diff --git a/.ci/coverage.sh b/.ci/coverage.sh new file mode 100644 index 000000000..d0524d922 --- /dev/null +++ b/.ci/coverage.sh @@ -0,0 +1,6 @@ + +lcov --directory . --capture --output-file coverage.info # capture coverage info +lcov --remove coverage.info '/usr/*' --output-file coverage.info # filter out system +lcov --list coverage.info #debug info +# Uploading report to CodeCov +bash <(curl -s https://codecov.io/bash) || echo "Codecov did not collect coverage reports" diff --git a/.ci/create_gource.sh b/.ci/create_gource.sh new file mode 100644 index 000000000..b0ed22b48 --- /dev/null +++ b/.ci/create_gource.sh @@ -0,0 +1,62 @@ +#!/bin/env bash + +# Generates gource video: https://gource.io/ +# To run it from the root directory +# Needs gource and ffmpeg for the video +# Usage: +# +# cd repository +# .ci/create_gource +# +# or, to save it into a video: +# +# create_gource --video +# + + +function is_installed () { + is_installed=$(which $1 2> /dev/null) + if [[ $? != 0 ]]; then + echo " ${1} is not available. Try installing it with" + echo " brew install ${1}" + exit 1 + fi +} + +pic_dir=".git/avatar" + +# name,github +cat < names.csv +Adrian Jackson,adrianjhpc +David Pérez-Suárez,dpshelio +Ilektra Christidi,ilectra +Jason McEwen,jasonmcewen +Luke Pratley,Luke-Pratley +Mayeul d'Avezac,mdavezac +Ole Streicher,olebole +Rafael Carrillo,rafael-carrillo +rc-softdev-admin,rc-softdev-admin +Roland Guichard,UCLGuichard +Sinan Shi,sinanshi +Xiaohao Cai,XiaohaoCai +EOF + +mkdir -p ${pic_dir} +url="https://github.com/username.png" +n_images=$(ls ${pic_dir} | wc -l) +n_names=$(wc -l names.csv) +if [[ ${n_images[1]} < ${n_names[1]} ]]; then + while IFS="," read fullname username; do + curl -L ${url/username/${username}} > "${pic_dir}/${fullname}.png" + done < names.csv +fi + +is_installed gource || exit 1 + + +if [[ ${1} == "--video" ]]; then + is_installed ffmpeg || exit 1 + gource --user-image-dir ${pic_dir} --seconds-per-day 0.05 -1280x720 -o - | ffmpeg -y -r 60 -f image2pipe -vcodec ppm -i - -vcodec libx264 -preset ultrafast -pix_fmt yuv420p -crf 1 -threads 0 -bf 0 gource.mp4 +else + gource --user-image-dir ${pic_dir} --seconds-per-day 0.05 -1280x720 +fi diff --git a/.ci/install_spack.sh b/.ci/install_spack.sh new file mode 100644 index 000000000..2559dbfb5 --- /dev/null +++ b/.ci/install_spack.sh @@ -0,0 +1,24 @@ +#!/bin/bash -xe + +cwd=$(pwd) +cd $HOME + +# Are we using the cache directory or it's empty? +if [ ! -f $HOME/spack/README.md ] +then + rm -rf spack + git clone https://github.com/spack/spack.git +fi + +. spack/share/spack/setup-env.sh + + +while sleep 540 ; do echo "=========== make is taking more than 9m - pinging travis =========="; done & +spack compiler list +spack compiler remove clang@10.0.0-apple +spack compiler list +# spack install -y gcc@7.2.0 +# spack compiler add `spack location -i gcc@7.2.0` +spack install -y openmpi@3.0.0 + +cd $cwd diff --git a/.ci/spack_env.sh b/.ci/spack_env.sh new file mode 100644 index 000000000..af7ae2282 --- /dev/null +++ b/.ci/spack_env.sh @@ -0,0 +1,5 @@ + +export SPACK_ROOT=$HOME/spack +. $SPACK_ROOT/share/spack/setup-env.sh + +spack load openmpi@3.0.0 diff --git a/.clang-format b/.clang-format index 55476bc7d..d19b9f893 100644 --- a/.clang-format +++ b/.clang-format @@ -1,60 +1,138 @@ --- Language: Cpp -# BasedOnStyle: LLVM -AccessModifierOffset: -2 -AlignAfterOpenBracket: true +# BasedOnStyle: Google +AccessModifierOffset: -1 +AlignAfterOpenBracket: Align AlignConsecutiveAssignments: false -AlignEscapedNewlinesLeft: false +AlignConsecutiveDeclarations: false +AlignEscapedNewlines: Left AlignOperands: true AlignTrailingComments: true AllowAllParametersOfDeclarationOnNextLine: true AllowShortBlocksOnASingleLine: false AllowShortCaseLabelsOnASingleLine: false AllowShortFunctionsOnASingleLine: All -AllowShortIfStatementsOnASingleLine: false -AllowShortLoopsOnASingleLine: false +AllowShortIfStatementsOnASingleLine: true +AllowShortLoopsOnASingleLine: true AlwaysBreakAfterDefinitionReturnType: None -AlwaysBreakBeforeMultilineStrings: false -AlwaysBreakTemplateDeclarations: false +AlwaysBreakAfterReturnType: None +AlwaysBreakBeforeMultilineStrings: true +AlwaysBreakTemplateDeclarations: true BinPackArguments: true BinPackParameters: true -BreakBeforeBinaryOperators: All +BraceWrapping: + AfterClass: false + AfterControlStatement: false + AfterEnum: false + AfterFunction: false + AfterNamespace: false + AfterObjCDeclaration: false + AfterStruct: false + AfterUnion: false + AfterExternBlock: false + BeforeCatch: false + BeforeElse: false + IndentBraces: false + SplitEmptyFunction: true + SplitEmptyRecord: true + SplitEmptyNamespace: true +BreakBeforeBinaryOperators: None BreakBeforeBraces: Attach -BreakBeforeTernaryOperators: false +BreakBeforeInheritanceComma: false +BreakBeforeTernaryOperators: true BreakConstructorInitializersBeforeComma: false +BreakConstructorInitializers: BeforeColon +BreakAfterJavaFieldAnnotations: false +BreakStringLiterals: true ColumnLimit: 100 CommentPragmas: '^ IWYU pragma:' -ConstructorInitializerAllOnOneLineOrOnePerLine: false +CompactNamespaces: false +ConstructorInitializerAllOnOneLineOrOnePerLine: true ConstructorInitializerIndentWidth: 4 ContinuationIndentWidth: 4 Cpp11BracedListStyle: true -DerivePointerAlignment: false +DerivePointerAlignment: true DisableFormat: false ExperimentalAutoDetectBinPacking: false -ForEachMacros: [ foreach, Q_FOREACH, BOOST_FOREACH ] +FixNamespaceComments: true +ForEachMacros: + - foreach + - Q_FOREACH + - BOOST_FOREACH +IncludeBlocks: Preserve +IncludeCategories: + - Regex: '^(<|")sopt/config.h(>|")$' + Priority: 2 + - Regex: '^(<|")sopt/wavelets/' + Priority: 10 + - Regex: '^(<|")sopt/' + Priority: 9 + - Regex: '^(<.*/.*>)' + Priority: 7 + - Regex: '^(<.*>)' + Priority: 6 + - Regex: '".*"' + Priority: 8 +IncludeIsMainRegex: '(Test)?$' IndentCaseLabels: false +IndentPPDirectives: None IndentWidth: 2 IndentWrappedFunctionNames: false -KeepEmptyLinesAtTheStartOfBlocks: true +JavaScriptQuotes: Leave +JavaScriptWrapImports: true +KeepEmptyLinesAtTheStartOfBlocks: false MacroBlockBegin: '' MacroBlockEnd: '' MaxEmptyLinesToKeep: 1 NamespaceIndentation: None ObjCBlockIndentWidth: 2 ObjCSpaceAfterProperty: false -ObjCSpaceBeforeProtocolList: true -PenaltyBreakBeforeFirstCallParameter: 19 +ObjCSpaceBeforeProtocolList: false +PenaltyBreakAssignment: 2 +PenaltyBreakBeforeFirstCallParameter: 1 PenaltyBreakComment: 300 PenaltyBreakFirstLessLess: 120 PenaltyBreakString: 1000 PenaltyExcessCharacter: 1000000 -PenaltyReturnTypeOnItsOwnLine: 10 -PointerAlignment: Right +PenaltyReturnTypeOnItsOwnLine: 200 +PointerAlignment: Left +RawStringFormats: + - Language: Cpp + Delimiters: + - cc + - CC + - cpp + - Cpp + - CPP + - 'c++' + - 'C++' + CanonicalDelimiter: '' + BasedOnStyle: google + - Language: TextProto + Delimiters: + - pb + - PB + - proto + - PROTO + EnclosingFunctions: + - EqualsProto + - EquivToProto + - PARSE_PARTIAL_TEXT_PROTO + - PARSE_TEST_PROTO + - PARSE_TEXT_PROTO + - ParseTextOrDie + - ParseTextProtoOrDie + CanonicalDelimiter: '' + BasedOnStyle: google +ReflowComments: true +SortIncludes: true +SortUsingDeclarations: true SpaceAfterCStyleCast: false +SpaceAfterTemplateKeyword: true SpaceBeforeAssignmentOperators: true -SpaceBeforeParens: false +SpaceBeforeParens: ControlStatements SpaceInEmptyParentheses: false -SpacesBeforeTrailingComments: 1 +SpacesBeforeTrailingComments: 2 SpacesInAngles: false SpacesInContainerLiterals: true SpacesInCStyleCastParentheses: false @@ -63,18 +141,4 @@ SpacesInSquareBrackets: false Standard: Cpp11 TabWidth: 8 UseTab: Never -IncludeCategories: - - Regex: '^(<|")sopt/config.h(>|")$' - Priority: 2 - - Regex: '^(<|")sopt/wavelets/' - Priority: 10 - - Regex: '^(<|")sopt/' - Priority: 9 - - Regex: '^(<.*/.*>)' - Priority: 7 - - Regex: '^(<.*>)' - Priority: 6 - - Regex: '".\*"' - Priority: 8 ... - diff --git a/.gitignore b/.gitignore index 28e751b1b..c0d4dcd19 100644 --- a/.gitignore +++ b/.gitignore @@ -78,3 +78,4 @@ build/ .*.swp .settings python/tests/__pycache__ +*.h.gch diff --git a/.mailmap b/.mailmap new file mode 100644 index 000000000..18b727408 --- /dev/null +++ b/.mailmap @@ -0,0 +1,29 @@ +Adrian Jackson Adrian Jackson +David Pérez-Suárez David Pérez-Suárez +David Pérez-Suárez David Perez-Suarez +David Pérez-Suárez dpshelio +Ilektra Christidi +Jason McEwen Jason McEwen +Jason McEwen Jason McEwen +Luke Pratley Luke Pratley +Luke Pratley luke +Luke Pratley Luke Pratley +Luke Pratley Luke Pratley +Mayeul d'Avezac Mayeul d'Avezac +Ole Streicher Ole Streicher +Rafael Carrillo Rafael Carrillo +Rafael Carrillo rafael-carrillo +Rafael Carrillo rafael-carrillo +Rafael Carrillo rafael-carrillo +Rafael Carrillo rafael-carrillo +Rafael Carrillo rafael-carrillo +Rafael Carrillo rafael-carrillo +rc-softdev-admin rc-softdev-admin +rc-softdev-admin ccsprsd on Legion@UCL +Roland Guichard Roland Guichard +Roland Guichard Roland +Roland Guichard UCLGuichard +Sinan Shi Sinan Shi +Sinan Shi sinanshi +Sinan Shi sinanshi +Xiaohao Cai Xiaohao Cai diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 000000000..0db451b59 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,300 @@ +language: cpp +sudo: required +dist: trusty + +env: + global: + - BUILD_CMD='make VERBOSE=1' + - TEST_CMD='ctest -T test --output-on-failure -V' + - OMP_NUM_THREADS=4 + - MPI_CONFIG='CMAKE_CMD_EXTRA="-DMPIEXEC:FILEPATH=$(which mpirun) -DMPIEXEC_MAX_NUMPROCS=${MPI_PROCS}"' + + +addons: + homebrew: + packages: &osx_sources + - gcc@7 + update: true + +cache: + directories: + - $HOME/spack + +matrix: + fast_finish: true + + include: + - os: osx + osx_image: xcode10.1 + env: + - TITLE="XCode 10.1 - GCC" + - MPI=OFF + - openMP=OFF + - DOCS=OFF + + - os: osx + osx_image: xcode10.1 + env: + - TITLE="XCode 10.1 - GCC - OMP" + - MPI=OFF + - openMP=ON + - DOCS=OFF + + - os: osx + osx_image: xcode10.1 + env: + - TITLE="XCode 10.1 - GCC - MPI" + - MPI=ON + - openMP=ON + - DOCS=OFF + - MPI_PROCS=2 + addons: + homebrew: + packages: + - *osx_sources + - modules + - lmod + + - os: osx + osx_image: xcode10.1 + env: + - TITLE="XCode 10.1 - Clang" + - MPI=OFF + - openMP=OFF + - DOCS=OFF + + - os: linux + addons: + apt: + sources: &basic_sources + - ubuntu-toolchain-r-test + - llvm-toolchain-trusty-5.0 + packages: + - &native_deps [ g++-7, clang-5.0, libtiff5-dev, libgomp1] + # libtiff5-dev version 5 ?; libgomp1 # version 4.8.4-2 + - &all_deps [ libfftw3-dev, libboost-all-dev, libeigen3-dev ] + # libfftw3 version 3.3.3; libboost-all-dev version 1.54; libeigen3-dev version 3.2.0 + + env: + - TITLE="All dependencies - GCC" + - DEBUG=True + - LDFLAGS='-pthread' + - MPI=OFF + - openMP=OFF + - DOCS=OFF + + - os: linux + addons: + apt: + sources: + - *basic_sources + packages: + - *native_deps + - *all_deps + + env: + - TITLE="All dependencies - GCC - OMP" + - DEBUG=True + - LDFLAGS='-pthread' + - MPI=OFF + - openMP=ON + - DOCS=OFF + + - os: linux + addons: + apt: + sources: + - *basic_sources + packages: + - *native_deps + - *all_deps + - openmpi-bin # Version 1.6.5-8 + - lcov + + env: + - TITLE="All dependencies - GCC - MPI" + - DEBUG=True + - LDFLAGS='-pthread' + - MPI=ON + - openMP=ON + - DOCS=OFF + - MPI_PROCS=4 + - COVERAGE=ON + + - os: linux + addons: + apt: + sources: + - *basic_sources + packages: + - *native_deps + - *all_deps + - mpich # version 3.0.4-6 + + env: + - TITLE="All dependencies - GCC - MPI - mpich" + - DEBUG=True + - LDFLAGS='-pthread' + - MPI=ON + - openMP=ON + - DOCS=OFF + - MPI_PROCS=4 + + + - os: linux + addons: + apt: + sources: + - *basic_sources + packages: + - *native_deps + - *all_deps + env: + - TITLE="All dependencies - Clang" + - DEBUG=True + - LDFLAGS='-pthread' + - MPI=OFF + - openMP=OFF + - DOCS=OFF + + - os: linux + addons: + apt: + sources: + - *basic_sources + packages: + - *native_deps + - openmpi-bin # Version 1.6.5-8 + + env: + - TITLE="No dependencies - GCC - MPI" + - DEBUG=True + - LDFLAGS='-pthread' + - MPI=ON + - openMP=ON + - DOCS=OFF + - MPI_PROCS=4 + + - os: linux + addons: + apt: + sources: + - *basic_sources + packages: + - *native_deps + - openmpi-bin # Version 1.6.5-8 + + env: + - TITLE="Benchmark (no deps) - GCC - MPI" + - DEBUG=True + - LDFLAGS='-pthread' + - MPI=ON + - openMP=ON + - DOCS=OFF + - MPI_PROCS=4 + - Benchmarks=ON + - TEST_CMD='cd cpp/benchmarks; ./wavelets; ./conjugate_gradient; ./l1_proximal' + - TRAVIS_ALLOW_FAILURE=true + + - os: linux + addons: + apt: + sources: + - *basic_sources + packages: + - *native_deps + - openmpi-bin # Version 1.6.5-8 + + env: + - TITLE="Examples (no deps) - GCC - MPI" + - DEBUG=True + - LDFLAGS='-pthread' + - MPI=ON + - openMP=ON + - DOCS=OFF + - MPI_PROCS=4 + - EXAMPLES=ON + - TEST_CMD='cd cpp/examples; find ./ -type f -perm /u=x -printf "Executing %p\n" -exec {} \; ' + - TRAVIS_ALLOW_FAILURE=true + + - os: linux + services: + - docker + env: + - TITLE="Documentation - GCC" + - DOCS=ON + - BUILD_CMD='make docweb VERBOSE=1' + script: + - chmod o+w . # To allow docker to create the build directory + - docker run --rm -v $(pwd):/mydata uclrits/sopt /bin/sh -c "mkdir build; cd build; cmake .. -Ddocs=${DOCS} -Dweb=ON; eval ${BUILD_CMD}" + + - os: linux + addons: + apt: + sources: + - *basic_sources + packages: + - *native_deps + env: + - TITLE="Lint" + - DEBUG=True + - LDFLAGS='-pthread' + - MPI=OFF + - openMP=OFF + - DOCS=OFF + - BUILD_CMD="find ../ -regex '.*\.\(cc\|h\)' -not -iname '*.in.h' | xargs -I{} -P 10 clang-format-7 -i -style=file {}; git diff" + - TEST_CMD="git diff --exit-code || (echo '## NOTE: your code is not linted properly - fix the above'; false)" + +deploy: + provider: pages + skip-cleanup: true + github-token: $GITHUB_TOKEN # Set in the settings page of your repository, as a secure variable + keep-history: true + local-dir: build/cpp/docs/html + verbose: true # FIXME: just at first to see logs + on: + branch: development + condition: $TITLE = "Documentation - GCC" + +before_install: + - echo "Travis Run!" + - if [ $TRAVIS_OS_NAME = linux ]; then ClangVer="-5.0"; fi + - if [[ ${TITLE} = *GCC* ]]; then CC=gcc-7; else CC=clang${ClangVer}; fi + - if [[ ${TITLE} = *GCC* ]]; then CXX=g++-7; else CXX=clang++${ClangVer}; fi + - if [ $TRAVIS_OS_NAME = osx ] && [[ $MPI = ON ]]; then bash .ci/install_spack.sh; source $(brew --prefix modules)/init/bash; source .ci/spack_env.sh ;fi + # As MPI is not installed already, this variable is not set properly; this + # way is set up for all the jobs in the same manner. + - if [[ $MPI = ON ]]; then eval $MPI_CONFIG; fi + - echo "==================== ${TITLE} =====================" + - if [[ ${TITLE} = *Documentation* ]]; then docker pull uclrits/sopt; fi + + +install: + +before_script: + - | + if [[ ${TITLE} = *Lint* ]]; then + curl https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add - + echo "deb http://apt.llvm.org/trusty/ llvm-toolchain-trusty-7 main" | sudo tee -a /etc/apt/sources.list + sudo apt-get update -y -qq + sudo apt-get install clang-format-7 + fi + +script: + - pwd + - mkdir build + - cd build + - | + cmake .. -DCMAKE_BUILD_TYPE=Release \ + -Ddompi=${MPI} \ + -Dexamples=${EXAMPLES-OFF} \ + -Dopenmp=${openMP} \ + -Ddocs=${DOCS} \ + -Dbenchmarks=${Benchmarks-OFF} \ + -Dcoverage=${COVERAGE-OFF} \ + ${CMAKE_CMD_EXTRA} + - eval $BUILD_CMD + - eval $TEST_CMD + +after_success: + - if [ "${TITLE}" = "All dependencies - GCC - MPI" ]; then cd ..; bash .ci/coverage.sh; fi diff --git a/.zenodo.json b/.zenodo.json new file mode 100644 index 000000000..032c33ab3 --- /dev/null +++ b/.zenodo.json @@ -0,0 +1,55 @@ +{ + "publication_date": "2019-02-01", + "title": "SOPT", + "version": "3.0.0", + "creators": [ + { + "affiliation": "University College London", + "name": "Luke Pratley", + "orcid": "0000-0002-4716-9933" + }, + { + "affiliation": "Imperial College", + "name": "Mayeul d'Avezac", + "orcid": "0000-0002-2615-8397" + }, + { + "name": "Rafael Carrillo", + "orcid": "0000-0001-7149-6304" + }, + { + "affiliation": "University College London", + "name": "Ilektra Christidi" + }, + { + "affiliation": "University College London", + "name": "Roland Guichard", + "orcid": "0000-0003-3969-4102" + }, + { + "affiliation": "University College London", + "name": "Jason D. McEwen", + "orcid": "0000-0002-5852-8890" + }, + { + "affiliation": "University College London", + "name": "David Pérez-Suárez", + "orcid": "0000-0003-0784-6909" + }, + { + "affiliation": "Heriot Watt University", + "name": "Yves Wiaux", + "orcid": "0000-0002-1658-0121" + } + ], + "keywords": [ + "convex optimization", + "sparse optimization", + "parallelization", + "big data" + ], + "license": "GPL-2.0", + "upload_type": "software", + "description": "Sparse OPTimisation using state-of-the-art convex optimisation algorithms.", + "access_right": "open" +} diff --git a/CMakeLists.txt b/CMakeLists.txt index f8a810471..f1d057d4a 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required(VERSION 2.8) +cmake_minimum_required(VERSION 3.0) project(Sopt CXX) # Location of extra cmake includes for the project @@ -13,12 +13,20 @@ set_version(2.0.0) get_gitref() option(tests "Enable testing" on) -option(python "Enable python" off) option(benchmarks "Enable benchmarking" off) option(examples "Enable Examples" on) option(logging "Enable logging" on) option(regressions "Enable regressions" off) option(openmp "Enable OpenMP" on) +option(dompi "Enable MPI" on) +option(docs "Build documentation" off) +option(coverage "Build coverage" off) + +if(NOT CMAKE_BUILD_TYPE) + message(STATUS "Setting build type to 'Release' as none was specified.") + set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Build Type" FORCE) +endif() +message(STATUS "Building sopt in ${CMAKE_BUILD_TYPE} mode") if(regressions) enable_language(C) @@ -30,14 +38,12 @@ endif() # Add c++11 stuff include(AddCPP11Flags) include(CheckCXX11Features) -if(tests AND python) - include(AddPyTest) -endif() cxx11_feature_check(REQUIRED unique_ptr nullptr override constructor_delegate) include(compilations) # search/install dependencies include(dependencies) + # sets rpath policy explicitly if(CMAKE_VERSION VERSION_LESS 3.0) set_property(GLOBAL PROPERTY MACOSX_RPATH ON) @@ -45,6 +51,12 @@ else() cmake_policy(SET CMP0042 NEW) endif() +if(SOPT_MPI) + include(DetectIntegerArchitecture) + DetectIntegerArchitecture(SOPT) +endif() + + if(tests OR examples) enable_testing() endif() @@ -57,18 +69,21 @@ if(examples) endif() if(benchmarks) + set(GBenchmark_GIT_TAG "v1.3.0") include(AddBenchmark) endif() if(regressions) include(AddRegression) endif() -if(python) - include(python_dependencies) - include(PythonModule) -endif() +if(tests AND coverage) + # Enable code coverage. + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") + + # Build with debugging information to make the output meaningful. + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g") -if(python) - add_subdirectory(python) + # Disable optimizations to get the most accurate results. + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O0") endif() add_subdirectory(cpp) diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 000000000..981e444dc --- /dev/null +++ b/Dockerfile @@ -0,0 +1,26 @@ +FROM uclrits/cppdev:18.10 + +USER root +WORKDIR /build +ENV LD_LIBRARY_PATH /usr/local/lib + +# Build sopt +RUN git clone https://github.com/astro-informatics/sopt.git +RUN mkdir -p /build/sopt/build && cd /build/sopt/build && \ + cmake .. -DCMAKE_BUILD_TYPE=Release \ + -Dtests=ON \ + -Dexamples=OFF \ + -Dbenchmarks=OFF \ + -DMPIEXEC:FILEPATH=$(which mpirun) -DMPIEXEC_MAX_NUMPROCS=4 \ + -DMPIEXEC_PREFLAGS="--oversubscribe" && \ + make && make install + +RUN useradd -ms /bin/bash purifier + +USER purifier +ENV HOME /home/purifier +RUN cp /etc/zsh/newuser.zshrc.recommended /home/purifier/.zshrc +WORKDIR /mydata +CMD ["zsh"] + +# docker build -t uclrits/sopt:18.10 diff --git a/README.md b/README.md index 661fb7f2b..853e3a6dd 100644 --- a/README.md +++ b/README.md @@ -1,78 +1,60 @@ +Sparse OPTimisation Library +=========================== -# SOPT: Sparse OPTimisation ------------------------------------------------------------------- +[![Build Status](https://travis-ci.com/astro-informatics/sopt.svg?branch=development)](https://travis-ci.com/astro-informatics/sopt) +[![codecov](https://codecov.io/gh/astro-informatics/sopt/branch/development/graph/badge.svg)](https://codecov.io/gh/astro-informatics/sopt) -## Description +Description +------------- -SOPT is a C++ package to perform Sparse OPTimisation. It solves a variety of sparse regularisation -problems, including the SARA algorithm. Prototype Matlab implementations of various algorithms are -also included. +**SOPT** is an open-source `C++` package available under the [license](#license) below. It performs Sparse OPTimisation using state-of-the-art convex optimisation algorithms. It solves a variety of sparse regularisation problems, including the Sparsity Averaging Reweighted Analysis (SARA) algorithm. -## Contributors +**SOPT** also has several MPI wrappers that can be adapted for computational distirbution of various linear operators and convex optimisation algorithms. Wavelet Operators with **SOPT** also support multi-threading through OpenMP. -SOPT was initially created by Rafael Carrillo, Jason McEwen and Yves Wiaux but major contributions -have since been made by a number of others. The full list of contributors is as follows: +**SOPT** is written in `C++` primarily but also contains partial and prototyped Matlab implementations of various algorithms. -* [Rafael E. Carrillo](https://www.researchgate.net/profile/Rafael_Carrillo2) -* [Jason D. McEwen](http://www.jasonmcewen.org) -* [Yves Wiaux](http://basp.eps.hw.ac.uk) -* [Vijay Kartik](https://people.epfl.ch/vijay.kartik) -* [Mayeul d'Avezac](https://github.com/mdavezac) -* [Luke Pratley](https://about.me/luke.pratley) -* [David Perez-Suarez](https://dpshelio.github.io) +**SOPT** is largely provided to support the [**PURIFY**](https://github.com/astro-informatics/purify) package, a companion open-source code to perform radio interferometric imaging, also written by the authors of **SOPT**. For further background please see the [reference](#references-and-citation) section. -## References -When referencing this code, please cite our related papers: +This documentation outlines the necessary and optional [dependencies](#dependencies-installation) upon which **SOPT** should be built, before describing [installation](#installing-and-building-SOPT) and [testing](#testing) details and [Matlab](#Matlab) support. [Contributors](#contributors), [references](#references-and-citation) and [license](#license) information then follows. -1. R. E. Carrillo, J. D. McEwen and Y. Wiaux. "Sparsity Averaging Reweighted - Analysis (SARA): a novel algorithm for radio-interferometric imaging", Mon. - Not. Roy. Astron. Soc., 426(2):1223-1234, 2012, - [arXiv:1205.3123](http://arxiv.org/abs/arXiv:1205.3123) -1. R. E. Carrillo, J. D. McEwen, D. Van De Ville, J.-P. Thiran, and Y. Wiaux. "Sparsity averaging - for compressive imaging", IEEE Signal Processing Letters, 20(6):591-594, 2013, - [arXiv:1208.2330](http://arxiv.org/abs/arXiv:1208.2330) -1. A. Onose, R. E. Carrillo, A. Repetti, J. D. McEwen, J.-P. Thiran, J.-C. Pesquet, and Y. Wiaux. - "Scalable splitting algorithms for big-data interferometric imaging in the SKA era". Mon. Not. - Roy. Astron. Soc., 462(4):4314-4335, 2016, - [arXiv:1601.04026](http://arxiv.org/abs/arXiv:1601.04026) +Dependencies installation +------------------------- -## Webpage +**SOPT** is mostly written in `C++11`. Pre-requisites and dependencies are listed in following and minimal versions required are tested against `Travis CI` meaning that they come natively with OSX and the Ubuntu Trusty release. These are also the default ones fetched by `CMake`. -http://basp-group.github.io/sopt/ +`C++` minimal dependencies: -## Installation - -### C++ pre-requisites and dependencies - -- [CMake](http://www.cmake.org/): a free software that allows cross-platform compilation -- [tiff](http://www.libtiff.org/): Tag Image File Format library -- [OpenMP](http://openmp.org/wp/): Optional. Speeds up some of the operations. -- [UCL/GreatCMakeCookOff](https://github.com/UCL/GreatCMakeCookOff): Collection of cmake recipes. +- [CMake](http://www.cmake.org/) v3.9.2 A free software that allows cross-platform compilation +- [GCC](https://gcc.gnu.org) v7.3.0 GNU compiler for `C++` +- [UCL/GreatCMakeCookOff](https://github.com/UCL/GreatCMakeCookOff) Collection of `CMake` recipes. Downloaded automatically if absent. -- [Eigen 3](http://eigen.tuxfamily.org/index.php?title=Main_Page): Modern C++ linear algebra. +- [Eigen3](http://eigen.tuxfamily.org/index.php?title=Main_Page) v3.2.0 (Trusty) Modern `C++` linear algebra. Downloaded automatically if absent. -- [spdlog](https://github.com/gabime/spdlog): Optional. Logging library. Downloaded automatically if +- [tiff](http://www.libtiff.org/) v4.0.3 (Trusty) Tag Image File Format library +- [OpenMP](http://openmp.org/wp/) v4.8.4 (Trusty) - Optional - Speeds up some of the operations. +- [spdlog](https://github.com/gabime/spdlog) v* - Optional - Logging library. Downloaded automatically if absent. -- [philsquared/Catch](https://github.com/philsquared/Catch): Optional - only for testing. A C++ - unit-testing framework. Downloaded automatically if absent. -- [google/benchmark](https://github.com/google/benchmar): Optional - only for benchmarks. A C++ - micro-benchmarking framework. Downloaded automatically if absent. - -### Python pre-requisites and dependencies - -- [numpy](http://www.numpy.org/): Fundamental package for scientific computing with Python -- [scipy](https://www.scipy.org/): User-friendly and efficient numerical routines such as routines - for numerical integration and optimization -- [pandas](http://pandas.pydata.org/): library providing high-performance, easy-to-use data - structures and data analysis tools -- [cython](http://cython.org/): Makes writing C extensions for Python as easy as Python itself. - Downloaded automatically if absent. -- [pytest](http://doc.pytest.org/en/latest/): Optional - for testing only. Unit-testing framework - for python. Downloaded automatically if absent and testing is not disabled. +- [Catch2](https://github.com/catchorg/Catch2) v2.2.3 - Optional - A `C++` + unit-testing framework only needed for testing. Downloaded automatically if absent. +- [google/benchmark](https://github.com/google/benchmark) - Optional - A `C++` + micro-benchmarking framework only needed for benchmarks. Downloaded automatically if absent. + +Installing and building SOPT +---------------------------- + +**SOPT** can be installed through the software packet manager on Linux Debian distributions: + +``` +apt-get install sopt +``` + +Alternatively, you can build **SOPT** entirely from the source code. Once the mandatory dependencies are present, `git clone` from the [GitHub repository](https://github.com/astro-informatics/sopt): -### Installing Sopt +``` +git clone https://github.com/astro-informatics/sopt.git +``` -Once the dependencies are present, the program can be built with: +Then, the program can be built with standard `CMake` command: ``` cd /path/to/code @@ -82,48 +64,106 @@ cmake -DCMAKE_BUILD_TYPE=Release .. make ``` -To test everything went all right: +To install in directory `/X`, with libraries going to `X/lib` do: ``` cd /path/to/code/build -ctest . +cmake -DCMAKE_INSTALL_PREFIX=/X .. +make install ``` -To install in directory `/X`, with libraries going to `X/lib`, python modules to -`X/lib/pythonA.B/site-packages/sopt`, etc, do: +Testing +------- + +To check everything went all right, run the test suite: ``` cd /path/to/code/build -cmake -DCMAKE_INSTALL_PREFIX=/X .. -make install +ctest . ``` +Docker +------- + +If you want to use Docker instead, you can build an image using the Dockerfile +available in the repository or pulling it from +[DockerHub](https://hub.docker.com/r/uclrits/sopt). + +``` +docker build -t sopt . +``` + +or + +``` +docker pull uclrits/sopt +``` + + +Matlab +------ + +A separate Matlab implementation is provided with **SOPT**. This implementation includes some (but not all) of the optimisation algorithms implemented in the `C++` code, including the SARA algorithm. + +The Matlab implementation is contained in the matlab directory. This is a stand-alone implementation and does not call any of the `C++` code. In future, Matlab interfaces to the `C++` code may also be included in **SOPT**. + +See `matlab/README.txt` for an overview of the Matlab implementation. The stand-alone Matlab implementation is also self-documenting; corresponding documentation can be found in `matlab/doc`. We thank Gilles Puy for contributing to this Matlab implementation. + +Contributors +------------ + +Check the [contributors](@ref sopt_contributors) page ([github](cpp/docs/SOPT_CONTRIBUTORS.md)). + +References and citation +----------------------- + +If you use **SOPT** for work that results in publication, please reference the [webpage](#webpage) and our related academic papers: + +1. L. Pratley _et al._ (to be published) +2. A. Onose, R. E. Carrillo, A. Repetti, J. D. McEwen, J.-P. Thiran, J.-C. Pesquet, and Y. Wiaux. + "Scalable splitting algorithms for big-data interferometric imaging in the SKA era" _Mon. Not. + Roy. Astron. Soc._ **462(4):4314-4335** (2016) [arXiv:1601.04026](http://arxiv.org/abs/arXiv:1601.04026) +3. R. E. Carrillo, J. D. McEwen, D. Van De Ville, J.-P. Thiran, and Y. Wiaux. "Sparsity averaging + for compressive imaging" _IEEE Signal Processing Letters_ **20(6):591-594** (2013) [arXiv:1208.2330](http://arxiv.org/abs/arXiv:1208.2330) +4. R. E. Carrillo, J. D. McEwen and Y. Wiaux. "Sparsity Averaging Reweighted + Analysis (SARA): a novel algorithm for radio-interferometric imaging" _Mon. + Not. Roy. Astron. Soc._ **426(2):1223-1234** (2012) [arXiv:1205.3123](http://arxiv.org/abs/arXiv:1205.3123) -## Support +License +------- -If you have any questions or comments, feel free to contact Rafael Carrillo or Jason McEwen, or add -an issue in the [issue tracker](https://github.com/basp-group/sopt/issues). +> SOPT: Sparse OPTimisation package +> Copyright (C) 2013-2019 +> +> This program is free software; you can redistribute it and/or +> modify it under the terms of the GNU General Public License as +> published by the Free Software Foundation; either version 2 of the +> License, or (at your option) any later version. +> +> This program is distributed in the hope that it will be useful, but +> WITHOUT ANY WARRANTY; without even the implied warranty of +> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +> General Public License for more details (LICENSE.txt). +> +> You should have received a copy of the GNU General Public License +> along with this program; if not, write to the Free Software +> Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA +> 02110-1301, USA. -## Notes +Webpage +------- -The code is given for educational purpose. For the matlab version of the code see the folder matlab. +- [Documentation](http://astro-informatics.github.io/sopt) +- [Repository](https://github.com/astro-informatics/sopt) -## License +Support +------- - SOPT: Sparse OPTimisation package - Copyright (C) 2013 Rafael Carrillo, Jason McEwen, Yves Wiaux +For any questions or comments, feel free to contact [Jason McEwen](http://www.jasonmcewen.org), or add +an issue to the [issue tracker](https://github.com/astro-informatics/sopt/issues). - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public License as - published by the Free Software Foundation; either version 2 of the - License, or (at your option) any later version. +Notes +----- - This program is distributed in the hope that it will be useful, but - WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - General Public License for more details (LICENSE.txt). +The code is given for educational purpose. For the `Matlab` version of the code see the folder matlab. - You should have received a copy of the GNU General Public License - along with this program; if not, write to the Free Software - Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA - 02110-1301, USA. diff --git a/cmake_files/DetectIntegerArchitecture.cmake b/cmake_files/DetectIntegerArchitecture.cmake new file mode 100644 index 000000000..860165c5a --- /dev/null +++ b/cmake_files/DetectIntegerArchitecture.cmake @@ -0,0 +1,78 @@ +# Detects whether char, int, etc have their equivalent int intx_t. +function(IsSimilarTo VARIABLE integer) + if(NOT "${${VARIABLE}}" STREQUAL "") + return() + endif() + list(GET ARGN 0 first_item) + list(REMOVE_AT ARGN 0) + set(staticasserts " std::is_same<${integer}, ${first_item}>::value\n") + foreach(var ${ARGN}) + set(staticasserts "${staticasserts} or std::is_same<${integer}, ${var}>::value\n") + endforeach() + + file(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/DetectIntegerArchitecture") + file(WRITE "${PROJECT_BINARY_DIR}/DetectIntegerArchitecture/equiv.cc" + "#include \n" + "#include \n" + "static_assert(\n" + "${staticasserts},\n" + " \"${integer} vs ${first_item};${ARGN}\");\n" + "int main(int nargs, char **argv) {\n" + " return 0;\n" + "}\n" + ) + file(WRITE "${PROJECT_BINARY_DIR}/DetectIntegerArchitecture/notequiv.cc" + "#include \n" + "#include \n" + "static_assert(not (\n" + "${staticasserts}), \n" + " \"${integer} vs ${ARGN}\");\n" + "int main(int nargs, char **argv) {\n" + " return 0;\n" + "}\n" + ) + try_compile(equiv + "${PROJECT_BINARY_DIR}/DetectIntegerArchitecture" + "${PROJECT_BINARY_DIR}/DetectIntegerArchitecture/equiv.cc" + OUTPUT_VARIABLE equiv_out + ) + try_compile(notequiv + "${PROJECT_BINARY_DIR}/DetectIntegerArchitecture" + "${PROJECT_BINARY_DIR}/DetectIntegerArchitecture/notequiv.cc" + OUTPUT_VARIABLE notequiv_out + ) + if(NOT notequiv AND NOT equiv) + message("${equiv_out}") + message("${notequiv_out}") + message(FATAL_ERROR "Could not acertain integer architecture ${integer}") + elseif(notequiv AND equiv) + message("${equiv_out}") + message("${notequiv_out}") + message(FATAL_ERROR "Could not acertain integer architecture ${integer}") + elseif(equiv) + message(STATUS "${integer} is equivalent to one of ${first_item};${ARGN}") + else() + message(STATUS "${integer} is not equivalent to any of ${first_item};${ARGN}") + endif() + set(${VARIABLE} "${equiv}" PARENT_SCOPE) +endfunction() + +function(DetectIntegerArchitecture PREFIX) + if(${PREFIX}_INTEGER_DETECTED) + return() + endif() + set(integers + "std::int8_t" "std::int16_t" "std::int32_t" "std::int64_t" + "std::uint8_t" "std::uint16_t" "std::uint32_t" "std::uint64_t") + IsSimilarTo(${PREFIX}_char char ${integers}) + IsSimilarTo(${PREFIX}_long long ${integers} int) + IsSimilarTo(${PREFIX}_unsigned_long "unsigned long" ${integers} "unsigned int") + set(${PREFIX}_CHAR_ARCH ${${PREFIX}_char} + CACHE BOOL "Integer equivalence for char") + set(${PREFIX}_LONG_ARCH ${${PREFIX}_long} + CACHE BOOL "Integer equivalence for long") + set(${PREFIX}_ULONG_ARCH ${${PREFIX}_unsigned_long} + CACHE BOOL "Integer equivalence for unsigned long") + set(${PREFIX}_INTEGER_DETECTED TRUE + CACHE BOOL "Whether to check integer architecture") +endfunction() diff --git a/cmake_files/LookUpSopt.cmake b/cmake_files/LookUpSopt.cmake index c2f589bc8..e9034b713 100644 --- a/cmake_files/LookUpSopt.cmake +++ b/cmake_files/LookUpSopt.cmake @@ -40,7 +40,6 @@ ExternalProject_Add( -DCMAKE_BUILD_TYPE=${Sopt_BUILD_TYPE} -DNOEXPORT=TRUE -Dtests=FALSE - -Dpython=FALSE -Dexamples=FALSE -Dlogging=FALSE -Dregressions=FALSE diff --git a/cmake_files/SoptConfig.in.cmake b/cmake_files/SoptConfig.in.cmake index 258ec345a..e65f229ab 100644 --- a/cmake_files/SoptConfig.in.cmake +++ b/cmake_files/SoptConfig.in.cmake @@ -17,4 +17,4 @@ if(TARGET libsopt) list(APPEND Sopt_LIBRARIES libsopt) set(Sopt_C_LIBRARY libsopt) endif() -set(Sopt_ABOUT_EXECUTABLE sopt_about) +set(Sopt_HAS_MPI @SOPT_MPI@) diff --git a/cmake_files/SoptConfigVersion.in.cmake b/cmake_files/SoptConfigVersion.in.cmake index 2689f99b7..296018a4c 100644 --- a/cmake_files/SoptConfigVersion.in.cmake +++ b/cmake_files/SoptConfigVersion.in.cmake @@ -1,4 +1,5 @@ set(PACKAGE_VERSION "@Sopt_VERSION@") +set(MPI_COMPONENT @SOPT_MPI@) if("${PACKAGE_VERSION}" VERSION_LESS "${PACKAGE_FIND_VERSION}") set(PACKAGE_VERSION_COMPATIBLE FALSE) else() @@ -7,3 +8,6 @@ else() set(PACKAGE_VERSION_EXACT FALSE) endif() endif() +if(Sopt_FIND_REQUIRED_MPI AND NOT MPI_COMPONENT) + set(PACKAGE_VERSION_COMPATIBLE FALSE) +endif() diff --git a/cmake_files/dependencies.cmake b/cmake_files/dependencies.cmake index 44a5f7235..16c325215 100644 --- a/cmake_files/dependencies.cmake +++ b/cmake_files/dependencies.cmake @@ -1,10 +1,20 @@ include(PackageLookup) # check for existence, or install external projects -lookup_package(Eigen3 ARGUMENTS URL "https://bitbucket.org/LukePratley/eigen/get/3.2.tar.gz" MD5 "f38e33505afbf4659cda191bbc992ca9") +lookup_package(Eigen3 REQUIRED DOWNLOAD_BY_DEFAULT ARGUMENTS URL "http://bitbucket.org/eigen/eigen/get/3.2.tar.gz" MD5 "035ccc791f046f48e90bb1fb42ce227e") if(logging) lookup_package(spdlog REQUIRED) endif() +if(docs) + cmake_policy(SET CMP0057 NEW) + find_package(Doxygen REQUIRED dot) + if(NOT DOXYGEN_FOUND) + mesage(STATUS "Could not find Doxygen or dot. No building documentation") + set(docs OFF) + endif() +endif() + + find_package(TIFF) if(examples OR regression) if(NOT TIFF_FOUND) @@ -12,6 +22,7 @@ if(examples OR regression) endif() endif() + if(regressions) find_package(FFTW3 REQUIRED DOUBLE) set(REGRESSION_ORACLE_ID "last_of_c" @@ -42,3 +53,9 @@ if(openmp) set(SOPT_OPENMP FALSE) endif() endif() + +set(SOPT_MPI FALSE) +if(dompi) + find_package(MPI) +endif() +set(SOPT_MPI ${MPI_FOUND}) diff --git a/cmake_files/python_dependencies.cmake b/cmake_files/python_dependencies.cmake deleted file mode 100644 index 90ab46b20..000000000 --- a/cmake_files/python_dependencies.cmake +++ /dev/null @@ -1,48 +0,0 @@ -# Scripts to run purify from build directory. Good for testing/debuggin. -include(EnvironmentScript) -# Function to install python files in python path ${PYTHON_PKG_DIR} -include(PythonInstall) -# Ability to find installed python packages -include(PythonPackage) -# Installs python packages that are missing. -# We choose to do this only for packages that are required to build purify. -# Leave it to the user to install packages that are needed for running -# purify. -include(PythonPackageLookup) -# Creates script for running python with the bempp package available -# Also makes python packages and selected directories available to the -# build system -add_to_python_path("${PROJECT_BINARY_DIR}/python") -add_to_python_path("${EXTERNAL_ROOT}/python") -add_python_eggs("${PROJECT_SOURCE_DIR}" - EXCLUDE - "${PROJECT_SOURCE_DIR}/purify*egg" - "${PROJECT_BINARY_DIR}/Purify*egg" -) -set(LOCAL_PYTHON_EXECUTABLE "${PROJECT_BINARY_DIR}/localpython.sh") -create_environment_script( - EXECUTABLE "${PYTHON_EXECUTABLE}" - PATH "${LOCAL_PYTHON_EXECUTABLE}" - PYTHON -) -# Python interpreter + libraries -find_package(CoherentPython) -# Only required for building -if(NOT cython_EXECUTABLE) - lookup_python_package(Cython REQUIRED PATH "${EXTERNAL_ROOT}/python") -endif() -# Also required for production -find_python_package(numpy) -find_python_package(scipy) -# Finds additional info, like libraries, include dirs... -# no need check numpy features, it's all handled by cython. -set(no_numpy_feature_tests TRUE) -find_package(Numpy REQUIRED) - -if(tests) - include(AddPyTest) - setup_pytest("${EXTERNAL_ROOT}/python" "${PROJECT_BINARY_DIR}/py.test.sh") - - lookup_python_package(pywt PIPNAME PyWavelets REQUIRED PATH "${EXTERNAL_ROOT}/python") -endif() - diff --git a/cmake_files/using.cc b/cmake_files/using.cc index f95849bbc..8317a837b 100644 --- a/cmake_files/using.cc +++ b/cmake_files/using.cc @@ -2,7 +2,7 @@ //! Sparsity Averaging Reweighted Analysis class SARA : public std::vector { -public: + public: // Constructors using std::vector::vector; }; diff --git a/cpp/CMakeLists.txt b/cpp/CMakeLists.txt index fd9247f70..3e5defede 100644 --- a/cpp/CMakeLists.txt +++ b/cpp/CMakeLists.txt @@ -20,7 +20,7 @@ list(GET version 2 Sopt_VERSION_PATCH) configure_file(sopt/config.in.h "${PROJECT_BINARY_DIR}/include/sopt/config.h") add_subdirectory(sopt) -if(regressions OR examples) +if(regressions OR examples OR tests) # Tiff wrappers and whatnot add_subdirectory(tools_for_tests) endif() @@ -36,3 +36,6 @@ endif() if(regressions) add_subdirectory(regressions) endif() +if (docs) + add_subdirectory(docs) +endif() diff --git a/cpp/benchmarks/conjugate_gradient.cc b/cpp/benchmarks/conjugate_gradient.cc index 51c4b3786..92bee7e31 100644 --- a/cpp/benchmarks/conjugate_gradient.cc +++ b/cpp/benchmarks/conjugate_gradient.cc @@ -2,7 +2,8 @@ #include #include -template void matrix_cg(benchmark::State &state) { +template +void matrix_cg(benchmark::State &state) { auto const N = state.range_x(); auto const epsilon = std::pow(10, -state.range_y()); auto const A = sopt::Image::Random(N, N).eval(); @@ -12,12 +13,12 @@ template void matrix_cg(benchmark::State &state) { auto const Ahb = A.matrix().transpose().conjugate() * b.matrix(); auto output = sopt::Vector::Zero(N).eval(); sopt::ConjugateGradient cg(0, epsilon); - while(state.KeepRunning()) - cg(output, AhA, Ahb); + while (state.KeepRunning()) cg(output, AhA, Ahb); state.SetBytesProcessed(int64_t(state.iterations()) * int64_t(N) * sizeof(TYPE)); } -template void function_cg(benchmark::State &state) { +template +void function_cg(benchmark::State &state) { auto const N = state.range_x(); auto const epsilon = std::pow(10, -state.range_y()); auto const A = sopt::Image::Random(N, N).eval(); @@ -29,8 +30,7 @@ template void function_cg(benchmark::State &state) { auto func = [&AhA](t_Vector &out, t_Vector const &input) { out = AhA * input; }; auto output = sopt::Vector::Zero(N).eval(); sopt::ConjugateGradient cg(0, epsilon); - while(state.KeepRunning()) - cg(output, func, Ahb); + while (state.KeepRunning()) cg(output, func, Ahb); state.SetBytesProcessed(int64_t(state.iterations()) * int64_t(N) * sizeof(TYPE)); } diff --git a/cpp/benchmarks/l1_proximal.cc b/cpp/benchmarks/l1_proximal.cc index 79ceb332d..5b923d3b2 100644 --- a/cpp/benchmarks/l1_proximal.cc +++ b/cpp/benchmarks/l1_proximal.cc @@ -4,13 +4,14 @@ #include #include -template void function_l1p(benchmark::State &state) { +template +void function_l1p(benchmark::State &state) { typedef typename sopt::real_type::type Real; auto const N = state.range_x(); auto const input = sopt::Vector::Random(N).eval(); auto const Psi = sopt::Matrix::Random(input.size(), input.size() * 10).eval(); - sopt::Vector const weights - = sopt::Vector::Random(Psi.cols()).normalized().array().abs(); + sopt::Vector const weights = + sopt::Vector::Random(Psi.cols()).normalized().array().abs(); auto const l1 = sopt::proximal::L1() .tolerance(std::pow(10, -state.range_y())) @@ -23,8 +24,7 @@ template void function_l1p(benchmark::State &state) { Real const gamma = 1e-2 / Psi.array().abs().sum(); auto output = sopt::Vector::Zero(N).eval(); - while(state.KeepRunning()) - l1(output, gamma, input); + while (state.KeepRunning()) l1(output, gamma, input); state.SetBytesProcessed(int64_t(state.iterations()) * int64_t(N) * sizeof(TYPE)); } diff --git a/cpp/benchmarks/wavelets.cc b/cpp/benchmarks/wavelets.cc index 5389dd29f..aa2c77de2 100644 --- a/cpp/benchmarks/wavelets.cc +++ b/cpp/benchmarks/wavelets.cc @@ -19,8 +19,7 @@ void direct_matrix(benchmark::State &state) { auto const input = sopt::Image::Random(Nx, Ny).eval(); auto output = sopt::Image::Zero(Nx, Ny).eval(); auto const wavelet = sopt::wavelets::factory(get_name(DB), LEVEL); - while(state.KeepRunning()) - wavelet.direct(output, input); + while (state.KeepRunning()) wavelet.direct(output, input); state.SetBytesProcessed(int64_t(state.iterations()) * int64_t(Nx) * int64_t(Ny) * sizeof(TYPE)); } @@ -31,8 +30,7 @@ void indirect_matrix(benchmark::State &state) { auto const input = sopt::Image::Random(Nx, Ny).eval(); auto output = sopt::Image::Zero(Nx, Ny).eval(); auto const wavelet = sopt::wavelets::factory(get_name(DB), LEVEL); - while(state.KeepRunning()) - wavelet.indirect(input, output); + while (state.KeepRunning()) wavelet.indirect(input, output); state.SetBytesProcessed(int64_t(state.iterations()) * int64_t(Nx) * int64_t(Ny) * sizeof(TYPE)); } @@ -42,8 +40,7 @@ void direct_vector(benchmark::State &state) { auto const input = sopt::Array::Random(Nx).eval(); auto output = sopt::Array::Zero(Nx).eval(); auto const wavelet = sopt::wavelets::factory(get_name(DB), LEVEL); - while(state.KeepRunning()) - wavelet.direct(output, input); + while (state.KeepRunning()) wavelet.direct(output, input); state.SetBytesProcessed(int64_t(state.iterations()) * int64_t(Nx) * sizeof(TYPE)); } template @@ -52,8 +49,7 @@ void indirect_vector(benchmark::State &state) { auto const input = sopt::Array::Random(Nx).eval(); auto output = sopt::Array::Zero(Nx).eval(); auto const wavelet = sopt::wavelets::factory(get_name(DB), LEVEL); - while(state.KeepRunning()) - wavelet.indirect(input, output); + while (state.KeepRunning()) wavelet.indirect(input, output); state.SetBytesProcessed(int64_t(state.iterations()) * int64_t(Nx) * sizeof(TYPE)); } diff --git a/cpp/docs/CMakeLists.txt b/cpp/docs/CMakeLists.txt new file mode 100644 index 000000000..a3da53998 --- /dev/null +++ b/cpp/docs/CMakeLists.txt @@ -0,0 +1,25 @@ +# Set some Doxygen flags +set(SOPT_DOXY_PROJECT_NAME "SOPT") +set(SOPT_DOXY_PROJECT_BRIEF "Sparse OPTimisation") +set(SOPT_DOXY_INPUT "${PROJECT_SOURCE_DIR}/cpp") + +configure_file( + ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in + ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile +) + +file(COPY + ${CMAKE_CURRENT_SOURCE_DIR}/DoxygenLayout.xml + DESTINATION ${CMAKE_CURRENT_BINARY_DIR} +) + + +add_custom_target(doc ALL + COMMAND doxygen + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + +if (web) + add_custom_target(docweb + COMMAND sed -i -e 's@namespacesopt@http://astro-informatics.github.io/sopt/&@g' -e 's@@&http://astro-informatics.github.io/sopt/@g' ${CMAKE_CURRENT_BINARY_DIR}/html/sopt.tag + DEPENDS doc) +endif() diff --git a/cpp/docs/Doxyfile.in b/cpp/docs/Doxyfile.in new file mode 100644 index 000000000..8de35a9b1 --- /dev/null +++ b/cpp/docs/Doxyfile.in @@ -0,0 +1,2482 @@ +# Doxyfile 1.8.14 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed in +# front of the TAG it is preceding. +# +# All text after a single hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists, items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (\" \"). + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all text +# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv +# built into libc) for the transcoding. See +# https://www.gnu.org/software/libiconv/ for the list of possible encodings. +# The default value is: UTF-8. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by +# double-quotes, unless you are using Doxywizard) that should identify the +# project for which the documentation is generated. This name is used in the +# title of most generated pages and in a few other places. +# The default value is: My Project. + +PROJECT_NAME = "${SOPT_DOXY_PROJECT_NAME}" + +# 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 +# control system is used. + +PROJECT_NUMBER = + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# 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 = "${SOPT_DOXY_PROJECT_BRIEF}" + +# With the PROJECT_LOGO tag one can specify a logo or an icon that is included +# in the documentation. The maximum height of the logo should not exceed 55 +# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy +# the logo to the output directory. + +PROJECT_LOGO = "${SOPT_DOXY_INPUT}/docs/assets/img/logo.png" + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path +# into which the generated documentation will be written. If a relative path is +# entered, it will be relative to the location where doxygen was started. If +# left blank the current directory will be used. + +OUTPUT_DIRECTORY = + +# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub- +# directories (in 2 levels) under the output directory of each output format and +# will distribute the generated files over these directories. Enabling this +# option can be useful when feeding doxygen a huge amount of source files, where +# putting all generated files in the same directory would otherwise causes +# performance problems for the file system. +# The default value is: NO. + +CREATE_SUBDIRS = NO + +# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII +# characters to appear in the names of generated files. If set to NO, non-ASCII +# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode +# U+3044. +# The default value is: NO. + +ALLOW_UNICODE_NAMES = YES + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese, +# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States), +# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian, +# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages), +# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian, +# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian, +# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish, +# Ukrainian and Vietnamese. +# The default value is: English. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member +# descriptions after the members that are listed in the file and class +# documentation (similar to Javadoc). Set to NO to disable this. +# The default value is: YES. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief +# description of a member or function before the detailed description +# +# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. +# The default value is: YES. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator that is +# used to form the text in various listings. Each string in this list, if found +# as the leading text of the brief description, will be stripped from the text +# and the result, after processing the whole list, is used as the annotated +# text. Otherwise, the brief description is used as-is. If left blank, the +# following values are used ($name is automatically replaced with the name of +# the entity):The $name class, The $name widget, The $name file, is, provides, +# specifies, contains, represents, a, an and the. + +ABBREVIATE_BRIEF = "The $name class" \ + "The $name widget" \ + "The $name file" \ + is \ + provides \ + specifies \ + contains \ + represents \ + a \ + an \ + the + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# doxygen will generate a detailed section even if there is only a brief +# description. +# The default value is: NO. + +ALWAYS_DETAILED_SEC = YES + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. +# The default value is: NO. + +INLINE_INHERITED_MEMB = NO + +# 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 +# shortest path that makes the file name unique will be used +# The default value is: YES. + +FULL_PATH_NAMES = YES + +# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. +# Stripping is only done if one of the specified strings matches the left-hand +# part of the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the path to +# strip. +# +# Note that you can specify absolute paths here, but also relative paths, which +# will be relative from the directory where doxygen is started. +# This tag requires that the tag FULL_PATH_NAMES is set to YES. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the +# path mentioned in the documentation of a class, which tells the reader which +# header file to include in order to use a class. If left blank only the name of +# the header file containing the class definition is used. Otherwise one should +# specify the list of include paths that are normally passed to the compiler +# using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but +# less readable) file names. This can be useful is your file systems doesn't +# support long names like on DOS, Mac, or CD-ROM. +# The default value is: NO. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the +# first line (until the first dot) of a Javadoc-style comment as the brief +# description. If set to NO, the Javadoc-style will behave just like regular Qt- +# style comments (thus requiring an explicit @brief command for a brief +# description.) +# The default value is: NO. + +JAVADOC_AUTOBRIEF = NO + +# 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 +# set to NO, the Qt-style will behave just like regular Qt-style comments (thus +# requiring an explicit \brief command for a brief description.) +# The default value is: NO. + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a +# multi-line C++ special comment block (i.e. a block of //! or /// comments) as +# a brief description. This used to be the default behavior. The new default is +# to treat a multi-line C++ comment block as a detailed description. Set this +# tag to YES if you prefer the old behavior instead. +# +# Note that setting this tag to YES also means that rational rose comments are +# not recognized any more. +# The default value is: NO. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the +# documentation from any documented member that it re-implements. +# The default value is: YES. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new +# page for each member. If set to NO, the documentation of a member will be part +# of the file/class/namespace that contains it. +# The default value is: NO. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen +# uses this value to replace tabs by spaces in code fragments. +# Minimum value: 1, maximum value: 16, default value: 4. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that act as commands in +# the documentation. An alias has the form: +# name=value +# For example adding +# "sideeffect=@par Side Effects:\n" +# will allow you to put the command \sideeffect (or @sideeffect) in the +# documentation, which will result in a user-defined paragraph with heading +# "Side Effects:". You can put \n's in the value part of an alias to insert +# newlines (in the resulting output). You can put ^^ in the value part of an +# alias to insert a newline as if a physical newline was in the original file. + +ALIASES = + +# This tag can be used to specify a number of word-keyword mappings (TCL only). +# A mapping has the form "name=value". For example adding "class=itcl::class" +# will allow you to use the command class in the itcl::class meaning. + +TCL_SUBST = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources +# only. Doxygen will then generate output that is more tailored for C. For +# instance, some of the names that are used will be different. The list of all +# members will be omitted, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or +# Python sources only. Doxygen will then generate output that is more tailored +# for that language. For instance, namespaces will be presented as packages, +# qualified scopes will look different, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources. Doxygen will then generate output that is tailored for Fortran. +# The default value is: NO. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for VHDL. +# The default value is: NO. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given +# extension. Doxygen has a built-in mapping, but you can override or extend it +# using this tag. The format is ext=language, where ext is a file extension, and +# language is one of the parsers supported by doxygen: IDL, Java, Javascript, +# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran: +# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran: +# Fortran. In the later case the parser tries to guess whether the code is fixed +# or free formatted code, this is the default for Fortran type files), VHDL. For +# instance to make doxygen treat .inc files as Fortran files (default is PHP), +# and .f files as C (default is Fortran), use: inc=Fortran f=C. +# +# Note: For files without extension you can use no_extension as a placeholder. +# +# Note that for custom extensions you also need to set FILE_PATTERNS otherwise +# the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments +# according to the Markdown format, which allows for more readable +# documentation. See http://daringfireball.net/projects/markdown/ for details. +# The output of markdown processing is further processed by doxygen, so you can +# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in +# case of backward compatibilities issues. +# The default value is: YES. + +MARKDOWN_SUPPORT = YES + +# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up +# to that level are automatically included in the table of contents, even if +# they do not have an id attribute. +# Note: This feature currently applies only to Markdown headings. +# Minimum value: 0, maximum value: 99, default value: 0. +# This tag requires that the tag MARKDOWN_SUPPORT is set to YES. + +TOC_INCLUDE_HEADINGS = 0 + +# When enabled doxygen tries to link words that correspond to documented +# classes, or namespaces to their corresponding documentation. Such a link can +# be prevented in individual cases by putting a % sign in front of the word or +# globally by setting AUTOLINK_SUPPORT to NO. +# The default value is: YES. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should set this +# tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); +# versus func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. +# The default value is: NO. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. +# The default value is: NO. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip (see: +# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen +# will parse them like normal C++ but will assume all classes use public instead +# of private inheritance when no explicit protection keyword is present. +# The default value is: NO. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES will make +# doxygen to replace the get and set methods by a property in the documentation. +# This will only work if the methods are indeed getting or setting a simple +# type. If this is not the case, or you want to show the methods anyway, you +# should set this option to NO. +# The default value is: YES. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. +# The default value is: NO. + +DISTRIBUTE_GROUP_DOC = NO + +# If one adds a struct or class to a group and this option is enabled, then also +# any nested class or struct is added to the same group. By default this option +# is disabled and one has to add nested compounds explicitly via \ingroup. +# The default value is: NO. + +GROUP_NESTED_COMPOUNDS = NO + +# Set the SUBGROUPING tag to YES to allow class member groups of the same type +# (for instance a group of public functions) to be put as a subgroup of that +# type (e.g. under the Public Functions section). Set it to NO to prevent +# subgrouping. Alternatively, this can be done per class using the +# \nosubgrouping command. +# The default value is: YES. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions +# are shown inside the group in which they are included (e.g. using \ingroup) +# instead of on a separate page (for HTML and Man pages) or section (for LaTeX +# and RTF). +# +# Note that this feature does not work in combination with +# SEPARATE_MEMBER_PAGES. +# The default value is: NO. + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions +# with only public data fields or simple typedef fields will be shown inline in +# the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO, structs, classes, and unions are shown on a separate page (for HTML and +# Man pages) or section (for LaTeX and RTF). +# The default value is: NO. + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or +# enum is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically be +# useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. +# The default value is: NO. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can be +# an expensive process and often the same symbol appears multiple times in the +# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small +# doxygen will become slower. If the cache is too large, memory is wasted. The +# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range +# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 +# symbols. At the end of a run doxygen will report the cache usage and suggest +# the optimal cache size from a speed point of view. +# Minimum value: 0, maximum value: 9, default value: 0. + +LOOKUP_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in +# documentation are documented, even if no documentation was available. Private +# class members and static file members will be hidden unless the +# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. +# Note: This will also disable the warnings about undocumented members that are +# normally produced when WARNINGS is set to YES. +# The default value is: NO. + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will +# be included in the documentation. +# The default value is: NO. + +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. +# The default value is: NO. + +EXTRACT_PACKAGE = NO + +# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be +# included in the documentation. +# The default value is: NO. + +EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO, +# only classes defined in header files are included. Does not have any effect +# for Java sources. +# The default value is: YES. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. If set to YES, local methods, +# which are defined in the implementation section but not in the interface are +# included in the documentation. If set to NO, only methods in the interface are +# included. +# The default value is: NO. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base name of +# the file that contains the anonymous namespace. By default anonymous namespace +# are hidden. +# The default value is: NO. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all +# undocumented members inside documented classes or files. If set to NO these +# members will be included in the various overviews, but no documentation +# section is generated. This option has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. If set +# to NO, these classes will be included in the various overviews. This option +# has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend +# (class|struct|union) declarations. If set to NO, these declarations will be +# included in the documentation. +# The default value is: NO. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any +# documentation blocks found inside the body of a function. If set to NO, these +# blocks will be appended to the function's detailed documentation block. +# The default value is: NO. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation that is typed after a +# \internal command is included. If the tag is set to NO then the documentation +# will be excluded. Set it to YES to include the internal documentation. +# The default value is: NO. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file +# names in lower-case letters. If set to YES, upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. +# The default value is: system dependent. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with +# their full class and namespace scopes in the documentation. If set to YES, the +# scope will be hidden. +# The default value is: NO. + +HIDE_SCOPE_NAMES = NO + +# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will +# append additional text to a page's title, such as Class Reference. If set to +# YES the compound reference will be hidden. +# The default value is: NO. + +HIDE_COMPOUND_REFERENCE= NO + +# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of +# the files that are included by a file in the documentation of that file. +# The default value is: YES. + +SHOW_INCLUDE_FILES = YES + +# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each +# grouped member an include statement to the documentation, telling the reader +# which file to include in order to use the member. +# The default value is: NO. + +SHOW_GROUPED_MEMB_INC = NO + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include +# files with double quotes in the documentation rather than with sharp brackets. +# The default value is: NO. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the +# documentation for inline members. +# The default value is: YES. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the +# (detailed) documentation of file and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. +# The default value is: YES. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief +# descriptions of file, namespace and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. Note that +# this will also influence the order of the classes in the class list. +# The default value is: NO. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the +# (brief and detailed) documentation of class members so that constructors and +# destructors are listed first. If set to NO the constructors will appear in the +# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. +# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief +# member documentation. +# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting +# detailed member documentation. +# The default value is: NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# 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 +# appear in their defined order. +# The default value is: NO. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by +# fully-qualified names, including namespaces. If set to NO, the class list will +# be sorted only by class name, not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the alphabetical +# list. +# The default value is: NO. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper +# type resolution of all parameters of a function it will reject a match between +# the prototype and the implementation of a member function even if there is +# only one candidate or it is obvious which candidate to choose by doing a +# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still +# accept a match between prototype and implementation in such cases. +# The default value is: NO. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo +# list. This list is created by putting \todo commands in the documentation. +# The default value is: YES. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test +# list. This list is created by putting \test commands in the documentation. +# The default value is: YES. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug +# list. This list is created by putting \bug commands in the documentation. +# The default value is: YES. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) +# the deprecated list. This list is created by putting \deprecated commands in +# the documentation. +# The default value is: YES. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional documentation +# sections, marked by \if ... \endif and \cond +# ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the +# initial value of a variable or macro / define can have for it to appear in the +# documentation. If the initializer consists of more lines than specified here +# it will be hidden. Use a value of 0 to hide initializers completely. The +# appearance of the value of individual variables and macros / defines can be +# controlled using \showinitializer or \hideinitializer command in the +# documentation regardless of this setting. +# Minimum value: 0, maximum value: 10000, default value: 30. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at +# the bottom of the documentation of classes and structs. If set to YES, the +# list will mention the files that were used to generate the documentation. +# The default value is: YES. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This +# will remove the Files entry from the Quick Index and from the Folder Tree View +# (if specified). +# The default value is: YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces +# page. This will remove the Namespaces entry from the Quick Index and from the +# Folder Tree View (if specified). +# The default value is: YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command command input-file, where command is the value of the +# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided +# by doxygen. Whatever the program writes to standard output is used as the file +# version. For an example see the documentation. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. You can +# optionally specify a file name after the option, if omitted DoxygenLayout.xml +# will be used as the name of the layout file. +# +# Note that if you run doxygen from a directory containing a file called +# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE +# tag is left empty. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files containing +# the reference definitions. This must be a list of .bib files. The .bib +# extension is automatically appended if omitted. This requires the bibtex tool +# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info. +# For LaTeX the style of the bibliography can be controlled using +# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the +# search path. See also \cite for info how to create references. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# Configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated to +# standard output by doxygen. If QUIET is set to YES this implies that the +# messages are off. +# The default value is: NO. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES +# this implies that the warnings are on. +# +# Tip: Turn warnings on while writing the documentation. +# The default value is: YES. + +WARNINGS = YES + +# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate +# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: YES. + +WARN_IF_UNDOCUMENTED = YES + +# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some parameters +# in a documented function, or documenting parameters that don't exist or using +# markup commands wrongly. +# The default value is: YES. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that +# are documented, but have no documentation for their parameters or return +# value. If set to NO, doxygen will only warn about wrong or incomplete +# parameter documentation, but not about the absence of documentation. +# The default value is: NO. + +WARN_NO_PARAMDOC = NO + +# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when +# a warning is encountered. +# The default value is: NO. + +WARN_AS_ERROR = NO + +# The WARN_FORMAT tag determines the format of the warning messages that doxygen +# can produce. The string should contain the $file, $line, and $text tags, which +# will be replaced by the file and line number from which the warning originated +# and the warning text. Optionally the format may contain $version, which will +# be replaced by the version of the file (if it could be obtained via +# FILE_VERSION_FILTER) +# The default value is: $file:$line: $text. + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning and error +# messages should be written. If left blank the output is written to standard +# error (stderr). + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# Configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag is used to specify the files and/or directories that contain +# documented source files. You may enter file names like myfile.cpp or +# directories like /usr/src/myproject. Separate the files or directories with +# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING +# Note: If this tag is empty the current directory is searched. + +INPUT = "${SOPT_DOXY_INPUT}" + +# 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 +# libiconv (or the iconv built into libc) for the transcoding. See the libiconv +# documentation (see: https://www.gnu.org/software/libiconv/) for the list of +# possible encodings. +# The default value is: UTF-8. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and +# *.h) to filter out the source-files in the directories. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# read by doxygen. +# +# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp, +# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, +# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, +# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, +# *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf. + +FILE_PATTERNS = *.c \ + *.cc \ + *.cxx \ + *.cpp \ + *.c++ \ + *.java \ + *.ii \ + *.ixx \ + *.ipp \ + *.i++ \ + *.inl \ + *.idl \ + *.ddl \ + *.odl \ + *.h \ + *.hh \ + *.hxx \ + *.hpp \ + *.h++ \ + *.cs \ + *.d \ + *.php \ + *.php4 \ + *.php5 \ + *.phtml \ + *.inc \ + *.m \ + *.markdown \ + *.md \ + *.mm \ + *.dox \ + *.py \ + *.pyw \ + *.f90 \ + *.f95 \ + *.f03 \ + *.f08 \ + *.f \ + *.for \ + *.tcl \ + *.vhd \ + *.vhdl \ + *.ucf \ + *.qsf + +# The RECURSIVE tag can be used to specify whether or not subdirectories should +# be searched for input files as well. +# The default value is: NO. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = + +# 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 +# from the input. +# The default value is: NO. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories use the pattern */test/* + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or directories +# that contain example code fragments that are included (see the \include +# command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank all +# files are included. + +EXAMPLE_PATTERNS = * + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude commands +# irrespective of the value of the RECURSIVE tag. +# The default value is: NO. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or directories +# that contain images that are to be included in the documentation (see the +# \image command). + +IMAGE_PATH = ${SOPT_DOXY_INPUT}/docs/assets/img + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command: +# +# +# +# where is the value of the INPUT_FILTER tag, and is the +# name of an input file. Doxygen will then use the output that the filter +# program writes to standard output. If FILTER_PATTERNS is specified, this tag +# will be ignored. +# +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: pattern=filter +# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how +# filters are used. If the FILTER_PATTERNS tag is empty or if none of the +# patterns match the file name, INPUT_FILTER is applied. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will also be used to filter the input files that are used for +# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). +# The default value is: NO. + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and +# it is also possible to disable source filtering for a specific pattern using +# *.ext= (so without naming a filter). +# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (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 = README.md + +#--------------------------------------------------------------------------- +# Configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will be +# generated. Documented entities will be cross-referenced with these sources. +# +# Note: To get rid of all source code in the generated output, make sure that +# also VERBATIM_HEADERS is set to NO. +# The default value is: NO. + +SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body of functions, +# classes and enums directly into the documentation. +# The default value is: NO. + +INLINE_SOURCES = YES + +# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any +# special comment blocks from generated source code fragments. Normal C, C++ and +# Fortran comments will always remain visible. +# The default value is: YES. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES then for each documented +# function all documented functions referencing it will be listed. +# The default value is: NO. + +REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES then for each documented function +# all documented entities called/used by that function will be listed. +# The default value is: NO. + +REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set +# to YES then the hyperlinks from functions in REFERENCES_RELATION and +# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will +# link to the documentation. +# The default value is: YES. + +REFERENCES_LINK_SOURCE = YES + +# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the +# source code will show a tooltip with additional information such as prototype, +# brief description and links to the definition and documentation. Since this +# will make the HTML file larger and loading of large files a bit slower, you +# can opt to disable this feature. +# The default value is: YES. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +SOURCE_TOOLTIPS = YES + +# If the USE_HTAGS tag is set to YES then the references to source code will +# point to the HTML generated by the htags(1) tool instead of doxygen built-in +# source browser. The htags tool is part of GNU's global source tagging system +# (see https://www.gnu.org/software/global/global.html). You will need version +# 4.8.6 or higher. +# +# To use it do the following: +# - Install the latest version of global +# - Enable SOURCE_BROWSER and USE_HTAGS in the config file +# - Make sure the INPUT points to the root of the source tree +# - Run doxygen as normal +# +# Doxygen will invoke htags (and that will in turn invoke gtags), so these +# tools must be available from the command line (i.e. in the search path). +# +# The result: instead of the source browser generated by doxygen, the links to +# source code will now point to the output of htags. +# The default value is: NO. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a +# verbatim copy of the header file for each class for which an include is +# specified. Set to NO to disable this. +# See also: Section \class. +# The default value is: YES. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# Configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all +# compounds will be generated. Enable this if the project contains a lot of +# classes, structs, unions or interfaces. +# The default value is: YES. + +ALPHABETICAL_INDEX = YES + +# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in +# which the alphabetical index list will be split. +# Minimum value: 1, maximum value: 20, default value: 5. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all classes will +# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag +# can be used to specify a prefix (or a list of prefixes) that should be ignored +# while generating the index headers. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output +# The default value is: YES. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each +# generated HTML page (for example: .htm, .php, .asp). +# The default value is: .html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a user-defined HTML header file for +# each generated HTML page. If the tag is left blank doxygen will generate a +# standard header. +# +# To get valid HTML the header file that includes any scripts and style sheets +# that doxygen needs, which is dependent on the configuration options used (e.g. +# the setting GENERATE_TREEVIEW). It is highly recommended to start with a +# default header using +# doxygen -w html new_header.html new_footer.html new_stylesheet.css +# YourConfigFile +# and then modify the file new_header.html. See also section "Doxygen usage" +# for information on how to generate the default header that doxygen normally +# uses. +# Note: The header is subject to change so you typically have to regenerate the +# default header when upgrading to a newer version of doxygen. For a description +# of the possible markers and block names see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each +# generated HTML page. If the tag is left blank doxygen will generate a standard +# footer. See HTML_HEADER for more information on how to generate a default +# footer and what special commands can be used inside the footer. See also +# section "Doxygen usage" for information on how to generate the default footer +# that doxygen normally uses. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style +# sheet that is used by each HTML page. It can be used to fine-tune the look of +# the HTML output. If left blank doxygen will generate a default style sheet. +# See also section "Doxygen usage" for information on how to generate the style +# sheet that doxygen normally uses. +# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as +# it is more robust and this tag (HTML_STYLESHEET) will in the future become +# obsolete. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# cascading style sheets that are included after the standard style sheets +# created by doxygen. Using this option one can overrule certain style aspects. +# This is preferred over using HTML_STYLESHEET since it does not replace the +# standard style sheet and is therefore more robust against future updates. +# Doxygen will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). For an example see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_STYLESHEET = ${SOPT_DOXY_INPUT}/docs/assets/css/style.css + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that the +# files will be copied as-is; there are no commands or markers available. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen +# will adjust the colors in the style sheet and background images according to +# this color. Hue is specified as an angle on a colorwheel, see +# https://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 +# purple, and 360 is red again. +# Minimum value: 0, maximum value: 359, default value: 220. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors +# in the HTML output. For a value of 0 the output will use grayscales only. A +# value of 255 will produce the most vivid colors. +# Minimum value: 0, maximum value: 255, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the +# luminance component of the colors in the HTML output. Values below 100 +# gradually make the output lighter, whereas values above 100 make the output +# darker. The value divided by 100 is the actual gamma applied, so 80 represents +# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not +# change the gamma. +# Minimum value: 40, maximum value: 240, default value: 80. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting this +# to YES can help to show when doxygen was last run and thus if the +# documentation is up to date. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_TIMESTAMP = NO + +# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML +# documentation will contain a main index with vertical navigation menus that +# are dynamically created via Javascript. If disabled, the navigation index will +# consists of multiple levels of tabs that are statically embedded in every HTML +# page. Disable this option to support browsers that do not have Javascript, +# like the Qt help browser. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_MENUS = 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 +# page has loaded. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_SECTIONS = YES + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries +# shown in the various tree structured indices initially; the user can expand +# and collapse entries dynamically later on. Doxygen will expand the tree to +# such a level that at most the specified number of entries are visible (unless +# a fully collapsed tree already exceeds this amount). So setting the number of +# entries 1 will produce a full collapsed tree by default. 0 is a special value +# representing an infinite number of entries and will result in a full expanded +# tree by default. +# Minimum value: 0, maximum value: 9999, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files will be +# generated that can be used as input for Apple's Xcode 3 integrated development +# environment (see: https://developer.apple.com/tools/xcode/), introduced with +# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a +# Makefile in the HTML output directory. Running make will produce the docset in +# that directory and running make install will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at +# startup. See https://developer.apple.com/tools/creatingdocsetswithdoxygen.html +# for more information. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_DOCSET = NO + +# This tag determines the name of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# The default value is: Doxygen generated docs. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# This tag specifies a string that should uniquely identify the documentation +# set bundle. This should be a reverse domain-name style string, e.g. +# com.mycompany.MyDocSet. Doxygen will append .docset to the name. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. +# The default value is: org.doxygen.Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. +# The default value is: Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three +# additional HTML index files: index.hhp, index.hhc, and index.hhk. The +# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop +# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on +# Windows. +# +# The HTML Help Workshop contains a compiler that can convert all HTML output +# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML +# files are now used as the Windows 98 help format, and will replace the old +# Windows help format (.hlp) on all Windows platforms in the future. Compressed +# HTML files also contain an index, a table of contents, and you can search for +# words in the documentation. The HTML workshop also contains a viewer for +# compressed HTML files. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_HTMLHELP = NO + +# The CHM_FILE tag can be used to specify the file name of the resulting .chm +# file. You can add a path in front of the file if the result should not be +# written to the html output directory. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_FILE = + +# The HHC_LOCATION tag can be used to specify the location (absolute path +# including file name) of the HTML help compiler (hhc.exe). If non-empty, +# doxygen will try to run the HTML help compiler on the generated index.hhp. +# The file has to be specified with full path. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +HHC_LOCATION = + +# The GENERATE_CHI flag controls if a separate .chi index file is generated +# (YES) or that it should be included in the master .chm file (NO). +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +GENERATE_CHI = NO + +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) +# and project file content. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_INDEX_ENCODING = + +# The BINARY_TOC flag controls whether a binary table of contents is generated +# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it +# enables the Previous and Next buttons. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members to +# the table of contents of the HTML help documentation and to the tree view. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that +# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help +# (.qch) of the generated HTML documentation. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify +# the file name of the resulting .qch file. The path specified is relative to +# the HTML output folder. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help +# Project output. For more information please see Qt Help Project / Namespace +# (see: http://doc.qt.io/qt-4.8/qthelpproject.html#namespace). +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt +# Help Project output. For more information please see Qt Help Project / Virtual +# Folders (see: http://doc.qt.io/qt-4.8/qthelpproject.html#virtual-folders). +# The default value is: doc. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_VIRTUAL_FOLDER = doc + +# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom +# filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://doc.qt.io/qt-4.8/qthelpproject.html#custom-filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://doc.qt.io/qt-4.8/qthelpproject.html#custom-filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's filter section matches. Qt Help Project / Filter Attributes (see: +# http://doc.qt.io/qt-4.8/qthelpproject.html#filter-attributes). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_SECT_FILTER_ATTRS = + +# The QHG_LOCATION tag can be used to specify the location of Qt's +# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the +# generated .qhp file. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be +# generated, together with the HTML files, they form an Eclipse help plugin. To +# install this plugin and make it available under the help contents menu in +# Eclipse, the contents of the directory containing the HTML and XML files needs +# to be copied into the plugins directory of eclipse. The name of the directory +# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. +# After copying Eclipse needs to be restarted before the help appears. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the Eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have this +# name. Each documentation set should have its own identifier. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# If you want full control over the layout of the generated HTML pages it might +# be necessary to disable the index and replace it with your own. The +# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top +# of each HTML page. A value of NO enables the index and the value YES disables +# it. Since the tabs in the index contain the same information as the navigation +# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. If the tag +# value is set to YES, a side panel will be generated containing a tree-like +# index structure (just like the one that is generated for HTML Help). For this +# to work a browser that supports JavaScript, DHTML, CSS and frames is required +# (i.e. any modern browser). Windows users are probably better off using the +# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can +# further fine-tune the look of the index. As an example, the default style +# sheet generated by doxygen has an example that shows how to put an image at +# the root of the tree instead of the PROJECT_NAME. Since the tree basically has +# the same information as the tab index, you could consider setting +# DISABLE_INDEX to YES when enabling this option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_TREEVIEW = NO + +# 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. +# +# Note that a value of 0 will completely suppress the enum values from appearing +# in the overview section. +# Minimum value: 0, maximum value: 20, default value: 4. +# This tag requires that the tag GENERATE_HTML is set to YES. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used +# to set the initial width (in pixels) of the frame in which the tree is shown. +# Minimum value: 0, maximum value: 1500, default value: 250. +# This tag requires that the tag GENERATE_HTML is set to YES. + +TREEVIEW_WIDTH = 250 + +# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to +# external symbols imported via tag files in a separate window. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +EXT_LINKS_IN_WINDOW = NO + +# 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 +# doxygen run you need to manually remove any form_*.png images from the HTML +# output directory to force them to be regenerated. +# Minimum value: 8, maximum value: 50, default value: 10. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANSPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are not +# supported properly for IE 6.0, but are supported on all modern browsers. +# +# Note that when changing this option you need to delete any form_*.png files in +# the HTML output directory before the changes have effect. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see +# https://www.mathjax.org) which uses client side Javascript for the rendering +# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX +# installed or if you want to formulas look prettier in the HTML output. When +# enabled you may also need to install MathJax separately and configure the path +# to it using the MATHJAX_RELPATH option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +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: +# http://docs.mathjax.org/en/latest/output.html) for more details. +# Possible values are: HTML-CSS (which is slower, but has the best +# compatibility), NativeMML (i.e. MathML) and SVG. +# The default value is: HTML-CSS. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the HTML +# output directory using the MATHJAX_RELPATH option. The destination directory +# should contain the MathJax.js script. For instance, if the mathjax directory +# is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax +# Content Delivery Network so you can quickly see the result without installing +# MathJax. However, it is strongly recommended to install a local copy of +# MathJax from https://www.mathjax.org before deployment. +# The default value is: https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2/. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_RELPATH = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2/ + +# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax +# extension names that should be enabled during MathJax rendering. For example +# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces +# of code that will be used on startup of the MathJax code. See the MathJax site +# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an +# example see the documentation. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for +# the HTML output. The underlying search engine uses javascript and DHTML and +# should work on any modern browser. Note that when using HTML help +# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) +# there is already a search function so this one should typically be disabled. +# For large projects the javascript based search engine can be slow, then +# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to +# search using the keyboard; to jump to the search box use + S +# (what the is depends on the OS and browser, but it is typically +# , /