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add modular simplifier#2752

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molpopgen wants to merge 88 commits intotskit-dev:maintskit-dev/tskit:mainfrom molpopgen:add_modular_simplifiermolpopgen/tskit:add_modular_simplifierCopy head branch name to clipboard

+1,368-8

Commits

Commits on Feb 5, 2024

• add prototypes

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  365de88

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• clang-format

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• add implementations

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• alloc array for tracking parent contiguity

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• check for contiguous parent processing

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• test skeleton

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• building up tests

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• whew

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• free

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• working on test

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• that was kinda brutal

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• more stress test

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• internal checks so we don't have to test internal details

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  4b49a7a

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• modularize, test that we can catch birth order violations

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• move comments

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  bcc9a15

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• FIXME

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• show some of the side effects that one can get

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  145abce

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• not detecting discontiguous parents

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• all tests fail when we try to check for non-contiguous parents

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  59ce926

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• fix array init to TSK_NULL

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• name field for what we use it for...

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• valgrind

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• testing pattern w/less duplication

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• found a goof. yay for testing

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  127106e

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• fix logic error

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  ac8236f

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• start treeseq comparison

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• tree time comparisons...

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• notes

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• TODO

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  ae005e6

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• fix typo

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  bddce27

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• update note

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  afe426f

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• fix setup comment

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  bfa2484

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• fix implicit integer cast flagged by circle CI

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• truly fix the cast

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• check that no new child is born before any child in the input tables.

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• use correct error codes

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  91734e3

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• add tests of null parent/child in edge

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• test for child time > that of any in the input tables

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• remove useless if

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• test node out of range

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• bad samples

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• note

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• input table integrity check fail

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• start on overlapping generation tests

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• big code duplication. ugh

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  fdbfac1

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• need to think now about how to handle overlapping gens w/o the actual edge buffer machinery in place.

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• note for tomorrow

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  b5eb446

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• more detailed notes

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  f5c23cb

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• update what to do

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  a890997

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• fix cast errors that aren't in printf

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• start mocking a buffer for internal testing. overlapping generations too hard otherwise

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  e95b671

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• not quite

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• remove memory leak

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  8bba18a

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• closer

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  c04efbb

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• tests pass

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• comment out unused code

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  aeea43b

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• fix compile fails on CI

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• allocate new edges as needed

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• be careful about setup

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• force a failing test

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• we don't need a particular order for the child nodes...

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• add test of parent time error

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• reinstate test failure

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• start refactor from temp buffer back into temp edge table. idea is to let us use a common runner routine later

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• at least no segfault any more...

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• some pring

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• we are not detecting parent time violations properly

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• now tests pass

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• clean

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• delete printf

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• start to abstract out the test runner step

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• streamline for new test runner

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• use new runner for most/all tests

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  8d25cc6

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• cleanup

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• add new .c

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• update the meson stuff

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• add some infrastructure

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• add some infrastructure

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• fmt

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• skeleton in place. we have a segfault

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• make valgrind happy

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  24a76bf

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• cleanup

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• cleanup

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• add death rate, update lots of the new example internals

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• overlapping gens seems to work

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• add an important note

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• Add basic simulation for development

  

  jeromekelleher

  authored and

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• Add almost-working version with Python simplifier

  

  jeromekelleher

  authored and

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