Remove daily-extend

Author: jeromekelleher

sc2ts/cli.py

@@ -360,139 +360,6 @@ def extend(
         add_provenance(ts_out, output_ts)
 
 
-@click.command()
-@click.argument("alignments", type=click.Path(exists=True, dir_okay=False))
-@click.argument("metadata", type=click.Path(exists=True, dir_okay=False))
-@click.argument("output-prefix")
-@click.option(
-    "-b",
-    "--base",
-    type=click.Path(dir_okay=False, exists=True),
-    default=None,
-    help=(
-        "The base tree sequence to match against. If not specified, create "
-        "a new initial base containing the reference. "
-    ),
-)
-@click.option("--num-mismatches", default=None, type=float, help="num-mismatches")
-@click.option("--max-hmm-cost", default=5, type=float, help="max-hmm-cost")
-@click.option(
-    "--min-group-size",
-    default=10,
-    type=int,
-    help="Minimum size of groups of reconsidered samples",
-)
-@click.option(
-    "--num-past-days",
-    default=None,
-    type=int,
-    help="Number of past days to retrieve filtered samples",
-)
-@click.option(
-    "--max-submission-delay",
-    default=None,
-    type=int,
-    help=(
-        "The maximum number of days between the sample and its submission date "
-        "for it to be included in the inference"
-    ),
-)
-@click.option(
-    "--max-daily-samples",
-    default=None,
-    type=int,
-    help=(
-        "The maximum number of samples to match in a single day. If the total "
-        "is greater than this, randomly subsample."
-    ),
-)
-@click.option("--num-threads", default=0, type=int, help="Number of match threads")
-@click.option("--random-seed", default=42, type=int, help="Random seed for subsampling")
-@click.option("--stop-date", default="2030-01-01", type=str, help="Stopping date")
-@click.option(
-    "--additional-problematic-sites",
-    default=None,
-    type=str,
-    help="File containing the list of additional problematic sites to exclude.",
-)
-@click.option("-p", "--precision", default=None, type=int, help="Match precision")
-@click.option("--no-progress", default=False, type=bool, help="Don't show progress")
-@click.option("-v", "--verbose", count=True)
-@click.option("-l", "--log-file", default=None, type=click.Path(dir_okay=False))
-def daily_extend(
-    alignments,
-    metadata,
-    output_prefix,
-    base,
-    num_mismatches,
-    max_hmm_cost,
-    min_group_size,
-    num_past_days,
-    max_submission_delay,
-    max_daily_samples,
-    num_threads,
-    random_seed,
-    stop_date,
-    additional_problematic_sites,
-    precision,
-    no_progress,
-    verbose,
-    log_file,
-):
-    """
-    Sequentially extend the trees by adding samples in daily batches.
-    """
-    setup_logging(verbose, log_file)
-    rng = random.Random(random_seed)
-
-    additional_problematic = []
-    if additional_problematic_sites is not None:
-        additional_problematic = (
-            np.loadtxt(additional_problematic_sites).astype(int).tolist()
-        )
-        logger.info(
-            f"Excluding additional {len(additional_problematic)} problematic sites"
-        )
-
-    match_db_path = f"{output_prefix}match.db"
-    if base is None:
-        base_ts = inference.initial_ts(additional_problematic)
-        match_db = inference.MatchDb.initialise(match_db_path)
-    else:
-        base_ts = tskit.load(base)
-
-    assert (
-        base_ts.metadata["sc2ts"]["additional_problematic_sites"]
-        == additional_problematic
-    )
-
-    with contextlib.ExitStack() as exit_stack:
-        alignment_store = exit_stack.enter_context(sc2ts.AlignmentStore(alignments))
-        metadata_db = exit_stack.enter_context(sc2ts.MetadataDb(metadata))
-        match_db = exit_stack.enter_context(inference.MatchDb(match_db_path))
-        ts_iter = inference.daily_extend(
-            alignment_store=alignment_store,
-            metadata_db=metadata_db,
-            base_ts=base_ts,
-            match_db=match_db,
-            num_mismatches=num_mismatches,
-            max_hmm_cost=max_hmm_cost,
-            min_group_size=min_group_size,
-            num_past_days=num_past_days,
-            max_submission_delay=max_submission_delay,
-            max_daily_samples=max_daily_samples,
-            rng=rng,
-            precision=precision,
-            num_threads=num_threads,
-            show_progress=not no_progress,
-        )
-        for ts, date in ts_iter:
-            output_ts = output_prefix + date + ".ts"
-            add_provenance(ts, output_ts)
-            if date >= stop_date:
-                break
-
-
 @click.command()
 @click.argument("alignment_db")
 @click.argument("ts_file")
@@ -658,6 +525,5 @@ def cli():
 cli.add_command(initialise)
 cli.add_command(list_dates)
 cli.add_command(extend)
-cli.add_command(daily_extend)
 cli.add_command(validate)
 cli.add_command(annotate_recombinants)