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feat: add analysis functions#92

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jjjermiah merged 41 commits intomainbhklab/readii:mainfrom katys/add-analysisbhklab/readii:katys/add-analysisCopy head branch name to clipboardDec 17, 2024

+3,906-782

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Commits on Dec 16, 2024

• feat: add functions for correlation matrix calculations and subsetting

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• style: change feature name if statements to be multi-line

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• build: updated pixi lock file

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• feat: add readii logger for errors and exceptions

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• test: add testing for getFeatureCorrelations

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• build: add seaborn for plotting

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• build: add pandas dependency

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• feat: add function to plot a correlation matrix as a seaborn heatmap

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• feat: add function for plotting correlation distribution as a histogram

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• feat: add correlation plot functions to init

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• feat: made writer class for plot figures

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• fix: removing what I think is a typo import

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• style: add space in import statement for plot correlation

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• feat: add function return types

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• feat: specify PlotWriter save object as matplotlib Figure

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• Merge remote-tracking branch 'origin/main' into katys/add-analysis

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• docs: correct docstring in getFeatureCorrelations for default feature name values

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• docs: make function docstring oneliners imperative form

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• docs: make docstring oneliner imperative

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• feat: add possible file extensions for plot figure, remove logger.exception calls

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• refactor: replace print statement with logger

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• docs: update triangle parameter description in plotCorrelationHeatmap

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• feat: add helper function to check if the subsetting of a dataframe is out of bounds for that dataframe

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• Merge remote-tracking branch 'origin/main' into katys/add-analysis for pixi.lock

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Commits on Dec 17, 2024

• docs/refactor: add parameter descriptions for PlotWriter save, change VALID_EXTENSIONS to a tuple

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• style: remove blank line after function docstring

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• refactor: remove unused import

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• refactor: remove unused error variables in loadFeatureFilesFromImageTypes

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• refactor: change fstring to regular string in error msgs

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• style: remove whitespace around docstrings

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• feat: add all io, data, analyze functions to ruff config

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• style: sorted imports

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• refactor: replaced matplotlib import to specifically import Figure

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• style: sort imports, remove whitespace in docstring

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• style: sort imports

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• feat: add error handling

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• refactor: correct help message for overwrite

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• refactor: replace matplotlib import with Figure import

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• style: sort imports

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• refactor: remove io readers and data directory for now, will add in separate branch

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• feat: add check for empty dataframes in getFeatureCorrelations

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