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Dev #88

Merged
merged 392 commits into from
Oct 15, 2022
Merged

Dev #88

merged 392 commits into from
Oct 15, 2022
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Dec 30, 2021

  1. drop debugging code

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    cscherrer committed Dec 30, 2021
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  2. small update for Likelihood, and a test

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    cscherrer committed Dec 30, 2021
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  3. fixing up likelihoods

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    cscherrer committed Dec 30, 2021
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  4. improve basemeasure_depth dispatch

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    cscherrer committed Dec 30, 2021
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  5. still some trouble with inferred basemeasure_depth

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    cscherrer committed Dec 30, 2021
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  6. clean up For dispatch

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    cscherrer committed Dec 30, 2021
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  7. simplify _logdensityof

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    cscherrer committed Dec 30, 2021
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Commits on Dec 31, 2021

  1. optimize for Returns{True} case

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    cscherrer committed Dec 31, 2021
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  2. Merge branch 'dev' of github.com:cscherrer/MeasureBase.jl into dev

    @cscherrer
    cscherrer committed Dec 31, 2021
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  3. rework basemeasure_depth

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    cscherrer committed Dec 31, 2021
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  4. aggressive tests passing!!

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    cscherrer committed Dec 31, 2021
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  5. drop type-level stuff

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    cscherrer committed Dec 31, 2021
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  6. drop help

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    cscherrer committed Dec 31, 2021
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Commits on Jan 3, 2022

  1. license

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Commits on Jan 5, 2022

  1. affero

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    cscherrer committed Jan 5, 2022
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  2. copyright notice

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Commits on Jan 22, 2022

  1. merge

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    cscherrer committed Jan 22, 2022
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  2. Merge branch 'dev' of github.com:cscherrer/MeasureBase.jl into dev

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    cscherrer committed Jan 22, 2022
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  3. Drop Create Commons

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    cscherrer committed Jan 22, 2022
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  4. Merge branch 'master' into dev

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    cscherrer committed Jan 22, 2022
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  5. cleanup after merge

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    cscherrer committed Jan 22, 2022
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Commits on Jan 24, 2022

  1. update support computations

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    cscherrer committed Jan 24, 2022
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  2. insupport(d::SuperpositionMeasure, x)

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    cscherrer committed Jan 24, 2022
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  3. dorp ParamWeighted

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    cscherrer committed Jan 24, 2022
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  4. insupport(d::FactoredBase, x)

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    cscherrer committed Jan 24, 2022
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  5. export unsafe_logdensityof

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    cscherrer committed Jan 24, 2022
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  6. call promote_type instead of promote_rule

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    cscherrer committed Jan 24, 2022
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  7. logdensity_def for named tuple product measures

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    cscherrer committed Jan 24, 2022
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  8. type annotation for now

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    cscherrer committed Jan 24, 2022
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Commits on Jan 25, 2022

  1. debugging

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    cscherrer committed Jan 25, 2022
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Commits on Jan 26, 2022

  1. drop shows

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    cscherrer committed Jan 26, 2022
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Commits on Feb 4, 2022

  1. speed up mapped arrays

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    cscherrer committed Feb 4, 2022
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  2. throw an error for Union{} types

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    cscherrer committed Feb 4, 2022
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Commits on Feb 7, 2022

  1. MT tests passing

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    cscherrer committed Feb 7, 2022
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Commits on Feb 9, 2022

  1. updates

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    cscherrer committed Feb 9, 2022
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Commits on Mar 16, 2022

  1. get tests passing

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    cscherrer committed Mar 16, 2022
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  2. MIT license for MeasureBase

    @cscherrer
    cscherrer committed Mar 16, 2022
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  3. bump version

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    cscherrer committed Mar 16, 2022
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Commits on Mar 29, 2022

  1. cleanup

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    cscherrer committed Mar 29, 2022
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  2. spacing

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    cscherrer committed Mar 29, 2022
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Commits on Mar 30, 2022

  1. Merge branch 'dev' of github.com:cscherrer/MeasureBase.jl into dev

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    cscherrer committed Mar 30, 2022
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Commits on Mar 31, 2022

  1. Move ConditionalMeasure to MeasureBase

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    cscherrer committed Mar 31, 2022
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Commits on Apr 1, 2022

  1. add LogarithmicNumbers

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    cscherrer committed Apr 1, 2022
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  2. export basemeasure_sequence

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    cscherrer committed Apr 1, 2022
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  3. update superpose

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    cscherrer committed Apr 1, 2022
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  4. fix logdensity_rel

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    cscherrer committed Apr 1, 2022
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  5. remove FIXME (it's fixed!!)

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  6. logdensityof(d::Density, x)

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    cscherrer committed Apr 1, 2022
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  7. Merge branch 'dev' of github.com:cscherrer/MeasureBase.jl into dev

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    cscherrer committed Apr 1, 2022
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  8. simplify insupport(::Lebesgue, ::Real)

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    cscherrer committed Apr 1, 2022
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  9. clean up

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    cscherrer committed Apr 1, 2022
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  10. assume insupport yields Bool

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  11. change logdensity_rel fall-through to warning and return NaN

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    cscherrer committed Apr 1, 2022
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  12. update logdensity_rel

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    cscherrer committed Apr 1, 2022
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  13. drop old code

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    cscherrer committed Apr 1, 2022
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  14. fix warning

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    cscherrer committed Apr 1, 2022
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  15. export logdensity_rel

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    cscherrer committed Apr 1, 2022
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  16. logdensity_def(μ::Dirac, ν::Dirac, x)

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  17. logdensity_def methods

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    cscherrer committed Apr 1, 2022
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  18. drop static

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    cscherrer committed Apr 1, 2022
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  19. ]add StatsFuns

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    cscherrer committed Apr 1, 2022
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  20. Fixing up superposition

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    cscherrer committed Apr 1, 2022
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  21. [compat] entries

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  22. trying to speed things up

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    cscherrer committed Apr 1, 2022
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  23. bugfixes

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    cscherrer committed Apr 1, 2022
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Commits on Apr 2, 2022

  1. logdensity_rel tests

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  2. logdensity_rel tests

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    cscherrer committed Apr 2, 2022
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  3. drop qualifier, and add a test

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    cscherrer committed Apr 2, 2022
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  4. more tests

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Commits on Apr 3, 2022

  1. type constraint in "logdensityof(μ::AbstractMeasure, x)" (was piracy,… 

    … oops)
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  2. add some docs

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    cscherrer committed Apr 3, 2022
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  3. docs

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  4. docs

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  5. typo

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Commits on Apr 4, 2022

  1. moar speed

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Commits on Apr 5, 2022

  1. Merge branch 'dev' of github.com:cscherrer/MeasureBase.jl into dev

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    cscherrer committed Apr 5, 2022
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  2. don't export Test

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    cscherrer committed Apr 5, 2022
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  3. some more updates

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Commits on Apr 6, 2022

  1. logdensity_rel for products

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  2. kleisli docs

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Commits on Apr 9, 2022

  1. update instance_type

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Commits on Apr 10, 2022

  1. instance_type => Core.Typeof

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Commits on Apr 11, 2022

  1. powermeasure bug fix

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    cscherrer committed Apr 11, 2022
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  2. fix logdensity_rel bug

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    cscherrer committed Apr 11, 2022
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  3. get commonbase to take x type into account

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    cscherrer committed Apr 11, 2022
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  4. test powers

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Commits on Apr 12, 2022

  1. commonbase docstring

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  2. deprecate instance_type

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Commits on Apr 13, 2022

  1. avoid breakage

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  2. switch || terms

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  3. @ifelse macro

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  4. simplify logdensity_rel

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  5. give up on this @ifelse business

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  6. bump version

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  7. Merge branch 'master' into dev

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Commits on Apr 21, 2022

  1. Make instance non-generated

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Commits on Apr 26, 2022

  1. working on likelihoods

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Commits on Apr 28, 2022

  1. update likelihood

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  2. powerweightedmeasure

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  3. powerweighted update

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  4. more powerweighted methods

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  5. bugfix

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Commits on May 2, 2022

  1. dropFactoredBase

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  2. drop FactoredBase

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Commits on May 3, 2022

  1. (::ProductMeasure) | constraint

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  2. update conditional measure

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  3. update Dirac

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  4. move conditional.jl down in the includes

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Commits on May 4, 2022

  1. Kleisli => TransitionKernel

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  2. simplify logdensity_def(::PowerMeasure, x)

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  3. rename kleisli.jl to kernel.jl

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  4. update Dirac tests

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  5. update Half

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  6. get tests passing

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Commits on May 5, 2022

  1. update kernel

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  2. Update Project.toml

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  3. Merge remote-tracking branch 'origin/master' into dev

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  4. no call-site inlining

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  5. restrict single-arg kernel to <:ParameterizedMeasure

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Commits on May 6, 2022

  1. export log_likelihood_ratio

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  2. Drop DensityKind(::Likelihood), at least for now

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  3. isfinite(x) instead of x>-Inf

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  4. add condition constructor

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  5. EOF newline

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Commits on May 9, 2022

  1. simplify logdensity_def for power measures

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  2. finishing up

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Commits on May 12, 2022

  1. Merge branch 'master' into dev

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Commits on May 18, 2022

  1. updates

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  2. kernel stuff

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Commits on May 23, 2022

  1. kernel stuff

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  2. update showe methods

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  3. ass a TODO

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  4. use dot instead of sum

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  5. drop old code

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  6. typo

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  7. Merge branch 'kernels' into dev

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  8. formatting

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  9. cleanup

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  10. kernel updates

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  11. uncomment

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  12. bugfix

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  13. drop old code

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  14. pretty printing

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Commits on May 24, 2022

  1. exports, cleanup

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  2. drop old for.jl

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  3. Make DensityKind(::AbstractLikelihood) = IsDensity()

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  4. update Compat version

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  5. Merge remote-tracking branch 'origin/master' into dev

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  6. Make likelihoods work with Distributions

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Commits on Jun 1, 2022

  1. _map(f, x::MappedArrays.ReadonlyMappedArray)

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  2. export productmeasure

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Commits on Aug 4, 2022

  1. Merge branch 'master' into dev

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  2. AbstractMeasure(::AbstractMeasure)

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Commits on Sep 2, 2022

  1. Merge branch 'master' into dev

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Commits on Sep 11, 2022

  1. Merge branch 'master' into dev

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  2. fixedrng

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  3. StdNormal

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  4. add SpecialFunctions

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  5. no need to qualify

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  6. update basemeasure

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  7. include stdnormal

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  8. include fixedrng

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  9. update tests

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Commits on Sep 12, 2022

  1. using SpecialFunctions

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  2. fixing transport_def

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  3. transport_def bugfix

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  4. StdMeasure(::typeof(randn))

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  5. checked_arg for LebesgueMeasure

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Commits on Sep 13, 2022

  1. NoTransformOrigin => NoTransportOrigin

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  2. transport interface for pushforwards

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  3. transporting pushforwards

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  4. Use LebesgueMeasure for basemeasure

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  5. updates

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  6. make testvalue fall back on FixedRNG approach

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  7. un-break testvalue

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  8. CI for Juila 1.8

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  9. fixes

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  10. rand on a pushforward calls rand on its parent

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Commits on Sep 14, 2022

  1. LebesgueMeasure => LebesgueBase 

    CountingMeasure => CountingBase
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  2. tests passing!

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  3. change invoke type

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  4. Change test_interface to check for 2-arg testvalue

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  5. manually-specifed inverses

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Commits on Sep 16, 2022

  1. more pushfwd stuff

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  2. A little less wrong

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Commits on Sep 19, 2022

  1. add mass interface

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  2. pullback

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  3. mass interface

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  4. working on mass interface

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  5. add some massof methods

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  6. Maybe <:Number is better for invalidations?

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  7. float instead of Int

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  8. logmassof

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Commits on Sep 20, 2022

  1. transports for proxies

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  2. drop latent-joint.jl

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Commits on Sep 21, 2022

  1. drop exports

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  2. Drop logmassof for now

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  3. reorganize Lebesgue measure

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  4. IntervalSets

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  5. proxy(::Lebesgue{MeasureBase.RealNumbers}) = LebesgueBase()

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  6. calling a "useproxy" measure calls its proxy

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  7. StdUniform()(s::Interval)

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  8. typo

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  9. (m::AbstractMeasure)(s::Interval)

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  10. bugfix

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Commits on Sep 22, 2022

  1. comment

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  2. IntervalSets version constraint

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  3. update dynamic_basemeasure_depth

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  4. format

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Commits on Sep 23, 2022

  1. Calling a measure calls massof

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  2. work on massof

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  3. AbstractSuperpositionMeasure

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Commits on Sep 26, 2022

  1. fix typo

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  2. typo

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  3. format

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Commits on Sep 27, 2022

  1. docstrings

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  2. remove massof(::PowerWeightedMeasure) method

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  3. make massof better

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Commits on Sep 28, 2022

  1. update testvalue

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  2. formatting

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  3. update _massof

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  4. Update transports for weighted measures

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Commits on Sep 29, 2022

  1. add chain rules

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  2. invariant mass under transport

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  3. typo

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Commits on Sep 30, 2022

  1. bugfix

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  2. hasmethod => Tricks.static_hasmethod

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Commits on Oct 1, 2022

  1. massof methods

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Commits on Oct 2, 2022

  1. Merge remote-tracking branch 'origin/master' into dev

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Commits on Oct 3, 2022

  1. roll back tranports for WeightedMeasure

    @cscherrer
    cscherrer committed Oct 3, 2022
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  2. Improve transport implementation and add product support (#97) 

    * Improve default transport implementation

Increases type stability.

* Rename NoTransformOrigin to NoTransportOrigin

* Add rrule for _origin_depth

* Fix ambiguities when forwarding NoTransportOrigin and NoTransportOrigin

* Define getdof for product measures

* Generalize test_transport to tuple-valued measures

* Implement transport for tuple-based products

Co-authored-by: Chad Scherrer <[email protected]>
    @oschulz @cscherrer
    oschulz and cscherrer authored Oct 3, 2022
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  3. @useproxy delegates massof

    @cscherrer
    cscherrer committed Oct 3, 2022
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Commits on Oct 4, 2022

  1. drop CI for nightly

    @cscherrer
    cscherrer committed Oct 4, 2022
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  2. callable densities (#85) 

    * callable densities

* separate `Density` and `LogDensity`, etc

* bugfix

* move some code around

* format

* updates

* working on densities

* update CI

* bugfix

* formatting

* reorg

* fix typos

* Drop LogDensityMeasure and refactor

* docstring

* inner type constructor with assertion

* type parameters

* 2-arg density_rel and logdensity_rel

* oops

* properties

* typo

* fix ambiguity

* bugfix

* bugfix

* updates

* drop densityof and logdensityof for AbstractDensity

* updates

* update tests

* update

* formatting

* bad calls throw errors

* drop CI for nightly
    @cscherrer
    cscherrer authored Oct 4, 2022
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Commits on Oct 6, 2022

  1. Pushfwd-inverses (#98) 

    * use InverseFunctions.setinverse

* bug fixes

* bugfix

* bugfix

* pushfwd of a pushfwd

* format

* drop old comment

* drop CI for nightly

* working on pushfwd

* bugfix

* inverse(f) => ν.finv

* separate logdensity functions from transport API

* format

* don't unwrap FunctionWithInverse

* drop redundant method

* leave logdensityof alone, instead write unsafe_logdensityof

* more tests

* more work on tests

* tests

* tests

* still messing with tests

* tests passing

* small edits

* formatting

* add some more failing tests

* add atol to isapprox in test

* getdof(μ::PushforwardMeasure) = getdof(transport_origin(μ))

* update atol

* small fix

* drop ((-) ∘ log1p ∘ (-), StdUniform(), StdExponential())
    @cscherrer
    cscherrer authored Oct 6, 2022
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Commits on Oct 10, 2022

  1. remove duplicate method

    @cscherrer
    cscherrer authored Oct 10, 2022
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  2. remove duplicate include

    @cscherrer
    cscherrer committed Oct 10, 2022
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Commits on Oct 11, 2022

  1. simplify getdof(::PushforwardMeasure)

    @cscherrer
    cscherrer committed Oct 11, 2022
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Commits on Oct 14, 2022

  1. Stieltjes measure function (#100) 

    * smf

* more smf stuff

* transport_to

* Lebesgue smf

* smf for std measures

* format

* transport_to

* oops

* smfinv

* bugfix

* more fixes

* minor refactoring

* formatting

* change x to p

* bugfix

* smfinv(::StdLogistic, p)

* add NoSMF and NoSMFInverse

* roll back some changes

* transport_def methods

* formatting

* another rollback

* make transport_def depend on smf(inv)

* update smf and transports for ::Half

* change `include` order

* test_smf

* more tests

* tests

* add tests

* formatting

* Drop unneeded type parameters

* smfinv => invsmf

* add some inverses

* Base.Fix1 versions

* some more methods
    @cscherrer
    cscherrer authored Oct 14, 2022
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Commits on Oct 15, 2022

  1. drop redundant transport_defs

    @cscherrer
    cscherrer committed Oct 15, 2022
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  2. update pushfwd

    @cscherrer
    cscherrer committed Oct 15, 2022
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  3. change name

    @cscherrer
    cscherrer committed Oct 15, 2022
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  4. add type

    @cscherrer
    cscherrer committed Oct 15, 2022
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  5. formatting

    @cscherrer
    cscherrer committed Oct 15, 2022
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  6. fix docstring

    @cscherrer
    cscherrer committed Oct 15, 2022
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  7. depend on FunctinoChains

    @cscherrer
    cscherrer committed Oct 15, 2022
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  8. Use fchain

    @cscherrer
    cscherrer committed Oct 15, 2022
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  9. simplify transport_def for StdLogistic

    @cscherrer
    cscherrer committed Oct 15, 2022
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  10. simplify transport_def for StdNormal

    @cscherrer
    cscherrer committed Oct 15, 2022
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  11. drop redundant method

    @cscherrer
    cscherrer committed Oct 15, 2022
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