           = "IOH"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
@@ -44,7 +44,7 @@ PROJECT_NUMBER         = "0.0.0.1"
 # for a project that appears at the top of each page and should give viewer a
 # quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          =
+PROJECT_BRIEF          = "Experimentation procedure for Iterative Optimization Heuristics"
 
 # With the PROJECT_LOGO tag one can specify a logo or an icon that is included
 # in the documentation. The maximum height of the logo should not exceed 55
@@ -143,7 +143,7 @@ ALWAYS_DETAILED_SEC    = NO
 # operators of the base classes will not be shown.
 # The default value is: NO.
 
-INLINE_INHERITED_MEMB  = NO
+INLINE_INHERITED_MEMB  = YES
 
 # If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
 # before files name in the file list and in the header files. If set to NO the
@@ -187,7 +187,7 @@ SHORT_NAMES            = NO
 # description.)
 # The default value is: NO.
 
-JAVADOC_AUTOBRIEF      = NO
+JAVADOC_AUTOBRIEF      = YES
 
 # If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
 # line (until the first dot) of a Qt-style comment as the brief description. If
@@ -441,7 +441,7 @@ EXTRACT_ALL            = NO
 # be included in the documentation.
 # The default value is: NO.
 
-EXTRACT_PRIVATE        = YES
+EXTRACT_PRIVATE        = NO
 
 # If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
 # scope will be included in the documentation.
@@ -590,7 +590,7 @@ SORT_BRIEF_DOCS        = NO
 # detailed member documentation.
 # The default value is: NO.
 
-SORT_MEMBERS_CTORS_1ST = NO
+SORT_MEMBERS_CTORS_1ST = YES
 
 # If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
 # of group names into alphabetical order. If set to NO the group names will
@@ -982,7 +982,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE =
+USE_MDFILE_AS_MAINPAGE = README.MD
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
@@ -1111,7 +1111,7 @@ GENERATE_HTML          = YES
 # The default directory is: html.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_OUTPUT            = html
+HTML_OUTPUT            = .
 
 # The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
 # generated HTML page (for example: .htm, .php, .asp).
@@ -1222,7 +1222,7 @@ HTML_COLORSTYLE_GAMMA  = 80
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_TIMESTAMP         = NO
+HTML_TIMESTAMP         = YES
 
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
@@ -1459,7 +1459,7 @@ DISABLE_INDEX          = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-GENERATE_TREEVIEW      = NO
+GENERATE_TREEVIEW      = YES
 
 # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
 # doxygen will group on one line in the generated HTML documentation.
@@ -1483,7 +1483,7 @@ TREEVIEW_WIDTH         = 250
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-EXT_LINKS_IN_WINDOW    = NO
+EXT_LINKS_IN_WINDOW    = YES
 
 # Use this tag to change the font size of LaTeX formulas included as images in
 # the HTML documentation. When you change the font size after a successful
@@ -1514,7 +1514,7 @@ FORMULA_TRANSPARENT    = YES
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
 
 # When MathJax is enabled you can set the default output format to be used for
 # the MathJax output. See the MathJax site (see:
@@ -1927,7 +1927,7 @@ MAN_LINKS              = NO
 # captures the structure of the code including all documentation.
 # The default value is: NO.
 
-GENERATE_XML           = YES
+GENERATE_XML           = NO
 
 # The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
@@ -2147,12 +2147,6 @@ EXTERNAL_GROUPS        = YES
 
 EXTERNAL_PAGES         = YES
 
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of 'which perl').
-# The default file (with absolute path) is: /usr/bin/perl.
-
-PERL_PATH              = /usr/bin/perl
-
 #---------------------------------------------------------------------------
 # Configuration options related to the dot tool
 #---------------------------------------------------------------------------
@@ -2166,15 +2160,6 @@ PERL_PATH              = /usr/bin/perl
 
 CLASS_DIAGRAMS         = YES
 
-# You can define message sequence charts within doxygen comments using the \msc
-# command. Doxygen will then run the mscgen tool (see:
-# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the
-# documentation. The MSCGEN_PATH tag allows you to specify the directory where
-# the mscgen tool resides. If left empty the tool is assumed to be found in the
-# default search path.
-
-MSCGEN_PATH            =
-
 # You can include diagrams made with dia in doxygen documentation. Doxygen will
 # then run dia to produce the diagram and insert it in the documentation. The
 # DIA_PATH tag allows you to specify the directory where the dia binary resides.