prepare next major release

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "include/hops/thirdparty/HighFive"]
-	path = include/hops/thirdparty/HighFive
+[submodule "include/hops/Third-party/HighFive"]
+	path = include/hops/Third-party/HighFive
 	url = https://github.com/BlueBrain/HighFive.git

.travis.yml

@@ -3,7 +3,7 @@ sudo: true
 
 env:
   global:
-    - MAKEFLAGS="-j 2"
+    - MAKEFLAGS="-j 3"
 
 language: cpp
 

AUTHORS

@@ -2,3 +2,4 @@ Johann Fredrik Jadebeck <j.jadebeck@fz-juelich.de>
 Samuel Leweke <s.leweke@fz-juelich.de>
 Axel Theorell <a.theorell@fz-juelich.de>
 Katharina Nöh <k.noeh@fz-juelich.de>
+Richard D. Paul <r.paul@fz-juelich.de>

CMakeLists.txt

@@ -1,6 +1,5 @@
 ########################################################################################################################
-# CMAKE Settings
-########################################################################################################################
+# CMAKE Settings ########################################################################################################################
 
 cmake_minimum_required(VERSION 3.14)
 set(CMAKE_TRY_COMPILE_TARGET_TYPE "STATIC_LIBRARY")
@@ -33,10 +32,15 @@ set(MKL_USE_interface lp64)
 # Set Options
 ########################################################################################################################
 
+option(HOPS_SBML_SUPPORT "Enables SBML support. Use -DHOPS_SBML_SUPPORT=ON to enable." OFF)
+option(HOPS_HDF5_SUPPORT "Enables HDF5 support with HighFive. Use -DHOPS_HDF5_SUPPORT=ON to enable." OFF)
 option(HOPS_BENCHMARKS "Enables compilation of Benchmarks (Requires Celero). Use -DHOPS_BENCHMARKS=ON to enable." OFF)
 option(HOPS_DOCS "Enables generation of documentation. Use -DHOPS_DOCS=OFF to disable." ON)
-option(HOPS_EXAMPLES "Enables compilation of Examples. Use -DHOPS_EXAMPLES=OFF to disable." ON)
+option(HOPS_BINARIES "Enables compilation of hops executables. Use -DHOPS_BINARIES=OFF to disable." ON)
 option(HOPS_TESTS "Enables compilation of unit tests. Use -DHOPS_TESTS=OFF to disable." ON)
+option(HOPS_NO_INSTALL "Disables installation. Use -DHOPS_NO_INSTALL=ON to disable installation." OFF)
+set(HOPS_LIBRARY_TYPE SHARED CACHE STRING "Type of library to build. Options are HEADER_ONLY, STATIC or SHARED")
+set_property(CACHE HOPS_LIBRARY_TYPE PROPERTY STRINGS HEADER_ONLY STATIC SHARED)
 
 ########################################################################################################################
 # C++-Compiler Settings
@@ -86,6 +90,7 @@ endif (NOT ${CMAKE_BUILD_TYPE} STREQUAL "Debug")
 find_package(Doxygen)
 find_package(Eigen3 REQUIRED)
 find_package(MKL)
+find_package(OpenMP)
 message(STATUS "FOUND MKL ? ${MKL_FOUND}")
 
 ########################################################################################################################
@@ -101,22 +106,58 @@ endif (MKL_LIBRARY_DIR)
 # HOPS
 ########################################################################################################################
 
-add_library(hops STATIC "" include/hops/FileReader/Hdf5Reader.hpp)
-target_include_directories(hops PUBLIC ${EIGEN3_INCLUDE_DIR})
+if (HOPS_LIBRARY_TYPE STREQUAL "HEADER_ONLY")
+    message(STATUS "Set to header-only installation")
+    set(SCOPE INTERFACE)
+    add_library(hops INTERFACE)
+
+    target_compile_definitions(hops INTERFACE HOPS_HEADER_ONLY)
+    if (HOPS_HDF5_SUPPORT)
+        target_compile_definitions(hops INTERFACE HOPS_HDF5_SUPPORT)
+    endif (HOPS_HDF5_SUPPORT)
+
+    target_include_directories(hops INTERFACE ${EIGEN3_INCLUDE_DIR}
+            $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+            $<INSTALL_INTERFACE:include>
+            )
+else (HOPS_LIBRARY_TYPE STREQUAL "HEADER_ONLY")
+    message(STATUS "Set to ${HOPS_LIBRARY_TYPE} library installation")
+    set(SCOPE PRIVATE)
+    add_library(hops ${HOPS_LIBRARY_TYPE})
+    target_compile_definitions(hops ${SCOPE} HOPS_HDF5_SUPPORT)
+
+    target_include_directories(hops PUBLIC ${EIGEN3_INCLUDE_DIR}
+            $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+            $<INSTALL_INTERFACE:include>
+            )
+endif (HOPS_LIBRARY_TYPE STREQUAL "HEADER_ONLY")
+
+if (OpenMP_CXX_FOUND)
+    target_link_libraries(hops INTERFACE OpenMP::OpenMP_CXX)
+    target_link_libraries(hops ${SCOPE} OpenMP::OpenMP_CXX)
+    target_link_options(hops INTERFACE ${OpenMP_CXX_LIBRARY} ${OpenMP_CXX_FLAGS})
+    target_link_options(hops ${SCOPE} ${OpenMP_CXX_LIBRARY} ${OpenMP_CXX_FLAGS})
+else (OpenMP_CXX_FOUND)
+    message(WARNING "OPENMP not found.")
+endif (OpenMP_CXX_FOUND)
+
+
+add_subdirectory(include)
+
+########################################################################################################################
+# MKL support for faster linear algebra
+########################################################################################################################
 
 if (MKL_INCLUDE_DIR)
-  target_include_directories(hops PRIVATE ${MKL_INCLUDE_DIR})
+    target_include_directories(hops ${SCOPE} ${MKL_INCLUDE_DIR})
 endif (MKL_INCLUDE_DIR)
 if (MKL_LIBRARY_DIR)
-  target_link_directories(hops PRIVATE ${MKL_LIBRARY_DIR})
+    target_link_directories(hops ${SCOPE} ${MKL_LIBRARY_DIR})
 endif (MKL_LIBRARY_DIR)
 if (MKL_LIBRARIES)
-  target_link_libraries(hops PRIVATE ${MKL_LIBRARIES})
+    target_link_libraries(hops ${SCOPE} ${MKL_LIBRARIES})
 endif (MKL_LIBRARIES)
 
-add_subdirectory(include)
-add_subdirectory(src)
-
 ########################################################################################################################
 # HOPS_DOCS
 ########################################################################################################################
@@ -129,12 +170,11 @@ if (HOPS_DOCS)
         message(STATUS "Enabled Doxygen documentation. Use -DHOPS_DOCS=OFF to disable.")
         set(DOCUMENTATION_DIR "docs")
 
-        set(HEADER_DIR "${CMAKE_CURRENT_SOURCE_DIR}/include/hops")
-        set(SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/src")
+        set(SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/include")
 
         set(doxy_main_page "${CMAKE_CURRENT_SOURCE_DIR}/README.md")
-        set(doxyfile_in "${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in")
-        set(doxyfile "${CMAKE_CURRENT_BINARY_DIR}/docs/Doxyfile")
+        set(doxyfile_in "${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in")
+        set(doxyfile "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile")
         configure_file(${doxyfile_in} ${doxyfile} @ONLY)
         add_custom_target(docs
                 COMMAND ${DOXYGEN_EXECUTABLE} ${doxyfile} && make -C ${CMAKE_CURRENT_BINARY_DIR}/docs/latex
@@ -159,14 +199,14 @@ else ()
 endif ()
 
 ########################################################################################################################
-# HOPS_EXAMPLES
+# HOPS_BINARIES
 ########################################################################################################################
 
-if (HOPS_EXAMPLES)
-    message(STATUS "Enabled compilation of examples. Use -DHOPS_EXAMPLES=OFF to disable.")
+if (HOPS_BINARIES)
+    message(STATUS "Enabled compilation of executables. Use -DHOPS_BINARIES=OFF to disable.")
     add_subdirectory(bin)
 else ()
-    message(STATUS "Disabled compilation of examples. Use -DHOPS_EXAMPLES=ON to enable.")
+    message(STATUS "Disabled compilation of executables. Use -DHOPS_BINARIES=ON to enable.")
 endif ()
 
 ########################################################################################################################
@@ -195,9 +235,16 @@ endif ()
 # Install
 ########################################################################################################################
 
-install(DIRECTORY include/ DESTINATION include/ FILES_MATCHING PATTERN "*.hpp")
-install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/include/hops/hops.hpp DESTINATION include/hops)
-install(TARGETS hops-sampler DESTINATION bin/)
-install(TARGETS hops EXPORT hops-config LIBRARY DESTINATION "lib")
-install(EXPORT hops-config DESTINATION "lib" CONFIGURATIONS RELEASE)
+if(NOT HOPS_NO_INSTALL)
+    install(DIRECTORY include/ DESTINATION include/ FILES_MATCHING PATTERN "*.hpp")
+    install(DIRECTORY include/ DESTINATION include/ FILES_MATCHING PATTERN "*.cpp")
+    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/include/hops/hops.hpp DESTINATION include/hops)
+
+    if (HOPS_BINARIES)
+        install(TARGETS hops-sampler DESTINATION bin/)
+    endif ()
+
+    install(TARGETS hops EXPORT hops-config LIBRARY DESTINATION "lib")
+    install(EXPORT hops-config DESTINATION "lib")
+endif()
 

Dockerfile

@@ -27,19 +27,18 @@ ADD cmake /home/hops_user/cmake
 ADD docs /home/hops_user/docs
 ADD include /home/hops_user/include
 ADD resources /home/hops_user/resources
-ADD src /home/hops_user/src
 ADD tests /home/hops_user/tests
 ADD CMakeLists.txt /home/hops_user/CMakeLists.txt
 
 RUN mkdir cmake-build-debug
 WORKDIR /home/hops_user/cmake-build-debug
 RUN cmake .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu
-RUN make -j8
+RUN make -j16
 RUN make test
 
 WORKDIR /home/hops_user/
 RUN mkdir cmake-build-release
 WORKDIR /home/hops_user/cmake-build-release
 RUN cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu
-RUN make -j8
+RUN make -j16
 RUN make test

docs/Doxyfile.in → Doxyfile.in

@@ -600,8 +600,8 @@ SORT_BY_SCOPE_NAME     = 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 GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the t0do
+# list. This list is created by putting \t0do commands in the documentation.
 # The default value is: YES.
 
 GENERATE_TODOLIST      = YES
@@ -772,8 +772,7 @@ WARN_LOGFILE           =
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  = @doxy_main_page@ \
-									@HEADER_DIR@ \
-									@SOURCE_DIR@
+                         @SOURCE_DIR@
 
 # 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
@@ -1473,7 +1472,7 @@ FORMULA_TRANSPARENT    = YES
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
 
 # When MathJax is enabled you can set the default output format to be used for
 # the MathJax output. See the MathJax site (see:
@@ -1661,7 +1660,7 @@ PAPER_TYPE             = a4
 # If left blank no extra packages will be included.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
-EXTRA_PACKAGES         =
+EXTRA_PACKAGES         ={amsmath}
 
 # The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
 # generated LaTeX document. The header should contain everything until the first

README.md

@@ -2,17 +2,18 @@
 
 [![Build Status](https://travis-ci.org/modsim/hops.svg?branch=master)](https://travis-ci.org/modsim/hops)
 
-
 The **H**ighly **O**ptimized **P**olytope **S**ampling toolbox is an open-source C++17
 library for efficient and scalable MCMC algorithms for sampling convex-constrained spaces possibly
 equipped with arbitrary target functions.
 
 For details and benchmarks see the application note https://doi.org/10.1093/bioinformatics/btaa872.
 Test data from the application note is downloadable at https://doi.org/10.26165/JUELICH-DATA/YXLFKJ.
 
+
 ## Documentation
 
-See https://modsim.github.io/hops/.
+Documentation, interactive demos and further resources can be found at https://modsim.github.io/hops/.
+
 
 ## Cloning from Github
 
@@ -23,54 +24,59 @@ For this reason, HOPS should be fetched recursively:
 git clone git@github.com:modsim/hops.git --recursive
 ```
 
+<img src="hops.png" alt="HOPS Logo" width="500"/>
+
+
 ## Installation
 
 HOPS uses CMake as build system.  
 See the Dockerfile for a demonstration on installing HOPS and its dependencies on Ubuntu 20.4.
 
+## Python Interface
+
+Python interface is available at https://github.com/modsim/hopsy.
+
+
 ### CMake options
 
-* HOPS\_BENCHMARKS (default OFF) - Enables compilation of Benchmarks (Requires Celero). Use -DHOPS\_BENCHMARKS=ON to enable.
-* HOPS\_DOCS (default ON) - Enables generation of documentation. Use -DHOPS\_DOCS=OFF to disable. (This creates the Doxygen file from which the docs have to be generated)
-* HOPS\_EXAMPLES (default ON) - Enables compilation of Examples. Use -DHOPS\_EXAMPLES=OFF to disable.
-* HOPS\_TESTS (default ON) - Enables compilation of unit tests. Use -DHOPS\_TESTS=OFF to disable.
+| Option Name               | Default   | Description                                                                                               |
+| ------------------------- | --------- | --------------------------------------------------------------------------------------------------------- |
+| HOPS\_HDF5\_SUPPORT       |       OFF | Enables HDF5 support with HighFive. Use -DHOPS\_BENCHMARKS=ON to enable.                                  |
+| HOPS\_BENCHMARKS          |       OFF | Enables compilation of Benchmarks (Requires Celero). Use -DHOPS\_BENCHMARKS=ON to enable.                 |
+| HOPS\_DOCS                |        ON | Enables generation of documentation. Use -DHOPS\_DOCS=OFF to disable. (This creates the Doxygen file fr om which the docs have to be generated) |
+| HOPS\_BINARIES            |        ON | Enables compilation of hops executables. Use -DHOPS\_EXAMPLES=OFF to disable.                             |
+| HOPS\_TESTS               |        ON | Enables compilation of unit tests. Use -DHOPS\_TESTS=OFF to disable.                                      |
+| HOPS\_LIBRARY\_TYPE       |    SHARED | Type of library to build. Options are HEADER\_ONLY, STATIC or SHARED                                      |
 
-When building HOPS with Tests, an internet connection is required in order to fetch Googletest (https://github.com/google/googletest).
 
 #### Install on Linux:
 
 ```
-# Create directory for out-of-source build
-$ mkdir cmake-build-release
-$ cd cmake-build-release
-# Run cmake
-$ cmake .. -DCMAKE_BUILD_TYPE=Release
-# Build HOPS
-$ make 
-# Run Tests
-$ make test
-# Alternatively run tests by calling runTests
-# cd tests
-$ ./runTests
-$ cd ..
-# Install
-$ sudo make install
+$ mkdir cmake-build-release cd cmake-build-release      # create and switch into 
+                                                        # directory for out-of-source build
+$ cmake .. -DCMAKE_BUILD_TYPE=Release                   # run cmake
+$ make                                                  # build hops
+$ make test                                             # run Tests
+$ sudo make install                                     # install
 ```
 
+
 #### Install on Windows 10:
 
 Use an IDE (e.g. CLion) to parse the project and its CMakeLists.txt.
 
 
-
 ## Examples
+
 See the examples directory for demonstrations on how to use the library.
 
+
 ## Supported Compilers
 * g++
 * Clang
 * Microsoft Visual C++
 
+
 ## Troubleshooting
 
 * If you run into trouble finding CLP on Linux (e.g. Ubuntu 20.04), try extending the cmake prefix path:

bin/CMakeLists.txt

@@ -1,21 +1,19 @@
-if (HOPS_MPI_SUPPORTED)
-    set(BIN_SOURCES ${EXAMPLE_SOURCES} ParallelTemperingDemo.cpp)
-endif (HOPS_MPI_SUPPORTED)
+find_package(MPI)
 
-foreach (BIN_SOURCE ${EXAMPLE_SOURCES})
-    get_filename_component(BIN_NAME ${EXAMPLE_SOURCE} NAME_WE)
-    add_executable(${BIN_NAME} ${EXAMPLE_SOURCE})
+if (MPI_FOUND)
+#    set(BIN_SOURCES ParallelTemperingDemo.cpp)
+    set(BIN_SOURCES )
+endif (MPI_FOUND)
+
+foreach (BIN_SOURCE ${BIN_SOURCES})
+    get_filename_component(BIN_NAME ${BIN_SOURCE} NAME_WE)
+    add_executable(${BIN_NAME} ${BIN_SOURCE})
     target_link_libraries(${BIN_NAME} hops)
-    target_include_directories(${BIN_NAME} PUBLIC ../include)
 endforeach (BIN_SOURCE)
 
 find_package(Boost COMPONENTS program_options REQUIRED)
 add_executable(hops-sampler hops-sampler.cpp hops-sampler.hpp)
-target_link_libraries(hops-sampler hops ${Boost_LIBRARIES})
-target_include_directories(hops-sampler PUBLIC
-        $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../include/${LIBRARY_NAME}>
-        $<INSTALL_INTERFACE:../include/${LIBRARY_NAME}>
-        )
+target_link_libraries(hops-sampler PRIVATE hops ${Boost_LIBRARIES})