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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.x.y] - 2024-nn-yy

Modified

  • Switched to using np.nan instead of np.NaN to be compatible with Numpy 2.0

[0.5.0] - 2024-04-15

Added

  • Added new rd.plot.debug_axes which draws guide lines to help with axis alignment.
  • Added new rd.plot.adjust_subplot_margins_inches which allows subplot configuring using inch offsets (instead of subfigure coordinate offsets)

Modified

  • rd.flow.load_csv_with_metadata and rd.flow.load_groups_with_metadata can now load a subset of columns.
  • The datadir.txt can include paths that use ~ to represent the home directory.
  • rd.plot.generate_xticklabels does not include metadata key labels in plots without yticklabels
  • rd.plot.generate_xticklabels no longer throws an error when xticklabels don't match the dictionary passed (instead leaves labels as-is)
  • rd.plot.generate_xticklabels now enables user-specified line spacing

[0.4.2] - 2023-07-27

Added

  • rd.plot.generate_xticklabels replaces a plot's existing xticklabels with specified metadata in a table-like format

[0.4.1] - 2023-06-27

Modified

  • Updated the rd.plot.plot_mapping command to properly handle the single-numeric case.

[0.4.0] - 2023-04-21

Added

  • rd.plot.plot_well_metadata to make nice plots corresponding to well metadata specified as a YAML file.

[0.3.0] - 2023-03-01

Added

  • rd.flow.load_groups_with_metadata loads files from several folders (groups, e.g. corresponding to plates) into a single dataframe

Modified

  • rd.flow.moi properly generates plots of MOI vs fraction infected for checking calculation accuracy
  • rd.well_mapper properly handles metadata concatenation

[0.2.0] - 2022-06-17

Added

  • rd.flow.moi calculates viral MOI, creating summary graphs and tables.

Modified

  • rd.outfile now creates necessary subdirectories within rootdir/datadir.
  • rd.flow.load_csv_with_metadata now allows str and Path arguments
  • rd.flow.load_csv_with_metadata properly handles well IDs up to A1-P24 (384-well plate)
  • rd.flow.load_csv_with_metadata fills unspecified metadata with NA

[0.1.0] - 2022-03-11

Added

  • Initial flow processing workflow

Modified

  • Automatic use of black, isort, and flake in CI