pycytominer
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cytomining
Python package for processing image-based profiling data
#387 introduced Bandit checks. A single S603 violations in `pycytominer.cyto_utils.collage` was left unaddressed at that time and was instead given `# noqa: S603` ignore. Acceptance Criteria: - There are no...
### Example code with output In `normalize.normalize`, this chunk explicitly recreates a `pd.DataFrame` from `feature_df` ```py feature_df = pd.DataFrame( fitted_scaler.transform(feature_df), columns=feature_df.columns, index=feature_df.index, ) ``` This fails when the ` fitted_scaler.transform(feature_df).columns`...
Since `ruff` is included as a Poetry dev group dependency, would it make sense to include a [repository local hook](https://pre-commit.com/#repository-local-hooks) so as to align versions used both during development as...
# Description Should be merged after #386 This applies the bugbear set of linting checks and makes appropriate fixes. The most commonly addressed linting failure that was fixed in this...
# Description This represents initial work toward an experimental `core` module that is intended to the basis of refactoring pycytominer towards a more modular and object oriented design. ## What...
# Description Thank you for your contribution to pycytominer! Please _succinctly_ summarize your proposed change. What motivated you to make this change? Please also link to any relevant issues that...
### Feature type - [X] Add new functionality - [ ] Change existing functionality ### General description of the proposed functionality Story: As a pycytominer user, I would like to...
### Feature type - [X] Add new functionality ### Story As a pycytominer developer, I would like to have descriptive dataclasses to use when working on pycytominer's main functions. Instead...
### Example code with output After turrning on isort (in this [branch](https://github.com/kenibrewer/pycytominer/tree/fix/circular-imports)), I received the following error: ``` (.venv) @kenibrewer ➜ /workspaces/pycytominer (fix/circular-imports) $ pytest ImportError while loading conftest '/workspaces/pycytominer/tests/test_cyto_utils/conftest.py'....
in #320, @shntnu introduced a function, which @kenibrewer and I recommended be removed from the PR to be added separately later. This issue documents @shntnu 's progress in this effort:...
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Python package for processing image-based profiling data