Move hasvalue and getvalue from DynamicPPL; implement extra Distributions-based methods (#125)

* Move hasvalue and getvalue to AbstractPPL; reimplement

* Add hasvalue for (some) distributions

* Bump min Julia to 1.10

* Make hasvalue and getvalue use the most specific value

* Specify getvalue semantics in docstring

* Simplify logic (can rely on normalisation)

* Add tests for composition of head/tail and init/last

* Finish implementing distributions methods

* Document

* Fix LinearAlgebra version bound

* Try to fix documentation for extension (why is this so complicated...)

* Fix extension documentation

* Implement fallback {has,get}value methods for NamedTuple + Distribution

* Fix wrong way round composition, add more tests

* Update src/hasvalue.jl

Co-authored-by: Markus Hauru <[email protected]>

* Update HISTORY.md

Co-authored-by: Markus Hauru <[email protected]>

* Minor bump

* Fix test (forgot to push this...)

* Add extra example for getvalue

* Tweak error message when value not found

* Format (?!)

* Fix doctests

* Add a docstring to the extension

* Add tests for colons

---------

Co-authored-by: Markus Hauru <[email protected]>

Author: penelopeysm

HISTORY.md

@@ -1,3 +1,17 @@
+## 0.13.0
+
+Minimum compatibility has been bumped to Julia 1.10.
+
+Added the new functions `hasvalue(container::T, ::VarName[, ::Distribution])` and `getvalue(container::T, ::VarName[, ::Distribution])`, where `T` is either `NamedTuple` or `AbstractDict{<:VarName}`.
+
+These functions check whether a given `VarName` has a value in the given `NamedTuple` or `AbstractDict`, and return the value if it exists.
+
+The optional `Distribution` argument allows one to reconstruct a full value from its component indices.
+For example, if `container` has `x[1]` and `x[2]`, then `hasvalue(container, @varname(x), dist)` will return true if `size(dist) == (2,)` (for example, `MvNormal(zeros(2), I)`).
+In this case plain `hasvalue(container, @varname(x))` would return `false`, since we can not know whether the vector-valued variable `x` has all of its elements specified in `container` (there might be an `x[3]` missing).
+
+These functions (without the `Distribution` argument) were previously in DynamicPPL.jl (albeit unexported).
+
 ## 0.12.0
 
 ### VarName constructors

Project.toml

@@ -3,7 +3,7 @@ uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf"
 keywords = ["probablistic programming"]
 license = "MIT"
 desc = "Common interfaces for probabilistic programming"
-version = "0.12.0"
+version = "0.13.0"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
@@ -13,11 +13,20 @@ JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 
+[weakdeps]
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+
+[extensions]
+AbstractPPLDistributionsExt = ["Distributions", "LinearAlgebra"]
+
 [compat]
 AbstractMCMC = "2, 3, 4, 5"
 Accessors = "0.1"
 DensityInterface = "0.4"
+Distributions = "0.25"
+LinearAlgebra = "<0.0.1, 1.10"
 JSON = "0.19 - 0.21"
 Random = "1.6"
 StatsBase = "0.32, 0.33, 0.34"
-julia = "~1.6.6, 1.7.3"
+julia = "1.10"

docs/Project.toml

@@ -1,2 +1,5 @@
 [deps]
+AbstractPPL = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"

docs/make.jl

@@ -1,12 +1,14 @@
 using Documenter
 using AbstractPPL
+# trigger DistributionsExt loading
+using Distributions, LinearAlgebra
 
 # Doctest setup
 DocMeta.setdocmeta!(AbstractPPL, :DocTestSetup, :(using AbstractPPL); recursive=true)
 
 makedocs(;
     sitename="AbstractPPL",
-    modules=[AbstractPPL],
+    modules=[AbstractPPL, Base.get_extension(AbstractPPL, :AbstractPPLDistributionsExt)],
     pages=["Home" => "index.md", "API" => "api.md"],
     checkdocs=:exports,
     doctest=false,

docs/src/api.md

@@ -21,6 +21,13 @@ prefix
 unprefix
 ```
 
+## Extracting values corresponding to a VarName
+
+```@docs
+hasvalue
+getvalue
+```
+
 ## VarName serialisation
 
 ```@docs