Upgrade to JSON v1 (#215)

* Upgrade to JSON v1

* Update documenter compat

* Warn only on missing docs etc

Author: BenCurran98

Project.toml

@@ -1,12 +1,12 @@
 name = "XGBoost"
 uuid = "009559a3-9522-5dbb-924b-0b6ed2b22bb9"
-version = "2.5.2"
+version = "2.5.3"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
 CEnum = "fa961155-64e5-5f13-b03f-caf6b980ea82"
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
-JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
@@ -29,13 +29,13 @@ XGBoostTermExt = "Term"
 AbstractTrees = "0.4"
 CEnum = "0.4, 0.5"
 CUDA = "3, 4, 5"
-JSON3 = "1"
+JSON = "1.4.0"
 OrderedCollections = "1"
 SparseMatricesCSR = "0.6"
 Tables = "1"
 Term = "1, 2"
-XGBoost_jll = "2.1"
 XGBoost_GPU_jll = "2.1"
+XGBoost_jll = "2.1"
 julia = "1.6"
 
 [extras]

docs/Project.toml

@@ -3,4 +3,4 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 XGBoost = "009559a3-9522-5dbb-924b-0b6ed2b22bb9"
 
 [compat]
-Documenter = "0.27"
+Documenter = "1"

docs/make.jl

@@ -17,6 +17,7 @@ makedocs(;
         "Additional Features" => "features.md",
         "API" => "api.md",
        ],
+    warnonly = [:missing_docs, :autodocs_block, :docs_block, :cross_references]
    )
 
 deploydocs(repo="github.com/dmlc/XGBoost.jl.git", devbranch="master")

src/XGBoost.jl

@@ -7,7 +7,7 @@ import SparseMatricesCSR
 using SparseMatricesCSR: SparseMatrixCSR
 using AbstractTrees
 using OrderedCollections
-using JSON3
+using JSON
 using Tables
 using Statistics: mean, std
 

src/booster.jl

@@ -196,7 +196,7 @@ function save(b::Booster, fname::AbstractString; kw...)
     fname
 end
 function save(b::Booster, ::Type{Vector{UInt8}}; format::AbstractString="json")
-    cfg = JSON3.write(Dict("format"=>format))
+    cfg = JSON.json(Dict("format"=>format))
     olen = Ref{Lib.bst_ulong}()
     o = Ref{Ptr{Int8}}()
     xgbcall(XGBoosterSaveModelToBuffer, b.handle, cfg, olen, o)
@@ -234,7 +234,7 @@ function dump(b::Booster;
               with_stats::Bool=false,
              )
     strs = dumpraw(b; fmap, with_stats)
-    JSON3.read.(strs)
+    JSON.parse.(strs)
 end
 
 """
@@ -302,7 +302,7 @@ function predict_nocopy(b::Booster, Xy::DMatrix;
                 "iteration_end"=>ntree_limit,
                 "strict_shape"=>false,
                 "training"=>training,
-               ) |> JSON3.write
+               ) |> JSON.json
     oshape = Ref{Ptr{Lib.bst_ulong}}()
     odim = Ref{Lib.bst_ulong}()
     o = Ref{Ptr{Cfloat}}()

src/dmatrix.jl

@@ -193,7 +193,7 @@ function load(::Type{DMatrix}, fname::AbstractString;
                # docs are inconsistent and don't explain this, so it's disabled
                #"data_split_mode"=>string(data_split_mode),
               )
-    xgbcall(XGDMatrixCreateFromURI, JSON3.write(cfg), o)
+    xgbcall(XGDMatrixCreateFromURI, JSON.json(cfg), o)
     DMatrix(o[], kw...)
 end
 
@@ -361,7 +361,7 @@ function getdata(dm::DMatrix)
     rowptr = Vector{UInt64}(undef, m+1)
     colval = Vector{UInt32}(undef, nnonmissing(dm))
     data = Vector{Float32}(undef, nnonmissing(dm))
-    cfg = JSON3.write(Dict())
+    cfg = JSON.json(Dict())
     xgbcall(XGDMatrixGetDataAsCSR, dm.handle, cfg, rowptr, colval, data)
     SparseMatrixCSR{0}(m, n, rowptr, UInt64.(colval), data)
 end
@@ -496,9 +496,9 @@ function numpy_json_dict(x::AbstractArray; read_only::Bool=false)
         )
 end
 
-numpy_json_info(x::AbstractArray; kw...) = JSON3.write(numpy_json_dict(x; kw...))
+numpy_json_info(x::AbstractArray; kw...) = JSON.json(numpy_json_dict(x; kw...))
 
-numpy_json_infos(cols::Tables.Columns; kw...) = JSON3.write(map(x -> numpy_json_dict(x; kw...), cols))
+numpy_json_infos(cols::Tables.Columns; kw...) = JSON.json(map(x -> numpy_json_dict(x; kw...), cols))
 
 #TODO: still a little worried about ownership here
 #TODO: sparse data for iterator and proper missings handling
@@ -597,7 +597,7 @@ function _dmatrix_caching_config_json(;cache_prefix::AbstractString,
         repr(missing_value)
     end
     # xgboost allows nan and inf which JSON3 thinks is invalid
-    replace(JSON3.write(d), "\"__NAN_STR__\""=>nanstr)
+    replace(JSON.json(d), "\"__NAN_STR__\""=>nanstr)
 end
 
 function DMatrix(itr::DataIterator;

src/introspection.jl

@@ -28,7 +28,7 @@ importances and [`importancereport`](@ref) for a convenient text display of it.
 function importance(b::Booster, type::AbstractString="gain")
     getnrounds(b) == 0 && return OrderedDict{String,Vector{Float32}}()
 
-    cfg = JSON3.write(Dict("importance_type"=>type))
+    cfg = JSON.json(Dict("importance_type"=>type))
 
     olen_fnames = Ref{Lib.bst_ulong}()
     o_fnames = Ref{Ptr{Ptr{Cchar}}}()

test/utils.jl

@@ -1,4 +1,4 @@
-using JSON3
+using JSON
 
 
 function testfilepath(name::AbstractString) 
@@ -27,7 +27,7 @@ end
 
 function load_classification()
     fname = joinpath(@__DIR__,"..","assets","data","blobs.json")
-    o = JSON3.read(String(open(read, fname)))
+    o = JSON.parse(String(open(read, fname)))
     X = Matrix{Float32}([o[:X1] o[:X2] o[:X3]])
     y = o[:y]
     (X, y)