Add Aqua tests #775

penelopeysm · 2025-01-08T16:27:37Z

There are quite a number of things to fix 😳

Method ambiguities

(fixed)

Ambiguity #1
DynamicPPL.SimpleVarInfo(values::NT, logp::T, transformation::C) where {NT, T, C<:AbstractTransformation} @ DynamicPPL ~/ppl/dppl/src/simple_varinfo.jl:192
DynamicPPL.SimpleVarInfo(model::DynamicPPL.Model, args...) @ DynamicPPL ~/ppl/dppl/src/simple_varinfo.jl:235

Possible fix, define
  DynamicPPL.SimpleVarInfo(::NT, ::T, ::C) where {NT<:DynamicPPL.Model, T, C<:DynamicPPL.AbstractTransformation}

(fixed)

Ambiguity #2
DynamicPPL.VarInfo(metadata::Tmeta, logp::Base.RefValue{Tlogp}, num_produce::Base.RefValue{Int64}) where {Tmeta, Tlogp} @ DynamicPPL ~/ppl/dppl/src/varinfo.jl:100
DynamicPPL.VarInfo(model::DynamicPPL.Model, args...) @ DynamicPPL ~/ppl/dppl/src/varinfo.jl:209

Possible fix, define
  DynamicPPL.VarInfo(::Tmeta, ::Base.RefValue{Tlogp}, ::Base.RefValue{Int64}) where {Tmeta<:DynamicPPL.Model, Tlogp}

(fixed)

Ambiguity #3
dot_tilde_assume(::DynamicPPL.IsParent, context::AbstractPPL.AbstractContext, args...) @ DynamicPPL ~/ppl/dppl/src/context_implementations.jl:298
dot_tilde_assume(::DynamicPPL.IsParent, rng, context::AbstractPPL.AbstractContext, args...) @ DynamicPPL ~/ppl/dppl/src/context_implementations.jl:301

Possible fix, define
  dot_tilde_assume(::DynamicPPL.IsParent, ::AbstractPPL.AbstractContext, ::AbstractPPL.AbstractContext, ::Vararg{Any})

Ambiguity #4
invlink!!(t::DynamicPPL.StaticTransformation{<:Bijectors.Transform}, vi::DynamicPPL.AbstractVarInfo, spl::AbstractMCMC.AbstractSampler, model::DynamicPPL.Model) @ DynamicPPL ~/ppl/dppl/src/abstract_varinfo.jl:615
invlink!!(t::DynamicPPL.AbstractTransformation, vi::DynamicPPL.ThreadSafeVarInfo, spl::AbstractMCMC.AbstractSampler, model::DynamicPPL.Model) @ DynamicPPL ~/ppl/dppl/src/threadsafe.jl:90

Possible fix, define
  invlink!!(::DynamicPPL.StaticTransformation{<:Bijectors.Transform}, ::DynamicPPL.ThreadSafeVarInfo, ::AbstractMCMC.AbstractSampler, ::DynamicPPL.Model)

Ambiguity #5
link!!(t::DynamicPPL.StaticTransformation{<:Bijectors.Transform}, vi::DynamicPPL.AbstractVarInfo, spl::AbstractMCMC.AbstractSampler, model::DynamicPPL.Model) @ DynamicPPL ~/ppl/dppl/src/abstract_varinfo.jl:600
link!!(t::DynamicPPL.AbstractTransformation, vi::DynamicPPL.ThreadSafeVarInfo, spl::AbstractMCMC.AbstractSampler, model::DynamicPPL.Model) @ DynamicPPL ~/ppl/dppl/src/threadsafe.jl:84

Possible fix, define
  link!!(::DynamicPPL.StaticTransformation{<:Bijectors.Transform}, ::DynamicPPL.ThreadSafeVarInfo, ::AbstractMCMC.AbstractSampler, ::DynamicPPL.Model)

(fixed)

Ambiguity #6
logpdf(d::Distributions.UnivariateDistribution, x::AbstractArray{<:Real, 0}) @ Distributions ~/.julia/packages/Distributions/j0ZcJ/src/univariates.jl:327
logpdf(dist::DynamicPPL.NamedDist, x::AbstractArray{<:Real}) @ DynamicPPL ~/ppl/dppl/src/distribution_wrappers.jl:20

Possible fix, define
  logpdf(::DynamicPPL.NamedDist{Distributions.Univariate, S, Td} where {S<:Distributions.ValueSupport, Td<:Distributions.UnivariateDistribution{S}}, ::AbstractArray{<:Real, 0})

Ambiguity #7
unwrap_right_left_vns(right::DynamicPPL.NamedDist, left, vns) @ DynamicPPL ~/ppl/dppl/src/compiler.jl:223
unwrap_right_left_vns(right::Distributions.MultivariateDistribution, left::AbstractMatrix, vn::AbstractPPL.VarName) @ DynamicPPL ~/ppl/dppl/src/compiler.jl:226

Possible fix, define
  unwrap_right_left_vns(::DynamicPPL.NamedDist{Distributions.Multivariate, support, Td} where {support<:Distributions.ValueSupport, Td<:Distributions.MultivariateDistribution{support}}, ::AbstractMatrix, ::AbstractPPL.VarName)

Ambiguity #8
unwrap_right_left_vns(right::DynamicPPL.NamedDist, left, vns) @ DynamicPPL ~/ppl/dppl/src/compiler.jl:223
unwrap_right_left_vns(right::Union{AbstractArray{<:Distributions.Distribution}, Distributions.Distribution}, left::AbstractArray, vn::AbstractPPL.VarName) @ DynamicPPL ~/ppl/dppl/src/compiler.jl:238

Possible fix, define
  unwrap_right_left_vns(::Union{DynamicPPL.NamedDist{F, S, Td} where {S<:Distributions.ValueSupport, Td<:Distributions.Distribution{F, S}}, DynamicPPL.NamedDist{F, support, Td} where {support<:Distributions.ValueSupport, Td<:Distributions.Distribution{F, support}}} where F<:Distributions.VariateForm, ::AbstractArray, ::AbstractPPL.VarName)

#776 should fix this

Ambiguity #9
|(x, ::Union{InitialValues.NonspecificInitialValue, InitialValues.SpecificInitialValue{typeof(|)}}) @ InitialValues ~/.julia/packages/InitialValues/OWP8V/src/InitialValues.jl:161
|(model::DynamicPPL.Model, values) @ DynamicPPL ~/ppl/dppl/src/model.jl:99

Possible fix, define
  |(::DynamicPPL.Model, ::Union{InitialValues.NonspecificInitialValue, InitialValues.SpecificInitialValue{typeof(|)}})

No compat bounds (fixed)

Base.PkgId(Base.UUID("366bfd00-2699-11ea-058f-f148b4cae6d8"), "DynamicPPL") does not declare a compat entry for the following deps:
1-element Vector{Base.PkgId}:
 InteractiveUtils [b77e0a4c-d291-57a0-90e8-8db25a27a240]

Type piracy (fixed)

Possible type-piracy detected:
[1] condition(context::AbstractContext, values::NTuple{var"#s77", Pair{<:VarName}} where var"#s77") @ DynamicPPL ~/ppl/dppl/src/contexts.jl:433
[2] condition(context::AbstractContext, value::Pair{<:VarName}, values::Pair{<:VarName}...) @ DynamicPPL ~/ppl/dppl/src/contexts.jl:428
[3] condition(context::AbstractContext; values...) @ DynamicPPL ~/ppl/dppl/src/contexts.jl:425
[4] condition(context::AbstractContext, values::Union{AbstractDict, NamedTuple}) @ DynamicPPL ~/ppl/dppl/src/contexts.jl:420
[5] condition(context::AbstractContext, values::NamedTuple{()}) @ DynamicPPL ~/ppl/dppl/src/contexts.jl:419
[6] condition(values::NTuple{var"#s77", var"#s76"} where {var"#s77", var"#s76"<:(Pair{<:VarName})}) @ DynamicPPL ~/ppl/dppl/src/contexts.jl:416
[7] condition(value::Pair{<:VarName}, values::Pair{<:VarName}...) @ DynamicPPL ~/ppl/dppl/src/contexts.jl:413
[8] condition(values::NamedTuple) @ DynamicPPL ~/ppl/dppl/src/contexts.jl:412
[9] condition(; values...) @ DynamicPPL ~/ppl/dppl/src/contexts.jl:411
[10] kwcall(::NamedTuple, ::typeof(condition)) @ DynamicPPL ~/ppl/dppl/src/contexts.jl:411
[11] kwcall(::NamedTuple, ::typeof(condition), context::AbstractContext) @ DynamicPPL ~/ppl/dppl/src/contexts.jl:425
[12] decondition(context, args...) @ DynamicPPL ~/ppl/dppl/src/contexts.jl:452
[13] getsym(::AbstractVector{<:VarName{sym}}) where sym @ DynamicPPL ~/ppl/dppl/src/varname.jl:46
Piracy: Test Failed at /Users/pyong/.julia/packages/Aqua/bBjXC/src/piracies.jl:240

coveralls · 2025-01-08T17:09:58Z

Pull Request Test Coverage Report for Build 12678919230

Details

0 of 11 (0.0%) changed or added relevant lines in 4 files are covered.
2849 unchanged lines in 26 files lost coverage.
Overall coverage decreased (-82.3%) to 3.951%

Changes Missing Coverage	Changed/Added Lines	%
src/distribution_wrappers.jl	2	0.0%
src/varinfo.jl	2	0.0%
src/simple_varinfo.jl	3	0.0%
src/context_implementations.jl	4	0.0%

Files with Coverage Reduction	New Missed Lines	%
src/selector.jl	5	0.0%
src/varname.jl	6	0.0%
src/test_utils/model_interface.jl	7	0.0%
src/model_utils.jl	11	0.0%
src/test_utils/contexts.jl	12	0.0%
src/distribution_wrappers.jl	13	0.0%
src/test_utils/varinfo.jl	23	0.0%
src/logdensityfunction.jl	23	0.0%
src/submodel_macro.jl	26	0.0%
src/extract_priors.jl	30	0.0%

Totals
Change from base Build 12657521724:	-82.3%
Covered Lines:	166
Relevant Lines:	4201

💛 - Coveralls

codecov · 2025-01-08T17:53:46Z

Codecov Report

Attention: Patch coverage is 0% with 11 lines in your changes missing coverage. Please review.

Project coverage is 3.86%. Comparing base (e673b69) to head (92b45d8).

Files with missing lines	Patch %	Lines
src/context_implementations.jl	0.00%	4 Missing ⚠️
src/simple_varinfo.jl	0.00%	3 Missing ⚠️
src/distribution_wrappers.jl	0.00%	2 Missing ⚠️
src/varinfo.jl	0.00%	2 Missing ⚠️

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HEAD has 21 uploads less than BASE

Flag BASE (e673b69) HEAD (92b45d8)

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Additional details and impacted files

@@            Coverage Diff             @@
##           master    #775       +/-   ##
==========================================
- Coverage   86.26%   3.86%   -82.40%     
==========================================
  Files          36      36               
  Lines        4332    4293       -39     
==========================================
- Hits         3737     166     -3571     
- Misses        595    4127     +3532

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See: https://discourse.julialang.org/t/psa-compat-requirements-in-the-general-registry-are-changing/104958

…guity)

penelopeysm force-pushed the py/aqua branch 3 times, most recently from bcb52e0 to 1092558 Compare January 8, 2025 20:59

penelopeysm mentioned this pull request Jan 9, 2025

Streamline internal de/conditioning interface #776

Merged

penelopeysm added 7 commits January 10, 2025 11:53

Add Aqua tests

c065ce7

(to drop) Comment out all non-Aqua tests

9b53194

Fix logpdf(::NamedDist) method ambiguity

04506ba

Fix SimpleVarInfo method ambiguity

7cd0355

Fix VarInfo method ambiguity

bf302ba

Add InteractiveUtils compat entry

bc93fe4

See: https://discourse.julialang.org/t/psa-compat-requirements-in-the-general-registry-are-changing/104958

Add Random.AbstractRNG type annotations (fixing dot_tilde_assume ambi…

1bf5497

…guity)

penelopeysm force-pushed the py/aqua branch from de4c661 to 1bf5497 Compare January 10, 2025 11:53

Remove unneeded getsym method

92b45d8

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Add Aqua tests #775

Add Aqua tests #775

penelopeysm commented Jan 8, 2025 •

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Add Aqua tests #775

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penelopeysm commented Jan 8, 2025 • edited Loading

Method ambiguities

No compat bounds (fixed)

Type piracy (fixed)

coveralls commented Jan 8, 2025 • edited Loading

Pull Request Test Coverage Report for Build 12678919230

Details

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Codecov Report

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