feat: set default for records

balajtimate commented 8 months ago

Description

Based on the results from running HTSinfer with various --records settings (https://github.com/zavolanlab/htsinfer/issues/109#issuecomment-1801481936), 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

[X] 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.

[X] I have performed a self-review of my own code
[X] My code follows the existing coding style, lints and generates no new warnings
[X] 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.
[X] I have commented my code in hard-to-understand areas
[X] I have added ["Google-style docstrings"] to all new modules, classes, methods/functions or updated previously existing ones
[X] I have added tests that prove my fix is effective or that my feature works
[X] New and existing unit tests pass locally with my changes and I have not reduced the code coverage relative to the previous state
[X] 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.

codecov[bot] commented 8 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

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

Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #148 +/- ## ========================================= Coverage 100.00% 100.00% ========================================= Files 13 13 Lines 1078 1078 ========================================= Hits 1078 1078 ``` | [Files](https://app.codecov.io/gh/zavolanlab/htsinfer/pull/148?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab) | Coverage Δ | | |---|---|---| | [htsinfer/cli.py](https://app.codecov.io/gh/zavolanlab/htsinfer/pull/148?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-aHRzaW5mZXIvY2xpLnB5) | `100.00% <ø> (ø)` | | | [htsinfer/models.py](https://app.codecov.io/gh/zavolanlab/htsinfer/pull/148?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-aHRzaW5mZXIvbW9kZWxzLnB5) | `100.00% <100.00%> (ø)` | |

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uniqueg commented 8 months ago

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 commented 8 months ago

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

zavolanlab / htsinfer