Fixes for Julia 1.6 (#212)

This PR fixes TuringLang/Turing.jl#1525 (comment) and fixes the model definition and some warning on Julia 1.6. It also includes a line number node of the call site instead of a reference to `src/compiler.jl` in the model definition for easier debugging. On Julia 1.6, initially I got warnings about method redefinitions (models of the same name) that all referred to line 344 in `src/compiler.jl` instead of the place where the model was defined by the user.

Turing tests are disabled currently since they crash (segmentation fault). Might be related to the fact that Libtask is not compatible with Julia 1.6 yet (therefore also an older version of Turing and Libtask would be used on Julia 1.6).

Co-authored-by: David Widmann <[email protected]>

Author: devmotion

.github/workflows/DynamicPPL-CI.yml renamed to .github/workflows/CI.yml

@@ -1,4 +1,4 @@
-name: DynamicPPL-CI
+name: CI
 
 on:
   push:
@@ -13,13 +13,11 @@ on:
 jobs:
   test:
     runs-on: ${{ matrix.os }}
-    continue-on-error: ${{ matrix.version == 'nightly' }}
     strategy:
       matrix:
         version:
-          - '1.3'
-          - '1'
-          # - 'nightly'
+          - '1.3' # minimum supported version
+          - '1' # current stable version
         os:
           - ubuntu-latest
           - macOS-latest

.github/workflows/JuliaNightly.yml

@@ -0,0 +1,33 @@
+name: JuliaNightly
+
+on:
+  push:
+    branches:
+      # This is where pull requests from "bors r+" are built.
+      - staging
+      # This is where pull requests from "bors try" are built.
+      - trying
+      # Build the master branch.
+      - master
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: 'nightly'
+          arch: x64
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/julia-runtest@latest

Project.toml

@@ -1,6 +1,6 @@
 name = "DynamicPPL"
 uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8"
-version = "0.10.5"
+version = "0.10.6"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
@@ -16,6 +16,6 @@ AbstractMCMC = "2"
 Bijectors = "0.5.2, 0.6, 0.7, 0.8"
 ChainRulesCore = "0.9.7"
 Distributions = "0.23.8, 0.24"
-MacroTools = "0.5.1"
+MacroTools = "0.5.6"
 NaturalSort = "1"
 julia = "1.3"

README.md

@@ -1,7 +1,8 @@
 # DynamicPPL.jl
 
-[![Build Status](https://travis-ci.com/TuringLang/DynamicPPL.jl.svg?branch=master)](https://travis-ci.com/TuringLang/DynamicPPL.jl)
-[![Build Status](https://github.com/TuringLang/DynamicPPL.jl/workflows/DynamicPPL-CI/badge.svg)](https://github.com/TuringLang/DynamicPPL.jl/actions?query=workflow%3ADynamicPPL-CI+branch%3Amaster)
+[![Build Status](https://github.com/TuringLang/DynamicPPL.jl/workflows/CI/badge.svg?branch=master)](https://github.com/TuringLang/DynamicPPL.jl/actions?query=workflow%3ACI+branch%3Amaster)
+[![Build Status](https://github.com/TuringLang/DynamicPPL.jl/workflows/JuliaNightly/badge.svg?branch=master)](https://github.com/TuringLang/DynamicPPL.jl/actions?query=workflow%3AJuliaNightly+branch%3Amaster)
+[![Coverage Status](https://coveralls.io/repos/github/TuringLang/DynamicPPL.jl/badge.svg?branch=master)](https://coveralls.io/github/TuringLang/DynamicPPL.jl?branch=master)
 [![Codecov](https://codecov.io/gh/TuringLang/DynamicPPL.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/TuringLang/DynamicPPL.jl)
 [![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://colprac.sciml.ai/)
 [![Bors enabled](https://bors.tech/images/badge_small.svg)](https://app.bors.tech/repositories/24589)

src/compiler.jl

@@ -62,18 +62,20 @@ end
 To generate a `Model`, call `model(xvalue)` or `model(xvalue, yvalue)`.
 """
 macro model(expr, warn=true)
-    esc(model(expr, warn))
+    # include `LineNumberNode` with information about the call site in the
+    # generated function for easier debugging and interpretation of error messages
+    esc(model(expr, __source__, warn))
 end
 
-function model(expr, warn)
+function model(expr, linenumbernode, warn)
     modelinfo = build_model_info(expr)
 
     # Generate main body
     modelinfo[:body] = generate_mainbody(
         modelinfo[:modeldef][:body], modelinfo[:allargs_syms], warn
     )
 
-    return build_output(modelinfo)
+    return build_output(modelinfo, linenumbernode)
 end
 
 """
@@ -301,11 +303,11 @@ hasmissing(T::Type{<:AbstractArray{>:Missing}}) = true
 hasmissing(T::Type) = false
 
 """
-    build_output(modelinfo)
+    build_output(modelinfo, linenumbernode)
 
 Builds the output expression.
 """
-function build_output(modelinfo)
+function build_output(modelinfo, linenumbernode)
     ## Build the anonymous evaluator from the user-provided model definition.
 
     # Remove the name.
@@ -340,8 +342,12 @@ function build_output(modelinfo)
     # We use a name for the anonymous evaluator that does not conflict with other variables.
     modeldef = modelinfo[:modeldef]
     @gensym evaluator
-    modeldef[:body] = quote
-        $evaluator = $(combinedef_anonymous(evaluatordef))
+    # We use `MacroTools.@q begin ... end` instead of regular `quote ... end` to ensure
+    # that no new `LineNumberNode`s are added apart from the reference `linenumbernode`
+    # to the call site
+    modeldef[:body] = MacroTools.@q begin
+        $(linenumbernode)
+        $evaluator = $(MacroTools.combinedef(evaluatordef))
         return $(DynamicPPL.Model)(
             $(QuoteNode(modeldef[:name])),
             $evaluator,

src/utils.jl

@@ -2,34 +2,6 @@
 struct NoDefault end
 const NO_DEFAULT = NoDefault()
 
-# FIXME: This is copied from MacroTools and should be removed when a MacroTools release with
-# support for anonymous functions is available (> 0.5.5).
-function combinedef_anonymous(dict::Dict)
-    rtype = get(dict, :rtype, nothing)
-    params = get(dict, :params, [])
-    wparams = get(dict, :whereparams, [])
-    body = MacroTools.block(dict[:body])
-
-    if isempty(dict[:kwargs])
-        arg = :($(dict[:args]...),)
-    else
-        arg = Expr(:tuple, Expr(:parameters, dict[:kwargs]...), dict[:args]...)
-    end
-    if isempty(wparams)
-        if rtype==nothing
-            MacroTools.@q($arg -> $body)
-        else
-            MacroTools.@q(($arg::$rtype) -> $body)
-        end
-    else
-        if rtype === nothing
-            MacroTools.@q(($arg where {$(wparams...)}) -> $body)
-        else
-            MacroTools.@q(($arg::$rtype where {$(wparams...)}) -> $body)
-        end
-    end
-end
-
 """
     @addlogprob!(ex)
 
@@ -52,6 +24,8 @@ function getargs_dottilde(expr::Expr)
     return MacroTools.@match expr begin
         (.~)(L_, R_) => (L, R)
         (~).(L_, R_) => (L, R)
+        # Julia 1.6: see https://github.com/TuringLang/Turing.jl/issues/1525
+        (L_ .~ R_) => (L, R)
         x_ => nothing
     end
 end

test/compiler.jl

@@ -20,30 +20,30 @@ end
         testmodel_comp(1.0, 1.2)
 
         # check if drawing from the prior works
-        @model function testmodel0(x = missing)
+        @model function testmodel01(x = missing)
             x ~ Normal()
             return x
         end
-        f0_mm = testmodel0()
+        f0_mm = testmodel01()
         @test mean(f0_mm() for _ in 1:1000) ≈ 0. atol=0.1
 
         # Test #544
-        @model function testmodel0(x = missing)
+        @model function testmodel02(x = missing)
             if x === missing
                 x = Vector{Float64}(undef, 2)
             end
             x[1] ~ Normal()
             x[2] ~ Normal()
             return x
         end
-        f0_mm = testmodel0()
+        f0_mm = testmodel02()
         @test all(x -> isapprox(x, 0; atol = 0.1), mean(f0_mm() for _ in 1:1000))
 
-        @model function testmodel01(x = missing)
+        @model function testmodel03(x = missing)
             x ~ Bernoulli(0.5)
             return x
         end
-        f01_mm = testmodel01()
+        f01_mm = testmodel03()
         @test mean(f01_mm() for _ in 1:1000) ≈ 0.5 atol=0.1
 
         # test if we get the correct return values
@@ -133,22 +133,22 @@ end
         @test_throws ArgumentError btest()
 
         # Test missing input arguments
-        @model function testmodel(x)
-            x ~ Bernoulli(0.5)
+        @model function testmodel_missing1(x)
+            x ~ Bernoulli(0.5)
             return x
         end
-        @test_throws MethodError testmodel()
+        @test_throws MethodError testmodel_missing1()
 
         # Test missing initialization for vector observation turned parameter
-        @model function testmodel(x)
-            x[1] ~ Bernoulli(0.5)
+        @model function testmodel_missing2(x)
+            x[1] ~ Bernoulli(0.5)
             return x
         end
-        @test_throws MethodError testmodel(missing)()
+        @test_throws MethodError testmodel_missing2(missing)()
 
         # Test use of internal names
-        @model function testmodel(x)
-            x[1] ~  Bernoulli(0.5)
+        @model function testmodel_missing3(x)
+            x[1] ~ Bernoulli(0.5)
             global varinfo_ = _varinfo
             global sampler_ = _sampler
             global model_ = _model
@@ -157,7 +157,7 @@ end
             global lp = getlogp(_varinfo)
             return x
         end
-        model = testmodel([1.0])
+        model = testmodel_missing3([1.0])
         varinfo = VarInfo(model)
         @test getlogp(varinfo) == lp
         @test varinfo_ isa AbstractVarInfo
@@ -167,8 +167,8 @@ end
         @test rng_ isa Random.AbstractRNG
 
         # disable warnings
-        @model function testmodel(x)
-            x[1] ~  Bernoulli(0.5)
+        @model function testmodel_missing4(x)
+            x[1] ~ Bernoulli(0.5)
             global varinfo_ = _varinfo
             global sampler_ = _sampler
             global model_ = _model
@@ -178,17 +178,17 @@ end
             return x
         end false
         lpold = lp
-        model = testmodel([1.0])
+        model = testmodel_missing4([1.0])
         varinfo = VarInfo(model)
         @test getlogp(varinfo) == lp == lpold
 
         # test DPPL#61
-        @model function testmodel(z)
+        @model function testmodel_missing5(z)
             m ~ Normal()
             z[1:end] ~ MvNormal(fill(m, length(z)), 1.0)
             return m
         end
-        model = testmodel(rand(10))
+        model = testmodel_missing5(rand(10))
         @test all(z -> isapprox(z, 0; atol = 0.2), mean(model() for _ in 1:1000))
 
         # test Turing#1464

test/runtests.jl

@@ -43,18 +43,20 @@ include("test_util.jl")
         include(joinpath("compat", "ad.jl"))
     end
 
-    @testset "turing" begin
-        # activate separate test environment
-        Pkg.activate(DIRECTORY_Turing_tests)
-        Pkg.develop(PackageSpec(path=DIRECTORY_DynamicPPL))
-        Pkg.instantiate()
-
-        # make sure that the new environment is considered `using` and `import` statements
-        # (not added automatically on Julia 1.3, see e.g. PR #209)
-        if !(joinpath(DIRECTORY_Turing_tests, "Project.toml") in Base.load_path())
-            pushfirst!(LOAD_PATH, DIRECTORY_Turing_tests)
+    @static if VERSION <= v"1.5.3"
+        @testset "turing" begin
+            # activate separate test environment
+            Pkg.activate(DIRECTORY_Turing_tests)
+            Pkg.develop(PackageSpec(path=DIRECTORY_DynamicPPL))
+            Pkg.instantiate()
+
+            # make sure that the new environment is considered `using` and `import` statements
+            # (not added automatically on Julia 1.3, see e.g. PR #209)
+            if !(joinpath(DIRECTORY_Turing_tests, "Project.toml") in Base.load_path())
+                pushfirst!(LOAD_PATH, DIRECTORY_Turing_tests)
+            end
+
+            include(joinpath("turing", "runtests.jl"))
         end
-
-        include(joinpath("turing", "runtests.jl"))
     end
 end

test/utils.jl

@@ -22,6 +22,7 @@
         @test getargs_dottilde(:(x ~ Normal(μ, σ))) === nothing
         @test getargs_dottilde(:((.~)(x, Normal(μ, σ)))) == (:x, :(Normal(μ, σ)))
         @test getargs_dottilde(:((~).(x, Normal(μ, σ)))) == (:x, :(Normal(μ, σ)))
+        @test getargs_dottilde(:(x .~ Normal(μ, σ))) == (:x, :(Normal(μ, σ)))
         @test getargs_dottilde(:(@. x ~ Normal(μ, σ))) === nothing
         @test getargs_dottilde(:(@. x ~ Normal(μ, $(Expr(:$, :(sqrt(v))))))) === nothing
         @test getargs_dottilde(:(@~ Normal.(μ, σ))) === nothing
@@ -41,4 +42,4 @@
         @test getargs_tilde(:(@. x ~ Normal(μ, $(Expr(:$, :(sqrt(v))))))) === nothing
         @test getargs_tilde(:(@~ Normal.(μ, σ))) === nothing
     end
-end
+end