merge upstream part1

src/Zigzag_persistence/concept/ZigzagOptions.h

@@ -34,7 +34,7 @@ struct FilteredZigzagOptions {
    * @brief Type for the face IDs used at insertion and in the boundaries given as argument.
    * Has to be usable as key in a hashtable, so "hashable" and comparable.
    */
-  using Face_key = unspecified;
+  using Cell_key = unspecified;
 
   /**
    * @brief Type for filtration values.

src/Zigzag_persistence/example/example_usage_filtered_zigzag_persistence.cpp

@@ -30,21 +30,21 @@ int main() {
   // filtration values are monotonous (ie., either only increasing or only decreasing).
 
   // inserts vertex 2 at filtration value 0.1 -> birth at 0.1 of 0-cycle
-  zp.insert_face(2, {}, 0, 0.1);
+  zp.insert_cell(2, {}, 0, 0.1);
   // inserts vertex 4 at filtration value 0.1 -> birth at 0.1 of 0-cycle
-  zp.insert_face(4, {}, 0, 0.1);
+  zp.insert_cell(4, {}, 0, 0.1);
   // inserts edge 5 = (2,4) at filtration value 0.3 -> death at 0.3 -> outputs (0, 0.1, 0.3)
-  zp.insert_face(5, {2, 4}, 1, 0.3);
+  zp.insert_cell(5, {2, 4}, 1, 0.3);
   // inserts vertex 3 at filtration value 0.4 -> birth at 0.4 of 0-cycle
-  zp.insert_face(3, {}, 0, 0.4);
+  zp.insert_cell(3, {}, 0, 0.4);
   // inserts edge 6 = (2,3) at filtration value 0.4 -> death at 0.4 of the cycle born at 0.4 -> outputs nothing
-  zp.insert_face(6, {2, 3}, 1, 0.4);
+  zp.insert_cell(6, {2, 3}, 1, 0.4);
   // inserts edge 9 = (3,4) at filtration value 1.2 -> birth at 1.2 of 1-cycle
-  zp.insert_face(9, {4, 3}, 1, 1.2);
+  zp.insert_cell(9, {4, 3}, 1, 1.2);
   // removes edge 6 at filtration value 1.5 -> death at 1.5 -> outputs (1, 1.2, 1.5)
-  zp.remove_face(6, 1.5);
+  zp.remove_cell(6, 1.5);
   // removes edge 5 at filtration value 2.0 -> birth at 2.0 of 0-cycle
-  zp.remove_face(5, 2.0);
+  zp.remove_cell(5, 2.0);
 
   // Only the closed bars where output so far, so the open/infinite bars still need to be retrieved.
 

src/Zigzag_persistence/example/example_usage_filtered_zigzag_persistence_with_storage.cpp

@@ -25,21 +25,21 @@ int main() {
   // filtration values are monotonous (ie., either only increasing or only decreasing).
 
   // inserts vertex 2 at filtration value 0.1 -> birth at 0.1 of 0-cycle
-  zp.insert_face(2, {}, 0, 0.1);
+  zp.insert_cell(2, {}, 0, 0.1);
   // inserts vertex 4 at filtration value 0.1 -> birth at 0.1 of 0-cycle
-  zp.insert_face(4, {}, 0, 0.1);
+  zp.insert_cell(4, {}, 0, 0.1);
   // inserts edge 5 = (2,4) at filtration value 0.3 -> death at 0.3 -> stores (0, 0.1, 0.3)
-  zp.insert_face(5, {2, 4}, 1, 0.3);
+  zp.insert_cell(5, {2, 4}, 1, 0.3);
   // inserts vertex 3 at filtration value 0.4 -> birth at 0.4 of 0-cycle
-  zp.insert_face(3, {}, 0, 0.4);
+  zp.insert_cell(3, {}, 0, 0.4);
   // inserts edge 6 = (2,3) at filtration value 0.4 -> death at 0.4 of the cycle born at 0.4 -> stores nothing
-  zp.insert_face(6, {2, 3}, 1, 0.4);
+  zp.insert_cell(6, {2, 3}, 1, 0.4);
   // inserts edge 9 = (3,4) at filtration value 1.2 -> birth at 1.2 of 1-cycle
-  zp.insert_face(9, {4, 3}, 1, 1.2);
+  zp.insert_cell(9, {4, 3}, 1, 1.2);
   // removes edge 6 at filtration value 1.5 -> death at 1.5 -> stores (1, 1.2, 1.5)
-  zp.remove_face(6, 1.5);
+  zp.remove_cell(6, 1.5);
   // removes edge 5 at filtration value 2.0 -> birth at 2.0 of 0-cycle
-  zp.remove_face(5, 2.0);
+  zp.remove_cell(5, 2.0);
 
   // The bars are stored within the class and where not output at all for now.
 

src/Zigzag_persistence/example/example_usage_zigzag_persistence.cpp

@@ -29,21 +29,21 @@ int main() {
   // A face has to be identified in the boundaries by the operation number the face was inserted with in the sequence.
 
   // inserts vertex 0 -> birth at 0 of 0-cycle
-  zp.insert_face({}, 0);
+  zp.insert_cell({}, 0);
   // inserts vertex 1 -> birth at 1 of 0-cycle
-  zp.insert_face({}, 0);
+  zp.insert_cell({}, 0);
   // inserts edge 2 = (0,1) -> death at 2 -> outputs (0, 1, 2)
-  zp.insert_face({0, 1}, 1);
+  zp.insert_cell({0, 1}, 1);
   // inserts vertex 3 -> birth at 3 of 0-cycle
-  zp.insert_face({}, 0);
+  zp.insert_cell({}, 0);
   // inserts edge 4 = (0,3) -> death at 4 -> outputs (0, 3, 4)
-  zp.insert_face({0, 3}, 1);
+  zp.insert_cell({0, 3}, 1);
   // inserts edge 5 = (1,3) -> birth at 5 of 1-cycle
-  zp.insert_face({1, 3}, 1);
+  zp.insert_cell({1, 3}, 1);
   // removes edge 4 -> death at 6 -> outputs (1, 5, 6)
-  zp.remove_face(4);
+  zp.remove_cell(4);
   // removes edge 2 -> birth at 7 of 0-cycle
-  zp.remove_face(2);
+  zp.remove_cell(2);
 
   // Only the closed bars were output so far, so the open/infinite bars still need to be retrieved.
 

src/Zigzag_persistence/example/example_zigzag_filtration_as_input_loop.cpp

@@ -14,7 +14,7 @@
 #include <gudhi/filtered_zigzag_persistence.h>
 
 using ZP = Gudhi::zigzag_persistence::Filtered_zigzag_persistence_with_storage<>;
-using Face_handle = ZP::Face_key;
+using Cell_handle = ZP::Cell_key;
 using Filtration_value = ZP::Filtration_value;
 using Interval_filtration = ZP::Filtration_value_interval;
 
@@ -50,7 +50,7 @@ void print_indices(ZP& zp) {
   }
 }
 
-std::vector<std::vector<Face_handle> > get_boundaries() {
+std::vector<std::vector<Cell_handle> > get_boundaries() {
   return {{},
           {},
           {},
@@ -114,7 +114,7 @@ int main(int argc, char* const argv[]) {
 
   ZP zp;
 
-  std::vector<std::vector<Face_handle> > simplices = get_boundaries();
+  std::vector<std::vector<Cell_handle> > simplices = get_boundaries();
   std::vector<Filtration_value> fils = get_filtration_values();
   std::vector<bool> dirs = get_directions();
 
@@ -125,10 +125,10 @@ int main(int argc, char* const argv[]) {
     }
     if (dirs[i]) {
       int dim = simplices[i].size() == 0 ? 0 : simplices[i].size() - 1;
-      zp.insert_face(i, simplices[i], dim, fils[i]);
+      zp.insert_cell(i, simplices[i], dim, fils[i]);
     } else {
       auto id = simplices[i][0];
-      zp.remove_face(id, fils[i]);
+      zp.remove_cell(id, fils[i]);
     }
   }
 

src/Zigzag_persistence/example/example_zzfiltration_from_file.cpp

@@ -16,7 +16,7 @@
 #include <gudhi/filtered_zigzag_persistence.h>
 
 using ZP = Gudhi::zigzag_persistence::Filtered_zigzag_persistence<>;
-using ID_handle = ZP::Face_key;
+using ID_handle = ZP::Cell_key;
 using Filtration_value = ZP::Filtration_value;
 using Dimension = ZP::Dimension;
 
@@ -89,7 +89,7 @@ int main(int argc, char* const argv[]) {
     while (getline(file, line, '\n') && read_operation(line, data, timestamp) == COMMENT);
     double lastTimestamp = timestamp;
     // first operation has to be an insertion.
-    zp.insert_face(id, data, 0, timestamp);
+    zp.insert_cell(id, data, 0, timestamp);
 
     while (getline(file, line, '\n')) {
       type = read_operation(line, data, timestamp);
@@ -100,10 +100,10 @@ int main(int argc, char* const argv[]) {
       if (type == INCLUSION) {
         ++id;
         int dim = data.size() == 0 ? 0 : data.size() - 1;
-        zp.insert_face(id, data, dim, timestamp);
+        zp.insert_cell(id, data, dim, timestamp);
       } else if (type == REMOVAL) {
         ++id;
-        zp.remove_face(data[0], timestamp);
+        zp.remove_cell(data[0], timestamp);
       }
     }
 

src/Zigzag_persistence/include/gudhi/Oscillating_rips_persistence.h

@@ -68,16 +68,16 @@ struct Simplex_tree_options_oscillating_rips {
 
 template <class StableFilteredComplex>
 struct Default_oscillating_rips_zigzag_options : Default_filtered_zigzag_options {
-  using Face_key = typename StableFilteredComplex::Simplex_handle;
+  using Cell_key = typename StableFilteredComplex::Simplex_handle;
   using Filtration_value = typename StableFilteredComplex::Filtration_value;
   using Dimension = int;  // it is `int` in the simplex tree
   struct Hash {
-    std::size_t operator()(const Face_key& sh) const {
+    std::size_t operator()(const Cell_key& sh) const {
       return sh->second.key();
     }
   };
   struct KeyEqual {
-    bool operator()(const Face_key& sh1, const Face_key& sh2) const {
+    bool operator()(const Cell_key& sh1, const Cell_key& sh2) const {
       return sh1->second.key() == sh2->second.key();
     }
   };
@@ -154,12 +154,12 @@ void compute_oscillating_rips_persistence(
 
   for (const auto& t : OscillatingRipsSimplexRange::get_iterator_range(start, end, st, maxDim)) {
     if (std::get<2>(t))
-      zp.insert_face(std::get<0>(t),
+      zp.insert_cell(std::get<0>(t),
                      st.boundary_simplex_range(std::get<0>(t)),
                      st.dimension(std::get<0>(t)),
                      std::get<1>(t));
     else
-      zp.remove_face(std::get<0>(t), std::get<1>(t));
+      zp.remove_cell(std::get<0>(t), std::get<1>(t));
   }
 
   zp.get_current_infinite_intervals([&](Dimension dim, Filtration_value birth) { outStream(dim, birth, Bar::inf); });
@@ -233,12 +233,12 @@ compute_oscillating_rips_persistence(
 
   for (const auto& t : OscillatingRipsSimplexRange::get_iterator_range(start, end, st, maxDim)) {
     if (std::get<2>(t))
-      zp.insert_face(std::get<0>(t),
+      zp.insert_cell(std::get<0>(t),
                      st.boundary_simplex_range(std::get<0>(t)),
                      st.dimension(std::get<0>(t)),
                      std::get<1>(t));
     else
-      zp.remove_face(std::get<0>(t), std::get<1>(t));
+      zp.remove_cell(std::get<0>(t), std::get<1>(t));
   }
 
   return zp.get_persistence_diagram();