Significantly improve performance

appveyor.yml

@@ -49,6 +49,10 @@ before_build:
   - git submodule update --init --recursive
 
 install:
+  - bash -lc "curl -O http://repo.msys2.org/msys/x86_64/msys2-keyring-r21.b39fb11-1-any.pkg.tar.xz"
+  - bash -lc "curl -O http://repo.msys2.org/msys/x86_64/msys2-keyring-r21.b39fb11-1-any.pkg.tar.xz.sig"
+  - bash -lc "pacman-key --verify msys2-keyring-r21.b39fb11-1-any.pkg.tar.xz.sig"
+  - bash -lc "pacman -U --noconfirm msys2-keyring-r21.b39fb11-1-any.pkg.tar.xz"
   - bash -lc "pacman --needed --noconfirm -Sy pacman-mirrors"
   - bash -lc "pacman --noconfirm -Sy"
   - bash -lc "pacman --noconfirm -S zstd"

include/GraphHelper.h

@@ -100,8 +100,6 @@ class Graph
     vector<size_t> const& get_neighbours(size_t v, igraph_neimode_t mode);
     size_t get_random_neighbour(size_t v, igraph_neimode_t mode, igraph_rng_t* rng);
 
-    pair<size_t, size_t> get_endpoints(size_t e);
-
     inline size_t get_random_node(igraph_rng_t* rng)
     {
       return get_random_int(0, this->vcount() - 1, rng);
@@ -113,7 +111,7 @@ class Graph
     inline size_t ecount() { return igraph_ecount(this->_graph); };
     inline double total_weight() { return this->_total_weight; };
     inline size_t total_size() { return this->_total_size; };
-    inline int is_directed() { return igraph_is_directed(this->_graph); };
+    inline int is_directed() { return this->_is_directed; };
     inline double density() { return this->_density; };
     inline int correct_self_loops() { return this->_correct_self_loops; };
     inline int is_weighted() { return this->_is_weighted; };
@@ -128,12 +126,15 @@ class Graph
       return this->_edge_weights[e];
     };
 
+    inline void edge(size_t eid, size_t &from, size_t &to) {
+      from = IGRAPH_FROM(this->get_igraph(), eid);
+      to = IGRAPH_TO(this->get_igraph(), eid);
+    }
+
     inline vector<size_t> edge(size_t e)
     {
-      igraph_integer_t v1, v2;
-      igraph_edge(this->_graph, e, &v1, &v2);
       vector<size_t> edge(2);
-      edge[0] = v1; edge[1] = v2;
+      this->edge(e, edge[0], edge[1]);
       return edge;
     }
 
@@ -147,7 +148,7 @@ class Graph
 
     inline size_t degree(size_t v, igraph_neimode_t mode)
     {
-      if (mode == IGRAPH_IN)
+      if (mode == IGRAPH_IN || !this->is_directed())
         return this->_degree_in[v];
       else if (mode == IGRAPH_OUT)
         return this->_degree_out[v];
@@ -159,7 +160,7 @@ class Graph
 
     inline double strength(size_t v, igraph_neimode_t mode)
     {
-      if (mode == IGRAPH_IN)
+      if (mode == IGRAPH_IN || !this->is_directed())
         return this->_strength_in[v];
       else if (mode == IGRAPH_OUT)
         return this->_strength_out[v];
@@ -173,6 +174,7 @@ class Graph
 
   private:
     igraph_t* _graph;
+    igraph_vector_t _temp_igraph_vector;
 
     // Utility variables to easily access the strength of each node
     vector<double> _strength_in;
@@ -199,6 +201,7 @@ class Graph
     double _total_weight;
     size_t _total_size;
     int _is_weighted;
+    bool _is_directed;
 
     int _correct_self_loops;
     double _density;

include/MutableVertexPartition.h

@@ -77,10 +77,11 @@ class MutableVertexPartition
     inline Graph* get_graph() { return this->graph; };
 
     void renumber_communities();
-    vector<size_t> renumber_communities(map<size_t, size_t> const& original_fixed_membership);
+    void renumber_communities(map<size_t, size_t> const& original_fixed_membership);
     void renumber_communities(vector<size_t> const& new_membership);
     void set_membership(vector<size_t> const& new_membership);
-    vector<size_t> static renumber_communities(vector<MutableVertexPartition*> partitions);
+    void relabel_communities(vector<size_t> const& new_comm_id);
+    vector<size_t> static rank_order_communities(vector<MutableVertexPartition*> partitions);
     size_t get_empty_community();
     size_t add_empty_community();
     void from_coarse_partition(vector<size_t> const& coarse_partition_membership);
@@ -97,8 +98,36 @@ class MutableVertexPartition
     inline double total_weight_in_all_comms()         { return this->_total_weight_in_all_comms; };
     inline size_t total_possible_edges_in_all_comms() { return this->_total_possible_edges_in_all_comms; };
 
-    double weight_to_comm(size_t v, size_t comm);
-    double weight_from_comm(size_t v, size_t comm);
+    inline double weight_to_comm(size_t v, size_t comm)
+    {
+      if (this->_current_node_cache_community_to != v)
+      {
+        this->cache_neigh_communities(v, IGRAPH_OUT);
+        this->_current_node_cache_community_to = v;
+      }
+
+      if (comm < this->_cached_weight_to_community.size())
+        return this->_cached_weight_to_community[comm];
+      else
+        return 0.0;
+    }
+
+    inline double weight_from_comm(size_t v, size_t comm)
+    {
+      if (!this->graph->is_directed())
+        return weight_to_comm(v, comm);
+
+      if (this->_current_node_cache_community_from != v)
+      {
+        this->cache_neigh_communities(v, IGRAPH_IN);
+        this->_current_node_cache_community_from = v;
+      }
+
+      if (comm < this->_cached_weight_from_community.size())
+        return this->_cached_weight_from_community[comm];
+      else
+        return 0.0;
+    }
 
     vector<size_t> const& get_neigh_comms(size_t v, igraph_neimode_t);
     set<size_t> get_neigh_comms(size_t v, igraph_neimode_t mode, vector<size_t> const& constrained_membership);