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-rw-r--r--CMakeGUDHIVersion.txt2
-rw-r--r--CMakeLists.txt12
-rw-r--r--data/points/human.COPYRIGHT77
-rwxr-xr-xscripts/create_gudhi_version.sh66
-rw-r--r--src/CMakeLists.txt14
-rw-r--r--src/GUDHIConfig.cmake.in7
-rw-r--r--src/GudhUI/CMakeLists.txt81
-rw-r--r--src/Nerve_GIC/include/gudhi/GIC.h88
-rw-r--r--src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h5
-rw-r--r--src/Simplex_tree/include/gudhi/Simplex_tree.h5
-rw-r--r--src/cmake/modules/GUDHI_doxygen_target.cmake8
-rw-r--r--src/cmake/modules/GUDHI_modules.cmake5
-rw-r--r--src/cmake/modules/GUDHI_third_party_libraries.cmake4
-rw-r--r--src/common/doc/installation.h24
-rw-r--r--src/cython/CMakeLists.txt686
-rw-r--r--src/cython/cython/nerve_gic.pyx30
-rw-r--r--src/cython/doc/nerve_gic_complex_sum.rst2
-rw-r--r--src/cython/include/Alpha_complex_interface.h2
18 files changed, 727 insertions, 391 deletions
diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index 6811d7e1..ebaddd47 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,5 +1,5 @@
set (GUDHI_MAJOR_VERSION 2)
-set (GUDHI_MINOR_VERSION 2)
+set (GUDHI_MINOR_VERSION 3)
set (GUDHI_PATCH_VERSION 0)
set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
diff --git a/CMakeLists.txt b/CMakeLists.txt
index afacede9..d61df992 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -6,6 +6,10 @@ include(CMakeGUDHIVersion.txt)
list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
+# Reset cache
+set(GUDHI_MODULES "" CACHE INTERNAL "GUDHI_MODULES")
+set(GUDHI_MISSING_MODULES "" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+
# This variable is used by Cython CMakeLists.txt and by GUDHI_third_party_libraries to know its path
set(GUDHI_CYTHON_PATH "src/cython")
@@ -37,8 +41,6 @@ add_gudhi_module(Tangential_complex)
add_gudhi_module(Witness_complex)
add_gudhi_module(Nerve_GIC)
-message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
-
# Include module CMake subdirectories
# GUDHI_SUB_DIRECTORIES is managed in CMAKE_MODULE_PATH/GUDHI_modules.cmake
foreach(GUDHI_MODULE ${GUDHI_MODULES})
@@ -54,9 +56,15 @@ add_subdirectory(src/GudhUI)
if (WITH_GUDHI_PYTHON)
# specific for cython module
add_subdirectory(${GUDHI_CYTHON_PATH})
+else()
+ message("++ Python module will not be compiled because WITH_GUDHI_PYTHON is set to OFF")
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python")
endif()
# For "make user_version" - Requires GUDHI_modules to be performed
include(GUDHI_user_version_target)
# For "make doxygen" - Requires GUDHI_USER_VERSION_DIR to be set - Done in GUDHI_user_version_target for dev version
include(GUDHI_doxygen_target)
+
+message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
+message("++ GUDHI_MISSING_MODULES list is:\"${GUDHI_MISSING_MODULES}\"")
diff --git a/data/points/human.COPYRIGHT b/data/points/human.COPYRIGHT
new file mode 100644
index 00000000..cb9bdb59
--- /dev/null
+++ b/data/points/human.COPYRIGHT
@@ -0,0 +1,77 @@
+The human.off point cloud is available at this webpage :
+http://segeval.cs.princeton.edu/
+
+LICENSE
+=======
+
+AIM@SHAPE General License for Shapes
+Applicable terms
+----------------
+
+This is the general AIM@SHAPE license applicable to models in the
+Shape Repository. It should be noted that each model is a
+representation of, and is distinct from, a shape, whether physical or
+imaginary. While the shape may be subject to its own terms, the terms
+governing the model you are about to download are described herein.
+
+For some models, the owners have defined specific licenses. The terms
+and conditions laid down in these licenses are in addition to the
+terms prescribed here, and are to be adhered to strictly when using
+such models.
+
+Acknowledgements
+----------------
+
+When including models from the Shape Repository in your website or
+research work, or when using them for other purposes allowed by the
+terms described herein, the AIM@SHAPE project and the model owner must
+be acknowledged as the sources of the models, for example with the
+phrase, "... model is provided courtesy of <model_owner> by the
+AIM@SHAPE Shape Repository."
+
+Information on <model_owner> is present in the accompanying metadata
+files and, where present, owner licenses.
+
+Metadata
+--------
+
+Each model is accompanied by its metadata file. Please keep this file
+with the model as it contains important information about the
+model. Please let us know if you find any errors in the metadata.
+
+(Im)proper use
+--------------
+
+Some models in the Shape Repository represent artifacts of religious,
+cultural and/or historical significance, e.g. the Max Planck
+model. Such models have been entrusted to the Shape Repository under
+the hope that they will be used respectfully and
+conscientiously. Please refrain from conducting experiments on them
+that may be rash or insensitive to people's feelings. Such experiments
+include, but are not limited to, morphing, animation, boolean
+operations, simulations of burning, breaking, exploding and melting.
+
+Models in the Shape Repository are made freely available for research
+and non-commercial purposes only. Use of these models for commercial
+purposes is permitted only after the express approval of the Shape
+Repository and the onwner has been obtained. Please contact us using
+the webform on our site in this regard.
+
+
+CITATION
+========
+
+If you use any part of this benchmark, please cite:
+Xiaobai Chen, Aleksey Golovinskiy, and Thomas Funkhouser,
+A Benchmark for 3D Mesh Segmentation
+ACM Transactions on Graphics (Proc. SIGGRAPH), 28(3), 2009.
+
+@article{Chen:2009:ABF,
+ author = "Xiaobai Chen and Aleksey Golovinskiy and Thomas Funkhouser",
+ title = "A Benchmark for {3D} Mesh Segmentation",
+ journal = "ACM Transactions on Graphics (Proc. SIGGRAPH)",
+ year = "2009",
+ month = aug,
+ volume = "28",
+ number = "3"
+} \ No newline at end of file
diff --git a/scripts/create_gudhi_version.sh b/scripts/create_gudhi_version.sh
new file mode 100755
index 00000000..f2a9233f
--- /dev/null
+++ b/scripts/create_gudhi_version.sh
@@ -0,0 +1,66 @@
+#!/bin/bash
+
+login="vrouvrea"
+version="2.3.0"
+cgaldir="/home/vincent/workspace/CGAL-4.11-HO/build"
+cpucount=7
+
+
+# We start from scripts dir in the dev branch
+cd ..
+RELATIVEURL=`svn info . |grep -F "Relative URL:" | awk '{print $NF}'`
+
+if [ "$RELATIVEURL" != "^/trunk" ]
+then
+echo "Script must be launched in trunk and not in $RELATIVEURL"
+exit
+fi
+
+rm -rf build; mkdir build; cd build; cmake -DCMAKE_BUILD_TYPE=Debug -DDEBUG_TRACES=ON -DCGAL_DIR=${cgaldir} -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_BENCHMARK=ON -DPython_ADDITIONAL_VERSIONS=3 ..
+cmake -DCMAKE_BUILD_TYPE=Debug .
+
+CURRENTDIRECTORY=`pwd`
+export PYTHONPATH=$CURRENTDIRECTORY/src/cython:$PYTHONPATH
+
+make -j ${cpucount} all test
+
+cd ..
+svn st | grep -v GUDHIVersion.cmake | grep "^\?" | awk "{print \$2}" | xargs rm -rf
+
+svn copy svn+ssh://${login}@scm.gforge.inria.fr/svnroot/gudhi/trunk svn+ssh://${login}@scm.gforge.inria.fr/svnroot/gudhi/tags/gudhi-release-${version} \
+ -m "Creating a tag of Gudhi release version ${version}."
+
+cd build
+make user_version
+
+userversiondir=`find . -type d -name "*_GUDHI_${version}" | sed 's/\.\///g'`
+echo "User version directory = ${userversiondir}"
+
+tar -czvf ${userversiondir}.tar.gz ${userversiondir}
+
+userdocdir=${userversiondir/GUDHI/GUDHI_DOC}
+echo "User documentation directory = ${userdocdir}"
+mkdir ${userdocdir}
+make doxygen
+
+cp -R ${userversiondir}/doc/html ${userdocdir}/cpp
+cd ${userversiondir}
+rm -rf build; mkdir build; cd build; cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./installed -DCGAL_DIR=${cgaldir} -DWITH_GUDHI_EXAMPLE=ON -DPython_ADDITIONAL_VERSIONS=3 ..
+
+CURRENTDIRECTORY=`pwd`
+export PYTHONPATH=$CURRENTDIRECTORY/cython:$PYTHONPATH
+
+make sphinx
+
+cp -R cython/sphinx ../../${userdocdir}/python
+cd ../..
+tar -czvf ${userdocdir}.tar.gz ${userdocdir}
+
+cd ${userversiondir}/build
+make -j ${cpucount} all test install
+
+cd ../..
+actualdir=`pwd`
+echo "Library is available at ${actualdir}/${userversiondir}.tar.gz"
+sha256sum ${userversiondir}.tar.gz
+echo "Documentation is available at ${actualdir}/${userdocdir}.tar.gz"
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index c60346d5..b40d506a 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -6,6 +6,9 @@ include(CMakeGUDHIVersion.txt)
list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/")
+set(GUDHI_MODULES "" CACHE INTERNAL "GUDHI_MODULES")
+set(GUDHI_MISSING_MODULES "" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+
# This variable is used by Cython CMakeLists.txt and by GUDHI_third_party_libraries to know its path
set(GUDHI_CYTHON_PATH "cython")
@@ -35,8 +38,6 @@ add_gudhi_module(Tangential_complex)
add_gudhi_module(Witness_complex)
add_gudhi_module(Nerve_GIC)
-message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
-
# For "make doxygen" - Requires GUDHI_USER_VERSION_DIR to be set
set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR})
include(GUDHI_doxygen_target)
@@ -60,7 +61,14 @@ add_subdirectory(GudhUI)
if (WITH_GUDHI_PYTHON)
# specific for cython module
add_subdirectory(${GUDHI_CYTHON_PATH})
+else()
+ message("++ Python module will not be compiled because WITH_GUDHI_PYTHON is set to OFF")
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python")
endif()
+
+message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
+message("++ GUDHI_MISSING_MODULES list is:\"${GUDHI_MISSING_MODULES}\"")
+
#---------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------
@@ -71,7 +79,7 @@ export(PACKAGE GUDHI)
message("++ make install will install ${PROJECT_NAME} in the following directory : ${CMAKE_INSTALL_PREFIX}")
# Create the GUDHIConfig.cmake and GUDHIConfigVersion files
-set(CONF_INCLUDE_DIRS "${CMAKE_INSTALL_PREFIX}/include")
+set(CONF_INCLUDE_DIRS "${CMAKE_SOURCE_DIR}/include;${CMAKE_INSTALL_PREFIX}/include")
configure_file(GUDHIConfig.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake" @ONLY)
configure_file(GUDHIConfigVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake" @ONLY)
diff --git a/src/GUDHIConfig.cmake.in b/src/GUDHIConfig.cmake.in
index 02b540dc..8d82f235 100644
--- a/src/GUDHIConfig.cmake.in
+++ b/src/GUDHIConfig.cmake.in
@@ -1,7 +1,12 @@
# - Config file for the GUDHI package
# It defines the following variables
# GUDHI_INCLUDE_DIRS - include directories for GUDHI
+#
+# Order is :
+# 1. user defined GUDHI_INCLUDE_DIRS
+# 2. ${CMAKE_SOURCE_DIR}/include => Where the 'cmake' has been done
+# 3. ${CMAKE_INSTALL_PREFIX}/include => Where the 'make install' has been performed
# Compute paths
-set(GUDHI_INCLUDE_DIRS "@CONF_INCLUDE_DIRS@")
+set(GUDHI_INCLUDE_DIRS "${GUDHI_INCLUDE_DIRS};@CONF_INCLUDE_DIRS@")
diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index b357b8f7..0945e758 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -1,40 +1,55 @@
project(GudhUI)
# Need to find OpenGL first as find_package(Qt5) tries to #include"GL/gl.h" on some platforms
-find_package(OpenGL)
+find_package(OpenGL QUIET)
if (OPENGL_FOUND)
- find_package(Qt5 COMPONENTS Widgets Xml OpenGL)
- find_package(QGLViewer)
-
- if ( CGAL_FOUND AND Qt5_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_VERSION VERSION_EQUAL 4.8.0)
-
- set(CMAKE_AUTOMOC ON)
- set(CMAKE_AUTOUIC ON)
- set(CMAKE_INCLUDE_CURRENT_DIR ON)
-
- SET(Boost_USE_STATIC_LIBS ON)
- SET(Boost_USE_MULTITHREAD OFF)
- include_directories (${QGLVIEWER_INCLUDE_DIR})
-
- add_executable ( GudhUI
- gui/gudhui.cpp
- gui/MainWindow.cpp
- gui/Menu_k_nearest_neighbors.cpp
- gui/Menu_uniform_neighbors.cpp
- gui/Menu_edge_contraction.cpp
- gui/Menu_persistence.cpp
- view/Viewer_instructor.cpp
- view/Viewer.cpp
- )
- target_link_libraries( GudhUI Qt5::Widgets Qt5::Xml Qt5::OpenGL )
- target_link_libraries( GudhUI ${QGLVIEWER_LIBRARIES} )
- target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} )
- if (TBB_FOUND)
- target_link_libraries( GudhUI ${TBB_LIBRARIES})
+ find_package(Qt5 COMPONENTS Widgets Xml OpenGL QUIET)
+ if (Qt5_FOUND)
+ find_package(QGLViewer QUIET)
+ if ( QGLVIEWER_FOUND)
+
+ if ( CGAL_FOUND AND NOT CGAL_VERSION VERSION_EQUAL 4.8.0)
+ set(CMAKE_AUTOMOC ON)
+ set(CMAKE_AUTOUIC ON)
+ set(CMAKE_INCLUDE_CURRENT_DIR ON)
+
+ SET(Boost_USE_STATIC_LIBS ON)
+ SET(Boost_USE_MULTITHREAD OFF)
+ include_directories (${QGLVIEWER_INCLUDE_DIR})
+
+ add_executable ( GudhUI
+ gui/gudhui.cpp
+ gui/MainWindow.cpp
+ gui/Menu_k_nearest_neighbors.cpp
+ gui/Menu_uniform_neighbors.cpp
+ gui/Menu_edge_contraction.cpp
+ gui/Menu_persistence.cpp
+ view/Viewer_instructor.cpp
+ view/Viewer.cpp
+ )
+ target_link_libraries( GudhUI Qt5::Widgets Qt5::Xml Qt5::OpenGL )
+ target_link_libraries( GudhUI ${QGLVIEWER_LIBRARIES} )
+ target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} )
+ if (TBB_FOUND)
+ target_link_libraries( GudhUI ${TBB_LIBRARIES})
+ endif()
+
+ install(TARGETS GudhUI DESTINATION bin)
+ set(GUDHI_MODULES ${GUDHI_MODULES} "GudhUI" CACHE INTERNAL "GUDHI_MODULES")
+ else()
+ message("++ GudhUI will not be compiled because CGAL < 4.8.0 or not found")
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "GudhUI" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+ endif()
+ else()
+ message("++ GudhUI will not be compiled because QGLViewer is not found")
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "GudhUI" CACHE INTERNAL "GUDHI_MISSING_MODULES")
endif()
-
- install(TARGETS GudhUI DESTINATION bin)
-
+ else()
+ message("++ GudhUI will not be compiled because Qt5 COMPONENTS Widgets Xml OpenGL are not found")
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "GudhUI" CACHE INTERNAL "GUDHI_MISSING_MODULES")
endif()
-endif(OPENGL_FOUND)
+else()
+ message("++ GudhUI will not be compiled because OpenGL is not found")
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "GudhUI" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+endif()
diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h
index fea0b861..30f89d65 100644
--- a/src/Nerve_GIC/include/gudhi/GIC.h
+++ b/src/Nerve_GIC/include/gudhi/GIC.h
@@ -226,7 +226,25 @@ class Cover_complex {
void set_mask(int nodemask) { mask = nodemask; }
public:
- /** \brief Reads and stores the input point cloud.
+
+
+ /** \brief Reads and stores the input point cloud from vector stored in memory.
+ *
+ * @param[in] cloud input vector representing the point cloud. Each row is a point and each coordinate is a vector.
+ *
+ */
+ template <class InputRange>
+ void set_point_cloud_from_range(InputRange const & cloud) {
+ n = cloud.size(); data_dimension = cloud[0].size(); point_cloud_name = "matrix";
+ for(int i = 0; i < n; i++){
+ point_cloud.emplace_back(cloud[i].begin(), cloud[i].begin() + data_dimension);
+ boost::add_vertex(one_skeleton_OFF);
+ vertices.push_back(boost::add_vertex(one_skeleton));
+ cover.emplace_back();
+ }
+ }
+
+ /** \brief Reads and stores the input point cloud from .(n)OFF file.
*
* @param[in] off_file_name name of the input .OFF or .nOFF file.
*
@@ -371,6 +389,28 @@ class Cover_complex {
distances[index[boost::source(*ei, one_skeleton)]][index[boost::target(*ei, one_skeleton)]]);
}
+ public:
+ /** \brief Reads and stores the distance matrices from vector stored in memory.
+ *
+ * @param[in] distance_matrix input vector representing the distance matrix.
+ *
+ */
+ template <class InputRange>
+ void set_distances_from_range(InputRange const & distance_matrix) {
+ if(point_cloud.size() == 0){
+ n = distance_matrix.size();
+ point_cloud_name = "matrix";
+ data_dimension = 0;
+ for(int i = 0; i < n; i++){
+ point_cloud.emplace_back();
+ boost::add_vertex(one_skeleton_OFF);
+ vertices.push_back(boost::add_vertex(one_skeleton));
+ cover.emplace_back();
+ }
+ }
+ distances = distance_matrix;
+ }
+
public: // Pairwise distances.
/** \private \brief Computes all pairwise distances.
*/
@@ -500,9 +540,17 @@ class Cover_complex {
*
*/
void set_function_from_coordinate(int k) {
- for (int i = 0; i < n; i++) func.push_back(point_cloud[i][k]);
- functional_cover = true;
- cover_name = "coordinate " + std::to_string(k);
+ if(point_cloud[0].size() > 0){
+ for (int i = 0; i < n; i++) func.push_back(point_cloud[i][k]);
+ functional_cover = true;
+ cover_name = "coordinate " + std::to_string(k);
+ }
+ else{
+ std::cout << "Only pairwise distances provided---cannot access " << k << "th coordinate; returning null vector instead" << std::endl;
+ for (int i = 0; i < n; i++) func.push_back(0.0);
+ functional_cover = true;
+ cover_name = "null";
+ }
}
public: // Set function from vector.
@@ -953,9 +1001,17 @@ class Cover_complex {
*
*/
void set_color_from_coordinate(int k = 0) {
- for (int i = 0; i < n; i++) func_color.push_back(point_cloud[i][k]);
- color_name = "coordinate ";
- color_name.append(std::to_string(k));
+ if(point_cloud[0].size() > 0){
+ for (int i = 0; i < n; i++) func_color.push_back(point_cloud[i][k]);
+ color_name = "coordinate ";
+ color_name.append(std::to_string(k));
+ }
+ else{
+ std::cout << "Only pairwise distances provided---cannot access " << k << "th coordinate; returning null vector instead" << std::endl;
+ for (int i = 0; i < n; i++) func.push_back(0.0);
+ functional_cover = true;
+ cover_name = "null";
+ }
}
public: // Set color from vector.
@@ -964,7 +1020,7 @@ class Cover_complex {
* @param[in] color input vector of values.
*
*/
- void set_color_from_vector(std::vector<double> color) {
+ void set_color_from_range(std::vector<double> color) {
for (unsigned int i = 0; i < color.size(); i++) func_color.push_back(color[i]);
}
@@ -1108,7 +1164,7 @@ class Cover_complex {
/** \brief Computes the extended persistence diagram of the complex.
*
*/
- void compute_PD() {
+ Persistence_diagram compute_PD() {
Simplex_tree st;
// Compute max and min
@@ -1121,15 +1177,18 @@ class Cover_complex {
// Build filtration
for (auto const& simplex : simplices) {
- std::vector<int> splx = simplex; splx.push_back(-2);
+ std::vector<int> splx = simplex;
+ splx.push_back(-2);
st.insert_simplex_and_subfaces(splx, -3);
}
for (std::map<int, double>::iterator it = cover_std.begin(); it != cover_std.end(); it++) {
int vertex = it->first; float val = it->second;
int vert[] = {vertex}; int edge[] = {vertex, -2};
- st.assign_filtration(st.find(vert), -2 + (val - minf)/(maxf - minf));
- st.assign_filtration(st.find(edge), 2 - (val - minf)/(maxf - minf));
+ if(st.find(vert) != st.null_simplex()){
+ st.assign_filtration(st.find(vert), -2 + (val - minf)/(maxf - minf));
+ st.assign_filtration(st.find(edge), 2 - (val - minf)/(maxf - minf));
+ }
}
st.make_filtration_non_decreasing();
@@ -1159,6 +1218,7 @@ class Cover_complex {
if (verbose) std::cout << " [" << birth << ", " << death << "]" << std::endl;
}
}
+ return PD;
}
public:
@@ -1184,7 +1244,7 @@ class Cover_complex {
Cboot.point_cloud.push_back(this->point_cloud[id]); Cboot.cover.emplace_back(); Cboot.func.push_back(this->func[id]);
boost::add_vertex(Cboot.one_skeleton_OFF); Cboot.vertices.push_back(boost::add_vertex(Cboot.one_skeleton));
}
- Cboot.set_color_from_vector(Cboot.func);
+ Cboot.set_color_from_range(Cboot.func);
for (int j = 0; j < n; j++) {
std::vector<double> dist(n);
@@ -1230,7 +1290,7 @@ class Cover_complex {
unsigned int N = distribution.size();
double level = 1;
for (unsigned int i = 0; i < N; i++)
- if (distribution[i] > d){ level = i * 1.0 / N; break; }
+ if (distribution[i] >= d){ level = i * 1.0 / N; break; }
if (verbose) std::cout << "Confidence level of distance " << d << " is " << level << std::endl;
return level;
}
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index c68b5c0b..c51e47a5 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -300,7 +300,10 @@ class Persistent_cohomology {
// with multiplicity. We used to sum the coefficients directly in
// annotations_in_boundary by using a map, we now do it later.
typedef std::pair<Column *, int> annotation_t;
- thread_local std::vector<annotation_t> annotations_in_boundary;
+#ifdef GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+ thread_local
+#endif // GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+ std::vector<annotation_t> annotations_in_boundary;
annotations_in_boundary.clear();
int sign = 1 - 2 * (dim_sigma % 2); // \in {-1,1} provides the sign in the
// alternate sum in the boundary.
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index ee96d5a2..3ab23c12 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -1057,7 +1057,10 @@ class Simplex_tree {
Dictionary_it next = siblings->members().begin();
++next;
- thread_local std::vector<std::pair<Vertex_handle, Node> > inter;
+#ifdef GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+ thread_local
+#endif // GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+ std::vector<std::pair<Vertex_handle, Node> > inter;
for (Dictionary_it s_h = siblings->members().begin();
s_h != siblings->members().end(); ++s_h, ++next) {
Simplex_handle root_sh = find_vertex(s_h->first);
diff --git a/src/cmake/modules/GUDHI_doxygen_target.cmake b/src/cmake/modules/GUDHI_doxygen_target.cmake
index 9e10e566..7a84c4e0 100644
--- a/src/cmake/modules/GUDHI_doxygen_target.cmake
+++ b/src/cmake/modules/GUDHI_doxygen_target.cmake
@@ -1,7 +1,7 @@
# add a target to generate API documentation with Doxygen
-find_package(Doxygen)
+find_package(Doxygen QUIET)
if(DOXYGEN_FOUND)
- # configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
+ set(GUDHI_MODULES ${GUDHI_MODULES} "cpp-documentation" CACHE INTERNAL "GUDHI_MODULES")
# starting from cmake 3.9 the usage of DOXYGEN_EXECUTABLE is deprecated
if(TARGET Doxygen::doxygen)
@@ -16,4 +16,6 @@ if(DOXYGEN_FOUND)
# In dev version, doxygen target depends on user_version target. Not existing in user version
add_dependencies(doxygen user_version)
endif()
-endif(DOXYGEN_FOUND)
+else()
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "cpp-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+endif()
diff --git a/src/cmake/modules/GUDHI_modules.cmake b/src/cmake/modules/GUDHI_modules.cmake
index f95d0c34..aab1dd08 100644
--- a/src/cmake/modules/GUDHI_modules.cmake
+++ b/src/cmake/modules/GUDHI_modules.cmake
@@ -1,11 +1,12 @@
# A function to add a new module in GUDHI
-set(GUDHI_MODULES "")
set(GUDHI_MODULES_FULL_LIST "")
function(add_gudhi_module file_path)
option("WITH_MODULE_GUDHI_${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)
+ set(GUDHI_MODULES ${GUDHI_MODULES} ${file_path} CACHE INTERNAL "GUDHI_MODULES")
+ else()
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} ${file_path} CACHE INTERNAL "GUDHI_MISSING_MODULES")
endif()
# Required by user_version
set(GUDHI_MODULES_FULL_LIST ${GUDHI_MODULES_FULL_LIST} ${file_path} PARENT_SCOPE)
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 1ad0c1fd..2464517c 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -21,11 +21,11 @@ endif()
# A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html
# or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
# but it implies to use cmake version 3.1 at least.
-find_package(CGAL)
+find_package(CGAL QUIET)
# Only CGAL versions > 4.4 supports what Gudhi uses from CGAL
if (CGAL_VERSION VERSION_LESS 4.4.0)
- message("CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.")
+ message("++ CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.")
unset(CGAL_FOUND)
endif()
if(CGAL_FOUND)
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index 12407c18..df7eed37 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -2,22 +2,34 @@
* \tableofcontents
* As GUDHI is a header only library, there is no need to install the library.
*
- * Examples of GUDHI headers inclusion can be found in \ref demos.
+ * Examples of GUDHI headers inclusion can be found in \ref utilities.
*
* \section compiling Compiling
* The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> &ge; 1.48.0
* and <a target="_blank" href="https://www.cmake.org/">CMake</a> &ge; 3.1.
* It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015.
*
- * \subsection demos Demos and examples
- * To build the demos and examples, run the following commands in a terminal:
+ * \subsection utilities Utilities and examples
+ * To build the utilities, run the following commands in a terminal:
\verbatim cd /path-to-gudhi/
mkdir build
cd build/
cmake ..
make \endverbatim
- * A list of examples is available <a href="examples.html">here</a>.
+ * By default, examples are disabled. You can activate their compilation with
+ * <a href="https://cmake.org/cmake/help/v3.0/manual/ccmake.1.html">ccmake</a> (on Linux and Mac OSX),
+ * <a href="https://cmake.org/cmake/help/v3.0/manual/cmake-gui.1.html">cmake-gui</a> (on Windows) or by modifying the
+ * cmake command as follows :
+\verbatim cmake -DWITH_GUDHI_EXAMPLE=ON ..
+make \endverbatim
+ * A list of utilities and examples is available <a href="examples.html">here</a>.
*
+ * \subsection libraryinstallation Installation
+ * To install the library (headers and activated utilities), run the following command in a terminal:
+ * \verbatim make install \endverbatim
+ * This action may require to be in the sudoer or administrator of the machine in function of the operating system and
+ * of <a href="https://cmake.org/cmake/help/v3.0/variable/CMAKE_INSTALL_PREFIX.html">CMAKE_INSTALL_PREFIX</a>.
+ *
* \subsection testsuites Test suites
* To test your build, run the following command in a terminal:
* \verbatim make test \endverbatim
@@ -31,6 +43,10 @@ make doxygen
# You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder`
\endverbatim
*
+ * \subsection helloworld Hello world !
+ * The <a target="_blank" href="https://gitlab.inria.fr/GUDHI/hello-gudhi-world">Hello world for GUDHI</a>
+ * project is an example to help developers to make their own C++ project on top of the GUDHI library.
+ *
* \section optionallibrary Optional third-party library
* \subsection gmp GMP
* The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 542be9b0..dc2e9278 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -31,360 +31,414 @@ function( add_gudhi_debug_info DEBUG_INFO )
set(GUDHI_CYTHON_DEBUG_INFO "${GUDHI_CYTHON_DEBUG_INFO} \"${DEBUG_INFO}\\n\" \\\n" PARENT_SCOPE)
endfunction( add_gudhi_debug_info )
+if(PYTHONINTERP_FOUND)
+ if(CYTHON_FOUND)
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}off_reader;")
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}simplex_tree;")
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}rips_complex;")
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}cubical_complex;")
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}periodic_cubical_complex;")
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}reader_utils;")
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}witness_complex;")
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}strong_witness_complex;")
+
+ add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}")
+ add_gudhi_debug_info("Cython version ${CYTHON_VERSION}")
+ if(PYTEST_FOUND)
+ add_gudhi_debug_info("Pytest version ${PYTEST_VERSION}")
+ endif()
+ if(MATPLOTLIB_FOUND)
+ add_gudhi_debug_info("Matplotlib version ${MATPLOTLIB_VERSION}")
+ endif()
+ if(NUMPY_FOUND)
+ add_gudhi_debug_info("Numpy version ${NUMPY_VERSION}")
+ endif()
+ if(SCIPY_FOUND)
+ add_gudhi_debug_info("Scipy version ${SCIPY_VERSION}")
+ endif()
+ if(MATPLOTLIB_FOUND AND NUMPY_FOUND AND SCIPY_FOUND)
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
+ else()
+ set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
+ endif()
-if(CYTHON_FOUND)
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}off_reader;")
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}simplex_tree;")
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}rips_complex;")
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}cubical_complex;")
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}periodic_cubical_complex;")
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}reader_utils;")
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}witness_complex;")
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}strong_witness_complex;")
-
- add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}")
- add_gudhi_debug_info("Cython version ${CYTHON_VERSION}")
- if(PYTEST_FOUND)
- add_gudhi_debug_info("Pytest version ${PYTEST_VERSION}")
- endif()
- if(MATPLOTLIB_FOUND)
- add_gudhi_debug_info("Matplotlib version ${MATPLOTLIB_VERSION}")
- endif()
- if(NUMPY_FOUND)
- add_gudhi_debug_info("Numpy version ${NUMPY_VERSION}")
- endif()
- if(SCIPY_FOUND)
- add_gudhi_debug_info("Scipy version ${SCIPY_VERSION}")
- endif()
-
- message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_VERSION} - 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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
- set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
-
- # Gudhi and CGAL compilation option
- if(MSVC)
- set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ")
- else(MSVC)
- set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-std=c++11', ")
- endif(MSVC)
- if(CMAKE_COMPILER_IS_GNUCXX)
- set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
- endif(CMAKE_COMPILER_IS_GNUCXX)
- if (CMAKE_CXX_COMPILER_ID MATCHES Intel)
- set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ")
- 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', ")
- endif()
-
- if (EIGEN3_FOUND)
- add_gudhi_debug_info("Eigen3 version ${EIGEN3_VERSION}")
- # No problem, even if no CGAL found
- set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
- endif (EIGEN3_FOUND)
-
- if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
- set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}bottleneck_distance;")
- set(GUDHI_CYTHON_NERVE_GIC "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/nerve_gic.pyx'")
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}nerve_gic;")
- else()
- set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}bottleneck_distance;")
- set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}nerve_gic;")
- endif ()
- if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
- set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}subsampling;")
- set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}tangential_complex;")
- else()
- set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}subsampling;")
- set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}tangential_complex;")
- endif ()
- if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
- set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}alpha_complex;")
- else()
- set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}alpha_complex;")
- endif ()
- if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
- set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
- "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n")
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_witness_complex;")
- set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_strong_witness_complex;")
- else()
- set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_witness_complex;")
- set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_strong_witness_complex;")
- endif ()
-
- add_gudhi_debug_info("Installed modules are: ${GUDHI_CYTHON_MODULES}")
- if(GUDHI_CYTHON_MISSING_MODULES)
- add_gudhi_debug_info("Missing modules are: ${GUDHI_CYTHON_MISSING_MODULES}")
- endif()
+ message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_VERSION} - 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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
+ set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
+
+ # Gudhi and CGAL compilation option
+ if(MSVC)
+ set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ")
+ else(MSVC)
+ set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-std=c++11', ")
+ endif(MSVC)
+ if(CMAKE_COMPILER_IS_GNUCXX)
+ set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
+ endif(CMAKE_COMPILER_IS_GNUCXX)
+ if (CMAKE_CXX_COMPILER_ID MATCHES Intel)
+ set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ")
+ endif(CMAKE_CXX_COMPILER_ID MATCHES Intel)
+ if (DEBUG_TRACES)
+ # For programs to be more verbose
+ set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ")
+ endif()
- if(CGAL_FOUND)
- can_cgal_use_cxx11_thread_local()
- if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
- add_gudhi_cython_lib(${Boost_THREAD_LIBRARY})
- set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
+ if (EIGEN3_FOUND)
+ add_gudhi_debug_info("Eigen3 version ${EIGEN3_VERSION}")
+ # No problem, even if no CGAL found
+ set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
+ endif (EIGEN3_FOUND)
+
+ if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+ set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}bottleneck_distance;")
+ set(GUDHI_CYTHON_NERVE_GIC "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/nerve_gic.pyx'")
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}nerve_gic;")
+ else()
+ set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}bottleneck_distance;")
+ set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}nerve_gic;")
+ endif ()
+ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+ set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}subsampling;")
+ set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}tangential_complex;")
+ else()
+ set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}subsampling;")
+ set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}tangential_complex;")
+ endif ()
+ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+ set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}alpha_complex;")
+ else()
+ set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}alpha_complex;")
+ endif ()
+ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+ set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
+ "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n")
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_witness_complex;")
+ set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_strong_witness_complex;")
+ else()
+ set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_witness_complex;")
+ set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_strong_witness_complex;")
+ endif ()
+
+ add_gudhi_debug_info("Installed modules are: ${GUDHI_CYTHON_MODULES}")
+ if(GUDHI_CYTHON_MISSING_MODULES)
+ add_gudhi_debug_info("Missing modules are: ${GUDHI_CYTHON_MISSING_MODULES}")
endif()
- # Add CGAL compilation args
- if(CGAL_HEADER_ONLY)
- add_gudhi_debug_info("CGAL header only version ${CGAL_VERSION}")
- set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
- else(CGAL_HEADER_ONLY)
- add_gudhi_debug_info("CGAL version ${CGAL_VERSION}")
- add_gudhi_cython_lib(${CGAL_LIBRARY})
- set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
- # If CGAL is not header only, CGAL library may link with boost system,
- add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY})
- set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
- endif(CGAL_HEADER_ONLY)
- # GMP and GMPXX are not required, but if present, CGAL will link with them.
- if(GMP_FOUND)
- add_gudhi_debug_info("GMP_LIBRARIES = ${GMP_LIBRARIES}")
- set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
- add_gudhi_cython_lib(${GMP_LIBRARIES})
- set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
- if(GMPXX_FOUND)
- add_gudhi_debug_info("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
- set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
- add_gudhi_cython_lib(${GMPXX_LIBRARIES})
- set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ")
- endif(GMPXX_FOUND)
- endif(GMP_FOUND)
- endif(CGAL_FOUND)
-
- # Specific for Mac
- if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
- set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-mmacosx-version-min=10.12', ")
- set(GUDHI_CYTHON_EXTRA_LINK_ARGS "${GUDHI_CYTHON_EXTRA_LINK_ARGS}'-mmacosx-version-min=10.12', ")
- endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
-
- # Loop on INCLUDE_DIRECTORIES PROPERTY
- get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES)
- foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
- set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ")
- endforeach()
- set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ")
-
- if (TBB_FOUND AND WITH_GUDHI_USE_TBB)
- add_gudhi_debug_info("TBB version ${TBB_INTERFACE_VERSION} found and used")
- set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ")
- add_gudhi_cython_lib(${TBB_RELEASE_LIBRARY})
- add_gudhi_cython_lib(${TBB_MALLOC_RELEASE_LIBRARY})
- set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ")
- set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ")
- endif()
- if(UNIX)
- set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}")
- endif(UNIX)
-
- # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention
- configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY)
- # Generate gudhi.pyx - Gudhi cython file
- configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY)
-
- add_custom_command(
- OUTPUT gudhi.so
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace")
-
- add_custom_target(cython ALL DEPENDS gudhi.so
- COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
-
- # For installation purpose
- # TODO(VR) : files matching pattern mechanism is copying all cython directory
- install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING
- PATTERN "*.so"
- PATTERN "*.dylib"
- PATTERN "*.pyd")
-
- # Test examples
- if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
- # Bottleneck and Alpha
- add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
- -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
+ if(CGAL_FOUND)
+ can_cgal_use_cxx11_thread_local()
+ if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
+ if(CMAKE_BUILD_TYPE MATCHES Debug)
+ add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_DEBUG}")
+ else()
+ add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_RELEASE}")
+ endif()
+ set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
+ endif()
+ # Add CGAL compilation args
+ if(CGAL_HEADER_ONLY)
+ add_gudhi_debug_info("CGAL header only version ${CGAL_VERSION}")
+ set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
+ else(CGAL_HEADER_ONLY)
+ add_gudhi_debug_info("CGAL version ${CGAL_VERSION}")
+ add_gudhi_cython_lib("${CGAL_LIBRARY}")
+ set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
+ # If CGAL is not header only, CGAL library may link with boost system,
+ if(CMAKE_BUILD_TYPE MATCHES Debug)
+ add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_DEBUG}")
+ else()
+ add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_RELEASE}")
+ endif()
+ set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
+ endif(CGAL_HEADER_ONLY)
+ # GMP and GMPXX are not required, but if present, CGAL will link with them.
+ if(GMP_FOUND)
+ add_gudhi_debug_info("GMP_LIBRARIES = ${GMP_LIBRARIES}")
+ set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
+ add_gudhi_cython_lib("${GMP_LIBRARIES}")
+ set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
+ if(GMPXX_FOUND)
+ add_gudhi_debug_info("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
+ set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
+ add_gudhi_cython_lib("${GMPXX_LIBRARIES}")
+ set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ")
+ endif(GMPXX_FOUND)
+ endif(GMP_FOUND)
+ endif(CGAL_FOUND)
+
+ # Specific for Mac
+ if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+ set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-mmacosx-version-min=10.12', ")
+ set(GUDHI_CYTHON_EXTRA_LINK_ARGS "${GUDHI_CYTHON_EXTRA_LINK_ARGS}'-mmacosx-version-min=10.12', ")
+ endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+
+ # Loop on INCLUDE_DIRECTORIES PROPERTY
+ get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES)
+ foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
+ set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ")
+ endforeach()
+ set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ")
+
+ if (TBB_FOUND AND WITH_GUDHI_USE_TBB)
+ add_gudhi_debug_info("TBB version ${TBB_INTERFACE_VERSION} found and used")
+ set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ")
+ if(CMAKE_BUILD_TYPE MATCHES Debug)
+ add_gudhi_cython_lib("${TBB_DEBUG_LIBRARY}")
+ add_gudhi_cython_lib("${TBB_MALLOC_DEBUG_LIBRARY}")
+ else()
+ add_gudhi_cython_lib("${TBB_RELEASE_LIBRARY}")
+ add_gudhi_cython_lib("${TBB_MALLOC_RELEASE_LIBRARY}")
+ endif()
+ set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ")
+ set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ")
+ endif()
- if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
- # Tangential
- add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
+ if(UNIX)
+ set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}")
+ endif(UNIX)
+
+ # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention
+ configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY)
+ # Generate gudhi.pyx - Gudhi cython file
+ configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY)
+
+ add_custom_command(
+ OUTPUT gudhi.so
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace")
+
+ add_custom_target(cython ALL DEPENDS gudhi.so
+ COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
+
+ # For installation purpose
+ # TODO(VR) : files matching pattern mechanism is copying all cython directory
+ install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING
+ PATTERN "*.so"
+ PATTERN "*.dylib"
+ PATTERN "*.pyd")
+
+ # Test examples
+ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+ # Bottleneck and Alpha
+ add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
+ -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
+
+ if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+ # Tangential
+ add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
+ --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+
+ add_gudhi_py_test(test_tangential_complex)
+
+ # Witness complex AND Subsampling
+ add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
+ add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+ endif()
+
+ # Subsampling
+ add_gudhi_py_test(test_subsampling)
+
+ endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+ if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+ # Bottleneck
+ add_test(NAME bottleneck_basic_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
- --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
- add_gudhi_py_test(test_tangential_complex)
+ add_gudhi_py_test(test_bottleneck_distance)
- # Witness complex AND Subsampling
- add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+ # Cover complex
+ file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+ file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+ file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+ add_test(NAME cover_complex_nerve_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
- --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py"
+ -f human.off -c 2 -r 10 -g 0.3)
- add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+ add_test(NAME cover_complex_coordinate_gic_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
- --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
- endif()
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py"
+ -f human.off -c 0 -v)
- # Subsampling
- add_gudhi_py_test(test_subsampling)
+ add_test(NAME cover_complex_functional_gic_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py"
+ -o lucky_cat.off
+ -f lucky_cat_PCA1 -v)
- endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
- if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
- # Bottleneck
- add_test(NAME bottleneck_basic_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
+ add_test(NAME cover_complex_voronoi_gic_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
+ -f human.off -n 700 -v)
- add_gudhi_py_test(test_bottleneck_distance)
+ add_gudhi_py_test(test_cover_complex)
+ endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
- # Cover complex
- file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
- file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
- file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
- add_test(NAME cover_complex_nerve_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py"
- -f human.off -c 2 -r 10 -g 0.3)
+ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+ # Alpha
+ add_test(NAME alpha_complex_from_points_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
- add_test(NAME cover_complex_coordinate_gic_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py"
- -f human.off -c 0 -v)
+ if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+ add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
+ endif()
- add_test(NAME cover_complex_functional_gic_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py"
- -o lucky_cat.off
- -f lucky_cat_PCA1 -v)
+ add_gudhi_py_test(test_alpha_complex)
- add_test(NAME cover_complex_voronoi_gic_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
- -f human.off -n 700 -v)
+ endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
- add_gudhi_py_test(test_cover_complex)
- endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+ # Euclidean witness
+ add_gudhi_py_test(test_euclidean_witness_complex)
- if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
- # Alpha
- add_test(NAME alpha_complex_from_points_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
+ endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
- if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
- add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
+ # Cubical
+ add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
- --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
- endif()
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
+ --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
- add_gudhi_py_test(test_alpha_complex)
-
- endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+ if(NUMPY_FOUND)
+ add_test(NAME random_cubical_complex_persistence_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
+ 10 10 10)
+ endif()
- if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
- # Euclidean witness
- add_gudhi_py_test(test_euclidean_witness_complex)
+ add_gudhi_py_test(test_cubical_complex)
- endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+ # Rips
+ if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+ add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
- # Cubical
- add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
- --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
+ add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3)
+ endif()
- if(NUMPY_FOUND)
- add_test(NAME random_cubical_complex_persistence_example_py_test
+ add_test(NAME rips_complex_from_points_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
- 10 10 10)
- endif()
+ ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
- add_gudhi_py_test(test_cubical_complex)
+ add_gudhi_py_test(test_rips_complex)
- # Rips
- if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
- add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
+ # Simplex tree
+ add_test(NAME simplex_tree_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
- --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
-
- add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
- --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3)
- endif()
-
- add_test(NAME rips_complex_from_points_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
+ ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
- add_gudhi_py_test(test_rips_complex)
+ add_gudhi_py_test(test_simplex_tree)
- # Simplex tree
- add_test(NAME simplex_tree_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
-
- add_gudhi_py_test(test_simplex_tree)
-
- # Witness
- add_test(NAME witness_complex_from_nearest_landmark_table_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
-
- add_gudhi_py_test(test_witness_complex)
-
- # Reader utils
- add_gudhi_py_test(test_reader_utils)
-
- # Documentation generation is available through sphinx - requires all modules
- if(SPHINX_PATH AND MATPLOTLIB_FOUND AND NUMPY_FOUND AND SCIPY_FOUND AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
- set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
- # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
- # Images and biblio warnings because not found on developper version
- if (GUDHI_CYTHON_PATH STREQUAL "src/cython")
- set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
- endif()
- # 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_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
- DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
- COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
-
- add_test(NAME sphinx_py_test
+ # Witness
+ add_test(NAME witness_complex_from_nearest_landmark_table_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}/doctest)
-
- endif()
-endif(CYTHON_FOUND)
+ ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
+
+ add_gudhi_py_test(test_witness_complex)
+
+ # Reader utils
+ add_gudhi_py_test(test_reader_utils)
+
+ # Documentation generation is available through sphinx - requires all modules
+ if(SPHINX_PATH)
+ if(MATPLOTLIB_FOUND)
+ if(NUMPY_FOUND)
+ if(SCIPY_FOUND)
+ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+ set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
+ # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
+ # Images and biblio warnings because not found on developper version
+ if (GUDHI_CYTHON_PATH STREQUAL "src/cython")
+ set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
+ endif()
+ # 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_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
+ DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+ COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
+
+ 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}/doctest)
+
+ # Set missing or not modules
+ set(GUDHI_MODULES ${GUDHI_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MODULES")
+ else(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+ message("++ Python documentation module will not be compiled because it requires a CGAL with Eigen3 version greater or equal than 4.8.1")
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+ endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+ else(SCIPY_FOUND)
+ message("++ Python documentation module will not be compiled because scipy was not found")
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+ endif(SCIPY_FOUND)
+ else(NUMPY_FOUND)
+ message("++ Python documentation module will not be compiled because numpy was not found")
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+ endif(NUMPY_FOUND)
+ else(MATPLOTLIB_FOUND)
+ message("++ Python documentation module will not be compiled because matplotlib was not found")
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+ endif(MATPLOTLIB_FOUND)
+ else(SPHINX_PATH)
+ message("++ Python documentation module will not be compiled because sphinx and sphinxcontrib-bibtex were not found")
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+ endif(SPHINX_PATH)
+
+
+ # Set missing or not modules
+ set(GUDHI_MODULES ${GUDHI_MODULES} "python" CACHE INTERNAL "GUDHI_MODULES")
+ else(CYTHON_FOUND)
+ message("++ Python module will not be compiled because cython was not found")
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+ endif(CYTHON_FOUND)
+else(PYTHONINTERP_FOUND)
+ message("++ Python module will not be compiled because no Python interpreter was found")
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+endif(PYTHONINTERP_FOUND)
diff --git a/src/cython/cython/nerve_gic.pyx b/src/cython/cython/nerve_gic.pyx
index 30a14d3b..5f01b379 100644
--- a/src/cython/cython/nerve_gic.pyx
+++ b/src/cython/cython/nerve_gic.pyx
@@ -38,14 +38,14 @@ cdef extern from "Nerve_gic_interface.h" namespace "Gudhi":
double compute_distance_from_confidence_level(double alpha)
void compute_distribution(int N)
double compute_p_value()
- void compute_PD()
+ vector[pair[double, double]] compute_PD()
void find_simplices()
void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree)
bool read_point_cloud(string off_file_name)
double set_automatic_resolution()
void set_color_from_coordinate(int k)
void set_color_from_file(string color_file_name)
- void set_color_from_vector(vector[double] color)
+ void set_color_from_range(vector[double] color)
void set_cover_from_file(string cover_file_name)
void set_cover_from_function()
void set_cover_from_Euclidean_Voronoi(int m)
@@ -67,6 +67,8 @@ cdef extern from "Nerve_gic_interface.h" namespace "Gudhi":
void write_info()
void plot_DOT()
void plot_OFF()
+ void set_point_cloud_from_range(vector[vector[double]] cloud)
+ void set_distances_from_range(vector[vector[double]] distance_matrix)
# CoverComplex python interface
cdef class CoverComplex:
@@ -102,6 +104,22 @@ cdef class CoverComplex:
"""
return self.thisptr != NULL
+ def set_point_cloud_from_range(self, cloud):
+ """ Reads and stores the input point cloud from a vector stored in memory.
+
+ :param cloud: Input vector containing the point cloud.
+ :type cloud: vector[vector[double]]
+ """
+ return self.thisptr.set_point_cloud_from_range(cloud)
+
+ def set_distances_from_range(self, distance_matrix):
+ """ Reads and stores the input distance matrix from a vector stored in memory.
+
+ :param distance_matrix: Input vector containing the distance matrix.
+ :type distance_matrix: vector[vector[double]]
+ """
+ return self.thisptr.set_distances_from_range(distance_matrix)
+
def compute_confidence_level_from_distance(self, distance):
"""Computes the confidence level of a specific bottleneck distance
threshold.
@@ -145,7 +163,7 @@ cdef class CoverComplex:
def compute_PD(self):
"""Computes the extended persistence diagram of the complex.
"""
- self.thisptr.compute_PD()
+ return self.thisptr.compute_PD()
def create_simplex_tree(self):
"""
@@ -162,7 +180,7 @@ cdef class CoverComplex:
self.thisptr.find_simplices()
def read_point_cloud(self, off_file):
- """Reads and stores the input point cloud.
+ """Reads and stores the input point cloud from .(n)OFF file.
:param off_file: Name of the input .OFF or .nOFF file.
:type off_file: string
@@ -206,14 +224,14 @@ cdef class CoverComplex:
else:
print("file " + color_file_name + " not found.")
- def set_color_from_vector(self, color):
+ def set_color_from_range(self, color):
"""Computes the function used to color the nodes of the simplicial
complex from a vector stored in memory.
:param color: Input vector of values.
:type color: vector[double]
"""
- self.thisptr.set_color_from_vector(color)
+ self.thisptr.set_color_from_range(color)
def set_cover_from_file(self, cover_file_name):
"""Creates the cover C from a file containing the cover elements of
diff --git a/src/cython/doc/nerve_gic_complex_sum.rst b/src/cython/doc/nerve_gic_complex_sum.rst
index 72782c7a..523c119f 100644
--- a/src/cython/doc/nerve_gic_complex_sum.rst
+++ b/src/cython/doc/nerve_gic_complex_sum.rst
@@ -1,5 +1,5 @@
================================================================= =================================== ===================================
-:Author: Mathieu Carrière :Introduced in: GUDHI 2.1.0 :Copyright: GPL v3
+:Author: Mathieu Carrière :Introduced in: GUDHI 2.3.0 :Copyright: GPL v3
:Requires: CGAL :math:`\geq` 4.8.1
================================================================= =================================== ===================================
diff --git a/src/cython/include/Alpha_complex_interface.h b/src/cython/include/Alpha_complex_interface.h
index 8cf527fc..faa059d1 100644
--- a/src/cython/include/Alpha_complex_interface.h
+++ b/src/cython/include/Alpha_complex_interface.h
@@ -60,7 +60,7 @@ class Alpha_complex_interface {
Point_d ph = alpha_complex_->get_point(vh);
for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++)
vd.push_back(*coord);
- } catch (std::out_of_range outofrange) {
+ } catch (std::out_of_range const&) {
// std::out_of_range is thrown in case not found. Other exceptions must be re-thrown
}
return vd;
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-01 02:47:13 +0000