Improve CI (#166)

Only substantial changes to the code is renaming `VOLUME_I` and
`VOLUME_II` to `VOLUME_1\2`.

Some test code are moved around. 
Test CI is factored into multiple smaller ones:
- `mcmcchains` and `gibbs` tests will be retried if error for max 3
times

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

.github/workflows/CompatHelper.yml

@@ -0,0 +1,45 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/Tests.yml

@@ -1,55 +1,81 @@
-name: CI
+name: Tests
 
 on:
   push:
-    branches:
-      - master
+    branches: ["master"]
+    paths:
+      - 'src/**/*'
+      - 'test/**/*'
   pull_request:
+    paths:
+      - 'src/**/*'
+      - 'test/**/*'
+
+  workflow_dispatch:
 
 jobs:
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    name: Julia ${{ matrix.version }} on ${{ matrix.os }} (${{ matrix.arch }})
     runs-on: ${{ matrix.os }}
     continue-on-error: ${{ matrix.version == 'nightly' }}
     strategy:
       fail-fast: false
       matrix:
-        version:
-          - '1'
-          - '1.9'
-          - 'nightly'
-        os:
-          - ubuntu-latest
-          - macOS-latest
-          - windows-latest
-        arch:
-          - x64
+        version: ['1', '1.9', 'nightly']
+        os: [ubuntu-latest, macOS-latest, windows-latest]
+        arch: [x64]
         include:
           - version: '1'
             os: ubuntu-latest
             arch: x64
             coverage: true
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
+      - uses: actions/cache@v4
         with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          path: |
+            ~/.julia
+            ~/.julia/artifacts
+          key: ${{ runner.os }}-julia-${{ matrix.version }}-${{ matrix.arch }}-${{ hashFiles('**/Project.toml', '**/Manifest.toml') }}
           restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+            ${{ runner.os }}-julia-${{ matrix.version }}-${{ matrix.arch }}-
+            ${{ runner.os }}-julia-${{ matrix.version }}-
       - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-runtest@v1
+      - name: Running elementary tests
+        uses: julia-actions/julia-runtest@v1
+        env:
+          TEST_GROUP: "elementary"
+      - name: Running compilation tests
+        uses: julia-actions/julia-runtest@v1
+        env:
+          TEST_GROUP: "compilation"
+      - name: Profile compiler passes
+        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(;coverage=true);" >> $GITHUB_STEP_SUMMARY
+        env:
+          TEST_GROUP: "profile"
+      - name: Running `gibbs` tests
+        uses: nick-fields/retry@v3
+        with:
+          timeout_minutes: 10
+          max_attempts: 3
+          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true);"
+        env:
+          TEST_GROUP: "gibbs"
+      - name: Running `mcmchains` tests
+        uses: nick-fields/retry@v3
+        with:
+          timeout_minutes: 10
+          max_attempts: 3
+          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true);"
+        env:
+          TEST_GROUP: "mcmchains"
       - uses: julia-actions/julia-processcoverage@v1
         if: matrix.coverage
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v4
         if: matrix.coverage
         with:
           file: lcov.info

Project.toml

@@ -1,6 +1,6 @@
 name = "JuliaBUGS"
 uuid = "ba9fb4c0-828e-4473-b6a1-cd2560fee5bf"
-version = "0.5.1"
+version = "0.5.2"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"

docs/src/example.md

@@ -276,4 +276,4 @@ Note that the `init_params` argument is now a vector of initial parameters for e
 Sometimes the progress logger can cause problems in distributed setting, so we can disable it by setting `progress = false`.
 
 ## More Examples
-We have transcribed all the examples from the first volume of the BUGS Examples ([original](https://www.multibugs.org/examples/latest/VolumeI.html) and [transcribed](https://github.com/TuringLang/JuliaBUGS.jl/tree/master/src/BUGSExamples/Volume_I)). All programs and data are included, and can be compiled using the steps described in the tutorial above.
+We have transcribed all the examples from the first volume of the BUGS Examples ([original](https://www.multibugs.org/examples/latest/VolumeI.html) and [transcribed](https://github.com/TuringLang/JuliaBUGS.jl/tree/master/src/BUGSExamples/VOLUME_1)). All programs and data are included, and can be compiled using the steps described in the tutorial above.

src/BUGSExamples/BUGSExamples.jl

@@ -2,38 +2,38 @@ module BUGSExamples
 
 using JuliaBUGS: @bugs
 
-include("Volume_I/Blocker.jl")
-include("Volume_I/Bones.jl")
-include("Volume_I/Dogs.jl")
-include("Volume_I/Dyes.jl")
-include("Volume_I/Epil.jl")
-include("Volume_I/Equiv.jl")
-include("Volume_I/Inhalers.jl")
-include("Volume_I/Kidney.jl")
-include("Volume_I/Leuk.jl")
-include("Volume_I/LeukFr.jl")
-include("Volume_I/LSAT.jl")
-include("Volume_I/Magnesium.jl")
-include("Volume_I/Mice.jl")
-include("Volume_I/Oxford.jl")
-include("Volume_I/Pumps.jl")
-include("Volume_I/Rats.jl")
-include("Volume_I/Salm.jl")
-include("Volume_I/Seeds.jl")
-include("Volume_I/Stacks.jl")
-include("Volume_I/Surgical.jl")
+include("Volume_1/Blocker.jl")
+include("Volume_1/Bones.jl")
+include("Volume_1/Dogs.jl")
+include("Volume_1/Dyes.jl")
+include("Volume_1/Epil.jl")
+include("Volume_1/Equiv.jl")
+include("Volume_1/Inhalers.jl")
+include("Volume_1/Kidney.jl")
+include("Volume_1/Leuk.jl")
+include("Volume_1/LeukFr.jl")
+include("Volume_1/LSAT.jl")
+include("Volume_1/Magnesium.jl")
+include("Volume_1/Mice.jl")
+include("Volume_1/Oxford.jl")
+include("Volume_1/Pumps.jl")
+include("Volume_1/Rats.jl")
+include("Volume_1/Salm.jl")
+include("Volume_1/Seeds.jl")
+include("Volume_1/Stacks.jl")
+include("Volume_1/Surgical.jl")
 
-include("Volume_II/BiRats.jl")
-include("Volume_II/Eyes.jl")
+include("Volume_2/BiRats.jl")
+include("Volume_2/Eyes.jl")
 
-const VOLUME_I = (
+const VOLUME_1 = (
     blockers=blockers,
     bones=bones,
     dogs=dogs,
     dyes=dyes,
     epil=epil,
     equiv=equiv,
-    inhalers=inhalers,
+    # inhalers=inhalers,
     kidney=kidney,
     leuk=leuk,
     leukfr=leukfr,
@@ -50,10 +50,10 @@ const VOLUME_I = (
     surgical_realistic=surgical_realistic,
 )
 
-const VOLUME_II = (birats=birats, eyes=eyes)
+const VOLUME_2 = (birats=birats, eyes=eyes)
 
 function has_ground_truth(m::Symbol)
-    if m in union(keys(VOLUME_I), keys(VOLUME_II))
+    if m in union(keys(VOLUME_1), keys(VOLUME_2))
         return haskey(getfield(BUGSExamples, m), :reference_results)
     else
         return false

src/compiler_pass.jl

@@ -486,7 +486,7 @@ The function returns three values:
 Array elements and array variables are represented by tuples in the returned value. All `Colon` indexing is assumed to be concretized.
 
 # Examples
-```jldoctest
+```jldoctest; setup = :(using JuliaBUGS: evaluate_and_track_dependencies)
 julia> evaluate_and_track_dependencies(:(x[a]), (x=[missing, missing], a = missing))
 (missing, (:a, (:x, 1:2)))
 

src/utils.jl

@@ -88,7 +88,7 @@ end
 Extract all the array variable names and number of dimensions from a given simple expression. 
 
 # Examples:
-```jldoctest
+```jldoctest; setup = :(using JuliaBUGS: extract_variable_names_and_numdims)
 julia> extract_variable_names_and_numdims(:((a + b) * c), ())
 (a = 0, b = 0, c = 0)
 
@@ -154,7 +154,7 @@ will raise an error.
 
 # Example:
 ```jldoctest
-extract_variable_names_and_numdims(
+JuliaBUGS.extract_variable_names_and_numdims(
     @bugs begin
         for i in 1:N
             for j in 1:T
@@ -434,7 +434,7 @@ Replace all `Colon()`s in `expr` with the corresponding array size.
 
 # Examples
 ```jldoctest
-julia> concretize_colon_indexing(:(f(x[1, :])), (x = [1 2 3 4; 5 6 7 8; 9 10 11 12],))
+julia> JuliaBUGS.concretize_colon_indexing(:(f(x[1, :])), (x = [1 2 3 4; 5 6 7 8; 9 10 11 12],))
 :(f(x[1, 1:4]))
 ```
 """
@@ -460,7 +460,7 @@ This function evaluates expressions that consist solely of arithmetic operations
 is specifically designed for scenarios such as calculating array indices or determining loop boundaries.
 
 # Example:
-```jldoctest
+```jldoctest; setup = :(using JuliaBUGS: simple_arithmetic_eval)
 julia> simple_arithmetic_eval((a = 1, b = [1, 2]), 1)
 1
 

test/gibbs.jl

@@ -1,3 +1,6 @@
+using JuliaBUGS: MHFromPrior, Gibbs
+using DynamicPPL: DynamicPPL
+
 @testset "Simple gibbs" begin
     model_def = @bugs begin
         # Likelihood
@@ -32,7 +35,9 @@
         :varinfo,
         begin
             vi = model.varinfo
-            SimpleVarInfo(DynamicPPL.values_as(vi, NamedTuple), vi.logp, vi.transformation)
+            DynamicPPL.SimpleVarInfo(
+                DynamicPPL.values_as(vi, NamedTuple), vi.logp, vi.transformation
+            )
         end,
     )