From 69433837adfa08e22d112bd18d6f17765fb58da6 Mon Sep 17 00:00:00 2001 From: BadPrograms Date: Mon, 30 Jun 2025 16:50:44 +0300 Subject: [PATCH 1/2] better_stems_for_writers --- src/LineageTree/lineageTree.py | 2 +- src/LineageTree/lineageTreeManager.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/LineageTree/lineageTree.py b/src/LineageTree/lineageTree.py index e8629ca..38c8c75 100644 --- a/src/LineageTree/lineageTree.py +++ b/src/LineageTree/lineageTree.py @@ -965,7 +965,7 @@ def write(self, fname: str) -> None: fname : str path to and name of the file to save """ - if os.path.splitext(fname)[-1] != ".lT": + if os.path.splitext(fname)[-1].upper() != ".LT": fname = os.path.extsep.join((fname, "lT")) if hasattr(self, "_protected_predecessor"): del self._protected_predecessor diff --git a/src/LineageTree/lineageTreeManager.py b/src/LineageTree/lineageTreeManager.py index 41c3677..6a777f3 100644 --- a/src/LineageTree/lineageTreeManager.py +++ b/src/LineageTree/lineageTreeManager.py @@ -6,7 +6,7 @@ from collections.abc import Callable, Iterable, Generator from functools import partial from typing import TYPE_CHECKING, Literal - +from pathlib import Path import matplotlib.colors as mcolors import numpy as np from matplotlib import colormaps @@ -140,7 +140,7 @@ def write(self, fname: str): fname : str The path and name of the file that is to be saved. """ - if os.path.splitext(fname)[-1] != ".lTM": + if os.path.splitext(fname)[-1].upper() != ".LTM": fname = os.path.extsep.join((fname, "lTM")) for _, lT in self: if hasattr(lT, "_protected_predecessor"): From aa98f826069399d4911fb611d5b43d40f60f2934 Mon Sep 17 00:00:00 2001 From: BadPrograms Date: Mon, 30 Jun 2025 16:51:55 +0300 Subject: [PATCH 2/2] ruff --- src/LineageTree/lineageTreeManager.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/LineageTree/lineageTreeManager.py b/src/LineageTree/lineageTreeManager.py index 6a777f3..89f7817 100644 --- a/src/LineageTree/lineageTreeManager.py +++ b/src/LineageTree/lineageTreeManager.py @@ -3,10 +3,10 @@ import os import pickle as pkl import warnings -from collections.abc import Callable, Iterable, Generator +from collections.abc import Callable, Generator, Iterable from functools import partial from typing import TYPE_CHECKING, Literal -from pathlib import Path + import matplotlib.colors as mcolors import numpy as np from matplotlib import colormaps