bump versions, update AD tests, update workflows (#166)

This fixes all the existing CompatHelper PRs

Closes #160
Closes #161
Closes #163 
Closes #164 

And also updates the AD testing to use Mooncake (and removes the
previously commented-out Tracker and Zygote tests).

And also updates the test and format workflows to more closely match the
rest of TuringLang. In particular:
- uses
[TuringLang/actions/Format](https://github.com/TuringLang/actions?tab=readme-ov-file#format)
for workflow standardisation
- tests on both Julia 1.10 and Julia 1.11
- removes the `arch=x64` matrix variable which is no longer appropriate
for macOS-latest (should be `aarch64`, but leaving it out is easier as
it will allow GitHub to automatically determine the right architecture)

---------

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

Author: penelopeysm

.github/workflows/CI.yml

@@ -6,38 +6,46 @@ on:
     tags: ["*"]
   pull_request:
   workflow_dispatch:
+
+# Cancel existing tests on the same PR if a new commit is added to a pull request
 concurrency:
-  # Skip intermediate builds: always.
-  # Cancel intermediate builds: only if it is a pull request build.
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: false
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
   test:
     name: Julia CI
     runs-on: ${{ matrix.os }}
     timeout-minutes: 90
-    continue-on-error: ${{ matrix.version == 'nightly' }}
     strategy:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
+          - 'lts'
+          - '1'
         os:
           - ubuntu-latest
           - windows-latest
           - macOS-latest
-        arch:
-          - x64
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
       - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
-        with:
-          coverage: "false"
         env:
           JULIA_NUM_THREADS: "auto"
+
+      - uses: julia-actions/julia-processcoverage@v1
+
+      - uses: codecov/codecov-action@v5
+        with:
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - uses: coverallsapp/github-action@v2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: lcov.info

.github/workflows/Format.yml

@@ -3,30 +3,19 @@ name: Format
 on:
   push:
     branches:
-      - "main"
-      - "release-"
-    tags: ["*"]
+      - main
   pull_request:
 
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
   format:
-    name: "Format Check"
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v2
-        with:
-          version: 1
-      - name: Install JuliaFormatter and format
-        run: |
-          using Pkg
-          Pkg.add(PackageSpec(name="JuliaFormatter"))
-          using JuliaFormatter
-          format("."; verbose=true)
-        shell: julia --color=yes {0}
-      - name: Suggest formatting changes
-        uses: reviewdog/action-suggester@v1
-        if: github.event_name == 'pull_request'
-        with:
-          tool_name: JuliaFormatter
-          fail_on_error: true
+      - name: Format code
+        uses: TuringLang/actions/Format@main

Project.toml

@@ -1,7 +1,7 @@
 name = "TuringGLM"
 uuid = "0004c1f4-53c5-4d43-a221-a1dac6cf6b74"
 authors = ["Jose Storopoli <[email protected]>", "Rik Huijzer <[email protected]>", "contributors"]
-version = "2.13.0"
+version = "2.14.0"
 
 [deps]
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
@@ -29,5 +29,5 @@ StatsBase = "0.33 - 0.34"
 StatsModels = "0.6.28 - 0.7"
 TableOperations = "1.2"
 Tables = "1.6"
-Turing = "0.20 - 0.37"
+Turing = "0.20 - 0.39"
 julia = "1"

README.md

@@ -5,7 +5,7 @@
 [![Build Status](https://github.com/TuringLang/TuringGLM.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/TuringLang/TuringGLM.jl/actions/workflows/CI.yml?query=branch%3Amain)
 [![Coverage](https://codecov.io/gh/TuringLang/TuringGLM.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/TuringLang/TuringGLM.jl)
 [![Coverage](https://coveralls.io/repos/github/TuringLang/TuringGLM.jl/badge.svg?branch=main)](https://coveralls.io/github/TuringLang/TuringGLM.jl?branch=main)
-[![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)
+[![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/JuliaDiff/BlueStyle)
 [![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
 
 TuringGLM makes easy to specify Bayesian **G**eneralized **L**inear **M**odels using the formula syntax and returns an instantiated [Turing](https://github.com/TuringLang/Turing.jl) model.

test/Project.toml

@@ -3,21 +3,19 @@ CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
-Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
-Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [compat]
 CSV = "0.10"
 CategoricalArrays = "0.10"
 DataFrames = "1"
-ForwardDiff = "0.10"
+ForwardDiff = "0.10, 1"
+Mooncake = "0.4.122"
 ReverseDiff = "1"
 Statistics = "1"
 TimerOutputs = "0.5"
-Tracker = "0.2"
-Zygote = "0.6"

test/ad_backends.jl

@@ -1,28 +1,20 @@
-@timed_testset "ad_backends" begin
+using ForwardDiff: ForwardDiff
+using ReverseDiff: ReverseDiff
+using Mooncake: Mooncake
+
+@timed_testset "ad_backends.jl" begin
     DATA_DIR = joinpath("..", "data")
     cheese = CSV.read(joinpath(DATA_DIR, "cheese.csv"), DataFrame)
     f = @formula(y ~ (1 | cheese) + background)
     m = turing_model(f, cheese)
-    # only running 2 samples to test if the different ADs runs
-    @timed_testset "ForwardDiff" begin
-        chn = sample(m, NUTS(; adtype=AutoForwardDiff(; chunksize=8)), 2)
-        @test chn isa Chains
-    end
-    # TODO: fix Tracker tests
-    # @timed_testset "Tracker" begin
-    #     using Tracker
-    #     chn = sample(m, NUTS(; adtype=AutoTracker()), 2)
-    #     @test chn isa Chains
-    # end
-    # TODO: fix Zygote tests
-    # @timed_testset "Zygote" begin
-    #     using Zygote
-    #     chn = sample(m, NUTS(; adtype=AutoZygote()), 2)
-    #     @test chn isa Chains
-    # end
-    @timed_testset "ReverseDiff" begin
-        using ReverseDiff
-        chn = sample(m, NUTS(; adtype=AutoReverseDiff(; compile=true)), 2)
-        @test chn isa Chains
+
+    ADTYPES = [
+        AutoForwardDiff(),
+        AutoReverseDiff(; compile=false),
+        AutoReverseDiff(; compile=true),
+        AutoMooncake(; config=nothing),
+    ]
+    @testset "$adtype" for adtype in ADTYPES
+        @test sample(m, NUTS(; adtype=adtype), 20) isa Chains
     end
 end