From 05c9c0060ec8ff4cbf8619ff74724c2eea426d84 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 8 Sep 2020 16:43:36 +0200 Subject: CMake > 3.5 to use Boost targets. Compile only what is available from boost targets --- src/common/doc/installation.h | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'src/common/doc') diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 6af645e2..9df1c2f0 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -6,7 +6,7 @@ * * \section compiling Compiling * The library uses c++14 and requires Boost ≥ 1.56.0 - * and CMake ≥ 3.1. + * and CMake ≥ 3.5. * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. * * \subsection utilities Utilities and examples @@ -17,8 +17,8 @@ cd build/ cmake -DCMAKE_BUILD_TYPE=Release .. make \endverbatim * By default, examples are disabled. You can activate their compilation with - * ccmake (on Linux and Mac OSX), - * cmake-gui (on Windows) or by modifying the + * ccmake (on Linux and Mac OSX), + * cmake-gui (on Windows) or by modifying the * cmake command as follows : \verbatim cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=ON .. make \endverbatim @@ -28,7 +28,7 @@ make \endverbatim * 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 CMAKE_INSTALL_PREFIX. + * of CMAKE_INSTALL_PREFIX. * * \subsection testsuites Test suites * To test your build, run the following command in a terminal: -- cgit v1.2.3 From 5db457afb8e3214bdd83bef51198b65e53267a8c Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 23 Sep 2020 10:12:22 +0200 Subject: Add coxeter on main page --- ...manifold_tracing_on_custom_function_example.png | Bin 0 -> 419483 bytes src/common/doc/main_page.md | 28 ++++++++++++++++++++- 2 files changed, 27 insertions(+), 1 deletion(-) create mode 100644 src/Coxeter_triangulation/doc/manifold_tracing_on_custom_function_example.png (limited to 'src/common/doc') diff --git a/src/Coxeter_triangulation/doc/manifold_tracing_on_custom_function_example.png b/src/Coxeter_triangulation/doc/manifold_tracing_on_custom_function_example.png new file mode 100644 index 00000000..1edbadf5 Binary files /dev/null and b/src/Coxeter_triangulation/doc/manifold_tracing_on_custom_function_example.png differ diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md index e19af537..c58b6994 100644 --- a/src/common/doc/main_page.md +++ b/src/common/doc/main_page.md @@ -135,7 +135,7 @@ -## Filtrations and reconstructions {#FiltrationsReconstructions} +## Filtrations ### Alpha complex @@ -298,6 +298,32 @@
+## Manifold reconstructions +### Coxeter triangulation + + + + + + + + + + +
+ \image html "manifold_tracing_on_custom_function_example.png" + + Coxeter triangulation module is designed to provide tools for constructing a piecewise-linear approximation of an + \f$m\f$-dimensional smooth manifold embedded in \f$ \mathbb{R}^d \f$ using an ambient triangulation. + + Author: Siargey Kachanovich
+ Introduced in: GUDHI 3.4.0
+ Copyright: MIT [(LGPL v3)](../../licensing/)
+ Requires: \ref cgal ≥ 4.11.0 +
+ User manual: \ref coxeter_triangulation +
+ ### Tangential complex -- cgit v1.2.3 From 2bbba93e7f0837b42def9bed13a6fa790c0eabda Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Sat, 31 Oct 2020 23:39:01 +0100 Subject: s/kernel/distance/ for choose_n_farthest_points argument --- .../include/gudhi/Sparse_rips_complex.h | 14 +---- src/Subsampling/example/CMakeLists.txt | 4 +- .../example/example_choose_n_farthest_points.cpp | 2 +- .../example/example_custom_distance.cpp | 44 +++++++++++++++ src/Subsampling/example/example_custom_kernel.cpp | 63 ---------------------- .../include/gudhi/choose_n_farthest_points.h | 26 +++++---- .../test/test_choose_n_farthest_points.cpp | 20 +++---- src/Witness_complex/doc/Witness_complex_doc.h | 6 +-- .../example/example_strong_witness_complex_off.cpp | 3 +- .../example/example_witness_complex_off.cpp | 3 +- .../example/example_witness_complex_sphere.cpp | 2 +- .../utilities/strong_witness_persistence.cpp | 3 +- .../utilities/weak_witness_persistence.cpp | 3 +- src/common/doc/examples.h | 2 +- src/common/doc/installation.h | 8 +-- src/python/include/Subsampling_interface.h | 10 ++-- 16 files changed, 93 insertions(+), 120 deletions(-) create mode 100644 src/Subsampling/example/example_custom_distance.cpp delete mode 100644 src/Subsampling/example/example_custom_kernel.cpp (limited to 'src/common/doc') diff --git a/src/Rips_complex/include/gudhi/Sparse_rips_complex.h b/src/Rips_complex/include/gudhi/Sparse_rips_complex.h index 1b250818..a5501004 100644 --- a/src/Rips_complex/include/gudhi/Sparse_rips_complex.h +++ b/src/Rips_complex/include/gudhi/Sparse_rips_complex.h @@ -67,8 +67,7 @@ class Sparse_rips_complex { : epsilon_(epsilon) { GUDHI_CHECK(epsilon > 0, "epsilon must be positive"); auto dist_fun = [&](Vertex_handle i, Vertex_handle j) { return distance(points[i], points[j]); }; - Ker kernel(dist_fun); - subsampling::choose_n_farthest_points(kernel, boost::irange(0, boost::size(points)), -1, -1, + subsampling::choose_n_farthest_points(dist_fun, boost::irange(0, boost::size(points)), -1, -1, std::back_inserter(sorted_points), std::back_inserter(params)); compute_sparse_graph(dist_fun, epsilon, mini, maxi); } @@ -128,17 +127,6 @@ class Sparse_rips_complex { } private: - // choose_n_farthest_points wants the distance function in this form... - template - struct Ker { - typedef std::size_t Point_d; // index into point range - Ker(Distance& d) : dist(d) {} - // Despite the name, this is not squared... - typedef Distance Squared_distance_d; - Squared_distance_d& squared_distance_d_object() const { return dist; } - Distance& dist; - }; - // PointRange must be random access. template void compute_sparse_graph(Distance& dist, double epsilon, Filtration_value mini, Filtration_value maxi) { diff --git a/src/Subsampling/example/CMakeLists.txt b/src/Subsampling/example/CMakeLists.txt index 28aab103..fb6875e1 100644 --- a/src/Subsampling/example/CMakeLists.txt +++ b/src/Subsampling/example/CMakeLists.txt @@ -3,7 +3,7 @@ project(Subsampling_examples) if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_executable(Subsampling_example_pick_n_random_points example_pick_n_random_points.cpp) add_executable(Subsampling_example_choose_n_farthest_points example_choose_n_farthest_points.cpp) - add_executable(Subsampling_example_custom_kernel example_custom_kernel.cpp) + add_executable(Subsampling_example_custom_distance example_custom_distance.cpp) add_executable(Subsampling_example_sparsify_point_set example_sparsify_point_set.cpp) target_link_libraries(Subsampling_example_sparsify_point_set ${CGAL_LIBRARY}) @@ -16,7 +16,7 @@ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) install(TARGETS Subsampling_example_pick_n_random_points DESTINATION bin) install(TARGETS Subsampling_example_choose_n_farthest_points DESTINATION bin) - install(TARGETS Subsampling_example_custom_kernel DESTINATION bin) + install(TARGETS Subsampling_example_custom_distance DESTINATION bin) install(TARGETS Subsampling_example_sparsify_point_set DESTINATION bin) endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Subsampling/example/example_choose_n_farthest_points.cpp b/src/Subsampling/example/example_choose_n_farthest_points.cpp index 27cf5d4e..e8b3ce2d 100644 --- a/src/Subsampling/example/example_choose_n_farthest_points.cpp +++ b/src/Subsampling/example/example_choose_n_farthest_points.cpp @@ -20,7 +20,7 @@ int main(void) { K k; std::vector results; - Gudhi::subsampling::choose_n_farthest_points(k, points, 100, + Gudhi::subsampling::choose_n_farthest_points(k.squared_distance_d_object(), points, 100, Gudhi::subsampling::random_starting_point, std::back_inserter(results)); std::clog << "Before sparsification: " << points.size() << " points.\n"; diff --git a/src/Subsampling/example/example_custom_distance.cpp b/src/Subsampling/example/example_custom_distance.cpp new file mode 100644 index 00000000..3325b12d --- /dev/null +++ b/src/Subsampling/example/example_custom_distance.cpp @@ -0,0 +1,44 @@ +#include + +#include +#include +#include + + +typedef unsigned Point; + +/* The class Distance contains a distance function defined on the set of points {0, 1, 2, 3} + * and computes a distance according to the matrix: + * 0 1 2 4 + * 1 0 4 2 + * 2 4 0 1 + * 4 2 1 0 + */ +class Distance { + private: + std::vector> matrix_; + + public: + Distance() { + matrix_.push_back({0, 1, 2, 4}); + matrix_.push_back({1, 0, 4, 2}); + matrix_.push_back({2, 4, 0, 1}); + matrix_.push_back({4, 2, 1, 0}); + } + + double operator()(Point p1, Point p2) const { + return matrix_[p1][p2]; + } +}; + +int main(void) { + std::vector points = {0, 1, 2, 3}; + std::vector results; + + Gudhi::subsampling::choose_n_farthest_points(Distance(), points, 2, + Gudhi::subsampling::random_starting_point, + std::back_inserter(results)); + std::clog << "Before sparsification: " << points.size() << " points.\n"; + std::clog << "After sparsification: " << results.size() << " points.\n"; + std::clog << "Result table: {" << results[0] << "," << results[1] << "}\n"; +} diff --git a/src/Subsampling/example/example_custom_kernel.cpp b/src/Subsampling/example/example_custom_kernel.cpp deleted file mode 100644 index 535bf42a..00000000 --- a/src/Subsampling/example/example_custom_kernel.cpp +++ /dev/null @@ -1,63 +0,0 @@ -#include - -#include -#include -#include - - -/* The class Kernel contains a distance function defined on the set of points {0, 1, 2, 3} - * and computes a distance according to the matrix: - * 0 1 2 4 - * 1 0 4 2 - * 2 4 0 1 - * 4 2 1 0 - */ -class Kernel { - public: - typedef double FT; - typedef unsigned Point_d; - - // Class Squared_distance_d - class Squared_distance_d { - private: - std::vector> matrix_; - - public: - Squared_distance_d() { - matrix_.push_back(std::vector({0, 1, 2, 4})); - matrix_.push_back(std::vector({1, 0, 4, 2})); - matrix_.push_back(std::vector({2, 4, 0, 1})); - matrix_.push_back(std::vector({4, 2, 1, 0})); - } - - FT operator()(Point_d p1, Point_d p2) { - return matrix_[p1][p2]; - } - }; - - // Constructor - Kernel() {} - - // Object of type Squared_distance_d - Squared_distance_d squared_distance_d_object() const { - return Squared_distance_d(); - } -}; - -int main(void) { - typedef Kernel K; - typedef typename K::Point_d Point_d; - - K k; - std::vector points = {0, 1, 2, 3}; - std::vector results; - - Gudhi::subsampling::choose_n_farthest_points(k, points, 2, - Gudhi::subsampling::random_starting_point, - std::back_inserter(results)); - std::clog << "Before sparsification: " << points.size() << " points.\n"; - std::clog << "After sparsification: " << results.size() << " points.\n"; - std::clog << "Result table: {" << results[0] << "," << results[1] << "}\n"; - - return 0; -} diff --git a/src/Subsampling/include/gudhi/choose_n_farthest_points.h b/src/Subsampling/include/gudhi/choose_n_farthest_points.h index b70af8a0..561dcf3e 100644 --- a/src/Subsampling/include/gudhi/choose_n_farthest_points.h +++ b/src/Subsampling/include/gudhi/choose_n_farthest_points.h @@ -38,33 +38,33 @@ enum : std::size_t { * \ingroup subsampling * \brief Subsample by a greedy strategy of iteratively adding the farthest point from the * current chosen point set to the subsampling. - * The iteration starts with the landmark `starting point` or, if `starting point==random_starting_point`, with a random landmark. - * \tparam Kernel must provide a type Kernel::Squared_distance_d which is a model of the - * concept Kernel_d::Squared_distance_d (despite the name, taken from CGAL, this can be any kind of metric or proximity measure). - * It must also contain a public member `squared_distance_d_object()` that returns an object of this type. - * \tparam Point_range Range whose value type is Kernel::Point_d. It must provide random-access - * via `operator[]` and the points should be stored contiguously in memory. - * \tparam PointOutputIterator Output iterator whose value type is Kernel::Point_d. + * The iteration starts with the landmark `starting point` or, if `starting point==random_starting_point`, + * with a random landmark. + * \tparam Distance must provide an operator() that takes 2 points (value type of the range) + * and returns their distance (or some more general proximity measure). + * \tparam Point_range Random access range of points. + * \tparam PointOutputIterator Output iterator whose value type is the point type. * \tparam DistanceOutputIterator Output iterator for distances. * \details It chooses `final_size` points from a random access range * `input_pts` (or the number of distinct points if `final_size` is larger) * and outputs them in the output iterator `output_it`. It also * outputs the distance from each of those points to the set of previous * points in `dist_it`. - * @param[in] k A kernel object. + * @param[in] dist A distance function. * @param[in] input_pts Const reference to the input points. * @param[in] final_size The size of the subsample to compute. * @param[in] starting_point The seed in the farthest point algorithm. * @param[out] output_it The output iterator for points. * @param[out] dist_it The optional output iterator for distances. + * + * \warning Older versions of this function took a CGAL kernel as argument. Users need to replace `k` with `k.squared_distance_d_object()` in the first argument of every call to `choose_n_farthest_points`. * */ -template < typename Kernel, +template < typename Distance, typename Point_range, typename PointOutputIterator, typename DistanceOutputIterator = Null_output_iterator> -void choose_n_farthest_points(Kernel const &k, +void choose_n_farthest_points(Distance dist, Point_range const &input_pts, std::size_t final_size, std::size_t starting_point, @@ -86,8 +86,6 @@ void choose_n_farthest_points(Kernel const &k, starting_point = dis(gen); } - typename Kernel::Squared_distance_d sqdist = k.squared_distance_d_object(); - std::size_t current_number_of_landmarks = 0; // counter for landmarks const double infty = std::numeric_limits::infinity(); // infinity (see next entry) std::vector< double > dist_to_L(nb_points, infty); // vector of current distances to L from input_pts @@ -100,7 +98,7 @@ void choose_n_farthest_points(Kernel const &k, *dist_it++ = dist_to_L[curr_max_w]; std::size_t i = 0; for (auto&& p : input_pts) { - double curr_dist = sqdist(p, input_pts[curr_max_w]); + double curr_dist = dist(p, input_pts[curr_max_w]); if (curr_dist < dist_to_L[i]) dist_to_L[i] = curr_dist; ++i; diff --git a/src/Subsampling/test/test_choose_n_farthest_points.cpp b/src/Subsampling/test/test_choose_n_farthest_points.cpp index b318d58e..94793295 100644 --- a/src/Subsampling/test/test_choose_n_farthest_points.cpp +++ b/src/Subsampling/test/test_choose_n_farthest_points.cpp @@ -44,7 +44,8 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(test_choose_farthest_point, Kernel, list_of_tested landmarks.clear(); Kernel k; - Gudhi::subsampling::choose_n_farthest_points(k, points, 100, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks)); + auto d = k.squared_distance_d_object(); + Gudhi::subsampling::choose_n_farthest_points(d, points, 100, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks)); BOOST_CHECK(landmarks.size() == 100); for (auto landmark : landmarks) @@ -61,32 +62,33 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(test_choose_farthest_point_limits, Kernel, list_of std::vector< FT > distances; landmarks.clear(); Kernel k; + auto d = k.squared_distance_d_object(); // Choose -1 farthest points in an empty point cloud - Gudhi::subsampling::choose_n_farthest_points(k, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); + Gudhi::subsampling::choose_n_farthest_points(d, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); BOOST_CHECK(landmarks.size() == 0); landmarks.clear(); distances.clear(); // Choose 0 farthest points in an empty point cloud - Gudhi::subsampling::choose_n_farthest_points(k, points, 0, -1, std::back_inserter(landmarks), std::back_inserter(distances)); + Gudhi::subsampling::choose_n_farthest_points(d, points, 0, -1, std::back_inserter(landmarks), std::back_inserter(distances)); BOOST_CHECK(landmarks.size() == 0); landmarks.clear(); distances.clear(); // Choose 1 farthest points in an empty point cloud - Gudhi::subsampling::choose_n_farthest_points(k, points, 1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); + Gudhi::subsampling::choose_n_farthest_points(d, points, 1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); BOOST_CHECK(landmarks.size() == 0); landmarks.clear(); distances.clear(); std::vector point({0.0, 0.0, 0.0, 0.0}); points.emplace_back(point.begin(), point.end()); // Choose -1 farthest points in a one point cloud - Gudhi::subsampling::choose_n_farthest_points(k, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); + Gudhi::subsampling::choose_n_farthest_points(d, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); BOOST_CHECK(landmarks.size() == 1 && distances.size() == 1); BOOST_CHECK(distances[0] == std::numeric_limits::infinity()); landmarks.clear(); distances.clear(); // Choose 0 farthest points in a one point cloud - Gudhi::subsampling::choose_n_farthest_points(k, points, 0, -1, std::back_inserter(landmarks), std::back_inserter(distances)); + Gudhi::subsampling::choose_n_farthest_points(d, points, 0, -1, std::back_inserter(landmarks), std::back_inserter(distances)); BOOST_CHECK(landmarks.size() == 0 && distances.size() == 0); landmarks.clear(); distances.clear(); // Choose 1 farthest points in a one point cloud - Gudhi::subsampling::choose_n_farthest_points(k, points, 1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); + Gudhi::subsampling::choose_n_farthest_points(d, points, 1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); BOOST_CHECK(landmarks.size() == 1 && distances.size() == 1); BOOST_CHECK(distances[0] == std::numeric_limits::infinity()); landmarks.clear(); distances.clear(); @@ -94,7 +96,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(test_choose_farthest_point_limits, Kernel, list_of std::vector point2({1.0, 0.0, 0.0, 0.0}); points.emplace_back(point2.begin(), point2.end()); // Choose all farthest points among 2 points - Gudhi::subsampling::choose_n_farthest_points(k, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); + Gudhi::subsampling::choose_n_farthest_points(d, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); BOOST_CHECK(landmarks.size() == 2 && distances.size() == 2); BOOST_CHECK(distances[0] == std::numeric_limits::infinity()); BOOST_CHECK(distances[1] == 1); @@ -102,7 +104,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(test_choose_farthest_point_limits, Kernel, list_of // Ignore duplicated points points.emplace_back(point.begin(), point.end()); - Gudhi::subsampling::choose_n_farthest_points(k, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); + Gudhi::subsampling::choose_n_farthest_points(d, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); BOOST_CHECK(landmarks.size() == 2 && distances.size() == 2); BOOST_CHECK(distances[0] == std::numeric_limits::infinity()); BOOST_CHECK(distances[1] == 1); diff --git a/src/Witness_complex/doc/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h index 62203054..202f4539 100644 --- a/src/Witness_complex/doc/Witness_complex_doc.h +++ b/src/Witness_complex/doc/Witness_complex_doc.h @@ -92,11 +92,11 @@ int main(int argc, char * const argv[]) { // Choose landmarks (one can choose either of the two methods below) // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); - Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks)); + Gudhi::subsampling::choose_n_farthest_points(K().squared_distance_d_object(), point_vector, nbL, + Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks)); // Compute witness complex - Witness_complex witness_complex(landmarks, - point_vector); + Witness_complex witness_complex(landmarks, point_vector); witness_complex.create_complex(simplex_tree, alpha2, lim_dim); } diff --git a/src/Witness_complex/example/example_strong_witness_complex_off.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp index 583a04ab..2bb135bf 100644 --- a/src/Witness_complex/example/example_strong_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp @@ -43,7 +43,8 @@ int main(int argc, char* const argv[]) { // Choose landmarks (decomment one of the following two lines) // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); - Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point, + Gudhi::subsampling::choose_n_farthest_points(K().squared_distance_d_object(), point_vector, + nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks)); // Compute witness complex diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp index 3635da78..e1384c73 100644 --- a/src/Witness_complex/example/example_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_witness_complex_off.cpp @@ -47,7 +47,8 @@ int main(int argc, char * const argv[]) { // Choose landmarks (decomment one of the following two lines) // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); - Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks)); + Gudhi::subsampling::choose_n_farthest_points(K().squared_distance_d_object(), point_vector, nbL, + Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks)); // Compute witness complex start = clock(); diff --git a/src/Witness_complex/example/example_witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp index 78d5db4f..12a56de4 100644 --- a/src/Witness_complex/example/example_witness_complex_sphere.cpp +++ b/src/Witness_complex/example/example_witness_complex_sphere.cpp @@ -53,7 +53,7 @@ int main(int argc, char* const argv[]) { // Choose landmarks start = clock(); // Gudhi::subsampling::pick_n_random_points(point_vector, number_of_landmarks, std::back_inserter(landmarks)); - Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, number_of_landmarks, + Gudhi::subsampling::choose_n_farthest_points(K().squared_distance_d_object(), point_vector, number_of_landmarks, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks)); diff --git a/src/Witness_complex/utilities/strong_witness_persistence.cpp b/src/Witness_complex/utilities/strong_witness_persistence.cpp index 1f61c77c..614de0d4 100644 --- a/src/Witness_complex/utilities/strong_witness_persistence.cpp +++ b/src/Witness_complex/utilities/strong_witness_persistence.cpp @@ -61,7 +61,8 @@ int main(int argc, char* argv[]) { // Choose landmarks (decomment one of the following two lines) // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); - Gudhi::subsampling::choose_n_farthest_points(K(), witnesses, nbL, Gudhi::subsampling::random_starting_point, + Gudhi::subsampling::choose_n_farthest_points(K().squared_distance_d_object(), witnesses, nbL, + Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks)); // Compute witness complex diff --git a/src/Witness_complex/utilities/weak_witness_persistence.cpp b/src/Witness_complex/utilities/weak_witness_persistence.cpp index 93050af5..5ea31d6b 100644 --- a/src/Witness_complex/utilities/weak_witness_persistence.cpp +++ b/src/Witness_complex/utilities/weak_witness_persistence.cpp @@ -61,7 +61,8 @@ int main(int argc, char* argv[]) { // Choose landmarks (decomment one of the following two lines) // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); - Gudhi::subsampling::choose_n_farthest_points(K(), witnesses, nbL, Gudhi::subsampling::random_starting_point, + Gudhi::subsampling::choose_n_farthest_points(K().squared_distance_d_object(), witnesses, nbL, + Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks)); // Compute witness complex diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h index c19b3444..474f8699 100644 --- a/src/common/doc/examples.h +++ b/src/common/doc/examples.h @@ -42,7 +42,7 @@ * @example Persistence_representations/persistence_landscape.cpp * @example Tangential_complex/example_basic.cpp * @example Tangential_complex/example_with_perturb.cpp - * @example Subsampling/example_custom_kernel.cpp + * @example Subsampling/example_custom_distance.cpp * @example Subsampling/example_choose_n_farthest_points.cpp * @example Subsampling/example_sparsify_point_set.cpp * @example Subsampling/example_pick_n_random_points.cpp diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 9df1c2f0..a6b9292b 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -113,8 +113,8 @@ make doxygen * Spatial_searching/example_spatial_searching.cpp * \li * Subsampling/example_choose_n_farthest_points.cpp - * \li - * Subsampling/example_custom_kernel.cpp + * \li + * Subsampling/example_custom_distance.cpp * \li * Subsampling/example_pick_n_random_points.cpp * \li @@ -153,8 +153,8 @@ make doxygen * Spatial_searching/example_spatial_searching.cpp * \li * Subsampling/example_choose_n_farthest_points.cpp - * \li - * Subsampling/example_custom_kernel.cpp + * \li + * Subsampling/example_custom_distance.cpp * \li * Subsampling/example_pick_n_random_points.cpp * \li diff --git a/src/python/include/Subsampling_interface.h b/src/python/include/Subsampling_interface.h index cdda851f..6aee7231 100644 --- a/src/python/include/Subsampling_interface.h +++ b/src/python/include/Subsampling_interface.h @@ -11,6 +11,7 @@ #ifndef INCLUDE_SUBSAMPLING_INTERFACE_H_ #define INCLUDE_SUBSAMPLING_INTERFACE_H_ +#include #include #include #include @@ -27,14 +28,13 @@ namespace subsampling { using Subsampling_dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; using Subsampling_point_d = Subsampling_dynamic_kernel::Point_d; -using Subsampling_ft = Subsampling_dynamic_kernel::FT; // ------ choose_n_farthest_points ------ std::vector> subsampling_n_farthest_points(const std::vector>& points, unsigned nb_points) { std::vector> landmarks; - Subsampling_dynamic_kernel k; - choose_n_farthest_points(k, points, nb_points, random_starting_point, std::back_inserter(landmarks)); + choose_n_farthest_points(Euclidean_distance(), points, nb_points, + random_starting_point, std::back_inserter(landmarks)); return landmarks; } @@ -42,8 +42,8 @@ std::vector> subsampling_n_farthest_points(const std::vector std::vector> subsampling_n_farthest_points(const std::vector>& points, unsigned nb_points, unsigned starting_point) { std::vector> landmarks; - Subsampling_dynamic_kernel k; - choose_n_farthest_points(k, points, nb_points, starting_point, std::back_inserter(landmarks)); + choose_n_farthest_points(Euclidean_distance(), points, nb_points, + starting_point, std::back_inserter(landmarks)); return landmarks; } -- cgit v1.2.3 From 20c50414163aabe6216c638b25c9568cfd1db458 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Sun, 1 Nov 2020 21:04:21 +0100 Subject: The example does not need CGAL/eigen anymore. I had done a search and replace without checking. I don't understand why there are "install" directives for examples... --- src/Subsampling/example/CMakeLists.txt | 5 +++-- src/common/doc/installation.h | 4 ---- 2 files changed, 3 insertions(+), 6 deletions(-) (limited to 'src/common/doc') diff --git a/src/Subsampling/example/CMakeLists.txt b/src/Subsampling/example/CMakeLists.txt index fb6875e1..bb02b37d 100644 --- a/src/Subsampling/example/CMakeLists.txt +++ b/src/Subsampling/example/CMakeLists.txt @@ -3,7 +3,6 @@ project(Subsampling_examples) if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_executable(Subsampling_example_pick_n_random_points example_pick_n_random_points.cpp) add_executable(Subsampling_example_choose_n_farthest_points example_choose_n_farthest_points.cpp) - add_executable(Subsampling_example_custom_distance example_custom_distance.cpp) add_executable(Subsampling_example_sparsify_point_set example_sparsify_point_set.cpp) target_link_libraries(Subsampling_example_sparsify_point_set ${CGAL_LIBRARY}) @@ -16,7 +15,9 @@ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) install(TARGETS Subsampling_example_pick_n_random_points DESTINATION bin) install(TARGETS Subsampling_example_choose_n_farthest_points DESTINATION bin) - install(TARGETS Subsampling_example_custom_distance DESTINATION bin) install(TARGETS Subsampling_example_sparsify_point_set DESTINATION bin) endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + +add_executable(Subsampling_example_custom_distance example_custom_distance.cpp) +install(TARGETS Subsampling_example_custom_distance DESTINATION bin) diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index a6b9292b..c2e63a24 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -113,8 +113,6 @@ make doxygen * Spatial_searching/example_spatial_searching.cpp * \li * Subsampling/example_choose_n_farthest_points.cpp - * \li - * Subsampling/example_custom_distance.cpp * \li * Subsampling/example_pick_n_random_points.cpp * \li @@ -153,8 +151,6 @@ make doxygen * Spatial_searching/example_spatial_searching.cpp * \li * Subsampling/example_choose_n_farthest_points.cpp - * \li - * Subsampling/example_custom_distance.cpp * \li * Subsampling/example_pick_n_random_points.cpp * \li -- cgit v1.2.3 From 29fa56b6768d7314fcddf39d7681aa6a82417b4e Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 21 Apr 2021 10:08:19 +0200 Subject: cell complex is only for coxeter. eigen is required for coxeter, not cgal --- src/Coxeter_triangulation/doc/intro_coxeter_triangulation.h | 5 +++++ src/Coxeter_triangulation/include/gudhi/Cell_complex.h | 10 +++------- src/common/doc/main_page.md | 2 +- 3 files changed, 9 insertions(+), 8 deletions(-) (limited to 'src/common/doc') diff --git a/src/Coxeter_triangulation/doc/intro_coxeter_triangulation.h b/src/Coxeter_triangulation/doc/intro_coxeter_triangulation.h index 3316bd81..99239e3a 100644 --- a/src/Coxeter_triangulation/doc/intro_coxeter_triangulation.h +++ b/src/Coxeter_triangulation/doc/intro_coxeter_triangulation.h @@ -166,6 +166,8 @@ The base function classes above can be composed or modified into new functions u The type of \f$T\f$ is required to be a model of the concept \ref Gudhi::coxeter_triangulation::TriangulationForManifoldTracing "TriangulationForManifoldTracing". +It is also possible to implement your own function as detailed in this \ref exampleswithcustomfunction. + \section cellcomplex Cell complex construction The output of the manifold tracing algorithm can be transformed into the Hasse diagram of a cell complex that @@ -194,6 +196,9 @@ triangulation. \li The method \ref Gudhi::coxeter_triangulation::Cell_complex::cell_point_map() "cell_point_map()" returns a map from the vertex cells in the cell complex to their Cartesian coordinates. +The use and interfaces of this \ref Gudhi::coxeter_triangulation::Cell_complex "Cell_complex" is limited to the +Coxeter_triangulation implementation. + \section example Examples \subsection examplewithoutboundaries Basic example without boundaries diff --git a/src/Coxeter_triangulation/include/gudhi/Cell_complex.h b/src/Coxeter_triangulation/include/gudhi/Cell_complex.h index b386e369..219f525b 100644 --- a/src/Coxeter_triangulation/include/gudhi/Cell_complex.h +++ b/src/Coxeter_triangulation/include/gudhi/Cell_complex.h @@ -25,18 +25,14 @@ namespace Gudhi { namespace coxeter_triangulation { -/** - * \ingroup coxeter_triangulation - */ - /** \class Cell_complex * \brief A class that constructs the cell complex from the output provided by the class - * Gudhi::Manifold_tracing. + * \ref Gudhi::coxeter_triangulation::Manifold_tracing. + * + * The use and interfaces of this cell complex is limited to the \ref coxeter_triangulation implementation. * * \tparam Out_simplex_map_ The type of a map from a simplex type that is a * model of SimplexInCoxeterTriangulation to Eigen::VectorXd. - * - * \ingroup coxeter_triangulation */ template class Cell_complex { diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md index c58b6994..17354179 100644 --- a/src/common/doc/main_page.md +++ b/src/common/doc/main_page.md @@ -314,7 +314,7 @@ Author: Siargey Kachanovich
Introduced in: GUDHI 3.4.0
Copyright: MIT [(LGPL v3)](../../licensing/)
- Requires: \ref cgal ≥ 4.11.0 + Requires: \ref eigen ≥ 3.1.0 -- cgit v1.2.3 From 1d7011f32573bb617894a3f263e2537c1f3a8649 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 22 Apr 2021 09:28:45 +0200 Subject: Add examples in doc and removes TBB link as not required by coxeter --- src/Coxeter_triangulation/example/CMakeLists.txt | 9 --------- src/Coxeter_triangulation/test/CMakeLists.txt | 3 --- src/common/doc/examples.h | 3 +++ src/common/doc/installation.h | 8 ++++++++ 4 files changed, 11 insertions(+), 12 deletions(-) (limited to 'src/common/doc') diff --git a/src/Coxeter_triangulation/example/CMakeLists.txt b/src/Coxeter_triangulation/example/CMakeLists.txt index 840e24e4..7f81c599 100644 --- a/src/Coxeter_triangulation/example/CMakeLists.txt +++ b/src/Coxeter_triangulation/example/CMakeLists.txt @@ -5,24 +5,15 @@ if (NOT EIGEN3_VERSION VERSION_LESS 3.1.0) if (NOT CGAL_VERSION VERSION_LESS 4.11.0) add_executable ( Coxeter_triangulation_manifold_tracing_flat_torus_with_boundary_example manifold_tracing_flat_torus_with_boundary.cpp ) target_link_libraries(Coxeter_triangulation_manifold_tracing_flat_torus_with_boundary_example ${CGAL_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(Coxeter_triangulation_manifold_tracing_flat_torus_with_boundary_example ${TBB_LIBRARIES}) - endif() add_test(NAME Coxeter_triangulation_manifold_tracing_flat_torus_with_boundary_example COMMAND $) endif() add_executable ( Coxeter_triangulation_manifold_tracing_custom_function_example manifold_tracing_custom_function.cpp ) - if (TBB_FOUND) - target_link_libraries(Coxeter_triangulation_manifold_tracing_custom_function_example ${TBB_LIBRARIES}) - endif() add_test(NAME Coxeter_triangulation_manifold_tracing_custom_function_example COMMAND $) add_executable ( Coxeter_triangulation_cell_complex_from_basic_circle_manifold_example cell_complex_from_basic_circle_manifold.cpp ) - if (TBB_FOUND) - target_link_libraries(Coxeter_triangulation_cell_complex_from_basic_circle_manifold_example ${TBB_LIBRARIES}) - endif() add_test(NAME Coxeter_triangulation_cell_complex_from_basic_circle_manifold_example COMMAND $) endif() \ No newline at end of file diff --git a/src/Coxeter_triangulation/test/CMakeLists.txt b/src/Coxeter_triangulation/test/CMakeLists.txt index 3da2410f..74ded91e 100644 --- a/src/Coxeter_triangulation/test/CMakeLists.txt +++ b/src/Coxeter_triangulation/test/CMakeLists.txt @@ -26,8 +26,5 @@ if (NOT EIGEN3_VERSION VERSION_LESS 3.1.0) gudhi_add_boost_test(Coxeter_triangulation_manifold_tracing_test) add_executable ( Coxeter_triangulation_cell_complex_test cell_complex_test.cpp ) - if (TBB_FOUND) - target_link_libraries(Coxeter_triangulation_cell_complex_test ${TBB_LIBRARIES}) - endif() gudhi_add_boost_test(Coxeter_triangulation_cell_complex_test) endif() \ No newline at end of file diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h index 474f8699..a8548f6a 100644 --- a/src/common/doc/examples.h +++ b/src/common/doc/examples.h @@ -92,5 +92,8 @@ * @example Persistence_representations/persistence_landscapes/create_landscapes.cpp * @example Persistence_representations/persistence_landscapes/compute_distance_of_landscapes.cpp * @example Persistence_representations/persistence_landscapes/plot_landscapes.cpp + * @example Coxeter_triangulation/cell_complex_from_basic_circle_manifold.cpp + * @example Coxeter_triangulation/manifold_tracing_custom_function.cpp + * @example Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp */ diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index c2e63a24..c0e36a59 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -125,6 +125,8 @@ make doxygen * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp * \li * Alpha_complex/alpha_complex_3d_persistence.cpp + * \li + * Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp * * \subsection eigen Eigen * Some GUDHI modules (cf. \ref main_page "modules list"), and few examples require @@ -169,6 +171,12 @@ make doxygen * Witness_complex/example_witness_complex_off.cpp * \li * Witness_complex/example_witness_complex_sphere.cpp + * \li + * Coxeter_triangulation/cell_complex_from_basic_circle_manifold.cpp + * \li + * Coxeter_triangulation/manifold_tracing_custom_function.cpp + * \li + * Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp * * \subsection tbb Threading Building Blocks * Intel® TBB lets you easily write parallel -- cgit v1.2.3 From 154596a39b2b26c90e46ec851b8f05ea08fa47d4 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 27 Apr 2021 09:17:53 +0200 Subject: Remove make install target from python and rewrite documentation accordingly --- src/common/doc/installation.h | 4 ++++ src/python/CMakeLists.txt | 2 -- src/python/doc/installation.rst | 14 ++++---------- 3 files changed, 8 insertions(+), 12 deletions(-) (limited to 'src/common/doc') diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index c2e63a24..ce393c38 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -30,6 +30,10 @@ make \endverbatim * This action may require to be in the sudoer or administrator of the machine in function of the operating system and * of CMAKE_INSTALL_PREFIX. * + * \note Python module will be compiled by the `make` command, but `make install` will not install it. Please refer to + * the Python + * module installation documentation. + * * \subsection testsuites Test suites * To test your build, run the following command in a terminal: * \verbatim make test \endverbatim diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 73303a24..a1440cbc 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -274,8 +274,6 @@ if(PYTHONINTERP_FOUND) add_custom_target(python ALL DEPENDS gudhi.so COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests") - install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install)") - set(GUDHI_PYTHON_PATH_ENV "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}:$ENV{PYTHONPATH}") # Documentation generation is available through sphinx - requires all modules # Make it first as sphinx test is by far the longest test which is nice when testing in parallel diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 66efe45a..2881055f 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -99,20 +99,14 @@ Or install it definitely in your Python packages folder: .. code-block:: bash cd /path-to-gudhi/build/python - # May require sudo or administrator privileges - make install + python setup.py install # add --user to the command if you do not have the permission + # Or 'pip install .' .. note:: - :code:`make install` is only a - `CMake custom targets `_ - to shortcut :code:`python setup.py install` command. It does not take into account :code:`CMAKE_INSTALL_PREFIX`. - But one can use :code:`python setup.py install ...` specific options in the python directory: - -.. code-block:: bash - - python setup.py install --prefix /home/gudhi # Install in /home/gudhi directory + But one can use + `alternate location installation `_. Test suites =========== -- cgit v1.2.3 From ce73a29d4fee67b7d20c213df81edf57b0de8770 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 27 Apr 2021 17:41:15 +0200 Subject: Doxygen documentation improvement --- .circleci/config.yml | 9 +- .../for_maintainers/new_gudhi_version_creation.md | 9 +- src/Alpha_complex/doc/Intro_alpha_complex.h | 14 +- .../doc/Intro_bottleneck_distance.h | 2 +- src/Cech_complex/doc/Intro_cech_complex.h | 6 +- src/Collapse/doc/intro_edge_collapse.h | 4 +- src/Doxyfile.in | 44 ++--- src/Nerve_GIC/doc/Intro_graph_induced_complex.h | 10 +- .../doc/Intro_persistent_cohomology.h | 14 +- src/Rips_complex/doc/Intro_rips_complex.h | 24 +-- src/Simplex_tree/doc/Intro_simplex_tree.h | 8 +- .../doc/Intro_spatial_searching.h | 2 +- src/Subsampling/doc/Intro_subsampling.h | 6 +- .../doc/Intro_tangential_complex.h | 4 +- src/Witness_complex/doc/Witness_complex_doc.h | 4 +- src/cmake/modules/GUDHI_doxygen_target.cmake | 47 +++++- src/cmake/modules/GUDHI_user_version_target.cmake | 11 +- src/common/doc/examples.h | 184 +++++++++++---------- src/common/doc/installation.h | 157 +++++++++--------- src/common/include/gudhi/Points_3D_off_io.h | 4 +- src/common/include/gudhi/Points_off_io.h | 4 +- 21 files changed, 302 insertions(+), 265 deletions(-) (limited to 'src/common/doc') diff --git a/.circleci/config.yml b/.circleci/config.yml index 7fa9ae05..f6a875dd 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -90,10 +90,15 @@ jobs: mkdir build cd build cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF -DUSER_VERSION_DIR=version .. + make user_version + cd version + mkdir build + cd build + cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF .. make doxygen 2>&1 | tee dox.log grep warning dox.log - cp dox.log version/doc/html/ - cp -R version/doc/html /tmp/doxygen + cp dox.log html/ + cp -R html /tmp/doxygen - store_artifacts: path: /tmp/doxygen diff --git a/.github/for_maintainers/new_gudhi_version_creation.md b/.github/for_maintainers/new_gudhi_version_creation.md index aadfae7d..d6c4cdd3 100644 --- a/.github/for_maintainers/new_gudhi_version_creation.md +++ b/.github/for_maintainers/new_gudhi_version_creation.md @@ -34,16 +34,21 @@ make -j 4 all && ctest -j 4 --output-on-failure ## Create the documentation ```bash mkdir gudhi.doc.@GUDHI_VERSION@ -make doxygen 2>&1 | tee dox.log && grep warning dox.log ``` ***[Check there are no error and the warnings]*** ```bash -cp -R gudhi.@GUDHI_VERSION@/doc/html gudhi.doc.@GUDHI_VERSION@/cpp cd gudhi.@GUDHI_VERSION@ rm -rf build; mkdir build; cd build cmake -DCMAKE_BUILD_TYPE=Release -DCGAL_DIR=/your/path/to/CGAL -DWITH_GUDHI_EXAMPLE=ON -DPython_ADDITIONAL_VERSIONS=3 .. +make doxygen 2>&1 | tee dox.log && grep warning dox.log +``` + +***[Check there are no error and the warnings]*** + +```bash +cp -R html ../../gudhi.doc.@GUDHI_VERSION@/cpp export LC_ALL=en_US.UTF-8 # cf. bug https://github.com/GUDHI/gudhi-devel/issues/111 make sphinx ``` diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index c068b268..f417ebb2 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -83,7 +83,7 @@ Table of Contents * * Then, it is asked to display information about the simplicial complex. * - * \include Alpha_complex/Alpha_complex_from_points.cpp + * \include Alpha_complex_from_points.cpp * * When launching: * @@ -92,7 +92,7 @@ Table of Contents * * the program output is: * - * \include Alpha_complex/alphaoffreader_for_doc_60.txt + * \include alphaoffreader_for_doc_60.txt * * \section createcomplexalgorithm Create complex algorithm * @@ -171,7 +171,7 @@ Table of Contents * * Then, it is asked to display information about the alpha complex. * - * \include Alpha_complex/Weighted_alpha_complex_from_points.cpp + * \include Weighted_alpha_complex_from_points.cpp * * When launching: * @@ -180,7 +180,7 @@ Table of Contents * * the program output is: * - * \include Alpha_complex/weightedalpha3dfrompoints_for_doc.txt + * \include weightedalpha3dfrompoints_for_doc.txt * * * \section offexample Example from OFF file @@ -190,7 +190,7 @@ Table of Contents * * Then, it is asked to display information about the alpha complex. * - * \include Alpha_complex/Alpha_complex_from_off.cpp + * \include Alpha_complex_from_off.cpp * * When launching: * @@ -199,7 +199,7 @@ Table of Contents * * the program output is: * - * \include Alpha_complex/alphaoffreader_for_doc_32.txt + * \include alphaoffreader_for_doc_32.txt * * * \section weighted3dexample 3d specific version @@ -215,7 +215,7 @@ Table of Contents * * Then, it is asked to display information about the alpha complex. * - * \include Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp + * \include Weighted_alpha_complex_3d_from_points.cpp * * The results will be the same as in \ref weightedversion . * diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h index 2a988b4b..4f5a956c 100644 --- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -64,7 +64,7 @@ int main() { * \section bottleneckbasicexample Basic example * * This other example computes the bottleneck distance from 2 persistence diagrams: - * \include Bottleneck_distance/bottleneck_basic_example.cpp + * \include bottleneck_basic_example.cpp * * \code Bottleneck distance = 0.75 diff --git a/src/Cech_complex/doc/Intro_cech_complex.h b/src/Cech_complex/doc/Intro_cech_complex.h index 80c88dc6..698f9749 100644 --- a/src/Cech_complex/doc/Intro_cech_complex.h +++ b/src/Cech_complex/doc/Intro_cech_complex.h @@ -71,7 +71,7 @@ namespace cech_complex { * \ref rips_complex but it offers more topological guarantees. * * If the Cech_complex interfaces are not detailed enough for your need, please refer to - * + * * cech_complex_step_by_step.cpp example, where the graph construction over the Simplex_tree is more detailed. * * \subsection cechpointscloudexample Example from a point cloud @@ -81,7 +81,7 @@ namespace cech_complex { * * Then, it is asked to display information about the simplicial complex. * - * \include Cech_complex/cech_complex_example_from_points.cpp + * \include cech_complex_example_from_points.cpp * * When launching (maximal enclosing ball radius is 1., is expanded until dimension 2): * @@ -90,7 +90,7 @@ namespace cech_complex { * * the program output is: * - * \include Cech_complex/cech_complex_example_from_points_for_doc.txt + * \include cech_complex_example_from_points_for_doc.txt * */ /** @} */ // end defgroup cech_complex diff --git a/src/Collapse/doc/intro_edge_collapse.h b/src/Collapse/doc/intro_edge_collapse.h index 81edd79f..fde39707 100644 --- a/src/Collapse/doc/intro_edge_collapse.h +++ b/src/Collapse/doc/intro_edge_collapse.h @@ -81,7 +81,7 @@ namespace collapse { * Then it collapses edges and displays a new list of `Filtered_edge` (with less edges) * that will preserve the persistence homology computation. * - * \include Collapse/edge_collapse_basic_example.cpp + * \include edge_collapse_basic_example.cpp * * When launching the example: * @@ -90,7 +90,7 @@ namespace collapse { * * the program output is: * - * \include Collapse/edge_collapse_example_basic.txt + * \include edge_collapse_example_basic.txt */ /** @} */ // end defgroup strong_collapse diff --git a/src/Doxyfile.in b/src/Doxyfile.in index 49e781bd..4784b915 100644 --- a/src/Doxyfile.in +++ b/src/Doxyfile.in @@ -32,7 +32,7 @@ DOXYFILE_ENCODING = UTF-8 # title of most generated pages and in a few other places. # The default value is: My Project. -PROJECT_NAME = "GUDHI" +PROJECT_NAME = "@CMAKE_PROJECT_NAME@" # The PROJECT_NUMBER tag can be used to enter a project or revision number. This # could be handy for archiving the generated documentation or if some version @@ -58,7 +58,7 @@ PROJECT_LOGO = # entered, it will be relative to the location where doxygen was started. If # left blank the current directory will be used. -OUTPUT_DIRECTORY = "doc/" +OUTPUT_DIRECTORY = # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 4096 sub- # directories (in 2 levels) under the output directory of each output format and @@ -672,9 +672,9 @@ LAYOUT_FILE = # search path. Do not use file names with spaces, bibtex cannot handle them. See # also \cite for info how to create references. -CITE_BIB_FILES = biblio/bibliography.bib \ - biblio/how_to_cite_cgal.bib \ - biblio/how_to_cite_gudhi.bib +CITE_BIB_FILES = @CMAKE_SOURCE_DIR@/biblio/bibliography.bib \ + @CMAKE_SOURCE_DIR@/biblio/how_to_cite_cgal.bib \ + @CMAKE_SOURCE_DIR@/biblio/how_to_cite_gudhi.bib #--------------------------------------------------------------------------- # Configuration options related to warning and progress messages @@ -745,7 +745,7 @@ WARN_LOGFILE = # spaces. # Note: If this tag is empty the current directory is searched. -INPUT = +INPUT = @CMAKE_SOURCE_DIR@ # This tag can be used to specify the character encoding of the source files # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses @@ -780,13 +780,14 @@ RECURSIVE = YES # Note that relative paths are relative to the directory from which doxygen is # run. -EXCLUDE = data/ \ - example/ \ - GudhUI/ \ - cmake/ \ - python/ \ - ext/ \ - README.md +EXCLUDE = @CMAKE_SOURCE_DIR@/data/ \ + @CMAKE_SOURCE_DIR@/ext/ \ + @CMAKE_SOURCE_DIR@/README.md \ + @CMAKE_SOURCE_DIR@/.github \ + @CMAKE_CURRENT_BINARY_DIR@/new_gudhi_version_creation.md \ + @GUDHI_DOXYGEN_SOURCE_PREFIX@/GudhUI/ \ + @GUDHI_DOXYGEN_SOURCE_PREFIX@/cmake/ \ + @GUDHI_DOXYGEN_SOURCE_PREFIX@/python/ \ # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or # directories that are symbolic links (a Unix file system feature) are excluded @@ -802,7 +803,7 @@ EXCLUDE_SYMLINKS = NO # Note that the wildcards are matched against the file with absolute path, so to # exclude all test directories for example use the pattern */test/* -EXCLUDE_PATTERNS = */utilities/*/*.md +EXCLUDE_PATTERNS = @GUDHI_DOXYGEN_SOURCE_PREFIX@/@GUDHI_DOXYGEN_UTILS_PATH@/*.md # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names # (namespaces, classes, functions, etc.) that should be excluded from the @@ -819,10 +820,9 @@ EXCLUDE_SYMBOLS = # that contain example code fragments that are included (see the \include # command). -EXAMPLE_PATH = biblio/ \ - example/ \ - utilities/ \ - data/ +EXAMPLE_PATH = @CMAKE_SOURCE_DIR@/biblio/ \ + @CMAKE_SOURCE_DIR@/data/ \ + @GUDHI_DOXYGEN_EXAMPLE_PATH@ # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and @@ -890,7 +890,7 @@ FILTER_SOURCE_PATTERNS = # (index.html). This can be useful if you have a project on for instance GitHub # and want to reuse the introduction page also for the doxygen output. -USE_MDFILE_AS_MAINPAGE = doc/common/main_page.md +USE_MDFILE_AS_MAINPAGE = @GUDHI_DOXYGEN_COMMON_DOC_PATH@/main_page.md #--------------------------------------------------------------------------- # Configuration options related to source browsing @@ -1046,7 +1046,7 @@ HTML_FILE_EXTENSION = .html # of the possible markers and block names see the documentation. # This tag requires that the tag GENERATE_HTML is set to YES. -HTML_HEADER = doc/common/header.html +HTML_HEADER = @GUDHI_DOXYGEN_COMMON_DOC_PATH@/header.html # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each # generated HTML page. If the tag is left blank doxygen will generate a standard @@ -1056,7 +1056,7 @@ HTML_HEADER = doc/common/header.html # that doxygen normally uses. # This tag requires that the tag GENERATE_HTML is set to YES. -HTML_FOOTER = doc/common/footer.html +HTML_FOOTER = @GUDHI_DOXYGEN_COMMON_DOC_PATH@/footer.html # The HTML_STYLESHEET tag can be used to specify a user-defined cascading style # sheet that is used by each HTML page. It can be used to fine-tune the look of @@ -1068,7 +1068,7 @@ HTML_FOOTER = doc/common/footer.html # obsolete. # This tag requires that the tag GENERATE_HTML is set to YES. -HTML_STYLESHEET = doc/common/stylesheet.css +HTML_STYLESHEET = @GUDHI_DOXYGEN_COMMON_DOC_PATH@/stylesheet.css # The HTML_EXTRA_STYLESHEET tag can be used to specify an additional user- # defined cascading style sheet that is included after the standard style sheets diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h index f9441b24..a6098860 100644 --- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h +++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h @@ -53,7 +53,7 @@ namespace cover_complex { * covering the height function (coordinate 2), * which are then refined into their connected components using the triangulation of the .OFF file. * - * \include Nerve_GIC/Nerve.cpp + * \include Nerve.cpp * * When launching: * @@ -62,7 +62,7 @@ namespace cover_complex { * * the program output is: * - * \include Nerve_GIC/Nerve.txt + * \include Nerve.txt * * The program also writes a file ../../data/points/human_sc.txt. The first three lines in this file are the location * of the input point cloud and the function used to compute the cover. @@ -96,7 +96,7 @@ namespace cover_complex { * comes from the triangulation of the human shape. Note that the resulting simplicial complex is in dimension 3 * in this example. * - * \include Nerve_GIC/VoronoiGIC.cpp + * \include VoronoiGIC.cpp * * When launching: * @@ -129,7 +129,7 @@ namespace cover_complex { * with automatic resolution and gain. Note that automatic threshold, resolution and gain * can be computed as well for the Nerve. * - * \include Nerve_GIC/CoordGIC.cpp + * \include CoordGIC.cpp * * When launching: * @@ -152,7 +152,7 @@ namespace cover_complex { * The function is now the first eigenfunction given by PCA, whose values * are written in a file (lucky_cat_PCA1). Threshold, resolution and gain are automatically selected as before. * - * \include Nerve_GIC/FuncGIC.cpp + * \include FuncGIC.cpp * * When launching: * diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index b4f9fd2c..a3613d0d 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -131,7 +131,7 @@ namespace persistent_cohomology { We provide several example files: run these examples with -h for details on their use, and read the README file. -\li +\li Rips_complex/rips_persistence.cpp computes the Rips complex of a point cloud and outputs its persistence diagram. \code $> ./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 \endcode @@ -144,11 +144,11 @@ diagram. More details on the Rips complex utilities dedicated page. -\li +\li Persistent_cohomology/rips_multifield_persistence.cpp computes the Rips complex of a point cloud and outputs its persistence diagram with a family of field coefficients. -\li +\li Rips_complex/rips_distance_matrix_persistence.cpp computes the Rips complex of a distance matrix and outputs its persistence diagram. @@ -158,7 +158,7 @@ Please refer to data/distance_matrix/lower_triangular_distance_matrix.csv for an More details on the Rips complex utilities dedicated page. -\li +\li Rips_complex/rips_correlation_matrix_persistence.cpp computes the Rips complex of a correlation matrix and outputs its persistence diagram. @@ -169,7 +169,7 @@ Please refer to data/correlation_matrix/lower_triangular_correlation_matrix.csv More details on the Rips complex utilities dedicated page. -\li +\li Alpha_complex/alpha_complex_3d_persistence.cpp computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. \code $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off -p 2 -m 0.45 \endcode @@ -235,7 +235,7 @@ Note that the lengths of the sides of the periodic cuboid have to be the same. +\li Alpha_complex/alpha_complex_persistence.cpp computes the persistent homology with \f$\mathbb{Z}/p\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. \code $> ./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off \endcode @@ -248,7 +248,7 @@ Simplex_tree dim: 3 More details on the Alpha complex utilities dedicated page. -\li +\li Persistent_cohomology/plain_homology.cpp computes the plain homology of a simple simplicial complex without filtration values. diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h index b2840686..3888ec8f 100644 --- a/src/Rips_complex/doc/Intro_rips_complex.h +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -64,7 +64,7 @@ namespace rips_complex { * And so on for simplex (0,1,2,3). * * If the Rips_complex interfaces are not detailed enough for your need, please refer to - * + * * rips_persistence_step_by_step.cpp example, where the constructions of the graph and * the Simplex_tree are more detailed. * @@ -111,7 +111,7 @@ namespace rips_complex { * * Then, it is asked to display information about the simplicial complex. * - * \include Rips_complex/example_one_skeleton_rips_from_points.cpp + * \include example_one_skeleton_rips_from_points.cpp * * When launching (Rips maximal distance between 2 points is 12.0, is expanded * until dimension 1 - one skeleton graph in other words): @@ -121,7 +121,7 @@ namespace rips_complex { * * the program output is: * - * \include Rips_complex/one_skeleton_rips_for_doc.txt + * \include one_skeleton_rips_for_doc.txt * * \subsection ripsoffexample Example from OFF file * @@ -132,7 +132,7 @@ namespace rips_complex { * * Then, it is asked to display information about the Rips complex. * - * \include Rips_complex/example_rips_complex_from_off_file.cpp + * \include example_rips_complex_from_off_file.cpp * * When launching: * @@ -141,7 +141,7 @@ namespace rips_complex { * * the program output is: * - * \include Rips_complex/full_skeleton_rips_for_doc.txt + * \include full_skeleton_rips_for_doc.txt * * * \subsection sparseripspointscloudexample Example of a sparse Rips from a point cloud @@ -149,7 +149,7 @@ namespace rips_complex { * This example builds the full sparse Rips of a set of 2D Euclidean points, then prints some minimal * information about the complex. * - * \include Rips_complex/example_sparse_rips.cpp + * \include example_sparse_rips.cpp * * When launching: * @@ -172,7 +172,7 @@ namespace rips_complex { * * Then, it is asked to display information about the simplicial complex. * - * \include Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp + * \include example_one_skeleton_rips_from_distance_matrix.cpp * * When launching (Rips maximal distance between 2 points is 1.0, is expanded until dimension 1 - one skeleton graph * with other words): @@ -182,7 +182,7 @@ namespace rips_complex { * * the program output is: * - * \include Rips_complex/one_skeleton_rips_for_doc.txt + * \include one_skeleton_rips_for_doc.txt * * \subsection ripscsvdistanceexample Example from a distance matrix read in a csv file * @@ -192,7 +192,7 @@ namespace rips_complex { * * Then, it is asked to display information about the Rips complex. * - * \include Rips_complex/example_rips_complex_from_csv_distance_matrix_file.cpp + * \include example_rips_complex_from_csv_distance_matrix_file.cpp * * When launching: * @@ -201,7 +201,7 @@ namespace rips_complex { * * the program output is: * - * \include Rips_complex/full_skeleton_rips_for_doc.txt + * \include full_skeleton_rips_for_doc.txt * * * \section ripscorrelationematrix Correlation matrix @@ -213,7 +213,7 @@ namespace rips_complex { * * Then, it is asked to display information about the simplicial complex. * - * \include Rips_complex/example_one_skeleton_rips_from_correlation_matrix.cpp + * \include example_one_skeleton_rips_from_correlation_matrix.cpp * * When launching: * @@ -222,7 +222,7 @@ namespace rips_complex { * * the program output is: * - * \include Rips_complex/one_skeleton_rips_from_correlation_matrix_for_doc.txt + * \include one_skeleton_rips_from_correlation_matrix_for_doc.txt * * All the other constructions discussed for Rips complex for distance matrix can be also performed for Rips complexes * construction from correlation matrices. diff --git a/src/Simplex_tree/doc/Intro_simplex_tree.h b/src/Simplex_tree/doc/Intro_simplex_tree.h index 800879fe..ef8dec91 100644 --- a/src/Simplex_tree/doc/Intro_simplex_tree.h +++ b/src/Simplex_tree/doc/Intro_simplex_tree.h @@ -39,10 +39,10 @@ namespace Gudhi { * \subsubsection filteredcomplexessimplextreeexamples Examples * * Here is a list of simplex tree examples : - * \li + * \li * Simplex_tree/simple_simplex_tree.cpp - Simple simplex tree construction and basic function use. * - * \li + * \li * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp - Simplex tree construction from cliques of graph read in * a file. * @@ -54,11 +54,11 @@ Expand the simplex tree in 3.8e-05 s. Information of the Simplex Tree: Number of vertices = 10 Number of simplices = 98 \endcode * - * \li + * \li * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp - Simplex tree is computed and displayed * from a 3D alpha complex (Requires CGAL, GMP and GMPXX to be installed). * - * \li + * \li * Simplex_tree/graph_expansion_with_blocker.cpp - Simple simplex tree construction from a one-skeleton graph with * a simple blocker expansion method. * diff --git a/src/Spatial_searching/doc/Intro_spatial_searching.h b/src/Spatial_searching/doc/Intro_spatial_searching.h index 30805570..81c5a3aa 100644 --- a/src/Spatial_searching/doc/Intro_spatial_searching.h +++ b/src/Spatial_searching/doc/Intro_spatial_searching.h @@ -36,7 +36,7 @@ namespace spatial_searching { * * This example generates 500 random points, then performs all-near-neighbors searches, and queries for nearest and furthest neighbors using different methods. * - * \include Spatial_searching/example_spatial_searching.cpp + * \include example_spatial_searching.cpp * */ /** @} */ // end defgroup spatial_searching diff --git a/src/Subsampling/doc/Intro_subsampling.h b/src/Subsampling/doc/Intro_subsampling.h index 1c84fb2e..1c366fe6 100644 --- a/src/Subsampling/doc/Intro_subsampling.h +++ b/src/Subsampling/doc/Intro_subsampling.h @@ -32,20 +32,20 @@ namespace subsampling { * squared distance between any two points * is greater than or equal to 0.4. * - * \include Subsampling/example_sparsify_point_set.cpp + * \include example_sparsify_point_set.cpp * * \section farthestpointexamples Example: choose_n_farthest_points * * This example outputs a subset of 100 points obtained by González algorithm, * starting with a random point. * - * \include Subsampling/example_choose_n_farthest_points.cpp + * \include example_choose_n_farthest_points.cpp * * \section randompointexamples Example: pick_n_random_points * * This example outputs a subset of 100 points picked randomly. * - * \include Subsampling/example_pick_n_random_points.cpp + * \include example_pick_n_random_points.cpp */ /** @} */ // end defgroup subsampling diff --git a/src/Tangential_complex/doc/Intro_tangential_complex.h b/src/Tangential_complex/doc/Intro_tangential_complex.h index ce277185..cb8c6122 100644 --- a/src/Tangential_complex/doc/Intro_tangential_complex.h +++ b/src/Tangential_complex/doc/Intro_tangential_complex.h @@ -88,7 +88,7 @@ This example builds the Tangential complex of point set. Note that the dimension of the kernel here is dynamic, which is slower, but more flexible: the intrinsic and ambient dimensions does not have to be known at compile-time. -\include Tangential_complex/example_basic.cpp +\include example_basic.cpp \section example_with_perturb Example with perturbation @@ -97,7 +97,7 @@ by perturbing the positions of points involved in inconsistent simplices. Note that the dimension of the kernel here is static, which is the best choice when the dimensions are known at compile-time. -\include Tangential_complex/example_with_perturb.cpp +\include example_with_perturb.cpp */ /** @} */ // end defgroup tangential_complex diff --git a/src/Witness_complex/doc/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h index 202f4539..c66b106e 100644 --- a/src/Witness_complex/doc/Witness_complex_doc.h +++ b/src/Witness_complex/doc/Witness_complex_doc.h @@ -108,14 +108,14 @@ int main(int argc, char * const argv[]) { Here is an example of constructing a strong witness complex filtration and computing persistence on it: - \include Witness_complex/strong_witness_persistence.cpp + \include strong_witness_persistence.cpp \section witnessexample3 Example3: Computing relaxed witness complex persistence from a distance matrix In this example we compute the relaxed witness complex persistence from a given matrix of closest landmarks to each witness. Each landmark is given as the couple (index, distance). - \include Witness_complex/example_nearest_landmark_table.cpp + \include example_nearest_landmark_table.cpp */ diff --git a/src/cmake/modules/GUDHI_doxygen_target.cmake b/src/cmake/modules/GUDHI_doxygen_target.cmake index 7a84c4e0..0f80b187 100644 --- a/src/cmake/modules/GUDHI_doxygen_target.cmake +++ b/src/cmake/modules/GUDHI_doxygen_target.cmake @@ -8,14 +8,47 @@ if(DOXYGEN_FOUND) get_property(DOXYGEN_EXECUTABLE TARGET Doxygen::doxygen PROPERTY IMPORTED_LOCATION) endif() - add_custom_target(doxygen ${DOXYGEN_EXECUTABLE} ${GUDHI_USER_VERSION_DIR}/Doxyfile - WORKING_DIRECTORY ${GUDHI_USER_VERSION_DIR} - COMMENT "Generating API documentation with Doxygen in ${GUDHI_USER_VERSION_DIR}/doc/html/" VERBATIM) - - if(TARGET user_version) - # In dev version, doxygen target depends on user_version target. Not existing in user version - add_dependencies(doxygen user_version) + message("++ Project = ${CMAKE_PROJECT_NAME}") + if (CMAKE_PROJECT_NAME STREQUAL "GUDHIdev") + # Set Doxyfile.in variables for the developer version + set(GUDHI_DOXYGEN_SOURCE_PREFIX "${CMAKE_SOURCE_DIR}/src") + foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST}) + if(EXISTS "${GUDHI_DOXYGEN_SOURCE_PREFIX}/${GUDHI_MODULE}/doc/") + set(GUDHI_DOXYGEN_IMAGE_PATH "${GUDHI_DOXYGEN_IMAGE_PATH} ${GUDHI_DOXYGEN_SOURCE_PREFIX}/${GUDHI_MODULE}/doc/ \\ \n") + endif() + if(EXISTS "${GUDHI_DOXYGEN_SOURCE_PREFIX}/${GUDHI_MODULE}/example/") + set(GUDHI_DOXYGEN_EXAMPLE_PATH "${GUDHI_DOXYGEN_EXAMPLE_PATH} ${GUDHI_DOXYGEN_SOURCE_PREFIX}/${GUDHI_MODULE}/example/ \\ \n") + endif() + if(EXISTS "${GUDHI_DOXYGEN_SOURCE_PREFIX}/${GUDHI_MODULE}/utilities/") + set(GUDHI_DOXYGEN_EXAMPLE_PATH "${GUDHI_DOXYGEN_EXAMPLE_PATH} ${GUDHI_DOXYGEN_SOURCE_PREFIX}/${GUDHI_MODULE}/utilities/ \\ \n") + endif() + endforeach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST}) + set(GUDHI_DOXYGEN_COMMON_DOC_PATH "${GUDHI_DOXYGEN_SOURCE_PREFIX}/common/doc") + set(GUDHI_DOXYGEN_UTILS_PATH "*/utilities") + endif() + if (CMAKE_PROJECT_NAME STREQUAL "GUDHI") + # Set Doxyfile.in variables for the user version + set(GUDHI_DOXYGEN_SOURCE_PREFIX "${CMAKE_SOURCE_DIR}") + foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST}) + if(EXISTS "${GUDHI_DOXYGEN_SOURCE_PREFIX}/doc/${GUDHI_MODULE}") + set(GUDHI_DOXYGEN_IMAGE_PATH "${GUDHI_DOXYGEN_IMAGE_PATH} ${GUDHI_DOXYGEN_SOURCE_PREFIX}/doc/${GUDHI_MODULE}/ \\ \n") + endif() + if(EXISTS "${GUDHI_DOXYGEN_SOURCE_PREFIX}/example/${GUDHI_MODULE}") + set(GUDHI_DOXYGEN_EXAMPLE_PATH "${GUDHI_DOXYGEN_EXAMPLE_PATH} ${GUDHI_DOXYGEN_SOURCE_PREFIX}/example/${GUDHI_MODULE}/ \\ \n") + endif() + if(EXISTS "${GUDHI_DOXYGEN_SOURCE_PREFIX}/utilities/${GUDHI_MODULE}") + set(GUDHI_DOXYGEN_EXAMPLE_PATH "${GUDHI_DOXYGEN_EXAMPLE_PATH} ${GUDHI_DOXYGEN_SOURCE_PREFIX}/utilities/${GUDHI_MODULE}/ \\ \n") + endif() + endforeach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST}) + set(GUDHI_DOXYGEN_COMMON_DOC_PATH "${GUDHI_DOXYGEN_SOURCE_PREFIX}/doc/common") + set(GUDHI_DOXYGEN_UTILS_PATH "utilities/*") endif() + + configure_file(${GUDHI_DOXYGEN_SOURCE_PREFIX}/Doxyfile.in "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile" @ONLY) + + add_custom_target(doxygen ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMENT "Generating API documentation with Doxygen in 'html' directory" VERBATIM) else() set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "cpp-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES") endif() diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake index e4f39aae..9e76c3d9 100644 --- a/src/cmake/modules/GUDHI_user_version_target.cmake +++ b/src/cmake/modules/GUDHI_user_version_target.cmake @@ -14,14 +14,7 @@ add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E make_directory ${GUDHI_USER_VERSION_DIR} COMMENT "user_version creation in ${GUDHI_USER_VERSION_DIR}") -foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST}) - set(GUDHI_DOXYGEN_IMAGE_PATH "${GUDHI_DOXYGEN_IMAGE_PATH} doc/${GUDHI_MODULE}/ \\ \n") -endforeach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST}) - -# Generate Doxyfile for Doxygen - cf. root CMakeLists.txt for explanation -configure_file(${CMAKE_SOURCE_DIR}/src/Doxyfile.in "${CMAKE_CURRENT_BINARY_DIR}/src/Doxyfile" @ONLY) -add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${CMAKE_CURRENT_BINARY_DIR}/src/Doxyfile ${GUDHI_USER_VERSION_DIR}/Doxyfile) +file(COPY "${CMAKE_SOURCE_DIR}/src/Doxyfile.in" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") # Generate bib files for Doxygen - cf. root CMakeLists.txt for explanation string(TIMESTAMP GUDHI_VERSION_YEAR "%Y") @@ -48,6 +41,8 @@ add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/src/GUDHIConfig.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIConfig.cmake.in) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/CMakeGUDHIVersion.txt ${GUDHI_USER_VERSION_DIR}/CMakeGUDHIVersion.txt) +add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E + copy ${CMAKE_SOURCE_DIR}/src/Doxyfile.in ${GUDHI_USER_VERSION_DIR}/Doxyfile.in) # As cython generates .cpp files in source, we have to copy all except cpp files from python directory file(GLOB_RECURSE PYTHON_FILES ${CMAKE_SOURCE_DIR}/${GUDHI_PYTHON_PATH}/*) diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h index 474f8699..b557727b 100644 --- a/src/common/doc/examples.h +++ b/src/common/doc/examples.h @@ -1,96 +1,98 @@ // List of GUDHI examples - Doxygen needs at least a file tag to analyse comments // In user_version, `find . -name "*.cpp"` in example and utilities folders /*! @file Examples - * @example Alpha_complex/Alpha_complex_from_off.cpp - * @example Alpha_complex/Alpha_complex_from_points.cpp - * @example Bottleneck_distance/bottleneck_basic_example.cpp - * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp - * @example Witness_complex/example_nearest_landmark_table.cpp - * @example Witness_complex/example_witness_complex_off.cpp - * @example Witness_complex/example_witness_complex_sphere.cpp - * @example Witness_complex/example_strong_witness_complex_off.cpp - * @example Simplex_tree/mini_simplex_tree.cpp - * @example Simplex_tree/graph_expansion_with_blocker.cpp - * @example Simplex_tree/simple_simplex_tree.cpp - * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp - * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp - * @example Simplex_tree/cech_complex_cgal_mini_sphere_3d.cpp - * @example Persistent_cohomology/plain_homology.cpp - * @example Persistent_cohomology/persistence_from_file.cpp - * @example Persistent_cohomology/rips_persistence_step_by_step.cpp - * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp - * @example Persistent_cohomology/custom_persistence_sort.cpp - * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp - * @example Persistent_cohomology/rips_multifield_persistence.cpp - * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp - * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp - * @example Skeleton_blocker/Skeleton_blocker_link.cpp - * @example Contraction/Garland_heckbert.cpp - * @example Contraction/Rips_contraction.cpp - * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp - * @example common/example_CGAL_3D_points_off_reader.cpp - * @example common/example_vector_double_points_off_reader.cpp - * @example common/example_CGAL_points_off_reader.cpp - * @example Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp - * @example Rips_complex/example_one_skeleton_rips_from_points.cpp - * @example Rips_complex/example_rips_complex_from_csv_distance_matrix_file.cpp - * @example Rips_complex/example_rips_complex_from_off_file.cpp - * @example Persistence_representations/persistence_intervals.cpp - * @example Persistence_representations/persistence_vectors.cpp - * @example Persistence_representations/persistence_heat_maps.cpp - * @example Persistence_representations/persistence_landscape_on_grid.cpp - * @example Persistence_representations/persistence_landscape.cpp - * @example Tangential_complex/example_basic.cpp - * @example Tangential_complex/example_with_perturb.cpp - * @example Subsampling/example_custom_distance.cpp - * @example Subsampling/example_choose_n_farthest_points.cpp - * @example Subsampling/example_sparsify_point_set.cpp - * @example Subsampling/example_pick_n_random_points.cpp - * @example Nerve_GIC/CoordGIC.cpp - * @example Nerve_GIC/Nerve.cpp - * @example Nerve_GIC/FuncGIC.cpp - * @example Nerve_GIC/VoronoiGIC.cpp - * @example Spatial_searching/example_spatial_searching.cpp - * @example Alpha_complex/alpha_complex_3d_persistence.cpp - * @example Alpha_complex/alpha_complex_persistence.cpp - * @example Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp - * @example Bottleneck_distance/bottleneck_distance.cpp - * @example Witness_complex/weak_witness_persistence.cpp - * @example Witness_complex/strong_witness_persistence.cpp - * @example Bitmap_cubical_complex/cubical_complex_persistence.cpp - * @example Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp - * @example common/off_file_from_shape_generator.cpp - * @example Rips_complex/rips_distance_matrix_persistence.cpp - * @example Rips_complex/rips_persistence.cpp - * @example Persistence_representations/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp - * @example Persistence_representations/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp - * @example Persistence_representations/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp - * @example Persistence_representations/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp - * @example Persistence_representations/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp - * @example Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp - * @example Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp - * @example Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp - * @example Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp - * @example Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp - * @example Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp - * @example Persistence_representations/persistence_heat_maps/create_pssk.cpp - * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp - * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp - * @example Persistence_representations/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp - * @example Persistence_representations/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp - * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp - * @example Persistence_representations/persistence_heat_maps/average_persistence_heat_maps.cpp - * @example Persistence_representations/persistence_heat_maps/plot_persistence_heat_map.cpp - * @example Persistence_representations/persistence_heat_maps/create_persistence_heat_maps.cpp - * @example Persistence_representations/persistence_vectors/plot_persistence_vectors.cpp - * @example Persistence_representations/persistence_vectors/compute_distance_of_persistence_vectors.cpp - * @example Persistence_representations/persistence_vectors/average_persistence_vectors.cpp - * @example Persistence_representations/persistence_vectors/create_persistence_vectors.cpp - * @example Persistence_representations/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp - * @example Persistence_representations/persistence_landscapes/average_landscapes.cpp - * @example Persistence_representations/persistence_landscapes/compute_scalar_product_of_landscapes.cpp - * @example Persistence_representations/persistence_landscapes/create_landscapes.cpp - * @example Persistence_representations/persistence_landscapes/compute_distance_of_landscapes.cpp - * @example Persistence_representations/persistence_landscapes/plot_landscapes.cpp + * \section Alpha_complex_examples Alpha complex + * @example Alpha_complex_from_off.cpp + * @example Alpha_complex_from_points.cpp + * \section bottleneck_examples bottleneck + * @example bottleneck_basic_example.cpp + * @example alpha_rips_persistence_bottleneck_distance.cpp + * @example example_nearest_landmark_table.cpp + * @example example_witness_complex_off.cpp + * @example example_witness_complex_sphere.cpp + * @example example_strong_witness_complex_off.cpp + * @example mini_simplex_tree.cpp + * @example graph_expansion_with_blocker.cpp + * @example simple_simplex_tree.cpp + * @example simplex_tree_from_cliques_of_graph.cpp + * @example example_alpha_shapes_3_simplex_tree_from_off_file.cpp + * @example cech_complex_cgal_mini_sphere_3d.cpp + * @example plain_homology.cpp + * @example persistence_from_file.cpp + * @example rips_persistence_step_by_step.cpp + * @example rips_persistence_via_boundary_matrix.cpp + * @example custom_persistence_sort.cpp + * @example persistence_from_simple_simplex_tree.cpp + * @example rips_multifield_persistence.cpp + * @example Skeleton_blocker_from_simplices.cpp + * @example Skeleton_blocker_iteration.cpp + * @example Skeleton_blocker_link.cpp + * @example Garland_heckbert.cpp + * @example Rips_contraction.cpp + * @example Random_bitmap_cubical_complex.cpp + * @example example_CGAL_3D_points_off_reader.cpp + * @example example_vector_double_points_off_reader.cpp + * @example example_CGAL_points_off_reader.cpp + * @example example_one_skeleton_rips_from_distance_matrix.cpp + * @example example_one_skeleton_rips_from_points.cpp + * @example example_rips_complex_from_csv_distance_matrix_file.cpp + * @example example_rips_complex_from_off_file.cpp + * @example persistence_intervals.cpp + * @example persistence_vectors.cpp + * @example persistence_heat_maps.cpp + * @example persistence_landscape_on_grid.cpp + * @example persistence_landscape.cpp + * @example example_basic.cpp + * @example example_with_perturb.cpp + * @example example_custom_distance.cpp + * @example example_choose_n_farthest_points.cpp + * @example example_sparsify_point_set.cpp + * @example example_pick_n_random_points.cpp + * @example CoordGIC.cpp + * @example Nerve.cpp + * @example FuncGIC.cpp + * @example VoronoiGIC.cpp + * @example example_spatial_searching.cpp + * @example alpha_complex_3d_persistence.cpp + * @example alpha_complex_persistence.cpp + * @example Weighted_alpha_complex_3d_from_points.cpp + * @example bottleneck_distance.cpp + * @example weak_witness_persistence.cpp + * @example strong_witness_persistence.cpp + * @example cubical_complex_persistence.cpp + * @example periodic_cubical_complex_persistence.cpp + * @example off_file_from_shape_generator.cpp + * @example rips_distance_matrix_persistence.cpp + * @example rips_persistence.cpp + * @example persistence_landscapes_on_grid/create_landscapes_on_grid.cpp + * @example persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp + * @example persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp + * @example persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp + * @example persistence_landscapes_on_grid/average_landscapes_on_grid.cpp + * @example persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp + * @example persistence_intervals/compute_number_of_dominant_intervals.cpp + * @example persistence_intervals/plot_persistence_Betti_numbers.cpp + * @example persistence_intervals/plot_persistence_intervals.cpp + * @example persistence_intervals/plot_histogram_of_intervals_lengths.cpp + * @example persistence_intervals/compute_bottleneck_distance.cpp + * @example persistence_heat_maps/create_pssk.cpp + * @example persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp + * @example persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp + * @example persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp + * @example persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp + * @example persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp + * @example persistence_heat_maps/average_persistence_heat_maps.cpp + * @example persistence_heat_maps/plot_persistence_heat_map.cpp + * @example persistence_heat_maps/create_persistence_heat_maps.cpp + * @example persistence_vectors/plot_persistence_vectors.cpp + * @example persistence_vectors/compute_distance_of_persistence_vectors.cpp + * @example persistence_vectors/average_persistence_vectors.cpp + * @example persistence_vectors/create_persistence_vectors.cpp + * @example persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp + * @example persistence_landscapes/average_landscapes.cpp + * @example persistence_landscapes/compute_scalar_product_of_landscapes.cpp + * @example persistence_landscapes/create_landscapes.cpp + * @example persistence_landscapes/compute_distance_of_landscapes.cpp + * @example persistence_landscapes/plot_landscapes.cpp */ diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index c2e63a24..313184b6 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -40,11 +40,8 @@ make \endverbatim * \subsection documentationgeneration Documentation * To generate the documentation, Doxygen is required. * Run the following command in a terminal: -\verbatim -make doxygen -# Documentation will be generated in the folder YYYY-MM-DD-hh-mm-ss_GUDHI_X.Y.Z/doc/html/ -# You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder` -\endverbatim + * \verbatim make doxygen \endverbatim + * Documentation will be generated in a folder named html. * * \subsection helloworld Hello world ! * The Hello world for GUDHI @@ -57,7 +54,7 @@ make doxygen * * The following example requires the GNU Multiple Precision Arithmetic * Library (GMP) and will not be built if GMP is not installed: - * \li + * \li * Persistent_cohomology/rips_multifield_persistence.cpp * * Having GMP version 4.2 or higher installed is recommended. @@ -75,55 +72,55 @@ make doxygen * * The following examples/utilities require the Computational Geometry Algorithms * Library (CGAL \cite cgal:eb-19b) and will not be built if CGAL version 4.11.0 or higher is not installed: - * \li + * \li * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp - * \li + * \li * Witness_complex/strong_witness_persistence.cpp - * \li + * \li * Witness_complex/weak_witness_persistence.cpp - * \li + * \li * Witness_complex/example_strong_witness_complex_off.cpp - * \li + * \li * Witness_complex/example_witness_complex_off.cpp - * \li + * \li * Witness_complex/example_witness_complex_sphere.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_off.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_points.cpp - * \li + * \li * Alpha_complex/alpha_complex_persistence.cpp - * \li + * \li * Persistent_cohomology/custom_persistence_sort.cpp - * \li + * \li * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp - * \li + * \li * Bottleneck_distance/bottleneck_basic_example.cpp - * \li + * \li * Bottleneck_distance/bottleneck_distance.cpp - * \li + * \li * Nerve_GIC/CoordGIC.cpp - * \li + * \li * Nerve_GIC/FuncGIC.cpp - * \li + * \li * Nerve_GIC/Nerve.cpp - * \li + * \li * Nerve_GIC/VoronoiGIC.cpp - * \li + * \li * Spatial_searching/example_spatial_searching.cpp - * \li + * \li * Subsampling/example_choose_n_farthest_points.cpp - * \li + * \li * Subsampling/example_pick_n_random_points.cpp - * \li + * \li * Subsampling/example_sparsify_point_set.cpp - * \li + * \li * Tangential_complex/example_basic.cpp - * \li + * \li * Tangential_complex/example_with_perturb.cpp - * \li + * \li * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp - * \li + * \li * Alpha_complex/alpha_complex_3d_persistence.cpp * * \subsection eigen Eigen @@ -133,41 +130,41 @@ make doxygen * * The following examples/utilities require the Eigen and will not be * built if Eigen is not installed: - * \li + * \li * Alpha_complex/Alpha_complex_from_off.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_points.cpp - * \li + * \li * Alpha_complex/alpha_complex_persistence.cpp - * \li + * \li * Alpha_complex/alpha_complex_3d_persistence.cpp - * \li + * \li * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp - * \li + * \li * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp - * \li + * \li * Persistent_cohomology/custom_persistence_sort.cpp - * \li + * \li * Spatial_searching/example_spatial_searching.cpp - * \li + * \li * Subsampling/example_choose_n_farthest_points.cpp - * \li + * \li * Subsampling/example_pick_n_random_points.cpp - * \li + * \li * Subsampling/example_sparsify_point_set.cpp - * \li + * \li * Tangential_complex/example_basic.cpp - * \li + * \li * Tangential_complex/example_with_perturb.cpp - * \li + * \li * Witness_complex/strong_witness_persistence.cpp - * \li + * \li * Witness_complex/weak_witness_persistence.cpp - * \li + * \li * Witness_complex/example_strong_witness_complex_off.cpp - * \li + * \li * Witness_complex/example_witness_complex_off.cpp - * \li + * \li * Witness_complex/example_witness_complex_sphere.cpp * * \subsection tbb Threading Building Blocks @@ -178,67 +175,67 @@ make doxygen * Having Intel® TBB installed is recommended to parallelize and accelerate some GUDHI computations. * * The following examples/utilities are using Intel® TBB if installed: - * \li + * \li * Alpha_complex/Alpha_complex_from_off.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_points.cpp - * \li + * \li * Alpha_complex/alpha_complex_3d_persistence.cpp - * \li + * \li * Alpha_complex/alpha_complex_persistence.cpp - * \li + * \li * Bitmap_cubical_complex/cubical_complex_persistence.cpp - * \li + * \li * Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp - * \li + * \li * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp - * \li + * \li * Nerve_GIC/CoordGIC.cpp - * \li + * \li * Nerve_GIC/FuncGIC.cpp - * \li + * \li * Nerve_GIC/Nerve.cpp - * \li + * \li * Nerve_GIC/VoronoiGIC.cpp - * \li + * \li * Simplex_tree/simple_simplex_tree.cpp - * \li + * \li * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp - * \li + * \li * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp - * \li + * \li * Simplex_tree/graph_expansion_with_blocker.cpp - * \li + * \li * Persistent_cohomology/alpha_complex_3d_persistence.cpp - * \li + * \li * Persistent_cohomology/alpha_complex_persistence.cpp - * \li + * \li * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp - * \li + * \li * Persistent_cohomology/persistence_from_file.cpp - * \li + * \li * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp - * \li + * \li * Persistent_cohomology/plain_homology.cpp - * \li + * \li * Persistent_cohomology/rips_multifield_persistence.cpp - * \li + * \li * Persistent_cohomology/rips_persistence_step_by_step.cpp - * \li + * \li * Persistent_cohomology/custom_persistence_sort.cpp - * \li + * \li * Rips_complex/example_one_skeleton_rips_from_points.cpp - * \li + * \li * Rips_complex/example_rips_complex_from_off_file.cpp - * \li + * \li * Rips_complex/rips_distance_matrix_persistence.cpp - * \li + * \li * Rips_complex/rips_persistence.cpp - * \li + * \li * Witness_complex/strong_witness_persistence.cpp - * \li + * \li * Witness_complex/weak_witness_persistence.cpp - * \li + * \li * Witness_complex/example_nearest_landmark_table.cpp * * \section Contributions Bug reports and contributions diff --git a/src/common/include/gudhi/Points_3D_off_io.h b/src/common/include/gudhi/Points_3D_off_io.h index 39b79c96..4f74fd4b 100644 --- a/src/common/include/gudhi/Points_3D_off_io.h +++ b/src/common/include/gudhi/Points_3D_off_io.h @@ -125,7 +125,7 @@ class Points_3D_off_visitor_reader { * This example loads points from an OFF file and builds a vector of CGAL points in dimension 3. * Then, it is asked to display the points. * - * @include common/example_CGAL_3D_points_off_reader.cpp + * @include example_CGAL_3D_points_off_reader.cpp * * When launching: * @@ -134,7 +134,7 @@ class Points_3D_off_visitor_reader { * * the program output is: * - * @include common/cgal3Doffreader_result.txt + * @include cgal3Doffreader_result.txt */ template class Points_3D_off_reader { diff --git a/src/common/include/gudhi/Points_off_io.h b/src/common/include/gudhi/Points_off_io.h index 9dc40568..3aa8afd8 100644 --- a/src/common/include/gudhi/Points_off_io.h +++ b/src/common/include/gudhi/Points_off_io.h @@ -107,7 +107,7 @@ class Points_off_visitor_reader { * This example loads points from an OFF file and builds a vector of points (vector of double). * Then, it is asked to display the points. * - * \include common/example_vector_double_points_off_reader.cpp + * \include example_vector_double_points_off_reader.cpp * * When launching: * @@ -116,7 +116,7 @@ class Points_off_visitor_reader { * * the program outputs a file ../../data/points/alphacomplexdoc.off.txt: * - * \include common/vectordoubleoffreader_result.txt + * \include vectordoubleoffreader_result.txt */ template class Points_off_reader { -- cgit v1.2.3 From c0cca8dbd60e3da5147517f6f8f37d9bdeefe511 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 25 Jun 2021 16:26:55 +0200 Subject: update headers, conf.py for the new theme and bottleneck image to be smaller --- src/Bottleneck_distance/doc/perturb_pd.png | Bin 20864 -> 15532 bytes src/common/doc/header.html | 1 + src/python/doc/_templates/layout.html | 1 + src/python/doc/conf.py | 3 --- 4 files changed, 2 insertions(+), 3 deletions(-) (limited to 'src/common/doc') diff --git a/src/Bottleneck_distance/doc/perturb_pd.png b/src/Bottleneck_distance/doc/perturb_pd.png index be638de0..eabf3c8c 100644 Binary files a/src/Bottleneck_distance/doc/perturb_pd.png and b/src/Bottleneck_distance/doc/perturb_pd.png differ diff --git a/src/common/doc/header.html b/src/common/doc/header.html index 9da20bbc..7c20478b 100644 --- a/src/common/doc/header.html +++ b/src/common/doc/header.html @@ -49,6 +49,7 @@ $extrastylesheet
  • Related projects
  • They are talking about us
  • GUDHI in action
    • +
  • Etymology
  • diff --git a/src/python/doc/_templates/layout.html b/src/python/doc/_templates/layout.html index cd40a51b..e074b6c7 100644 --- a/src/python/doc/_templates/layout.html +++ b/src/python/doc/_templates/layout.html @@ -194,6 +194,7 @@
  • Related projects
  • They are talking about us
  • GUDHI in action
    • +
  • Etymology
  • diff --git a/src/python/doc/conf.py b/src/python/doc/conf.py index 46debd87..e69e2751 100755 --- a/src/python/doc/conf.py +++ b/src/python/doc/conf.py @@ -126,9 +126,6 @@ html_theme = 'python_docs_theme' # further. For a list of options available for each theme, see the # documentation. html_theme_options = { - "sidebarbgcolor": "#A1ADCD", - "sidebartextcolor": "black", - "sidebarlinkcolor": "#334D5C", "body_max_width": "100%", } -- cgit v1.2.3 From a91e3bc16d511ef66bb296da6a990a0723100657 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 5 Aug 2021 18:00:40 +0200 Subject: mailing lists migration and rephrase contributions in installation guides --- .github/for_maintainers/new_gudhi_version_creation.md | 4 ++-- src/common/doc/installation.h | 8 +++++--- src/python/doc/installation.rst | 9 +++++---- src/python/setup.py.in | 2 +- 4 files changed, 13 insertions(+), 10 deletions(-) (limited to 'src/common/doc') diff --git a/.github/for_maintainers/new_gudhi_version_creation.md b/.github/for_maintainers/new_gudhi_version_creation.md index d6c4cdd3..3e5295c5 100644 --- a/.github/for_maintainers/new_gudhi_version_creation.md +++ b/.github/for_maintainers/new_gudhi_version_creation.md @@ -128,5 +128,5 @@ docker image on docker hub. ## Mail sending Send version mail to the following lists : -* gudhi-devel@lists.gforge.inria.fr -* gudhi-users@lists.gforge.inria.fr (not for release candidate) +* gudhi-devel@inria.fr +* gudhi-users@inria.fr (not for release candidate) diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 610aa17e..5d40a48e 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -243,10 +243,12 @@ make \endverbatim * Witness_complex/example_nearest_landmark_table.cpp * * \section Contributions Bug reports and contributions - * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: - * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim + * Please help us improving the quality of the GUDHI library. + * You may report bugs or + * contact us for any suggestions. * - * GUDHI is open to external contributions. If you want to join our development team, please contact us. + * GUDHI is open to external contributions. If you want to join our development team, please take some time to read our + * contributing guide. * */ diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 9c16b04e..56f27b21 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -396,8 +396,9 @@ TensorFlow Bug reports and contributions ***************************** -Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: +Please help us improving the quality of the GUDHI library. +You may `report bugs `_ or +`contact us `_ for any suggestions. - Contact: gudhi-users@lists.gforge.inria.fr - -GUDHI is open to external contributions. If you want to join our development team, please contact us. +GUDHI is open to external contributions. If you want to join our development team, please take some time to read our +`contributing guide `_. diff --git a/src/python/setup.py.in b/src/python/setup.py.in index 759ec8d8..c400b601 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -71,7 +71,7 @@ setup( name = 'gudhi', packages=find_packages(), # find_namespace_packages(include=["gudhi*"]) author='GUDHI Editorial Board', - author_email='gudhi-contact@lists.gforge.inria.fr', + author_email='gudhi-contact@inria.fr', version='@GUDHI_VERSION@', url='https://gudhi.inria.fr/', project_urls={ -- cgit v1.2.3 From 4db14bad8006638fc8249cb867a1720f581e044d Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 31 Aug 2021 18:18:51 +0200 Subject: Fix broken links. Add a tool to generate cpp example page --- biblio/bibliography.bib | 1 - scripts/cpp_examples_for_doxygen.py | 16 ++ .../utilities/bottleneckdistance.md | 4 +- src/common/doc/examples.h | 164 ++++++++++++--------- src/common/doc/installation.h | 40 ++--- src/python/doc/installation.rst | 2 +- 6 files changed, 137 insertions(+), 90 deletions(-) create mode 100644 scripts/cpp_examples_for_doxygen.py (limited to 'src/common/doc') diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib index 16fa29d0..eed871be 100644 --- a/biblio/bibliography.bib +++ b/biblio/bibliography.bib @@ -15,7 +15,6 @@ title = {{Statistical analysis and parameter selection for Mapper}}, volume = {19}, year = {2018}, url = {http://jmlr.org/papers/v19/17-291.html}, -doi = {10.5555/3291125.3291137} } @inproceedings{Dey13, diff --git a/scripts/cpp_examples_for_doxygen.py b/scripts/cpp_examples_for_doxygen.py new file mode 100644 index 00000000..5c091c4f --- /dev/null +++ b/scripts/cpp_examples_for_doxygen.py @@ -0,0 +1,16 @@ +import os +import glob + +for gd_mod in glob.glob("src/*/"): + mod_files = [] + for paths in [gd_mod + 'utilities', gd_mod + 'example']: + if os.path.isdir(paths): + for root, dirs, files in os.walk(paths): + for file in files: + if file.endswith(".cpp"): + mod_files.append(str(os.path.join(root, file)).split(paths)[1][1:]) + if len(mod_files) > 0: + mod = str(gd_mod).split('/')[1] + print(' * \section ' + mod + '_example_section ' + mod) + for file in mod_files: + print(' * @example ' + file) diff --git a/src/Bottleneck_distance/utilities/bottleneckdistance.md b/src/Bottleneck_distance/utilities/bottleneckdistance.md index a81426cf..2f5dedc9 100644 --- a/src/Bottleneck_distance/utilities/bottleneckdistance.md +++ b/src/Bottleneck_distance/utilities/bottleneckdistance.md @@ -10,14 +10,14 @@ Leave the lines above as it is required by the web site generator 'Jekyll' {:/comment} -## bottleneck_read_file_example ## +## bottleneck_distance ## This program computes the Bottleneck distance between two persistence diagram files. **Usage** ``` - bottleneck_read_file_example [] + bottleneck_distance [] ``` where diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h index b557727b..a2de4335 100644 --- a/src/common/doc/examples.h +++ b/src/common/doc/examples.h @@ -1,98 +1,130 @@ -// List of GUDHI examples - Doxygen needs at least a file tag to analyse comments -// In user_version, `find . -name "*.cpp"` in example and utilities folders +// List of GUDHI examples and utils - Doxygen needs at least a file tag to analyse comments +// Generated from scripts/cpp_examples_for_doxygen.py /*! @file Examples - * \section Alpha_complex_examples Alpha complex - * @example Alpha_complex_from_off.cpp + * \section Skeleton_blocker_example_section Skeleton_blocker + * @example Skeleton_blocker_iteration.cpp + * @example Skeleton_blocker_from_simplices.cpp + * @example Skeleton_blocker_link.cpp + * \section Alpha_complex_example_section Alpha_complex + * @example alpha_complex_persistence.cpp + * @example alpha_complex_3d_persistence.cpp * @example Alpha_complex_from_points.cpp - * \section bottleneck_examples bottleneck - * @example bottleneck_basic_example.cpp - * @example alpha_rips_persistence_bottleneck_distance.cpp - * @example example_nearest_landmark_table.cpp - * @example example_witness_complex_off.cpp - * @example example_witness_complex_sphere.cpp - * @example example_strong_witness_complex_off.cpp + * @example Alpha_complex_3d_from_points.cpp + * @example Weighted_alpha_complex_3d_from_points.cpp + * @example Fast_alpha_complex_from_off.cpp + * @example Alpha_complex_from_off.cpp + * @example Weighted_alpha_complex_from_points.cpp + * \section Simplex_tree_example_section Simplex_tree + * @example cech_complex_cgal_mini_sphere_3d.cpp * @example mini_simplex_tree.cpp + * @example example_alpha_shapes_3_simplex_tree_from_off_file.cpp * @example graph_expansion_with_blocker.cpp * @example simple_simplex_tree.cpp * @example simplex_tree_from_cliques_of_graph.cpp - * @example example_alpha_shapes_3_simplex_tree_from_off_file.cpp - * @example cech_complex_cgal_mini_sphere_3d.cpp - * @example plain_homology.cpp - * @example persistence_from_file.cpp - * @example rips_persistence_step_by_step.cpp + * \section Collapse_example_section Collapse + * @example point_cloud_edge_collapse_rips_persistence.cpp + * @example distance_matrix_edge_collapse_rips_persistence.cpp + * @example edge_collapse_basic_example.cpp + * @example edge_collapse_conserve_persistence.cpp + * \section Persistent_cohomology_example_section Persistent_cohomology * @example rips_persistence_via_boundary_matrix.cpp + * @example rips_persistence_step_by_step.cpp + * @example plain_homology.cpp * @example custom_persistence_sort.cpp * @example persistence_from_simple_simplex_tree.cpp + * @example persistence_from_file.cpp * @example rips_multifield_persistence.cpp - * @example Skeleton_blocker_from_simplices.cpp - * @example Skeleton_blocker_iteration.cpp - * @example Skeleton_blocker_link.cpp - * @example Garland_heckbert.cpp - * @example Rips_contraction.cpp - * @example Random_bitmap_cubical_complex.cpp - * @example example_CGAL_3D_points_off_reader.cpp - * @example example_vector_double_points_off_reader.cpp - * @example example_CGAL_points_off_reader.cpp - * @example example_one_skeleton_rips_from_distance_matrix.cpp - * @example example_one_skeleton_rips_from_points.cpp - * @example example_rips_complex_from_csv_distance_matrix_file.cpp - * @example example_rips_complex_from_off_file.cpp - * @example persistence_intervals.cpp - * @example persistence_vectors.cpp - * @example persistence_heat_maps.cpp - * @example persistence_landscape_on_grid.cpp - * @example persistence_landscape.cpp - * @example example_basic.cpp - * @example example_with_perturb.cpp - * @example example_custom_distance.cpp - * @example example_choose_n_farthest_points.cpp - * @example example_sparsify_point_set.cpp - * @example example_pick_n_random_points.cpp - * @example CoordGIC.cpp + * \section Nerve_GIC_example_section Nerve_GIC + * @example VoronoiGIC.cpp * @example Nerve.cpp * @example FuncGIC.cpp - * @example VoronoiGIC.cpp - * @example example_spatial_searching.cpp - * @example alpha_complex_3d_persistence.cpp - * @example alpha_complex_persistence.cpp - * @example Weighted_alpha_complex_3d_from_points.cpp - * @example bottleneck_distance.cpp - * @example weak_witness_persistence.cpp - * @example strong_witness_persistence.cpp - * @example cubical_complex_persistence.cpp - * @example periodic_cubical_complex_persistence.cpp - * @example off_file_from_shape_generator.cpp - * @example rips_distance_matrix_persistence.cpp + * @example CoordGIC.cpp + * \section Rips_complex_example_section Rips_complex * @example rips_persistence.cpp + * @example sparse_rips_persistence.cpp + * @example rips_correlation_matrix_persistence.cpp + * @example rips_distance_matrix_persistence.cpp + * @example example_one_skeleton_rips_from_correlation_matrix.cpp + * @example example_rips_complex_from_csv_distance_matrix_file.cpp + * @example example_sparse_rips.cpp + * @example example_one_skeleton_rips_from_distance_matrix.cpp + * @example example_rips_complex_from_off_file.cpp + * @example example_one_skeleton_rips_from_points.cpp + * \section Persistence_representations_example_section Persistence_representations + * @example persistence_landscapes_on_grid/average_landscapes_on_grid.cpp * @example persistence_landscapes_on_grid/create_landscapes_on_grid.cpp + * @example persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp * @example persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp * @example persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp - * @example persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp - * @example persistence_landscapes_on_grid/average_landscapes_on_grid.cpp * @example persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp - * @example persistence_intervals/compute_number_of_dominant_intervals.cpp - * @example persistence_intervals/plot_persistence_Betti_numbers.cpp * @example persistence_intervals/plot_persistence_intervals.cpp * @example persistence_intervals/plot_histogram_of_intervals_lengths.cpp * @example persistence_intervals/compute_bottleneck_distance.cpp - * @example persistence_heat_maps/create_pssk.cpp - * @example persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp + * @example persistence_intervals/plot_persistence_Betti_numbers.cpp + * @example persistence_intervals/compute_number_of_dominant_intervals.cpp + * @example persistence_heat_maps/average_persistence_heat_maps.cpp * @example persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp - * @example persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp - * @example persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp + * @example persistence_heat_maps/create_pssk.cpp * @example persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp - * @example persistence_heat_maps/average_persistence_heat_maps.cpp + * @example persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp + * @example persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp * @example persistence_heat_maps/plot_persistence_heat_map.cpp + * @example persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp * @example persistence_heat_maps/create_persistence_heat_maps.cpp - * @example persistence_vectors/plot_persistence_vectors.cpp - * @example persistence_vectors/compute_distance_of_persistence_vectors.cpp * @example persistence_vectors/average_persistence_vectors.cpp + * @example persistence_vectors/plot_persistence_vectors.cpp * @example persistence_vectors/create_persistence_vectors.cpp * @example persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp - * @example persistence_landscapes/average_landscapes.cpp - * @example persistence_landscapes/compute_scalar_product_of_landscapes.cpp + * @example persistence_vectors/compute_distance_of_persistence_vectors.cpp * @example persistence_landscapes/create_landscapes.cpp + * @example persistence_landscapes/average_landscapes.cpp * @example persistence_landscapes/compute_distance_of_landscapes.cpp * @example persistence_landscapes/plot_landscapes.cpp + * @example persistence_landscapes/compute_scalar_product_of_landscapes.cpp + * @example persistence_heat_maps.cpp + * @example sliced_wasserstein.cpp + * @example persistence_intervals.cpp + * @example persistence_vectors.cpp + * @example persistence_landscape.cpp + * @example persistence_landscape_on_grid.cpp + * \section common_example_section common + * @example off_file_from_shape_generator.cpp + * @example example_CGAL_points_off_reader.cpp + * @example example_vector_double_points_off_reader.cpp + * @example example_CGAL_3D_points_off_reader.cpp + * \section Subsampling_example_section Subsampling + * @example example_pick_n_random_points.cpp + * @example example_choose_n_farthest_points.cpp + * @example example_sparsify_point_set.cpp + * @example example_custom_distance.cpp + * \section Contraction_example_section Contraction + * @example Rips_contraction.cpp + * @example Garland_heckbert.cpp + * \section Bottleneck_distance_example_section Bottleneck_distance + * @example bottleneck_distance.cpp + * @example bottleneck_basic_example.cpp + * @example alpha_rips_persistence_bottleneck_distance.cpp + * \section Tangential_complex_example_section Tangential_complex + * @example example_basic.cpp + * @example example_with_perturb.cpp + * \section Cech_complex_example_section Cech_complex + * @example cech_persistence.cpp + * @example cech_complex_example_from_points.cpp + * @example cech_complex_step_by_step.cpp + * \section Spatial_searching_example_section Spatial_searching + * @example example_spatial_searching.cpp + * \section Bitmap_cubical_complex_example_section Bitmap_cubical_complex + * @example periodic_cubical_complex_persistence.cpp + * @example cubical_complex_persistence.cpp + * @example Random_bitmap_cubical_complex.cpp + * \section Toplex_map_example_section Toplex_map + * @example simple_toplex_map.cpp + * \section Witness_complex_example_section Witness_complex + * @example weak_witness_persistence.cpp + * @example strong_witness_persistence.cpp + * @example example_witness_complex_sphere.cpp + * @example example_strong_witness_complex_off.cpp + * @example example_nearest_landmark_table.cpp + * @example example_witness_complex_off.cpp */ diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 5d40a48e..609f2f2f 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -88,9 +88,9 @@ make \endverbatim * Witness_complex/example_witness_complex_off.cpp * \li * Witness_complex/example_witness_complex_sphere.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_off.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_points.cpp * \li * Alpha_complex/alpha_complex_persistence.cpp @@ -100,15 +100,15 @@ make \endverbatim * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp * \li * Bottleneck_distance/bottleneck_basic_example.cpp - * \li + * \li * Bottleneck_distance/bottleneck_distance.cpp - * \li + * \li * Nerve_GIC/CoordGIC.cpp - * \li + * \li * Nerve_GIC/FuncGIC.cpp - * \li + * \li * Nerve_GIC/Nerve.cpp - * \li + * \li * Nerve_GIC/VoronoiGIC.cpp * \li * Spatial_searching/example_spatial_searching.cpp @@ -122,7 +122,7 @@ make \endverbatim * Tangential_complex/example_basic.cpp * \li * Tangential_complex/example_with_perturb.cpp - * \li + * \li * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp * \li * Alpha_complex/alpha_complex_3d_persistence.cpp @@ -134,15 +134,15 @@ make \endverbatim * * The following examples/utilities require the Eigen and will not be * built if Eigen is not installed: - * \li + * \li * Alpha_complex/Alpha_complex_from_off.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_points.cpp * \li * Alpha_complex/alpha_complex_persistence.cpp * \li * Alpha_complex/alpha_complex_3d_persistence.cpp - * \li + * \li * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp * \li * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp @@ -179,27 +179,27 @@ make \endverbatim * Having Intel® TBB installed is recommended to parallelize and accelerate some GUDHI computations. * * The following examples/utilities are using Intel® TBB if installed: - * \li + * \li * Alpha_complex/Alpha_complex_from_off.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_points.cpp * \li * Alpha_complex/alpha_complex_3d_persistence.cpp * \li * Alpha_complex/alpha_complex_persistence.cpp - * \li + * \li * Bitmap_cubical_complex/cubical_complex_persistence.cpp - * \li + * \li * Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp - * \li + * \li * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp - * \li + * \li * Nerve_GIC/CoordGIC.cpp - * \li + * \li * Nerve_GIC/FuncGIC.cpp - * \li + * \li * Nerve_GIC/Nerve.cpp - * \li + * \li * Nerve_GIC/VoronoiGIC.cpp * \li * Simplex_tree/simple_simplex_tree.cpp diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index cb7700ce..35c344e3 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -359,7 +359,7 @@ Python Optimal Transport ------------------------ The :doc:`Wasserstein distance ` -module requires `POT `_, a library that provides +module requires `POT `_, a library that provides several solvers for optimization problems related to Optimal Transport. PyTorch -- cgit v1.2.3 From 4fc331267735a3368160ea7cd001b7fa45d720f7 Mon Sep 17 00:00:00 2001 From: Vincent Rouvreau Date: Thu, 10 Feb 2022 10:32:18 +0100 Subject: Boost 1.66.0 is now the minimal version as required from cgal 5.1 - Also remove useless include boost/version.h --- .github/next_release.md | 3 +++ src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 1 - src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h | 1 - src/Subsampling/include/gudhi/sparsify_point_set.h | 5 ----- src/cmake/modules/GUDHI_third_party_libraries.cmake | 2 +- src/common/doc/installation.h | 2 +- src/common/include/gudhi/reader_utils.h | 4 ---- src/python/doc/installation.rst | 2 +- 8 files changed, 6 insertions(+), 14 deletions(-) (limited to 'src/common/doc') diff --git a/.github/next_release.md b/.github/next_release.md index 65a92816..e21b25c7 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -13,6 +13,9 @@ Below is a list of changes made since GUDHI 3.5.0: - [Representations](https://gudhi.inria.fr/python/latest/representations.html#gudhi.representations.vector_methods.BettiCurve) - A more flexible Betti curve class capable of computing exact curves +- Installation + - Boost ≥ 1.66.0 is now required (was ≥ 1.56.0). + - [Module](link) - ... diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index ccc3d852..df5c630e 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -12,7 +12,6 @@ #ifndef ALPHA_COMPLEX_3D_H_ #define ALPHA_COMPLEX_3D_H_ -#include #include #include #include diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h index ee64a277..e5522cc7 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h @@ -14,7 +14,6 @@ #include #include -#include #include #include diff --git a/src/Subsampling/include/gudhi/sparsify_point_set.h b/src/Subsampling/include/gudhi/sparsify_point_set.h index 4571b8f3..b325fe3c 100644 --- a/src/Subsampling/include/gudhi/sparsify_point_set.h +++ b/src/Subsampling/include/gudhi/sparsify_point_set.h @@ -11,12 +11,7 @@ #ifndef SPARSIFY_POINT_SET_H_ #define SPARSIFY_POINT_SET_H_ -#include -#if BOOST_VERSION < 106600 -# include -#else # include -#endif #include #ifdef GUDHI_SUBSAMPLING_PROFILING diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index b316740d..68ffaee1 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 1.56.0 QUIET OPTIONAL_COMPONENTS filesystem unit_test_framework program_options) +find_package(Boost 1.66.0 QUIET OPTIONAL_COMPONENTS filesystem unit_test_framework program_options) # Boost_FOUND is not reliable if(NOT Boost_VERSION) diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index ef668dfb..67d026bd 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -5,7 +5,7 @@ * Examples of GUDHI headers inclusion can be found in \ref utilities. * * \section compiling Compiling - * The library uses c++14 and requires Boost ≥ 1.56.0 + * The library uses c++14 and requires Boost ≥ 1.66.0 * and CMake ≥ 3.5. * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. * diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index a1b104e2..29d5423d 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -14,11 +14,7 @@ #include #include -#if BOOST_VERSION < 106600 -# include -#else # include -#endif #include #include diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 35c344e3..c2c3db34 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -39,7 +39,7 @@ If you are instead using a git checkout, beware that the paths are a bit different, and in particular the `python/` subdirectory is actually `src/python/` there. -The library uses c++14 and requires `Boost `_ :math:`\geq` 1.56.0, +The library uses c++14 and requires `Boost `_ :math:`\geq` 1.66.0, `CMake `_ :math:`\geq` 3.5 to generate makefiles, `NumPy `_ :math:`\geq` 1.15.0, `Cython `_ and `pybind11 `_ to compile -- cgit v1.2.3