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Anopheles refactor part 6 - haplotype data#401

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alimanfoo merged 13 commits intomalariagen:masterfrom
alimanfoo:refactor-part-size-hap-data-2023-05-20
May 23, 2023
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Anopheles refactor part 6 - haplotype data#401
alimanfoo merged 13 commits intomalariagen:masterfrom
alimanfoo:refactor-part-size-hap-data-2023-05-20

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@alimanfoo alimanfoo commented May 20, 2023 •
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Continue working towards #366, refactoring haplotype data access functions.

Also some other changes:

  • All parameter definitions have been moved to separate dedicated modules, to make it easier to find them. E.g., the base_params are now available via from malariagen_data.anoph import base_params.
  • Haplotype data access tests have been refactored to use simulated data rather than real data for speed.
  • Some other general improvements to the fast unit tests for speed and simplicity.

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codecov bot commented May 20, 2023 •
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Codecov Report

Attention: Patch coverage is 97.50693% with 9 lines in your changes missing coverage. Please review.

Project coverage is 96.19%. Comparing base (c3e76e2) to head (2f295f7).
Report is 595 commits behind head on master.

Files with missing lines Patch % Lines
malariagen_data/anoph/hap_data.py 94.57% 7 Missing ⚠️
malariagen_data/anoph/base_params.py 97.05% 1 Missing ⚠️
malariagen_data/anoph/sample_metadata.py 87.50% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##           master     #401      +/-   ##
==========================================
+ Coverage   95.73%   96.19%   +0.46%     
==========================================
  Files           5       21      +16     
  Lines        1242     1525     +283     
==========================================
+ Hits         1189     1467     +278     
- Misses         53       58       +5

☔ View full report in Codecov by Sentry.
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@alimanfoo alimanfoo marked this pull request as ready for review May 23, 2023 17:16
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alimanfoo commented May 23, 2023

Hi @leehart, FYI more spring cleaning coming in here.

@alimanfoo alimanfoo merged commit 962b54b into malariagen:master May 23, 2023
@alimanfoo alimanfoo deleted the refactor-part-size-hap-data-2023-05-20 branch May 23, 2023 19:05
@alimanfoo alimanfoo mentioned this pull request May 23, 2023
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leehart commented May 25, 2023

Awesome stuff @alimanfoo

It would be nice if the max_cohort_size base param could assimilate the cohort_size base param.

@alimanfoo alimanfoo added the BMGF-001927 Work supported by BMGF grant INV-001927 (MalariaGEN 2019-2024). label Dec 4, 2024
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