Move hera to submodule

.gitmodules

@@ -5,3 +5,6 @@
 	path = gtda/externals/gudhi-devel
 	url = https://github.com/giotto-ai/gudhi-devel
 	branch = giotto
+[submodule "gtda/externals/hera"]
+	path = gtda/externals/hera
+	url = https://github.com/grey-narn/hera

CMakeLists.txt

@@ -11,6 +11,7 @@ find_package(OpenMP)
 
 set(RIPSER_SRC_DIR "gtda/externals/ripser")
 set(GUDHI_SRC_DIR "gtda/externals/gudhi-devel/src")
+set(HERA_DIR "gtda/externals/hera")
 
 #######################################################################
 #                               Ripser                                #
@@ -56,10 +57,13 @@ endif()
 #                             Wasserstein                             #
 #######################################################################
 
-pybind11_add_module(gtda_wasserstein "${BINDINGS_DIR}/wasserstein_bindings.cpp")
+pybind11_add_module(gtda_wasserstein ${BINDINGS_DIR}/wasserstein_bindings.cpp)
 target_link_libraries(gtda_wasserstein LINK_PUBLIC ${Boost_LIBRARIES})
 target_compile_definitions(gtda_wasserstein PRIVATE BOOST_RESULT_OF_USE_DECLTYPE=1 BOOST_ALL_NO_LIB=1 BOOST_SYSTEM_NO_DEPRECATED=1)
 
+target_include_directories(gtda_wasserstein PRIVATE "${HERA_DIR}")
+target_include_directories(gtda_wasserstein PRIVATE "${HERA_DIR}/wasserstein/include")
+
 if(MSVC)
     target_compile_options(gtda_wasserstein PUBLIC $<$<CONFIG:RELEASE>: /Wall /O2>)
     target_compile_options(gtda_wasserstein PUBLIC $<$<CONFIG:DEBUG>:/O1 /DEBUG:FULL /Zi /Zo>)
@@ -76,6 +80,9 @@ pybind11_add_module(gtda_bottleneck "${BINDINGS_DIR}/bottleneck_bindings.cpp")
 target_link_libraries(gtda_bottleneck LINK_PUBLIC ${Boost_LIBRARIES})
 target_compile_definitions(gtda_bottleneck PRIVATE BOOST_RESULT_OF_USE_DECLTYPE=1 BOOST_ALL_NO_LIB=1 BOOST_SYSTEM_NO_DEPRECATED=1)
 
+target_include_directories(gtda_bottleneck PRIVATE "${HERA_DIR}")
+target_include_directories(gtda_bottleneck PRIVATE "${HERA_DIR}/bottleneck/include")
+
 if(MSVC)
     target_compile_options(gtda_bottleneck PUBLIC $<$<CONFIG:RELEASE>: /Wall /O2>)
     target_compile_options(gtda_bottleneck PUBLIC $<$<CONFIG:DEBUG>:/O1 /DEBUG:FULL /Zi /Zo>)

azure-pipelines.yml

@@ -38,7 +38,7 @@ jobs:
 
   - task: Cache@2
     inputs:
-      key: '"ccache-wheels-v2020.03.12" | $(Agent.OS) | "$(python.version)"'
+      key: '"ccache-wheels-v2020.03.18" | $(Agent.OS) | "$(python.version)"'
       path: $(CCACHE_DIR)
     displayName: ccache
 
@@ -133,7 +133,7 @@ jobs:
 
   - task: Cache@2
     inputs:
-      key: '"ccache-v2020.03.12" | $(Agent.OS) | "$(python.version)"'
+      key: '"ccache-v2020.03.18" | $(Agent.OS) | "$(python.version)"'
       path: $(CCACHE_DIR)
     displayName: ccache
 

gtda/externals/bindings/bottleneck_bindings.cpp

@@ -4,14 +4,23 @@
  * License:          Apache 2.0
  *****************************************************************************/
 
-#include "../hera/bottleneck/bottleneck.h"
+/* ssize_t is not standard C, it is a typedef from Posix.
+ * Following solution is copy/pasted from solution found in
+ * https://stackoverflow.com/a/35368387
+ */
+#if defined(_MSC_VER)
+#include <BaseTsd.h>
+typedef SSIZE_T ssize_t;
+#endif
+
+#include <bottleneck/include/bottleneck.h>
 
 // PYBIND11
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 
-double bottleneck_distance(const std::vector<std::pair<double, double>>& dgm1,
-                           const std::vector<std::pair<double, double>>& dgm2,
+double bottleneck_distance(std::vector<std::pair<double, double>>& dgm1,
+                           std::vector<std::pair<double, double>>& dgm2,
                            double delta) {
   if (delta == 0.0)
     return hera::bottleneckDistExact(dgm1, dgm2);

gtda/externals/bindings/wasserstein_bindings.cpp

@@ -3,7 +3,7 @@
  * License:          Apache 2.0
  *****************************************************************************/
 
-#include "../hera/wasserstein/wasserstein.h"
+#include <wasserstein/include/wasserstein.h>
 
 // PYBIND11
 #include <pybind11/pybind11.h>
@@ -12,17 +12,18 @@
 double wasserstein_distance(const std::vector<std::pair<double, double>>& dgm1,
                             const std::vector<std::pair<double, double>>& dgm2,
                             double q, double delta, double internal_p,
-                            double initial_eps, double eps_factor) {
+                            double initial_eps, double eps_factor,
+                            int max_bids_per_round) {
   hera::AuctionParams<double> params;
   params.wasserstein_power = q;
   params.delta = delta;
   params.internal_p = internal_p;
+  params.max_bids_per_round = max_bids_per_round;
+  params.epsilon_common_ratio = eps_factor;
 
   if (initial_eps != 0) params.initial_epsilon = initial_eps;
 
-  if (eps_factor != 0.) params.epsilon_common_ratio = eps_factor;
-
-  return hera::wasserstein_dist(dgm1, dgm2, params);
+  return hera::wasserstein_dist<>(dgm1, dgm2, params);
 }
 
 namespace py = pybind11;
@@ -34,5 +35,8 @@ PYBIND11_MODULE(gtda_wasserstein, m) {
         py::arg("q") = 2.0, py::arg("delta") = .01,
         py::arg("internal_p") = hera::get_infinity<double>(),
         py::arg("initial_eps") = 0., py::arg("eps_factor") = 0.,
+        py::arg("max_bids_per_round") = 1,
         "compute Wasserstein distance between two persistence diagrams");
+  m.def("hera_get_infinity", hera::get_infinity<double>,
+        "hera infinity is not equal float('inf'), but -1, be careful");
 }