Housekeeping

.JuliaFormatter.toml

@@ -0,0 +1 @@
+style = "blue"

.github/workflows/Docs.yml

@@ -1,30 +1,37 @@
-name: Docs
+name: Documentation
 
 on:
   push:
     branches:
-      - master
+      - master # update to match your development branch (master, main, dev, trunk, ...)
     tags: '*'
   pull_request:
 
 jobs:
-  docs:
-    name: Documentation
+  build:
+    # These permissions are needed to:
+    # - Deploy the documentation: https://documenter.juliadocs.org/stable/man/hosting/#Permissions
+    # - Delete old caches: https://github.com/julia-actions/cache#usage
+    permissions:
+      actions: write
+      contents: write
+      pull-requests: read
+      statuses: write
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: '1'
-      - name: Install dependencies, build and deploy
+      - uses: julia-actions/cache@v2
+      - name: Install dependencies
+        shell: julia --color=yes --project=docs {0}
         run: |
           using Pkg
           Pkg.develop(PackageSpec(path=pwd()))
           Pkg.instantiate()
-          include(joinpath(pwd(), "docs", "make.jl"))
+      - name: Build and deploy
+        run: julia --color=yes --project=docs docs/make.jl
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
-          GKSwstype: nul # turn off GR's interactive plotting for notebooks
-          JULIA_PKG_SERVER: ''
-        shell: julia --color=yes --project=docs/ {0}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/ci.yml

@@ -20,12 +20,12 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
+      - uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:
@@ -38,6 +38,8 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v5
         with:
-          file: lcov.info
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false

NEWS.md

@@ -6,6 +6,20 @@ between versions, and discuss new features.
 If you find a breaking change this is not reported here, please either raise an issue or
 make a PR to ammend this document.
 
+## 0.9.0
+
+This version is largely a tidying up job. It simplies much of the test suite, bumps the
+required version to Julia LTS. It additionally drops the various ChainRules that were
+implemented, in favour of assuming that users make use of a more powerful AD system than was
+available when this package was originally written. For example, you may wish to make use of
+Mooncake to differentiate code in this package.
+
+### Breaking Changes
+
+Removal of dependency on ChainRulesCore.jl, and associated rules. This means that this
+package almost certainly no longer supports Zygote.jl, but achieves a great reduction in the
+amount of testing which much be performed.
+
 ## 0.8.0
 
 ### Breaking Changes

Project.toml

@@ -1,22 +1,25 @@
 name = "Stheno"
 uuid = "8188c328-b5d6-583d-959b-9690869a5511"
-version = "0.8.2"
+version = "0.9.0"
 
 [deps]
 AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918"
 BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e"
-ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 
 [compat]
-AbstractGPs = "0.4, 0.5"
-BlockArrays = "0.15, 0.16"
-ChainRulesCore = "1"
-KernelFunctions = "0.9.6, 0.10"
-MacroTools = "0.4, 0.5"
-Reexport = "0.2, 1"
-julia = "1.3"
+AbstractGPs = "0.5"
+BlockArrays = "1"
+KernelFunctions = "0.10"
+MacroTools = "0.5"
+Test = "1"
+julia = "1.10"
+
+[extras]
+KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["KernelFunctions", "Test"]

README.md

@@ -242,7 +242,7 @@ See the docs for more examples.
 
 ## Hyperparameter learning and inference
 
-Fortunately, there is really no need for this package to explicitly provide support for hyperparameter optimisation as the functionality is already available elsewhere -- it's sufficient that it plays nicely with other standard packages in the ecosystem such as [Zygote.jl](https://github.com/FluxML/Zygote.jl/) (reverse-mode algorithmic differentiation), [Optim.jl](https://github.com/JuliaNLSolvers/Optim.jl) (non-linear optimisation), [AdvancedHMC.jl](https://github.com/TuringLang/AdvancedHMC.jl/) (Hamiltonian Monte Carlo / NUTS), [ParameterHandling.jl](https://github.com/invenia/ParameterHandling.jl/), [Soss.jl](https://github.com/cscherrer/Soss.jl/) / [Turing.jl](https://github.com/TuringLang/Turing.jl). For concrete examples of the use of each of these packages in conjunction with Stheno, see the `Getting Started` section of the [(dev) docs](https://juliagaussianprocesses.github.io/Stheno.jl/dev).
+Fortunately, there is really no need for this package to explicitly provide support for hyperparameter optimisation as the functionality is already available elsewhere -- it's sufficient that it plays nicely with other standard packages in the ecosystem such as [Mooncake.jl](https://github.com/compintell/Mooncake.jl/) (reverse-mode algorithmic differentiation), [Optim.jl](https://github.com/JuliaNLSolvers/Optim.jl) (non-linear optimisation), [AdvancedHMC.jl](https://github.com/TuringLang/AdvancedHMC.jl/) (Hamiltonian Monte Carlo / NUTS), [ParameterHandling.jl](https://github.com/invenia/ParameterHandling.jl/), [Soss.jl](https://github.com/cscherrer/Soss.jl/) / [Turing.jl](https://github.com/TuringLang/Turing.jl). For concrete examples of the use of each of these packages in conjunction with Stheno, see the `Getting Started` section of the [(dev) docs](https://juliagaussianprocesses.github.io/Stheno.jl/dev).
 
 
 

docs/Project.toml

@@ -4,6 +4,6 @@ Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Stheno = "8188c328-b5d6-583d-959b-9690869a5511"
 
 [compat]
-Documenter = "0.27"
-julia = "1.6"
-Stheno = "0.8"
+Documenter = "1"
+julia = "1.10"
+Pkg = "1"

docs/make.jl

@@ -1,8 +1,7 @@
 using Pkg
-Pkg.develop(path=joinpath(@__DIR__, ".."))
+Pkg.develop(; path=joinpath(@__DIR__, ".."))
 
-using Documenter
-using Stheno
+using Documenter, Stheno
 
 ### Process examples
 
@@ -48,6 +47,7 @@ dev_command = "Pkg.develop(PackageSpec(; path=relpath(\"$(pkgdir(Stheno))\", pwd
 
 let script = "using Pkg; Pkg.activate(ARGS[1]); $dev_command Pkg.instantiate()"
     for example in example_locations
+        @show example
         if !success(`$(Base.julia_cmd()) -e $script $example`)
             error(
                 "project environment of example ",
@@ -75,8 +75,6 @@ end
 # Check that all examples were run successfully
 isempty(processes) || success(processes) || error("some examples were not run successfully")
 
-
-
 ### Build documentation
 DocMeta.setdocmeta!(
     Stheno,
@@ -85,7 +83,7 @@ DocMeta.setdocmeta!(
     recursive=true,
 )
 
-makedocs(
+makedocs(;
     modules=[Stheno],
     format=Documenter.HTML(),
     sitename="Stheno.jl",

examples/getting_started/Project.toml

@@ -1,10 +1,11 @@
 [deps]
 AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918"
 AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
+DifferentiationInterface = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 ParameterHandling = "2412ca09-6db7-441c-8e3a-88d5709968c5"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Stheno = "8188c328-b5d6-583d-959b-9690869a5511"
-Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"