From e2e0bea1c4208a213d09846b0dfc204d074d9b41 Mon Sep 17 00:00:00 2001 From: Yan Wong Date: Tue, 4 Jun 2024 19:02:57 +0100 Subject: [PATCH] Remove "ignore-oldest" option from the CLI --- CHANGELOG.md | 4 ++++ tsdate/cli.py | 12 ------------ 2 files changed, 4 insertions(+), 12 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4dd91513..0f80ecaf 100644 --- a/CHANGELOG.md +++ b/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** diff --git a/tsdate/cli.py b/tsdate/cli.py index dfa40119..d7f8d1e9 100644 --- a/tsdate/cli.py +++ b/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)