Add extra tests

tests/test_cli.py

@@ -243,6 +243,18 @@ def test_verbosity(self, tmp_path, caplog, flag, log_status):
         self.run_tsdate_cli(tmp_path, input_ts, flag, cmd="preprocess")
         assert log_status in caplog.text
 
+    @pytest.mark.parametrize(
+        "method", ["inside_outside", "maximization", "variational_gamma"]
+    )
+    def test_no_progress(self, method, tmp_path, capfd):
+        input_ts = msprime.simulate(4, random_seed=123)
+        params = f"-m 0.1 --method {method}"
+        self.run_tsdate_cli(tmp_path, input_ts, f"{self.popsize} {params}")
+        (out, err) = capfd.readouterr()
+        assert out == ""
+        # run_tsdate_cli print logging to stderr
+        assert err == ""
+
     def test_progress(self, tmp_path, capfd):
         input_ts = msprime.simulate(4, random_seed=123)
         params = "--method inside_outside --progress"

tests/test_inference.py

@@ -23,8 +23,6 @@
 """
 Test cases for the python API for tsdate.
 """
-import unittest
-
 import msprime
 import numpy as np
 import pytest
@@ -37,7 +35,7 @@
 from tsdate.demography import PopulationSizeHistory
 
 
-class TestPrebuilt(unittest.TestCase):
+class TestPrebuilt:
     """
     Tests for tsdate on prebuilt tree sequences
     """
@@ -47,6 +45,12 @@ def test_no_population_size(self):
         with pytest.raises(ValueError, match="Must specify population size"):
             tsdate.date(ts, mutation_rate=None)
 
+    @pytest.mark.parametrize("method", ["maximization", "variational_gamma"])
+    def test_no_mutation(self, method):
+        ts = utility_functions.two_tree_mutation_ts()
+        with pytest.raises(ValueError, match="method requires mutation rate"):
+            tsdate.date(ts, method=method, population_size=1, mutation_rate=None)
+
     def test_not_needed_population_size(self):
         ts = utility_functions.two_tree_mutation_ts()
         prior = tsdate.build_prior_grid(ts, population_size=1, timepoints=10)

tests/test_provenance.py

@@ -49,10 +49,13 @@ def test_date_params_recorded(self):
         ts = utility_functions.single_tree_ts_n2()
         mu = 0.123
         Ne = 9
-        dated_ts = tsdate.date(ts, population_size=Ne, mutation_rate=mu)
+        dated_ts = tsdate.date(
+            ts, population_size=Ne, mutation_rate=mu, method="maximization"
+        )
         rec = json.loads(dated_ts.provenance(-1).record)
         assert np.isclose(rec["parameters"]["mutation_rate"], mu)
         assert np.isclose(rec["parameters"]["population_size"], Ne)
+        assert rec["parameters"]["method"] == "maximization"
 
     @pytest.mark.parametrize(
         "popdict",

tsdate/core.py

@@ -1572,6 +1572,9 @@ def variational_dates(
     if not max_iterations >= 1:
         raise ValueError("Maximum number of iterations must be greater than 0")
 
+    if mutation_rate is None:
+        raise ValueError("Variational gamma method requires mutation rate")
+
     # Parameters below are not used in variational dating, but are here
     # to match the signature of get_dates(). We may be able to remove some
     # if we move to specifying some params via a control dictionary