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[pre-commit.ci] pre-commit autoupdate #268

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[pre-commit.ci] pre-commit autoupdate #268

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e4cdae0
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot] Mar 3, 2025
9885d6f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 3, 2025
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10 changes: 5 additions & 5 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
exclude: ^\.vscode/.*
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.6.0
rev: v5.0.0
hooks:
- id: check-added-large-files
- id: check-case-conflict
Expand All @@ -16,7 +16,7 @@ repos:
- id: requirements-txt-fixer
- id: trailing-whitespace
- repo: https://github.com/PyCQA/isort
rev: "5.13.2"
rev: "6.0.1"
hooks:
- id: isort
- repo: https://github.com/PyCQA/autoflake
Expand All @@ -25,16 +25,16 @@ repos:
- id: autoflake
args: [--in-place, --remove-all-unused-imports]
- repo: https://github.com/psf/black
rev: '24.8.0'
rev: '25.1.0'
hooks:
- id: black
- repo: https://github.com/PyCQA/flake8
rev: "7.1.1"
rev: "7.1.2"
hooks:
- id: flake8
additional_dependencies: [flake8-typing-imports]
- repo: https://github.com/pre-commit/mirrors-mypy
rev: v1.11.1
rev: v1.15.0
hooks:
- id: mypy
additional_dependencies: [types-requests, types-PyYAML]
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4 changes: 2 additions & 2 deletions steinbock/preprocessing/external.py
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Expand Up @@ -43,7 +43,7 @@ def list_image_files(ext_img_dir: Union[str, PathLike]) -> List[Path]:


def create_panel_from_image_files(
ext_img_files: Sequence[Union[str, PathLike]]
ext_img_files: Sequence[Union[str, PathLike]],
) -> pd.DataFrame:
num_channels = None
for ext_img_file in ext_img_files:
Expand Down Expand Up @@ -75,7 +75,7 @@ def create_panel_from_image_files(


def try_preprocess_images_from_disk(
ext_img_files: Sequence[Union[str, PathLike]]
ext_img_files: Sequence[Union[str, PathLike]],
) -> Generator[Tuple[Path, np.ndarray], None, None]:
for ext_img_file in ext_img_files:
try:
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2 changes: 1 addition & 1 deletion steinbock/segmentation/cellprofiler/_cellprofiler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@


def create_and_save_segmentation_pipeline(
segmentation_pipeline_file: Union[str, PathLike]
segmentation_pipeline_file: Union[str, PathLike],
) -> None:
with resources.open_binary(cellprofiler_data, "cell_segmentation.cppipe") as fsrc:
with open(segmentation_pipeline_file, mode="wb") as fdst:
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2 changes: 1 addition & 1 deletion steinbock/utils/_cli/mosaics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@


def _collect_tiff_files(
img_files_or_dirs: Sequence[Union[str, PathLike]]
img_files_or_dirs: Sequence[Union[str, PathLike]],
) -> List[Path]:
img_files = []
for img_file_or_dir in img_files_or_dirs:
Expand Down