Run extension tests in separate workflow (#317)

* Use correct imports in helpers * Define extension tests * Delete old tests * Remove weakdeps from extras * Define workflow for testing extensions * Run extension tests on older Julia versions * Run MCMCChains tests separately * Create Project for MCMCChains tests * Run ArviZMCMCChainsExt tests * Remove unused test deps * Add missing DimensionalData compats * Don't include helpers if unneeded * Update extension test deps with CompatHelper * Add back weak deps to extras
arviz-devs · Dec 19, 2023 · f479d37 · f479d37
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diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml
@@ -16,4 +16,5 @@ jobs:
           COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
         run: |
           using CompatHelper
-          CompatHelper.main(; subdirs=["", "docs"])
+          subdirs = ["", "docs", readdir("test/ext"; join=true)...]
+          CompatHelper.main(; subdirs)
diff --git a/.github/workflows/ExtensionTest.yml b/.github/workflows/ExtensionTest.yml
@@ -0,0 +1,36 @@
+name: ExtensionTest
+on:
+  push:
+    branches: [main]
+    tags: [v*]
+  pull_request:
+jobs:
+  test:
+    name: ${{ matrix.extension }} - Julia ${{ matrix.julia-version }} 
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        julia-version: [1.6, 1]
+        extension:
+          - ArviZMCMCChainsExt
+          - ArviZSampleChainsExt
+          - ArviZSampleChainsDynamicHMCExt
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+          arch: x64
+      - uses: julia-actions/julia-buildpkg@v1
+      - run: |
+          julia --code-coverage=user -e '
+            using Pkg
+            test_path = joinpath(pwd(), "test", "ext", "${{ matrix.extension }}")
+            Pkg.activate(test_path)
+            Pkg.develop(PackageSpec(path=pwd()))
+            include(joinpath(test_path, "runtests.jl"))'
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v2
+        with:
+          files: lcov.info
diff --git a/Project.toml b/Project.toml
@@ -36,13 +36,10 @@ StatsBase = "0.32, 0.33, 0.34"
 julia = "1.6"
 
 [extras]
-DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
 MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
-OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SampleChains = "754583d1-7fc4-4dab-93b5-5eaca5c9622e"
 SampleChainsDynamicHMC = "6d9fd711-e8b2-4778-9c70-c1dfb499d4c4"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["DimensionalData", "MCMCChains", "OrderedCollections", "Random", "SampleChains", "SampleChainsDynamicHMC", "Test"]
+test = ["Test"]
diff --git a/test/ext/ArviZMCMCChainsExt/Project.toml b/test/ext/ArviZMCMCChainsExt/Project.toml
@@ -0,0 +1,15 @@
+[deps]
+ArviZ = "131c737c-5715-5e2e-ad31-c244f01c1dc7"
+DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
+MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
+OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[compat]
+ArviZ = "0.10.3"
+DimensionalData = "0.24, 0.25"
+MCMCChains = "6"
+OrderedCollections = "1"
+Random = "1.6"
+Test = "1.6"
diff --git a/test/test_mcmcchains.jl → test/ext/ArviZMCMCChainsExt/runtests.jl b/test/test_mcmcchains.jl → test/ext/ArviZMCMCChainsExt/runtests.jl
@@ -3,6 +3,7 @@ using ArviZ
 using DimensionalData
 using MCMCChains: MCMCChains
 using OrderedCollections
+using Random
 
 function makechains(
     names, ndraws, nchains, domains=[Float64 for _ in names]; seed=42, internal_names=[]

diff --git a/test/ext/ArviZSampleChainsDynamicHMCExt/Project.toml b/test/ext/ArviZSampleChainsDynamicHMCExt/Project.toml
@@ -0,0 +1,15 @@
+[deps]
+ArviZ = "131c737c-5715-5e2e-ad31-c244f01c1dc7"
+DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+SampleChains = "754583d1-7fc4-4dab-93b5-5eaca5c9622e"
+SampleChainsDynamicHMC = "6d9fd711-e8b2-4778-9c70-c1dfb499d4c4"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[compat]
+ArviZ = "0.10.3"
+DimensionalData = "0.24, 0.25"
+Random = "1.6"
+SampleChains = "0.5"
+SampleChainsDynamicHMC = "0.3"
+Test = "1.6"
diff --git a/test/ext/ArviZSampleChainsDynamicHMCExt/runtests.jl b/test/ext/ArviZSampleChainsDynamicHMCExt/runtests.jl
@@ -0,0 +1,38 @@
+using ArviZ
+using SampleChains: SampleChains
+using SampleChains.TupleVectors: TupleVectors
+using SampleChainsDynamicHMC: SampleChainsDynamicHMC
+using SampleChainsDynamicHMC.TransformVariables
+using Test
+
+include("../../helpers.jl")
+
+function samplechains_dynamichmc_sample(nchains, ndraws)
+    # μ ~ Normal(0, 1) |> iid(2, 3), σ ~ HalfNormal(0, 1), y[i] ~ Normal(μ[i], σ)
+    y = [0.74 0.15 -1.08; -0.42 1.08 -0.52]
+    function ℓ(nt)
+        μ = nt.μ
+        σ = nt.σ
+        return -(sum(abs2, μ) + σ^2 + sum((y .- μ) .^ 2) / σ^2) / 2 - length(y) * log(σ)
+    end
+    t = as((μ=as(Array, 2, 3), σ=asℝ₊))
+    chain = SampleChains.newchain(nchains, SampleChainsDynamicHMC.dynamichmc(), ℓ, t)
+    return SampleChains.sample!(chain, ndraws - 1)
+end
+
+@testset "SampleChainsDynamicHMC" begin
+    expected_stats_vars = (
+        :acceptance_rate, :n_steps, :diverging, :energy, :tree_depth, :turning
+    )
+
+    multichain = samplechains_dynamichmc_sample(4, 10)
+    idata = convert_to_inference_data(multichain)
+    @test InferenceObjects.groupnames(idata) === (:posterior, :sample_stats)
+    @test issubset(expected_stats_vars, keys(idata.sample_stats))
+    @test size(idata.posterior.μ) == (10, 4, 2, 3)
+    @test size(idata.posterior.σ) == (10, 4)
+
+    idata = convert_to_inference_data(multichain; group=:prior)
+    @test InferenceObjects.groupnames(idata) === (:prior, :sample_stats_prior)
+    @test issubset(expected_stats_vars, keys(idata.sample_stats_prior))
+end
diff --git a/test/ext/ArviZSampleChainsExt/Project.toml b/test/ext/ArviZSampleChainsExt/Project.toml
@@ -0,0 +1,13 @@
+[deps]
+ArviZ = "131c737c-5715-5e2e-ad31-c244f01c1dc7"
+DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+SampleChains = "754583d1-7fc4-4dab-93b5-5eaca5c9622e"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[compat]
+ArviZ = "0.10.3"
+DimensionalData = "0.24, 0.25"
+Random = "1.6"
+SampleChains = "0.5"
+Test = "1.6"
diff --git a/test/test_samplechains.jl → test/ext/ArviZSampleChainsExt/runtests.jl b/test/test_samplechains.jl → test/ext/ArviZSampleChainsExt/runtests.jl
@@ -1,11 +1,10 @@
 using ArviZ
-using DimensionalData
 using SampleChains: SampleChains
 using SampleChains.TupleVectors: TupleVectors
-using SampleChainsDynamicHMC: SampleChainsDynamicHMC
-using SampleChainsDynamicHMC.TransformVariables
 using Test
 
+include("../../helpers.jl")
+
 # minimal AbstractChain implementation
 struct TestChain{T} <: SampleChains.AbstractChain{T}
     samples::TupleVectors.TupleVector{T}
@@ -14,19 +13,6 @@ end
 SampleChains.samples(chain::TestChain) = getfield(chain, :samples)
 SampleChains.info(chain::TestChain) = getfield(chain, :info)
 
-function samplechains_dynamichmc_sample(nchains, ndraws)
-    # μ ~ Normal(0, 1) |> iid(2, 3), σ ~ HalfNormal(0, 1), y[i] ~ Normal(μ[i], σ)
-    y = [0.74 0.15 -1.08; -0.42 1.08 -0.52]
-    function ℓ(nt)
-        μ = nt.μ
-        σ = nt.σ
-        return -(sum(abs2, μ) + σ^2 + sum((y .- μ) .^ 2) / σ^2) / 2 - length(y) * log(σ)
-    end
-    t = as((μ=as(Array, 2, 3), σ=asℝ₊))
-    chain = SampleChains.newchain(nchains, SampleChainsDynamicHMC.dynamichmc(), ℓ, t)
-    return SampleChains.sample!(chain, ndraws - 1)
-end
-
 @testset "SampleChains" begin
     @testset "TestChain with $nchains chains" for nchains in (1, 4)
         ndraws = 10
@@ -70,20 +56,4 @@ end
             end
         end
     end
-    @testset "SampleChainsDynamicHMC" begin
-        expected_stats_vars = (
-            :acceptance_rate, :n_steps, :diverging, :energy, :tree_depth, :turning
-        )
-
-        multichain = samplechains_dynamichmc_sample(4, 10)
-        idata = convert_to_inference_data(multichain)
-        @test InferenceObjects.groupnames(idata) === (:posterior, :sample_stats)
-        @test issubset(expected_stats_vars, keys(idata.sample_stats))
-        @test size(idata.posterior.μ) == (10, 4, 2, 3)
-        @test size(idata.posterior.σ) == (10, 4)
-
-        idata = convert_to_inference_data(multichain; group=:prior)
-        @test InferenceObjects.groupnames(idata) === (:prior, :sample_stats_prior)
-        @test issubset(expected_stats_vars, keys(idata.sample_stats_prior))
-    end
 end
diff --git a/test/helpers.jl b/test/helpers.jl
@@ -1,5 +1,6 @@
-using Random
 using ArviZ
+using DimensionalData
+using Random
 
 function random_dim_array(var_name, dims, coords, default_dims=())
     _dims = (default_dims..., dims...)

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -2,8 +2,5 @@ using ArviZ
 using Test
 
 @testset "ArviZ" begin
-    include("helpers.jl")
     include("test_utils.jl")
-    include("test_samplechains.jl")
-    include("test_mcmcchains.jl")
 end