Add iterative python parsimony

tree_performance/benchmark.py

@@ -5,8 +5,8 @@
 import sys
 import os
 import pathlib
-import benchmarks.numba
-import benchmarks.numba_vectorised
+import benchmarks.numba_recursive
+import benchmarks.numba_recursive_vectorised
 import benchmarks.pythran
 import pandas as pd
 import numpy as np

tree_performance/benchmarks/numba_iterative.py

@@ -0,0 +1,74 @@
+import tskit
+import util
+import functools
+import numba
+import numpy as np
+import msprime
+
+VECTORISED = False
+
+@numba.njit()
+def _iterative_hartigan_parsimony(genotypes, samples, left_child, parent, postorder, preorder, root):
+    num_nodes = len(postorder)
+    num_alleles = np.max(genotypes) + 1
+    optimal_set = np.zeros((num_nodes, num_alleles), dtype=np.int8)
+    # Simple version assuming non missing data and one root
+    for allele, u in zip(genotypes, samples):
+        optimal_set[u, allele] = 1
+
+    allele_count = np.zeros((num_nodes, num_alleles), dtype=np.int32)
+    for node_j in postorder:
+        if left_child[node_j] != tskit.NULL:
+            max_allele_count = 0
+            for allele_k in range(num_alleles):
+                if allele_count[node_j, allele_k] > max_allele_count:
+                    max_allele_count = allele_count[node_j, allele_k]
+            for allele_k in range(num_alleles):
+                if allele_count[node_j, allele_k] == max_allele_count:
+                    optimal_set[node_j, allele_k] = 1
+        for allele_k in range(num_alleles):
+            allele_count[parent[node_j], allele_k] += optimal_set[node_j, allele_k]
+
+    anc_index, max_val = -1, -1
+    for i in range(len(optimal_set[root])):
+        if optimal_set[root, i] > max_val:
+            anc_index, max_val = i, optimal_set[root, i]
+
+    state = np.zeros((num_nodes), dtype=np.int32)
+    state[:] = anc_index
+    mutations = 0
+    for node_j in preorder:
+        state[node_j] = state[parent[node_j]]
+        if optimal_set[node_j, state[node_j]] == 0:
+            maxval, argmax = -1, -1
+            for k in range(num_alleles):
+                if optimal_set[node_j, k] > maxval:
+                    maxval = optimal_set[node_j, k]
+                    argmax = k
+            state[node_j] = argmax
+            mutations += 1
+    return mutations
+
+def iterative_hartigan_parsimony(tree, genotypes, alleles):
+    samples = tree.tree_sequence.samples()
+    left_child = tree.left_child_array
+    parent = tree.parent_array
+    postorder = tree.postorder()
+    preorder = tree.preorder()
+    return _iterative_hartigan_parsimony(genotypes, samples, left_child, parent, postorder, preorder, tree.root)
+
+def run(ts_path, max_sites):
+    ts = tskit.load(ts_path)
+    assert ts.num_trees == 1
+    tree = ts.first()
+    return util.benchmark_python(
+        ts,
+        functools.partial(iterative_hartigan_parsimony, tree),
+        "py_numba_iterative",
+        max_sites=max_sites,
+    )
+
+def warmup():
+    ts = msprime.sim_ancestry(100, sequence_length=100000, random_seed=43)
+    genotypes = np.zeros(ts.num_samples, dtype=np.int8)
+    iterative_hartigan_parsimony(ts.first(), genotypes, ["0"])

tree_performance/benchmarks/numba.py → tree_performance/benchmarks/numba_recursive.py

@@ -75,7 +75,7 @@ def run(ts_path, max_sites):
     return util.benchmark_python(
         ts,
         functools.partial(numba_hartigan_parsimony, tree),
-        "py_numba",
+        "py_numba_recursive",
         max_sites=max_sites,
     )