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Simpler lineage struct #2296

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merged 3 commits into from
Jul 30, 2024

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@jeromekelleher jeromekelleher commented Jul 23, 2024

Work towards #2294

Work on adding a lineage struct that we store in the algorithm state in preference to using just segments. This does the initial bit where we just define this structure minimally in C and Python. Actually using it to some advantage can be done in follow-ups.

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codecov bot commented Jul 23, 2024

Codecov Report

Attention: Patch coverage is 83.42857% with 29 lines in your changes missing coverage. Please review.

Project coverage is 90.96%. Comparing base (ad3f625) to head (8ee8cb1).

Files Patch % Lines
lib/msprime.c 83.42% 18 Missing and 11 partials ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #2296      +/-   ##
==========================================
- Coverage   91.09%   90.96%   -0.14%     
==========================================
  Files          20       20              
  Lines       11921    12003      +82     
  Branches     2435     2444       +9     
==========================================
+ Hits        10860    10919      +59     
- Misses        581      598      +17     
- Partials      480      486       +6     
Flag Coverage Δ
C 90.96% <83.42%> (-0.14%) ⬇️
python 98.70% <ø> (ø)

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Cover all the easy cases

Get SMCK working

Add a "lineage" attr to Segment and fixup sweeps code

Basic DTWF seems to work

Fixup algorithms minimally
Make some progress. Disable DTWF tests for now

Minimal changes to get smck working

Fix DTWF simulations

Fixup incorrectly failing test

Make results reproducible by seed

Revert back to old seed for failing test

Skip segfaulting pedigree and sweep tests

Fix sweeps

Fix pedigree sims

Keep track of lineages
Newer versions of jsonschema emit a DeprecationWarning
@jeromekelleher jeromekelleher force-pushed the simpler-lineage-struct branch from a74a21c to 8ee8cb1 Compare July 25, 2024 12:45
@jeromekelleher jeromekelleher marked this pull request as ready for review July 25, 2024 12:45
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I think this is the basic changes needed to start with. Would you mind having a quick look over to see if I've made any obvious mistakes (like keeping an msp_verify() left over from debugging etc) please @GertjanBisschop?

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I'm going to go ahead and merge this, there's no point in keeping a big diff like this lying around. Sorry to anyone who's code is clobbered!

@jeromekelleher jeromekelleher merged commit 89f8770 into tskit-dev:main Jul 30, 2024
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@jeromekelleher jeromekelleher deleted the simpler-lineage-struct branch July 30, 2024 15:19
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