From 6f249d41ec5f554aaabba68ed61569c822e8e646 Mon Sep 17 00:00:00 2001 From: GavinHuttley Date: Fri, 8 Nov 2024 01:15:13 +0000 Subject: [PATCH] STY: pre-commit linting with ruff --- src/diverse_seq/cli.py | 1 - src/diverse_seq/cluster.py | 6 ++++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/src/diverse_seq/cli.py b/src/diverse_seq/cli.py index 4446cf5..a12f47a 100644 --- a/src/diverse_seq/cli.py +++ b/src/diverse_seq/cli.py @@ -7,7 +7,6 @@ import click import rich.progress as rich_progress -from cogent3 import make_unaligned_seqs from cogent3.app import data_store as c3_data_store from scitrack import CachingLogger diff --git a/src/diverse_seq/cluster.py b/src/diverse_seq/cluster.py index 8140e0d..5fcfd18 100644 --- a/src/diverse_seq/cluster.py +++ b/src/diverse_seq/cluster.py @@ -242,7 +242,6 @@ def make_cluster_tree( return tree - class DvsParCtreeMixin: def _mash_dist(self, seq_arrays: Sequence[SeqArray]) -> numpy.ndarray: """Calculates pairwise mash distances between sequences in parallel. @@ -624,7 +623,10 @@ def main(self, seq_names: list[str]) -> PhyloNode: seq_arrays = seq_arrays[: self._limit] if self._limit else seq_arrays seq_arrays = [ SeqArray( - member.unique_id, member.read(), self._moltype, member.data_store.source + member.unique_id, + member.read(), + self._moltype, + member.data_store.source, ) for member in seq_arrays ]