Merge branch 'main' into compathelper/new_version/2024-09-19-01-00-46…

…-351-01475325828

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/CI.yml

@@ -39,16 +39,18 @@ jobs:
         with:
           distribution: 'temurin'
           java-version: '11'
-      - uses: julia-actions/setup-julia@latest
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
       - uses: julia-actions/cache@v2
-      - uses: julia-actions/julia-buildpkg@latest
-      - uses: julia-actions/julia-runtest@latest
-      - uses: julia-actions/julia-processcoverage@latest
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v4
         with:
-          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false  # or true if you want CI to fail when Codecov fails
+          file: lcov.info
 
 
   # test OpenMPI by requesting it with MPIPreferences
@@ -71,7 +73,7 @@ jobs:
     - name: Checkout
       uses: actions/checkout@v4
 
-    - uses: julia-actions/setup-julia@latest
+    - uses: julia-actions/setup-julia@v2
       with:
         version: ${{ matrix.version }}
     - uses: julia-actions/cache@v2
@@ -85,7 +87,7 @@ jobs:
         MPIPreferences.use_jll_binary("OpenMPI_jll")
         rm("test/Manifest.toml")
 
-    - uses: julia-actions/julia-runtest@latest
+    - uses: julia-actions/julia-runtest@v1
 
 
   # # CI is getting too slow! 
@@ -98,7 +100,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1'
+          - '1.10'
         os:
           - macos-13
         mpi:
@@ -119,7 +121,7 @@ jobs:
           distribution: 'temurin'
           java-version: '11'
 
-      - uses: julia-actions/setup-julia@latest
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
 
@@ -137,7 +139,7 @@ jobs:
           run(`sed -i.bu 's/unknown/MPICH/' test/LocalPreferences.toml`) # fix wrong abi detection for mpich
           rm("test/Manifest.toml")
       
-      - uses: julia-actions/julia-runtest@latest
+      - uses: julia-actions/julia-runtest@v1
 
 
   docs:
@@ -151,11 +153,11 @@ jobs:
         with:
           distribution: 'temurin'
           java-version: '11'
-      - uses: julia-actions/setup-julia@latest
+      - uses: julia-actions/setup-julia@v2
         with:
-          version: '1.9'
-      - uses: julia-actions/julia-buildpkg@latest
-      - uses: julia-actions/julia-docdeploy@latest
+          version: '1.10'
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-docdeploy@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - run: |

.github/workflows/CompatHelper.yml

@@ -15,7 +15,7 @@ jobs:
         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
+        uses: julia-actions/setup-julia@v2
         with:
           version: '1'
           arch: ${{ runner.arch }}

CONTRIBUTING.md

@@ -0,0 +1,22 @@
+# Contributing Guide
+
+Thank you for your interest in contributing to Pigeons.jl! There are multiple ways to contribute, and we appreciate all contributions.
+
+## Ways to Contribute
+
+### Bug Reports and Feature Requests
+
+If you are working with Pigeons, and run into a bug, or require additional features, we definitely want to know about it. Please let us know by creating a [GitHub Issue](https://github.com/PigeonsAD/Pigeons.jl/issues).
+
+### How to Submit a Pull Request
+
+If you would like to contribute, please feel free to open a pull request. The pull request should:
+
+- Include a small unit test
+- Not contain any unrelated changes
+- Be an isolated change. Independent changes should be submitted as separate pull requests as this makes reviewing easier.
+
+## Code of Conduct
+
+As a Julia Project we expect all participants to abide by the [Julia Community Standards](https://julialang.org/community/standards/).
+

Project.toml

@@ -1,7 +1,7 @@
 name = "Pigeons"
 uuid = "0eb8d820-af6a-4919-95ae-11206f830c31"
 authors = ["Alexandre Bouchard-Côté <[email protected]>, Nikola Surjanovic <[email protected]>, Paul Tiede <[email protected]>, Trevor Campbell, Miguel Biron-Lattes, Saifuddin Syed"]
-version = "0.4.5"
+version = "0.4.7"
 
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
@@ -59,7 +59,7 @@ BridgeStan = "2"
 DataFrames = "1"
 Distributions = "0.25"
 DocStringExtensions = "0.9"
-DynamicPPL = "0.23, 0.24, 0.25, 0.26, 0.27, 0.28"
+DynamicPPL = "0.23, 0.24, 0.25, 0.26, 0.27, 0.28, 0.30"
 Enzyme = "0.12, 0.13"
 Expect = "0.3"
 FillArrays = "1"

docs/make.jl

@@ -72,6 +72,7 @@ InferenceReport.headless() do
             "More on distributed PT" => "distributed.md",
             "Interfaces" => Pigeons.informal_doc(@__DIR__, Pigeons),
             "Reference" => "reference.md",
+            "About Us" => "about-us.md",
             "Google Summer of Code" => "gsoc.md"
         ],
     )

docs/src/about-us.md

@@ -0,0 +1,103 @@
+```@meta
+CurrentModule = Pigeons
+```
+# [The Pigeons Team - About Us](@id about)
+
+Planning for the Pigeons project started taking place in the summer of 2022. 
+Since then, we have grown as a team and have added various features to the software. 
+We still have great ambitions and a swath of features to add; if you would like 
+to become a part of our team feel free to reach out!
+
+## Team Members (chronological order)
+
+```@raw html
+<div style="display: flex; align-items: center; margin-bottom: 20px;">
+    <img src="https://raw.githubusercontent.com/Julia-Tempering/Pigeons.jl/27ee86b8e0827ba9e7eead6374960ba8673e1006/docs/img/alex.png" alt="Alexandre Bouchard-Côté" style="width: 100px; height: 100px; border-radius: 50%; margin-right: 20px;">
+    <div>
+        <b>Alexandre Bouchard-Côté</b>
+        </br>
+        University of British Columbia 
+    </div>
+</div>
+
+<div style="display: flex; align-items: center; margin-bottom: 20px;">
+    <img src="https://raw.githubusercontent.com/Julia-Tempering/Pigeons.jl/27ee86b8e0827ba9e7eead6374960ba8673e1006/docs/img/nikola.jpg" alt="Nikola Surjanovic" style="width: 100px; height: 100px; border-radius: 50%; margin-right: 20px;">
+    <div>
+        <b>Nikola Surjanovic</b>
+        </br>
+        University of British Columbia 
+    </div>
+</div>
+
+<div style="display: flex; align-items: center; margin-bottom: 20px;">
+    <img src="https://raw.githubusercontent.com/Julia-Tempering/Pigeons.jl/27ee86b8e0827ba9e7eead6374960ba8673e1006/docs/img/paul.jpg" alt="Paul Tiede" style="width: 100px; height: 100px; border-radius: 50%; margin-right: 20px;">
+    <div>
+        <b>Paul Tiede</b>
+        </br>
+        Harvard University, Event Horizon Telescope
+    </div>
+</div>
+
+<div style="display: flex; align-items: center; margin-bottom: 20px;">
+    <img src="https://raw.githubusercontent.com/Julia-Tempering/Pigeons.jl/27ee86b8e0827ba9e7eead6374960ba8673e1006/docs/img/saif.jpg" alt="Saifuddin Syed" style="width: 100px; height: 100px; border-radius: 50%; margin-right: 20px;">
+    <div>
+        <b>Saifuddin Syed</b>
+        </br>
+        University of Oxford 
+    </div>
+</div>
+
+<div style="display: flex; align-items: center; margin-bottom: 20px;">
+    <img src="https://raw.githubusercontent.com/Julia-Tempering/Pigeons.jl/27ee86b8e0827ba9e7eead6374960ba8673e1006/docs/img/trevor.jpg" alt="Trevor Campbell" style="width: 100px; height: 100px; border-radius: 50%; margin-right: 20px;">
+    <div>
+        <b>Trevor Campbell</b>
+        </br>
+        University of British Columbia 
+    </div>
+</div>
+
+<div style="display: flex; align-items: center; margin-bottom: 20px;">
+    <img src="https://raw.githubusercontent.com/Julia-Tempering/Pigeons.jl/27ee86b8e0827ba9e7eead6374960ba8673e1006/docs/img/miguel.jpg" alt="Miguel Biron-Lattes" style="width: 100px; height: 100px; border-radius: 50%; margin-right: 20px;">
+    <div>
+        <b>Miguel Biron-Lattes</b>
+        </br>
+        University of British Columbia 
+    </div>
+</div>
+
+<div style="display: flex; align-items: center; margin-bottom: 20px;">
+    <img src="https://raw.githubusercontent.com/Julia-Tempering/Pigeons.jl/27ee86b8e0827ba9e7eead6374960ba8673e1006/docs/img/william.png" alt="William Thompson" style="width: 100px; height: 100px; border-radius: 50%; margin-right: 20px;">
+    <div>
+        <b>William Thompson</b>
+        </br>
+        Herzberg Astronomy and Astrophysics Research Centre
+    </div>
+</div>
+
+<div style="display: flex; align-items: center; margin-bottom: 20px;">
+    <img src="https://raw.githubusercontent.com/Julia-Tempering/Pigeons.jl/27ee86b8e0827ba9e7eead6374960ba8673e1006/docs/img/yujia.jpg" alt="Yujia Ma" style="width: 100px; height: 100px; border-radius: 50%; margin-right: 20px;">
+    <div>
+        <b>Yujia Ma</b>
+        </br>
+        University of British Columbia 
+    </div>
+</div>
+
+<div style="display: flex; align-items: center; margin-bottom: 20px;">
+    <img src="https://raw.githubusercontent.com/Julia-Tempering/Pigeons.jl/27ee86b8e0827ba9e7eead6374960ba8673e1006/docs/img/lucas.jpg" alt="Lucas Wong" style="width: 100px; height: 100px; border-radius: 50%; margin-right: 20px;">
+    <div>
+        <b>Lucas Wong</b>
+        </br>
+        University of British Columbia 
+    </div>
+</div>
+
+<div style="display: flex; align-items: center; margin-bottom: 20px;">
+    <img src="https://raw.githubusercontent.com/Julia-Tempering/Pigeons.jl/27ee86b8e0827ba9e7eead6374960ba8673e1006/docs/img/son.jpg" alt="Son Luu" style="width: 100px; height: 100px; border-radius: 50%; margin-right: 20px;">
+    <div>
+        <b>Son Luu</b>
+        </br>
+        University of British Columbia 
+    </div>
+</div>
+```

ext/PigeonsEnzymeExt/PigeonsEnzymeExt.jl

@@ -13,26 +13,32 @@ else
     using ..LogDensityProblemsAD
 end
 
-# TODO: currently, the concrete versions of ADGradientWrapper are defined only
-# in the extensions of LogDensityProblemsAD. Therefore, it is impossible to 
-# dispatch on them; see 
-#   https://github.com/tpapp/LogDensityProblemsAD.jl/issues/32
-# This is a HACK to extract that type 
-const EnzymeGradientLogDensity = if isdefined(Base, :get_extension)
-    Base.get_extension(LogDensityProblemsAD, :LogDensityProblemsADEnzymeExt).EnzymeGradientLogDensity
-else
-    LogDensityProblemsAD.LogDensityProblemsADEnzymeExt.EnzymeGradientLogDensity
+# A simpler version of the wrapper defined in LogDensityProblemsAD's extension
+struct EnzymeWrapper{TLP} <: Pigeons.ADWrapper
+    log_potential::TLP
+end
+
+# special ADgradient constructor for Enzyme
+function LogDensityProblemsAD.ADgradient(
+    kind::Val{:Enzyme}, 
+    log_potential, 
+    buffers::Pigeons.Augmentation
+    )
+    d = LogDensityProblems.dimension(log_potential)
+    buffer = Pigeons.get_buffer(buffers, :gradient_buffer, d)
+    enclosed = EnzymeWrapper(log_potential)
+    Pigeons.BufferedAD(enclosed, buffer, nothing, nothing)
 end
 
 # adapted from LogDensityProblemsAD to use the Replica's buffer
 function LogDensityProblems.logdensity_and_gradient(
-    b::Pigeons.BufferedAD{<:EnzymeGradientLogDensity},
+    b::Pigeons.BufferedAD{<:EnzymeWrapper},
     x::AbstractVector
     )
     ∂ℓ_∂x = fill!(b.buffer, zero(eltype(b.buffer))) # NB: Enzyme gives erroneous answer if buffer is not zeroed first
     _, y = Enzyme.autodiff(
         Enzyme.ReverseWithPrimal, LogDensityProblems.logdensity, Enzyme.Active,
-        Enzyme.Const(b.enclosed.ℓ), Enzyme.Duplicated(x, ∂ℓ_∂x)
+        Enzyme.Const(b.enclosed.log_potential), Enzyme.Duplicated(x, ∂ℓ_∂x)
     )
     y, ∂ℓ_∂x
 end

ext/PigeonsForwardDiffExt/PigeonsForwardDiffExt.jl

@@ -15,15 +15,10 @@ else
     import ..ForwardDiff: DiffResults
 end
 
-# TODO: currently, the concrete versions of ADGradientWrapper are defined only
-# in the extensions of LogDensityProblemsAD. Therefore, it is impossible to 
-# dispatch on them; see 
-#   https://github.com/tpapp/LogDensityProblemsAD.jl/issues/32
-# This is a HACK to extract that type 
-const ForwardDiffLogDensity = if isdefined(Base, :get_extension)
-    Base.get_extension(LogDensityProblemsAD, :LogDensityProblemsADForwardDiffExt).ForwardDiffLogDensity
-else
-    LogDensityProblemsAD.LogDensityProblemsADForwardDiffExt.ForwardDiffLogDensity
+# A simpler version of the wrapper defined in LogDensityProblemsAD's extension
+struct ForwardDiffWrapper{TLP, TGC <: ForwardDiff.GradientConfig} <: Pigeons.ADWrapper
+    log_potential::TLP
+    gradient_config::TGC
 end
 
 # special ADgradient constructor for ForwardDiff
@@ -33,21 +28,22 @@ function LogDensityProblemsAD.ADgradient(
     buffers::Pigeons.Augmentation
     )
     d = LogDensityProblems.dimension(log_potential)
-    buffer = Pigeons.get_buffer(buffers, :gradient_buffer, d) 
-    enclosed = ADgradient(kind, log_potential; x = buffer)
+    buffer = Pigeons.get_buffer(buffers, :gradient_buffer, d)
+    lp_fix = Base.Fix1(LogDensityProblems.logdensity, log_potential)
+    gradient_config = ForwardDiff.GradientConfig(lp_fix, buffer, ForwardDiff.Chunk(d))
+    enclosed = ForwardDiffWrapper(log_potential, gradient_config)
     diff_result = DiffResults.MutableDiffResult(zero(eltype(buffer)), (buffer, ))
     Pigeons.BufferedAD(enclosed, diff_result, nothing, nothing)
 end
 
 # adapted from LogDensityProblemsAD to use the Replica's buffer
 function LogDensityProblems.logdensity_and_gradient(
-    b::Pigeons.BufferedAD{<:ForwardDiffLogDensity},
+    b::Pigeons.BufferedAD{<:ForwardDiffWrapper},
     x::AbstractVector
     )
     diff_result = b.buffer
-    ℓ_fix = Base.Fix1(LogDensityProblems.logdensity, b.enclosed.ℓ)
-    ForwardDiff.gradient!(diff_result, ℓ_fix, x, b.enclosed.gradient_config)
-
+    lp_fix = Base.Fix1(LogDensityProblems.logdensity, b.enclosed.log_potential)
+    ForwardDiff.gradient!(diff_result, lp_fix, x, b.enclosed.gradient_config)
     return (DiffResults.value(diff_result), DiffResults.gradient(diff_result))
 end