From 82117377c043f8a9a21cc933977e902fb5624129 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Fri, 25 Oct 2024 20:36:26 +0100 Subject: [PATCH] Bump Turing/DynamicPPL compat (#214) * Bump compat for Turing -> 0.35, DynamicPPL -> 0.29 * Fix links to old Turing website * Bump patch version * Increment patch number --------- Co-authored-by: Seth Axen --- Project.toml | 6 +++--- docs/Project.toml | 2 +- docs/src/examples/initializing-hmc.md | 4 ++-- docs/src/examples/turing.md | 2 +- test/integration/Turing/Project.toml | 2 +- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/Project.toml b/Project.toml index 1fa4d281b..ff179da06 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Pathfinder" uuid = "b1d3bc72-d0e7-4279-b92f-7fa5d6d2d454" authors = ["Seth Axen and contributors"] -version = "0.9.3" +version = "0.9.4" [deps] ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" @@ -41,7 +41,7 @@ ADTypes = "0.2, 1" Accessors = "0.1.12" Distributions = "0.25.87" DynamicHMC = "3.4.0" -DynamicPPL = "0.25.2, 0.27, 0.28" +DynamicPPL = "0.25.2, 0.27, 0.28, 0.29" Folds = "0.2.9" ForwardDiff = "0.10.19" IrrationalConstants = "0.1.1, 0.2" @@ -62,7 +62,7 @@ SciMLBase = "1.95.0, 2" Statistics = "1.6" StatsBase = "0.33.7, 0.34" Transducers = "0.4.81" -Turing = "0.31.4, 0.32, 0.33, 0.34" +Turing = "0.31.4, 0.32, 0.33, 0.34, 0.35" UnPack = "1" julia = "1.6" diff --git a/docs/Project.toml b/docs/Project.toml index 17946eaca..91a8f13cd 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -30,4 +30,4 @@ StatsFuns = "1" StatsPlots = "0.14.21, 0.15" TransformVariables = "0.6.2, 0.7, 0.8" TransformedLogDensities = "1.0.2" -Turing = "0.31.4, 0.32, 0.33, 0.34" +Turing = "0.31.4, 0.32, 0.33, 0.34, 0.35" diff --git a/docs/src/examples/initializing-hmc.md b/docs/src/examples/initializing-hmc.md index 2a0bbe704..0777ed93d 100644 --- a/docs/src/examples/initializing-hmc.md +++ b/docs/src/examples/initializing-hmc.md @@ -17,7 +17,7 @@ Pathfinder can be used to initialize MCMC, and in particular HMC, in 3 ways: This tutorial demonstrates all three approaches with [DynamicHMC.jl](https://tamaspapp.eu/DynamicHMC.jl/stable/) and [AdvancedHMC.jl](https://github.com/TuringLang/AdvancedHMC.jl). Both of these packages have standalone implementations of adaptive HMC (aka NUTS) and can be used independently of any probabilistic programming language (PPL). -Both the [Turing](https://turing.ml/stable/) and [Soss](https://github.com/cscherrer/Soss.jl) PPLs have some DynamicHMC integration, while Turing also integrates with AdvancedHMC. +Both the [Turing](https://turinglang.org/) and [Soss](https://github.com/cscherrer/Soss.jl) PPLs have some DynamicHMC integration, while Turing also integrates with AdvancedHMC. For demonstration purposes, we'll use the following dummy data: @@ -234,4 +234,4 @@ samples_ahmc3, stats_ahmc3 = sample( ) ``` -[^1]: https://mc-stan.org/docs/reference-manual/hmc-algorithm-parameters.html \ No newline at end of file +[^1]: https://mc-stan.org/docs/reference-manual/hmc-algorithm-parameters.html diff --git a/docs/src/examples/turing.md b/docs/src/examples/turing.md index 0de997359..e2774e93d 100644 --- a/docs/src/examples/turing.md +++ b/docs/src/examples/turing.md @@ -1,6 +1,6 @@ # Running Pathfinder on Turing.jl models -This tutorial demonstrates how [Turing](https://turing.ml/stable/) can be used with Pathfinder. +This tutorial demonstrates how [Turing](https://turinglang.org/) can be used with Pathfinder. We'll demonstrate with a regression example. diff --git a/test/integration/Turing/Project.toml b/test/integration/Turing/Project.toml index e59b1e29c..1938c556c 100644 --- a/test/integration/Turing/Project.toml +++ b/test/integration/Turing/Project.toml @@ -9,5 +9,5 @@ Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" [compat] LogDensityProblems = "2.1.0" Pathfinder = "0.9" -Turing = "0.31.4, 0.32, 0.33, 0.34" +Turing = "0.31.4, 0.32, 0.33, 0.34, 0.35" julia = "1.6"