From 54f23e3ae4a672ba2f08d0df34ac7e5a3bd2d9f6 Mon Sep 17 00:00:00 2001
From: Aoife <aoife1hughes@gmail.com>
Date: Thu, 18 Sep 2025 13:31:38 +0100
Subject: [PATCH 01/23] Add download button for Jupyter notebooks in tutorial
 pages

---
 .github/workflows/publish.yml    |  2 +-
 .gitignore                       |  3 +-
 _includes/download-notebook.html | 56 ++++++++++++++++++++++++++++++++
 _quarto.yml                      |  6 ++++
 4 files changed, 65 insertions(+), 2 deletions(-)
 create mode 100644 _includes/download-notebook.html

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 5cb81b4f0..c13c570e6 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -83,7 +83,7 @@ jobs:
           sh assets/scripts/versions.sh
 
       - name: Render Quarto site
-        run: quarto render
+        run: quarto render --to html,ipynb
 
       - name: Rename original search index
         run: mv _site/search.json _site/search_original.json
diff --git a/.gitignore b/.gitignore
index 3c097ca05..c50c42e25 100644
--- a/.gitignore
+++ b/.gitignore
@@ -28,4 +28,5 @@ venv
 site_libs
 .DS_Store
 index_files
-digest.txt
\ No newline at end of file
+digest.txt
+**/*.quarto_ipynb
diff --git a/_includes/download-notebook.html b/_includes/download-notebook.html
new file mode 100644
index 000000000..db5ba4d55
--- /dev/null
+++ b/_includes/download-notebook.html
@@ -0,0 +1,56 @@
+<script>
+document.addEventListener('DOMContentLoaded', function() {
+  // Only add button if we're on a tutorial page
+  const path = window.location.pathname;
+  if (path.includes('/tutorials/') || path.includes('/usage/')) {
+    // Extract the notebook name from the URL
+    const pathParts = path.split('/');
+    const section = pathParts[pathParts.length - 2];
+
+    // Create download button
+    const downloadBtn = document.createElement('a');
+    downloadBtn.className = 'btn btn-primary download-notebook-btn';
+    downloadBtn.innerHTML = '<i class="bi bi-download"></i> Download as Notebook';
+
+    // Generate GitHub raw URL for the notebook
+    const baseUrl = 'https://raw.githubusercontent.com/TuringLang/docs/main';
+    const notebookPath = path.replace('.html', '.ipynb');
+    downloadBtn.href = baseUrl + notebookPath;
+    downloadBtn.download = section + '.ipynb';
+
+    // Insert button after title or in TOC area
+    const tocTitle = document.querySelector('.toc-title');
+    if (tocTitle) {
+      tocTitle.parentNode.insertBefore(downloadBtn, tocTitle.nextSibling);
+    } else {
+      const articleHeader = document.querySelector('header.quarto-title-block');
+      if (articleHeader) {
+        articleHeader.appendChild(downloadBtn);
+      }
+    }
+  }
+});
+</script>
+
+<style>
+.download-notebook-btn {
+  display: inline-block;
+  margin: 1rem 0;
+  padding: 0.5rem 1rem;
+  background-color: var(--bs-primary);
+  color: white;
+  text-decoration: none;
+  border-radius: 0.25rem;
+  font-size: 0.9rem;
+}
+
+.download-notebook-btn:hover {
+  background-color: var(--bs-primary-dark);
+  color: white;
+  text-decoration: none;
+}
+
+.download-notebook-btn i {
+  margin-right: 0.5rem;
+}
+</style>
\ No newline at end of file
diff --git a/_quarto.yml b/_quarto.yml
index 47c5159f3..8d2f93920 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -153,6 +153,11 @@ format:
     toc-title: "Table of Contents"
     code-fold: false
     code-overflow: scroll
+    code-tools:
+      source: true
+      toggle: false
+      caption: none
+    downloads: [ipynb]
     include-in-header:
       - text: |
           <style>
@@ -163,6 +168,7 @@ format:
               text-decoration: underline;
             }
           </style>
+      - _includes/download-notebook.html
     include-after-body:
       - text: |
           <footer class="custom-footer">

From ff55d5a8980a7c13042f7b531cf93bb53965c1cf Mon Sep 17 00:00:00 2001
From: Aoife <aoife1hughes@gmail.com>
Date: Mon, 22 Sep 2025 10:54:31 +0100
Subject: [PATCH 02/23] Refactor Quarto rendering and remove download notebook
 script

---
 .github/workflows/publish.yml    |  2 +-
 _includes/download-notebook.html | 56 --------------------------------
 _quarto.yml                      |  8 ++---
 3 files changed, 3 insertions(+), 63 deletions(-)
 delete mode 100644 _includes/download-notebook.html

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index c13c570e6..5cb81b4f0 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -83,7 +83,7 @@ jobs:
           sh assets/scripts/versions.sh
 
       - name: Render Quarto site
-        run: quarto render --to html,ipynb
+        run: quarto render
 
       - name: Rename original search index
         run: mv _site/search.json _site/search_original.json
diff --git a/_includes/download-notebook.html b/_includes/download-notebook.html
deleted file mode 100644
index db5ba4d55..000000000
--- a/_includes/download-notebook.html
+++ /dev/null
@@ -1,56 +0,0 @@
-<script>
-document.addEventListener('DOMContentLoaded', function() {
-  // Only add button if we're on a tutorial page
-  const path = window.location.pathname;
-  if (path.includes('/tutorials/') || path.includes('/usage/')) {
-    // Extract the notebook name from the URL
-    const pathParts = path.split('/');
-    const section = pathParts[pathParts.length - 2];
-
-    // Create download button
-    const downloadBtn = document.createElement('a');
-    downloadBtn.className = 'btn btn-primary download-notebook-btn';
-    downloadBtn.innerHTML = '<i class="bi bi-download"></i> Download as Notebook';
-
-    // Generate GitHub raw URL for the notebook
-    const baseUrl = 'https://raw.githubusercontent.com/TuringLang/docs/main';
-    const notebookPath = path.replace('.html', '.ipynb');
-    downloadBtn.href = baseUrl + notebookPath;
-    downloadBtn.download = section + '.ipynb';
-
-    // Insert button after title or in TOC area
-    const tocTitle = document.querySelector('.toc-title');
-    if (tocTitle) {
-      tocTitle.parentNode.insertBefore(downloadBtn, tocTitle.nextSibling);
-    } else {
-      const articleHeader = document.querySelector('header.quarto-title-block');
-      if (articleHeader) {
-        articleHeader.appendChild(downloadBtn);
-      }
-    }
-  }
-});
-</script>
-
-<style>
-.download-notebook-btn {
-  display: inline-block;
-  margin: 1rem 0;
-  padding: 0.5rem 1rem;
-  background-color: var(--bs-primary);
-  color: white;
-  text-decoration: none;
-  border-radius: 0.25rem;
-  font-size: 0.9rem;
-}
-
-.download-notebook-btn:hover {
-  background-color: var(--bs-primary-dark);
-  color: white;
-  text-decoration: none;
-}
-
-.download-notebook-btn i {
-  margin-right: 0.5rem;
-}
-</style>
\ No newline at end of file
diff --git a/_quarto.yml b/_quarto.yml
index 8d2f93920..e40b37aa5 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -153,11 +153,7 @@ format:
     toc-title: "Table of Contents"
     code-fold: false
     code-overflow: scroll
-    code-tools:
-      source: true
-      toggle: false
-      caption: none
-    downloads: [ipynb]
+    format-links: [ipynb]
     include-in-header:
       - text: |
           <style>
@@ -168,7 +164,6 @@ format:
               text-decoration: underline;
             }
           </style>
-      - _includes/download-notebook.html
     include-after-body:
       - text: |
           <footer class="custom-footer">
@@ -216,6 +211,7 @@ format:
               </div>
             </div>
           </footer>
+  ipynb: default
 
 execute:
   echo: true

From 091e1a1ba24b63aa23df686a00f4814d460bdb01 Mon Sep 17 00:00:00 2001
From: Markus Hauru <mhauru@turing.ac.uk>
Date: Wed, 13 Aug 2025 17:08:18 +0100
Subject: [PATCH 03/23] Update to Turing 0.40

---
 Manifest.toml | 419 +++++++++++++++++++++++---------------------------
 Project.toml  |   3 +-
 2 files changed, 196 insertions(+), 226 deletions(-)

diff --git a/Manifest.toml b/Manifest.toml
index c5d7a04ff..2f8687805 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -2,12 +2,12 @@
 
 julia_version = "1.11.6"
 manifest_format = "2.0"
-project_hash = "2db94c909342da49eb3ff313436b75e25977ace6"
+project_hash = "0250fe85007baf77c93e2189ee544ed354b8099e"
 
 [[deps.ADTypes]]
-git-tree-sha1 = "27cecae79e5cc9935255f90c53bb831cc3c870d7"
+git-tree-sha1 = "60665b326b75db6517939d0e1875850bc4a54368"
 uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
-version = "1.18.0"
+version = "1.17.0"
 weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"]
 
     [deps.ADTypes.extensions]
@@ -34,15 +34,19 @@ version = "0.5.24"
 
 [[deps.AbstractMCMC]]
 deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "FillArrays", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers", "UUIDs"]
-git-tree-sha1 = "2b33cfcb3f32819e02bf949e7546a1d59247884e"
+git-tree-sha1 = "e4b6a25ba2e033c74ea11720daacafbc2ab50a7e"
 uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
-version = "5.8.0"
+version = "5.7.2"
 
 [[deps.AbstractPPL]]
 deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "Random", "StatsBase"]
-git-tree-sha1 = "478b0b6176125cf0a5e6e9fd69fdd0923754531c"
+git-tree-sha1 = "b7a856399119394a573141c553aeb5b674a500b5"
 uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf"
-version = "0.12.0"
+version = "0.13.0"
+weakdeps = ["Distributions", "LinearAlgebra"]
+
+    [deps.AbstractPPL.extensions]
+    AbstractPPLDistributionsExt = ["Distributions", "LinearAlgebra"]
 
 [[deps.AbstractTrees]]
 git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177"
@@ -86,9 +90,9 @@ weakdeps = ["SparseArrays", "StaticArrays"]
 
 [[deps.AdvancedHMC]]
 deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Setfield", "Statistics", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "e5625ace51e1f11f479b24017193bc7fdfef73a2"
+git-tree-sha1 = "22496647c061d00217759e95a18d601c959df0c9"
 uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-version = "0.8.2"
+version = "0.8.1"
 
     [deps.AdvancedHMC.extensions]
     AdvancedHMCADTypesExt = "ADTypes"
@@ -177,9 +181,9 @@ version = "3.5.1+1"
 
 [[deps.ArrayInterface]]
 deps = ["Adapt", "LinearAlgebra"]
-git-tree-sha1 = "dbd8c3bbbdbb5c2778f85f4422c39960eac65a42"
+git-tree-sha1 = "9606d7832795cbef89e06a550475be300364a8aa"
 uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
-version = "7.20.0"
+version = "7.19.0"
 
     [deps.ArrayInterface.extensions]
     ArrayInterfaceBandedMatricesExt = "BandedMatrices"
@@ -189,7 +193,6 @@ version = "7.20.0"
     ArrayInterfaceChainRulesCoreExt = "ChainRulesCore"
     ArrayInterfaceChainRulesExt = "ChainRules"
     ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore"
-    ArrayInterfaceMetalExt = "Metal"
     ArrayInterfaceReverseDiffExt = "ReverseDiff"
     ArrayInterfaceSparseArraysExt = "SparseArrays"
     ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore"
@@ -203,7 +206,6 @@ version = "7.20.0"
     ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2"
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
     GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
-    Metal = "dde4c033-4e86-420c-a63e-0dd931031962"
     ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
     SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
     StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
@@ -249,9 +251,9 @@ version = "1.1.0"
 
 [[deps.AxisArrays]]
 deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"]
-git-tree-sha1 = "4126b08903b777c88edf1754288144a0492c05ad"
+git-tree-sha1 = "16351be62963a67ac4083f748fdb3cca58bfd52f"
 uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
-version = "0.4.8"
+version = "0.4.7"
 
 [[deps.BandedMatrices]]
 deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"]
@@ -300,10 +302,10 @@ version = "0.1.1"
 
 [[deps.Bijectors]]
 deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Distributions", "DocStringExtensions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Roots", "SparseArrays", "Statistics"]
-git-tree-sha1 = "1f8e2022a4f6dbbe3c7b60f728647973e7b514ef"
+git-tree-sha1 = "35ba30573d4f83242f1e788c87ca792c83553c9e"
 uuid = "76274a88-744f-5084-9051-94815aaf08c4"
-version = "0.15.10"
-weakdeps = ["ChainRules", "DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyArrays", "Mooncake", "ReverseDiff"]
+version = "0.15.9"
+weakdeps = ["ChainRules", "DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyArrays", "Mooncake", "ReverseDiff", "Tracker"]
 
     [deps.Bijectors.extensions]
     BijectorsDistributionsADExt = "DistributionsAD"
@@ -313,6 +315,7 @@ weakdeps = ["ChainRules", "DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyA
     BijectorsMooncakeExt = "Mooncake"
     BijectorsReverseDiffChainRulesExt = ["ChainRules", "ReverseDiff"]
     BijectorsReverseDiffExt = "ReverseDiff"
+    BijectorsTrackerExt = "Tracker"
 
 [[deps.BitFlags]]
 git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d"
@@ -375,9 +378,9 @@ version = "1.9.0"
 
 [[deps.BracketingNonlinearSolve]]
 deps = ["CommonSolve", "ConcreteStructs", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"]
-git-tree-sha1 = "90740f16aef91d898424bc11c1cabada475435e0"
+git-tree-sha1 = "a9014924595b7a2c1dd14aac516e38fa10ada656"
 uuid = "70df07ce-3d50-431d-a3e7-ca6ddb60ac1e"
-version = "1.4.0"
+version = "1.3.0"
 weakdeps = ["ChainRulesCore", "ForwardDiff"]
 
     [deps.BracketingNonlinearSolve.extensions]
@@ -493,9 +496,9 @@ version = "0.7.8"
 
 [[deps.ColorSchemes]]
 deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"]
-git-tree-sha1 = "b0fd3f56fa442f81e0a47815c92245acfaaa4e34"
+git-tree-sha1 = "a656525c8b46aa6a1c76891552ed5381bb32ae7b"
 uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
-version = "3.31.0"
+version = "3.30.0"
 
 [[deps.ColorTypes]]
 deps = ["FixedPointNumbers", "Random"]
@@ -653,9 +656,9 @@ version = "1.16.0"
 
 [[deps.DataFrames]]
 deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
-git-tree-sha1 = "c967271c27a95160e30432e011b58f42cd7501b5"
+git-tree-sha1 = "fb61b4812c49343d7ef0b533ba982c46021938a6"
 uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-version = "1.8.0"
+version = "1.7.0"
 
 [[deps.DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
@@ -686,9 +689,9 @@ version = "0.1.2"
 
 [[deps.DelayDiffEq]]
 deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "FastBroadcast", "ForwardDiff", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqRosenbrock", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack", "SymbolicIndexingInterface"]
-git-tree-sha1 = "c50981fb5b6441a1213debb1423385a462e88032"
+git-tree-sha1 = "d9b1e66070ce15bc2b9c3d5af6b94f693fc03ba4"
 uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb"
-version = "5.56.0"
+version = "5.58.0"
 
 [[deps.DelimitedFiles]]
 deps = ["Mmap"]
@@ -703,14 +706,15 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d"
 version = "0.4.0"
 
 [[deps.DiffEqBase]]
-deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "TruncatedStacktraces"]
-git-tree-sha1 = "087632db966c90079a5534e4147afea9136ca39a"
+deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "TruncatedStacktraces"]
+git-tree-sha1 = "6fecfae8b2d9983e939378c8eacff6562e8a2567"
 uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
-version = "6.190.2"
+version = "6.183.0"
 
     [deps.DiffEqBase.extensions]
     DiffEqBaseCUDAExt = "CUDA"
     DiffEqBaseChainRulesCoreExt = "ChainRulesCore"
+    DiffEqBaseDistributionsExt = "Distributions"
     DiffEqBaseEnzymeExt = ["ChainRulesCore", "Enzyme"]
     DiffEqBaseForwardDiffExt = ["ForwardDiff"]
     DiffEqBaseGTPSAExt = "GTPSA"
@@ -777,9 +781,9 @@ version = "7.16.1"
 
 [[deps.DifferentiationInterface]]
 deps = ["ADTypes", "LinearAlgebra"]
-git-tree-sha1 = "16946a4d305607c3a4af54ff35d56f0e9444ed0e"
+git-tree-sha1 = "54d7b8c74408048aea9c055ac8573b2b5c5ec11f"
 uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
-version = "0.7.7"
+version = "0.7.4"
 
     [deps.DifferentiationInterface.extensions]
     DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore"
@@ -894,10 +898,10 @@ uuid = "bbc10e6e-7c05-544b-b16e-64fede858acb"
 version = "3.5.1"
 
 [[deps.DynamicPPL]]
-deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Chairmarks", "Compat", "ConstructionBase", "DifferentiationInterface", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Requires", "Statistics", "Test"]
-git-tree-sha1 = "07218fc45d4f1abc9de4498e8cf966b6672c84f0"
+deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Chairmarks", "Compat", "ConstructionBase", "DifferentiationInterface", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Printf", "Random", "Requires", "Statistics", "Test"]
+git-tree-sha1 = "e36add2952240379bd53b83e76cfd3a8c56748d6"
 uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8"
-version = "0.36.15"
+version = "0.37.0"
 
     [deps.DynamicPPL.extensions]
     DynamicPPLChainRulesCoreExt = ["ChainRulesCore"]
@@ -929,9 +933,9 @@ version = "1.0.5"
 
 [[deps.Enzyme]]
 deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "InteractiveUtils", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"]
-git-tree-sha1 = "8bd38788cad934e433f944678885d8525cccc009"
+git-tree-sha1 = "1a9c9e3401f5d024612a70d24a19517b2dbc1824"
 uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9"
-version = "0.13.76"
+version = "0.13.67"
 
     [deps.Enzyme.extensions]
     EnzymeBFloat16sExt = "BFloat16s"
@@ -950,9 +954,9 @@ version = "0.13.76"
     StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [[deps.EnzymeCore]]
-git-tree-sha1 = "787f5e2efb33af12cc3fde313c1b0195a3f08eba"
+git-tree-sha1 = "8272a687bca7b5c601c0c24fc0c71bff10aafdfd"
 uuid = "f151be2c-9106-41f4-ab19-57ee4f262869"
-version = "0.8.13"
+version = "0.8.12"
 weakdeps = ["Adapt"]
 
     [deps.EnzymeCore.extensions]
@@ -960,9 +964,9 @@ weakdeps = ["Adapt"]
 
 [[deps.Enzyme_jll]]
 deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"]
-git-tree-sha1 = "440abfda8e1329662bed574250dde0dcd91f3181"
+git-tree-sha1 = "a357a553f8dfd461756ff8ed66fd541bdf2d1588"
 uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef"
-version = "0.0.197+0"
+version = "0.0.188+0"
 
 [[deps.EpollShim_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -978,9 +982,9 @@ version = "0.1.11"
 
 [[deps.Expat_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "7bb1361afdb33c7f2b085aa49ea8fe1b0fb14e58"
+git-tree-sha1 = "d55dffd9ae73ff72f1c0482454dcf2ec6c6c4a63"
 uuid = "2e619515-83b5-522b-bb60-26c02a35a201"
-version = "2.7.1+0"
+version = "2.6.5+0"
 
 [[deps.ExponentialUtilities]]
 deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"]
@@ -1015,10 +1019,10 @@ uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5"
 version = "7.1.1+0"
 
 [[deps.FFTW]]
-deps = ["AbstractFFTs", "FFTW_jll", "Libdl", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"]
-git-tree-sha1 = "97f08406df914023af55ade2f843c39e99c5d969"
+deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"]
+git-tree-sha1 = "797762812ed063b9b94f6cc7742bc8883bb5e69e"
 uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
-version = "1.10.0"
+version = "1.9.0"
 
 [[deps.FFTW_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -1111,9 +1115,9 @@ version = "1.11.0"
 
 [[deps.FillArrays]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "173e4d8f14230a7523ae11b9a3fa9edb3e0efd78"
+git-tree-sha1 = "6a70198746448456524cb442b8af316927ff3e1a"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "1.14.0"
+version = "1.13.0"
 weakdeps = ["PDMats", "SparseArrays", "Statistics"]
 
     [deps.FillArrays.extensions]
@@ -1123,9 +1127,9 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"]
 
 [[deps.FiniteDiff]]
 deps = ["ArrayInterface", "LinearAlgebra", "Setfield"]
-git-tree-sha1 = "31fd32af86234b6b71add76229d53129aa1b87a9"
+git-tree-sha1 = "d84e026183bb3fc764110ae98792c2e004f8c240"
 uuid = "6a86dc24-6348-571c-b903-95158fe2bd41"
-version = "2.28.1"
+version = "2.28.0"
 
     [deps.FiniteDiff.extensions]
     FiniteDiffBandedMatricesExt = "BandedMatrices"
@@ -1169,9 +1173,9 @@ version = "0.16.5"
 
 [[deps.Fontconfig_jll]]
 deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"]
-git-tree-sha1 = "f85dac9a96a01087df6e3a749840015a0ca3817d"
+git-tree-sha1 = "301b5d5d731a0654825f1f2e906990f7141a106b"
 uuid = "a3f928ae-7b40-5064-980b-68af3947d34b"
-version = "2.17.1+0"
+version = "2.16.0+0"
 
 [[deps.Format]]
 git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc"
@@ -1180,9 +1184,9 @@ version = "1.3.7"
 
 [[deps.ForwardDiff]]
 deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"]
-git-tree-sha1 = "dc41303865a16274ecb8450c220021ce1e0cf05f"
+git-tree-sha1 = "910febccb28d493032495b7009dce7d7f7aee554"
 uuid = "f6369f11-7733-5829-9624-2563aa707210"
-version = "1.2.1"
+version = "1.0.1"
 weakdeps = ["StaticArrays"]
 
     [deps.ForwardDiff.extensions]
@@ -1276,17 +1280,11 @@ git-tree-sha1 = "45288942190db7c5f760f59c04495064eedf9340"
 uuid = "b0724c58-0f36-5564-988d-3bb0596ebc4a"
 version = "0.22.4+0"
 
-[[deps.Ghostscript_jll]]
-deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Zlib_jll"]
-git-tree-sha1 = "38044a04637976140074d0b0621c1edf0eb531fd"
-uuid = "61579ee1-b43e-5ca0-a5da-69d92c66a64b"
-version = "9.55.1+0"
-
 [[deps.Glib_jll]]
 deps = ["Artifacts", "GettextRuntime_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"]
-git-tree-sha1 = "50c11ffab2a3d50192a228c313f05b5b5dc5acb2"
+git-tree-sha1 = "35fbd0cefb04a516104b8e183ce0df11b70a3f1a"
 uuid = "7746bdde-850d-59dc-9ae8-88ece973131d"
-version = "2.86.0+0"
+version = "2.84.3+0"
 
 [[deps.Graphite2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -1296,9 +1294,9 @@ version = "1.3.15+0"
 
 [[deps.Graphs]]
 deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
-git-tree-sha1 = "7a98c6502f4632dbe9fb1973a4244eaa3324e84d"
+git-tree-sha1 = "c5abfa0ae0aaee162a3fbb053c13ecda39be545b"
 uuid = "86223c79-3864-5bf0-83f7-82e725a168b6"
-version = "1.13.1"
+version = "1.13.0"
 
 [[deps.Grisu]]
 git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2"
@@ -1360,9 +1358,9 @@ uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c"
 version = "0.3.1"
 
 [[deps.InlineStrings]]
-git-tree-sha1 = "8f3d257792a522b4601c24a577954b0a8cd7334d"
+git-tree-sha1 = "8594fac023c5ce1ef78260f24d1ad18b4327b420"
 uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48"
-version = "1.4.5"
+version = "1.4.4"
 
     [deps.InlineStrings.extensions]
     ArrowTypesExt = "ArrowTypes"
@@ -1460,9 +1458,9 @@ version = "0.2.1"
 
 [[deps.JpegTurbo_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "4255f0032eafd6451d707a51d5f0248b8a165e4d"
+git-tree-sha1 = "eac1206917768cb54957c65a615460d87b455fc1"
 uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8"
-version = "3.1.3+0"
+version = "3.1.1+0"
 
 [[deps.JuliaVariables]]
 deps = ["MLStyle", "NameResolution"]
@@ -1471,10 +1469,10 @@ uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec"
 version = "0.2.4"
 
 [[deps.JumpProcesses]]
-deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "PoissonRandom", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"]
-git-tree-sha1 = "905a2a28770e23f3ed750306ef48eb8c46c3a002"
+deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"]
+git-tree-sha1 = "f5b57507a36f05509e72120aa84d5c3747dbd70e"
 uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
-version = "9.19.1"
+version = "9.17.0"
 weakdeps = ["Adapt", "FastBroadcast", "KernelAbstractions"]
 
     [deps.JumpProcesses.extensions]
@@ -1570,10 +1568,10 @@ uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 version = "1.4.0"
 
 [[deps.Latexify]]
-deps = ["Format", "Ghostscript_jll", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"]
-git-tree-sha1 = "44f93c47f9cd6c7e431f2f2091fcba8f01cd7e8f"
+deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"]
+git-tree-sha1 = "52e1296ebbde0db845b356abbbe67fb82a0a116c"
 uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
-version = "0.16.10"
+version = "0.16.9"
 
     [deps.Latexify.extensions]
     DataFramesExt = "DataFrames"
@@ -1595,9 +1593,9 @@ version = "0.1.17"
 
 [[deps.LazyArrays]]
 deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"]
-git-tree-sha1 = "21057b6f4f5db1475e653735fda7d1de1c267b46"
+git-tree-sha1 = "76627adb8c542c6b73f68d4bfd0aa71c9893a079"
 uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02"
-version = "2.6.3"
+version = "2.6.2"
 
     [deps.LazyArrays.extensions]
     LazyArraysBandedMatricesExt = "BandedMatrices"
@@ -1695,9 +1693,9 @@ version = "1.18.0+0"
 
 [[deps.Libmount_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "706dfd3c0dd56ca090e86884db6eda70fa7dd4af"
+git-tree-sha1 = "a31572773ac1b745e0343fe5e2c8ddda7a37e997"
 uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9"
-version = "2.41.1+0"
+version = "2.41.0+0"
 
 [[deps.Libtask]]
 deps = ["MistyClosures", "Test"]
@@ -1713,9 +1711,9 @@ version = "4.7.1+0"
 
 [[deps.Libuuid_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "d3c8af829abaeba27181db4acb485b18d15d89c6"
+git-tree-sha1 = "321ccef73a96ba828cd51f2ab5b9f917fa73945a"
 uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700"
-version = "2.41.1+0"
+version = "2.41.0+0"
 
 [[deps.LineSearch]]
 deps = ["ADTypes", "CommonSolve", "ConcreteStructs", "FastClosures", "LinearAlgebra", "MaybeInplace", "SciMLBase", "SciMLJacobianOperators", "StaticArraysCore"]
@@ -1739,10 +1737,10 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 version = "1.11.0"
 
 [[deps.LinearSolve]]
-deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "OpenBLAS_jll", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"]
-git-tree-sha1 = "e479c96c20e3fe6067d7ee6618839236d156f060"
+deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"]
+git-tree-sha1 = "1c597eceb5ead73dae17ffa4dcc1160e3e4da1f3"
 uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
-version = "3.40.1"
+version = "3.28.0"
 
     [deps.LinearSolve.extensions]
     LinearSolveAMDGPUExt = "AMDGPU"
@@ -1752,7 +1750,6 @@ version = "3.40.1"
     LinearSolveCUDAExt = "CUDA"
     LinearSolveCUDSSExt = "CUDSS"
     LinearSolveCUSOLVERRFExt = ["CUSOLVERRF", "SparseArrays"]
-    LinearSolveCliqueTreesExt = ["CliqueTrees", "SparseArrays"]
     LinearSolveEnzymeExt = "EnzymeCore"
     LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices"
     LinearSolveFastLapackInterfaceExt = "FastLapackInterface"
@@ -1774,7 +1771,6 @@ version = "3.40.1"
     CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
     CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e"
     CUSOLVERRF = "a8cc9031-bad2-4722-94f5-40deabb4245c"
-    CliqueTrees = "60701a23-6482-424a-84db-faee86b9b1f8"
     EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
     FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e"
     FastLapackInterface = "29a986be-02c6-4525-aec4-84b980013641"
@@ -1849,9 +1845,9 @@ version = "1.1.0"
 
 [[deps.Lux]]
 deps = ["ADTypes", "Adapt", "ArgCheck", "ArrayInterface", "ChainRulesCore", "Compat", "ConcreteStructs", "DiffResults", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "GPUArraysCore", "LinearAlgebra", "LuxCore", "LuxLib", "MLDataDevices", "MacroTools", "Markdown", "NNlib", "Optimisers", "Preferences", "Random", "Reexport", "SIMDTypes", "Setfield", "Static", "StaticArraysCore", "Statistics", "WeightInitializers"]
-git-tree-sha1 = "c300d2df439a343a840dd8ef6b0910ce4cafc8c6"
+git-tree-sha1 = "c05e5c3dca1810e728429771763b485057322ad2"
 uuid = "b2108857-7c20-44ae-9111-449ecde12c47"
-version = "1.21.1"
+version = "1.16.0"
 
     [deps.Lux.extensions]
     LuxComponentArraysExt = "ComponentArrays"
@@ -1888,9 +1884,9 @@ version = "1.21.1"
 
 [[deps.LuxCore]]
 deps = ["Compat", "DispatchDoctor", "Random"]
-git-tree-sha1 = "cf12c8eba464132e781d7e000bcc4090e2b6e115"
+git-tree-sha1 = "a72b6b530f39a87d1327b90f5def4bce48eb1a52"
 uuid = "bb33d45b-7691-41d6-9220-0943567d0623"
-version = "1.4.1"
+version = "1.3.0"
 
     [deps.LuxCore.extensions]
     LuxCoreArrayInterfaceReverseDiffExt = ["ArrayInterface", "ReverseDiff"]
@@ -1907,7 +1903,6 @@ version = "1.4.1"
     ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
     EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
-    Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
     Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
     MLDataDevices = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40"
     Reactant = "3c362404-f566-11ee-1572-e11a4b42c853"
@@ -1917,9 +1912,9 @@ version = "1.4.1"
 
 [[deps.LuxLib]]
 deps = ["ArrayInterface", "CPUSummary", "ChainRulesCore", "Compat", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "KernelAbstractions", "LinearAlgebra", "LuxCore", "MLDataDevices", "Markdown", "NNlib", "Polyester", "Preferences", "Random", "Reexport", "Static", "StaticArraysCore", "Statistics"]
-git-tree-sha1 = "109240d7ba4698e7eb60b11f190424b8ca018318"
+git-tree-sha1 = "bf64921ca8182e3ee34a56b05b9f1ed568141a13"
 uuid = "82251201-b29d-42c6-8e01-566dec8acb11"
-version = "1.11.2"
+version = "1.10.1"
 
     [deps.LuxLib.extensions]
     LuxLibAppleAccelerateExt = "AppleAccelerate"
@@ -1928,8 +1923,9 @@ version = "1.11.2"
     LuxLibEnzymeExt = "Enzyme"
     LuxLibLoopVectorizationExt = "LoopVectorization"
     LuxLibMKLExt = "MKL"
+    LuxLibMooncakeExt = "Mooncake"
     LuxLibOctavianExt = ["Octavian", "LoopVectorization"]
-    LuxLibReactantExt = ["Reactant", "ReactantCore"]
+    LuxLibReactantExt = "Reactant"
     LuxLibReverseDiffExt = "ReverseDiff"
     LuxLibSLEEFPiratesExt = "SLEEFPirates"
     LuxLibTrackerAMDGPUExt = ["AMDGPU", "Tracker"]
@@ -1944,9 +1940,9 @@ version = "1.11.2"
     Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
     LoopVectorization = "bdcacae8-1622-11e9-2a5c-532679323890"
     MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
+    Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
     Octavian = "6fd5a793-0b7e-452c-907f-f8bfe9c57db4"
     Reactant = "3c362404-f566-11ee-1572-e11a4b42c853"
-    ReactantCore = "a3311ec8-5e00-46d5-b541-4f83e724a433"
     ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
     SLEEFPirates = "476501e8-09a2-5ece-8869-fb82de89a1fa"
     Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
@@ -1954,9 +1950,9 @@ version = "1.11.2"
 
 [[deps.MCMCChains]]
 deps = ["AbstractMCMC", "AxisArrays", "DataAPI", "Dates", "Distributions", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"]
-git-tree-sha1 = "902175f1618baa58dc50dc2894d382bbd484adf4"
+git-tree-sha1 = "a1b9bf62acb012e4a717562f83f859257c5b6fec"
 uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
-version = "7.3.0"
+version = "7.1.0"
 
 [[deps.MCMCDiagnosticTools]]
 deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"]
@@ -1978,9 +1974,9 @@ version = "1.0.0"
 
 [[deps.MLDataDevices]]
 deps = ["Adapt", "Compat", "Functors", "Preferences", "Random"]
-git-tree-sha1 = "39bac90ff3e88e086426f05a3e97646f91088a7f"
+git-tree-sha1 = "0ad0d8f83ddf28a7eba28ed94d0d68015ce645b7"
 uuid = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40"
-version = "1.12.0"
+version = "1.11.1"
 
     [deps.MLDataDevices.extensions]
     MLDataDevicesAMDGPUExt = "AMDGPU"
@@ -2148,9 +2144,9 @@ version = "0.8.1"
 
 [[deps.Mooncake]]
 deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "DispatchDoctor", "ExprTools", "FunctionWrappers", "GPUArraysCore", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Test"]
-git-tree-sha1 = "bc28c3170e7c78d671ff512ca80487ce7e375bb5"
+git-tree-sha1 = "88bb6e5054ba4a341c8fb7047af859720669628d"
 uuid = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
-version = "0.4.160"
+version = "0.4.142"
 
     [deps.Mooncake.extensions]
     MooncakeAllocCheckExt = "AllocCheck"
@@ -2158,7 +2154,7 @@ version = "0.4.160"
     MooncakeDynamicExpressionsExt = "DynamicExpressions"
     MooncakeFluxExt = "Flux"
     MooncakeJETExt = "JET"
-    MooncakeLuxLibExt = ["LuxLib", "MLDataDevices", "Static"]
+    MooncakeLuxLibExt = "LuxLib"
     MooncakeLuxLibSLEEFPiratesExtension = ["LuxLib", "SLEEFPirates"]
     MooncakeNNlibExt = "NNlib"
     MooncakeSpecialFunctionsExt = "SpecialFunctions"
@@ -2170,11 +2166,9 @@ version = "0.4.160"
     Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
     JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
     LuxLib = "82251201-b29d-42c6-8e01-566dec8acb11"
-    MLDataDevices = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40"
     NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
     SLEEFPirates = "476501e8-09a2-5ece-8869-fb82de89a1fa"
     SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
-    Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
 
 [[deps.Moshi]]
 deps = ["ExproniconLite", "Jieko"]
@@ -2285,10 +2279,10 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 version = "1.2.0"
 
 [[deps.NonlinearSolve]]
-deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "StaticArraysCore", "SymbolicIndexingInterface"]
-git-tree-sha1 = "627967f6e36aac9f5afb2fb285e33b676a6892f9"
+deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface"]
+git-tree-sha1 = "d2ec18c1e4eccbb70b64be2435fc3b06fbcdc0a1"
 uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
-version = "4.11.0"
+version = "4.10.0"
 
     [deps.NonlinearSolve.extensions]
     NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt"
@@ -2297,7 +2291,7 @@ version = "4.11.0"
     NonlinearSolveMINPACKExt = "MINPACK"
     NonlinearSolveNLSolversExt = "NLSolvers"
     NonlinearSolveNLsolveExt = ["NLsolve", "LineSearches"]
-    NonlinearSolvePETScExt = ["PETSc", "MPI", "SparseArrays"]
+    NonlinearSolvePETScExt = ["PETSc", "MPI"]
     NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations"
     NonlinearSolveSpeedMappingExt = "SpeedMapping"
     NonlinearSolveSundialsExt = "Sundials"
@@ -2313,51 +2307,46 @@ version = "4.11.0"
     NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
     PETSc = "ace2c81b-2b5f-4b1e-a30d-d662738edfe0"
     SIAMFANLEquations = "084e46ad-d928-497d-ad5e-07fa361a48c4"
-    SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
     SpeedMapping = "f1835b91-879b-4a3f-a438-e4baacf14412"
     Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"
 
 [[deps.NonlinearSolveBase]]
-deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "SciMLStructures", "Setfield", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"]
-git-tree-sha1 = "bc0c764f8d4cbd75dc8e4968e62194495c2c6637"
+deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"]
+git-tree-sha1 = "1d42a315ba627ca0027d49d0efb44e3d88db24aa"
 uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0"
-version = "1.16.0"
-weakdeps = ["BandedMatrices", "ChainRulesCore", "Enzyme", "ForwardDiff", "LineSearch", "LinearSolve", "Mooncake", "ReverseDiff", "SparseArrays", "SparseMatrixColorings", "Tracker"]
+version = "1.14.0"
+weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearSolve", "SparseArrays", "SparseMatrixColorings"]
 
     [deps.NonlinearSolveBase.extensions]
     NonlinearSolveBaseBandedMatricesExt = "BandedMatrices"
-    NonlinearSolveBaseChainRulesCoreExt = "ChainRulesCore"
-    NonlinearSolveBaseEnzymeExt = ["ChainRulesCore", "Enzyme"]
+    NonlinearSolveBaseDiffEqBaseExt = "DiffEqBase"
     NonlinearSolveBaseForwardDiffExt = "ForwardDiff"
     NonlinearSolveBaseLineSearchExt = "LineSearch"
     NonlinearSolveBaseLinearSolveExt = "LinearSolve"
-    NonlinearSolveBaseMooncakeExt = "Mooncake"
-    NonlinearSolveBaseReverseDiffExt = "ReverseDiff"
     NonlinearSolveBaseSparseArraysExt = "SparseArrays"
     NonlinearSolveBaseSparseMatrixColoringsExt = "SparseMatrixColorings"
-    NonlinearSolveBaseTrackerExt = "Tracker"
 
 [[deps.NonlinearSolveFirstOrder]]
-deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"]
-git-tree-sha1 = "b9702235120d1161f8041b326eccebd334340de2"
+deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"]
+git-tree-sha1 = "3f1198ae5cbf21e84b8251a9e62fa1f888f3e4cb"
 uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d"
-version = "1.8.0"
+version = "1.7.0"
 
 [[deps.NonlinearSolveQuasiNewton]]
-deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"]
-git-tree-sha1 = "4e0e34601c6c9890aa9443003180967f75c6929d"
+deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"]
+git-tree-sha1 = "40dfaf1bf74f1f700f81d0002d4dd90999598eb2"
 uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114"
-version = "1.9.0"
+version = "1.8.0"
 weakdeps = ["ForwardDiff"]
 
     [deps.NonlinearSolveQuasiNewton.extensions]
     NonlinearSolveQuasiNewtonForwardDiffExt = "ForwardDiff"
 
 [[deps.NonlinearSolveSpectralMethods]]
-deps = ["CommonSolve", "ConcreteStructs", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"]
-git-tree-sha1 = "6c613302febe2bb408a888105d07073cf6824911"
+deps = ["CommonSolve", "ConcreteStructs", "DiffEqBase", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"]
+git-tree-sha1 = "84de5a469e119eb2c22ae07c543dc4e7f7001ee7"
 uuid = "26075421-4e9a-44e1-8bd1-420ed7ad02b2"
-version = "1.4.0"
+version = "1.3.0"
 weakdeps = ["ForwardDiff"]
 
     [deps.NonlinearSolveSpectralMethods.extensions]
@@ -2452,16 +2441,16 @@ version = "0.4.6"
     Reactant = "3c362404-f566-11ee-1572-e11a4b42c853"
 
 [[deps.Optimization]]
-deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Printf", "ProgressLogging", "Random", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"]
-git-tree-sha1 = "1e02b79bf6175d723a40745f622e9513253bab55"
+deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Printf", "ProgressLogging", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"]
+git-tree-sha1 = "41902230755effe29a8599ea4b61dc3ffc2c952d"
 uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
-version = "4.7.0"
+version = "4.5.0"
 
 [[deps.OptimizationBase]]
-deps = ["ADTypes", "ArrayInterface", "DifferentiationInterface", "DocStringExtensions", "FastClosures", "LinearAlgebra", "PDMats", "Reexport", "SciMLBase", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"]
-git-tree-sha1 = "4f6098addb09203f35de1b21d5e668315544ff26"
+deps = ["ADTypes", "ArrayInterface", "DifferentiationInterface", "DocStringExtensions", "FastClosures", "LinearAlgebra", "PDMats", "Reexport", "Requires", "SciMLBase", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"]
+git-tree-sha1 = "474b2fa6de9288d34b8ad42c9c500088132621a7"
 uuid = "bca83a33-5cc9-4baa-983d-23429ab6bcbb"
-version = "2.11.0"
+version = "2.10.0"
 
     [deps.OptimizationBase.extensions]
     OptimizationEnzymeExt = "Enzyme"
@@ -2487,15 +2476,15 @@ version = "2.11.0"
 
 [[deps.OptimizationNLopt]]
 deps = ["NLopt", "Optimization", "Random", "Reexport"]
-git-tree-sha1 = "83e469a5b058250e95121afeea71da14034b24a4"
+git-tree-sha1 = "da55bae039168c0ef977bd5926cd5208c6cd13cf"
 uuid = "4e6fcdb7-1186-4e1f-a706-475e75c168bb"
-version = "0.3.3"
+version = "0.3.2"
 
 [[deps.OptimizationOptimJL]]
 deps = ["Optim", "Optimization", "PrecompileTools", "Reexport", "SparseArrays"]
-git-tree-sha1 = "a6194340cb4f7d61cec9d6f605848d6a187c64b6"
+git-tree-sha1 = "6f228118b81ce4e849091ee0d00805f2ecb18f54"
 uuid = "36348300-93cb-4f02-beb5-3c3902f8871e"
-version = "0.4.4"
+version = "0.4.3"
 
 [[deps.Opus_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -2509,10 +2498,10 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 version = "1.8.1"
 
 [[deps.OrdinaryDiffEq]]
-deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqAdamsBashforthMoulton", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqExplicitRK", "OrdinaryDiffEqExponentialRK", "OrdinaryDiffEqExtrapolation", "OrdinaryDiffEqFIRK", "OrdinaryDiffEqFeagin", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqHighOrderRK", "OrdinaryDiffEqIMEXMultistep", "OrdinaryDiffEqLinear", "OrdinaryDiffEqLowOrderRK", "OrdinaryDiffEqLowStorageRK", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqNordsieck", "OrdinaryDiffEqPDIRK", "OrdinaryDiffEqPRK", "OrdinaryDiffEqQPRK", "OrdinaryDiffEqRKN", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqSDIRK", "OrdinaryDiffEqSSPRK", "OrdinaryDiffEqStabilizedIRK", "OrdinaryDiffEqStabilizedRK", "OrdinaryDiffEqSymplecticRK", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
-git-tree-sha1 = "89cd4e81d7a668f8858fba6779212f41a0360260"
+deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqAdamsBashforthMoulton", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqExplicitRK", "OrdinaryDiffEqExponentialRK", "OrdinaryDiffEqExtrapolation", "OrdinaryDiffEqFIRK", "OrdinaryDiffEqFeagin", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqHighOrderRK", "OrdinaryDiffEqIMEXMultistep", "OrdinaryDiffEqLinear", "OrdinaryDiffEqLowOrderRK", "OrdinaryDiffEqLowStorageRK", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqNordsieck", "OrdinaryDiffEqPDIRK", "OrdinaryDiffEqPRK", "OrdinaryDiffEqQPRK", "OrdinaryDiffEqRKN", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqSDIRK", "OrdinaryDiffEqSSPRK", "OrdinaryDiffEqStabilizedIRK", "OrdinaryDiffEqStabilizedRK", "OrdinaryDiffEqSymplecticRK", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
+git-tree-sha1 = "55c21fdb4626037cdbcb04fec3afa192345a24de"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.102.1"
+version = "6.101.0"
 
 [[deps.OrdinaryDiffEqAdamsBashforthMoulton]]
 deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"]
@@ -2528,9 +2517,9 @@ version = "1.10.1"
 
 [[deps.OrdinaryDiffEqCore]]
 deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FastPower", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "SymbolicIndexingInterface", "TruncatedStacktraces"]
-git-tree-sha1 = "688c717e8eee84dcfef02ddf71c8028215b329ca"
+git-tree-sha1 = "e579c9a4f9102e82da3d97c349a74d6bc11cf8dc"
 uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8"
-version = "1.34.0"
+version = "1.30.0"
 weakdeps = ["EnzymeCore", "Mooncake"]
 
     [deps.OrdinaryDiffEqCore.extensions]
@@ -2544,14 +2533,10 @@ uuid = "50262376-6c5a-4cf5-baba-aaf4f84d72d7"
 version = "1.8.0"
 
 [[deps.OrdinaryDiffEqDifferentiation]]
-deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SciMLOperators", "SparseMatrixColorings", "StaticArrayInterface", "StaticArrays"]
-git-tree-sha1 = "1fff7356ccb79ca1b1ff3276135fda68d4d661be"
+deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseMatrixColorings", "StaticArrayInterface", "StaticArrays"]
+git-tree-sha1 = "4c270747152db513dd80bfd5f2f9df48befff28a"
 uuid = "4302a76b-040a-498a-8c04-15b101fed76b"
-version = "1.16.0"
-weakdeps = ["SparseArrays"]
-
-    [deps.OrdinaryDiffEqDifferentiation.extensions]
-    OrdinaryDiffEqDifferentiationSparseArraysExt = "SparseArrays"
+version = "1.14.0"
 
 [[deps.OrdinaryDiffEqExplicitRK]]
 deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"]
@@ -2567,9 +2552,9 @@ version = "1.8.0"
 
 [[deps.OrdinaryDiffEqExtrapolation]]
 deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastPower", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase"]
-git-tree-sha1 = "9e1b11cf448a2c1bca640103c1c848a20aa2f967"
+git-tree-sha1 = "ee2cba2533e9faf71b09a319a910d4886931e7a6"
 uuid = "becaefa8-8ca2-5cf9-886d-c06f3d2bd2c4"
-version = "1.9.0"
+version = "1.8.0"
 
 [[deps.OrdinaryDiffEqFIRK]]
 deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastGaussQuadrature", "FastPower", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators"]
@@ -2615,9 +2600,9 @@ version = "1.6.0"
 
 [[deps.OrdinaryDiffEqLowStorageRK]]
 deps = ["Adapt", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "StaticArrays"]
-git-tree-sha1 = "e6bd0a7fb6643a57b06a90415608a81aaf7bd772"
+git-tree-sha1 = "9291cdfd2e8c91e900c48d71d76618de47daeede"
 uuid = "b0944070-b475-4768-8dec-fb6eb410534d"
-version = "1.7.0"
+version = "1.6.0"
 
 [[deps.OrdinaryDiffEqNonlinearSolve]]
 deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "PreallocationTools", "RecursiveArrayTools", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "StaticArrays"]
@@ -2657,9 +2642,9 @@ version = "1.5.0"
 
 [[deps.OrdinaryDiffEqRosenbrock]]
 deps = ["ADTypes", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"]
-git-tree-sha1 = "f60d7201a2ceaa7e9a406942f0a2fa3e920715fa"
+git-tree-sha1 = "a06c1263d71ea42a1881b4d49c8a087035d4a3ff"
 uuid = "43230ef6-c299-4910-a778-202eb28ce4ce"
-version = "1.18.0"
+version = "1.16.1"
 
 [[deps.OrdinaryDiffEqSDIRK]]
 deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"]
@@ -2669,9 +2654,9 @@ version = "1.7.0"
 
 [[deps.OrdinaryDiffEqSSPRK]]
 deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "StaticArrays"]
-git-tree-sha1 = "3bce87977264916bd92455754ab336faec68bf8a"
+git-tree-sha1 = "af955c61407631d281dd4c2e8331cdfea1af49be"
 uuid = "669c94d9-1f4b-4b64-b377-1aa079aa2388"
-version = "1.7.0"
+version = "1.6.0"
 
 [[deps.OrdinaryDiffEqStabilizedIRK]]
 deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqStabilizedRK", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays"]
@@ -2722,9 +2707,9 @@ weakdeps = ["Requires", "TOML"]
 
 [[deps.Pango_jll]]
 deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "1f7f9bbd5f7a2e5a9f7d96e51c9754454ea7f60b"
+git-tree-sha1 = "275a9a6d85dc86c24d03d1837a0010226a96f540"
 uuid = "36c8627f-9965-5494-a995-c6b170f724f3"
-version = "1.56.4+0"
+version = "1.56.3+0"
 
 [[deps.Parameters]]
 deps = ["OrderedCollections", "UnPack"]
@@ -2767,9 +2752,9 @@ version = "1.4.3"
 
 [[deps.Plots]]
 deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"]
-git-tree-sha1 = "bfe839e9668f0c58367fb62d8757315c0eac8777"
+git-tree-sha1 = "9a9216c0cf706cb2cc58fd194878180e3e51e8c0"
 uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-version = "1.40.20"
+version = "1.40.18"
 
     [deps.Plots.extensions]
     FileIOExt = "FileIO"
@@ -2817,9 +2802,9 @@ version = "0.2.4"
 
 [[deps.PreallocationTools]]
 deps = ["Adapt", "ArrayInterface", "PrecompileTools"]
-git-tree-sha1 = "c05b4c6325262152483a1ecb6c69846d2e01727b"
+git-tree-sha1 = "a0d5f963cfee70bee26dfa137a732e759e24436a"
 uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46"
-version = "0.4.34"
+version = "0.4.31"
 weakdeps = ["ForwardDiff", "ReverseDiff", "SparseConnectivityTracer"]
 
     [deps.PreallocationTools.extensions]
@@ -2863,9 +2848,9 @@ version = "0.1.5"
 
 [[deps.ProgressMeter]]
 deps = ["Distributed", "Printf"]
-git-tree-sha1 = "fbb92c6c56b34e1a2c4c36058f68f332bec840e7"
+git-tree-sha1 = "13c5103482a8ed1536a54c08d0e742ae3dca2d42"
 uuid = "92933f4c-e287-5a05-a399-4b506db050ca"
-version = "1.11.0"
+version = "1.10.4"
 
 [[deps.PtrArrays]]
 git-tree-sha1 = "1d36ef11a9aaf1e8b74dacc6a731dd1de8fd493d"
@@ -2975,9 +2960,9 @@ version = "0.6.12"
 
 [[deps.RecursiveArrayTools]]
 deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
-git-tree-sha1 = "96bef5b9ac123fff1b379acf0303cf914aaabdfd"
+git-tree-sha1 = "7c7ac305885b1e0292585d087ecd60331a705965"
 uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
-version = "3.37.1"
+version = "3.37.0"
 
     [deps.RecursiveArrayTools.extensions]
     RecursiveArrayToolsFastBroadcastExt = "FastBroadcast"
@@ -3048,9 +3033,9 @@ version = "0.5.1+0"
 
 [[deps.Roots]]
 deps = ["Accessors", "CommonSolve", "Printf"]
-git-tree-sha1 = "8a433b1ede5e9be9a7ba5b1cc6698daa8d718f1d"
+git-tree-sha1 = "668e411c0616a70860249b4c96e5d35296631a1d"
 uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
-version = "2.2.10"
+version = "2.2.8"
 
     [deps.Roots.extensions]
     RootsChainRulesCoreExt = "ChainRulesCore"
@@ -3058,7 +3043,6 @@ version = "2.2.10"
     RootsIntervalRootFindingExt = "IntervalRootFinding"
     RootsSymPyExt = "SymPy"
     RootsSymPyPythonCallExt = "SymPyPythonCall"
-    RootsUnitfulExt = "Unitful"
 
     [deps.Roots.weakdeps]
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
@@ -3066,7 +3050,6 @@ version = "2.2.10"
     IntervalRootFinding = "d2bf35a9-74e0-55ec-b149-d360ff49b807"
     SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6"
     SymPyPythonCall = "bc8888f7-b21e-4b7c-a06a-5d9c9496438c"
-    Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [[deps.RuntimeGeneratedFunctions]]
 deps = ["ExprTools", "SHA", "Serialization"]
@@ -3085,64 +3068,48 @@ version = "0.1.0"
 
 [[deps.SSMProblems]]
 deps = ["AbstractMCMC", "Distributions", "Random"]
-git-tree-sha1 = "5dd0431563784b468db06335ce8777653092d621"
+git-tree-sha1 = "b00814e67e8aacda2073865a3832e6cc378ea504"
 uuid = "26aad666-b158-4e64-9d35-0e672562fa48"
-version = "0.5.2"
+version = "0.5.1"
 
 [[deps.SciMLBase]]
-deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PreallocationTools", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
-git-tree-sha1 = "16fa030fb4bd4df373a677eca0460c3eee791ab2"
+deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
+git-tree-sha1 = "95ce48fe76b9530799429244392853b5405469c1"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "2.120.0"
+version = "2.109.0"
 
     [deps.SciMLBase.extensions]
     SciMLBaseChainRulesCoreExt = "ChainRulesCore"
-    SciMLBaseDistributionsExt = "Distributions"
-    SciMLBaseEnzymeExt = "Enzyme"
-    SciMLBaseForwardDiffExt = "ForwardDiff"
     SciMLBaseMLStyleExt = "MLStyle"
     SciMLBaseMakieExt = "Makie"
-    SciMLBaseMeasurementsExt = "Measurements"
-    SciMLBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements"
-    SciMLBaseMooncakeExt = "Mooncake"
     SciMLBasePartialFunctionsExt = "PartialFunctions"
     SciMLBasePyCallExt = "PyCall"
     SciMLBasePythonCallExt = "PythonCall"
     SciMLBaseRCallExt = "RCall"
-    SciMLBaseReverseDiffExt = "ReverseDiff"
-    SciMLBaseTrackerExt = "Tracker"
     SciMLBaseZygoteExt = ["Zygote", "ChainRulesCore"]
 
     [deps.SciMLBase.weakdeps]
     ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2"
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-    Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
-    Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
-    ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
     MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
     Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
-    Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"
-    MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca"
-    Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
     PartialFunctions = "570af359-4316-4cb7-8c74-252c00c2016b"
     PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
     PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
     RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
-    ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
-    Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
     Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [[deps.SciMLJacobianOperators]]
 deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"]
-git-tree-sha1 = "a273b291c90909ba6fe08402dd68e09aae423008"
+git-tree-sha1 = "3414071e3458f3065de7fa5aed55283b236b4907"
 uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e"
-version = "0.1.11"
+version = "0.1.8"
 
 [[deps.SciMLOperators]]
 deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"]
-git-tree-sha1 = "024d829102878141aaee5cf8f8288bcabd2f57a0"
+git-tree-sha1 = "aea915a39b547c48a18ee041120db1ae8df5a691"
 uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961"
-version = "1.7.2"
+version = "1.5.0"
 weakdeps = ["SparseArrays", "StaticArraysCore"]
 
     [deps.SciMLOperators.extensions]
@@ -3172,9 +3139,9 @@ version = "3.0.0"
 
 [[deps.ScopedValues]]
 deps = ["HashArrayMappedTries", "Logging"]
-git-tree-sha1 = "c3b2323466378a2ba15bea4b2f73b081e022f473"
+git-tree-sha1 = "7f44eef6b1d284465fafc66baf4d9bdcc239a15b"
 uuid = "7e506255-f358-4e82-b7e4-beb19740aa63"
-version = "1.5.0"
+version = "1.4.0"
 
 [[deps.Scratch]]
 deps = ["Dates"]
@@ -3226,13 +3193,14 @@ version = "1.2.0"
 
 [[deps.SimpleNonlinearSolve]]
 deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"]
-git-tree-sha1 = "782c67176b473abf62a6786399c4b7ddcc1a2d77"
+git-tree-sha1 = "09d986e27a606f172c5b6cffbd8b8b2f10bf1c75"
 uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7"
-version = "2.8.0"
-weakdeps = ["ChainRulesCore", "ReverseDiff", "Tracker"]
+version = "2.7.0"
+weakdeps = ["ChainRulesCore", "DiffEqBase", "ReverseDiff", "Tracker"]
 
     [deps.SimpleNonlinearSolve.extensions]
     SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore"
+    SimpleNonlinearSolveDiffEqBaseExt = "DiffEqBase"
     SimpleNonlinearSolveReverseDiffExt = "ReverseDiff"
     SimpleNonlinearSolveTrackerExt = "Tracker"
 
@@ -3264,13 +3232,12 @@ version = "1.11.0"
 
 [[deps.SparseConnectivityTracer]]
 deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"]
-git-tree-sha1 = "3c3a42a29f696f16273741ffe589b4003f539088"
+git-tree-sha1 = "7bd2b8981cc57adcf5cf1add282aba2713a7058f"
 uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5"
-version = "1.1.0"
-weakdeps = ["ChainRulesCore", "LogExpFunctions", "NNlib", "NaNMath", "SpecialFunctions"]
+version = "1.0.0"
+weakdeps = ["LogExpFunctions", "NNlib", "NaNMath", "SpecialFunctions"]
 
     [deps.SparseConnectivityTracer.extensions]
-    SparseConnectivityTracerChainRulesCoreExt = "ChainRulesCore"
     SparseConnectivityTracerLogExpFunctionsExt = "LogExpFunctions"
     SparseConnectivityTracerNNlibExt = "NNlib"
     SparseConnectivityTracerNaNMathExt = "NaNMath"
@@ -3339,9 +3306,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"]
 
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
-git-tree-sha1 = "b8693004b385c842357406e3af647701fe783f98"
+git-tree-sha1 = "cbea8a6bd7bed51b1619658dec70035e07b8502f"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.9.15"
+version = "1.9.14"
 weakdeps = ["ChainRulesCore", "Statistics"]
 
     [deps.StaticArrays.extensions]
@@ -3394,9 +3361,9 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"]
 
 [[deps.StatsModels]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsAPI", "StatsBase", "StatsFuns", "Tables"]
-git-tree-sha1 = "85a43f6fc30dd80c61342519ca2fc36dac912eae"
+git-tree-sha1 = "728d276a5adc2f1cbb800eec4b63d0a8221024b4"
 uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
-version = "0.7.6"
+version = "0.7.5"
 
 [[deps.StatsPlots]]
 deps = ["AbstractFFTs", "Clustering", "DataStructures", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "NaNMath", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"]
@@ -3412,15 +3379,15 @@ version = "2.5.0"
 
 [[deps.StochasticDiffEq]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FastPower", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "StaticArrays", "UnPack"]
-git-tree-sha1 = "d9540e35a902512f6c86a6817120eddc8912f651"
+git-tree-sha1 = "c3a55a2a1e180e249a0550d30a58c700487aa7ef"
 uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
-version = "6.82.0"
+version = "6.81.0"
 
 [[deps.StrideArraysCore]]
 deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"]
-git-tree-sha1 = "83151ba8065a73f53ca2ae98bc7274d817aa30f2"
+git-tree-sha1 = "f35f6ab602df8413a50c4a25ca14de821e8605fb"
 uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da"
-version = "0.5.8"
+version = "0.5.7"
 
 [[deps.Strided]]
 deps = ["LinearAlgebra", "StridedViews", "TupleTools"]
@@ -3494,9 +3461,9 @@ version = "5.2.3+0"
 
 [[deps.SymbolicIndexingInterface]]
 deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"]
-git-tree-sha1 = "b19cf024a2b11d72bef7c74ac3d1cbe86ec9e4ed"
+git-tree-sha1 = "93104ca226670c0cb92ba8bc6998852ad55a2d4c"
 uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
-version = "0.3.44"
+version = "0.3.43"
 weakdeps = ["PrettyTables"]
 
     [deps.SymbolicIndexingInterface.extensions]
@@ -3599,9 +3566,9 @@ weakdeps = ["PDMats"]
 
 [[deps.Tracy]]
 deps = ["ExprTools", "LibTracyClient_jll", "Libdl"]
-git-tree-sha1 = "73e3ff50fd3990874c59fef0f35d10644a1487bc"
+git-tree-sha1 = "91dbaee0f50faa4357f7e9fc69442c7b6364dfe5"
 uuid = "e689c965-62c8-4b79-b2c5-8359227902fd"
-version = "0.1.6"
+version = "0.1.5"
 
     [deps.Tracy.extensions]
     TracyProfilerExt = "TracyProfiler_jll"
@@ -3615,10 +3582,10 @@ uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 version = "0.11.3"
 
 [[deps.Transducers]]
-deps = ["Accessors", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "SplittablesBase", "Tables"]
-git-tree-sha1 = "4aa1fdf6c1da74661f6f5d3edfd96648321dade9"
+deps = ["Accessors", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "SplittablesBase", "Tables"]
+git-tree-sha1 = "7deeab4ff96b85c5f72c824cae53a1398da3d1cb"
 uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999"
-version = "0.4.85"
+version = "0.4.84"
 
     [deps.Transducers.extensions]
     TransducersAdaptExt = "Adapt"
@@ -3655,9 +3622,9 @@ version = "1.6.0"
 
 [[deps.Turing]]
 deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "58ad6cfe65311dc4ddc0e13e6747f3fad26f1034"
+git-tree-sha1 = "ed944065575fd4a6d9d2b802bbd914b53f08bce8"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-version = "0.39.10"
+version = "0.40.1"
 weakdeps = ["DynamicHMC", "Optim"]
 
     [deps.Turing.extensions]
@@ -3742,23 +3709,27 @@ version = "1.4.2"
 
 [[deps.WeightInitializers]]
 deps = ["ArgCheck", "ConcreteStructs", "GPUArraysCore", "LinearAlgebra", "Random", "SpecialFunctions", "Statistics"]
-git-tree-sha1 = "2fe6d8bd39dc8d1f575963eef137f77bd47200c9"
+git-tree-sha1 = "dd2e8eb0120c12eed3446cedee395ca7ac42a5db"
 uuid = "d49dbf32-c5c2-4618-8acc-27bb2598ef2d"
-version = "1.2.0"
+version = "1.1.4"
 
     [deps.WeightInitializers.extensions]
-    WeightInitializersAMDGPUExt = "AMDGPU"
-    WeightInitializersCUDAExt = "CUDA"
+    WeightInitializersAMDGPUExt = ["AMDGPU", "GPUArrays"]
+    WeightInitializersCUDAExt = ["CUDA", "GPUArrays"]
     WeightInitializersChainRulesCoreExt = "ChainRulesCore"
     WeightInitializersGPUArraysExt = "GPUArrays"
+    WeightInitializersMetalExt = ["Metal", "GPUArrays"]
     WeightInitializersReactantExt = "Reactant"
+    WeightInitializersoneAPIExt = ["oneAPI", "GPUArrays"]
 
     [deps.WeightInitializers.weakdeps]
     AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e"
     CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
     GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
+    Metal = "dde4c033-4e86-420c-a63e-0dd931031962"
     Reactant = "3c362404-f566-11ee-1572-e11a4b42c853"
+    oneAPI = "8f75cd03-7ff8-4ecb-9b8f-daf728133b1b"
 
 [[deps.Widgets]]
 deps = ["Colors", "Dates", "Observables", "OrderedCollections"]
diff --git a/Project.toml b/Project.toml
index 68ca649e1..3498eed33 100644
--- a/Project.toml
+++ b/Project.toml
@@ -56,5 +56,4 @@ Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
 UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 
 [compat]
-Turing = "0.39"
-DelayDiffEq = "~5.56"
+Turing = "0.40"

From fc4df949787606ea69474b9924d08cf33a41b6d9 Mon Sep 17 00:00:00 2001
From: Markus Hauru <mhauru@turing.ac.uk>
Date: Wed, 13 Aug 2025 17:24:40 +0100
Subject: [PATCH 04/23] Update version in _quarto.yml

---
 _quarto.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_quarto.yml b/_quarto.yml
index 1b2264e7e..4cbdd369c 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -43,7 +43,7 @@ website:
         href: https://turinglang.org/team/
     right:
       # Current version
-      - text: "v0.39"
+      - text: "v0.40"
         menu:
           - text: Changelog
             href: https://turinglang.org/docs/changelog.html

From df1f9cda639dc928c3a179522413d549dbd0b684 Mon Sep 17 00:00:00 2001
From: Markus Hauru <mhauru@turing.ac.uk>
Date: Wed, 13 Aug 2025 17:45:44 +0100
Subject: [PATCH 05/23] Fix DPPL 0.37 run_ad change

---
 usage/automatic-differentiation/index.qmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/usage/automatic-differentiation/index.qmd b/usage/automatic-differentiation/index.qmd
index 768845942..5ae168473 100755
--- a/usage/automatic-differentiation/index.qmd
+++ b/usage/automatic-differentiation/index.qmd
@@ -91,7 +91,7 @@ model = gdemo(1.5, 2)
 
 for adtype in [AutoForwardDiff(), AutoReverseDiff()]
     result = run_ad(model, adtype; benchmark=true)
-    @show result.time_vs_primal
+    @show result.grad_time / result.primal_time
 end
 ```
 

From 14973adead84351c31450ad3029a8debaf530479 Mon Sep 17 00:00:00 2001
From: Markus Hauru <mhauru@turing.ac.uk>
Date: Wed, 20 Aug 2025 10:08:46 +0100
Subject: [PATCH 06/23] Fix VI tutorial

---
 tutorials/variational-inference/index.qmd | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/tutorials/variational-inference/index.qmd b/tutorials/variational-inference/index.qmd
index cd814b156..7d89ba904 100755
--- a/tutorials/variational-inference/index.qmd
+++ b/tutorials/variational-inference/index.qmd
@@ -182,8 +182,8 @@ Usually, `q_avg` will perform better than the last-iterate `q_last`.
 For instance, we can compare the ELBO of the two:
 ```{julia}
 @info("Objective of q_avg and q_last",
-    ELBO_q_avg = estimate_objective(AdvancedVI.RepGradELBO(32), q_avg, Turing.Variational.make_logdensity(m)),
-    ELBO_q_last = estimate_objective(AdvancedVI.RepGradELBO(32), q_last, Turing.Variational.make_logdensity(m)) 
+    ELBO_q_avg = estimate_objective(AdvancedVI.RepGradELBO(32), q_avg, LogDensityFunction(m)),
+    ELBO_q_last = estimate_objective(AdvancedVI.RepGradELBO(32), q_last, LogDensityFunction(m))
 )
 ```
 We can see that `ELBO_q_avg` is slightly more optimal.
@@ -205,9 +205,9 @@ For example, the following callback function estimates the ELBO on `q_avg` every
 ```{julia}
 function callback(; stat, averaged_params, restructure, kwargs...)
     if mod(stat.iteration, 10) == 1
-        q_avg    = restructure(averaged_params)
-        obj      = AdvancedVI.RepGradELBO(128)
-        elbo_avg = estimate_objective(obj, q_avg, Turing.Variational.make_logdensity(m))
+        q_avg = restructure(averaged_params)
+        obj = AdvancedVI.RepGradELBO(128)
+        elbo_avg = estimate_objective(obj, q_avg, LogDensityFunction(m))
         (elbo_avg = elbo_avg,)
     else
         nothing
@@ -223,7 +223,7 @@ q_mf, _, info_mf, _ = vi(m, q_init, n_iters; show_progress=false, callback=callb
 
 Let's plot the result:
 ```{julia}
-iters   = 1:10:length(info_mf)
+iters = 1:10:length(info_mf)
 elbo_mf = [i.elbo_avg for i in info_mf[iters]]
 Plots.plot!(iters, elbo_mf, xlabel="Iterations", ylabel="ELBO", label="callback", ylims=(-200,Inf))
 ```
@@ -247,7 +247,7 @@ _, _, info_adam, _ = vi(m, q_init, n_iters; show_progress=false, callback=callba
 ```
 
 ```{julia}
-iters     = 1:10:length(info_mf)
+iters = 1:10:length(info_mf)
 elbo_adam = [i.elbo_avg for i in info_adam[iters]]
 Plots.plot(iters, elbo_mf, xlabel="Iterations", ylabel="ELBO", label="DoWG")
 Plots.plot!(iters, elbo_adam, xlabel="Iterations", ylabel="ELBO", label="Adam")

From 06bb33d85cdb981e8e0a0dde2b5ba44cf715c87b Mon Sep 17 00:00:00 2001
From: Markus Hauru <mhauru@turing.ac.uk>
Date: Thu, 21 Aug 2025 16:25:34 +0100
Subject: [PATCH 07/23] Fix model-manual's use of contexts

---
 developers/compiler/model-manual/index.qmd | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/developers/compiler/model-manual/index.qmd b/developers/compiler/model-manual/index.qmd
index 4571254c8..a3e404122 100755
--- a/developers/compiler/model-manual/index.qmd
+++ b/developers/compiler/model-manual/index.qmd
@@ -33,21 +33,21 @@ Taking the `gdemo` model above as an example, the macro-based definition can be
 using DynamicPPL
 
 # Create the model function.
-function gdemo2(model, varinfo, context, x)
+function gdemo2(model, varinfo, x)
     # Assume s² has an InverseGamma distribution.
     s², varinfo = DynamicPPL.tilde_assume!!(
-        context, InverseGamma(2, 3), @varname(s²), varinfo
+        model.context, InverseGamma(2, 3), @varname(s²), varinfo
     )
 
     # Assume m has a Normal distribution.
     m, varinfo = DynamicPPL.tilde_assume!!(
-        context, Normal(0, sqrt(s²)), @varname(m), varinfo
+        model.context, Normal(0, sqrt(s²)), @varname(m), varinfo
     )
 
     # Observe each value of x[i] according to a Normal distribution.
     for i in eachindex(x)
         _retval, varinfo = DynamicPPL.tilde_observe!!(
-            context, Normal(m, sqrt(s²)), x[i], @varname(x[i]), varinfo
+            model.context, Normal(m, sqrt(s²)), x[i], @varname(x[i]), varinfo
         )
     end
 

From e7519c9f5531b2be655bae638e790b0bc21705d2 Mon Sep 17 00:00:00 2001
From: Markus Hauru <mhauru@turing.ac.uk>
Date: Thu, 21 Aug 2025 16:42:10 +0100
Subject: [PATCH 08/23] Fix references to __context__

---
 developers/contexts/submodel-condition/index.qmd | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/developers/contexts/submodel-condition/index.qmd b/developers/contexts/submodel-condition/index.qmd
index 69fad0bd8..0294ce9e8 100755
--- a/developers/contexts/submodel-condition/index.qmd
+++ b/developers/contexts/submodel-condition/index.qmd
@@ -108,13 +108,13 @@ unwrap_sampling_context(ctx::DynamicPPL.SamplingContext) = ctx.context
 unwrap_sampling_context(ctx::DynamicPPL.AbstractContext) = ctx
 
 @model function inner()
-    println("inner context: $(unwrap_sampling_context(__context__))")
+    println("inner context: $(unwrap_sampling_context(model.context))")
     x ~ Normal()
     return y ~ Normal()
 end
 
 @model function outer()
-    println("outer context: $(unwrap_sampling_context(__context__))")
+    println("outer context: $(unwrap_sampling_context(model.context))")
     return a ~ to_submodel(inner())
 end
 
@@ -124,7 +124,7 @@ 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(__context__))")
+    println("outer context: $(unwrap_sampling_context(model.context))")
     return a ~ to_submodel(inner_cond)
 end
 with_inner_cond = outer2()

From 45302476cfe89a00e1b0bffab679ec3ad5201e24 Mon Sep 17 00:00:00 2001
From: Markus Hauru <mhauru@turing.ac.uk>
Date: Thu, 21 Aug 2025 16:45:30 +0100
Subject: [PATCH 09/23] Fix use of addlogprob for log prior

---
 usage/modifying-logprob/index.qmd | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/usage/modifying-logprob/index.qmd b/usage/modifying-logprob/index.qmd
index b3de9e7ee..0eb6f8b30 100755
--- a/usage/modifying-logprob/index.qmd
+++ b/usage/modifying-logprob/index.qmd
@@ -47,13 +47,10 @@ using LinearAlgebra
 end
 ```
 
-Note that `@addlogprob!` always increases the accumulated log probability, regardless of the provided
-sampling context.
-For instance, if you do not want to apply `@addlogprob!` when evaluating the prior of your model but only when computing the log likelihood and the log joint probability, then you should [check the type of the internal variable `__context_`](https://github.com/TuringLang/DynamicPPL.jl/issues/154), as in the following example:
+Note that `@addlogprob!` increases the accumulated log likelihood.
+If instead you want to add to the log prior, you can use
 
 ```{julia}
 #| eval: false
-if DynamicPPL.leafcontext(__context__) !== Turing.PriorContext()
-    @addlogprob! myloglikelihood(x, μ)
-end
+@addlogprob! (; logprior=value_goes_here)
 ```

From 57c31626d199ebda82ac666cbe8daf51ab7a5c8c Mon Sep 17 00:00:00 2001
From: Markus Hauru <mhauru@turing.ac.uk>
Date: Tue, 16 Sep 2025 16:31:02 +0100
Subject: [PATCH 10/23] Fix typo

---
 developers/contexts/submodel-condition/index.qmd | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/developers/contexts/submodel-condition/index.qmd b/developers/contexts/submodel-condition/index.qmd
index 0294ce9e8..3519116bf 100755
--- a/developers/contexts/submodel-condition/index.qmd
+++ b/developers/contexts/submodel-condition/index.qmd
@@ -108,13 +108,13 @@ 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: $(unwrap_sampling_context(__model__.context))")
     x ~ Normal()
     return y ~ Normal()
 end
 
 @model function outer()
-    println("outer context: $(unwrap_sampling_context(model.context))")
+    println("outer context: $(unwrap_sampling_context(__model__.context))")
     return a ~ to_submodel(inner())
 end
 
@@ -124,7 +124,7 @@ 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: $(unwrap_sampling_context(__model__.context))")
     return a ~ to_submodel(inner_cond)
 end
 with_inner_cond = outer2()

From 2065a14f8770c2766d0b359b9ae294db05d5ea77 Mon Sep 17 00:00:00 2001
From: Markus Hauru <mhauru@turing.ac.uk>
Date: Tue, 16 Sep 2025 16:55:56 +0100
Subject: [PATCH 11/23] Regenerate manifest

---
 Manifest.toml | 406 +++++++++++++++++++++++++++-----------------------
 1 file changed, 219 insertions(+), 187 deletions(-)

diff --git a/Manifest.toml b/Manifest.toml
index 2f8687805..0a95cce1c 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -2,12 +2,12 @@
 
 julia_version = "1.11.6"
 manifest_format = "2.0"
-project_hash = "0250fe85007baf77c93e2189ee544ed354b8099e"
+project_hash = "9f86f29e94eb0d08fa3f55118bf3765e18345c9e"
 
 [[deps.ADTypes]]
-git-tree-sha1 = "60665b326b75db6517939d0e1875850bc4a54368"
+git-tree-sha1 = "27cecae79e5cc9935255f90c53bb831cc3c870d7"
 uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
-version = "1.17.0"
+version = "1.18.0"
 weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"]
 
     [deps.ADTypes.extensions]
@@ -34,19 +34,19 @@ version = "0.5.24"
 
 [[deps.AbstractMCMC]]
 deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "FillArrays", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers", "UUIDs"]
-git-tree-sha1 = "e4b6a25ba2e033c74ea11720daacafbc2ab50a7e"
+git-tree-sha1 = "2b33cfcb3f32819e02bf949e7546a1d59247884e"
 uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
-version = "5.7.2"
+version = "5.8.0"
 
 [[deps.AbstractPPL]]
-deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "Random", "StatsBase"]
-git-tree-sha1 = "b7a856399119394a573141c553aeb5b674a500b5"
+deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "LinearAlgebra", "Random", "StatsBase"]
+git-tree-sha1 = "3a9c1e6e7418494454260b0c8efd7b00fca251bc"
 uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf"
-version = "0.13.0"
-weakdeps = ["Distributions", "LinearAlgebra"]
+version = "0.13.1"
+weakdeps = ["Distributions"]
 
     [deps.AbstractPPL.extensions]
-    AbstractPPLDistributionsExt = ["Distributions", "LinearAlgebra"]
+    AbstractPPLDistributionsExt = ["Distributions"]
 
 [[deps.AbstractTrees]]
 git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177"
@@ -90,9 +90,9 @@ weakdeps = ["SparseArrays", "StaticArrays"]
 
 [[deps.AdvancedHMC]]
 deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Setfield", "Statistics", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "22496647c061d00217759e95a18d601c959df0c9"
+git-tree-sha1 = "e5625ace51e1f11f479b24017193bc7fdfef73a2"
 uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-version = "0.8.1"
+version = "0.8.2"
 
     [deps.AdvancedHMC.extensions]
     AdvancedHMCADTypesExt = "ADTypes"
@@ -181,9 +181,9 @@ version = "3.5.1+1"
 
 [[deps.ArrayInterface]]
 deps = ["Adapt", "LinearAlgebra"]
-git-tree-sha1 = "9606d7832795cbef89e06a550475be300364a8aa"
+git-tree-sha1 = "dbd8c3bbbdbb5c2778f85f4422c39960eac65a42"
 uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
-version = "7.19.0"
+version = "7.20.0"
 
     [deps.ArrayInterface.extensions]
     ArrayInterfaceBandedMatricesExt = "BandedMatrices"
@@ -193,6 +193,7 @@ version = "7.19.0"
     ArrayInterfaceChainRulesCoreExt = "ChainRulesCore"
     ArrayInterfaceChainRulesExt = "ChainRules"
     ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore"
+    ArrayInterfaceMetalExt = "Metal"
     ArrayInterfaceReverseDiffExt = "ReverseDiff"
     ArrayInterfaceSparseArraysExt = "SparseArrays"
     ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore"
@@ -206,6 +207,7 @@ version = "7.19.0"
     ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2"
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
     GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
+    Metal = "dde4c033-4e86-420c-a63e-0dd931031962"
     ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
     SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
     StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
@@ -251,9 +253,9 @@ version = "1.1.0"
 
 [[deps.AxisArrays]]
 deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"]
-git-tree-sha1 = "16351be62963a67ac4083f748fdb3cca58bfd52f"
+git-tree-sha1 = "4126b08903b777c88edf1754288144a0492c05ad"
 uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
-version = "0.4.7"
+version = "0.4.8"
 
 [[deps.BandedMatrices]]
 deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"]
@@ -302,10 +304,10 @@ version = "0.1.1"
 
 [[deps.Bijectors]]
 deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Distributions", "DocStringExtensions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Roots", "SparseArrays", "Statistics"]
-git-tree-sha1 = "35ba30573d4f83242f1e788c87ca792c83553c9e"
+git-tree-sha1 = "1f8e2022a4f6dbbe3c7b60f728647973e7b514ef"
 uuid = "76274a88-744f-5084-9051-94815aaf08c4"
-version = "0.15.9"
-weakdeps = ["ChainRules", "DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyArrays", "Mooncake", "ReverseDiff", "Tracker"]
+version = "0.15.10"
+weakdeps = ["ChainRules", "DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyArrays", "Mooncake", "ReverseDiff"]
 
     [deps.Bijectors.extensions]
     BijectorsDistributionsADExt = "DistributionsAD"
@@ -315,7 +317,6 @@ weakdeps = ["ChainRules", "DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyA
     BijectorsMooncakeExt = "Mooncake"
     BijectorsReverseDiffChainRulesExt = ["ChainRules", "ReverseDiff"]
     BijectorsReverseDiffExt = "ReverseDiff"
-    BijectorsTrackerExt = "Tracker"
 
 [[deps.BitFlags]]
 git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d"
@@ -378,9 +379,9 @@ version = "1.9.0"
 
 [[deps.BracketingNonlinearSolve]]
 deps = ["CommonSolve", "ConcreteStructs", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"]
-git-tree-sha1 = "a9014924595b7a2c1dd14aac516e38fa10ada656"
+git-tree-sha1 = "90740f16aef91d898424bc11c1cabada475435e0"
 uuid = "70df07ce-3d50-431d-a3e7-ca6ddb60ac1e"
-version = "1.3.0"
+version = "1.4.0"
 weakdeps = ["ChainRulesCore", "ForwardDiff"]
 
     [deps.BracketingNonlinearSolve.extensions]
@@ -496,9 +497,9 @@ version = "0.7.8"
 
 [[deps.ColorSchemes]]
 deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"]
-git-tree-sha1 = "a656525c8b46aa6a1c76891552ed5381bb32ae7b"
+git-tree-sha1 = "b0fd3f56fa442f81e0a47815c92245acfaaa4e34"
 uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
-version = "3.30.0"
+version = "3.31.0"
 
 [[deps.ColorTypes]]
 deps = ["FixedPointNumbers", "Random"]
@@ -656,9 +657,9 @@ version = "1.16.0"
 
 [[deps.DataFrames]]
 deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
-git-tree-sha1 = "fb61b4812c49343d7ef0b533ba982c46021938a6"
+git-tree-sha1 = "c967271c27a95160e30432e011b58f42cd7501b5"
 uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-version = "1.7.0"
+version = "1.8.0"
 
 [[deps.DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
@@ -689,9 +690,9 @@ version = "0.1.2"
 
 [[deps.DelayDiffEq]]
 deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "FastBroadcast", "ForwardDiff", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqRosenbrock", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack", "SymbolicIndexingInterface"]
-git-tree-sha1 = "d9b1e66070ce15bc2b9c3d5af6b94f693fc03ba4"
+git-tree-sha1 = "c50981fb5b6441a1213debb1423385a462e88032"
 uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb"
-version = "5.58.0"
+version = "5.56.0"
 
 [[deps.DelimitedFiles]]
 deps = ["Mmap"]
@@ -706,15 +707,14 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d"
 version = "0.4.0"
 
 [[deps.DiffEqBase]]
-deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "TruncatedStacktraces"]
-git-tree-sha1 = "6fecfae8b2d9983e939378c8eacff6562e8a2567"
+deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "TruncatedStacktraces"]
+git-tree-sha1 = "6df3b15d504315ec306118aed14f9d7af9f83db1"
 uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
-version = "6.183.0"
+version = "6.189.1"
 
     [deps.DiffEqBase.extensions]
     DiffEqBaseCUDAExt = "CUDA"
     DiffEqBaseChainRulesCoreExt = "ChainRulesCore"
-    DiffEqBaseDistributionsExt = "Distributions"
     DiffEqBaseEnzymeExt = ["ChainRulesCore", "Enzyme"]
     DiffEqBaseForwardDiffExt = ["ForwardDiff"]
     DiffEqBaseGTPSAExt = "GTPSA"
@@ -781,9 +781,9 @@ version = "7.16.1"
 
 [[deps.DifferentiationInterface]]
 deps = ["ADTypes", "LinearAlgebra"]
-git-tree-sha1 = "54d7b8c74408048aea9c055ac8573b2b5c5ec11f"
+git-tree-sha1 = "16946a4d305607c3a4af54ff35d56f0e9444ed0e"
 uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
-version = "0.7.4"
+version = "0.7.7"
 
     [deps.DifferentiationInterface.extensions]
     DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore"
@@ -899,9 +899,9 @@ version = "3.5.1"
 
 [[deps.DynamicPPL]]
 deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Chairmarks", "Compat", "ConstructionBase", "DifferentiationInterface", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Printf", "Random", "Requires", "Statistics", "Test"]
-git-tree-sha1 = "e36add2952240379bd53b83e76cfd3a8c56748d6"
+git-tree-sha1 = "65649377104973412c10fb00ebc2f8430dcf8b93"
 uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8"
-version = "0.37.0"
+version = "0.37.2"
 
     [deps.DynamicPPL.extensions]
     DynamicPPLChainRulesCoreExt = ["ChainRulesCore"]
@@ -933,9 +933,9 @@ version = "1.0.5"
 
 [[deps.Enzyme]]
 deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "InteractiveUtils", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"]
-git-tree-sha1 = "1a9c9e3401f5d024612a70d24a19517b2dbc1824"
+git-tree-sha1 = "66ec698bd4791c8d2b2be2fe2a472d1dd76a5c7d"
 uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9"
-version = "0.13.67"
+version = "0.13.75"
 
     [deps.Enzyme.extensions]
     EnzymeBFloat16sExt = "BFloat16s"
@@ -954,9 +954,9 @@ version = "0.13.67"
     StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [[deps.EnzymeCore]]
-git-tree-sha1 = "8272a687bca7b5c601c0c24fc0c71bff10aafdfd"
+git-tree-sha1 = "787f5e2efb33af12cc3fde313c1b0195a3f08eba"
 uuid = "f151be2c-9106-41f4-ab19-57ee4f262869"
-version = "0.8.12"
+version = "0.8.13"
 weakdeps = ["Adapt"]
 
     [deps.EnzymeCore.extensions]
@@ -964,9 +964,9 @@ weakdeps = ["Adapt"]
 
 [[deps.Enzyme_jll]]
 deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"]
-git-tree-sha1 = "a357a553f8dfd461756ff8ed66fd541bdf2d1588"
+git-tree-sha1 = "bf15bd2b3ddff92fc5bb5687ffe074ebd814c756"
 uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef"
-version = "0.0.188+0"
+version = "0.0.196+0"
 
 [[deps.EpollShim_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -982,9 +982,9 @@ version = "0.1.11"
 
 [[deps.Expat_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "d55dffd9ae73ff72f1c0482454dcf2ec6c6c4a63"
+git-tree-sha1 = "7bb1361afdb33c7f2b085aa49ea8fe1b0fb14e58"
 uuid = "2e619515-83b5-522b-bb60-26c02a35a201"
-version = "2.6.5+0"
+version = "2.7.1+0"
 
 [[deps.ExponentialUtilities]]
 deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"]
@@ -1019,10 +1019,10 @@ uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5"
 version = "7.1.1+0"
 
 [[deps.FFTW]]
-deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"]
-git-tree-sha1 = "797762812ed063b9b94f6cc7742bc8883bb5e69e"
+deps = ["AbstractFFTs", "FFTW_jll", "Libdl", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"]
+git-tree-sha1 = "97f08406df914023af55ade2f843c39e99c5d969"
 uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
-version = "1.9.0"
+version = "1.10.0"
 
 [[deps.FFTW_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -1115,9 +1115,9 @@ version = "1.11.0"
 
 [[deps.FillArrays]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "6a70198746448456524cb442b8af316927ff3e1a"
+git-tree-sha1 = "173e4d8f14230a7523ae11b9a3fa9edb3e0efd78"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "1.13.0"
+version = "1.14.0"
 weakdeps = ["PDMats", "SparseArrays", "Statistics"]
 
     [deps.FillArrays.extensions]
@@ -1127,9 +1127,9 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"]
 
 [[deps.FiniteDiff]]
 deps = ["ArrayInterface", "LinearAlgebra", "Setfield"]
-git-tree-sha1 = "d84e026183bb3fc764110ae98792c2e004f8c240"
+git-tree-sha1 = "31fd32af86234b6b71add76229d53129aa1b87a9"
 uuid = "6a86dc24-6348-571c-b903-95158fe2bd41"
-version = "2.28.0"
+version = "2.28.1"
 
     [deps.FiniteDiff.extensions]
     FiniteDiffBandedMatricesExt = "BandedMatrices"
@@ -1173,9 +1173,9 @@ version = "0.16.5"
 
 [[deps.Fontconfig_jll]]
 deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"]
-git-tree-sha1 = "301b5d5d731a0654825f1f2e906990f7141a106b"
+git-tree-sha1 = "f85dac9a96a01087df6e3a749840015a0ca3817d"
 uuid = "a3f928ae-7b40-5064-980b-68af3947d34b"
-version = "2.16.0+0"
+version = "2.17.1+0"
 
 [[deps.Format]]
 git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc"
@@ -1184,9 +1184,9 @@ version = "1.3.7"
 
 [[deps.ForwardDiff]]
 deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"]
-git-tree-sha1 = "910febccb28d493032495b7009dce7d7f7aee554"
+git-tree-sha1 = "dc41303865a16274ecb8450c220021ce1e0cf05f"
 uuid = "f6369f11-7733-5829-9624-2563aa707210"
-version = "1.0.1"
+version = "1.2.1"
 weakdeps = ["StaticArrays"]
 
     [deps.ForwardDiff.extensions]
@@ -1280,11 +1280,17 @@ git-tree-sha1 = "45288942190db7c5f760f59c04495064eedf9340"
 uuid = "b0724c58-0f36-5564-988d-3bb0596ebc4a"
 version = "0.22.4+0"
 
+[[deps.Ghostscript_jll]]
+deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Zlib_jll"]
+git-tree-sha1 = "38044a04637976140074d0b0621c1edf0eb531fd"
+uuid = "61579ee1-b43e-5ca0-a5da-69d92c66a64b"
+version = "9.55.1+0"
+
 [[deps.Glib_jll]]
 deps = ["Artifacts", "GettextRuntime_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"]
-git-tree-sha1 = "35fbd0cefb04a516104b8e183ce0df11b70a3f1a"
+git-tree-sha1 = "50c11ffab2a3d50192a228c313f05b5b5dc5acb2"
 uuid = "7746bdde-850d-59dc-9ae8-88ece973131d"
-version = "2.84.3+0"
+version = "2.86.0+0"
 
 [[deps.Graphite2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -1294,9 +1300,9 @@ version = "1.3.15+0"
 
 [[deps.Graphs]]
 deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
-git-tree-sha1 = "c5abfa0ae0aaee162a3fbb053c13ecda39be545b"
+git-tree-sha1 = "7a98c6502f4632dbe9fb1973a4244eaa3324e84d"
 uuid = "86223c79-3864-5bf0-83f7-82e725a168b6"
-version = "1.13.0"
+version = "1.13.1"
 
 [[deps.Grisu]]
 git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2"
@@ -1358,9 +1364,9 @@ uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c"
 version = "0.3.1"
 
 [[deps.InlineStrings]]
-git-tree-sha1 = "8594fac023c5ce1ef78260f24d1ad18b4327b420"
+git-tree-sha1 = "8f3d257792a522b4601c24a577954b0a8cd7334d"
 uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48"
-version = "1.4.4"
+version = "1.4.5"
 
     [deps.InlineStrings.extensions]
     ArrowTypesExt = "ArrowTypes"
@@ -1458,9 +1464,9 @@ version = "0.2.1"
 
 [[deps.JpegTurbo_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "eac1206917768cb54957c65a615460d87b455fc1"
+git-tree-sha1 = "4255f0032eafd6451d707a51d5f0248b8a165e4d"
 uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8"
-version = "3.1.1+0"
+version = "3.1.3+0"
 
 [[deps.JuliaVariables]]
 deps = ["MLStyle", "NameResolution"]
@@ -1469,10 +1475,10 @@ uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec"
 version = "0.2.4"
 
 [[deps.JumpProcesses]]
-deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"]
-git-tree-sha1 = "f5b57507a36f05509e72120aa84d5c3747dbd70e"
+deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "PoissonRandom", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"]
+git-tree-sha1 = "905a2a28770e23f3ed750306ef48eb8c46c3a002"
 uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
-version = "9.17.0"
+version = "9.19.1"
 weakdeps = ["Adapt", "FastBroadcast", "KernelAbstractions"]
 
     [deps.JumpProcesses.extensions]
@@ -1568,10 +1574,10 @@ uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 version = "1.4.0"
 
 [[deps.Latexify]]
-deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"]
-git-tree-sha1 = "52e1296ebbde0db845b356abbbe67fb82a0a116c"
+deps = ["Format", "Ghostscript_jll", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"]
+git-tree-sha1 = "44f93c47f9cd6c7e431f2f2091fcba8f01cd7e8f"
 uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
-version = "0.16.9"
+version = "0.16.10"
 
     [deps.Latexify.extensions]
     DataFramesExt = "DataFrames"
@@ -1693,9 +1699,9 @@ version = "1.18.0+0"
 
 [[deps.Libmount_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "a31572773ac1b745e0343fe5e2c8ddda7a37e997"
+git-tree-sha1 = "706dfd3c0dd56ca090e86884db6eda70fa7dd4af"
 uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9"
-version = "2.41.0+0"
+version = "2.41.1+0"
 
 [[deps.Libtask]]
 deps = ["MistyClosures", "Test"]
@@ -1711,9 +1717,9 @@ version = "4.7.1+0"
 
 [[deps.Libuuid_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "321ccef73a96ba828cd51f2ab5b9f917fa73945a"
+git-tree-sha1 = "d3c8af829abaeba27181db4acb485b18d15d89c6"
 uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700"
-version = "2.41.0+0"
+version = "2.41.1+0"
 
 [[deps.LineSearch]]
 deps = ["ADTypes", "CommonSolve", "ConcreteStructs", "FastClosures", "LinearAlgebra", "MaybeInplace", "SciMLBase", "SciMLJacobianOperators", "StaticArraysCore"]
@@ -1737,10 +1743,10 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 version = "1.11.0"
 
 [[deps.LinearSolve]]
-deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"]
-git-tree-sha1 = "1c597eceb5ead73dae17ffa4dcc1160e3e4da1f3"
+deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "OpenBLAS_jll", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"]
+git-tree-sha1 = "69cee52e516c859e64adba702ac382c0498a4e29"
 uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
-version = "3.28.0"
+version = "3.40.0"
 
     [deps.LinearSolve.extensions]
     LinearSolveAMDGPUExt = "AMDGPU"
@@ -1750,6 +1756,7 @@ version = "3.28.0"
     LinearSolveCUDAExt = "CUDA"
     LinearSolveCUDSSExt = "CUDSS"
     LinearSolveCUSOLVERRFExt = ["CUSOLVERRF", "SparseArrays"]
+    LinearSolveCliqueTreesExt = ["CliqueTrees", "SparseArrays"]
     LinearSolveEnzymeExt = "EnzymeCore"
     LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices"
     LinearSolveFastLapackInterfaceExt = "FastLapackInterface"
@@ -1771,6 +1778,7 @@ version = "3.28.0"
     CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
     CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e"
     CUSOLVERRF = "a8cc9031-bad2-4722-94f5-40deabb4245c"
+    CliqueTrees = "60701a23-6482-424a-84db-faee86b9b1f8"
     EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
     FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e"
     FastLapackInterface = "29a986be-02c6-4525-aec4-84b980013641"
@@ -1845,9 +1853,9 @@ version = "1.1.0"
 
 [[deps.Lux]]
 deps = ["ADTypes", "Adapt", "ArgCheck", "ArrayInterface", "ChainRulesCore", "Compat", "ConcreteStructs", "DiffResults", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "GPUArraysCore", "LinearAlgebra", "LuxCore", "LuxLib", "MLDataDevices", "MacroTools", "Markdown", "NNlib", "Optimisers", "Preferences", "Random", "Reexport", "SIMDTypes", "Setfield", "Static", "StaticArraysCore", "Statistics", "WeightInitializers"]
-git-tree-sha1 = "c05e5c3dca1810e728429771763b485057322ad2"
+git-tree-sha1 = "c300d2df439a343a840dd8ef6b0910ce4cafc8c6"
 uuid = "b2108857-7c20-44ae-9111-449ecde12c47"
-version = "1.16.0"
+version = "1.21.1"
 
     [deps.Lux.extensions]
     LuxComponentArraysExt = "ComponentArrays"
@@ -1884,9 +1892,9 @@ version = "1.16.0"
 
 [[deps.LuxCore]]
 deps = ["Compat", "DispatchDoctor", "Random"]
-git-tree-sha1 = "a72b6b530f39a87d1327b90f5def4bce48eb1a52"
+git-tree-sha1 = "cf12c8eba464132e781d7e000bcc4090e2b6e115"
 uuid = "bb33d45b-7691-41d6-9220-0943567d0623"
-version = "1.3.0"
+version = "1.4.1"
 
     [deps.LuxCore.extensions]
     LuxCoreArrayInterfaceReverseDiffExt = ["ArrayInterface", "ReverseDiff"]
@@ -1903,6 +1911,7 @@ version = "1.3.0"
     ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
     EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
+    Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
     Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
     MLDataDevices = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40"
     Reactant = "3c362404-f566-11ee-1572-e11a4b42c853"
@@ -1912,9 +1921,9 @@ version = "1.3.0"
 
 [[deps.LuxLib]]
 deps = ["ArrayInterface", "CPUSummary", "ChainRulesCore", "Compat", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "KernelAbstractions", "LinearAlgebra", "LuxCore", "MLDataDevices", "Markdown", "NNlib", "Polyester", "Preferences", "Random", "Reexport", "Static", "StaticArraysCore", "Statistics"]
-git-tree-sha1 = "bf64921ca8182e3ee34a56b05b9f1ed568141a13"
+git-tree-sha1 = "109240d7ba4698e7eb60b11f190424b8ca018318"
 uuid = "82251201-b29d-42c6-8e01-566dec8acb11"
-version = "1.10.1"
+version = "1.11.2"
 
     [deps.LuxLib.extensions]
     LuxLibAppleAccelerateExt = "AppleAccelerate"
@@ -1923,9 +1932,8 @@ version = "1.10.1"
     LuxLibEnzymeExt = "Enzyme"
     LuxLibLoopVectorizationExt = "LoopVectorization"
     LuxLibMKLExt = "MKL"
-    LuxLibMooncakeExt = "Mooncake"
     LuxLibOctavianExt = ["Octavian", "LoopVectorization"]
-    LuxLibReactantExt = "Reactant"
+    LuxLibReactantExt = ["Reactant", "ReactantCore"]
     LuxLibReverseDiffExt = "ReverseDiff"
     LuxLibSLEEFPiratesExt = "SLEEFPirates"
     LuxLibTrackerAMDGPUExt = ["AMDGPU", "Tracker"]
@@ -1940,9 +1948,9 @@ version = "1.10.1"
     Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
     LoopVectorization = "bdcacae8-1622-11e9-2a5c-532679323890"
     MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
-    Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
     Octavian = "6fd5a793-0b7e-452c-907f-f8bfe9c57db4"
     Reactant = "3c362404-f566-11ee-1572-e11a4b42c853"
+    ReactantCore = "a3311ec8-5e00-46d5-b541-4f83e724a433"
     ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
     SLEEFPirates = "476501e8-09a2-5ece-8869-fb82de89a1fa"
     Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
@@ -1950,9 +1958,9 @@ version = "1.10.1"
 
 [[deps.MCMCChains]]
 deps = ["AbstractMCMC", "AxisArrays", "DataAPI", "Dates", "Distributions", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"]
-git-tree-sha1 = "a1b9bf62acb012e4a717562f83f859257c5b6fec"
+git-tree-sha1 = "902175f1618baa58dc50dc2894d382bbd484adf4"
 uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
-version = "7.1.0"
+version = "7.3.0"
 
 [[deps.MCMCDiagnosticTools]]
 deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"]
@@ -1974,9 +1982,9 @@ version = "1.0.0"
 
 [[deps.MLDataDevices]]
 deps = ["Adapt", "Compat", "Functors", "Preferences", "Random"]
-git-tree-sha1 = "0ad0d8f83ddf28a7eba28ed94d0d68015ce645b7"
+git-tree-sha1 = "39bac90ff3e88e086426f05a3e97646f91088a7f"
 uuid = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40"
-version = "1.11.1"
+version = "1.12.0"
 
     [deps.MLDataDevices.extensions]
     MLDataDevicesAMDGPUExt = "AMDGPU"
@@ -2144,9 +2152,9 @@ version = "0.8.1"
 
 [[deps.Mooncake]]
 deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "DispatchDoctor", "ExprTools", "FunctionWrappers", "GPUArraysCore", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Test"]
-git-tree-sha1 = "88bb6e5054ba4a341c8fb7047af859720669628d"
+git-tree-sha1 = "2aa902cb9f45dbeaaae5eaa98559d600b1f5deb7"
 uuid = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
-version = "0.4.142"
+version = "0.4.159"
 
     [deps.Mooncake.extensions]
     MooncakeAllocCheckExt = "AllocCheck"
@@ -2154,7 +2162,7 @@ version = "0.4.142"
     MooncakeDynamicExpressionsExt = "DynamicExpressions"
     MooncakeFluxExt = "Flux"
     MooncakeJETExt = "JET"
-    MooncakeLuxLibExt = "LuxLib"
+    MooncakeLuxLibExt = ["LuxLib", "MLDataDevices", "Static"]
     MooncakeLuxLibSLEEFPiratesExtension = ["LuxLib", "SLEEFPirates"]
     MooncakeNNlibExt = "NNlib"
     MooncakeSpecialFunctionsExt = "SpecialFunctions"
@@ -2166,9 +2174,11 @@ version = "0.4.142"
     Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
     JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
     LuxLib = "82251201-b29d-42c6-8e01-566dec8acb11"
+    MLDataDevices = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40"
     NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
     SLEEFPirates = "476501e8-09a2-5ece-8869-fb82de89a1fa"
     SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+    Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
 
 [[deps.Moshi]]
 deps = ["ExproniconLite", "Jieko"]
@@ -2311,42 +2321,46 @@ version = "4.10.0"
     Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"
 
 [[deps.NonlinearSolveBase]]
-deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"]
-git-tree-sha1 = "1d42a315ba627ca0027d49d0efb44e3d88db24aa"
+deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "SciMLStructures", "Setfield", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"]
+git-tree-sha1 = "99a400f7ad42e56431c76f3eadee0755f2123fda"
 uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0"
-version = "1.14.0"
-weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearSolve", "SparseArrays", "SparseMatrixColorings"]
+version = "1.15.0"
+weakdeps = ["BandedMatrices", "ChainRulesCore", "Enzyme", "ForwardDiff", "LineSearch", "LinearSolve", "Mooncake", "ReverseDiff", "SparseArrays", "SparseMatrixColorings", "Tracker"]
 
     [deps.NonlinearSolveBase.extensions]
     NonlinearSolveBaseBandedMatricesExt = "BandedMatrices"
-    NonlinearSolveBaseDiffEqBaseExt = "DiffEqBase"
+    NonlinearSolveBaseChainRulesCoreExt = "ChainRulesCore"
+    NonlinearSolveBaseEnzymeExt = ["ChainRulesCore", "Enzyme"]
     NonlinearSolveBaseForwardDiffExt = "ForwardDiff"
     NonlinearSolveBaseLineSearchExt = "LineSearch"
     NonlinearSolveBaseLinearSolveExt = "LinearSolve"
+    NonlinearSolveBaseMooncakeExt = "Mooncake"
+    NonlinearSolveBaseReverseDiffExt = "ReverseDiff"
     NonlinearSolveBaseSparseArraysExt = "SparseArrays"
     NonlinearSolveBaseSparseMatrixColoringsExt = "SparseMatrixColorings"
+    NonlinearSolveBaseTrackerExt = "Tracker"
 
 [[deps.NonlinearSolveFirstOrder]]
-deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"]
-git-tree-sha1 = "3f1198ae5cbf21e84b8251a9e62fa1f888f3e4cb"
+deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"]
+git-tree-sha1 = "b9702235120d1161f8041b326eccebd334340de2"
 uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d"
-version = "1.7.0"
+version = "1.8.0"
 
 [[deps.NonlinearSolveQuasiNewton]]
-deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"]
-git-tree-sha1 = "40dfaf1bf74f1f700f81d0002d4dd90999598eb2"
+deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"]
+git-tree-sha1 = "4e0e34601c6c9890aa9443003180967f75c6929d"
 uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114"
-version = "1.8.0"
+version = "1.9.0"
 weakdeps = ["ForwardDiff"]
 
     [deps.NonlinearSolveQuasiNewton.extensions]
     NonlinearSolveQuasiNewtonForwardDiffExt = "ForwardDiff"
 
 [[deps.NonlinearSolveSpectralMethods]]
-deps = ["CommonSolve", "ConcreteStructs", "DiffEqBase", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"]
-git-tree-sha1 = "84de5a469e119eb2c22ae07c543dc4e7f7001ee7"
+deps = ["CommonSolve", "ConcreteStructs", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"]
+git-tree-sha1 = "6c613302febe2bb408a888105d07073cf6824911"
 uuid = "26075421-4e9a-44e1-8bd1-420ed7ad02b2"
-version = "1.3.0"
+version = "1.4.0"
 weakdeps = ["ForwardDiff"]
 
     [deps.NonlinearSolveSpectralMethods.extensions]
@@ -2441,16 +2455,16 @@ version = "0.4.6"
     Reactant = "3c362404-f566-11ee-1572-e11a4b42c853"
 
 [[deps.Optimization]]
-deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Printf", "ProgressLogging", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"]
-git-tree-sha1 = "41902230755effe29a8599ea4b61dc3ffc2c952d"
+deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Printf", "ProgressLogging", "Random", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"]
+git-tree-sha1 = "1e02b79bf6175d723a40745f622e9513253bab55"
 uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
-version = "4.5.0"
+version = "4.7.0"
 
 [[deps.OptimizationBase]]
-deps = ["ADTypes", "ArrayInterface", "DifferentiationInterface", "DocStringExtensions", "FastClosures", "LinearAlgebra", "PDMats", "Reexport", "Requires", "SciMLBase", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"]
-git-tree-sha1 = "474b2fa6de9288d34b8ad42c9c500088132621a7"
+deps = ["ADTypes", "ArrayInterface", "DifferentiationInterface", "DocStringExtensions", "FastClosures", "LinearAlgebra", "PDMats", "Reexport", "SciMLBase", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"]
+git-tree-sha1 = "4f6098addb09203f35de1b21d5e668315544ff26"
 uuid = "bca83a33-5cc9-4baa-983d-23429ab6bcbb"
-version = "2.10.0"
+version = "2.11.0"
 
     [deps.OptimizationBase.extensions]
     OptimizationEnzymeExt = "Enzyme"
@@ -2476,15 +2490,15 @@ version = "2.10.0"
 
 [[deps.OptimizationNLopt]]
 deps = ["NLopt", "Optimization", "Random", "Reexport"]
-git-tree-sha1 = "da55bae039168c0ef977bd5926cd5208c6cd13cf"
+git-tree-sha1 = "83e469a5b058250e95121afeea71da14034b24a4"
 uuid = "4e6fcdb7-1186-4e1f-a706-475e75c168bb"
-version = "0.3.2"
+version = "0.3.3"
 
 [[deps.OptimizationOptimJL]]
 deps = ["Optim", "Optimization", "PrecompileTools", "Reexport", "SparseArrays"]
-git-tree-sha1 = "6f228118b81ce4e849091ee0d00805f2ecb18f54"
+git-tree-sha1 = "a6194340cb4f7d61cec9d6f605848d6a187c64b6"
 uuid = "36348300-93cb-4f02-beb5-3c3902f8871e"
-version = "0.4.3"
+version = "0.4.4"
 
 [[deps.Opus_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -2498,10 +2512,10 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 version = "1.8.1"
 
 [[deps.OrdinaryDiffEq]]
-deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqAdamsBashforthMoulton", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqExplicitRK", "OrdinaryDiffEqExponentialRK", "OrdinaryDiffEqExtrapolation", "OrdinaryDiffEqFIRK", "OrdinaryDiffEqFeagin", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqHighOrderRK", "OrdinaryDiffEqIMEXMultistep", "OrdinaryDiffEqLinear", "OrdinaryDiffEqLowOrderRK", "OrdinaryDiffEqLowStorageRK", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqNordsieck", "OrdinaryDiffEqPDIRK", "OrdinaryDiffEqPRK", "OrdinaryDiffEqQPRK", "OrdinaryDiffEqRKN", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqSDIRK", "OrdinaryDiffEqSSPRK", "OrdinaryDiffEqStabilizedIRK", "OrdinaryDiffEqStabilizedRK", "OrdinaryDiffEqSymplecticRK", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
-git-tree-sha1 = "55c21fdb4626037cdbcb04fec3afa192345a24de"
+deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqAdamsBashforthMoulton", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqExplicitRK", "OrdinaryDiffEqExponentialRK", "OrdinaryDiffEqExtrapolation", "OrdinaryDiffEqFIRK", "OrdinaryDiffEqFeagin", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqHighOrderRK", "OrdinaryDiffEqIMEXMultistep", "OrdinaryDiffEqLinear", "OrdinaryDiffEqLowOrderRK", "OrdinaryDiffEqLowStorageRK", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqNordsieck", "OrdinaryDiffEqPDIRK", "OrdinaryDiffEqPRK", "OrdinaryDiffEqQPRK", "OrdinaryDiffEqRKN", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqSDIRK", "OrdinaryDiffEqSSPRK", "OrdinaryDiffEqStabilizedIRK", "OrdinaryDiffEqStabilizedRK", "OrdinaryDiffEqSymplecticRK", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
+git-tree-sha1 = "89cd4e81d7a668f8858fba6779212f41a0360260"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.101.0"
+version = "6.102.1"
 
 [[deps.OrdinaryDiffEqAdamsBashforthMoulton]]
 deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"]
@@ -2517,9 +2531,9 @@ version = "1.10.1"
 
 [[deps.OrdinaryDiffEqCore]]
 deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FastPower", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "SymbolicIndexingInterface", "TruncatedStacktraces"]
-git-tree-sha1 = "e579c9a4f9102e82da3d97c349a74d6bc11cf8dc"
+git-tree-sha1 = "688c717e8eee84dcfef02ddf71c8028215b329ca"
 uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8"
-version = "1.30.0"
+version = "1.34.0"
 weakdeps = ["EnzymeCore", "Mooncake"]
 
     [deps.OrdinaryDiffEqCore.extensions]
@@ -2533,10 +2547,14 @@ uuid = "50262376-6c5a-4cf5-baba-aaf4f84d72d7"
 version = "1.8.0"
 
 [[deps.OrdinaryDiffEqDifferentiation]]
-deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseMatrixColorings", "StaticArrayInterface", "StaticArrays"]
-git-tree-sha1 = "4c270747152db513dd80bfd5f2f9df48befff28a"
+deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SciMLOperators", "SparseMatrixColorings", "StaticArrayInterface", "StaticArrays"]
+git-tree-sha1 = "1fff7356ccb79ca1b1ff3276135fda68d4d661be"
 uuid = "4302a76b-040a-498a-8c04-15b101fed76b"
-version = "1.14.0"
+version = "1.16.0"
+weakdeps = ["SparseArrays"]
+
+    [deps.OrdinaryDiffEqDifferentiation.extensions]
+    OrdinaryDiffEqDifferentiationSparseArraysExt = "SparseArrays"
 
 [[deps.OrdinaryDiffEqExplicitRK]]
 deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"]
@@ -2552,9 +2570,9 @@ version = "1.8.0"
 
 [[deps.OrdinaryDiffEqExtrapolation]]
 deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastPower", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase"]
-git-tree-sha1 = "ee2cba2533e9faf71b09a319a910d4886931e7a6"
+git-tree-sha1 = "9e1b11cf448a2c1bca640103c1c848a20aa2f967"
 uuid = "becaefa8-8ca2-5cf9-886d-c06f3d2bd2c4"
-version = "1.8.0"
+version = "1.9.0"
 
 [[deps.OrdinaryDiffEqFIRK]]
 deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastGaussQuadrature", "FastPower", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators"]
@@ -2600,9 +2618,9 @@ version = "1.6.0"
 
 [[deps.OrdinaryDiffEqLowStorageRK]]
 deps = ["Adapt", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "StaticArrays"]
-git-tree-sha1 = "9291cdfd2e8c91e900c48d71d76618de47daeede"
+git-tree-sha1 = "e6bd0a7fb6643a57b06a90415608a81aaf7bd772"
 uuid = "b0944070-b475-4768-8dec-fb6eb410534d"
-version = "1.6.0"
+version = "1.7.0"
 
 [[deps.OrdinaryDiffEqNonlinearSolve]]
 deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "PreallocationTools", "RecursiveArrayTools", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "StaticArrays"]
@@ -2642,9 +2660,9 @@ version = "1.5.0"
 
 [[deps.OrdinaryDiffEqRosenbrock]]
 deps = ["ADTypes", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"]
-git-tree-sha1 = "a06c1263d71ea42a1881b4d49c8a087035d4a3ff"
+git-tree-sha1 = "f60d7201a2ceaa7e9a406942f0a2fa3e920715fa"
 uuid = "43230ef6-c299-4910-a778-202eb28ce4ce"
-version = "1.16.1"
+version = "1.18.0"
 
 [[deps.OrdinaryDiffEqSDIRK]]
 deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"]
@@ -2654,9 +2672,9 @@ version = "1.7.0"
 
 [[deps.OrdinaryDiffEqSSPRK]]
 deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "StaticArrays"]
-git-tree-sha1 = "af955c61407631d281dd4c2e8331cdfea1af49be"
+git-tree-sha1 = "3bce87977264916bd92455754ab336faec68bf8a"
 uuid = "669c94d9-1f4b-4b64-b377-1aa079aa2388"
-version = "1.6.0"
+version = "1.7.0"
 
 [[deps.OrdinaryDiffEqStabilizedIRK]]
 deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqStabilizedRK", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays"]
@@ -2707,9 +2725,9 @@ weakdeps = ["Requires", "TOML"]
 
 [[deps.Pango_jll]]
 deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "275a9a6d85dc86c24d03d1837a0010226a96f540"
+git-tree-sha1 = "1f7f9bbd5f7a2e5a9f7d96e51c9754454ea7f60b"
 uuid = "36c8627f-9965-5494-a995-c6b170f724f3"
-version = "1.56.3+0"
+version = "1.56.4+0"
 
 [[deps.Parameters]]
 deps = ["OrderedCollections", "UnPack"]
@@ -2752,9 +2770,9 @@ version = "1.4.3"
 
 [[deps.Plots]]
 deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"]
-git-tree-sha1 = "9a9216c0cf706cb2cc58fd194878180e3e51e8c0"
+git-tree-sha1 = "bfe839e9668f0c58367fb62d8757315c0eac8777"
 uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-version = "1.40.18"
+version = "1.40.20"
 
     [deps.Plots.extensions]
     FileIOExt = "FileIO"
@@ -2802,9 +2820,9 @@ version = "0.2.4"
 
 [[deps.PreallocationTools]]
 deps = ["Adapt", "ArrayInterface", "PrecompileTools"]
-git-tree-sha1 = "a0d5f963cfee70bee26dfa137a732e759e24436a"
+git-tree-sha1 = "c05b4c6325262152483a1ecb6c69846d2e01727b"
 uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46"
-version = "0.4.31"
+version = "0.4.34"
 weakdeps = ["ForwardDiff", "ReverseDiff", "SparseConnectivityTracer"]
 
     [deps.PreallocationTools.extensions]
@@ -2848,9 +2866,9 @@ version = "0.1.5"
 
 [[deps.ProgressMeter]]
 deps = ["Distributed", "Printf"]
-git-tree-sha1 = "13c5103482a8ed1536a54c08d0e742ae3dca2d42"
+git-tree-sha1 = "fbb92c6c56b34e1a2c4c36058f68f332bec840e7"
 uuid = "92933f4c-e287-5a05-a399-4b506db050ca"
-version = "1.10.4"
+version = "1.11.0"
 
 [[deps.PtrArrays]]
 git-tree-sha1 = "1d36ef11a9aaf1e8b74dacc6a731dd1de8fd493d"
@@ -2960,9 +2978,9 @@ version = "0.6.12"
 
 [[deps.RecursiveArrayTools]]
 deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
-git-tree-sha1 = "7c7ac305885b1e0292585d087ecd60331a705965"
+git-tree-sha1 = "96bef5b9ac123fff1b379acf0303cf914aaabdfd"
 uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
-version = "3.37.0"
+version = "3.37.1"
 
     [deps.RecursiveArrayTools.extensions]
     RecursiveArrayToolsFastBroadcastExt = "FastBroadcast"
@@ -3033,9 +3051,9 @@ version = "0.5.1+0"
 
 [[deps.Roots]]
 deps = ["Accessors", "CommonSolve", "Printf"]
-git-tree-sha1 = "668e411c0616a70860249b4c96e5d35296631a1d"
+git-tree-sha1 = "8a433b1ede5e9be9a7ba5b1cc6698daa8d718f1d"
 uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
-version = "2.2.8"
+version = "2.2.10"
 
     [deps.Roots.extensions]
     RootsChainRulesCoreExt = "ChainRulesCore"
@@ -3043,6 +3061,7 @@ version = "2.2.8"
     RootsIntervalRootFindingExt = "IntervalRootFinding"
     RootsSymPyExt = "SymPy"
     RootsSymPyPythonCallExt = "SymPyPythonCall"
+    RootsUnitfulExt = "Unitful"
 
     [deps.Roots.weakdeps]
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
@@ -3050,6 +3069,7 @@ version = "2.2.8"
     IntervalRootFinding = "d2bf35a9-74e0-55ec-b149-d360ff49b807"
     SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6"
     SymPyPythonCall = "bc8888f7-b21e-4b7c-a06a-5d9c9496438c"
+    Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [[deps.RuntimeGeneratedFunctions]]
 deps = ["ExprTools", "SHA", "Serialization"]
@@ -3068,48 +3088,64 @@ version = "0.1.0"
 
 [[deps.SSMProblems]]
 deps = ["AbstractMCMC", "Distributions", "Random"]
-git-tree-sha1 = "b00814e67e8aacda2073865a3832e6cc378ea504"
+git-tree-sha1 = "5dd0431563784b468db06335ce8777653092d621"
 uuid = "26aad666-b158-4e64-9d35-0e672562fa48"
-version = "0.5.1"
+version = "0.5.2"
 
 [[deps.SciMLBase]]
-deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
-git-tree-sha1 = "95ce48fe76b9530799429244392853b5405469c1"
+deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PreallocationTools", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
+git-tree-sha1 = "dfec1fce27c829814348266486b4cb8fdcb263fb"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "2.109.0"
+version = "2.119.0"
 
     [deps.SciMLBase.extensions]
     SciMLBaseChainRulesCoreExt = "ChainRulesCore"
+    SciMLBaseDistributionsExt = "Distributions"
+    SciMLBaseEnzymeExt = "Enzyme"
+    SciMLBaseForwardDiffExt = "ForwardDiff"
     SciMLBaseMLStyleExt = "MLStyle"
     SciMLBaseMakieExt = "Makie"
+    SciMLBaseMeasurementsExt = "Measurements"
+    SciMLBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements"
+    SciMLBaseMooncakeExt = "Mooncake"
     SciMLBasePartialFunctionsExt = "PartialFunctions"
     SciMLBasePyCallExt = "PyCall"
     SciMLBasePythonCallExt = "PythonCall"
     SciMLBaseRCallExt = "RCall"
+    SciMLBaseReverseDiffExt = "ReverseDiff"
+    SciMLBaseTrackerExt = "Tracker"
     SciMLBaseZygoteExt = ["Zygote", "ChainRulesCore"]
 
     [deps.SciMLBase.weakdeps]
     ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2"
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+    Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+    Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
+    ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
     MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
     Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+    Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"
+    MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca"
+    Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
     PartialFunctions = "570af359-4316-4cb7-8c74-252c00c2016b"
     PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
     PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
     RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
+    ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
+    Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
     Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [[deps.SciMLJacobianOperators]]
 deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"]
-git-tree-sha1 = "3414071e3458f3065de7fa5aed55283b236b4907"
+git-tree-sha1 = "a273b291c90909ba6fe08402dd68e09aae423008"
 uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e"
-version = "0.1.8"
+version = "0.1.11"
 
 [[deps.SciMLOperators]]
 deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"]
-git-tree-sha1 = "aea915a39b547c48a18ee041120db1ae8df5a691"
+git-tree-sha1 = "024d829102878141aaee5cf8f8288bcabd2f57a0"
 uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961"
-version = "1.5.0"
+version = "1.7.2"
 weakdeps = ["SparseArrays", "StaticArraysCore"]
 
     [deps.SciMLOperators.extensions]
@@ -3139,9 +3175,9 @@ version = "3.0.0"
 
 [[deps.ScopedValues]]
 deps = ["HashArrayMappedTries", "Logging"]
-git-tree-sha1 = "7f44eef6b1d284465fafc66baf4d9bdcc239a15b"
+git-tree-sha1 = "c3b2323466378a2ba15bea4b2f73b081e022f473"
 uuid = "7e506255-f358-4e82-b7e4-beb19740aa63"
-version = "1.4.0"
+version = "1.5.0"
 
 [[deps.Scratch]]
 deps = ["Dates"]
@@ -3193,14 +3229,13 @@ version = "1.2.0"
 
 [[deps.SimpleNonlinearSolve]]
 deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"]
-git-tree-sha1 = "09d986e27a606f172c5b6cffbd8b8b2f10bf1c75"
+git-tree-sha1 = "782c67176b473abf62a6786399c4b7ddcc1a2d77"
 uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7"
-version = "2.7.0"
-weakdeps = ["ChainRulesCore", "DiffEqBase", "ReverseDiff", "Tracker"]
+version = "2.8.0"
+weakdeps = ["ChainRulesCore", "ReverseDiff", "Tracker"]
 
     [deps.SimpleNonlinearSolve.extensions]
     SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore"
-    SimpleNonlinearSolveDiffEqBaseExt = "DiffEqBase"
     SimpleNonlinearSolveReverseDiffExt = "ReverseDiff"
     SimpleNonlinearSolveTrackerExt = "Tracker"
 
@@ -3232,9 +3267,9 @@ version = "1.11.0"
 
 [[deps.SparseConnectivityTracer]]
 deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"]
-git-tree-sha1 = "7bd2b8981cc57adcf5cf1add282aba2713a7058f"
+git-tree-sha1 = "e49c106eb7c78f55cdfa39e8bddeda24e1e09fce"
 uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5"
-version = "1.0.0"
+version = "1.0.2"
 weakdeps = ["LogExpFunctions", "NNlib", "NaNMath", "SpecialFunctions"]
 
     [deps.SparseConnectivityTracer.extensions]
@@ -3306,9 +3341,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"]
 
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
-git-tree-sha1 = "cbea8a6bd7bed51b1619658dec70035e07b8502f"
+git-tree-sha1 = "b8693004b385c842357406e3af647701fe783f98"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.9.14"
+version = "1.9.15"
 weakdeps = ["ChainRulesCore", "Statistics"]
 
     [deps.StaticArrays.extensions]
@@ -3361,9 +3396,9 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"]
 
 [[deps.StatsModels]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsAPI", "StatsBase", "StatsFuns", "Tables"]
-git-tree-sha1 = "728d276a5adc2f1cbb800eec4b63d0a8221024b4"
+git-tree-sha1 = "85a43f6fc30dd80c61342519ca2fc36dac912eae"
 uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
-version = "0.7.5"
+version = "0.7.6"
 
 [[deps.StatsPlots]]
 deps = ["AbstractFFTs", "Clustering", "DataStructures", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "NaNMath", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"]
@@ -3379,15 +3414,15 @@ version = "2.5.0"
 
 [[deps.StochasticDiffEq]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FastPower", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "StaticArrays", "UnPack"]
-git-tree-sha1 = "c3a55a2a1e180e249a0550d30a58c700487aa7ef"
+git-tree-sha1 = "d9540e35a902512f6c86a6817120eddc8912f651"
 uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
-version = "6.81.0"
+version = "6.82.0"
 
 [[deps.StrideArraysCore]]
 deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"]
-git-tree-sha1 = "f35f6ab602df8413a50c4a25ca14de821e8605fb"
+git-tree-sha1 = "83151ba8065a73f53ca2ae98bc7274d817aa30f2"
 uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da"
-version = "0.5.7"
+version = "0.5.8"
 
 [[deps.Strided]]
 deps = ["LinearAlgebra", "StridedViews", "TupleTools"]
@@ -3566,9 +3601,9 @@ weakdeps = ["PDMats"]
 
 [[deps.Tracy]]
 deps = ["ExprTools", "LibTracyClient_jll", "Libdl"]
-git-tree-sha1 = "91dbaee0f50faa4357f7e9fc69442c7b6364dfe5"
+git-tree-sha1 = "73e3ff50fd3990874c59fef0f35d10644a1487bc"
 uuid = "e689c965-62c8-4b79-b2c5-8359227902fd"
-version = "0.1.5"
+version = "0.1.6"
 
     [deps.Tracy.extensions]
     TracyProfilerExt = "TracyProfiler_jll"
@@ -3582,10 +3617,10 @@ uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 version = "0.11.3"
 
 [[deps.Transducers]]
-deps = ["Accessors", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "SplittablesBase", "Tables"]
-git-tree-sha1 = "7deeab4ff96b85c5f72c824cae53a1398da3d1cb"
+deps = ["Accessors", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "SplittablesBase", "Tables"]
+git-tree-sha1 = "4aa1fdf6c1da74661f6f5d3edfd96648321dade9"
 uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999"
-version = "0.4.84"
+version = "0.4.85"
 
     [deps.Transducers.extensions]
     TransducersAdaptExt = "Adapt"
@@ -3622,9 +3657,9 @@ version = "1.6.0"
 
 [[deps.Turing]]
 deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "ed944065575fd4a6d9d2b802bbd914b53f08bce8"
+git-tree-sha1 = "8e1e790cfdffd15524575b84c4709033d1ea9550"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-version = "0.40.1"
+version = "0.40.3"
 weakdeps = ["DynamicHMC", "Optim"]
 
     [deps.Turing.extensions]
@@ -3658,15 +3693,16 @@ version = "0.4.1"
 
 [[deps.Unitful]]
 deps = ["Dates", "LinearAlgebra", "Random"]
-git-tree-sha1 = "6258d453843c466d84c17a58732dda5deeb8d3af"
+git-tree-sha1 = "cec2df8cf14e0844a8c4d770d12347fda5931d72"
 uuid = "1986cc42-f94f-5a68-af5c-568840ba703d"
-version = "1.24.0"
-weakdeps = ["ConstructionBase", "ForwardDiff", "InverseFunctions", "Printf"]
+version = "1.25.0"
+weakdeps = ["ConstructionBase", "ForwardDiff", "InverseFunctions", "LaTeXStrings", "Latexify", "Printf"]
 
     [deps.Unitful.extensions]
     ConstructionBaseUnitfulExt = "ConstructionBase"
     ForwardDiffExt = "ForwardDiff"
     InverseFunctionsUnitfulExt = "InverseFunctions"
+    LatexifyExt = ["Latexify", "LaTeXStrings"]
     PrintfExt = "Printf"
 
 [[deps.UnitfulLatexify]]
@@ -3709,27 +3745,23 @@ version = "1.4.2"
 
 [[deps.WeightInitializers]]
 deps = ["ArgCheck", "ConcreteStructs", "GPUArraysCore", "LinearAlgebra", "Random", "SpecialFunctions", "Statistics"]
-git-tree-sha1 = "dd2e8eb0120c12eed3446cedee395ca7ac42a5db"
+git-tree-sha1 = "2fe6d8bd39dc8d1f575963eef137f77bd47200c9"
 uuid = "d49dbf32-c5c2-4618-8acc-27bb2598ef2d"
-version = "1.1.4"
+version = "1.2.0"
 
     [deps.WeightInitializers.extensions]
-    WeightInitializersAMDGPUExt = ["AMDGPU", "GPUArrays"]
-    WeightInitializersCUDAExt = ["CUDA", "GPUArrays"]
+    WeightInitializersAMDGPUExt = "AMDGPU"
+    WeightInitializersCUDAExt = "CUDA"
     WeightInitializersChainRulesCoreExt = "ChainRulesCore"
     WeightInitializersGPUArraysExt = "GPUArrays"
-    WeightInitializersMetalExt = ["Metal", "GPUArrays"]
     WeightInitializersReactantExt = "Reactant"
-    WeightInitializersoneAPIExt = ["oneAPI", "GPUArrays"]
 
     [deps.WeightInitializers.weakdeps]
     AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e"
     CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
     GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
-    Metal = "dde4c033-4e86-420c-a63e-0dd931031962"
     Reactant = "3c362404-f566-11ee-1572-e11a4b42c853"
-    oneAPI = "8f75cd03-7ff8-4ecb-9b8f-daf728133b1b"
 
 [[deps.Widgets]]
 deps = ["Colors", "Dates", "Observables", "OrderedCollections"]

From 2babb2da0ee1e976a3a45f8cd74aad746125052b Mon Sep 17 00:00:00 2001
From: Markus Hauru <mhauru@turing.ac.uk>
Date: Thu, 18 Sep 2025 12:03:30 +0100
Subject: [PATCH 12/23] Remove version pin of DelayDiffEq and update Manifest

---
 Manifest.toml | 71 +++++++++++++++++++++++++--------------------------
 1 file changed, 35 insertions(+), 36 deletions(-)

diff --git a/Manifest.toml b/Manifest.toml
index 0a95cce1c..c0c40d833 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -1,8 +1,8 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.11.6"
+julia_version = "1.11.7"
 manifest_format = "2.0"
-project_hash = "9f86f29e94eb0d08fa3f55118bf3765e18345c9e"
+project_hash = "6ed163b5c6c108dfaae31b757b21ff71e297872f"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "27cecae79e5cc9935255f90c53bb831cc3c870d7"
@@ -690,9 +690,9 @@ version = "0.1.2"
 
 [[deps.DelayDiffEq]]
 deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "FastBroadcast", "ForwardDiff", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqRosenbrock", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack", "SymbolicIndexingInterface"]
-git-tree-sha1 = "c50981fb5b6441a1213debb1423385a462e88032"
+git-tree-sha1 = "bb84c7ab3de56ada66430b5671db3b3cdaadcd61"
 uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb"
-version = "5.56.0"
+version = "5.61.0"
 
 [[deps.DelimitedFiles]]
 deps = ["Mmap"]
@@ -708,9 +708,9 @@ version = "0.4.0"
 
 [[deps.DiffEqBase]]
 deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "TruncatedStacktraces"]
-git-tree-sha1 = "6df3b15d504315ec306118aed14f9d7af9f83db1"
+git-tree-sha1 = "087632db966c90079a5534e4147afea9136ca39a"
 uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
-version = "6.189.1"
+version = "6.190.2"
 
     [deps.DiffEqBase.extensions]
     DiffEqBaseCUDAExt = "CUDA"
@@ -933,9 +933,9 @@ version = "1.0.5"
 
 [[deps.Enzyme]]
 deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "InteractiveUtils", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"]
-git-tree-sha1 = "66ec698bd4791c8d2b2be2fe2a472d1dd76a5c7d"
+git-tree-sha1 = "8bd38788cad934e433f944678885d8525cccc009"
 uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9"
-version = "0.13.75"
+version = "0.13.76"
 
     [deps.Enzyme.extensions]
     EnzymeBFloat16sExt = "BFloat16s"
@@ -964,9 +964,9 @@ weakdeps = ["Adapt"]
 
 [[deps.Enzyme_jll]]
 deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"]
-git-tree-sha1 = "bf15bd2b3ddff92fc5bb5687ffe074ebd814c756"
+git-tree-sha1 = "440abfda8e1329662bed574250dde0dcd91f3181"
 uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef"
-version = "0.0.196+0"
+version = "0.0.197+0"
 
 [[deps.EpollShim_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -1599,9 +1599,9 @@ version = "0.1.17"
 
 [[deps.LazyArrays]]
 deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"]
-git-tree-sha1 = "76627adb8c542c6b73f68d4bfd0aa71c9893a079"
+git-tree-sha1 = "21057b6f4f5db1475e653735fda7d1de1c267b46"
 uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02"
-version = "2.6.2"
+version = "2.6.3"
 
     [deps.LazyArrays.extensions]
     LazyArraysBandedMatricesExt = "BandedMatrices"
@@ -1743,10 +1743,10 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 version = "1.11.0"
 
 [[deps.LinearSolve]]
-deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "OpenBLAS_jll", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"]
-git-tree-sha1 = "69cee52e516c859e64adba702ac382c0498a4e29"
+deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"]
+git-tree-sha1 = "1c597eceb5ead73dae17ffa4dcc1160e3e4da1f3"
 uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
-version = "3.40.0"
+version = "3.28.0"
 
     [deps.LinearSolve.extensions]
     LinearSolveAMDGPUExt = "AMDGPU"
@@ -1756,7 +1756,6 @@ version = "3.40.0"
     LinearSolveCUDAExt = "CUDA"
     LinearSolveCUDSSExt = "CUDSS"
     LinearSolveCUSOLVERRFExt = ["CUSOLVERRF", "SparseArrays"]
-    LinearSolveCliqueTreesExt = ["CliqueTrees", "SparseArrays"]
     LinearSolveEnzymeExt = "EnzymeCore"
     LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices"
     LinearSolveFastLapackInterfaceExt = "FastLapackInterface"
@@ -1778,7 +1777,6 @@ version = "3.40.0"
     CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
     CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e"
     CUSOLVERRF = "a8cc9031-bad2-4722-94f5-40deabb4245c"
-    CliqueTrees = "60701a23-6482-424a-84db-faee86b9b1f8"
     EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
     FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e"
     FastLapackInterface = "29a986be-02c6-4525-aec4-84b980013641"
@@ -2152,9 +2150,9 @@ version = "0.8.1"
 
 [[deps.Mooncake]]
 deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "DispatchDoctor", "ExprTools", "FunctionWrappers", "GPUArraysCore", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Test"]
-git-tree-sha1 = "2aa902cb9f45dbeaaae5eaa98559d600b1f5deb7"
+git-tree-sha1 = "bc28c3170e7c78d671ff512ca80487ce7e375bb5"
 uuid = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
-version = "0.4.159"
+version = "0.4.160"
 
     [deps.Mooncake.extensions]
     MooncakeAllocCheckExt = "AllocCheck"
@@ -2289,10 +2287,10 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 version = "1.2.0"
 
 [[deps.NonlinearSolve]]
-deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface"]
-git-tree-sha1 = "d2ec18c1e4eccbb70b64be2435fc3b06fbcdc0a1"
+deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "StaticArraysCore", "SymbolicIndexingInterface"]
+git-tree-sha1 = "627967f6e36aac9f5afb2fb285e33b676a6892f9"
 uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
-version = "4.10.0"
+version = "4.11.0"
 
     [deps.NonlinearSolve.extensions]
     NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt"
@@ -2301,7 +2299,7 @@ version = "4.10.0"
     NonlinearSolveMINPACKExt = "MINPACK"
     NonlinearSolveNLSolversExt = "NLSolvers"
     NonlinearSolveNLsolveExt = ["NLsolve", "LineSearches"]
-    NonlinearSolvePETScExt = ["PETSc", "MPI"]
+    NonlinearSolvePETScExt = ["PETSc", "MPI", "SparseArrays"]
     NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations"
     NonlinearSolveSpeedMappingExt = "SpeedMapping"
     NonlinearSolveSundialsExt = "Sundials"
@@ -2317,14 +2315,15 @@ version = "4.10.0"
     NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
     PETSc = "ace2c81b-2b5f-4b1e-a30d-d662738edfe0"
     SIAMFANLEquations = "084e46ad-d928-497d-ad5e-07fa361a48c4"
+    SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
     SpeedMapping = "f1835b91-879b-4a3f-a438-e4baacf14412"
     Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"
 
 [[deps.NonlinearSolveBase]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "SciMLStructures", "Setfield", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"]
-git-tree-sha1 = "99a400f7ad42e56431c76f3eadee0755f2123fda"
+git-tree-sha1 = "bc0c764f8d4cbd75dc8e4968e62194495c2c6637"
 uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0"
-version = "1.15.0"
+version = "1.16.0"
 weakdeps = ["BandedMatrices", "ChainRulesCore", "Enzyme", "ForwardDiff", "LineSearch", "LinearSolve", "Mooncake", "ReverseDiff", "SparseArrays", "SparseMatrixColorings", "Tracker"]
 
     [deps.NonlinearSolveBase.extensions]
@@ -3094,9 +3093,9 @@ version = "0.5.2"
 
 [[deps.SciMLBase]]
 deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PreallocationTools", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
-git-tree-sha1 = "dfec1fce27c829814348266486b4cb8fdcb263fb"
+git-tree-sha1 = "16fa030fb4bd4df373a677eca0460c3eee791ab2"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "2.119.0"
+version = "2.120.0"
 
     [deps.SciMLBase.extensions]
     SciMLBaseChainRulesCoreExt = "ChainRulesCore"
@@ -3267,12 +3266,13 @@ version = "1.11.0"
 
 [[deps.SparseConnectivityTracer]]
 deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"]
-git-tree-sha1 = "e49c106eb7c78f55cdfa39e8bddeda24e1e09fce"
+git-tree-sha1 = "3c3a42a29f696f16273741ffe589b4003f539088"
 uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5"
-version = "1.0.2"
-weakdeps = ["LogExpFunctions", "NNlib", "NaNMath", "SpecialFunctions"]
+version = "1.1.0"
+weakdeps = ["ChainRulesCore", "LogExpFunctions", "NNlib", "NaNMath", "SpecialFunctions"]
 
     [deps.SparseConnectivityTracer.extensions]
+    SparseConnectivityTracerChainRulesCoreExt = "ChainRulesCore"
     SparseConnectivityTracerLogExpFunctionsExt = "LogExpFunctions"
     SparseConnectivityTracerNNlibExt = "NNlib"
     SparseConnectivityTracerNaNMathExt = "NaNMath"
@@ -3496,9 +3496,9 @@ version = "5.2.3+0"
 
 [[deps.SymbolicIndexingInterface]]
 deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"]
-git-tree-sha1 = "93104ca226670c0cb92ba8bc6998852ad55a2d4c"
+git-tree-sha1 = "b19cf024a2b11d72bef7c74ac3d1cbe86ec9e4ed"
 uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
-version = "0.3.43"
+version = "0.3.44"
 weakdeps = ["PrettyTables"]
 
     [deps.SymbolicIndexingInterface.extensions]
@@ -3693,16 +3693,15 @@ version = "0.4.1"
 
 [[deps.Unitful]]
 deps = ["Dates", "LinearAlgebra", "Random"]
-git-tree-sha1 = "cec2df8cf14e0844a8c4d770d12347fda5931d72"
+git-tree-sha1 = "6258d453843c466d84c17a58732dda5deeb8d3af"
 uuid = "1986cc42-f94f-5a68-af5c-568840ba703d"
-version = "1.25.0"
-weakdeps = ["ConstructionBase", "ForwardDiff", "InverseFunctions", "LaTeXStrings", "Latexify", "Printf"]
+version = "1.24.0"
+weakdeps = ["ConstructionBase", "ForwardDiff", "InverseFunctions", "Printf"]
 
     [deps.Unitful.extensions]
     ConstructionBaseUnitfulExt = "ConstructionBase"
     ForwardDiffExt = "ForwardDiff"
     InverseFunctionsUnitfulExt = "InverseFunctions"
-    LatexifyExt = ["Latexify", "LaTeXStrings"]
     PrintfExt = "Printf"
 
 [[deps.UnitfulLatexify]]

From b41a4cbdd08e620d35f194ab471acb8e9a89e530 Mon Sep 17 00:00:00 2001
From: Markus Hauru <mhauru@turing.ac.uk>
Date: Thu, 18 Sep 2025 17:49:11 +0100
Subject: [PATCH 13/23] Fix call to evaluate

---
 developers/transforms/dynamicppl/index.qmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/developers/transforms/dynamicppl/index.qmd b/developers/transforms/dynamicppl/index.qmd
index ae7722d48..a02dde7af 100644
--- a/developers/transforms/dynamicppl/index.qmd
+++ b/developers/transforms/dynamicppl/index.qmd
@@ -351,7 +351,7 @@ Hence, one might expect that if we try to evaluate the model using this `VarInfo
 Here, `evaluate!!` returns two things: the model's return value itself (which we defined above to be a `NamedTuple`), and the resulting `VarInfo` post-evaluation.
 
 ```{julia}
-retval, ret_varinfo = DynamicPPL.evaluate!!(model, vi_linked, DefaultContext())
+retval, ret_varinfo = DynamicPPL.evaluate!!(model, vi_linked)
 getlogp(ret_varinfo)
 ```
 

From 425539d974a319aa86f0b17af75cc3044b124250 Mon Sep 17 00:00:00 2001
From: Markus Hauru <mhauru@turing.ac.uk>
Date: Fri, 19 Sep 2025 17:08:32 +0100
Subject: [PATCH 14/23] Add note about contexts tutorial being out of date

---
 developers/compiler/minituring-contexts/index.qmd | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/developers/compiler/minituring-contexts/index.qmd b/developers/compiler/minituring-contexts/index.qmd
index 4fcdda02b..b178e9708 100755
--- a/developers/compiler/minituring-contexts/index.qmd
+++ b/developers/compiler/minituring-contexts/index.qmd
@@ -14,6 +14,8 @@ Pkg.instantiate();
 
 In the [Mini Turing]({{< meta minituring >}}) tutorial we developed a miniature version of the Turing language, to illustrate its core design. A passing mention was made of contexts. In this tutorial we develop that aspect of our mini Turing language further to demonstrate how and why contexts are an important part of Turing's design.
 
+Note: The way Turing actually uses contexts changed somewhat in releases 0.39 and 0.40. The content of this page remains relevant, the principles of how contexts operate remain the same, and concepts like leaf and parent contexts still exist. However, we've moved away from using contexts for quite as many things as we used to. Most importantly, whether to accumulate the log joint, log prior, or log likelihood is no longer done using different contexts. Please keep this in mind as you read this page: The principles remain, but the details have changed. We will update this page once the refactoring of internals that is happening around releases like 0.39 and 0.40 is done.
+
 # Mini Turing expanded, now with more contexts
 
 If you haven't read [Mini Turing]({{< meta minituring >}}) yet, you should do that first. We start by repeating verbatim much of the code from there. Define the type for holding values for variables:

From dde0ed371ad066fbfa527f8589c49f2ff104a655 Mon Sep 17 00:00:00 2001
From: Markus Hauru <mhauru@turing.ac.uk>
Date: Mon, 22 Sep 2025 12:48:38 +0100
Subject: [PATCH 15/23] Apply suggestions from code review

Co-authored-by: Penelope Yong <penelopeysm@gmail.com>
---
 developers/compiler/minituring-contexts/index.qmd | 2 ++
 usage/modifying-logprob/index.qmd                 | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/developers/compiler/minituring-contexts/index.qmd b/developers/compiler/minituring-contexts/index.qmd
index b178e9708..aa125b703 100755
--- a/developers/compiler/minituring-contexts/index.qmd
+++ b/developers/compiler/minituring-contexts/index.qmd
@@ -14,7 +14,9 @@ Pkg.instantiate();
 
 In the [Mini Turing]({{< meta minituring >}}) tutorial we developed a miniature version of the Turing language, to illustrate its core design. A passing mention was made of contexts. In this tutorial we develop that aspect of our mini Turing language further to demonstrate how and why contexts are an important part of Turing's design.
 
+::: {.callout-important}
 Note: The way Turing actually uses contexts changed somewhat in releases 0.39 and 0.40. The content of this page remains relevant, the principles of how contexts operate remain the same, and concepts like leaf and parent contexts still exist. However, we've moved away from using contexts for quite as many things as we used to. Most importantly, whether to accumulate the log joint, log prior, or log likelihood is no longer done using different contexts. Please keep this in mind as you read this page: The principles remain, but the details have changed. We will update this page once the refactoring of internals that is happening around releases like 0.39 and 0.40 is done.
+:::
 
 # Mini Turing expanded, now with more contexts
 
diff --git a/usage/modifying-logprob/index.qmd b/usage/modifying-logprob/index.qmd
index 0eb6f8b30..892ac7ba8 100755
--- a/usage/modifying-logprob/index.qmd
+++ b/usage/modifying-logprob/index.qmd
@@ -47,7 +47,7 @@ using LinearAlgebra
 end
 ```
 
-Note that `@addlogprob!` increases the accumulated log likelihood.
+Note that `@addlogprob! (p::Float64)` adds `p` to the log likelihood.
 If instead you want to add to the log prior, you can use
 
 ```{julia}

From a32ec1b954254c2b66cbd32cd8b685e6ea94f76f Mon Sep 17 00:00:00 2001
From: AoifeHughes <aoife1hughes@gmail.com>
Date: Wed, 24 Sep 2025 11:25:31 +0100
Subject: [PATCH 16/23] Add ipynb format support

---
 _quarto.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/_quarto.yml b/_quarto.yml
index 632cea199..4cbdd369c 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -153,6 +153,7 @@ format:
     toc-title: "Table of Contents"
     code-fold: false
     code-overflow: scroll
+    format-links: [ipynb]
     include-in-header:
       - text: |
           <style>
@@ -210,6 +211,7 @@ format:
               </div>
             </div>
           </footer>
+  ipynb: default
 
 execute:
   echo: true

From 1e7f351f931ea941820b549ba20c32d9870578a4 Mon Sep 17 00:00:00 2001
From: AoifeHughes <aoife1hughes@gmail.com>
Date: Wed, 24 Sep 2025 11:34:43 +0100
Subject: [PATCH 17/23] maybe added links to dl?

---
 tutorials/bayesian-differential-equations/index.qmd         | 3 +++
 tutorials/bayesian-linear-regression/index.qmd              | 3 +++
 tutorials/bayesian-logistic-regression/index.qmd            | 3 +++
 tutorials/bayesian-neural-networks/index.qmd                | 3 +++
 tutorials/bayesian-poisson-regression/index.qmd             | 3 +++
 tutorials/bayesian-time-series-analysis/index.qmd           | 3 +++
 tutorials/coin-flipping/index.qmd                           | 3 +++
 tutorials/gaussian-mixture-models/index.qmd                 | 3 +++
 tutorials/gaussian-process-latent-variable-models/index.qmd | 3 +++
 tutorials/gaussian-processes-introduction/index.qmd         | 3 +++
 tutorials/hidden-markov-models/index.qmd                    | 3 +++
 tutorials/infinite-mixture-models/index.qmd                 | 3 +++
 tutorials/multinomial-logistic-regression/index.qmd         | 3 +++
 tutorials/probabilistic-pca/index.qmd                       | 3 +++
 tutorials/variational-inference/index.qmd                   | 3 +++
 15 files changed, 45 insertions(+)

diff --git a/tutorials/bayesian-differential-equations/index.qmd b/tutorials/bayesian-differential-equations/index.qmd
index 6da7f9eef..946d27d82 100755
--- a/tutorials/bayesian-differential-equations/index.qmd
+++ b/tutorials/bayesian-differential-equations/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Bayesian Differential Equations
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../10-bayesian-differential-equations/index.html
 ---
diff --git a/tutorials/bayesian-linear-regression/index.qmd b/tutorials/bayesian-linear-regression/index.qmd
index c28148371..f4bd0d763 100755
--- a/tutorials/bayesian-linear-regression/index.qmd
+++ b/tutorials/bayesian-linear-regression/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Bayesian Linear Regression
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../05-linear-regression/index.html
 ---
diff --git a/tutorials/bayesian-logistic-regression/index.qmd b/tutorials/bayesian-logistic-regression/index.qmd
index bfa4e68fc..2f944228a 100755
--- a/tutorials/bayesian-logistic-regression/index.qmd
+++ b/tutorials/bayesian-logistic-regression/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Bayesian Logistic Regression
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../02-logistic-regression/index.html
 ---
diff --git a/tutorials/bayesian-neural-networks/index.qmd b/tutorials/bayesian-neural-networks/index.qmd
index c5652c057..0b24d48a1 100755
--- a/tutorials/bayesian-neural-networks/index.qmd
+++ b/tutorials/bayesian-neural-networks/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Bayesian Neural Networks
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../03-bayesian-neural-network/index.html
 ---
diff --git a/tutorials/bayesian-poisson-regression/index.qmd b/tutorials/bayesian-poisson-regression/index.qmd
index e8e51cb1a..8d55cbcb0 100755
--- a/tutorials/bayesian-poisson-regression/index.qmd
+++ b/tutorials/bayesian-poisson-regression/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Bayesian Poisson Regression
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../07-poisson-regression/index.html
 ---
diff --git a/tutorials/bayesian-time-series-analysis/index.qmd b/tutorials/bayesian-time-series-analysis/index.qmd
index 0cdf201d6..fbe68cb21 100755
--- a/tutorials/bayesian-time-series-analysis/index.qmd
+++ b/tutorials/bayesian-time-series-analysis/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Bayesian Time Series Analysis
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../13-seasonal-time-series/index.html
 ---
diff --git a/tutorials/coin-flipping/index.qmd b/tutorials/coin-flipping/index.qmd
index 757525249..e0463d314 100755
--- a/tutorials/coin-flipping/index.qmd
+++ b/tutorials/coin-flipping/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: "Introduction: Coin Flipping"
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases: 
   - ../00-introduction/index.html
   - ../00-introduction/
diff --git a/tutorials/gaussian-mixture-models/index.qmd b/tutorials/gaussian-mixture-models/index.qmd
index 99db86bc2..0845435df 100755
--- a/tutorials/gaussian-mixture-models/index.qmd
+++ b/tutorials/gaussian-mixture-models/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Gaussian Mixture Models
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../01-gaussian-mixture-model/index.html
 ---
diff --git a/tutorials/gaussian-process-latent-variable-models/index.qmd b/tutorials/gaussian-process-latent-variable-models/index.qmd
index e6a9c3f62..b9fc89b90 100755
--- a/tutorials/gaussian-process-latent-variable-models/index.qmd
+++ b/tutorials/gaussian-process-latent-variable-models/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Gaussian Process Latent Variable Models
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../12-gplvm/index.html
 ---
diff --git a/tutorials/gaussian-processes-introduction/index.qmd b/tutorials/gaussian-processes-introduction/index.qmd
index 6db5a1388..d5dfd4a55 100755
--- a/tutorials/gaussian-processes-introduction/index.qmd
+++ b/tutorials/gaussian-processes-introduction/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: "Gaussian Processes: Introduction"
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../15-gaussian-processes/index.html
 ---
diff --git a/tutorials/hidden-markov-models/index.qmd b/tutorials/hidden-markov-models/index.qmd
index 9448b5794..cee9cdd71 100755
--- a/tutorials/hidden-markov-models/index.qmd
+++ b/tutorials/hidden-markov-models/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Hidden Markov Models
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../04-hidden-markov-model/index.html
 ---
diff --git a/tutorials/infinite-mixture-models/index.qmd b/tutorials/infinite-mixture-models/index.qmd
index 8b14aac49..1c67a8b79 100755
--- a/tutorials/infinite-mixture-models/index.qmd
+++ b/tutorials/infinite-mixture-models/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Infinite Mixture Models
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../06-infinite-mixture-model/index.html
 ---
diff --git a/tutorials/multinomial-logistic-regression/index.qmd b/tutorials/multinomial-logistic-regression/index.qmd
index e788475e8..9fb15649c 100755
--- a/tutorials/multinomial-logistic-regression/index.qmd
+++ b/tutorials/multinomial-logistic-regression/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Multinomial Logistic Regression
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../08-multinomial-logistic-regression/index.html
 ---
diff --git a/tutorials/probabilistic-pca/index.qmd b/tutorials/probabilistic-pca/index.qmd
index 6f8982923..ee9ff2464 100755
--- a/tutorials/probabilistic-pca/index.qmd
+++ b/tutorials/probabilistic-pca/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Probabilistic PCA
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../11-probabilistic-pca/index.html
 ---
diff --git a/tutorials/variational-inference/index.qmd b/tutorials/variational-inference/index.qmd
index 7d89ba904..d49adb2a7 100755
--- a/tutorials/variational-inference/index.qmd
+++ b/tutorials/variational-inference/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Variational Inference
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../09-variational-inference/index.html
 ---

From d1bacacae60d1f38a15d8528b3228658c8cae54d Mon Sep 17 00:00:00 2001
From: AoifeHughes <aoife1hughes@gmail.com>
Date: Wed, 24 Sep 2025 12:38:45 +0100
Subject: [PATCH 18/23] reset mainifest

---
 Manifest.toml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Manifest.toml b/Manifest.toml
index c0c40d833..d2970bf3c 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -1743,10 +1743,10 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 version = "1.11.0"
 
 [[deps.LinearSolve]]
-deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"]
-git-tree-sha1 = "1c597eceb5ead73dae17ffa4dcc1160e3e4da1f3"
+deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "OpenBLAS_jll", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"]
+git-tree-sha1 = "e479c96c20e3fe6067d7ee6618839236d156f060"
 uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
-version = "3.28.0"
+version = "3.40.1"
 
     [deps.LinearSolve.extensions]
     LinearSolveAMDGPUExt = "AMDGPU"

From a78fac461f6123a1b1d2b311a87d168c15177177 Mon Sep 17 00:00:00 2001
From: AoifeHughes <aoife1hughes@gmail.com>
Date: Wed, 24 Sep 2025 15:13:39 +0100
Subject: [PATCH 19/23] dont execute ipynb

---
 _quarto.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/_quarto.yml b/_quarto.yml
index 4cbdd369c..4bc507829 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -211,7 +211,9 @@ format:
               </div>
             </div>
           </footer>
-  ipynb: default
+  ipynb:
+    execute:
+      enabled: false
 
 execute:
   echo: true

From 98bf999901d43d6f4d6200d5605f4a4dd80cc017 Mon Sep 17 00:00:00 2001
From: AoifeHughes <aoife1hughes@gmail.com>
Date: Thu, 25 Sep 2025 09:22:36 +0100
Subject: [PATCH 20/23] bump local changes

---
 _quarto.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/_quarto.yml b/_quarto.yml
index 4bc507829..efd93b7d2 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -213,7 +213,8 @@ format:
           </footer>
   ipynb:
     execute:
-      enabled: false
+      eval: false
+      echo: true
 
 execute:
   echo: true

From af7ceb4ddd87c45d327d4b546247c83209668a67 Mon Sep 17 00:00:00 2001
From: AoifeHughes <aoife1hughes@gmail.com>
Date: Fri, 26 Sep 2025 10:46:52 +0100
Subject: [PATCH 21/23] add post-render script for converting .quarto_ipynb
 files to .ipynb

---
 _quarto.yml | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/_quarto.yml b/_quarto.yml
index efd93b7d2..f874c122a 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -4,6 +4,24 @@ project:
     # Change port if it's busy in your system or just remove this line so that It will automatically use any free port
     port: 4200
     browser: true
+  post-render:
+    - |
+      echo "Converting .quarto_ipynb files to .ipynb..."
+      find . -name "*.quarto_ipynb" -type f | while read -r file; do
+        base="${file%.quarto_ipynb}"
+        ipynb_file="${base}.ipynb"
+        site_path="_site${base#.}.ipynb"
+
+        # Copy to local directory
+        cp "$file" "$ipynb_file"
+
+        # Copy to _site directory
+        mkdir -p "$(dirname "$site_path")"
+        cp "$file" "$site_path"
+
+        echo "Created: $ipynb_file and $site_path"
+      done
+      echo "Notebook conversion complete!"
 
 # These cannot be used as variables. They are reserved for the project configuration.
 website:
@@ -213,9 +231,8 @@ format:
           </footer>
   ipynb:
     execute:
-      eval: false
-      echo: true
-
+      enabled: false
+    jupyter: julia-1.11
 execute:
   echo: true
   output: true

From 7f0045335fd7199936ed6fecb50324e14f9d8d6e Mon Sep 17 00:00:00 2001
From: Aoife <aoife1hughes@gmail.com>
Date: Mon, 29 Sep 2025 10:39:12 +0100
Subject: [PATCH 22/23] Refactor notebook generation process and clean up
 tutorial metadata

---
 _quarto.yml                                   | 23 +-----
 scripts/generate_notebooks.sh                 | 77 +++++++++++++++++++
 .../bayesian-differential-equations/index.qmd |  3 -
 .../bayesian-linear-regression/index.qmd      |  3 -
 .../bayesian-logistic-regression/index.qmd    |  3 -
 tutorials/bayesian-neural-networks/index.qmd  |  3 -
 .../bayesian-poisson-regression/index.qmd     |  3 -
 .../bayesian-time-series-analysis/index.qmd   |  3 -
 tutorials/coin-flipping/index.qmd             |  3 -
 tutorials/gaussian-mixture-models/index.qmd   |  3 -
 .../index.qmd                                 |  3 -
 .../gaussian-processes-introduction/index.qmd |  3 -
 tutorials/hidden-markov-models/index.qmd      |  3 -
 tutorials/infinite-mixture-models/index.qmd   |  3 -
 .../multinomial-logistic-regression/index.qmd |  3 -
 tutorials/probabilistic-pca/index.qmd         |  3 -
 tutorials/variational-inference/index.qmd     |  3 -
 17 files changed, 79 insertions(+), 66 deletions(-)
 create mode 100755 scripts/generate_notebooks.sh

diff --git a/_quarto.yml b/_quarto.yml
index f874c122a..cd46af249 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -5,23 +5,7 @@ project:
     port: 4200
     browser: true
   post-render:
-    - |
-      echo "Converting .quarto_ipynb files to .ipynb..."
-      find . -name "*.quarto_ipynb" -type f | while read -r file; do
-        base="${file%.quarto_ipynb}"
-        ipynb_file="${base}.ipynb"
-        site_path="_site${base#.}.ipynb"
-
-        # Copy to local directory
-        cp "$file" "$ipynb_file"
-
-        # Copy to _site directory
-        mkdir -p "$(dirname "$site_path")"
-        cp "$file" "$site_path"
-
-        echo "Created: $ipynb_file and $site_path"
-      done
-      echo "Notebook conversion complete!"
+    - bash scripts/generate_notebooks.sh
 
 # These cannot be used as variables. They are reserved for the project configuration.
 website:
@@ -229,10 +213,7 @@ format:
               </div>
             </div>
           </footer>
-  ipynb:
-    execute:
-      enabled: false
-    jupyter: julia-1.11
+
 execute:
   echo: true
   output: true
diff --git a/scripts/generate_notebooks.sh b/scripts/generate_notebooks.sh
new file mode 100755
index 000000000..484507469
--- /dev/null
+++ b/scripts/generate_notebooks.sh
@@ -0,0 +1,77 @@
+#!/bin/bash
+
+# Script to generate Jupyter notebooks from QMD files without executing code
+# This runs as part of the Quarto post-render process
+
+echo "Generating Jupyter notebooks from QMD files..."
+
+# Check if quarto is available
+if ! command -v quarto &> /dev/null; then
+    echo "Warning: quarto command not found. Skipping notebook generation."
+    exit 0
+fi
+
+# Find all tutorial QMD files that have Julia engine
+tutorial_files=$(find tutorials -name "index.qmd" -type f 2>/dev/null | grep -v "_site" || true)
+
+for qmd_file in $tutorial_files; do
+    # Check if file contains "engine: julia"
+    if [ -f "$qmd_file" ] && grep -q "engine: julia" "$qmd_file" 2>/dev/null; then
+        # Get the directory path
+        dir_path=$(dirname "$qmd_file")
+        base_name=$(basename "$dir_path")
+
+        # Generate notebook without executing code
+        echo "Converting $qmd_file to notebook..."
+
+        # Use quarto to render to ipynb format without execution
+        # Using --no-execute to skip code execution entirely
+        if quarto render "$qmd_file" --to ipynb --no-execute 2>/dev/null; then
+            # The notebook will be created as index.ipynb in the same directory
+            ipynb_file="${dir_path}/index.ipynb"
+
+            if [ -f "$ipynb_file" ]; then
+                # Create the _site directory structure if it doesn't exist
+                site_dir="_site/${dir_path}"
+                mkdir -p "$site_dir"
+
+                # Copy the notebook to the _site directory
+                cp "$ipynb_file" "$site_dir/index.ipynb"
+                echo "Created notebook: $site_dir/index.ipynb"
+
+                # Remove the local ipynb file (keep only in _site)
+                rm "$ipynb_file"
+            fi
+        else
+            echo "Warning: Failed to convert $qmd_file to notebook. Skipping."
+        fi
+    fi
+done
+
+# Also handle special pages if they have Julia code
+special_pages=("core-functionality/index.qmd" "faq/index.qmd")
+
+for qmd_file in "${special_pages[@]}"; do
+    if [ -f "$qmd_file" ] && grep -q "engine: julia" "$qmd_file" 2>/dev/null; then
+        echo "Converting $qmd_file to notebook..."
+
+        # Generate notebook without executing
+        if quarto render "$qmd_file" --to ipynb --no-execute 2>/dev/null; then
+            # Get paths
+            dir_path=$(dirname "$qmd_file")
+            ipynb_file="${dir_path}/index.ipynb"
+
+            if [ -f "$ipynb_file" ]; then
+                site_dir="_site/${dir_path}"
+                mkdir -p "$site_dir"
+                cp "$ipynb_file" "$site_dir/index.ipynb"
+                echo "Created notebook: $site_dir/index.ipynb"
+                rm "$ipynb_file"
+            fi
+        else
+            echo "Warning: Failed to convert $qmd_file to notebook. Skipping."
+        fi
+    fi
+done
+
+echo "Notebook generation complete!"
\ No newline at end of file
diff --git a/tutorials/bayesian-differential-equations/index.qmd b/tutorials/bayesian-differential-equations/index.qmd
index 946d27d82..6da7f9eef 100755
--- a/tutorials/bayesian-differential-equations/index.qmd
+++ b/tutorials/bayesian-differential-equations/index.qmd
@@ -1,9 +1,6 @@
 ---
 title: Bayesian Differential Equations
 engine: julia
-format:
-  html: default
-  ipynb: default
 aliases:
  - ../10-bayesian-differential-equations/index.html
 ---
diff --git a/tutorials/bayesian-linear-regression/index.qmd b/tutorials/bayesian-linear-regression/index.qmd
index f4bd0d763..c28148371 100755
--- a/tutorials/bayesian-linear-regression/index.qmd
+++ b/tutorials/bayesian-linear-regression/index.qmd
@@ -1,9 +1,6 @@
 ---
 title: Bayesian Linear Regression
 engine: julia
-format:
-  html: default
-  ipynb: default
 aliases:
  - ../05-linear-regression/index.html
 ---
diff --git a/tutorials/bayesian-logistic-regression/index.qmd b/tutorials/bayesian-logistic-regression/index.qmd
index 2f944228a..bfa4e68fc 100755
--- a/tutorials/bayesian-logistic-regression/index.qmd
+++ b/tutorials/bayesian-logistic-regression/index.qmd
@@ -1,9 +1,6 @@
 ---
 title: Bayesian Logistic Regression
 engine: julia
-format:
-  html: default
-  ipynb: default
 aliases:
  - ../02-logistic-regression/index.html
 ---
diff --git a/tutorials/bayesian-neural-networks/index.qmd b/tutorials/bayesian-neural-networks/index.qmd
index 0b24d48a1..c5652c057 100755
--- a/tutorials/bayesian-neural-networks/index.qmd
+++ b/tutorials/bayesian-neural-networks/index.qmd
@@ -1,9 +1,6 @@
 ---
 title: Bayesian Neural Networks
 engine: julia
-format:
-  html: default
-  ipynb: default
 aliases:
  - ../03-bayesian-neural-network/index.html
 ---
diff --git a/tutorials/bayesian-poisson-regression/index.qmd b/tutorials/bayesian-poisson-regression/index.qmd
index 8d55cbcb0..e8e51cb1a 100755
--- a/tutorials/bayesian-poisson-regression/index.qmd
+++ b/tutorials/bayesian-poisson-regression/index.qmd
@@ -1,9 +1,6 @@
 ---
 title: Bayesian Poisson Regression
 engine: julia
-format:
-  html: default
-  ipynb: default
 aliases:
  - ../07-poisson-regression/index.html
 ---
diff --git a/tutorials/bayesian-time-series-analysis/index.qmd b/tutorials/bayesian-time-series-analysis/index.qmd
index fbe68cb21..0cdf201d6 100755
--- a/tutorials/bayesian-time-series-analysis/index.qmd
+++ b/tutorials/bayesian-time-series-analysis/index.qmd
@@ -1,9 +1,6 @@
 ---
 title: Bayesian Time Series Analysis
 engine: julia
-format:
-  html: default
-  ipynb: default
 aliases:
  - ../13-seasonal-time-series/index.html
 ---
diff --git a/tutorials/coin-flipping/index.qmd b/tutorials/coin-flipping/index.qmd
index e0463d314..757525249 100755
--- a/tutorials/coin-flipping/index.qmd
+++ b/tutorials/coin-flipping/index.qmd
@@ -1,9 +1,6 @@
 ---
 title: "Introduction: Coin Flipping"
 engine: julia
-format:
-  html: default
-  ipynb: default
 aliases: 
   - ../00-introduction/index.html
   - ../00-introduction/
diff --git a/tutorials/gaussian-mixture-models/index.qmd b/tutorials/gaussian-mixture-models/index.qmd
index 0845435df..99db86bc2 100755
--- a/tutorials/gaussian-mixture-models/index.qmd
+++ b/tutorials/gaussian-mixture-models/index.qmd
@@ -1,9 +1,6 @@
 ---
 title: Gaussian Mixture Models
 engine: julia
-format:
-  html: default
-  ipynb: default
 aliases:
  - ../01-gaussian-mixture-model/index.html
 ---
diff --git a/tutorials/gaussian-process-latent-variable-models/index.qmd b/tutorials/gaussian-process-latent-variable-models/index.qmd
index b9fc89b90..e6a9c3f62 100755
--- a/tutorials/gaussian-process-latent-variable-models/index.qmd
+++ b/tutorials/gaussian-process-latent-variable-models/index.qmd
@@ -1,9 +1,6 @@
 ---
 title: Gaussian Process Latent Variable Models
 engine: julia
-format:
-  html: default
-  ipynb: default
 aliases:
  - ../12-gplvm/index.html
 ---
diff --git a/tutorials/gaussian-processes-introduction/index.qmd b/tutorials/gaussian-processes-introduction/index.qmd
index d5dfd4a55..6db5a1388 100755
--- a/tutorials/gaussian-processes-introduction/index.qmd
+++ b/tutorials/gaussian-processes-introduction/index.qmd
@@ -1,9 +1,6 @@
 ---
 title: "Gaussian Processes: Introduction"
 engine: julia
-format:
-  html: default
-  ipynb: default
 aliases:
  - ../15-gaussian-processes/index.html
 ---
diff --git a/tutorials/hidden-markov-models/index.qmd b/tutorials/hidden-markov-models/index.qmd
index cee9cdd71..9448b5794 100755
--- a/tutorials/hidden-markov-models/index.qmd
+++ b/tutorials/hidden-markov-models/index.qmd
@@ -1,9 +1,6 @@
 ---
 title: Hidden Markov Models
 engine: julia
-format:
-  html: default
-  ipynb: default
 aliases:
  - ../04-hidden-markov-model/index.html
 ---
diff --git a/tutorials/infinite-mixture-models/index.qmd b/tutorials/infinite-mixture-models/index.qmd
index 1c67a8b79..8b14aac49 100755
--- a/tutorials/infinite-mixture-models/index.qmd
+++ b/tutorials/infinite-mixture-models/index.qmd
@@ -1,9 +1,6 @@
 ---
 title: Infinite Mixture Models
 engine: julia
-format:
-  html: default
-  ipynb: default
 aliases:
  - ../06-infinite-mixture-model/index.html
 ---
diff --git a/tutorials/multinomial-logistic-regression/index.qmd b/tutorials/multinomial-logistic-regression/index.qmd
index 9fb15649c..e788475e8 100755
--- a/tutorials/multinomial-logistic-regression/index.qmd
+++ b/tutorials/multinomial-logistic-regression/index.qmd
@@ -1,9 +1,6 @@
 ---
 title: Multinomial Logistic Regression
 engine: julia
-format:
-  html: default
-  ipynb: default
 aliases:
  - ../08-multinomial-logistic-regression/index.html
 ---
diff --git a/tutorials/probabilistic-pca/index.qmd b/tutorials/probabilistic-pca/index.qmd
index ee9ff2464..6f8982923 100755
--- a/tutorials/probabilistic-pca/index.qmd
+++ b/tutorials/probabilistic-pca/index.qmd
@@ -1,9 +1,6 @@
 ---
 title: Probabilistic PCA
 engine: julia
-format:
-  html: default
-  ipynb: default
 aliases:
  - ../11-probabilistic-pca/index.html
 ---
diff --git a/tutorials/variational-inference/index.qmd b/tutorials/variational-inference/index.qmd
index d49adb2a7..7d89ba904 100755
--- a/tutorials/variational-inference/index.qmd
+++ b/tutorials/variational-inference/index.qmd
@@ -1,9 +1,6 @@
 ---
 title: Variational Inference
 engine: julia
-format:
-  html: default
-  ipynb: default
 aliases:
  - ../09-variational-inference/index.html
 ---

From 64c62a4cd490a6c21d2ebc89f144ee416e9f1764 Mon Sep 17 00:00:00 2001
From: Aoife <aoife1hughes@gmail.com>
Date: Mon, 29 Sep 2025 11:33:34 +0100
Subject: [PATCH 23/23] please work :(

---
 _quarto.yml                                   |  7 +-
 scripts/generate_notebooks.sh                 | 77 -------------------
 .../bayesian-differential-equations/index.qmd |  3 +
 .../bayesian-linear-regression/index.qmd      |  3 +
 .../bayesian-logistic-regression/index.qmd    |  3 +
 tutorials/bayesian-neural-networks/index.qmd  |  3 +
 .../bayesian-poisson-regression/index.qmd     |  3 +
 .../bayesian-time-series-analysis/index.qmd   |  3 +
 tutorials/coin-flipping/index.qmd             |  5 +-
 tutorials/gaussian-mixture-models/index.qmd   |  3 +
 .../index.qmd                                 |  3 +
 .../gaussian-processes-introduction/index.qmd |  3 +
 tutorials/hidden-markov-models/index.qmd      |  3 +
 tutorials/infinite-mixture-models/index.qmd   |  3 +
 .../multinomial-logistic-regression/index.qmd |  3 +
 tutorials/probabilistic-pca/index.qmd         |  3 +
 tutorials/variational-inference/index.qmd     |  3 +
 17 files changed, 50 insertions(+), 81 deletions(-)
 delete mode 100755 scripts/generate_notebooks.sh

diff --git a/_quarto.yml b/_quarto.yml
index cd46af249..c6dfe3d55 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -4,8 +4,6 @@ project:
     # Change port if it's busy in your system or just remove this line so that It will automatically use any free port
     port: 4200
     browser: true
-  post-render:
-    - bash scripts/generate_notebooks.sh
 
 # These cannot be used as variables. They are reserved for the project configuration.
 website:
@@ -213,7 +211,10 @@ format:
               </div>
             </div>
           </footer>
-
+  ipynb:
+    execute:
+      cache: true
+      freeze: auto
 execute:
   echo: true
   output: true
diff --git a/scripts/generate_notebooks.sh b/scripts/generate_notebooks.sh
deleted file mode 100755
index 484507469..000000000
--- a/scripts/generate_notebooks.sh
+++ /dev/null
@@ -1,77 +0,0 @@
-#!/bin/bash
-
-# Script to generate Jupyter notebooks from QMD files without executing code
-# This runs as part of the Quarto post-render process
-
-echo "Generating Jupyter notebooks from QMD files..."
-
-# Check if quarto is available
-if ! command -v quarto &> /dev/null; then
-    echo "Warning: quarto command not found. Skipping notebook generation."
-    exit 0
-fi
-
-# Find all tutorial QMD files that have Julia engine
-tutorial_files=$(find tutorials -name "index.qmd" -type f 2>/dev/null | grep -v "_site" || true)
-
-for qmd_file in $tutorial_files; do
-    # Check if file contains "engine: julia"
-    if [ -f "$qmd_file" ] && grep -q "engine: julia" "$qmd_file" 2>/dev/null; then
-        # Get the directory path
-        dir_path=$(dirname "$qmd_file")
-        base_name=$(basename "$dir_path")
-
-        # Generate notebook without executing code
-        echo "Converting $qmd_file to notebook..."
-
-        # Use quarto to render to ipynb format without execution
-        # Using --no-execute to skip code execution entirely
-        if quarto render "$qmd_file" --to ipynb --no-execute 2>/dev/null; then
-            # The notebook will be created as index.ipynb in the same directory
-            ipynb_file="${dir_path}/index.ipynb"
-
-            if [ -f "$ipynb_file" ]; then
-                # Create the _site directory structure if it doesn't exist
-                site_dir="_site/${dir_path}"
-                mkdir -p "$site_dir"
-
-                # Copy the notebook to the _site directory
-                cp "$ipynb_file" "$site_dir/index.ipynb"
-                echo "Created notebook: $site_dir/index.ipynb"
-
-                # Remove the local ipynb file (keep only in _site)
-                rm "$ipynb_file"
-            fi
-        else
-            echo "Warning: Failed to convert $qmd_file to notebook. Skipping."
-        fi
-    fi
-done
-
-# Also handle special pages if they have Julia code
-special_pages=("core-functionality/index.qmd" "faq/index.qmd")
-
-for qmd_file in "${special_pages[@]}"; do
-    if [ -f "$qmd_file" ] && grep -q "engine: julia" "$qmd_file" 2>/dev/null; then
-        echo "Converting $qmd_file to notebook..."
-
-        # Generate notebook without executing
-        if quarto render "$qmd_file" --to ipynb --no-execute 2>/dev/null; then
-            # Get paths
-            dir_path=$(dirname "$qmd_file")
-            ipynb_file="${dir_path}/index.ipynb"
-
-            if [ -f "$ipynb_file" ]; then
-                site_dir="_site/${dir_path}"
-                mkdir -p "$site_dir"
-                cp "$ipynb_file" "$site_dir/index.ipynb"
-                echo "Created notebook: $site_dir/index.ipynb"
-                rm "$ipynb_file"
-            fi
-        else
-            echo "Warning: Failed to convert $qmd_file to notebook. Skipping."
-        fi
-    fi
-done
-
-echo "Notebook generation complete!"
\ No newline at end of file
diff --git a/tutorials/bayesian-differential-equations/index.qmd b/tutorials/bayesian-differential-equations/index.qmd
index 6da7f9eef..946d27d82 100755
--- a/tutorials/bayesian-differential-equations/index.qmd
+++ b/tutorials/bayesian-differential-equations/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Bayesian Differential Equations
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../10-bayesian-differential-equations/index.html
 ---
diff --git a/tutorials/bayesian-linear-regression/index.qmd b/tutorials/bayesian-linear-regression/index.qmd
index c28148371..f4bd0d763 100755
--- a/tutorials/bayesian-linear-regression/index.qmd
+++ b/tutorials/bayesian-linear-regression/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Bayesian Linear Regression
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../05-linear-regression/index.html
 ---
diff --git a/tutorials/bayesian-logistic-regression/index.qmd b/tutorials/bayesian-logistic-regression/index.qmd
index bfa4e68fc..2f944228a 100755
--- a/tutorials/bayesian-logistic-regression/index.qmd
+++ b/tutorials/bayesian-logistic-regression/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Bayesian Logistic Regression
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../02-logistic-regression/index.html
 ---
diff --git a/tutorials/bayesian-neural-networks/index.qmd b/tutorials/bayesian-neural-networks/index.qmd
index c5652c057..0b24d48a1 100755
--- a/tutorials/bayesian-neural-networks/index.qmd
+++ b/tutorials/bayesian-neural-networks/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Bayesian Neural Networks
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../03-bayesian-neural-network/index.html
 ---
diff --git a/tutorials/bayesian-poisson-regression/index.qmd b/tutorials/bayesian-poisson-regression/index.qmd
index e8e51cb1a..8d55cbcb0 100755
--- a/tutorials/bayesian-poisson-regression/index.qmd
+++ b/tutorials/bayesian-poisson-regression/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Bayesian Poisson Regression
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../07-poisson-regression/index.html
 ---
diff --git a/tutorials/bayesian-time-series-analysis/index.qmd b/tutorials/bayesian-time-series-analysis/index.qmd
index 0cdf201d6..fbe68cb21 100755
--- a/tutorials/bayesian-time-series-analysis/index.qmd
+++ b/tutorials/bayesian-time-series-analysis/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Bayesian Time Series Analysis
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../13-seasonal-time-series/index.html
 ---
diff --git a/tutorials/coin-flipping/index.qmd b/tutorials/coin-flipping/index.qmd
index 757525249..9b5d2f49a 100755
--- a/tutorials/coin-flipping/index.qmd
+++ b/tutorials/coin-flipping/index.qmd
@@ -1,7 +1,10 @@
 ---
 title: "Introduction: Coin Flipping"
 engine: julia
-aliases: 
+format:
+  html: default
+  ipynb: default
+aliases:
   - ../00-introduction/index.html
   - ../00-introduction/
 ---
diff --git a/tutorials/gaussian-mixture-models/index.qmd b/tutorials/gaussian-mixture-models/index.qmd
index 99db86bc2..0845435df 100755
--- a/tutorials/gaussian-mixture-models/index.qmd
+++ b/tutorials/gaussian-mixture-models/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Gaussian Mixture Models
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../01-gaussian-mixture-model/index.html
 ---
diff --git a/tutorials/gaussian-process-latent-variable-models/index.qmd b/tutorials/gaussian-process-latent-variable-models/index.qmd
index e6a9c3f62..b9fc89b90 100755
--- a/tutorials/gaussian-process-latent-variable-models/index.qmd
+++ b/tutorials/gaussian-process-latent-variable-models/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Gaussian Process Latent Variable Models
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../12-gplvm/index.html
 ---
diff --git a/tutorials/gaussian-processes-introduction/index.qmd b/tutorials/gaussian-processes-introduction/index.qmd
index 6db5a1388..d5dfd4a55 100755
--- a/tutorials/gaussian-processes-introduction/index.qmd
+++ b/tutorials/gaussian-processes-introduction/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: "Gaussian Processes: Introduction"
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../15-gaussian-processes/index.html
 ---
diff --git a/tutorials/hidden-markov-models/index.qmd b/tutorials/hidden-markov-models/index.qmd
index 9448b5794..cee9cdd71 100755
--- a/tutorials/hidden-markov-models/index.qmd
+++ b/tutorials/hidden-markov-models/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Hidden Markov Models
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../04-hidden-markov-model/index.html
 ---
diff --git a/tutorials/infinite-mixture-models/index.qmd b/tutorials/infinite-mixture-models/index.qmd
index 8b14aac49..1c67a8b79 100755
--- a/tutorials/infinite-mixture-models/index.qmd
+++ b/tutorials/infinite-mixture-models/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Infinite Mixture Models
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../06-infinite-mixture-model/index.html
 ---
diff --git a/tutorials/multinomial-logistic-regression/index.qmd b/tutorials/multinomial-logistic-regression/index.qmd
index e788475e8..9fb15649c 100755
--- a/tutorials/multinomial-logistic-regression/index.qmd
+++ b/tutorials/multinomial-logistic-regression/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Multinomial Logistic Regression
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../08-multinomial-logistic-regression/index.html
 ---
diff --git a/tutorials/probabilistic-pca/index.qmd b/tutorials/probabilistic-pca/index.qmd
index 6f8982923..ee9ff2464 100755
--- a/tutorials/probabilistic-pca/index.qmd
+++ b/tutorials/probabilistic-pca/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Probabilistic PCA
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../11-probabilistic-pca/index.html
 ---
diff --git a/tutorials/variational-inference/index.qmd b/tutorials/variational-inference/index.qmd
index 7d89ba904..d49adb2a7 100755
--- a/tutorials/variational-inference/index.qmd
+++ b/tutorials/variational-inference/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Variational Inference
 engine: julia
+format:
+  html: default
+  ipynb: default
 aliases:
  - ../09-variational-inference/index.html
 ---