Merge pull request #253 from hyanwong/tidying

Tidy tests and unpin numba

Author: hyanwong

requirements.txt

@@ -1,4 +1,4 @@
-tskit>=0.4.0
+tskit>=0.5.0
 tsinfer>=0.3.0
 flake8
 numpy
@@ -7,7 +7,7 @@ daiquiri
 msprime>=1.0.0
 scipy
 codecov
-numba==0.53.1
+numba
 appdirs
 pre-commit
 pytest

tests/test_cli.py

@@ -218,7 +218,7 @@ def compare_python_api(self, input_ts, cmd, Ne, mutation_rate, method):
         dated_ts = tsdate.date(
             input_ts, population_size=Ne, mutation_rate=mutation_rate, method=method
         )
-        print(dated_ts.tables.nodes.time, output_ts.tables.nodes.time)
+        # print(dated_ts.tables.nodes.time, output_ts.tables.nodes.time)
         assert np.array_equal(dated_ts.tables.nodes.time, output_ts.tables.nodes.time)
 
     def test_ts(self):
@@ -284,7 +284,7 @@ def preprocess_compare_python_api(self, input_ts):
             input_ts.dump(input_filename)
             output_filename = pathlib.Path(tmpdir) / "output.trees"
             full_cmd = "preprocess " + str(input_filename) + f" {output_filename}"
-            print(full_cmd)
+            # print(full_cmd)
             cli.tsdate_main(full_cmd.split())
             output_ts = tskit.load(output_filename)
         preprocessed_ts = tsdate.preprocess_ts(input_ts)

tests/test_functions.py

@@ -26,6 +26,7 @@
 """
 import collections
 import json
+import logging
 import unittest
 
 import msprime
@@ -457,9 +458,13 @@ def test_single_tree_ts_disallow_unary(self):
         with pytest.raises(ValueError, match="unary"):
             self.get_mixture_prior_params(ts, "gamma")
 
-    def test_single_tree_ts_with_unary(self):
+    def test_single_tree_ts_with_unary(self, caplog):
         ts = utility_functions.single_tree_ts_with_unary()
-        mixture_priors = self.get_mixture_prior_params(ts, "gamma", allow_unary=True)
+        with caplog.at_level(logging.WARNING):
+            mixture_priors = self.get_mixture_prior_params(
+                ts, "gamma", allow_unary=True
+            )
+        assert "tsdate may give poor results" in caplog.text
         # Root is a 3 tip prior
         assert np.allclose(mixture_priors[7, self.alpha_beta], [1.6, 1.2])
         # Node 6 should be a 50:50 mixture between 1 and 3 tips
@@ -1093,8 +1098,8 @@ def test_two_tree_mutation_ts(self):
 
     def test_dangling_fails(self):
         ts = utility_functions.single_tree_ts_n2_dangling()
-        print(ts.draw_text())
-        print("Samples:", ts.samples())
+        # print(ts.draw_text())
+        # print("Samples:", ts.samples())
         Ne = 0.5
         with pytest.raises(ValueError, match="simplified"):
             tsdate.build_prior_grid(ts, Ne, timepoints=np.array([0, 1.2, 2]))