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shift the migrant flag from metadata to the flags column - #668

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bhaller merged 4 commits into
multitraitfrom
fix_666
Aug 26, 2026
Merged

shift the migrant flag from metadata to the flags column#668
bhaller merged 4 commits into
multitraitfrom
fix_666

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@bhaller

@bhaller bhaller commented Aug 26, 2026

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fix #666, shift the migrant flag from metadata to the flags column

@bhaller bhaller linked an issue Aug 26, 2026 that may be closed by this pull request
@bhaller
bhaller requested a review from petrelharp August 26, 2026 11:47
@codecov

codecov Bot commented Aug 26, 2026

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Codecov Report

❌ Patch coverage is 55.55556% with 8 lines in your changes missing coverage. Please review.
✅ Project coverage is 76.80%. Comparing base (98ed022) to head (04f4051).

Files with missing lines Patch % Lines
core/species.cpp 55.55% 8 Missing ⚠️
Additional details and impacted files

Impacted file tree graph

@@             Coverage Diff             @@
##           multitrait     #668   +/-   ##
===========================================
  Coverage       76.80%   76.80%           
===========================================
  Files             117      117           
  Lines           78760    78763    +3     
  Branches        14296    14301    +5     
===========================================
+ Hits            60491    60496    +5     
+ Misses          18269    18267    -2     
Files with missing lines Coverage Δ
core/slim_globals.cpp 69.25% <ø> (ø)
core/slim_globals.h 57.89% <ø> (ø)
core/species.h 91.80% <ø> (ø)
core/species.cpp 64.82% <55.55%> (-0.02%) ⬇️

... and 7 files with indirect coverage changes

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@petrelharp petrelharp left a comment

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LGTM! I'll have a look at the python tests next.

Comment thread core/species.cpp
Comment thread core/species.cpp Outdated
@petrelharp

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So far I'm pretty sure the test errors are because the individual metadata isn't getting written out correctly. Trying to figure out how to verify that.

Comment thread core/species.h
slim_age_t age_; // 4 bytes (int32_t): the age of the individual (-1 for WF models)
slim_objectid_t subpopulation_id_; // 4 bytes (int32_t): the subpopulation the individual belongs to

int16_t sex_; // 2 bytes (int16_t): the sex of the individual, as defined by the IndividualSex enum

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here the number of bytes changed, but it didn't change in the schema

Comment thread core/slim_globals.cpp Outdated
@bhaller

bhaller commented Aug 26, 2026

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OK, good to go! Thanks for the review, and for finding that bug!

@bhaller
bhaller merged commit 1d8386c into multitrait Aug 26, 2026
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remove flags from individual metadata?

2 participants