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changelog: - previously, unique sample IDs were being assigned to samples with the same metadata parameters due to improper grouping of duplicate samples. The code has been updated to correct sample ID assignment to require uniqueness.
changelog: - add bmdrc code to main build pipeline via `fitCurveFiles` function. validated to work locally
changelog: - style: reformat and lint code using ruff - refactor: change output filename format - refactor: file cleanup-- e.g. move large list/dict params to separate params file to make code easier to follow. - style: add some documentation - feat: add new CLI args for specifying filename format
changelog: - Manifest handler object for interfacing with and downloading files from the manifest now exists. - Schema parser to pull columns and slots from schema classes.
changelog: - feat: add schema checks and update related functions to correctly parse class name from file name types with and without underscores. - refactor: rename `res` variable -> `result` for clearer code
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I converted PR to draft status, just to keep track :) |
changelog: - refactor: previously, zebrafish chemical and sample file generation code was occurring across two separate files (map_samples_to_chemicals.py and build_script.py). Sample files were being produced by the build_script.py, but were not being produced correctly. Code has been updated to remove the code generating incorrect zebrafish sample files and moving all zebrafish file combination code to build_script.py. This also involved moving code dependencies to src/samples.py. - fix: fix the generation of incorrect sample files (see above)
(note: code has been updated to remove trailing spaces from fields in the dataframe when loaded, but the file itself has been updated as well)
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Note: IN PROGRESS
Ideally, I would like to update the build manifest to fully use figshare files, but not all github data has been uploaded to figshare yet. However, if we want to merge changes and open a separate branch to update the manifest, that's fine too.
Summary
Fixes duplication of
Sample_IDand updates pipeline to fully produce zebrafish benchmark dose curve response files using new data files. Includes several QOL improvements to the code.Changelog
Sample_IDs from non-unique samples (i.e. duplicates)is_aconstruct as a template for Dose, Fits, and BMD types.Issues