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multitrait changes - #531

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bhaller wants to merge 426 commits into

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multitrait

Open

multitrait changes#531
bhaller wants to merge 426 commits into
masterfrom
multitrait

This pull request is big! We're only showing the most recent 250 commits

Commits on Feb 26, 2026
- add a small optimization for trait calculation in WF models
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  committed
  9d51625
Commits on Feb 28, 2026
- merge to resolve cherry-pick of *add zygosityOfMutations([No<Mutation> mutations = NULL], [integer$ hemizygousValue = 1], [integer$ haploidValue = 1]) for assessing zygosity (see also mutationsFrom…
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  93d918e
- clean up some FIXME MULTITRAIT comments
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  973e673
Commits on Mar 3, 2026
- first pass at SLiMgui multitrait support
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  d86672b
Commits on Mar 5, 2026
- fix some warnings
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  10059fe
- fixes for the SLiMgui trait bar in multispecies models
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  48bd826
- fix a mutrun experiment timing bug causing logging
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  af785ef
Commits on Mar 8, 2026
- multi-trait changes for chromosome and haplotype displays
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  303f297
- show gray for individuals with a NAN trait value
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  93a1fa2
- remember display trait choice across recycles
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Commits on Mar 10, 2026
- typo fix
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  8c048c0
- fix excessive trait-related initialize warnings
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  69ab6de
- add AddFloatString() to EidosCallSignature
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  f9fd60c
- square off (miter) the corners of rects drawn with rects()
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  a2785a0
- decrease minimum size for custom plots to 100x100
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  edb2fd9
Commits on Mar 12, 2026
- decrease minimum size of custom plot windows
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  e63dfb1
- add Palette class, add support for plotting palettes with image()
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  777f9fe
- fix CI warnings and errors
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  c3c3674
- move to current tskit, incl current (not final) `json+struct` codec
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  002daf7
Commits on Mar 14, 2026
- switch to Palette for coloring individuals/mutations
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Commits on Mar 16, 2026
- invalidate trait values without baseline accumulation
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  18e91f7
- customizability of trait/species palettes; shift to Qt 5.15.2 minimum
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  766a831
- extend Palette methods to accept `numeric` values
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  02c29dd
- add defaultPalette() method to class SLiMgui
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  c759119
- image() plotting of palettes should use the fixed point
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Commits on Mar 17, 2026
- extend call signatures with "ellipsis variants" for overloading
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Commits on Mar 19, 2026
- switch SpatialMap over to using Palette for its colors
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  637fd1e
Commits on Mar 21, 2026
- remove the restriction that ellipsis variants cannot contain an ellipsis
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  734fb08
- add ellipsis variants for class constructors
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  4c9a755
Commits on Mar 22, 2026
- display ellipsis variants in QtSLiM's status bar
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  c5d2dd2
- tighten up fitnessScaling handling and fix a (post-5.1) bug with it
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  cb6c779
Commits on Mar 23, 2026
- add Palette() variants, refine ellipsis variant treatment
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  c0f0fbb
Commits on Mar 25, 2026
- improve SLiMgui code completion
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  221c93c
- fix a few CI build issues
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  684b56c
- more CI build errors
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  f6cedb8
Commits on Mar 29, 2026
- add a line in the color scales panel about gray for NAN
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  78b1208
- add code completion support for ellipsis variant arguments
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Commits on Mar 30, 2026
- fix an independent-dominance caching bug
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  1f82264
- fix an excessively broad warning
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  7a6db60
Commits on Mar 31, 2026
- fix Plot's "no data" message in an erroneous case
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  fb66111
- improve autofixes for some multitrait API changes
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  0eb999b
Commits on Apr 1, 2026
- disable debug logs
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  ffafa7c
- change Plot.matrix() to take a Palette object for coloring
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  75f2208
- fix a bug with mutationEffect() callback trait specifiers
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  671b240
- minor fixen for mutationEffect()/fitnessEffect() callback handling
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  e44f37f
Commits on Apr 2, 2026
- a little clarification of the `homozygous` pseudo-parameter
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  abc9732
- add Plot() for quick default plots of single objects/things
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  05c77c7
Commits on Apr 3, 2026
- fix an optimization flag bug with addNewDrawnMutation()
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  e59ffc3
- fix an optimization flag bug with autogenerated mutations
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  aedebd7
- fix a timing check regression in removeSubpopulation()
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  9b6e51f
Commits on Apr 4, 2026
- fix a bug with ellipsis variant argument handling
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  21dc221
- detect stochastic mutationEffect() callbacks to disable DEBUG crosschecks
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  be013ae
Commits on Apr 6, 2026
- cleanup of ellipsis variant handling
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  88e21d0
- Merge branch 'master' into multitrait
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  901784a
- finish the previous merge
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  c1d9787
Commits on Apr 7, 2026
- doc typo fix
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  2c8e0a0
- bringing changes back to the master branch
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  c5499e7
Commits on Apr 8, 2026
- Merge branch 'master' into multitrait
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  committed
  431c19e
- fix some annoying build warnings
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  cd4d80a
- Merge branch 'master' into multitrait
  bhaller
  committed
  e020be6
- clean up the doc after merge
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  b1a636f
- Merge branch 'master' into multitrait
  bhaller
  committed
  1140695
- doc cleanup after merge
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  4005b16
- Merge branch 'master' into multitrait
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  b8230b1
Commits on Apr 9, 2026
- Merge branch 'master' into multitrait
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  committed
  7ab317d
- enable SIMD/SLEEF in Xcode
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  dfb878d
- Merge branch 'master' into multitrait
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  committed
  aeaf063
- clean up project file after merge
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  committed
  2a5af83
- another try with the project file
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  53edcd7
Commits on Apr 10, 2026
- Merge branch 'master' into multitrait
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  e13904c
Commits on Apr 13, 2026
- Merge branch 'master' into multitrait
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  committed
  e3fbaf2
- remove SIMD warning suppression that doesn't work anyway
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  8f8a022
Commits on Apr 14, 2026
- update recipes for multitrait
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  committed
  3e6bf13
- fix recipes that re-seed the RNG to use rdunif64()
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  47253ad
Commits on Apr 24, 2026
- comment fixes for QtSLiM autofixing
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  56be5e3
Commits on May 30, 2026
- Merge branch 'master' into multitrait
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  committed
  6d6d06d
- fix doc merge
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  b6440db
- improve error messages for top-level SLiM script syntax errors
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  2e4d664
- bump tskit/msprime requirements up to current to get json+binary codec
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  b18cadf
- Merge branch 'master' into multitrait
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  committed
  cd8d650
- remove obsolete custom changes to tskit
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  21edb35
- Merge branch 'master' into multitrait
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  b4e960e
Commits on May 31, 2026
- fixes to sync SLiM with the final `json+struct` design
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  ee148f7
- fix header path issue in CI
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  d715aab
Commits on Jun 2, 2026
- schema improvements
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  13ef056
- fix occasional memory bug in previous commit
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  cdd13c5
Commits on Jun 13, 2026
- fix an error position involving variants
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  81f6a83
Commits on Jun 16, 2026
- add unit tests for Palette, fix various issues
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  bdd9e19
Commits on Jul 5, 2026
- fix #638, setMutationType() can produce inconsistencies
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  3cd5670
- fix CI build issue
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  0451eef
- fix #633: persist the various tag properties of individual in .trees
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  b5a7b2c
Commits on Jul 8, 2026
- boolean not bool in schema types
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  74eb175
- Merge pull request #639 from petrelharp/schema_fix
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  authored
  6fbadc8
- fix a remaining metadata schema issue
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  committed
  952a139
- new chapter 13 recipes for multitrait
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  f307178
- fix #640, not all mutations recorded in metadata
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  7987154
Commits on Jul 9, 2026
- update remaining QTL-based recipes for multitrait
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  d55f25d
- deprecate sumOfMutationsOfType()
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  37ca94b
- fix overbars in the object tables window
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  307b734
Commits on Jul 11, 2026
- minor recipe fixen, add recipe 13.14 (sexual dimorphism)
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  916a211
- chapter 13 recipe cleanup (keywords, seeds)
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  af8dc6b
- doc tweak for treeSeqMetadata()
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  03b0959
- tweak signature mismatch output
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  1f1e34d
- fix calcInbreedingLoad(), + preliminary calcVA/VD/VG()
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  9b0d739
- fix calcVG, whoops
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  dc0898c
Commits on Jul 16, 2026
- fix #641, crash after expanding mutation block buffers
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  d727954
- disable old calcVA() self-tests that no longer work
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  3b66ac3
- fix #642, unreferenced mutation from multiple reload
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  051b47d
- add info about the mutation table to implementation.md
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  cfcecf5
- fix #643, phenotypes not initialized from TreeSeq file
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  cd8816f
- fix #644, remapping subpops causes a raise
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  0e2f682
Commits on Jul 17, 2026
- remove spurious setSeed() call from recipe 9.12
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  99d1f32
- fix #645, save-and-reload can remove mutations
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  committed
  61ddfdb
- update recipe 13.9 with logMutationData()
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  07fc977
- small update to implementation of mutation storing
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  e09adce
- Merge pull request #647 from petrelharp/multitrait
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Commits on Jul 19, 2026
- fix #648: rearchitect the "retained by the tree sequence" design
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  committed
  cc2e6f4
- Merge branch 'multitrait' of https://github.com/MesserLab/SLiM into multitrait
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  committed
  09ad501
- update implementation.md
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  9425692
- add some mutation retain debugging code
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  537f340
- fix a whoopsie
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  e5f7364
- fix another wee typo
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  572ff36
- fix #646, #648: rearchitecture needed (see previous commits)
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  47325fd
- fix build error in CI
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  ec0a6b4
Commits on Jul 20, 2026
- copyright tweaks and such
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  8acab57
- update seed for recipe 14.16
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Commits on Jul 21, 2026
- fix out-of-date recipe numbers
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  d667f94
- a little endline cleanup in debug output
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  ea5067c
- tweak method timing restrictions
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  a73466b
Commits on Jul 23, 2026
- fix multitrait_REVERT_TO_NEUTRAL test
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  7491b91
- for #649: move substitution info to Chromosome
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  930b9db
- for #649: move muts_tracked_by_treeseq_ to Chromosome
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Commits on Jul 24, 2026
- for #649: move the mutation registry to Chromosome
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  ba36a6f
- fix #649: shift more state to being kept per-chromosome
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  049fad9
- add a note related to #649
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  52353b7
- Merge branch 'master' into multitrait
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  f672e5c
Commits on Jul 25, 2026
- doc update for mutationEffect() callbacks for multitrait
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  1baf68a
- doc cleanup for mutationEffect() and fitnessEffect() callbacks
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  8fe4e47
- fix incorrectly curled quote
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  a3410f1
- increase the default size of the Eidos console and Help windows
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  fcb1b51
- fix #651, font size in Help window doesn't scale with user pref
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  952b0f6
- fix #653, spurious error in zygosityOfMutations()
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  1e54a08
Commits on Jul 29, 2026
- fix estimated last tick at simulation end
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  21f48d0
- add "Multispecies Multitrait Phenotype ~ Time" plot
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  98a4422
- somehow excluded from the previous commit
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Commits on Jul 30, 2026
- add phenotype ~ time plot, tweak other plots
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  263f38a
- some auto and const usage cleanup
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  6218ee3
- more auto and const usage cleanup
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Commits on Aug 11, 2026
- some pedigree ID design cleanup
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  45edaf7
- little comment tweaks and such
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  0657f03
Commits on Aug 14, 2026
- draft fix for metadata inefficiency
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  36d89fe
- fixup of python recipe
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  1a1214a
Commits on Aug 15, 2026
- bug fixup
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  d6def05
- Merge pull request #659 from petrelharp/efficient_metadata
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  1321d0d
- final (?) revisions
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  316e7a0
- add newlines since they fit
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  37054fe
- remove semicolons, sigh
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  0b1dd8b
- Merge pull request #658 from MesserLab/efficient_metadata
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Commits on Aug 19, 2026
- fix #661, baseline offset needs to be split into subcomponents
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Commits on Aug 22, 2026
- put binary derived state info in the mutation table metadata
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Commits on Aug 23, 2026
- fix #663, revert filtering of unused mutation types
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Commits on Aug 25, 2026
- suggestions from petrelharp code review
  
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  fb2c56b
- switch to using tsk_mutation_table_takeset_columns()
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  committed
  ff92bb8
- add some comments after discussion with Peter
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  c98f248
- Merge pull request #665 from MesserLab/derived_state_metadata
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Commits on Aug 26, 2026
- shift the migrant flag from metadata to the flags column
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  fb295de
- error in schema and test machinery
  petrelharp
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  3d45be3
- Merge pull request #669 from petrelharp/fix_666
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  9a65a4d
- a little cleanup of SLIM_TSK_INDIVIDUAL_MIGRATED handling
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  committed
  04f4051
- Merge pull request #668 from MesserLab/fix_666
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  1d8386c
- add mutrun count hint to top-level metadata, for use later
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  a2849c3
Commits on Aug 27, 2026
- improve error handlign when reading .trees files
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  b6f698d
- polish up another error message
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  e9e1a24
- more error message polish
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Commits on Aug 28, 2026
- add a VERSIONS note about SLiMv6MutationModel
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  1899c60
- fix #637, fix #650: VCF I/O ##contig and #CHROM should use name
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Commits on Aug 29, 2026
- removing mutrun count hint from top-level metadata
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  53984b4
Commits on Sep 2, 2026
- fix #536: add stacking policy "a" and recipe 13.15
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  488fa85
- fix #670, sort derived states by mutation ID
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Commits on Sep 4, 2026
- fix { 1.0; } typos in doc
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Commits on Sep 5, 2026
- a little cleanup of typedef struct usage
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Commits on Sep 6, 2026
- back out a few typedef struct usage changes
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  9370cd6
- tweak __AccumulateStackedEffects() a bit
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  d749377
- back out another typedef struct change
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Commits on Sep 7, 2026
- fix #671, separate trait offsets by sex and by baseline vs. substitution
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Commits on Sep 10, 2026
- fix remaining references to baselineOffset etc.
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Commits on Sep 11, 2026
- insert new recipe 13.15, sexual dimorphism and differential selection
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Commits on Sep 12, 2026
- fix #673, segfault when reloading a model that had been executed
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  beef64a
- fix #662, add `skip` parameter to readCSV() and others
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  cb81790
- fix #634: add [f$ failureScaling] to drawByStrength()
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  7b36094
- fix #631: support pedigree IDs as individual IDs in VCF output
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  committed
  a99cbc1
- tweaks to the fix for #673, segfault when reloading
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  92935c7
- fix #609, rare error about parents with coalescence checking on
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Commits on Sep 13, 2026
- add recipe 16.12 (monozygotic twins)
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Commits on Sep 14, 2026
- add impplementation.md info on derived state metadata
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  84cf290
- use the new smaller minimum size only for custom plots
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  21c13cf
- fix build errors using DEBUG_TRAIT_DEMAND
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  committed
  8a0f8d5
- added clarifications about derived state info
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  0057bcf
- trait tests in python
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  committed
  8774a7a
- relax the requirement of `ticks all` in multispecies models
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  4004364
- remove obsolete units tests about `ticks all`
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  129802b
- clamp effects
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Commits on Sep 15, 2026
- zero out ancestral state on reading in
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  committed
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Commits on Sep 16, 2026
- Merge pull request #672 from petrelharp/pytests
  bhaller
  authored
  53d6bc2
- first pass on #387, needs polish and unit tests
  bhaller
  committed
  1ba42f3
- Merge branch 'multitrait' of https://github.com/MesserLab/SLiM into multitrait
  bhaller
  committed
  ef871d3
- Merge pull request #680 from petrelharp/zero_ancestral_state
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  authored
  097d0d9
- Merge branch 'multitrait' of https://github.com/MesserLab/SLiM into multitrait
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  committed
  42c1225
- minor note in implementation
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  committed
  f72a318
- Merge pull request #681 from petrelharp/implnote
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  authored
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Commits on Sep 17, 2026
Commits on Sep 18, 2026
- try a fix for the new SelfConsistencyCheck() raises
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  2a8c761
- remove MINGW64 from CI for the CLI and GUI builds
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  11a8ef6
- restore code that was Not The Problem
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  committed
  2b6208e
- add a bit more diagnostic output
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  5b75851
- change self consistency check to use an error tolerance
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  67d9de9
- raise reporting threshold
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  committed
  ca68936
- raise threshold again
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  25f040d
- final tweaks to the self-consistency problem workaround
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  committed
  6772106
- new calcVA/VD/VG/VP() functions for multitrait from Vitor Sudbrack!
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  committed
  0de018d
- tweaks to my calcVADGP() commit to fix things I messed up, whoops
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Commits on Sep 19, 2026
- update recipe 13.16 to show all the calcVX() functions
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  f2c74f5
- extend calcVG() and calcVP() to support [No<Mutation> muts = NULL]
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  f1a4527
Commits on Sep 22, 2026
- fix #433: use tspop to assess ancestry in recipe 18.5
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  committed
  7cfe3dd
- protect calculateFitness() and calculatePhenotype() from changes mid-calculation
  bhaller
  committed
  8e7d419
- fix a tiny loophole in trait invalidation
  bhaller
  committed
  ceb3deb
- invalidate trait values after reading from VCF/MS files
  bhaller
  committed
  5708047
- sex-specific trait invalidation for sex-specific baseline offset changes
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  committed
  c5014b9
- a little comment cleanup
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  committed
  3738797
- fix stochastic tests that were failing too often
  bhaller
  committed
  239d8c2
Commits on Sep 23, 2026
- add shuffle buffer usage to phenotype demand calculations
  bhaller
  committed
  1aed48d
- doc tweaks from Vitor
  bhaller
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  9c4274c
- tweak recipe 18.8 to avoid warning
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  daba252
- recipes needed patching up for metadata/pyslim changes
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  e58b23e
Commits on Sep 24, 2026
- fix a bug in the calcVG() implementation
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  dcfa40c
Commits on Sep 25, 2026
- extend addNewMutation() for multitrait
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  committed
  0278e1a
- add a couple more unit tests for multitrait addNewMutation()
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  995f493
- remove the _RunMultitraitTests() log for now
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  54d52e6
Commits on Sep 26, 2026
- do a pass with include-what-you-use
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  committed
  c32a151
Commits on Sep 27, 2026
- increment version to 6.0b1
  bhaller
  committed
  1221642
Commits on Oct 23, 2026
- fix SLiMgui layout/size issues on Linux and macOS
  bhaller
  committed
  ef69ca4

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