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CHANGELOG.md

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Change Log

Unreleased

Changed repo name from brainspin to cvasl

Added

  • cli module for command line interface
  • file_handler module for configuring and hashing data
  • carve module for handeling DICOM data
  • mold module for plotting and debiasing images
  • seperated module for dealing csv and tsv derived data
  • a changelog
  • tests/test.py for testing

Changed

Release 0.0.0-alpha

Added

  • First version of this Python project to follow the Netherlands eScience Center software development guide, containing (added to this version):

    • License
    • Notice
    • seperate environments for harmonization experiments inside harmonization_paper folder
    • notebook showing how showable standard was generated
    • file with standard for submitting to package inside researcher_interface folder
    • preliminary linear regression models as baseline for brain age models

Release 0.0.1

Added

  • Second version of this Python project to follow the Netherlands eScience Center software development guide, containing (added to this version):

    • additional experiments inside harmonization_paper folder
    • example of correct format for csv of derived values to use with library

Release 0.0.2

Added

  • Third version of this Python project containing (added to this version):

    • haromnzation_abstract_one folder to save and make reproducible work for brain mapping abstract

    • exact freeze of environment in precise_working_environment

    • harmony module for functions related to implementing common harmonization algorithms

    • harmony also includes new graphing functions in harmony module to illustrate harmonization effects e.g. compare_harm_one_site_violins and compare_harm_multi_site_violins

    • updates to seperated module including:

    • new functons in seperated to bin data on a continous variable

    • generalized functions for k-folding as specific to project in seperated module

    • k folding which allows splitting on two variables (one continuous, one categorical) with
      stratified_cat_and_cont_categories_shuffle_split function

    • command-line sex recoding over a folder

    • command-line loging of columns over a folder

    • command-line loging of columns over a file

    • command-line cleaning off unwanted columns run over a folder

Release 0.0.3

Added

  • Fourth version of this Python project containing (added to this version):

    • testing has been changed to use pytest ( all unit-test formatted tests will still run)
    • testing has been split into two files so CI can run a docker based testing, and a general (multi-os) test
    • testing platform (what makes venv + run) switched to tox
    • possibility to test notebooks with nbmake module added, but not in CI due to time and data issues
    • vendor module of cvasl, harmonization code from outside packages previously without releases, original open licenses copied
    • vendor module versions for RELIEF, neurocombat, autocombat, Combat++, covbat and open nested combat

Release 0.0.4

Added

  • Fifth version of this Python project containing (added to this version):

    • work for first long paper in secluded notebooks = reworked environment to run all pythonharmonizations from venfor in one environment
    • change to setup to include vendor