diff --git a/refgenconf/refgenconf_v03.py b/refgenconf/refgenconf_v03.py index a4cd47b..e4f66e6 100644 --- a/refgenconf/refgenconf_v03.py +++ b/refgenconf/refgenconf_v03.py @@ -9,7 +9,7 @@ import sys import urllib.request import warnings -from collections import Iterable, Mapping, OrderedDict +from collections.abc import Iterable, Mapping from functools import partial from inspect import getfullargspec as finspect from tempfile import TemporaryDirectory @@ -223,7 +223,7 @@ def list(self, genome=None, order=None, include_tags=False): ) if include_tags: self.run_plugins(POST_LIST_HOOK) - return OrderedDict( + return dict( [ ( g, @@ -238,7 +238,7 @@ def list(self, genome=None, order=None, include_tags=False): ] ) self.run_plugins(POST_LIST_HOOK) - return OrderedDict( + return dict( [ ( g, @@ -677,7 +677,7 @@ def listr( :param list[str] | str genome: genomes that the assets should be found for :param function(str) -> object order: how to key genome IDs and asset names for sort - :return dict[OrderedDict[list]]: remotely available genomes and assets + :return dict[dict[list]]: remotely available genomes and assets keyed by genome keyed by source server endpoint """ data_by_server = {} @@ -1575,7 +1575,7 @@ def _invert_genomes(self, order=None): asset ID. :param function(str) -> object order: how to key genome IDs and asset names for sort - :return OrderedDict[str, Iterable[str]] binding between asset kind/key/name + :return dict[str, Iterable[str]] binding between asset kind/key/name and collection of reference genome assembly names for which the asset type is available """ @@ -1584,7 +1584,7 @@ def _invert_genomes(self, order=None): for a in am[CFG_ASSETS_KEY].keys(): genomes.setdefault(a, []).append(g) assets = sorted(genomes.keys(), key=order) - return OrderedDict([(a, sorted(genomes[a], key=order)) for a in assets]) + return dict([(a, sorted(genomes[a], key=order)) for a in assets]) def _chk_digest_if_avail(self, genome, remote_asset_name, server_url): """ @@ -1910,7 +1910,7 @@ def _list_remote(url, genome, order=None, as_str=True): ) if not refgens: return None, None if as_str else dict() - filtered_genomes_data = OrderedDict( + filtered_genomes_data = dict( [(rg, sorted(genomes_data[rg], key=order)) for rg in refgens] ) if not as_str: diff --git a/tests/test_utils.py b/tests/test_utils.py index 3995a3a..c0ffa8f 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -1,4 +1,4 @@ -from collections import Mapping +from collections.abc import Mapping import pytest