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feat: set default for records #148

Merged
merged 1 commit into from
Nov 12, 2023
Merged

feat: set default for records #148

merged 1 commit into from
Nov 12, 2023

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balajtimate
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@balajtimate balajtimate commented Nov 10, 2023

Description

Based on the results from running HTSinfer with various --records settings (#109 (comment)), and the discussion that followed, the optimal number for this parameter was found to be 1000000. Records set to 1 million resulted in the lowest number of mismatches for organisms, with an average runtime for the whole process of 540.1 seconds (~9 minutes).

  • Set default parameter for --records to 1000000

Closes #109

Type of change

  • New feature (non-breaking change which adds functionality)

Checklist

Please carefully read these items and tick them off if the statements are true
or do not apply.

  • I have performed a self-review of my own code
  • My code follows the existing coding style, lints and generates no new
    warnings
  • I have added type annotations to all function/method signatures, and I
    have added type annotations for any local variables that are non-trivial,
    potentially ambiguous or might otherwise benefit from explicit typing.
  • I have commented my code in hard-to-understand areas
  • I have added ["Google-style docstrings"] to all new modules, classes,
    methods/functions or updated previously existing ones
  • I have added tests that prove my fix is effective or that my feature
    works
  • New and existing unit tests pass locally with my changes and I have not
    reduced the code coverage relative to the previous state
  • I have updated any sections of the app's documentation that are affected
    by the proposed changes

If for some reason you are unable to tick off all boxes, please leave a
comment explaining the issue you are facing so that we can work on it
together.

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codecov bot commented Nov 10, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (172eb99) 100.00% compared to head (40204b2) 100.00%.

Additional details and impacted files
@@            Coverage Diff            @@
##               dev      #148   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           13        13           
  Lines         1078      1078           
=========================================
  Hits          1078      1078           
Files Coverage Δ
htsinfer/cli.py 100.00% <ø> (ø)
htsinfer/models.py 100.00% <100.00%> (ø)

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@balajtimate balajtimate requested a review from uniqueg November 10, 2023 14:28
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uniqueg commented Nov 10, 2023

Good stuff! Maybe link to the issue with the test results in the PR description. Otherwise LGTM.

Of course, after merging, you need to again merge these changes into your other feature branch, commit and push, to update the corresponding PR in #147

@balajtimate
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I think the issue with the results was already linked, but I added a link to the comment containing the results instead.

@balajtimate balajtimate merged commit 5ef3322 into dev Nov 12, 2023
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@balajtimate balajtimate deleted the set_def_rec branch November 12, 2023 21:29
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Optimize performance
2 participants