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CHANGELOG.md

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Changelog

Currently, GlyTrait is in development and no stable version has been released yet. The following is a list of changes that have been made to the project.

v2.0.0

Changed:

  • Experiment class and CLI can accept a meta-property table instead of a glycan structure or composition file. This allows further cumstomization of the trait calculation. To accommodate the change, the second argument of CLI ("glycan-file") is now an option, and another "mp-file" option was added. See README for details.

Removed:

  • The input_data argument from Experiment was removed.
  • The Experiment.extract_meta_properties method was removed. Meta-property table is extracted from glycan structures or compositions automatically after Experiment initialization.
  • load_data and GlyTraitInputData were removed.

v0.1.7

Fixed:

  • Fix the bug that type checks failed when the abundance data type is integer.

v0.1.6

Changed:

  • The Experiment class now can be initialized from file paths directly. The old way of initializing from a GlyTraitInputData instance could be done by the keyword argument: Experiment(input_data=input_data).
  • The file format instructions in the Streamlit app are updated to be more clear.

v0.1.5

Added:

  • A new try_formulas method for Experiment. This method returned the calculated derived trait DataFrame directly based on given formula expressions. It might be useful for glycomics EDA.
  • Example data are added to the Streamlit app.

Changed:

  • Experiment.extract_meta_properties method was removed for less confusion to users. Calling Experiment.preprocess will automatically extract meta properties.

v0.1.4

Added:

  • Sialic acid linkage configuration in the Streamlit app.
  • A spinner is shown now when the Streamlit app is running.

Fixed:

  • Fix the bug that the "mode" configuration was ignored by the Streamlit app.

v0.1.3

Added:

  • The Streamlit app!
  • A new method for the Experiment class: Experiment.run_workflow().

v0.1.2

Added:

  • Experiment class is added as the new api of GlyTrait, instead of the old GlyTrait. This might be part of the python package api in the future.

Changed:

  • The formula file format is much simpler: any non-blank lines not starting with "#" will be parsed as a formula. The formula descriptions are converted into comments (starting with "#").
  • GlyTraitInputData now checks the validity of data. This allows dynamic change the input data after a GlyTraitInputData instance is created.

Removed:

  • GlyTrait class is removed.

v0.1.1

Changed:

  • When provided a custom formula file, the built-in formula file is no longer used.

v0.1.0

Initial release of GlyTrait.