Update CI and test deps (#188)

* Update CI and test deps

* Update JET

* KrylovKit

* Add KrylovKit

* Switch to 1.11 since Zygote fails on 1.12

Author: gdalle

.github/dependabot.yml

@@ -0,0 +1,20 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+enable-beta-ecosystems: true # Julia ecosystem
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: "julia"
+    directories: # Location of Julia projects
+      - "/"
+      - "/docs"
+      - "/test"
+    schedule:
+      interval: "weekly"
+    groups:
+      # Group all Julia package updates into a single PR:
+      all-julia-packages:
+        patterns:
+          - "*"

.github/workflows/CI.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        version: ['1.10', '1']
+        version: ['1.10', '1.11']
         os: [ubuntu-latest]
         arch: [x64]
         allow_failure: [false]
@@ -47,12 +47,12 @@ jobs:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
         with:
-          version: '1'
+          version: '1.11'
       - uses: julia-actions/cache@v1
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.Registry.update(); Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
-        run: julia --project=docs/ docs/make.jl
+        run: julia --project=docs/ docs/make.jl

.github/workflows/CompatHelper.yml

@@ -0,0 +1,13 @@
+name: Format suggestions
+on:
+  pull_request:
+    # this argument is not required if you don't use the `suggestion-label` input
+    types: [opened, reopened, synchronize, labeled, unlabeled]
+jobs:
+  code-style:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: julia-actions/julia-format@v4
+        with:
+          version: '1' # Set `version` to '1.0.54' if you need to use JuliaFormatter.jl v1.0.54 (default: '1')
+          suggestion-label: 'format-suggest' # leave this unset or empty to show suggestions for all PRs

.github/workflows/Format.yml

@@ -21,78 +21,10 @@ ImplicitDifferentiationZygoteExt = "Zygote"
 
 [compat]
 ADTypes = "1.9.0"
-Aqua = "0.8.13"
 ChainRulesCore = "1.25.0"
-ChainRulesTestUtils = "1.13.0"
-ComponentArrays = "0.15.27"
 DifferentiationInterface = "0.6.1,0.7"
-Documenter = "1.12.0"
-ExplicitImports = "1"
-FiniteDiff = "2.27.0"
 ForwardDiff = "0.10.36, 1"
-JET = "0.9, 0.10"
-JuliaFormatter = "2.1.2"
-Krylov = "0.9.6, 0.10"
 KrylovKit = "0.10.0"
 LinearAlgebra = "1"
-NLsolve = "4.5.1"
-Optim = "1.12.0"
-Random = "1"
-SparseArrays = "1"
-StaticArrays = "1.9.13"
-Test = "1"
-TestItemRunner = "1.1.0"
-TestItems = "1.0.0"
 Zygote = "0.7.4"
 julia = "1.10"
-
-[extras]
-ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
-Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
-ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-ChainRulesTestUtils = "cdddcdb0-9152-4a09-a978-84456f9df70a"
-ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
-DifferentiationInterface = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
-Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
-FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
-ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
-JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
-JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
-Krylov = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
-LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
-Optim = "429524aa-4258-5aef-a3af-852621145aeb"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
-StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"
-TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe"
-Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
-
-[targets]
-test = [
-    "ADTypes",
-    "Aqua",
-    "ChainRulesCore",
-    "ChainRulesTestUtils",
-    "ComponentArrays",
-    "DifferentiationInterface",
-    "Documenter",
-    "ExplicitImports",
-    "FiniteDiff",
-    "ForwardDiff",
-    "JET",
-    "JuliaFormatter",
-    "LinearAlgebra",
-    "NLsolve",
-    "Optim",
-    "Random",
-    "SparseArrays",
-    "StaticArrays",
-    "Test",
-    "TestItems",
-    "TestItemRunner",
-    "Zygote",
-]

Project.toml

@@ -0,0 +1,52 @@
+[deps]
+ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+ChainRulesTestUtils = "cdddcdb0-9152-4a09-a978-84456f9df70a"
+ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
+DifferentiationInterface = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
+FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
+ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+ImplicitDifferentiation = "57b37032-215b-411a-8a7c-41a003a55207"
+JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
+Optim = "429524aa-4258-5aef-a3af-852621145aeb"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"
+TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe"
+Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
+
+[sources]
+ImplicitDifferentiation = { path = ".." }
+
+[compat]
+ADTypes = "1.9.0"
+Aqua = "0.8.13"
+ChainRulesCore = "1.25.0"
+ChainRulesTestUtils = "1.13.0"
+ComponentArrays = "0.15.27"
+DifferentiationInterface = "0.6.1,0.7"
+Documenter = "1.12.0"
+ExplicitImports = "1"
+FiniteDiff = "2.27.0"
+ForwardDiff = "0.10.36, 1"
+JET = "0.9, 0.10, 0.11"
+KrylovKit = "0.10.2"
+LinearAlgebra = "1"
+NLsolve = "4.5.1"
+Optim = "1.12.0"
+Random = "1"
+SparseArrays = "1"
+StaticArrays = "1.9.13"
+Test = "1"
+TestItemRunner = "1.1.0"
+TestItems = "1.0.0"
+Zygote = "0.7.4"
+julia = "1.10"

test/Project.toml

@@ -7,16 +7,11 @@ using TestItems
     Aqua.test_all(ImplicitDifferentiation; ambiguities=false, undocumented_names=true)
 end
 
-@testitem "Formatting" begin
-    using JuliaFormatter
-    @test format(ImplicitDifferentiation; verbose=false, overwrite=false)
-end
-
 @testitem "Static checking" begin
     using JET
     using ForwardDiff: ForwardDiff
     using Zygote: Zygote
-    JET.test_package(ImplicitDifferentiation; target_defined_modules=true)
+    JET.test_package(ImplicitDifferentiation; target_modules=(ImplicitDifferentiation,))
 end
 
 @testitem "Imports" begin