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Speedup mask filter. #40

Merged
merged 3 commits into from
Dec 16, 2023
Merged

Speedup mask filter. #40

merged 3 commits into from
Dec 16, 2023

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FloWuenne
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@FloWuenne FloWuenne commented Dec 15, 2023 •
edited by kbestak
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PR checklist

This PR replaces the mask filtering code by more efficient code that speeds up the function, particularly for larger datasets.

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

@FloWuenne FloWuenne added the enhancement Improvement for existing functionality label Dec 15, 2023
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Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

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github-actions bot commented Dec 15, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1d68330

+| ✅ 158 tests passed       |+
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in main.nf.test: Once you have added the required tests, please run the following command to build this file:
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-16 11:31:20

@FloWuenne FloWuenne mentioned this pull request Dec 16, 2023
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@FloWuenne
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This PR will resolve #38 !

kbestak
kbestak reviewed Dec 16, 2023
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If only max_area is provided, small_labels is not defined.

bin/maskfilter.py Show resolved Hide resolved
@FloWuenne @kbestak
Update bin/maskfilter.py
1d68330 
Co-authored-by: Krešimir Beštak <[email protected]>
kbestak
kbestak approved these changes Dec 16, 2023
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LGTM!

@kbestak kbestak merged commit eecf921 into dev Dec 16, 2023
6 checks passed
@kbestak kbestak deleted the speedup_maskfilter branch December 16, 2023 11:54
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@FloWuenne @kbestak