multitrait changes - #531

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bhaller wants to merge 361 commits into

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Commits on Jan 28, 2026

Commits on Jan 29, 2026

iver renaming for better searchability
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1cc4da9
minimize the independent-dominance cache size
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b810674
fix CI build error
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2095f49

Commits on Feb 1, 2026

Commits on Feb 2, 2026

add optimizations for all mutations being nonneutral
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11113c9
versions log cleanup
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97dc657
shift MutationType logging info into a separate struct
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b818e2f

Commits on Feb 3, 2026

improve trait pure neutral inference
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1de2654
fix CI build failures
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8296572
a little doc cleanup
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949227b
add comment regarding failed MutationTraitInfo experiment
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2c6cac9
push copyrights to 2026
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d315b2a

Commits on Feb 4, 2026

fix an occasional CI error due to a test script bug
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730823d
improve "all neutral mutations" inference
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b10edb7
optimization and bug fixes
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483a83d

Commits on Feb 5, 2026

Commits on Feb 6, 2026

add invalidation of trait values due to non-constant mutationEffect() callbacks
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667d5ba
finish up trait invalidation work
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f0bc459

Commits on Feb 7, 2026

add notes to self
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916d9a2

Commits on Feb 9, 2026

fix #613, doc bug for mmJukesCantor()/mmKimura()
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e2bd7c6
hand-merge of C changes from tskit #3306, json_struct codec
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3ef6709

Commits on Feb 12, 2026

first wave of changes for multitrait metadata
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6da30a1
fix CI build error due to use of private API
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4a052cd
tweak write order to match metadata
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c81891f

Commits on Feb 13, 2026

fix #617, %d left in metadata schema
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15dfd0b
fix requirements for `struct` schemas
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fbe4686
add comment about schema validation
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88c261c
fix missing "type" for "per_trait" arrays
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2c2d593
fix index bugs in schemas
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c9d7dd3
fix incorrect binary length due to aligner
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41947eb
fix pointer_t build issue
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7a6be65
fix the pointer_t build issue again
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ddc1350

Commits on Feb 14, 2026

fix mutation metadata schema
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77f974d
remove stray commit
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9dacca7
remove const from tsk_json_struct_metadata_get_blob()
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c99488d
fixes for tree sequence reading
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63553e8
ensure that all mutations needed are in the metadata table
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00f55f8
fix CI build error
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d82e647

Commits on Feb 15, 2026

try again with CI build error
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3d60aba
multitrait edits for implementation.md
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88ea343
fix treeSeqMetadata() to use `json+struct"
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4306882
Merge pull request #614 from MesserLab/multitrait-metadata
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authored
53a1ee6
add implementation.md text about metadata in SLiM 4.3
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8d622e1
make a couple of self-tests less likely to fail
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bd91eee

Commits on Feb 24, 2026

add haploid trait calculation regimes and haploid caches
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bdc542d
fix a few CI issues
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ed32398

Commits on Feb 25, 2026

Commits on Feb 26, 2026

fix a multitrait bug involving trait invalidation with migration
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e70a2f6
comment tweaks
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84992a0
add comment on path not taken
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3a70160
don't allow trait names beginning with an underscore
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9c62949
hide deprecated APIs in auto-completion
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03f0be8
clean up nonneutral cache invalidation
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58f353a
add a small optimization for trait calculation in WF models
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9d51625

Commits on Feb 28, 2026

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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dcbd85a

Commits on Mar 10, 2026

Commits on Mar 12, 2026

Commits on Mar 14, 2026

switch to Palette for coloring individuals/mutations
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60f7d53

Commits on Mar 16, 2026

Commits on Mar 17, 2026

extend call signatures with "ellipsis variants" for overloading
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bfe4678

Commits on Mar 19, 2026

switch SpatialMap over to using Palette for its colors
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637fd1e

Commits on Mar 21, 2026

Commits on Mar 22, 2026

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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0387b0f

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

Commits on Apr 2, 2026

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

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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431c19e
fix some annoying build warnings
bhaller
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cd4d80a
Merge branch 'master' into multitrait
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e020be6
clean up the doc after merge
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b1a636f
Merge branch 'master' into multitrait
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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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7ab317d
enable SIMD/SLEEF in Xcode
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dfb878d
Merge branch 'master' into multitrait
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aeaf063
clean up project file after merge
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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
bhaller
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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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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
bhaller
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6d6d06d
fix doc merge
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b6440db
improve error messages for top-level SLiM script syntax errors
bhaller
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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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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

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

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

Commits on Jul 19, 2026

fix #648: rearchitect the "retained by the tree sequence" design
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cc2e6f4
Merge branch 'multitrait' of https://github.com/MesserLab/SLiM into multitrait
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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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c2e474f

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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2fc5600

Commits on Jul 24, 2026

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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00025a3

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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c4c1d0c

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
petrelharp
committed
1a1214a

Commits on Aug 15, 2026

bug fixup
petrelharp
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d6def05
Merge pull request #659 from petrelharp/efficient_metadata
bhaller
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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
bhaller
authored
d9aa4a6

Commits on Aug 19, 2026

fix #661, baseline offset needs to be split into subcomponents
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3d2c471

Commits on Aug 22, 2026

put binary derived state info in the mutation table metadata
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f31ec10

Commits on Aug 23, 2026

fix #663, revert filtering of unused mutation types
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8faf2b8

Commits on Aug 25, 2026

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
committed
3d45be3
Merge pull request #669 from petrelharp/fix_666
bhaller
authored
9a65a4d
a little cleanup of SLIM_TSK_INDIVIDUAL_MIGRATED handling
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04f4051
Merge pull request #668 from MesserLab/fix_666
bhaller
authored
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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30e0056

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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72bbc55

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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0a0d915

Commits on Sep 4, 2026

fix { 1.0; } typos in doc
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e3b88b9

Commits on Sep 5, 2026

a little cleanup of typedef struct usage
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committed
1b36c96

Commits on Sep 6, 2026

back out a few typedef struct usage changes
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committed
9370cd6
tweak __AccumulateStackedEffects() a bit
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d749377
back out another typedef struct change
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committed
c57c1eb

Commits on Sep 7, 2026

fix #671, separate trait offsets by sex and by baseline vs. substitution
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committed
bb87daf