First public commit

.gitignore

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+### CMake ###
+CMakeCache.txt
+CMakeFiles
+CMakeScripts
+Makefile
+cmake_install.cmake
+install_manifest.txt
+.deps
+.dirstamp
+
+### C++ ###
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+doc

.travis.yml

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+language: cpp
+os:
+  - linux
+  - osx
+compiler: 
+  - gcc
+  - clang
+cache:
+  apt: true
+addons:
+  apt:
+    sources:
+      - llvm-toolchain-precise
+      - ubuntu-toolchain-r-test
+      - boost-latest
+    packages:
+      - clang-3.7
+      - g++-4.7
+      - gcc-4.7
+      - libboost1.55-all-dev
+notifications:
+  email: false
+script: 
+  - cmake .; make; ./spa_networks -c test_conf.txt  | tee /dev/tty | wc -l;
+  - cmake -DOPTMEM_MODE=ON -DDEBUG_MODE=OFF .; make; ./spa_networks -c test_conf.txt  | tee /dev/tty | wc -l;
+  - cmake -DOPTMEM_MODE=OFF -DDEBUG_MODE=ON .; make; ./spa_networks -c test_conf.txt  | tee /dev/tty | wc -l;
+  - cmake -DHPC_MODE=OFF -DDEBUG_MODE=OFF -DOPTMEM_MODE=OFF .; make; ./spa_networks -c test_conf.txt  | tee /dev/tty | wc -l;
+  - cmake -DFORCE_NO_BOOST=ON .; make; ./spa_networks -c test_conf.txt  | tee /dev/tty | wc -l;
+  - cmake -DFORCE_NO_STEADY_CLOCK=ON .; make; ./spa_networks -c test_conf.txt  | tee /dev/tty | wc -l;

AUTHORS

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+Authors of SPA
+
+Jean-Gabriel Young implemented this simulation of the SPA (Structural 
+Preferential Attachment) stochastic process.
+
+The SPA process is introduced in :
+
+  "Structural preferential attachment: 
+     Network organization beyond the link"
+  L. Hébert-Dufresne, A. Allard, V. Marceau, P.-A. Noël, and L.J. Dubé
+  Phys. Rev. Lett. 107, 158702, (2011)
+  http://arxiv.org/abs/1105.5980
+
+and the community structure it creates is studied extensively in :
+
+  "Structural preferential attachment: 
+     Stochastic process for the growth of scale-free, 
+     modular and self-similar systems"
+   L. Hébert-Dufresne, A. Allard, V. Marceau, P.-A. Noël, and L.J. Dubé
+   Phys. Rev. E 85, 026108, (2012)
+   http://arxiv.org/abs/1109.0034
+
+A local extension that incorporates an explicit link creation mechanism 
+is presented in  :
+
+  "Structural preferential attachment of community structure 
+     and its relation to Dunbar’s number"
+  J.-G. Young, L. Hébert-Dufresne, A. Allard and L.J. Dubé
+
+This C++11 simulation implements the complete version (all three 
+publications).

CMakeLists.txt

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+# ~~~~~~~~~~~~~~~~~~~~~~~~~
+# Project
+# ~~~~~~~~~~~~~~~~~~~~~~~~~
+cmake_minimum_required(VERSION 2.8)
+project (SPA_networks_generator)
+
+# ~~~~~~~~~~~~~~~~~~~~~~~~~
+# Check for functionalities 
+# ~~~~~~~~~~~~~~~~~~~~~~~~~
+
+# Check for C++ 11 with CMAKE v.2.8 
+# Note: there exists a cleaner method in CMAKE 3.1+ [target_compile_features()]
+#       but stable Debian distributions tend to distribute CMAKE 2.8 as the default.
+#
+# Solution found @ http://stackoverflow.com/a/25836953/1851837.
+include(CheckCXXCompilerFlag)
+CHECK_CXX_COMPILER_FLAG("-std=c++11" COMPILER_SUPPORTS_CXX11)
+CHECK_CXX_COMPILER_FLAG("-std=c++0x" COMPILER_SUPPORTS_CXX0X)
+if(COMPILER_SUPPORTS_CXX11)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+elseif(COMPILER_SUPPORTS_CXX0X)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x")
+else()
+    message(STATUS "The compiler ${CMAKE_CXX_COMPILER} has no C++11 support. Please use a different C++ compiler.")
+endif()
+
+# Boost
+find_package( Boost 1.40 COMPONENTS program_options )
+if (Boost_FOUND)
+    set(HAVE_LIBBOOST_PROGRAM_OPTIONS 1)
+else()
+    message(STATUS "C++ Boost::program_options is not installed. Using limited interface.")
+    set(HAVE_LIBBOOST_PROGRAM_OPTIONS 0)
+endif ()
+
+# Steady clock (Google code)
+include(cmake_tests/CXXFeatureCheck.cmake)
+# If successful, then HAVE_STEADY_CLOCK is set to 1
+set(HAVE_STEADY_CLOCK 0)
+cxx_feature_check(STEADY_CLOCK)
+
+# ~~~~~~~~~~~~~~~~~~~~~~~~~
+# Options
+# ~~~~~~~~~~~~~~~~~~~~~~~~~
+
+option(HPC_MODE 
+        "Enable high-performance mode: no output and compiles assertions out." OFF)
+
+option(OPTMEM_MODE 
+        "Enable memory optimized mode, i.e. a small memory footprint is preferred over speed." OFF)
+
+option (DEBUG_MODE
+        "Enable debugging, i.e. full logging and assertion checks. (overrides HPC mode)." OFF)
+
+option (FORCE_NO_BOOST
+        "Do not use boost::program_options." OFF)
+
+option (FORCE_NO_STEADY_CLOCK
+        "Do not use std::steady_clock." OFF)
+
+# Defaults
+set (MEMORY_OPTIMIZED 0)
+set (REMOVE_ASSERTS 1)
+set (LOGGER_LEVEL 2)
+
+if (HPC_MODE)
+  set (LOGGER_LEVEL 3)
+endif()
+
+if (OPTMEM_MODE)
+  set (MEMORY_OPTIMIZED 1)
+endif()
+
+if (DEBUG_MODE)
+  set (LOGGER_LEVEL 0)
+  set (REMOVE_ASSERTS 0)
+endif()
+
+if (FORCE_NO_BOOST)
+  set (HAVE_LIBBOOST_PROGRAM_OPTIONS 0)
+endif()
+
+if (FORCE_NO_STEADY_CLOCK)
+  set (STEADY_CLOCK 0)
+endif()
+# ~~~~~~~~~~~~~~~~~~~~~~~~~
+# Build
+# ~~~~~~~~~~~~~~~~~~~~~~~~~
+
+configure_file (
+  "${PROJECT_SOURCE_DIR}/src/config.h.in"
+  "${PROJECT_BINARY_DIR}/src/config.h"
+  )
+include_directories("${PROJECT_BINARY_DIR}")
+
+add_subdirectory(src) 

COPYING

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+The MIT License (MIT)
+
+Copyright (c) 2014-2015 Jean-Gabriel Young
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

README.md

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+# Structural Preferential Attachment Simulation [![Build Status](https://travis-ci.org/spa-networks/spa.svg?branch=master)](https://travis-ci.org/spa-networks/spa)
+
+## About:
+
+This is a C++ implementation of the stochastic growth process dubbed Structural Preferential Attachment (SPA).
+See [our official website](http://www.spa-networks.org/) for more informations.
+
+## Quick start
+
+### Compilation
+
+
+`spa_networks` uses features from C++11 and must therefore be compiled with `gcc-4.6` or `clang-3.7` (or a newer version).
+
+#### Using cmake
+
+Compiling with cmake should be straightforward:
+
+    cmake .
+    make
+
+The available options for `cmake` are
+
+* `OPTMEM_MODE`
+* `HPC_MODE`
+* `FORCE_NO_BOOST`
+
+`OPTMEM_MODE` favors a small memory footprint over speed.
+
+`HPC_MODE` silences all output and compiles assertions out.
+
+The options can be passed to the usual GUI or through the command line interface:
+
+    cmake -DOPTMEM_MODE=ON .
+    make
+
+The build [has been test](https://magnum.travis-ci.com/jg-you/spa) with `cmake-2.8` and `cmake-3.4`.
+
+#### Using g++
+
+The explicit compilation call below should work on most Unix systems
+
+    g++ -o3 -W -Wall -Wextra -pedantic -std=c++0x  spa_main.cpp modular_structure.cpp spa_network.cpp subgraph.cpp spa_algorithm.cpp interface.cpp output_functions.cpp misc_functions.cpp includes/logger.cpp -lboost_program_options -o SPA
+
+Compilations options can be manually adjusted in the [src/config.h](src/config.h) file.
+
+### Execution
+
+Multiple parameters must be set for each simulation of the SPA process.
+These parameters can be passed through a configuration file 
+
+    ./spa_networks -c path/to/config/file.txt
+
+Note that `./spa_networks -g` generates an empty configuration file template.
+If `boost::program_options` is installed and properly linked to the binary, parameters will also be accepted directly from the command line. See
+
+    ./spa_networks -h 
+
+for more information about each flags.
+
+### Output
+
+The results of a simulation run are outputted in the directory from which `spa_networks` is called.
+This default behavior can be modified with the `-B / --base_path=` flag (by specifying a new absolute or relative path).
+Note that outputs are *not* computed unless specifically requested.
+So, for example, there won't be an edge list file, unless the user specifies a file name for the edge_list. e.g. `--edge_list=TestEdgeList.txt`.
+
+## Papers:
+
+More information about the SPA process is available in the following papers.
+
+### Growth at the level of communities:
+
+* [Structural preferential attachment: Network organization beyond the link](http://arxiv.org/abs/1105.5980)
+* [Structural preferential attachment: Stochastic process for the growth of scale-free, modular and self-similar systems](http://arxiv.org/abs/1109.0034)
+
+### Growth within a community
+

cmake_tests/CXXFeatureCheck.cmake

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+# This files has been copied from https://github.com/google/benchmark/cmake/
+# Distributed under the Apache License Version 2.0.
+#   https://github.com/google/benchmark/LICENSE
+# Modified on Dec. 22th 2015 by Jean-Gabriel Young <jean.gabriel.young@gmail.com>
+# 
+# - Compile and run code to check for C++ features
+#
+# This functions compiles a source file under the `cmake` folder
+# and adds the corresponding `HAVE_[FILENAME]` flag to the CMake
+# environment
+#
+#  cxx_feature_check(<FLAG> [<VARIANT>])
+#
+# - Example
+#
+# include(CXXFeatureCheck)
+# cxx_feature_check(STD_REGEX)
+# Requires CMake 2.6+
+
+if(__cxx_feature_check)
+  return()
+endif()
+set(__cxx_feature_check INCLUDED)
+
+function(cxx_feature_check FILE)
+  string(TOLOWER ${FILE} FILE)
+  string(TOUPPER ${FILE} VAR)
+  string(TOUPPER "HAVE_${VAR}" FEATURE)
+  message("-- Performing Test ${FEATURE}")
+  try_run(RUN_${FEATURE} COMPILE_${FEATURE}
+          ${CMAKE_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/cmake_tests/${FILE}.cpp)
+  if(RUN_${FEATURE} EQUAL 0)
+    message("-- Performing Test ${FEATURE} -- success")
+    set(HAVE_${VAR} 1 PARENT_SCOPE)
+    add_definitions(-DHAVE_${VAR})
+  else()
+    if(NOT COMPILE_${FEATURE})
+      message("-- Performing Test ${FEATURE} -- failed to compile")
+    else()
+      message("-- Performing Test ${FEATURE} -- compiled but failed to run")
+    endif()
+  endif()
+endfunction()

cmake_tests/steady_clock.cpp

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+// This files has been copied from https://github.com/google/benchmark/cmake/
+// Distributed under the Apache License Version 2.0.
+//   https://github.com/google/benchmark/LICENSE
+// Modified on Dec. 22th 2015 by Jean-Gabriel Young <jean.gabriel.young@gmail.com>
+#include <chrono>
+
+int main() {
+    typedef std::chrono::steady_clock Clock;
+    Clock::time_point tp = Clock::now();
+    ((void)tp);
+}

src/CMakeLists.txt

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+add_subdirectory(includes) 
+
+if (Boost_FOUND)
+    include_directories(${BOOST_INCLUDEDIR})
+endif (Boost_FOUND)
+
+add_executable(spa_networks  spa_main.cpp modular_structure.cpp spa_network.cpp subgraph.cpp spa_algorithm.cpp interface.cpp output_functions.cpp misc_functions.cpp)
+target_link_libraries (spa_networks logger)
+set_target_properties(spa_networks PROPERTIES RUNTIME_OUTPUT_DIRECTORY ../ )
+
+if (Boost_FOUND)
+    target_link_libraries(spa_networks ${Boost_LIBRARIES})
+endif (Boost_FOUND)
+

src/config.h.in

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+#define HAVE_LIBBOOST_PROGRAM_OPTIONS @HAVE_LIBBOOST_PROGRAM_OPTIONS@
+#define HAVE_STEADY_CLOCK @HAVE_STEADY_CLOCK@
+#define LOGGER_LEVEL @LOGGER_LEVEL@
+#define MEMORY_OPTIMIZED @MEMORY_OPTIMIZED@
+#define REMOVE_ASSERTS @REMOVE_ASSERTS@
+
+#if REMOVE_ASSERTS == 1
+    #define NDEBUG 1
+#endif

src/errors.hpp

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+#ifndef ERRORS_HPP
+#define ERRORS_HPP
+
+#define STOP_WITH_SUCCESS 100
+#define FILE_ERROR 101
+#define LOGIC_ERROR 102
+#define ELEM_MISSING_ERROR 103
+
+#endif // ERRORS_HPP

src/includes/CMakeLists.txt

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+add_library(logger logger.cpp)