Merge branch 'develop'

* develop: (24 commits)
  Added build status tag.
  Added example and jupyter notebook. Tidying up everything…
  Rewrote the Python extension quite a bit. Can now reproduce the results from the C++ tests.
  Fixed the Python tests and the files used for the benchmark.
  Fixed benchmark runner. Additional: * added COPYRIGHT * updated README * minor fixes
  Documentations: * updated Doxygen doc * added Sphinx doc
  Removed legacy code + some cython cleaning.
  Cleaning Windows compilation by adding headers hack for debug config. Additional: * reduced tests duration by limiting tests to 100 iterations * removed legacy tests
  Added benchmark functionality from Caterina. Additional: * cmake updated * minor cleaning and updating the README
  Reorganized cmake and repository for making the code cross-platform and setting the CI. This includes: * builds passing on Win10, OSX, and Linux * python extension, including the infrastructure to build wheels * cleaning of the cmake
  Added a python wrapper to the algorithm.
  Added assortative case. Additional: * many tests including some for the algorithm types * added template for initializing w * major refactoring * printing out likelihood * minor review comments
  Implemented case when affinity is specified in a file. Additional: * added test for undirected graphs * cleaning + bug fixes in the solver and the application * a bit more consistency + comments as suggested by Ivan
  Improved interface, writing files is now part of the application. Additional: * random generator is now a template. Added CLI for the user to specify the seed * added tensor tests. * labels must be extracted to write the output files * writing files is now part of the application. * implementation of undirected graphs;
  Some general improvements: * added template types (vertex_t, weight_t…) * reorganized tests inside fixtures * added report class * added termination reason * initialization is now a template of the solver * added report output file * API simplified * more tests * documentation updated
  Removing unnecessary Makefile
  Added a lot of unit tests and ctests. Additional: * refactored of the network logic * comments from review * moved headers to separate folder. * added methods writing outputs into files
  Awesome documentation and consistent versioning across the project. Additional: * number of groups is now a required argument. * fixed some warnings during compilation
  Some additional changes: * reverted back legacy code * added timer * removed dependency on boost program options - not easy to handle required arguments
  First implementation finished. Reproduces the results for an non-assortative, undirected network with the adjacency data file.
  ...

Author: jcpassy

.DS_Store

@@ -1,29 +1,18 @@
-# Compiled Object files
-*.slo
-*.lo
+build
+release
+debug
+*.DS_Store
 *.o
-*.obj
-
-# Precompiled Headers
-*.gch
-*.pch
-
-# Compiled Dynamic libraries
-*.so
-*.dylib
-*.dll
-
-# Fortran module files
-*.mod
-*.smod
-
-# Compiled Static libraries
-*.lai
-*.la
-*.a
-*.lib
-
-# Executables
 *.exe
-*.out
-*.app
+*.vs*
+__pycache__
+dist/
+*egg-*
+.noseids
+
+# data from tests
+u_*.dat
+v_*.dat
+w_*.dat
+*out*.dat
+results/

.gitignore

@@ -0,0 +1,182 @@
+# Copyright (c) 2019, Max Planck Society / Software Workshop - Max Planck Institute for Intelligent Systems
+# Distributed under the GNU GPL license version 3
+# See file LICENSE.md or at https://github.com/MPI-IS/multitensor/LICENSE.md
+
+
+cmake_minimum_required (VERSION 3.5)
+cmake_policy(SET CMP0054 NEW)
+
+if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.13")
+    cmake_policy(SET CMP0076 OLD)
+endif()
+
+set_property(GLOBAL PROPERTY USE_FOLDERS ON)
+
+# Extract version number
+file(READ ${CMAKE_SOURCE_DIR}/version.txt ver)
+project(MultiTensor VERSION ${ver})
+message(STATUS "Project ${CMAKE_PROJECT_NAME} v${CMAKE_PROJECT_VERSION}")
+
+enable_testing()
+
+option(ENABLE_PYTHON_WRAPPER "Enable the python extensions" ON)
+option(ENABLE_BENCHMARK "Enable the benchmark" ON)
+
+# 0:silent
+add_definitions(-DMULTITENSOR_VERBOSE=1)
+
+#################################
+# thirdparties and configurations
+include(cmake/compiler_settings.cmake)
+include(cmake/thirdparty.cmake)
+
+
+################################
+# Main libraries and executables
+set(multitensor_src
+    ${CMAKE_SOURCE_DIR}/include/multitensor/graph.hpp
+    ${CMAKE_SOURCE_DIR}/include/multitensor/initialization.hpp
+    ${CMAKE_SOURCE_DIR}/include/multitensor/params.hpp
+    ${CMAKE_SOURCE_DIR}/include/multitensor/solver.hpp
+    ${CMAKE_SOURCE_DIR}/include/multitensor/tensor.hpp
+    ${CMAKE_SOURCE_DIR}/include/multitensor/utils.hpp
+    ${CMAKE_SOURCE_DIR}/include/multitensor/main.hpp)
+
+# libraries
+add_library(multitensor INTERFACE)
+target_include_directories(multitensor
+    INTERFACE
+        ${CMAKE_SOURCE_DIR}/include/
+        ${CMAKE_SOURCE_DIR}/src/)
+target_sources(multitensor
+    INTERFACE
+        $<BUILD_INTERFACE:${multitensor_src} >) # for the IDE to see the library
+
+add_library(multitensor_utils
+    ${CMAKE_SOURCE_DIR}/applications/include/app_params.hpp
+    ${CMAKE_SOURCE_DIR}/applications/include/app_utils.hpp
+    ${CMAKE_SOURCE_DIR}/applications/src/app_utils.cpp)
+target_link_libraries(multitensor_utils PUBLIC multitensor Boost::filesystem)
+target_include_directories(multitensor_utils
+    PUBLIC
+    ${CMAKE_SOURCE_DIR}/applications/include/
+    ${CMAKE_SOURCE_DIR}/applications/src/)
+
+# executables
+add_executable(Multitensor applications/src/multitensor.cpp)
+target_link_libraries(Multitensor multitensor multitensor_utils)
+
+# Unit tests
+add_executable(test_multitensor
+    tests/fixtures.hpp
+    tests/test_graph.cpp
+    tests/test_initialization.cpp
+    tests/test_multitensor.cpp
+    tests/test_solver.cpp
+    tests/test_tensor.cpp
+    tests/test_utils.cpp)
+target_link_libraries(test_multitensor
+    multitensor
+    Boost::unit_test_framework
+    Boost::system
+    Boost::filesystem)
+add_test(
+    NAME multitensor_unit_tests
+    COMMAND test_multitensor)
+
+# Functional tests
+# Helper for command line run
+function(add_test_cmd_line
+    test_name
+    test_program)
+
+    # Set test folder and copy adjacency file
+    set(test_folder ${CMAKE_BINARY_DIR}/tests/${test_name})
+    file(COPY ${CMAKE_SOURCE_DIR}/data/${test_name}/ DESTINATION ${test_folder}/)
+    file(COPY ${CMAKE_SOURCE_DIR}/tests/data/compare.sh DESTINATION ${test_folder}/)
+    file(COPY ${CMAKE_SOURCE_DIR}/tests/data/${test_name}/ DESTINATION ${test_folder}/)
+
+    # Run
+    add_test(
+        NAME "command-line-${test_name}-run"
+        COMMAND ${test_program} ${ARGN}
+        WORKING_DIRECTORY ${test_folder}
+    )
+
+    if("${test_program}" STREQUAL "Multitensor")
+        add_test(
+            NAME "command-line-${test_name}-verify-content"
+            COMMAND ${CMAKE_COMMAND}
+                "-Dresults=${test_folder}/results"
+                "-Dground_truth=${CMAKE_SOURCE_DIR}/tests/data/${test_name}"
+                -P ${CMAKE_SOURCE_DIR}/cmake/verify_content.cmake
+        )
+
+        set_tests_properties(
+            "command-line-${test_name}-verify-content"
+            PROPERTIES
+            DEPENDS "command-line-${test_name}-run"
+        )
+    endif()
+
+endfunction()
+
+add_test_cmd_line(
+    "main"
+    Multitensor
+    --a adjacency.dat
+    --k 2
+    --s 5489
+    --maxit 100)
+
+add_test_cmd_line(
+    "undirected"
+    Multitensor
+    --a adjacency.dat
+    --k 2
+    --s 5489
+    --undirected
+    --maxit 100)
+
+add_test_cmd_line(
+    "w_input"
+    Multitensor
+    --a adjacency_k2L4.dat
+    --k 2
+    --s 5489
+    --w w_k2_k2L4_A.dat
+    --maxit 100)
+
+add_test_cmd_line(
+    "multi_real"
+    Multitensor
+    --a adjacency_k2L4.dat
+    --k 2
+    --s 5489
+    --w w_k2_k2L4_r2.dat
+    --r 2
+    --maxit 100)
+
+add_test_cmd_line(
+    "assortative"
+    Multitensor
+    --a adjacency_assortative_k3L4.dat
+    --k 3
+    --s 5489
+    --assortative
+    --maxit 100)
+
+
+#########################
+# Python Bindings + Tests
+include(cmake/python.cmake)
+
+
+#########################
+# Documentation (Doxygen)
+include(cmake/doxygen_doc.cmake)
+
+
+###########
+# Benchmark
+include(cmake/benchmark.cmake)