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Parallel parsimony score calculation #35

Merged
merged 1 commit into from
Nov 8, 2022
Merged

Parallel parsimony score calculation #35

merged 1 commit into from
Nov 8, 2022

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Billyzhang1229
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@Billyzhang1229 Billyzhang1229 commented Aug 23, 2022 •
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coveralls commented Aug 23, 2022 •
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Pull Request Test Coverage Report for Build 3323008394

  • 39 of 87 (44.83%) changed or added relevant lines in 2 files are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage decreased (-7.8%) to 89.779%
Changes Missing Coverage Covered Lines Changed/Added Lines %
phylokit/parsimony/hartigan.py 36 84 42.86%
Totals Coverage Status
Change from base Build 3114111723: -7.8%
Covered Lines: 527
Relevant Lines: 587
💛 - Coveralls

@Billyzhang1229 Billyzhang1229 force-pushed the feature/parsimony_score branch 2 times, most recently from a341575 to bfff6d1 Compare August 24, 2022 11:04
@Billyzhang1229 Billyzhang1229 force-pushed the feature/parsimony_score branch 6 times, most recently from 56dba71 to 91b27f2 Compare October 24, 2022 18:28
@Billyzhang1229 Billyzhang1229 marked this pull request as ready for review October 25, 2022 14:04
jeromekelleher
jeromekelleher reviewed Oct 25, 2022
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Looks good, just need to test against tskit's parsimony over a range of chunk sizes to test out the vectorisation.

tests/test_parsimony.py Outdated Show resolved Hide resolved
@Billyzhang1229
Add hartigan parsimony functions and tests
8d8c0f2 
Add example notebook for parallel computing
@Billyzhang1229 Billyzhang1229 force-pushed the feature/parsimony_score branch from 91b27f2 to 8d8c0f2 Compare October 25, 2022 17:30
jeromekelleher
jeromekelleher approved these changes Nov 8, 2022
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LGTM!

@jeromekelleher jeromekelleher merged commit c666035 into jeromekelleher:main Nov 8, 2022
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@jeromekelleher jeromekelleher jeromekelleher approved these changes

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@Billyzhang1229 @coveralls @jeromekelleher