Merge pull request #21 from crvs/python3

Python3

.gitignore

@@ -1,6 +1,3 @@
-# ignore all files
-*
-
 # tags file
 tags
 

.gitmodules

@@ -10,3 +10,6 @@
 [submodule "yaml-cpp"]
 	path = yaml-cpp
 	url = https://github.com/jbeder/yaml-cpp
+[submodule "pybind11"]
+	path = pybind11
+	url = https://github.com/pybind/pybind11

CMakeLists.txt

@@ -5,7 +5,6 @@ project(coefficient-flow CXX)
 #   * Gudhi under /usr/include/gudhi
 #   * Eigen3 under /usr/include/eigen3
 #   * boost under /usr/include/boost
-#
 
 # in case Eigen, and/or GUDHI are not found by find_package
 # try setting the paths to them manually
@@ -21,6 +20,9 @@ project(coefficient-flow CXX)
 add_subdirectory(yaml-cpp)
 include_directories("./yaml-cpp/include/")
 
+add_subdirectory(pybind11)
+include_directories("./pybind11/include/")
+
 add_subdirectory(KDTree)
 include_directories("./KDTree")
 
@@ -56,7 +58,6 @@ set(CMAKE_BUILD_TYPE Release)
 
 include_directories( "./lib" )
 
-
 add_library(scomplex SHARED "./lib/scomplex/simplicial_complex.cpp")
 add_library(pathsnap SHARED "./lib/scomplex/path_snapper.cpp")
 target_link_libraries(pathsnap KDTree)
@@ -75,3 +76,7 @@ add_custom_target(timing_test
     COMMAND "${CMAKE_CURRENT_BINARY_DIR}/run_dumb_tests.sh" "1"
     DEPENDS yamltest qhull2ply "test/run_dumb_tests.sh" "test/dumbexample.yaml")
 
+#Python bindings:
+add_library(coeffflow MODULE python/bindings.cpp)
+target_link_libraries(coeffflow PRIVATE scomplex pybind11::module)
+set_target_properties(coeffflow PROPERTIES PREFIX "" SUFFIX .so)

README.md

@@ -49,6 +49,23 @@ make timing-test
 
 to run the timing tests, the files for the other tests, are still not provided.
 
+### Using Python bindings
+
+In the python bindings we provide bindings for the `simplicial_complex` which uses only cells to for construction, and provides also bindings for the functions `cell_to_index` and `index_to_cell`. Furthermore we provide bindings for `coeff_flow` and `coeff_flow_embedded`. Below is a toy example run:
+
+```{python}
+>>> import coeffflow
+>>> a = coeffflow.simplicial_complex([[0,1,2]])
+>>> a.cell_to_index([0,2])
+1
+>>> a.index_to_cell(0,1)
+[1]
+>>> a.index_to_cell(1,2)
+[2, 1]
+>>> coeffflow.coeff_flow_embedded(a ,(1, [1,-1,1]))
+(2, [1.0])
+```
+
 ### References/links
 
 [1]: Carvalho JF, Vejdemo-Johansson M, Kragic D, Pokorny FT. _An algorithm for calculating top-dimensional bounding chains._ 2017 [PeerJ Preprints 5:e3151v1](https://doi.org/10.7287/peerj.preprints.3151v1)

python/bindings.cpp

@@ -0,0 +1,23 @@
+#include <vector>
+
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
+#include "scomplex/coeff_flow.hpp"
+#include "scomplex/simplicial_complex.hpp"
+#include "scomplex/types.hpp"
+
+using namespace gsimp;
+
+namespace py = pybind11;
+
+PYBIND11_MODULE(coeffflow, m) {
+    py::class_< simplicial_complex >(m, "simplicial_complex")      //
+        .def(py::init< std::vector< cell_t >& >())                 //
+        .def("cell_to_index", &simplicial_complex::cell_to_index)  //
+        .def("index_to_cell", &simplicial_complex::index_to_cell);
+
+    m.def("coeff_flow", coeff_flow);
+
+    m.def("coeff_flow_embedded", coeff_flow_embedded);
+};