Warn if no inference sites

Author: hyanwong

CHANGELOG.rst

@@ -2,6 +2,11 @@
 [0.2.4] - 2022-06-xx
 ********************
 
+**Features**
+
+- matching routines warn if no inference sites
+  (:pr:`685`, :issue:`683` :user:`hyanwong`)
+
 **Fixes**
 
 - sample_data.subset() now accepts a sequence_length  (:pr:`681`, :user:`hyanwong`)

tests/test_inference.py

@@ -22,6 +22,7 @@
 import io
 import itertools
 import json
+import logging
 import os.path
 import random
 import string
@@ -729,6 +730,14 @@ class TestZeroInferenceSites:
     Tests for the degenerate case in which we have no inference sites.
     """
 
+    @classmethod
+    def setup_class(cls):
+        logging.disable(logging.CRITICAL)
+
+    @classmethod
+    def teardown_class(cls):
+        logging.disable(logging.NOTSET)
+
     def verify(self, genotypes):
         genotypes = np.array(genotypes, dtype=np.int8)
         m = genotypes.shape[0]
@@ -774,6 +783,18 @@ def test_three_sites(self):
         self.verify([[1, 1], [1, 1], [1, 1]])
 
 
+class TestZeroInferenceSitesWarning:
+    def test_warning_match_ancestors(self, caplog):
+        with tsinfer.SampleData(sequence_length=10) as sd:
+            sd.add_site(1, [0, 0])
+        ancestors = tsinfer.generate_ancestors(sd)
+        with caplog.at_level(logging.WARNING):
+            ats = tsinfer.match_ancestors(sd, ancestors)
+            assert caplog.text.count("No sites used") == 1
+            _ = tsinfer.match_samples(sd, ats)
+            assert caplog.text.count("No sites used") == 2
+
+
 def random_string(rng, max_len=10):
     """
     Uses the specified random generator to generate a random string.

tsinfer/inference.py

@@ -1027,6 +1027,8 @@ def __init__(
         self.path_compression = path_compression
         self.num_samples = self.sample_data.num_samples
         self.num_sites = len(inference_site_position)
+        if self.num_sites == 0:
+            logging.warning("No sites used for inference")
         num_intervals = max(self.num_sites - 1, 0)
         self.progress_monitor = _get_progress_monitor(progress_monitor)
         self.match_progress = None  # Allocated by subclass