Add support for dynamic neighbour-joining (#647)

* upgrade anjl

* add support for dynamic nj

Author: alimanfoo

malariagen_data/anoph/distance.py

@@ -367,8 +367,13 @@ def _njt(
         # neighbour-joining iterations.
         progress_options = dict(desc="Construct neighbour-joining tree", leave=False)
 
-        # Decide which algorithm to use and run the neighbour-joining.
-        if algorithm == "rapid":
+        # Decide which algorithm to use and run the neighbour-joining. The "dynamic"
+        # algorithm is fastest.
+        if algorithm == "dynamic":
+            Z = anjl.dynamic_nj(
+                D=D, progress=self._progress, progress_options=progress_options
+            )
+        elif algorithm == "rapid":
             Z = anjl.rapid_nj(
                 D=D, progress=self._progress, progress_options=progress_options
             )

malariagen_data/anoph/distance_params.py

@@ -14,8 +14,8 @@
 default_distance_metric: distance_metric = "cityblock"
 
 nj_algorithm: TypeAlias = Annotated[
-    Literal["rapid", "canonical"],
-    "Neighbour-joining algorithm to use.",
+    Literal["dynamic", "rapid", "canonical"],
+    "Neighbour-joining algorithm to use. The 'dynamic' algorithm is fastest.",
 ]
 
-default_nj_algorithm: nj_algorithm = "rapid"
+default_nj_algorithm: nj_algorithm = "dynamic"