From 643cc01300e7b5b6c37f8407ff37e65b5c61e9d3 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 1 Aug 2026 12:34:27 +0000 Subject: [PATCH 1/3] Bump the python-packages group with 4 updates Updates the requirements on [ome-arrow](https://github.com/wayscience/ome-arrow), [opencv-python](https://github.com/opencv/opencv-python), [poethepoet](https://github.com/nat-n/poethepoet) and [pydata-sphinx-theme](https://github.com/pydata/pydata-sphinx-theme) to permit the latest version. Updates `ome-arrow` to 0.1.0 - [Release notes](https://github.com/wayscience/ome-arrow/releases) - [Commits](https://github.com/wayscience/ome-arrow/compare/v0.0.3...v0.1.0) Updates `opencv-python` to 5.0.0.93 - [Release notes](https://github.com/opencv/opencv-python/releases) - [Commits](https://github.com/opencv/opencv-python/commits) Updates `poethepoet` to 0.48.0 - [Release notes](https://github.com/nat-n/poethepoet/releases) - [Commits](https://github.com/nat-n/poethepoet/compare/v0.37.0...v0.48.0) Updates `pydata-sphinx-theme` to 0.20.0 - [Release notes](https://github.com/pydata/pydata-sphinx-theme/releases) - [Changelog](https://github.com/pydata/pydata-sphinx-theme/blob/main/RELEASE.md) - [Commits](https://github.com/pydata/pydata-sphinx-theme/compare/v0.16.0...v0.20.0) --- updated-dependencies: - dependency-name: ome-arrow dependency-version: 0.1.0 dependency-type: direct:production dependency-group: python-packages - dependency-name: opencv-python dependency-version: 5.0.0.93 dependency-type: direct:production dependency-group: python-packages - dependency-name: poethepoet dependency-version: 0.48.0 dependency-type: direct:development dependency-group: python-packages - dependency-name: pydata-sphinx-theme dependency-version: 0.20.0 dependency-type: direct:development dependency-group: python-packages ... Signed-off-by: dependabot[bot] --- pyproject.toml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 13e8ecc..7593311 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,8 +27,8 @@ dependencies = [ "ipywidgets>=8.1.7,<9", "matplotlib>=3.9.3,<4", "nest-asyncio2>=1.7,<2", - "ome-arrow>=0.0.3,<0.0.12", - "opencv-python>=4.10.0.84,<5", + "ome-arrow>=0.0.3,<0.1.1", + "opencv-python>=4.10.0.84,<6", "pandas>=2.2.2,<4", "pyarrow>=16", "pyvista>=0.46.4", @@ -50,7 +50,7 @@ dev = [ "jupyterlab>=4.3,<5", "jupyterlab-code-formatter>=3.0.2,<4", "jupytext>=1.16.4,<2", - "poethepoet>=0.37,<0.48", + "poethepoet>=0.37,<0.49", "pytest>=8.3.3,<10", "pytest-cov>=5,<8", "sqlalchemy>=1.3.6,<3", @@ -59,7 +59,7 @@ docs = [ "dunamai>=1.22,<2", "myst-nb>=1.1.2,<2", "myst-parser>=3,<6", - "pydata-sphinx-theme>=0.16,<0.20", + "pydata-sphinx-theme>=0.16,<0.21", "sphinx>=9,<9.1", "sphinx-multiversion", ] From a05d8d59f4706f3d2dc7b07025b0a28067402d22 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Sat, 1 Aug 2026 12:37:11 +0000 Subject: [PATCH 2/3] chore: auto-apply pre-commit fixes --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c4297f4..89a00e9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -15,11 +15,11 @@ repos: - id: check-yaml - id: detect-private-key - repo: https://github.com/tox-dev/pyproject-fmt - rev: "v2.25.1" + rev: "v2.26.0" hooks: - id: pyproject-fmt - repo: https://github.com/codespell-project/codespell - rev: v2.4.2 + rev: v2.4.3 hooks: - id: codespell exclude: | @@ -50,7 +50,7 @@ repos: hooks: - id: actionlint - repo: https://github.com/astral-sh/ruff-pre-commit - rev: "v0.15.20" + rev: "v0.16.1" hooks: - id: ruff-format - id: ruff-check From dfd6c059a459bcee46e0bb4e080efdbb68ce0788 Mon Sep 17 00:00:00 2001 From: Dave Bunten Date: Sat, 1 Aug 2026 12:48:37 -0600 Subject: [PATCH 3/3] Resolve Ruff checks after dependency update --- src/cytodataframe/frame.py | 12 ++++++------ src/cytodataframe/volume.py | 4 ++-- tests/test_frame.py | 2 +- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/cytodataframe/frame.py b/src/cytodataframe/frame.py index 92c46f5..6cd5249 100644 --- a/src/cytodataframe/frame.py +++ b/src/cytodataframe/frame.py @@ -112,7 +112,7 @@ class CytoDataFrame(pd.DataFrame): # while avoiding oversized outputs in typical Jupyter viewports. _DEFAULT_TABLE_MAX_HEIGHT: ClassVar[str] = "700px" - def __init__( # noqa: PLR0913 + def __init__( # noqa: PLR0913, PLR0917 self: CytoDataFrame_type, data: Union[CytoDataFrame_type, pd.DataFrame, str, pathlib.Path], data_context_dir: Optional[str] = None, @@ -840,7 +840,7 @@ def _slider_relative_position(value: float, slider_domain: np.ndarray) -> float: return position @staticmethod - def _build_filter_distribution_html( # noqa: C901, PLR0912, PLR0913, PLR0915 + def _build_filter_distribution_html( # noqa: C901, PLR0912, PLR0913, PLR0915, PLR0917 values: pd.Series, selected_range: Tuple[float, float], threshold_x: Optional[float] = None, @@ -2035,7 +2035,7 @@ def find_image_path_columns( and str(col).replace("FileName", "PathName") in all_cols } - def search_for_mask_or_outline( # noqa: PLR0913, PLR0911, C901 + def search_for_mask_or_outline( # noqa: PLR0913, PLR0911, PLR0917, C901 self: CytoDataFrame_type, data_value: str, pattern_map: dict, @@ -2644,7 +2644,7 @@ def _load_enhanced_image_for_display( # noqa: C901 return orig_image_array - def _prepare_cropped_image_layers( # noqa: C901, PLR0915, PLR0912, PLR0913 + def _prepare_cropped_image_layers( # noqa: C901, PLR0915, PLR0912, PLR0913, PLR0917 self: CytoDataFrame_type, data_value: Any, bounding_box: Tuple[int, int, int, int], @@ -3630,7 +3630,7 @@ def _find_3d_columns_for_display( return columns_3d - def _add_label_overlay_to_plotter( # noqa: PLR0913 + def _add_label_overlay_to_plotter( # noqa: PLR0913, PLR0917 self: CytoDataFrame_type, plotter: Any, volume: np.ndarray, @@ -3969,7 +3969,7 @@ def _toggle_overlay_actors_visibility( with contextlib.suppress(Exception): plotter.render() - def _build_pyvista_viewer( # noqa: C901, PLR0912, PLR0913, PLR0915 + def _build_pyvista_viewer( # noqa: C901, PLR0912, PLR0913, PLR0915, PLR0917 self: CytoDataFrame_type, volume: np.ndarray, backend: str, diff --git a/src/cytodataframe/volume.py b/src/cytodataframe/volume.py index b7e588c..4227931 100644 --- a/src/cytodataframe/volume.py +++ b/src/cytodataframe/volume.py @@ -82,7 +82,7 @@ def _resolve_vtk_js_url(display_options: Optional[dict]) -> str: return str(configured) if configured else VTK_JS_CDN_URL -def build_3d_image_html_view( # noqa: C901, PLR0912, PLR0913, PLR0915 +def build_3d_image_html_view( # noqa: C901, PLR0912, PLR0913, PLR0915, PLR0917 volume: np.ndarray, dims: Tuple[int, int, int], data_value: str, @@ -443,7 +443,7 @@ def extract_volume_from_ome_arrow( # noqa: C901, PLR0912 return None -def build_3d_html_from_path( # noqa: PLR0913 +def build_3d_html_from_path( # noqa: PLR0913, PLR0917 data_value: str, candidate_path: pathlib.Path, display_options: Optional[dict], diff --git a/tests/test_frame.py b/tests/test_frame.py index fb613ad..b907fd9 100644 --- a/tests/test_frame.py +++ b/tests/test_frame.py @@ -530,7 +530,7 @@ def test_find_matching_segmentation_path_prefers_candidate_parent_tree( assert matched.parent.name == "plate_a" -def test_cytodataframe_input( +def test_cytodataframe_input( # noqa: PLR0917 tmp_path: pathlib.Path, basic_outlier_dataframe: pd.DataFrame, basic_outlier_csv: str,