Disable float versions in Python bindings, add Decomposition ctor fro…

…m MatrixData

CMakeLists.txt

@@ -5,6 +5,7 @@ project(oineus LANGUAGES CXX)
 option(oin_use_spdlog "Use spdlog" OFF)
 option(oin_use_jemalloc "Use jemalloc" OFF)
 option(oin_build_tests "Build tests" ON)
+option(oin_build_examples "Build examples" ON)
 option(oin_gather_add_stats "Gather statistics about summand sizes" OFF)
 option(oin_caliper "Enable profiling with Caliper" OFF)
 
@@ -40,7 +41,10 @@ if(oin_caliper)
 endif()
 
 
-add_subdirectory(examples)
+if (oin_build_examples)
+    add_subdirectory(examples)
+endif ()
+
 add_subdirectory(bindings/python)
 
 if (oin_build_tests)

bindings/python/oineus.cpp

@@ -8,16 +8,16 @@ PYBIND11_MODULE(_oineus, m)
 {
     m.doc() = "Oineus python bindings";
 
-    std::string float_suffix = "_float";
+//    std::string float_suffix = "_float";
     std::string double_suffix = "_double";
 //    std::string double_suffix = "";
 
     init_oineus_common_int(m);
     init_oineus_common_diagram_int(m);
     init_oineus_common_decomposition_int(m);
 
-    init_oineus_functions_float(m, float_suffix);
-    init_oineus_fil_dgm_simplex_float(m, float_suffix);
+//    init_oineus_functions_float(m, float_suffix);
+//    init_oineus_fil_dgm_simplex_float(m, float_suffix);
 
     init_oineus_functions_double(m, double_suffix);
     init_oineus_fil_dgm_simplex_double(m, double_suffix);

bindings/python/oineus_persistence_bindings.h

@@ -561,6 +561,7 @@ void init_oineus_common_decomposition(py::module& m)
             .def(py::init<const SimplexFiltrationFloat&, bool>())
             .def(py::init<const ProdSimplexFiltrationDouble&, bool>())
             .def(py::init<const ProdSimplexFiltrationFloat&, bool>())
+            .def(py::init<const typename Decomposition::MatrixData&, size_t>())
             .def_readwrite("r_data", &Decomposition::r_data)
             .def_readwrite("v_data", &Decomposition::v_data)
             .def_readwrite("u_data_t", &Decomposition::u_data_t)
@@ -904,6 +905,7 @@ void init_oineus_fil_dgm_simplex(py::module& m, std::string suffix)
             .def("get_sorted_id_by_vertices", &Filtration::get_sorted_id_by_vertices, py::arg("vertices"))
             .def("cell_by_uid", &Filtration::get_cell_by_uid, py::arg("uid"))
             .def("boundary_matrix", &Filtration::boundary_matrix_full)
+            .def("coboundary_matrix", &Filtration::coboundary_matrix)
             .def("boundary_matrix_rel", &Filtration::boundary_matrix_full_rel)
             .def("reset_ids_to_sorted_ids", &Filtration::reset_ids_to_sorted_ids)
             .def("__repr__", [](const Filtration& fil) {

include/oineus/decomposition.h

@@ -261,7 +261,7 @@ namespace oineus {
         template<class C, class R>
         VRUDecomposition(const Filtration<C, R>& fil, bool _dualize)
                 :
-                d_data(!_dualize ? fil.boundary_matrix_full() : antitranspose(fil.boundary_matrix_full(), fil.size())),
+                d_data(!_dualize ? fil.boundary_matrix_full() : fil.coboundary_matrix()),
                 r_data(d_data),
                 dualize_(_dualize),
                 dim_first(fil.dim_first()),

include/oineus/filtration.h

@@ -123,6 +123,7 @@ namespace oineus {
 
         dim_type max_dim() const { return dim_last_.size() - 1; }
 
+
         BoundaryMatrix boundary_matrix_full() const
         {
             CALI_CXX_MARK_FUNCTION;
@@ -203,6 +204,10 @@ namespace oineus {
             return result;
         }
 
+        BoundaryMatrix coboundary_matrix() const
+        {
+            return antitranspose(boundary_matrix_full(), size());
+        }
 
         template<typename I, typename R, size_t D>
         friend class Grid;

requirements.txt

@@ -1,46 +1,3 @@
-ansi2html==1.8.0
-certifi==2023.7.22
-charset-normalizer==3.3.1
-click==8.1.7
-dash==2.14.0
-dash-core-components==2.0.0
-dash-html-components==2.0.0
-dash-table==5.0.0
-filelock==3.12.4
-Flask==2.2.5
-fsspec==2023.10.0
-idna==3.4
-importlib-metadata==6.8.0
-itsdangerous==2.1.2
-Jinja2==3.1.2
-MarkupSafe==2.1.3
-mpmath==1.3.0
-nest-asyncio==1.5.8
-networkx==3.2
-numpy==1.26.1
-nvidia-cublas-cu12==12.1.3.1
-nvidia-cuda-cupti-cu12==12.1.105
-nvidia-cuda-nvrtc-cu12==12.1.105
-nvidia-cuda-runtime-cu12==12.1.105
-nvidia-cudnn-cu12==8.9.2.26
-nvidia-cufft-cu12==11.0.2.54
-nvidia-curand-cu12==10.3.2.106
-nvidia-cusolver-cu12==11.4.5.107
-nvidia-cusparse-cu12==12.1.0.106
-nvidia-nccl-cu12==2.18.1
-nvidia-nvjitlink-cu12==12.3.52
-nvidia-nvtx-cu12==12.1.105
-packaging==23.2
-plotly==5.18.0
-requests==2.31.0
-retrying==1.3.4
-scipy==1.11.3
-six==1.16.0
-sympy==1.12
-tenacity==8.2.3
-torch==2.1.0
-triton==2.1.0
-typing_extensions==4.8.0
-urllib3==2.0.7
-Werkzeug==2.2.3
-zipp==3.17.0
+scipy
+numpy
+eagerpy