fix cli tests

Author: nspope

tests/test_cli.py

@@ -57,7 +57,8 @@ def test_default_values(self):
         assert args.population_size is None
         assert args.mutation_rate is None
         assert args.recombination_rate is None
-        assert args.epsilon == 1e-10
+        assert args.epsilon == 1e-8
+        assert args.min_branch_length == 1e-8
         assert args.num_threads is None
         assert args.probability_space is None  # Use the defaults
         assert args.method == "variational_gamma"

tests/test_functions.py

@@ -1546,7 +1546,7 @@ def test_node_metadata_inside_outside(self):
         )
         algorithm = InsideOutsideMethod(ts, mutation_rate=1, population_size=10000)
         mn_post, *_ = algorithm.run(
-            eps=1e-10,
+            eps=1e-8,
             outside_standardize=True,
             ignore_oldest_root=False,
             probability_space=tsdate.node_time_class.LOG_GRID,
@@ -1743,7 +1743,7 @@ def test_sites_time_insideoutside(self):
         dated = tsdate.inside_outside(ts, mutation_rate=1, population_size=1)
         algorithm = InsideOutsideMethod(ts, mutation_rate=1, population_size=1)
         mn_post, *_ = algorithm.run(
-            eps=1e-10,
+            eps=1e-8,
             outside_standardize=True,
             ignore_oldest_root=False,
             probability_space=LOG_GRID,

tsdate/cli.py

@@ -124,11 +124,20 @@ def tsdate_cli_parser():
         type=float,
         default=core.DEFAULT_EPSILON,
         help=(
-            "Specify minimum distance separating time points. Also "
-            "specifies the error factor in time difference calculations. "
+            "Specify the error factor in time difference calculations. "
             f"Default: {core.DEFAULT_EPSILON}"
         ),
     )
+    parser.add_argument(
+        "-b",
+        "--min-branch-length",
+        type=float,
+        default=core.DEFAULT_MIN_BRANCH_LENGTH,
+        help=(
+            "Specify the minimum difference in age between parent and child nodes. "
+            f"Default: {core.DEFAULT_MIN_BRANCH_LENGTH}"
+        ),
+    )
     parser.add_argument(
         "--method",
         choices=["inside_outside", "maximization", "variational_gamma"],
@@ -169,7 +178,7 @@ def tsdate_cli_parser():
         ),
         default=None,
     )
-    # TODO array specification from file?
+    # arguments for discrete time methods
     parser.add_argument(
         "-n",
         "--population_size",
@@ -283,7 +292,7 @@ def run_date(args):
         params = dict(
             recombination_rate=args.recombination_rate,
             method=args.method,
-            eps=args.epsilon,
+            min_branch_length=args.min_branch_length,
             progress=args.progress,
             max_iterations=args.max_iterations,
             rescaling_intervals=args.rescaling_intervals,
@@ -299,6 +308,7 @@ def run_date(args):
             population_size=args.population_size,
             recombination_rate=args.recombination_rate,
             method=args.method,
+            min_branch_length=args.min_branch_length,
             eps=args.epsilon,
             progress=args.progress,
             probability_space=args.probability_space,