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v1.0.0 #7

Merged
merged 12 commits into from
Mar 24, 2025
Merged

v1.0.0 #7

merged 12 commits into from
Mar 24, 2025

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sage-wright
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@sage-wright sage-wright commented Mar 14, 2025

This PR does a lot -- enough that I'm bumping this to v1.0.0 woohoo!

  • generally tries to implement pep8 standards (thanks, autopep8)
  • adds several new validation criteria and customizations:
    • a range comparison (essentially is the diffference between the values +- the threshold)
    • add your own delimiter for set comparisons and you can use many at a time without issue -- e.g, (";,\[])
    • combine multiple different criteria (0.01,50) so that if at least one test succeeds the sample passeswith fancy recursive stuff
    • allow for lists of numbers and values to be compared in the %DIFF and RANGE comparisons (especially helpful for results like BUSCO where we've got a lot of different percentages)
  • edits the output validation criteria failure excel file for clarity: when an entire column passes it is now excluded and sets now only show what's missing from the either one -- less visual clutter and scrolling which is awesome!
  • updates the examples to show new functionality and provides the command in a .sh file to recreate the examples
  • updates the documentation

Also, this closes #4 by requiring a header row in the column_translation TSV file and closes #6 by preventing the issue from occurring in the first place.

v1.0.0 is backwards compatible with v0.1.0 input parameters.

@sage-wright sage-wright requested a review from a team as a code owner March 14, 2025 03:20
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@Michal-Babins Michal-Babins left a comment

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Updated flow in theiavalidate has been reviewed and the examples have been tested. Range comparisons & delimiter updates for list comparisons like busco are explicit in example. Final report clearly states validation criteria and the number of samples failing, if any. Good work on the updates.

@sage-wright sage-wright merged commit 0bef54c into main Mar 24, 2025
@sage-wright sage-wright deleted the dev branch March 24, 2025 14:26
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Successfully merging this pull request may close these issues.

[BUG] Empty cells not being converted correctly to 0 Column Translation TSV file bug
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