Merge pull request #389 from hyanwong/remove_oldest_node_cli

Remove "ignore-oldest" option from the CLI

CHANGELOG.md

@@ -27,6 +27,10 @@
 - The `mutation_rate` and `population_size` parameters are now keyword-only, and
   therefore these parameter names need to be explicitly typed out.
 
+- The `ignore-oldest` option has been removed from the command-line interface,
+  as it is no longer very helpful with new _tsinfer_ output, which has the root
+  node split. The option is stall accessible from the Python API.
+
 ## [0.1.6] - 2024-01-07
 
 **Breaking changes**

tsdate/cli.py

@@ -163,14 +163,6 @@ def tsdate_cli_parser():
             "continuous-time approximation. Current default: 'inside_outside'"
         ),
     )
-    parser.add_argument(
-        "--ignore-oldest",
-        action="store_true",
-        help=(
-            "Ignore the oldest node in the tree sequence: in older tsinfer versions "
-            "this could be of low quality when using empirical data."
-        ),
-    )
     parser.add_argument(
         "-p", "--progress", action="store_true", help="Show progress bar."
     )
@@ -288,10 +280,6 @@ def run_date(args):
             probability_space=args.probability_space,
             num_threads=args.num_threads,
         )
-        if args.method == "inside_outside":
-            params["ignore_oldest_root"] = args.ignore_oldest  # For backwards compat
-        # TODO: remove and error out if ignore_oldest_root is set,
-        # see https://github.com/tskit-dev/tsdate/issues/262
     dated_ts = tsdate.date(ts, mutation_rate=args.mutation_rate, **params)
     dated_ts.dump(args.output)