From c09268a046c43b4311f0f29ac4bfb14dcb2da30d Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 2 Jun 2017 14:10:20 +0000
Subject: Try to remove boost system

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2504 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: fd12c45af5ebeb72c4b49142abab91b46ce1a9da
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'src/cmake')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 8cb01d3c..7b0cda3b 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -99,6 +99,8 @@ add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
 add_definitions(-DBOOST_ALL_NO_LIB)
 # problem with Visual Studio link on Boost program_options
 add_definitions( -DBOOST_ALL_DYN_LINK )
+# problem on Mac with boost_system and boost_thread
+#add_definitions( -DBOOST_SYSTEM_NO_DEPRECATED )
 
 INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
 LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
-- 
cgit v1.2.3


From f5d28342ee398c739c7345d8db4fbd653e9a0413 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 8 Jun 2017 07:17:36 +0000
Subject: Add modules as CMake options in order to be able to
 activate/desactivate compilation

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cmake_modules_for_gudhi@2515 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 53d5e669ad310c9d8d17c7f95f1e07c3bf658d77
---
 CMakeLists.txt                                    | 18 ++++--------------
 src/CMakeLists.txt                                |  8 ++++----
 src/cmake/modules/GUDHI_modules.cmake             | 23 +++++++++++++++++++----
 src/cmake/modules/GUDHI_user_version_target.cmake |  4 ++--
 4 files changed, 29 insertions(+), 24 deletions(-)

(limited to 'src/cmake')

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c9ceb92b..fbb359e1 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -3,10 +3,7 @@ project(GUDHIdev)
 
 include(CMakeGUDHIVersion.txt)
 
-set(CMAKE_PREFIX_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
-set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
-message("CMAKE_PREFIX_PATH = ${CMAKE_PREFIX_PATH}")
-message("CMAKE_MODULE_PATH = ${CMAKE_MODULE_PATH}")
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
 
 enable_testing()
 
@@ -34,10 +31,8 @@ if (DEBUG_TRACES)
   add_definitions(-DDEBUG_TRACES)
 endif()
 
-# Modules list can be found in CMAKE_MODULE_PATH/GUDHI_modules.cmake
-include(GUDHI_modules)
-
 # Add your new module in the list, order is not important
+include(GUDHI_modules)
 
 add_gudhi_module(common)
 add_gudhi_module(Alpha_complex)
@@ -54,12 +49,7 @@ add_gudhi_module(Subsampling)
 add_gudhi_module(Tangential_complex)
 add_gudhi_module(Witness_complex)
 
-# Include module headers
-foreach(GUDHI_MODULE ${GUDHI_MODULES})
-  if(IS_DIRECTORY ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/include/)
-    include_directories(src/${GUDHI_MODULE}/include/)
-  endif()
-endforeach()
+message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
 
 # Include module CMake subdirectories
 # GUDHI_SUB_DIRECTORIES is managed in CMAKE_MODULE_PATH/GUDHI_modules.cmake
@@ -73,7 +63,7 @@ endforeach()
 
 add_subdirectory(src/GudhUI)
 
-if (NOT WITHOUT_GUDHI_PYTHON)
+if (WITH_GUDHI_PYTHON)
   # specific for cython module
   add_subdirectory(${GUDHI_CYTHON_PATH})
 endif()
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 8abfcf44..795005b1 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -7,10 +7,8 @@ enable_testing()
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/")
 
-# To be done first - Modules list can be found in CMAKE_MODULE_PATH/GUDHI_modules.cmake
-include(GUDHI_modules)
-
 # Add your new module in the list, order is not important
+include(GUDHI_modules)
 
 add_gudhi_module(common)
 add_gudhi_module(Alpha_complex)
@@ -27,6 +25,8 @@ add_gudhi_module(Subsampling)
 add_gudhi_module(Tangential_complex)
 add_gudhi_module(Witness_complex)
 
+message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
+
 # For "make doxygen" - Requires GUDHI_USER_VERSION_DIR to be set
 set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR})
 include(GUDHI_doxygen_target)
@@ -71,7 +71,7 @@ endforeach()
 
 add_subdirectory(GudhUI)
 
-if (NOT WITHOUT_GUDHI_PYTHON)
+if (WITH_GUDHI_PYTHON)
   # specific for cython module
   add_subdirectory(${GUDHI_CYTHON_PATH})
 endif()
diff --git a/src/cmake/modules/GUDHI_modules.cmake b/src/cmake/modules/GUDHI_modules.cmake
index 20fc8d17..f95d0c34 100644
--- a/src/cmake/modules/GUDHI_modules.cmake
+++ b/src/cmake/modules/GUDHI_modules.cmake
@@ -1,11 +1,26 @@
 # A function to add a new module in GUDHI
 
 set(GUDHI_MODULES "")
+set(GUDHI_MODULES_FULL_LIST "")
 function(add_gudhi_module file_path)
+  option("WITH_MODULE_GUDHI_${file_path}" "Activate/desactivate ${file_path} compilation and installation" ON)
+  if (WITH_MODULE_GUDHI_${file_path})
     set(GUDHI_MODULES ${GUDHI_MODULES} ${file_path} PARENT_SCOPE)
+  endif()
+  # Required by user_version
+  set(GUDHI_MODULES_FULL_LIST ${GUDHI_MODULES_FULL_LIST} ${file_path} PARENT_SCOPE)
+  # Include module headers is independant - You may ask for no Alpha complex module but Python interface i.e.
+  if(IS_DIRECTORY ${CMAKE_SOURCE_DIR}/src/${file_path}/include/)
+    include_directories(src/${file_path}/include/)
+  endif()
+
 endfunction(add_gudhi_module)
 
-# message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
+option(WITH_GUDHI_BENCHMARK "Activate/desactivate benchmark compilation" OFF)
+option(WITH_GUDHI_EXAMPLE "Activate/desactivate examples compilation and installation" OFF)
+option(WITH_GUDHI_PYTHON "Activate/desactivate python module compilation and installation" ON)
+option(WITH_GUDHI_TEST "Activate/desactivate examples compilation and installation" ON)
+option(WITH_GUDHI_UTILITIES "Activate/desactivate utilities compilation and installation" ON)
 
 if (WITH_GUDHI_BENCHMARK)
   set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};benchmark")
@@ -13,10 +28,10 @@ endif()
 if (WITH_GUDHI_EXAMPLE)
   set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};example")
 endif()
-if (NOT WITHOUT_GUDHI_TEST)
-    set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};test")
+if (WITH_GUDHI_TEST)
+  set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};test")
 endif()
-if (NOT WITHOUT_GUDHI_UTILITIES)
+if (WITH_GUDHI_UTILITIES)
   set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};utilities")
 endif()
 
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
index 8642d3bf..cff64ad2 100644
--- a/src/cmake/modules/GUDHI_user_version_target.cmake
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -50,7 +50,7 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
   set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
   set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches")
 
-  foreach(GUDHI_MODULE ${GUDHI_MODULES})
+  foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
     foreach(GUDHI_DIRECTORY ${GUDHI_DIRECTORIES})
       # Find files
       file(GLOB GUDHI_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/${GUDHI_DIRECTORY}/*)
@@ -85,6 +85,6 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
       endforeach()
     endforeach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
 
-  endforeach(GUDHI_MODULE ${GUDHI_MODULES})
+  endforeach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
 
 endif()
-- 
cgit v1.2.3


From 41991433af57269f1328c7c67e26eb111b060fa2 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 06:19:25 +0000
Subject: Add BOOST_SYSTEM_NO_DEPRECATED definition

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2524 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4718264666a9289a46f282cfcf3200481966c0db
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'src/cmake')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 7b0cda3b..5bee774a 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -100,7 +100,7 @@ add_definitions(-DBOOST_ALL_NO_LIB)
 # problem with Visual Studio link on Boost program_options
 add_definitions( -DBOOST_ALL_DYN_LINK )
 # problem on Mac with boost_system and boost_thread
-#add_definitions( -DBOOST_SYSTEM_NO_DEPRECATED )
+add_definitions( -DBOOST_SYSTEM_NO_DEPRECATED )
 
 INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
 LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
-- 
cgit v1.2.3


From 4adbd857ff2ac187b5dfcfa25c37f32b887ae69b Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 07:48:54 +0000
Subject: No more need of find_the_lib cmake macro to find Windows boost lib
 name Fix cmake warning on if with quotes

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2527 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a352820ab0a596961b9851d4a30c40196a70ff98
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 13 -------------
 src/cython/CMakeLists.txt                           |  4 ++--
 2 files changed, 2 insertions(+), 15 deletions(-)

(limited to 'src/cmake')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 5bee774a..b4f3eb52 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -108,19 +108,6 @@ LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
 message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
 message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
 
-macro( find_the_lib placeholder THE_LIBS )
-  set (THE_LIB_WE_FOUND "NO")
-  foreach(THE_LIB ${THE_LIBS})
-    if(EXISTS ${THE_LIB})
-      get_filename_component(THE_LIB_WE ${THE_LIB} NAME_WE)
-      if (NOT THE_LIB_WE_FOUND)
-        set (THE_LIB_WE_FOUND "YES")
-        set(returnValue "${THE_LIB_WE}")
-      endif(NOT THE_LIB_WE_FOUND)
-    endif(EXISTS ${THE_LIB})
-  endforeach(THE_LIB ${THE_LIBS})
-endmacro( find_the_lib )
-
 # Find the correct Python interpreter.
 # Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance.
 find_package(Cython)
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 4b56122d..adcc64e4 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -17,9 +17,9 @@ if(CYTHON_FOUND)
   if(CMAKE_COMPILER_IS_GNUCXX)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
   endif(CMAKE_COMPILER_IS_GNUCXX)
-  if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
+  if (CMAKE_CXX_COMPILER_ID MATCHES Intel)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ")
-  endif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
+  endif(CMAKE_CXX_COMPILER_ID MATCHES Intel)
   if (DEBUG_TRACES)
     # For programs to be more verbose
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ")
-- 
cgit v1.2.3


From 26ccabbd6892ddc5313a7f75c98a92c268f15747 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 08:39:16 +0000
Subject: Remove boost timer and chrono dependencies

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2528 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5bfb8bd5a6e49dbea9fbfbdc1d748423fc930913
---
 src/Contraction/example/CMakeLists.txt                      | 4 ----
 src/Contraction/example/Garland_heckbert.cpp                | 3 ---
 src/Contraction/example/Rips_contraction.cpp                | 6 ------
 src/Skeleton_blocker/example/CMakeLists.txt                 | 2 --
 src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp | 4 ----
 src/cmake/modules/GUDHI_third_party_libraries.cmake         | 2 +-
 6 files changed, 1 insertion(+), 20 deletions(-)

(limited to 'src/cmake')

diff --git a/src/Contraction/example/CMakeLists.txt b/src/Contraction/example/CMakeLists.txt
index 6443323d..83594c0e 100644
--- a/src/Contraction/example/CMakeLists.txt
+++ b/src/Contraction/example/CMakeLists.txt
@@ -5,10 +5,6 @@ project(Contraction_examples)
 add_executable(RipsContraction Rips_contraction.cpp)
 add_executable(GarlandHeckbert Garland_heckbert.cpp)
 
-target_link_libraries(RipsContraction ${Boost_TIMER_LIBRARY})
-target_link_libraries(GarlandHeckbert ${Boost_TIMER_LIBRARY})
-
-
 add_test(NAME Contraction_example_tore3D_0.2 COMMAND $<TARGET_FILE:RipsContraction>
     "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "0.2")
 # TODO(DS) : These tests are too long under Windows
diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp
index 8b5a6a6c..2b0dc973 100644
--- a/src/Contraction/example/Garland_heckbert.cpp
+++ b/src/Contraction/example/Garland_heckbert.cpp
@@ -30,7 +30,6 @@
 #include <gudhi/Skeleton_blocker.h>
 #include <gudhi/Off_reader.h>
 
-#include <boost/timer/timer.hpp>
 #include <iostream>
 
 #include "Garland_heckbert/Error_quadric.h"
@@ -165,8 +164,6 @@ int main(int argc, char *argv[]) {
 
   int num_contractions = atoi(argv[3]);
 
-  boost::timer::auto_cpu_timer t;
-
   // constructs the contractor object with Garland Heckbert policies.
   Complex_contractor contractor(complex,
                                 new GH_cost(complex),
diff --git a/src/Contraction/example/Rips_contraction.cpp b/src/Contraction/example/Rips_contraction.cpp
index 8289b1d3..1b97f877 100644
--- a/src/Contraction/example/Rips_contraction.cpp
+++ b/src/Contraction/example/Rips_contraction.cpp
@@ -24,7 +24,6 @@
 #include <gudhi/Off_reader.h>
 #include <gudhi/Point.h>
 
-#include <boost/timer/timer.hpp>
 #include <iostream>
 
 struct Geometry_trait {
@@ -68,8 +67,6 @@ int main(int argc, char *argv[]) {
 
   build_rips(complex, atof(argv[2]));
 
-  boost::timer::auto_cpu_timer t;
-
   std::cout << "Initial complex has " <<
       complex.num_vertices() << " vertices and " <<
       complex.num_edges() << " edges" << std::endl;
@@ -90,9 +87,6 @@ int main(int argc, char *argv[]) {
       complex.num_blockers() << " blockers and " <<
       num_simplices << " simplices" << std::endl;
 
-
-  std::cout << "Time to simplify and enumerate simplices:\n";
-
   return EXIT_SUCCESS;
 }
 
diff --git a/src/Skeleton_blocker/example/CMakeLists.txt b/src/Skeleton_blocker/example/CMakeLists.txt
index 6d685717..de70f089 100644
--- a/src/Skeleton_blocker/example/CMakeLists.txt
+++ b/src/Skeleton_blocker/example/CMakeLists.txt
@@ -5,8 +5,6 @@ add_executable(Skeleton_blocker_example_from_simplices Skeleton_blocker_from_sim
 add_executable(Skeleton_blocker_example_iteration Skeleton_blocker_iteration.cpp)
 add_executable(Skeleton_blocker_example_link Skeleton_blocker_link.cpp)
 
-target_link_libraries(Skeleton_blocker_example_iteration ${Boost_TIMER_LIBRARY})
-
 add_test(NAME Skeleton_blocker_example_from_simplices COMMAND $<TARGET_FILE:Skeleton_blocker_example_from_simplices>)
 add_test(NAME Skeleton_blocker_example_iteration COMMAND $<TARGET_FILE:Skeleton_blocker_example_iteration>)
 add_test(NAME Skeleton_blocker_example_link COMMAND $<TARGET_FILE:Skeleton_blocker_example_link>)
diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
index 6a1bc480..4a0044e1 100644
--- a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
+++ b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
@@ -22,8 +22,6 @@
 
 #include <gudhi/Skeleton_blocker.h>
 
-#include <boost/timer/timer.hpp>
-
 #include <stdio.h>
 #include <stdlib.h>
 #include <string>
@@ -47,8 +45,6 @@ Complex build_complete_complex(int n) {
 }
 
 int main(int argc, char *argv[]) {
-  boost::timer::auto_cpu_timer t;
-
   const int n = 15;
 
   // build a full complex with n vertices and 2^n-1 simplices
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index b4f3eb52..2be79ee4 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -1,6 +1,6 @@
 # This files manage third party libraries required by GUDHI
 
-find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework chrono timer date_time program_options thread)
+find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework date_time program_options thread)
 
 if(NOT Boost_FOUND)
   message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
-- 
cgit v1.2.3


From 05de4e9f4ed8f74e53a11455bc50470beba908eb Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 09:40:52 +0000
Subject: Remove boost date_time dependencies

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2529 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: daa13fc0046ffdd72577bb1b399fcbdc8ef5033c
---
 src/Tangential_complex/benchmark/CMakeLists.txt     |  3 +--
 src/Tangential_complex/example/CMakeLists.txt       |  4 ++--
 src/Tangential_complex/test/CMakeLists.txt          |  2 +-
 src/cmake/modules/GUDHI_third_party_libraries.cmake |  2 +-
 src/common/include/gudhi/Clock.h                    | 18 +++++++++---------
 5 files changed, 14 insertions(+), 15 deletions(-)

(limited to 'src/cmake')

diff --git a/src/Tangential_complex/benchmark/CMakeLists.txt b/src/Tangential_complex/benchmark/CMakeLists.txt
index 8cb16e8c..8729e394 100644
--- a/src/Tangential_complex/benchmark/CMakeLists.txt
+++ b/src/Tangential_complex/benchmark/CMakeLists.txt
@@ -3,8 +3,7 @@ project(Tangential_complex_benchmark)
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   add_executable(Tangential_complex_benchmark benchmark_tc.cpp)
-  target_link_libraries(Tangential_complex_benchmark
-    ${Boost_DATE_TIME_LIBRARY} ${CGAL_LIBRARY})
+  target_link_libraries(Tangential_complex_benchmark ${CGAL_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Tangential_complex_benchmark ${TBB_LIBRARIES})
   endif(TBB_FOUND)
diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt
index 45c7642b..16d1339d 100644
--- a/src/Tangential_complex/example/CMakeLists.txt
+++ b/src/Tangential_complex/example/CMakeLists.txt
@@ -3,9 +3,9 @@ project(Tangential_complex_examples)
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   add_executable( Tangential_complex_example_basic example_basic.cpp )
-  target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY})
+  target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY})
   add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp )
-  target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY})
+  target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Tangential_complex_example_basic ${TBB_LIBRARIES})
     target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES})
diff --git a/src/Tangential_complex/test/CMakeLists.txt b/src/Tangential_complex/test/CMakeLists.txt
index 63e51c3e..1948c8f6 100644
--- a/src/Tangential_complex/test/CMakeLists.txt
+++ b/src/Tangential_complex/test/CMakeLists.txt
@@ -5,7 +5,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   include(GUDHI_test_coverage)
 
   add_executable( Tangential_complex_test_TC test_tangential_complex.cpp )
-  target_link_libraries(Tangential_complex_test_TC ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}  ${Boost_DATE_TIME_LIBRARY})
+  target_link_libraries(Tangential_complex_test_TC ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Tangential_complex_test_TC ${TBB_LIBRARIES})
   endif()
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 2be79ee4..8f486118 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -1,6 +1,6 @@
 # This files manage third party libraries required by GUDHI
 
-find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework date_time program_options thread)
+find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework program_options thread)
 
 if(NOT Boost_FOUND)
   message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
diff --git a/src/common/include/gudhi/Clock.h b/src/common/include/gudhi/Clock.h
index 77f196ca..eff48e41 100644
--- a/src/common/include/gudhi/Clock.h
+++ b/src/common/include/gudhi/Clock.h
@@ -23,9 +23,9 @@
 #ifndef CLOCK_H_
 #define CLOCK_H_
 
-#include <boost/date_time/posix_time/posix_time.hpp>
-
+#include <iostream>
 #include <string>
+#include <chrono>
 
 namespace Gudhi {
 
@@ -33,20 +33,20 @@ class Clock {
  public:
   // Construct and start the timer
   Clock(const std::string& msg_ = std::string())
-      : startTime(boost::posix_time::microsec_clock::local_time()),
+      : startTime(std::chrono::system_clock::now()),
       end_called(false),
       msg(msg_) { }
 
   // Restart the timer
   void begin() const {
     end_called = false;
-    startTime = boost::posix_time::microsec_clock::local_time();
+    startTime = std::chrono::system_clock::now();
   }
 
   // Stop the timer
   void end() const {
     end_called = true;
-    endTime = boost::posix_time::microsec_clock::local_time();
+    endTime = std::chrono::system_clock::now();
   }
 
   std::string message() const {
@@ -71,15 +71,15 @@ class Clock {
   // - or now otherwise. In this case, the timer is not stopped.
   double num_seconds() const {
     if (!end_called) {
-      auto end = boost::posix_time::microsec_clock::local_time();
-      return (end - startTime).total_milliseconds() / 1000.;
+      auto end = std::chrono::system_clock::now();
+      return std::chrono::duration_cast<std::chrono::milliseconds>(end-startTime).count() / 1000.;
     } else {
-      return (endTime - startTime).total_milliseconds() / 1000.;
+      return std::chrono::duration_cast<std::chrono::milliseconds>(endTime-startTime).count() / 1000.;
     }
   }
 
  private:
-  mutable boost::posix_time::ptime startTime, endTime;
+  mutable std::chrono::time_point<std::chrono::system_clock> startTime, endTime;
   mutable bool end_called;
   std::string msg;
 };
-- 
cgit v1.2.3


From 547a7c9cb50d1818c9412d10cca9655503db625c Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 13 Jun 2017 20:42:51 +0000
Subject: Try to fix Windows compilation for Conda

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2541 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: afa1b10e300aafbc92a85b3519f4b39add2ae6e4
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 4 ++++
 src/cython/CMakeLists.txt                           | 3 +++
 2 files changed, 7 insertions(+)

(limited to 'src/cmake')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 8f486118..7cd57b25 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -10,6 +10,10 @@ find_package(GMP)
 if(GMP_FOUND)
   message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}")
   INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
+  get_filename_component(lib_we ${GMP_LIBRARIES} NAME_WE)
+
+  message("++ lib_we = ${lib_we}")
+
   find_package(GMPXX)
   if(GMPXX_FOUND)
     message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index adcc64e4..2a0a3844 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -8,6 +8,9 @@ if(CYTHON_FOUND)
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
 
+  if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+    set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'boost_thread', ")
+  endif()
   # Gudhi and CGAL compilation option
   if(MSVC)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ")
-- 
cgit v1.2.3


From f6d8aaaacf4a2802d3aaad6d326f9510fdb2ddf7 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 14 Jun 2017 05:24:01 +0000
Subject: Add traces for debug

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2542 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a9e8098443114a4fe6e9c19e6410169580c134c6
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake |  4 ----
 src/cython/CMakeLists.txt                           | 10 ++++++++--
 2 files changed, 8 insertions(+), 6 deletions(-)

(limited to 'src/cmake')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 7cd57b25..8f486118 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -10,10 +10,6 @@ find_package(GMP)
 if(GMP_FOUND)
   message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}")
   INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
-  get_filename_component(lib_we ${GMP_LIBRARIES} NAME_WE)
-
-  message("++ lib_we = ${lib_we}")
-
   find_package(GMPXX)
   if(GMPXX_FOUND)
     message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 2a0a3844..eff36f93 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -8,6 +8,7 @@ if(CYTHON_FOUND)
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
 
+  message("++ Boost_THREAD_LIBRARY=${Boost_THREAD_LIBRARY} - Boost_thread_LIBRARY=${Boost_thread_LIBRARY} - ")
   if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
     set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'boost_thread', ")
   endif()
@@ -106,6 +107,7 @@ if(CYTHON_FOUND)
 
   if(CGAL_FOUND)
     # Add CGAL compilation args
+    message("++ CGAL_LIBRARIES = ${CGAL_LIBRARIES}")
     if(CGAL_HEADER_ONLY)
       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
     else(CGAL_HEADER_ONLY)
@@ -119,10 +121,14 @@ if(CYTHON_FOUND)
     # GMP and GMPXX are not required, but if present, CGAL will link with them.
     if(GMP_FOUND)
       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
+      get_filename_component(GMP_LIBRARY_FILE_NAME ${GMP_LIBRARIES} NAME_WE)
+      message("++ GMP_LIBRARY_FILE_NAME = ${GMP_LIBRARY_FILE_NAME}")
       if(WIN32)
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'libgmp-10', ")
+        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${GMP_LIBRARY_FILE_NAME}', ")
       else(WIN32)
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmp', ")
+        STRING(REGEX REPLACE "lib" "" UNIX_GMP_LIBRARY_FILE_NAME ${GMP_LIBRARY_FILE_NAME})
+        message("++ UNIX_GMP_LIBRARY_FILE_NAME = ${UNIX_GMP_LIBRARY_FILE_NAME}")
+        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${UNIX_GMP_LIBRARY_FILE_NAME}', ")
       endif(WIN32)
         set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
       if(GMPXX_FOUND)
-- 
cgit v1.2.3


From 2fc118133e76f05fc55d86cf32883223191fe473 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 17 Aug 2017 16:10:46 +0000
Subject: Add file formats for Python. Binding for persistence write files
 Launch py.test with the command "python -m pytest" (shall work everywhere)

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2611 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9443a7eb5b580ece7708ff57949ad08339c1c5c3
---
 .../include/gudhi/Persistent_cohomology.h          | 13 +++++++---
 .../modules/GUDHI_third_party_libraries.cmake      |  2 --
 src/common/doc/file_formats.h                      |  6 ++++-
 src/cython/CMakeLists.txt                          | 14 +++++-----
 src/cython/cython/simplex_tree.pyx                 | 22 +++++++++++++++-
 src/cython/doc/_templates/layout.html              |  1 +
 src/cython/doc/fileformats.rst                     | 30 ++++++++++++++++++++++
 src/cython/doc/reader_utils_ref.rst                | 11 ++++++++
 8 files changed, 84 insertions(+), 15 deletions(-)
 create mode 100644 src/cython/doc/fileformats.rst
 create mode 100644 src/cython/doc/reader_utils_ref.rst

(limited to 'src/cmake')

diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index 672fda48..e0a147b3 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -591,10 +591,17 @@ class Persistent_cohomology {
     std::ofstream diagram_out(diagram_name.c_str());
     cmp_intervals_by_length cmp(cpx_);
     std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp);
+    bool has_infinity = std::numeric_limits<Filtration_value>::has_infinity;
     for (auto pair : persistent_pairs_) {
-    diagram_out << cpx_->dimension(get<0>(pair)) << " "
-          << cpx_->filtration(get<0>(pair)) << " "
-          << cpx_->filtration(get<1>(pair)) << std::endl;
+      // Special case on windows, inf is "1.#INF"
+      if (has_infinity && cpx_->filtration(get<1>(pair)) == std::numeric_limits<Filtration_value>::infinity()) {
+        diagram_out << cpx_->dimension(get<0>(pair)) << " "
+              << cpx_->filtration(get<0>(pair)) << " inf" << std::endl;
+      } else {
+        diagram_out << cpx_->dimension(get<0>(pair)) << " "
+              << cpx_->filtration(get<0>(pair)) << " "
+              << cpx_->filtration(get<1>(pair)) << std::endl;
+      }
     }
   }
 
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 8f486118..e29ba40c 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -117,8 +117,6 @@ if(NOT GUDHI_CYTHON_PATH)
 endif(NOT GUDHI_CYTHON_PATH)
 
 if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
-  # Unitary tests are available through py.test
-  find_program( PYTEST_PATH py.test )
   # Default found version 2
   if(PYTHON_VERSION_MAJOR EQUAL 2)
     # Documentation generation is available through sphinx
diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index 9d0415b1..d715aa4d 100644
--- a/src/common/doc/file_formats.h
+++ b/src/common/doc/file_formats.h
@@ -26,7 +26,7 @@
 namespace Gudhi {
 
 /*! \page fileformats File formats
- 
+
  \tableofcontents
 
  \section FileFormatsPers Persistence Diagram
@@ -49,6 +49,10 @@ namespace Gudhi {
  \endverbatim
 
  Other sample files can be found in the `data/persistence_diagram` folder.
+
+ Such files can be generated with `Gudhi::persistent_cohomology::Persistent_cohomology::output_diagram()` and read with
+ `Gudhi::read_persistence_intervals_and_dimension()`, `Gudhi::read_persistence_intervals_grouped_by_dimension()` or
+ `Gudhi::read_persistence_intervals_in_dimension()`.
 */
 }  // namespace Gudhi
 
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index f427b3c5..a06be008 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -16,7 +16,7 @@ function( add_gudhi_cython_lib THE_LIB )
 endfunction( add_gudhi_cython_lib )
 
 if(CYTHON_FOUND)
-  message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}")
+  message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - Sphinx is ${SPHINX_PATH}")
 
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ")
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
@@ -305,13 +305,11 @@ if(CYTHON_FOUND)
   set_tests_properties(witness_complex_from_nearest_landmark_table_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   # Unitary tests are available through py.test
-  if(PYTEST_PATH)
-    add_test(
-        NAME gudhi_cython_py_test
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${PYTHON_EXECUTABLE} "${PYTEST_PATH}")
-    set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
-  endif(PYTEST_PATH)
+  add_test(
+      NAME gudhi_cython_py_test
+      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+      COMMAND ${PYTHON_EXECUTABLE} -m pytest)
+  set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   # Documentation generation is available through sphinx
   if(SPHINX_PATH)
diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index 2acdac3c..9e3b2345 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -61,6 +61,7 @@ cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
         vector[int] betti_numbers()
         vector[int] persistent_betti_numbers(double from_value, double to_value)
         vector[pair[double,double]] intervals_in_dimension(int dimension)
+        void write_output_diagram(string diagram_file_name)
 
 # SimplexTree python interface
 cdef class SimplexTree:
@@ -385,7 +386,7 @@ cdef class SimplexTree:
         complex in a specific dimension.
 
         :param dimension: The specific dimension.
-        :type from_value: int.
+        :type dimension: int.
         :returns: The persistence intervals.
         :rtype:  list of pair of float
 
@@ -399,3 +400,22 @@ cdef class SimplexTree:
             print("intervals_in_dim function requires persistence function"
                   " to be launched first.")
         return intervals_result
+
+    def write_persistence_diagram(self, persistence_file=''):
+        """This function writes the persistence intervals of the simplicial
+        complex in a user given file name.
+
+        :param persistence_file: The specific dimension.
+        :type persistence_file: string.
+
+        :note: intervals_in_dim function requires persistence function to be
+            launched first.
+        """
+        if self.pcohptr != NULL:
+            if persistence_file != '':
+                self.pcohptr.write_output_diagram(str.encode(persistence_file))
+            else:
+                print("persistence_file must be specified")
+        else:
+            print("intervals_in_dim function requires persistence function"
+                  " to be launched first.")
diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html
index b11c1236..243f33c6 100644
--- a/src/cython/doc/_templates/layout.html
+++ b/src/cython/doc/_templates/layout.html
@@ -65,6 +65,7 @@
             {#- old style sidebars: using blocks -- should be deprecated #}
             {%- block sidebartoc %}
 <h2><a href="index.html">GUDHI</a></h2>
+<h2><a href="fileformats.html">File formats</a></h2>
 <h2><a href="installation.html">GUDHI installation</a></h2>
 <h2><a href="citation.html">Acknowledging the GUDHI library</a></h2>
 <h2><a href="genindex.html">Index</a></h2>
diff --git a/src/cython/doc/fileformats.rst b/src/cython/doc/fileformats.rst
new file mode 100644
index 00000000..36225b6d
--- /dev/null
+++ b/src/cython/doc/fileformats.rst
@@ -0,0 +1,30 @@
+File formats
+############
+
+To find the correct function to read the files, please refer to :doc:`reader_utils_ref`
+
+Persistence Diagram
+*******************
+
+Such a file, whose extension is usually ``.pers``, contains a list of persistence intervals.
+
+Lines starting with ``#`` are ignored (comments).
+
+Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines)::
+
+    [[field] dimension] birth death
+
+Here is a simple sample file::
+
+    # Persistence diagram example
+    2 2.7 3.7
+    2 9.6 14.
+    # Some comments
+    3 34.2 34.974
+    4 3. inf
+
+Other sample files can be found in the data/persistence_diagram folder.
+
+Such files can be generated with :meth:`gudhi.SimplexTree.write_persistence_diagram` and read with
+:meth:`gudhi.read_persistence_intervals_grouped_by_dimension`, or
+:meth:`gudhi.read_persistence_intervals_in_dimension`.
diff --git a/src/cython/doc/reader_utils_ref.rst b/src/cython/doc/reader_utils_ref.rst
new file mode 100644
index 00000000..9c1ea6fc
--- /dev/null
+++ b/src/cython/doc/reader_utils_ref.rst
@@ -0,0 +1,11 @@
+=============================
+Reader utils reference manual
+=============================
+
+.. autofunction:: gudhi.read_off
+
+.. autofunction:: gudhi.read_lower_triangular_matrix_from_csv_file
+
+.. autofunction:: gudhi.read_persistence_intervals_grouped_by_dimension
+
+.. autofunction:: gudhi.read_persistence_intervals_in_dimension
-- 
cgit v1.2.3


From ef36c8b63bc353ac9d4e6982b9bba6797d546e51 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 18 Aug 2017 09:40:19 +0000
Subject: Fix sphinx bug when python3 is not in /usr/bin

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2613 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 07f67d4cc1f3b558b191115e0979ce3ce0580206
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake |  2 +-
 src/cython/CMakeLists.txt                           |  1 +
 src/cython/doc/python3-sphinx-build                 | 11 -----------
 src/cython/doc/python3-sphinx-build.in              | 11 +++++++++++
 4 files changed, 13 insertions(+), 12 deletions(-)
 delete mode 100755 src/cython/doc/python3-sphinx-build
 create mode 100755 src/cython/doc/python3-sphinx-build.in

(limited to 'src/cmake')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index e29ba40c..dbf2106a 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -123,7 +123,7 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
     find_program( SPHINX_PATH sphinx-build )
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
     # No sphinx-build in Pyton3, just hack it
-    set(SPHINX_PATH "${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
+    set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
   else()
     message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
   endif(PYTHON_VERSION_MAJOR EQUAL 2)
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index a06be008..ab5ea9ef 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -194,6 +194,7 @@ if(CYTHON_FOUND)
   endif(UNIX)
 
   # set sphinx-build in make files
+  configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY)
   configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY)
   configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY)
 
diff --git a/src/cython/doc/python3-sphinx-build b/src/cython/doc/python3-sphinx-build
deleted file mode 100755
index 44b94169..00000000
--- a/src/cython/doc/python3-sphinx-build
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/python3
-
-"""
-Emulate sphinx-build for python3
-"""
-
-from sys import exit, argv
-from sphinx import main
-
-if __name__ == '__main__':
-    exit(main(argv))
diff --git a/src/cython/doc/python3-sphinx-build.in b/src/cython/doc/python3-sphinx-build.in
new file mode 100755
index 00000000..c97965f5
--- /dev/null
+++ b/src/cython/doc/python3-sphinx-build.in
@@ -0,0 +1,11 @@
+#!@PYTHON_EXECUTABLE@
+
+"""
+Emulate sphinx-build for python3
+"""
+
+from sys import exit, argv
+from sphinx import main
+
+if __name__ == '__main__':
+    exit(main(argv))
-- 
cgit v1.2.3


From 5470c3565cfb4b9e3827a42bfdc3fbec461638a5 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 10:05:46 +0000
Subject: Fix in Python3 if sphinx is not installed

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2663 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0005d7fe2e7e8513a276543295c02351456595cc
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

(limited to 'src/cmake')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index dbf2106a..4cf2f445 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -122,8 +122,12 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
     # Documentation generation is available through sphinx
     find_program( SPHINX_PATH sphinx-build )
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
-    # No sphinx-build in Pyton3, just hack it
-    set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
+    execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "from sphinx import main"
+                    RESULT_VARIABLE SPHINX_MODULE_IS_INSTALLED)
+    if(SPHINX_MODULE_IS_INSTALLED)
+      # No sphinx-build in Pyton3, just hack it
+      set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
+    endif(SPHINX_MODULE_IS_INSTALLED)
   else()
     message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
   endif(PYTHON_VERSION_MAJOR EQUAL 2)
-- 
cgit v1.2.3


From 3dd4db9ad872eecae58e6edf3c16915ca1ec7ccc Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 11:26:30 +0000
Subject: Add debug traces

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2664 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: e4c572d98f4628e7f9b36fd9925ba7ce68e3cf81
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 1 +
 1 file changed, 1 insertion(+)

(limited to 'src/cmake')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 4cf2f445..799d28b6 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -124,6 +124,7 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
     execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "from sphinx import main"
                     RESULT_VARIABLE SPHINX_MODULE_IS_INSTALLED)
+    message("  --- SPHINX_MODULE_IS_INSTALLED --- ${SPHINX_MODULE_IS_INSTALLED}")
     if(SPHINX_MODULE_IS_INSTALLED)
       # No sphinx-build in Pyton3, just hack it
       set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
-- 
cgit v1.2.3


From 90f4783f287e266d3d8787d0d18b84d27f8b96b6 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 12:45:20 +0000
Subject: Modification rollback

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2665 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 2f977f8b93c6104d2b7c8f16c13da974b36f1535
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

(limited to 'src/cmake')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 799d28b6..dbf2106a 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -122,13 +122,8 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
     # Documentation generation is available through sphinx
     find_program( SPHINX_PATH sphinx-build )
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
-    execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "from sphinx import main"
-                    RESULT_VARIABLE SPHINX_MODULE_IS_INSTALLED)
-    message("  --- SPHINX_MODULE_IS_INSTALLED --- ${SPHINX_MODULE_IS_INSTALLED}")
-    if(SPHINX_MODULE_IS_INSTALLED)
-      # No sphinx-build in Pyton3, just hack it
-      set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
-    endif(SPHINX_MODULE_IS_INSTALLED)
+    # No sphinx-build in Pyton3, just hack it
+    set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
   else()
     message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
   endif(PYTHON_VERSION_MAJOR EQUAL 2)
-- 
cgit v1.2.3


From 8a22b7c6111b41e91766cdd53c0116b845e068b5 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 21:47:19 +0000
Subject: Fix sphinx build for python3 on Ubuntu

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2667 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c720b8be2919344e06f3d71cefdd7693439f63f0
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake |  2 +-
 src/cython/CMakeLists.txt                           |  9 +++------
 src/cython/doc/python3-sphinx-build.in              | 11 -----------
 src/cython/doc/python3-sphinx-build.py              | 11 +++++++++++
 4 files changed, 15 insertions(+), 18 deletions(-)
 delete mode 100755 src/cython/doc/python3-sphinx-build.in
 create mode 100755 src/cython/doc/python3-sphinx-build.py

(limited to 'src/cmake')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index dbf2106a..f2bbafdc 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -123,7 +123,7 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
     find_program( SPHINX_PATH sphinx-build )
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
     # No sphinx-build in Pyton3, just hack it
-    set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
+    set(SPHINX_PATH "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build.py")
   else()
     message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
   endif(PYTHON_VERSION_MAJOR EQUAL 2)
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index baeeb203..d1761f47 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -75,7 +75,7 @@ if(CYTHON_FOUND)
 
   if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
     set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
     set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
@@ -300,20 +300,17 @@ if(CYTHON_FOUND)
 
   # Documentation generation is available through sphinx - requires all modules
   if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-    # set sphinx-build in make files
-    configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY)
-
     # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
     add_custom_target(sphinx
         WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
         COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-        ${SPHINX_PATH} -b html . "${CMAKE_CURRENT_BINARY_DIR}/sphinx"
+        ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc sphinx
         DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so")
 
     add_test(NAME sphinx_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc "${CMAKE_CURRENT_BINARY_DIR}/sphinx")
+             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc doctest)
 
   endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 endif(CYTHON_FOUND)
diff --git a/src/cython/doc/python3-sphinx-build.in b/src/cython/doc/python3-sphinx-build.in
deleted file mode 100755
index c97965f5..00000000
--- a/src/cython/doc/python3-sphinx-build.in
+++ /dev/null
@@ -1,11 +0,0 @@
-#!@PYTHON_EXECUTABLE@
-
-"""
-Emulate sphinx-build for python3
-"""
-
-from sys import exit, argv
-from sphinx import main
-
-if __name__ == '__main__':
-    exit(main(argv))
diff --git a/src/cython/doc/python3-sphinx-build.py b/src/cython/doc/python3-sphinx-build.py
new file mode 100755
index 00000000..44b94169
--- /dev/null
+++ b/src/cython/doc/python3-sphinx-build.py
@@ -0,0 +1,11 @@
+#!/usr/bin/python3
+
+"""
+Emulate sphinx-build for python3
+"""
+
+from sys import exit, argv
+from sphinx import main
+
+if __name__ == '__main__':
+    exit(main(argv))
-- 
cgit v1.2.3