Temporarily disable --recombination-map in cli

Author: hyanwong

tests/test_cli.py

@@ -311,7 +311,7 @@ def test_infer(self):
 
     @pytest.mark.skip(
         reason="Ancestors not saving provenance:"
-        "see https://github.com/tskit-dev/tsinfer/issues/743"
+        "see https://github.com/tskit-dev/tsinfer/issues/753"
     )
     def test_ancestors(self):
         sd = tsinfer.load(self.sample_file)
@@ -357,9 +357,9 @@ def test_separate_calls(self):
                 [
                     "match-ancestors",
                     self.sample_file,
-                    "--recombination_rate",
+                    "--recombination-rate",
                     "0.001",
-                    "--mismatch_ratio",
+                    "--mismatch-ratio",
                     "0.01",
                 ]
             )
@@ -372,9 +372,9 @@ def test_separate_calls(self):
                 [
                     "match-samples",
                     self.sample_file,
-                    "--recombination_rate",
+                    "--recombination-rate",
                     "10",
-                    "--mismatch_ratio",
+                    "--mismatch-ratio",
                     "100",
                 ]
             )
@@ -386,9 +386,9 @@ def test_infer(self):
         command = [
             "infer",
             self.sample_file,
-            "--recombination_rate",
+            "--recombination-rate",
             "0.1",
-            "--mismatch_ratio",
+            "--mismatch-ratio",
             "10",
         ]
         with mock.patch("tsinfer.infer") as infer:
@@ -397,6 +397,7 @@ def test_infer(self):
             assert kwargs["recombination_rate"] == 0.1
             assert kwargs["mismatch_ratio"] == 10
 
+    @pytest.mark.skip(reason="https://github.com/tskit-dev/tsinfer/issues/753")
     @pytest.mark.skipif(
         sys.platform == "win32", reason="windows simultaneous file permissions issue"
     )
@@ -409,14 +410,15 @@ def test_map(self):
         command = [
             "infer",
             self.sample_file,
-            "--recombination_map",
+            "--recombination-map",
             ratemap,
         ]
         with mock.patch("tsinfer.infer") as infer:
             self.run_command(command)
             args, kwargs = infer.call_args
             assert isinstance(kwargs["recombination_rate"], msprime.RateMap)
 
+    @pytest.mark.skip(reason="https://github.com/tskit-dev/tsinfer/issues/753")
     @pytest.mark.skipif(
         sys.platform == "win32", reason="windows simultaneous file permissions issue"
     )
@@ -433,7 +435,7 @@ def test_fails_on_bad_map(self):
         command = [
             "infer",
             self.sample_file,
-            "--recombination_map",
+            "--recombination-map",
             ratemap,
             "-O",
             output_trees,

tsinfer/cli.py

@@ -32,7 +32,7 @@
     resource = None  # resource.getrusage absent on windows, so skip outputting max mem
 
 import daiquiri
-import msprime  # for the RateMap class
+
 import tskit
 import humanize
 import time
@@ -89,8 +89,9 @@ def get_output_trees_path(path, input_path):
 def get_recombination_map(args):
     if args.recombination_rate is not None:
         return args.recombination_rate
-    if args.recombination_map is not None:
-        return msprime.RateMap.read_hapmap(args.recombination_map)
+    # uncomment below when https://github.com/tskit-dev/tsinfer/issues/753 fixed
+    # if args.recombination_map is not None:
+    #     return msprime.RateMap.read_hapmap(args.recombination_map)
     return None
 
 
@@ -354,25 +355,26 @@ def add_postprocess_argument(parser):
 def add_recombination_arguments(parser):
     group = parser.add_mutually_exclusive_group()
     group.add_argument(
-        "--recombination_rate",
+        "--recombination-rate",
         default=None,
         type=float,
         help="The recombination rate per unit genome",
     )
-    group.add_argument(
-        "--recombination_map",
-        default=None,
-        help=(
-            "The path to a file containing recombination rates along the chromosome "
-            "in HapMap format (see https://tskit.dev/msprime/docs/latest/api.html"
-            "#msprime.RateMap.read_hapmap for details of the format)"
-        ),
-    )
+    # Uncomment below when https://github.com/tskit-dev/tsinfer/issues/753 fixed
+    # group.add_argument(
+    #     "--recombination-map",
+    #     default=None,
+    #     help=(
+    #         "The path to a file containing recombination rates along the chromosome "
+    #         "in HapMap format (see https://tskit.dev/msprime/docs/latest/api.html"
+    #         "#msprime.RateMap.read_hapmap for details of the format)"
+    #     ),
+    # )
 
 
 def add_mismatch_argument(parser):
     parser.add_argument(
-        "--mismatch_ratio",
+        "--mismatch-ratio",
         type=float,
         default=None,
         help=(