From 978537e9c2d03d4b5c13f8ffd3d4a13a70f27173 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 1 Dec 2025 16:28:54 +0000 Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.1 → v0.14.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.1...v0.14.7) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f052d43..3171329 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -9,7 +9,7 @@ repos: - id: check-case-conflict - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.14.1 + rev: v0.14.7 hooks: - id: ruff types_or: [python, pyi, jupyter] From 353f71b320f1ce169ac027cc4ae5dd7b94cacdb6 Mon Sep 17 00:00:00 2001 From: Nezar Abdennur Date: Mon, 1 Dec 2025 13:36:44 -0500 Subject: [PATCH 2/2] style: RUF059 fixes --- bioframe/core/checks.py | 6 +++--- bioframe/core/construction.py | 2 +- bioframe/ops.py | 10 +++++----- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/bioframe/core/checks.py b/bioframe/core/checks.py index ba00ddd..88a413b 100644 --- a/bioframe/core/checks.py +++ b/bioframe/core/checks.py @@ -169,7 +169,7 @@ def is_overlapping(df, cols=None): """ from ..ops import merge - ck1, sk1, ek1 = _get_default_colnames() if cols is None else cols + _ck1, sk1, ek1 = _get_default_colnames() if cols is None else cols df_merged = merge(df, cols=cols) @@ -297,8 +297,8 @@ def is_contained( """ from ..ops import trim - ck1, sk1, ek1 = _get_default_colnames() if cols is None else cols - ck2, sk2, ek2 = _get_default_colnames() if cols_view is None else cols_view + _ck1, sk1, ek1 = _get_default_colnames() if cols is None else cols + _ck2, sk2, ek2 = _get_default_colnames() if cols_view is None else cols_view if df_view_col is None: try: df_view_assigned = ops.overlap(df, view_df, cols1=cols, cols2=cols_view) diff --git a/bioframe/core/construction.py b/bioframe/core/construction.py index b7363a5..481adf5 100644 --- a/bioframe/core/construction.py +++ b/bioframe/core/construction.py @@ -229,7 +229,7 @@ def make_viewframe( view_df:dataframe satisfying properties of a view """ - ck1, sk1, ek1 = _get_default_colnames() if cols is None else cols + ck1, _sk1, _ek1 = _get_default_colnames() if cols is None else cols view_df = from_any(regions, name_col=view_name_col, cols=cols) diff --git a/bioframe/ops.py b/bioframe/ops.py index dfc42d4..8318075 100644 --- a/bioframe/ops.py +++ b/bioframe/ops.py @@ -880,8 +880,8 @@ def coverage( """ - ck1, sk1, ek1 = _get_default_colnames() if cols1 is None else cols1 - ck2, sk2, ek2 = _get_default_colnames() if cols2 is None else cols2 + _ck1, sk1, ek1 = _get_default_colnames() if cols1 is None else cols1 + _ck2, _sk2, _ek2 = _get_default_colnames() if cols2 is None else cols2 df1.reset_index(inplace=True, drop=True) @@ -1365,8 +1365,8 @@ def setdiff(df1, df2, cols1=None, cols2=None, on=None): df_setdiff : pandas.DataFrame """ - ck1, sk1, ek1 = _get_default_colnames() if cols1 is None else cols1 - ck2, sk2, ek2 = _get_default_colnames() if cols2 is None else cols2 + _ck1, _sk1, _ek1 = _get_default_colnames() if cols1 is None else cols1 + _ck2, _sk2, _ek2 = _get_default_colnames() if cols2 is None else cols2 events1, _ = _overlap_intidxs( df1, df2, how="inner", cols1=cols1, cols2=cols2, on=on @@ -1866,7 +1866,7 @@ def assign_view( """ - ck1, sk1, ek1 = _get_default_colnames() if cols is None else cols + _ck1, sk1, ek1 = _get_default_colnames() if cols is None else cols df = df.copy() df.reset_index(inplace=True, drop=True)