fix: add parameter use_cached to BlackholeGraph._get_blackhole_plasmi…

…ds(), solving the slowdown introduced in releases v0.3.3 and v0.3.4

use_cached allows us to get the blackhole plasmids already computed in a previous call to this method, instead of always recomputing them from scratch.

plasnet/blackhole_graph.py

@@ -23,44 +23,51 @@ def __init__(
         self._edge_density = edge_density
 
     def _get_node_shape(self, node: str) -> str:
-        if node in self._get_blackhole_plasmids():
+        if node in self._get_blackhole_plasmids(use_cached=True):
             return "star"
         return "circle"
 
     def _add_special_node_attributes(self, node: str, attrs: dict[str, Any]) -> None:
-        if node in self._get_blackhole_plasmids():
-            attrs["is_blackhole"] = True
-        else:
-            attrs["is_blackhole"] = False
+        attrs["is_blackhole"] = node in self._get_blackhole_plasmids(use_cached=True)
 
-    def _get_blackhole_plasmids(self) -> list[str]:
-        blackhole_plasmids_in_graph = []
-        for node in self.nodes:
-            if self.degree(node) >= self._blackhole_connectivity_threshold:
-                neighbors = list(self.neighbors(node))
-                subgraph = nx.induced_subgraph(self, neighbors)
-                nb_of_edges_between_neighbours = subgraph.number_of_edges()
-                max_nb_of_edges_between_neighbours = (len(neighbors) * (len(neighbors) - 1)) // 2
-                edge_rate = nb_of_edges_between_neighbours / max_nb_of_edges_between_neighbours
-                if edge_rate <= self._edge_density:
-                    blackhole_plasmids_in_graph.append(node)
-                    logging.debug(f"{node} is a blackhole plasmid")
-                else:
-                    logging.debug(
-                        f"{node} is highly connected but does not connect "
-                        f"unrelated plasmids, not a blackhole plasmid"
-                    )
-        return blackhole_plasmids_in_graph
+    def _get_blackhole_plasmids(self, use_cached: bool = False) -> list[str]:
+        need_to_compute_the_blackhole_plasmids = not use_cached or not hasattr(
+            self, "_blackhole_plasmids"
+        )
+        if need_to_compute_the_blackhole_plasmids:
+            blackhole_plasmids_in_graph = []
+            for node in self.nodes:
+                if self.degree(node) >= self._blackhole_connectivity_threshold:
+                    neighbors = list(self.neighbors(node))
+                    subgraph = nx.induced_subgraph(self, neighbors)
+                    nb_of_edges_between_neighbours = subgraph.number_of_edges()
+                    max_nb_of_edges_between_neighbours = (
+                        len(neighbors) * (len(neighbors) - 1)
+                    ) // 2
+                    edge_rate = nb_of_edges_between_neighbours / max_nb_of_edges_between_neighbours
+                    if edge_rate <= self._edge_density:
+                        blackhole_plasmids_in_graph.append(node)
+                        logging.debug(f"{node} is a blackhole plasmid")
+                    else:
+                        logging.debug(
+                            f"{node} is highly connected but does not connect "
+                            f"unrelated plasmids, not a blackhole plasmid"
+                        )
+            self._blackhole_plasmids = blackhole_plasmids_in_graph
 
-    def get_nb_of_blackhole_plasmids(self) -> int:
-        return len(self._get_blackhole_plasmids())
+        return self._blackhole_plasmids
 
     def remove_blackhole_plasmids(self) -> None:
-        while self.get_nb_of_blackhole_plasmids() > 0:
-            self.remove_nodes_from(self._get_blackhole_plasmids())
+        while True:
+            blackhole_plasmids = self._get_blackhole_plasmids()
+            there_are_still_blackhole_plasmids = len(blackhole_plasmids) > 0
+            if there_are_still_blackhole_plasmids:
+                self.remove_nodes_from(blackhole_plasmids)
+            else:
+                break
 
     def _get_filters_HTML(self) -> str:
-        nb_of_black_holes = len(self._get_blackhole_plasmids())
+        nb_of_black_holes = len(self._get_blackhole_plasmids(use_cached=True))
         return (
             f'<label for="hide_blackholes">'
             f"Hide blackhole plasmids ({nb_of_black_holes} present)"
@@ -74,7 +81,7 @@ def _get_custom_buttons_HTML(self) -> str:
     @property
     def description(self) -> str:
         description = super().description
-        blackholes_detected = self.get_nb_of_blackhole_plasmids() > 0
+        blackholes_detected = len(self._get_blackhole_plasmids(use_cached=True)) > 0
         if blackholes_detected:
             description += " - WARNING: BLACKHOLE SPOTTED!"
         return description