Merge pull request #22 from peekxc/dev

v.0.1.2 patched

.github/workflows/build_linux.yml

@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"] 
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
     - name: Checkout 
       uses: actions/checkout@v3

.github/workflows/build_macos.yml

@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["macos-latest"] 
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
     - name: Checkout 
       uses: actions/checkout@v3

.github/workflows/build_windows.yml

@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["windows-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
     - name: Checkout 
       uses: actions/checkout@v3

.github/workflows/wheels.yml

@@ -15,7 +15,7 @@ jobs:
       matrix:
         os: [windows-latest]
         cibw_arch: ["AMD64"]
-        cibw_python: ["cp38-*", "cp39-*", "cp310-*", "cp311-*"]
+        cibw_python: ["cp38-*", "cp39-*", "cp310-*", "cp311-*", "cp312-*"]
 
     steps:
       - uses: actions/checkout@v3
@@ -77,7 +77,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos-latest]
-        cibw_python: ["cp38-*", "cp39-*", "cp310-*", "cp311-*"]
+        cibw_python: ["cp38-*", "cp39-*", "cp310-*", "cp311-*", "cp312-*"]
         cibw_arch: ["x86_64", "arm64"]  # TODO: add "universal2" once a universal2 libomp is available
 
     steps:
@@ -159,7 +159,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        cibw_python: ["cp38-*", "cp39-*", "cp310-*", "cp311-*"]
+        cibw_python: ["cp38-*", "cp39-*", "cp310-*", "cp311-*", "cp312-*"]
         cibw_manylinux: [manylinux2014]
         cibw_arch: ["x86_64"]
 

CHANGELOG.md

@@ -7,7 +7,8 @@ This project loosely adheres to [semantic versioning](https://semver.org/spec/v2
 ## Unreleased [v0.1.2]
 
 - Exported underlying `st.reindex()` function to allow node relabeling
-
+- Added ability to chaneg the default simplex output type via the `s_type` Callable
+- Re-added vertex/edge contraction to the API
 
 ## [v0.1.1](https://github.com/peekxc/simplextree-py/releases/tag/v0.1.1) - 2023-08-20
 

include/simplextree.h

@@ -74,7 +74,8 @@ struct SimplexTree {
 	struct less_ptr {
     bool operator() (const node_uptr& lhs, const node_uptr& rhs) const { return (*lhs) < (*rhs); }
   };
-	using node_set_t = set< node_uptr, less_ptr >;
+	// using node_set_t = set< node_uptr, less_ptr >;
+  using node_set_t = vector< node_uptr >;
   using simplex_t = vector< idx_t >; 
   using cousin_map_t = std::map< idx_t, vector< node_ptr > >;
   using difference_type = std::ptrdiff_t;
@@ -217,15 +218,15 @@ struct SimplexTree {
   auto collapse(node_ptr, node_ptr) -> bool;
   auto vertex_collapse(idx_t, idx_t, idx_t) -> bool;
   auto vertex_collapse(node_ptr, node_ptr, node_ptr) -> bool;
-  auto contract(simplex_t) -> void;
+  auto contract(simplex_t) -> bool;
 
   auto expansion(const idx_t k) -> void;
 
   template < typename Lambda >
   auto expansion_f(const idx_t, Lambda&&) -> void;
 
   template < typename Lambda >
-  auto expand_f(node_set_t&, const idx_t, size_t, Lambda&&) -> void;
+  auto expand_f(node_set_t&, const idx_t, size_t, Lambda&&, SmallVector< node_ptr >&, SmallVector< node_ptr >&) -> void;
 
   template < typename Lambda > 
 	void traverse_up(node_ptr, const size_t, Lambda&&) const noexcept;

include/simplextree/st.hpp

@@ -212,7 +212,8 @@ inline void SimplexTree::remove(node_ptr cn){
 
 template< typename Iter >
 inline auto SimplexTree::append_node(Iter pos, node_ptr cn, idx_t label, size_t depth) -> node_set_t::iterator {
-  auto new_it = cn->children.emplace_hint(pos, make_unique< node >(label, cn));
+  // auto new_it = cn->children.emplace_hint(pos, make_unique< node >(label, cn)); // set 
+  auto new_it = cn->children.emplace(pos, make_unique< node >(label, cn)); // vector
   add_cousin((*new_it).get(), depth);
   record_new_simplexes(depth-1, 1);
   return(new_it);
@@ -264,13 +265,22 @@ inline void SimplexTree::insert_it(Iter s, Iter e, node_ptr c_node, const idx_t
     //   }
     //   record_new_simplexes(child_depth-1, 1);
     // } else {
-      auto it = std::find_if(begin(node_children(c_node)), end(node_children(c_node)), [label](const node_uptr& cn){
-        return(cn->label == label);
+      // original 
+      // auto it = std::find_if(begin(node_children(c_node)), end(node_children(c_node)), [label](const node_uptr& cn){
+      //   return(cn->label == label);
+      // });
+      auto it = std::lower_bound(begin(node_children(c_node)), end(node_children(c_node)), label, [](const node_uptr& cn, idx_t c_label){
+        return cn->label < c_label;
       });
-      if (it == end(c_node->children)){
-        auto new_it = c_node->children.emplace_hint(it, make_unique< node >(label, c_node));
+      if (it == end(c_node->children) || (*it)->label != label){
+        // auto new_it = c_node->children.emplace_hint(it, make_unique< node >(label, c_node)); // set 
+        // auto& new_it = c_node->children.emplace_back(make_unique< node >(label, c_node)); // vector
+        auto new_it = c_node->children.emplace(it, make_unique< node >(label, c_node)); // vector
+
         if (child_depth > 1){ // keep track of nodes which share ids at the same depth
-          add_cousin((*new_it).get(), child_depth);
+          // add_cousin((*new_it).get(), child_depth); // set 
+          // add_cousin(new_it.get(), child_depth); // vector
+          add_cousin((*new_it).get(), child_depth); // vector emplace 
         }
         record_new_simplexes(child_depth-1, 1);
       }
@@ -439,38 +449,51 @@ inline void SimplexTree::print_simplex(OutputStream& os, node_ptr cn, bool newli
 
 // Performs the default expansion of order k, reconstructing the k-skeleton flag complex via an in-depth expansion of the 1-skeleton.
 inline void SimplexTree::expansion(const idx_t k){
-  expansion_f(k, [this](node_ptr parent, idx_t depth, idx_t label){
-    std::array< idx_t, 1 > int_label = { label };
+  std::array< idx_t, 1 > int_label = { 0 };
+  expansion_f(k, [this, &int_label](node_ptr parent, idx_t depth, idx_t label){
+    // std::array< idx_t, 1 > int_label = { label };
+    int_label[0] = label; 
     insert_it(begin(int_label), end(int_label), parent, depth);
   });
 }
 
 // Global expansion operation: calls expand_f on all children of the root node
 template < typename Lambda >
 inline void SimplexTree::expansion_f(const idx_t k, Lambda&& f){
+  SmallVector< node_ptr >::allocator_type::arena_type arena1;
+  SmallVector< node_ptr > intersection { arena1 };
+  SmallVector< node_ptr >::allocator_type::arena_type arena2;
+  SmallVector< node_ptr > sib_ptrs { arena2 } ;
   for (auto& cn: node_children(root)){ 
     if (!node_children(cn).empty()){ 
-			expand_f(cn->children, k-1, 2, f); 
+			expand_f(cn->children, k-1, 2, f, intersection, sib_ptrs); 
 		}
   }
 }
 
 // Local expand operation checks A \cap N^+(vj) \neq \emptyset
 // If they have a non-empty intersection, then the intersection is added as a child to the head node and expand is recursivey called. 
 template < typename Lambda >
-inline void SimplexTree::expand_f(node_set_t& c_set, const idx_t k, size_t depth, Lambda&& f){
+inline void SimplexTree::expand_f(
+  node_set_t& c_set, const idx_t k, size_t depth, 
+  Lambda&& f, 
+  SmallVector< node_ptr >& intersection, 
+  SmallVector< node_ptr >& sib_ptrs
+){
   if (k == 0 || c_set.empty()){ return; }
   // Traverse the children
   auto siblings = std::next(begin(c_set), 1);
-  SmallVector< node_ptr >::allocator_type::arena_type arena1;
-  SmallVector< node_ptr > intersection { arena1 };
+  // SmallVector< node_ptr >::allocator_type::arena_type arena1;
+  // SmallVector< node_ptr > intersection { arena1 };
+  intersection.clear();
   for (auto& cn: c_set){
     node_ptr top_v = find_by_id(root->children, cn->label);
     if (top_v != nullptr && (!top_v->children.empty())){
 
 			// Temporary 
-			SmallVector< node_ptr >::allocator_type::arena_type arena2;
-			SmallVector< node_ptr > sib_ptrs { arena2 } ;
+			// SmallVector< node_ptr >::allocator_type::arena_type arena2;
+			// SmallVector< node_ptr > sib_ptrs { arena2 } ;
+      sib_ptrs.clear();
 			std::transform(siblings, end(c_set), std::back_inserter(sib_ptrs), [](const node_uptr& n){
 				return (node_ptr) n.get();
 			});
@@ -492,7 +515,7 @@ inline void SimplexTree::expand_f(node_set_t& c_set, const idx_t k, size_t depth
             f((node_ptr) cn.get(), depth, int_node->label);
           }
         }
-        expand_f(cn->children, k-1, depth+1, f); // recurse
+        expand_f(cn->children, k-1, depth+1, f, intersection, sib_ptrs); // recurse
       }
     }
     if (siblings != end(c_set)){ ++siblings; }
@@ -684,7 +707,8 @@ inline vector< idx_t > SimplexTree::connected_components() const{
 }
 
 // Edge contraction 
-inline void SimplexTree::contract(vector< idx_t > edge){
+inline bool SimplexTree::contract(vector< idx_t > edge){
+  if (edge.size() != 2){ return false; }
   vector< simplex_t > to_remove;
   vector< simplex_t > to_insert; 
   traverse(st::preorder< true >(this, root.get()), [this, edge, &to_remove, &to_insert](node_ptr np, idx_t depth, simplex_t sigma){
@@ -707,11 +731,14 @@ inline void SimplexTree::contract(vector< idx_t > edge){
     return true; 
   });
 
-  // for (auto& edge: to_remove){ print_simplex(std::cout, edge, true); }
-
   // Remove the simplices containing vb
-	for (auto& edge: to_remove){ remove(find(edge)); }
-	for (auto& edge: to_insert){ insert(edge); }
+  if (to_remove.size() > 0 || to_insert.size() > 0){
+    for (auto& edge: to_remove){ remove(find(edge)); }
+	  for (auto& edge: to_insert){ insert(edge); }
+    return true; 
+  } else {
+    return false;
+  }
 }
 
 template < typename Lambda > // Assume lambda is boolean return 

meson.build

@@ -3,9 +3,11 @@ project(
   license: 'Apache-2.0',
   meson_version: '>= 0.64.0',
   default_options : [
-    'buildtype=debugoptimized', 
+    'buildtype=release', 
+    'b_ndebug=if-release',
     'cpp_std=c++17', 
-    'warning_level=2'
+    'warning_level=2', 
+    'pkgconfig.relocatable=true'
   ]
 )
 
@@ -26,6 +28,33 @@ inc_local = include_directories('include')
 incdir_numpy = run_command(py, ['-c', 'import os; os.chdir(".."); import numpy; print(numpy.get_include())'], check : true).stdout().strip()
 inc_np = include_directories(incdir_numpy)
 
+## Begin compiler arguments
+compiler = meson.get_compiler('cpp')
+message('Compiler = '+compiler.get_id())
+_cpp_args = []
+if get_option('buildtype') == 'debugoptimized'
+  _cpp_args += compiler.get_supported_arguments(
+    '-O2',
+    # '-fsanitize=address', 
+    # '-fno-omit-frame-pointer',
+    '-g',
+    '-Wall'
+  )
+else
+  ## Release
+  _cpp_args += compiler.get_supported_arguments(
+    '-flto=thin',   # think LTO
+    # '-flto',      # monolithic LTO
+    '-O3',          # full optimizations
+    '-DNDEBUG',     # remove assertions
+    '-Wl,-s',       # strip symbols to reduce binary size
+    # '-march=native' # either this or lto seems to not work on multiple builds
+  )
+endif
+
+
+
+
 ## Compile the package directory
 subdir('simplextree')