Merge branch 'master' into kx/general-relativistic

xukai92 · web-flow · commit 62077db9a8c2 · 2024-10-26T12:07:24.000-04:00
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -6,42 +6,41 @@ on:
       - master
   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:
   test:
+    # needed to allow julia-actions/cache to delete old caches that it has created
+    permissions:
+      actions: write
+      contents: read
     runs-on: ${{ matrix.os }}
-    continue-on-error: ${{ matrix.version == 'nightly' }}
+    continue-on-error: ${{ matrix.version == 'pre' }}
     strategy:
       matrix:
         version:
-          - '1.6'
+          - 'min'
           - '1'
-          - 'nightly'
+          - 'pre'
         os:
           - ubuntu-latest
           - macOS-latest
           - windows-latest
         arch:
-          - x86
           - x64
-        exclude:
-          - os: ubuntu-latest
-            arch: x86
-          - os: macOS-latest
-            arch: x86
-          - os: windows-latest
-            arch: x86
-          # GitHub Action seems to have issue of running julia-nightly with windows-latest
-          # TODO Revisit in the future
-          - version: 'nightly'
-            os: windows-latest
     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: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
       - name: Run tests
-        uses: julia-actions/julia-runtest@latest
+        uses: julia-actions/julia-runtest@v1
         env:
           AHMC_TEST_GROUP: AdvancedHMC
diff --git a/.github/workflows/ExperimentalTests.yml b/.github/workflows/ExperimentalTests.yml
@@ -6,8 +6,18 @@ on:
       - master
   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:
   test:
+    # needed to allow julia-actions/cache to delete old caches that it has created
+    permissions:
+      actions: write
+      contents: read
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -18,23 +28,16 @@ jobs:
           - macOS-latest
           - windows-latest
         arch:
-          - x86
           - x64
-        exclude:
-          - os: ubuntu-latest
-            arch: x86
-          - os: macOS-latest
-            arch: x86
-          - os: windows-latest
-            arch: x86
     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: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
       - name: Run integration tests
-        uses: julia-actions/julia-runtest@latest
+        uses: julia-actions/julia-runtest@v1
         env:
           AHMC_TEST_GROUP: Experimental
diff --git a/.github/workflows/Format.yml b/.github/workflows/Format.yml
@@ -5,7 +5,6 @@ on:
   push:
     branches:
       - master
-      - main
 
 concurrency:
   # Skip intermediate builds: always.
@@ -17,8 +16,8 @@ jobs:
   format:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: 1
       - name: Format code
diff --git a/.github/workflows/IntegrationTests.yml b/.github/workflows/IntegrationTests.yml
@@ -6,8 +6,18 @@ on:
       - master
   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:
   test:
+    # needed to allow julia-actions/cache to delete old caches that it has created
+    permissions:
+      actions: write
+      contents: read
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -18,23 +28,16 @@ jobs:
           - macOS-latest
           - windows-latest
         arch:
-          - x86
           - x64
-        exclude:
-          - os: ubuntu-latest
-            arch: x86
-          - os: macOS-latest
-            arch: x86
-          - os: windows-latest
-            arch: x86
     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: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
       - name: Run integration tests
-        uses: julia-actions/julia-runtest@latest
+        uses: julia-actions/julia-runtest@v1
         env:
           AHMC_TEST_GROUP: Downstream
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -9,12 +9,14 @@ on:
 
 jobs:
   build:
+    permissions:
+      statuses: write # Used to report documentation build statuses
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
-          version: '1.7'
+          version: '1'
       - name: Install dependencies
         run: julia --project=docs/ -e '
               using Pkg; 
@@ -24,4 +26,3 @@ jobs:
         env:
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
         run: julia --project=docs/ docs/make.jl
-
diff --git a/Project.toml b/Project.toml
@@ -1,6 +1,6 @@
 name = "AdvancedHMC"
 uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-version = "0.6.1"
+version = "0.6.2"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
@@ -31,7 +31,7 @@ AdvancedHMCMCMCChainsExt = "MCMCChains"
 AdvancedHMCOrdinaryDiffEqExt = "OrdinaryDiffEq"
 
 [compat]
-AbstractMCMC = "4.2, 5"
+AbstractMCMC = "5"
 AdaptiveRejectionSampling = "0.1.1"
 ArgCheck = "1, 2"
 CUDA = "3, 4, 5"
@@ -50,7 +50,9 @@ SimpleUnPack = "1.1"
 Statistics = "1.6"
 StatsBase = "0.31, 0.32, 0.33, 0.34"
 StatsFuns = "0.8, 0.9, 1"
-julia = "1.6"
+LinearAlgebra = "1.6"
+Random = "1.6"
+julia = "1.6.7"
 
 [extras]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
diff --git a/README.md b/README.md
@@ -128,7 +128,7 @@ samples = AbstractMCMC.sample(
       model,
       sampler,
       n_adapts + n_samples;
-      nadapts = n_adapts,
+      n_adapts = n_adapts,
       initial_params = initial_θ,
   )
 ```
diff --git a/src/abstractmcmc.jl b/src/abstractmcmc.jl
@@ -47,6 +47,14 @@ function AbstractMCMC.sample(
     callback = nothing,
     kwargs...,
 )
+    if haskey(kwargs, :nadapts)
+        throw(
+            ArgumentError(
+                "keyword argument `nadapts` is unsupported. Please use `n_adapts` to specify the number of adaptation steps.",
+            ),
+        )
+    end
+
     if callback === nothing
         callback = HMCProgressCallback(N, progress = progress, verbose = verbose)
         progress = false # don't use AMCMC's progress-funtionality
@@ -78,6 +86,13 @@ function AbstractMCMC.sample(
     callback = nothing,
     kwargs...,
 )
+    if haskey(kwargs, :nadapts)
+        throw(
+            ArgumentError(
+                "keyword argument `nadapts` is unsupported. Please use `n_adapts` to specify the number of adaptation steps.",
+            ),
+        )
+    end
 
     if callback === nothing
         callback = HMCProgressCallback(N, progress = progress, verbose = verbose)
@@ -141,8 +156,17 @@ function AbstractMCMC.step(
     model::AbstractMCMC.LogDensityModel,
     spl::AbstractHMCSampler,
     state::HMCState;
+    n_adapts::Int = 0,
     kwargs...,
 )
+    if haskey(kwargs, :nadapts)
+        throw(
+            ArgumentError(
+                "keyword argument `nadapts` is unsupported. Please use `n_adapts` to specify the number of adaptation steps.",
+            ),
+        )
+    end
+
     # Compute transition.
     i = state.i + 1
     t_old = state.transition
@@ -158,7 +182,6 @@ function AbstractMCMC.step(
 
     # Adapt h and spl.
     tstat = stat(t)
-    n_adapts = kwargs[:n_adapts]
     h, κ, isadapted = adapt!(h, κ, adaptor, i, n_adapts, t.z.θ, tstat.acceptance_rate)
     tstat = merge(tstat, (is_adapt = isadapted,))
 
@@ -189,8 +212,8 @@ struct HMCProgressCallback{P}
     "If `progress` is not specified and this is `true` some information will be logged upon completion of adaptation."
     verbose::Bool
     "Number of divergent transitions fo far."
-    num_divergent_transitions::Ref{Int}
-    num_divergent_transitions_during_adaption::Ref{Int}
+    num_divergent_transitions::Base.RefValue{Int}
+    num_divergent_transitions_during_adaption::Base.RefValue{Int}
 end
 
 function HMCProgressCallback(n_samples; progress = true, verbose = false)
@@ -200,7 +223,16 @@ function HMCProgressCallback(n_samples; progress = true, verbose = false)
     HMCProgressCallback(pm, progress, verbose, Ref(0), Ref(0))
 end
 
-function (cb::HMCProgressCallback)(rng, model, spl, t, state, i; nadapts = 0, kwargs...)
+function (cb::HMCProgressCallback)(
+    rng,
+    model,
+    spl,
+    t,
+    state,
+    i;
+    n_adapts::Int = 0,
+    kwargs...,
+)
     progress = cb.progress
     verbose = cb.verbose
     pm = cb.pm
@@ -243,8 +275,8 @@ function (cb::HMCProgressCallback)(rng, model, spl, t, state, i; nadapts = 0, kw
             ),
         )
         # Report finish of adapation
-    elseif verbose && isadapted && i == nadapts
-        @info "Finished $nadapts adapation steps" adaptor κ.τ.integrator metric
+    elseif verbose && isadapted && i == n_adapts
+        @info "Finished $(n_adapts) adapation steps" adaptor κ.τ.integrator metric
     end
 end
 
diff --git a/test/abstractmcmc.jl b/test/abstractmcmc.jl
@@ -32,6 +32,30 @@ using Statistics: mean
         verbose = false,
     )
 
+    # Error if keyword argument `nadapts` is used
+    @test_throws ArgumentError AbstractMCMC.sample(
+        rng,
+        model,
+        nuts,
+        n_adapts + n_samples;
+        nadapts = n_adapts,
+        initial_params = θ_init,
+        progress = false,
+        verbose = false,
+    )
+    @test_throws ArgumentError AbstractMCMC.sample(
+        rng,
+        model,
+        nuts,
+        MCMCThreads(),
+        n_adapts + n_samples,
+        2;
+        nadapts = n_adapts,
+        initial_params = θ_init,
+        progress = false,
+        verbose = false,
+    )
+
     # Transform back to original space.
     # NOTE: We're not correcting for the `logabsdetjac` here since, but
     # we're only interested in the mean it doesn't matter.
diff --git a/test/mcmcchains.jl b/test/mcmcchains.jl
@@ -23,7 +23,7 @@ using Statistics: mean
         model,
         sampler,
         n_adapts + n_samples;
-        nadapts = n_adapts,
+        n_adapts = n_adapts,
         initial_params = θ_init,
         chain_type = Chains,
         progress = false,

Original file line number	Diff line number	Diff line change
`@@ -128,7 +128,7 @@ samples = AbstractMCMC.sample(`
`128`	`128`	`model,`
`129`	`129`	`sampler,`
`130`	`130`	`n_adapts + n_samples;`
`131`		`- nadapts = n_adapts,`
	`131`	`+ n_adapts = n_adapts,`
`132`	`132`	`initial_params = initial_θ,`
`133`	`133`	`)`
`134`	`134`	```