Extract plot_haplotype_network into AnophelesHapNetAnalysis mixin#1310
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AswaniSahoo wants to merge 1 commit intomalariagen:masterfrom
Open
Extract plot_haplotype_network into AnophelesHapNetAnalysis mixin#1310AswaniSahoo wants to merge 1 commit intomalariagen:masterfrom
AswaniSahoo wants to merge 1 commit intomalariagen:masterfrom
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@jonbrenas Ready for review when you get a chance. Let me know if you'd like any changes to the test coverage or the MRO placement. |
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Relates to #366
Extracts
plot_haplotype_networkfromAnophelesDataResourceinto a newAnophelesHapNetAnalysismixin, as outlined in my comment on the issue.What this does
malariagen_data/anoph/hapnet.py— mixin withplot_haplotype_networkand its internal helpers (_median_joining_network,_mjn_graph)malariagen_data/anopheles.py— removed method, added mixin to MRO, cleaned up unused importshapnet_params.py— kept as-istests/anoph/test_hapnet.py— simulated-data tests following the existinghapclust.pypatternVerification
test_hapclusttests pass (no regressions)ruff checkandruff formatclean