Merge branch 'main' into ah-grammar

Author: penelopeysm

.github/workflows/create_release.yml

@@ -23,9 +23,6 @@ jobs:
 
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
-        with:
-          # Needs Quarto 1.6 (which is currently a pre-release version) to fix #533
-          version: pre-release
 
       - name: Restore cached _freeze folder
         id: cache-restore

Manifest.toml

@@ -3,23 +3,18 @@ ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
 AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918"
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
 AbstractPPL = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf"
-AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
 AdvancedMH = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170"
 AdvancedVI = "b5ca4192-6429-45e5-a2d9-87aec30a685c"
 Bijectors = "76274a88-744f-5084-9051-94815aaf08c4"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
+Chairmarks = "0ca39b1e-fe0b-4e98-acfc-b1656634c4de"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-DelayDiffEq = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
-DistributionsAD = "ced4e74d-a319-5a8a-b0ac-84af2272839c"
 DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb"
 DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
-Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
 GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
@@ -29,31 +24,31 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LogDensityProblems = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c"
 LogDensityProblemsAD = "996a588d-648d-4e1f-a8f0-a84b347e47b1"
 LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
+Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 Lux = "b2108857-7c20-44ae-9111-449ecde12c47"
 MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
 MLDataUtils = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d"
 MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 Measures = "442fdcdd-2543-5da2-b0f3-8c86c306513e"
-Memoization = "6fafb56a-5788-4b4e-91ca-c0cea6611c73"
 Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
 NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
 Optimisers = "3bd65402-5787-11e9-1adc-39752487f4e2"
-Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
 OptimizationNLopt = "4e6fcdb7-1186-4e1f-a706-475e75c168bb"
 OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
 PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
 SciMLSensitivity = "1ed8b502-d754-442c-8d5d-10ac956f44a1"
+StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
 StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd"
 Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 
 [compat]
-Turing = "0.40"
+Turing = "0.41"

Project.toml

@@ -1,3 +1,11 @@
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="https://turinglang.org/assets/logo/turing-logo-dark.svg">
+    <img src="https://turinglang.org/assets/logo/turing-logo-light.svg" alt="Turing.jl logo" width="300">
+  </picture>
+</p>
+<p align="center"><i>Bayesian inference with probabilistic programming</i></p>
+
 # Turing.jl Documentation and Tutorials
 
 **https://turinglang.org/docs/**

README.md

@@ -0,0 +1,4 @@
+logo:
+  medium:
+    light: https://turinglang.org/assets/logo/turing-logo-light.svg
+    dark: https://turinglang.org/assets/logo/turing-logo-dark.svg

_brand.yml

@@ -0,0 +1,45 @@
+<footer class="custom-footer">
+  <div class="footer-container">
+    <div class="footer-grid">
+      <div class="footer-links-wrapper">
+        <div class="footer-column footer-explore">
+          <h5>Explore</h5>
+          <a href="https://turinglang.org/docs/getting-started/">Get Started</a>
+          <a href="https://turinglang.org/docs/tutorials/">Tutorials</a>
+          <a href="https://turinglang.org/docs/faq/">FAQ</a>
+          <a href="https://turinglang.org/library/">Libraries</a>
+          <a href="https://turinglang.org/news/">News</a>
+          <a href="https://turinglang.org/team/">Team</a>
+        </div>
+
+        <div class="footer-column footer-connect">
+          <h5>Connect</h5>
+          <a href="https://github.com/TuringLang" target="_blank" rel="noopener"><i class="bi bi-github"></i> GitHub</a>
+          <a href="https://x.com/TuringLang" target="_blank" rel="noopener"><i class="bi bi-twitter-x"></i> Twitter</a>
+          <a href="https://julialang.slack.com/archives/CCYDC34A0" target="_blank" rel="noopener"><i class="bi bi-slack"></i> Slack</a>
+          <a href="https://discourse.julialang.org/c/domain/probprog/48" target="_blank" rel="noopener"><i class="bi bi-chat-dots"></i> Discourse</a>
+        </div>
+      </div>
+
+      <div class="footer-column footer-brands">
+        <h5>Supported by leading researchers</h5>
+        <p>Turing.jl is developed by researchers and engineers at the following research institutions.</p>
+        <div class="logo-grid">
+          <a href="https://mlg.eng.cam.ac.uk/" class="partner-logo" target="_blank" rel="noopener">
+            <img src="/assets/images/brands/university-cambridge-logo-black-example-640x132.png" alt="University of Cambridge Logo" class="brands-light-mode-logo">
+            <img src="/assets/images/brands/university-cambridge-logo-white-example-640x133.png" alt="University of Cambridge Logo Dark" class="brands-dark-mode-logo">
+          </a>
+          <a href="https://www.turing.ac.uk/" class="partner-logo" target="_blank" rel="noopener">
+            <img src="/assets/images/brands/Turing_Logo_1000x400px_Black.webp" alt="The Alan Turing Institute Logo" class="brands-light-mode-logo">
+            <img src="/assets/images/brands/Turing_Logo_1000x400px_White.webp" alt="The Alan Turing Institute Logo Dark" class="brands-dark-mode-logo">
+          </a>
+        </div>
+      </div>
+
+    </div>
+    <div class="footer-bottom">
+      <p>Turing.jl was created by <a href="https://mlg.eng.cam.ac.uk/hong/" target="_blank" rel="noopener">Hong Ge</a>, and maintained by the core <a href="https://turinglang.org/team/" target="_blank" rel="noopener">team</a> of developers and <a href="https://github.com/TuringLang/Turing.jl/graphs/contributors" target="_blank" rel="noopener">contributors</a>.<br>© 2025 The Turing Project Contributors. <a href="https://github.com/TuringLang/Turing.jl/blob/master/LICENCE" target="_blank" rel="noopener">MIT License</a>.</p>
+      <a href="https://github.com/TuringLang/docs/" target="_blank" rel="noopener" class="footer-source-link"><i class="bi bi-github"></i> Website Source</a>
+    </div>
+  </div>
+</footer>

_includes/footer.html

@@ -26,7 +26,7 @@ website:
     location: navbar
     type: overlay
   navbar:
-    logo: "/assets/images/turing-logo.svg"
+    title: false
     logo-href: https://turinglang.org/
     left:
       - text: Get Started
@@ -43,7 +43,7 @@ website:
         href: https://turinglang.org/team/
     right:
       # Current version
-      - text: "v0.40"
+      - text: "v0.41"
         menu:
           - text: Changelog
             href: https://turinglang.org/docs/changelog.html
@@ -117,6 +117,11 @@ website:
               - developers/compiler/minituring-contexts/index.qmd
               - developers/compiler/design-overview/index.qmd
 
+          - section: "DynamicPPL Models"
+            collapse-level: 1
+            contents:
+              - developers/models/varinfo-overview/index.qmd
+
           - section: "DynamicPPL Contexts"
             collapse-level: 1
             contents:
@@ -167,52 +172,7 @@ format:
             }
           </style>
     include-after-body:
-      - text: |
-          <footer class="custom-footer">
-            <div class="footer-container">
-              <div class="footer-grid">
-                <div class="footer-links-wrapper">
-                  <div class="footer-column footer-explore">
-                    <h5>Explore</h5>
-                    <a href="https://turinglang.org/docs/getting-started/">Get Started</a>
-                    <a href="https://turinglang.org/docs/tutorials/">Tutorials</a>
-                    <a href="https://turinglang.org/docs/faq/">FAQ</a>
-                    <a href="https://turinglang.org/library/">Libraries</a>
-                    <a href="https://turinglang.org/news/">News</a>
-                    <a href="https://turinglang.org/team/">Team</a>
-                  </div>
-
-                  <div class="footer-column footer-connect">
-                    <h5>Connect</h5>
-                    <a href="https://github.com/TuringLang" target="_blank" rel="noopener"><i class="bi bi-github"></i> GitHub</a>
-                    <a href="https://x.com/TuringLang" target="_blank" rel="noopener"><i class="bi bi-twitter-x"></i> Twitter</a>
-                    <a href="https://julialang.slack.com/archives/CCYDC34A0" target="_blank" rel="noopener"><i class="bi bi-slack"></i> Slack</a>
-                    <a href="https://discourse.julialang.org/c/domain/probprog/48" target="_blank" rel="noopener"><i class="bi bi-chat-dots"></i> Discourse</a>
-                  </div>
-                </div>
-
-                <div class="footer-column footer-brands">
-                  <h5>Supported by leading researchers</h5>
-                  <p>Turing.jl is developed by researchers and engineers at the following research institutions.</p>
-                  <div class="logo-grid">
-                    <a href="https://mlg.eng.cam.ac.uk/" class="partner-logo" target="_blank" rel="noopener">
-                      <img src="/assets/images/brands/university-cambridge-logo-black-example-640x132.png" alt="University of Cambridge Logo" class="brands-light-mode-logo">
-                      <img src="/assets/images/brands/university-cambridge-logo-white-example-640x133.png" alt="University of Cambridge Logo Dark" class="brands-dark-mode-logo">
-                    </a>
-                    <a href="https://www.turing.ac.uk/" class="partner-logo" target="_blank" rel="noopener">
-                      <img src="/assets/images/brands/Turing_Logo_1000x400px_Black.webp" alt="The Alan Turing Institute Logo" class="brands-light-mode-logo">
-                      <img src="/assets/images/brands/Turing_Logo_1000x400px_White.webp" alt="The Alan Turing Institute Logo Dark" class="brands-dark-mode-logo">
-                    </a>
-                  </div>
-                </div>
-
-              </div>
-              <div class="footer-bottom">
-                <p>Turing.jl was created by <a href="https://mlg.eng.cam.ac.uk/hong/" target="_blank" rel="noopener">Hong Ge</a>, and maintained by the core <a href="https://turinglang.org/team/" target="_blank" rel="noopener">team</a> of developers and <a href="https://github.com/TuringLang/Turing.jl/graphs/contributors" target="_blank" rel="noopener">contributors</a>.<br>© 2025 The Turing Project Contributors. <a href="https://github.com/TuringLang/Turing.jl/blob/master/LICENCE" target="_blank" rel="noopener">MIT Licence</a>.</p>
-                <a href="https://github.com/TuringLang/docs/" target="_blank" rel="noopener" class="footer-source-link"><i class="bi bi-github"></i> Website Source</a>
-              </div>
-            </div>
-          </footer>
+      file: _includes/footer.html
 
 execute:
   echo: true
@@ -267,3 +227,4 @@ dev-transforms-distributions: developers/transforms/distributions
 dev-transforms-bijectors: developers/transforms/bijectors
 dev-transforms-dynamicppl: developers/transforms/dynamicppl
 dev-contexts-submodel-condition: developers/contexts/submodel-condition
+dev-models-varinfo-overview: developers/models/varinfo-overview

_quarto.yml

@@ -36,6 +36,7 @@ The following are the main jobs of the `@model` macro:
 
 ## The model
 
+<!-- Very outdated
 A `model::Model` is a callable struct that one can sample from by calling
 
 ```{julia}
@@ -273,4 +274,4 @@ Note that in order to make `md::Metadata` type stable, all the `md.vns` must hav
 
 However, in `Turing` models one cannot have this restriction, so we must use a type unstable `Metadata` if we want to use one `Metadata` instance for the whole model. This is what `UntypedVarInfo` does. A type unstable `Metadata` will still work but will have inferior performance.
 
-To strike a balance between flexibility and performance when constructing the `spl::Sampler` instance, the model is first run by sampling the parameters in `P` from their priors using an `UntypedVarInfo`, i.e. a type unstable `Metadata` is used for all the variables. Then once all the symbols and distribution types have been identified, a `vi::TypedVarInfo` is constructed where `vi.metadata` is a `NamedTuple` mapping each symbol in `P` to a specialized instance of `Metadata`. So as long as each symbol in `P` is sampled from only one type of distributions, `vi::TypedVarInfo` will have fully concretely typed fields which brings out the peak performance of Julia.
+To strike a balance between flexibility and performance when constructing the `spl::Sampler` instance, the model is first run by sampling the parameters in `P` from their priors using an `UntypedVarInfo`, i.e. a type unstable `Metadata` is used for all the variables. Then once all the symbols and distribution types have been identified, a `vi::TypedVarInfo` is constructed where `vi.metadata` is a `NamedTuple` mapping each symbol in `P` to a specialized instance of `Metadata`. So as long as each symbol in `P` is sampled from only one type of distributions, `vi::TypedVarInfo` will have fully concretely typed fields which brings out the peak performance of Julia.

developers/compiler/design-overview/index.qmd

@@ -102,19 +102,14 @@ We begin by mentioning some high-level desiderata for their joint behaviour.
 Take these models, for example:
 
 ```{julia}
-# We define a helper function to unwrap a layer of SamplingContext, to
-# avoid cluttering the print statements.
-unwrap_sampling_context(ctx::DynamicPPL.SamplingContext) = ctx.context
-unwrap_sampling_context(ctx::DynamicPPL.AbstractContext) = ctx
-
 @model function inner()
-    println("inner context: $(unwrap_sampling_context(__model__.context))")
+    println("inner context: $(__model__.context)")
     x ~ Normal()
     return y ~ Normal()
 end
 
 @model function outer()
-    println("outer context: $(unwrap_sampling_context(__model__.context))")
+    println("outer context: $(__model__.context)")
     return a ~ to_submodel(inner())
 end
 
@@ -124,7 +119,7 @@ with_outer_cond = outer() | (@varname(a.x) => 1.0)
 # 'Inner conditioning'
 inner_cond = inner() | (@varname(x) => 1.0)
 @model function outer2()
-    println("outer context: $(unwrap_sampling_context(__model__.context))")
+    println("outer context: $(__model__.context)")
     return a ~ to_submodel(inner_cond)
 end
 with_inner_cond = outer2()