bat · oschulz · Aug 1, 2024 · Aug 1, 2024 · Aug 1, 2024 · Aug 1, 2024
diff --git a/.github/workflows/DocPreviewCleanup.yml b/.github/workflows/DocPreviewCleanup.yml
@@ -0,0 +1,33 @@
+name: Doc Preview Cleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+# Ensure that only one "Doc Preview Cleanup" workflow is force pushing at a time
+concurrency:
+  group: doc-preview-cleanup
+  cancel-in-progress: false
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+          if [ -d "${preview_dir}" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "documenter@juliadocs.github.io"
+              git rm -rf "${preview_dir}"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+          fi
+        env:
+          preview_dir: previews/PR${{ github.event.number }}
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -29,9 +29,9 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
+          - '1.10'
           - '1'
-          # - 'nightly'
+          - 'pre'
         os:
           - ubuntu-latest
         arch:

diff --git a/Project.toml b/Project.toml
@@ -1,6 +1,6 @@
 name = "BAT"
 uuid = "c0cd4b16-88b7-57fa-983b-ab80aecada7e"
-version = "3.2.1"
+version = "3.3.0"
 
 [deps]
 Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
@@ -51,7 +51,6 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Random123 = "74087812-796a-5b5d-8853-05524746bad3"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Sobol = "ed01d8cd-4d21-5b2a-85b4-cc3bdc58bad4"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
@@ -146,7 +145,6 @@ Printf = "1"
 Random = "1"
 Random123 = "1.2"
 RecipesBase = "0.7, 0.8, 1.0"
-Requires = "0.5, 1"
 Sobol = "1.4"
 StableRNGs = "1"
 StaticArrays = "0.12, 1.0"
@@ -160,17 +158,4 @@ TypedTables = "1.2"
 UltraNest = "0.1"
 ValueShapes = "0.11"
 ZygoteRules = "0.2"
-julia = "1.6"
-
-[extras]
-ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
-AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-Cuba = "8a292aeb-7a57-582c-b821-06e4c11590b1"
-Folds = "41a02a25-b8f0-4f67-bc48-60067656b558"
-HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
-NestedSamplers = "41ceaf6f-1696-4a54-9b49-2e7a9ec3782e"
-Optim = "429524aa-4258-5aef-a3af-852621145aeb"
-Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-Transducers = "28d57a85-8fef-5791-bfe6-a80928e7c999"
-UltraNest = "6822f173-b0be-4018-9ee2-28bf56348d09"
+julia = "1.10"
diff --git a/README.md b/README.md
@@ -23,7 +23,9 @@ julia> using Pkg
 julia> pkg"add BAT"
 ```
 
-**Note:** BAT.jl requires Julia >= v1.6, we recommend to use Julia >= v1.10 for optimal performance.
+Note: BAT.jl requires Julia >= v1.10, we recommend to use
+[the latest stable Julia version](https://julialang.org/downloads/)
+for optimal performance.
 
 
 ## Documentation

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -12,7 +12,7 @@ BAT.jl originated as a rewrite/redesign of [BAT](https://github.com/bat/bat), th
 
 !!! note
 
-    BAT.jl requires Julia >= v1.6, we recommend to use Julia >= v1.9 for optimal performance.
+    BAT.jl requires Julia >= v1.10, we recommend to use [the latest stable Julia version](https://julialang.org/downloads/) for optimal performance.
 
 
 ## Table of contents

diff --git a/docs/src/installation.md b/docs/src/installation.md
@@ -21,7 +21,7 @@ Julia is available for Linux, OS-X and Windows, and easy to install:
 
 !!! note
 
-    BAT.jl requires Julia >= v1.6, we strongly recommend to use the latest Julia version for optimal performance.
+    BAT.jl requires Julia >= v1.10, we recommend to use [the latest stable Julia version](https://julialang.org/downloads/) for optimal performance.
 
 
 ## Installing BAT.jl and related Julia packages

diff --git a/ext/BATAdvancedHMCExt.jl b/ext/BATAdvancedHMCExt.jl
@@ -2,11 +2,7 @@
 
 module BATAdvancedHMCExt
 
-@static if isdefined(Base, :get_extension)
-    using AdvancedHMC
-else
-    using ..AdvancedHMC
-end
+using AdvancedHMC
 
 using BAT
 BAT.pkgext(::Val{:AdvancedHMC}) = BAT.PackageExtension{:AdvancedHMC}()

diff --git a/ext/BATCubaExt.jl b/ext/BATCubaExt.jl
@@ -2,11 +2,7 @@
 
 module BATCubaExt
 
-@static if isdefined(Base, :get_extension)
-    using Cuba
-else
-    using ..Cuba
-end
+using Cuba
 
 using BAT
 BAT.pkgext(::Val{:Cuba}) = BAT.PackageExtension{:Cuba}()

diff --git a/ext/BATFoldsExt.jl b/ext/BATFoldsExt.jl
@@ -2,11 +2,7 @@
 
 module BATFoldsExt
 
-@static if isdefined(Base, :get_extension)
-    using Folds, Transducers
-else
-    using ..Folds, ..Transducers
-end
+using Folds, Transducers
 
 using BAT
 

diff --git a/ext/BATHDF5Ext.jl b/ext/BATHDF5Ext.jl
@@ -2,13 +2,8 @@
 
 module BATHDF5Ext
 
-@static if isdefined(Base, :get_extension)
-    using HDF5
-    using HDF5: H5DataStore
-else
-    using ..HDF5
-    using ..HDF5: H5DataStore
-end
+using HDF5
+using HDF5: H5DataStore
 
 using BAT
 using BAT: MCMCSampleIDVector

diff --git a/ext/BATNestedSamplersExt.jl b/ext/BATNestedSamplersExt.jl
@@ -2,11 +2,7 @@
 
 module BATNestedSamplersExt
 
-@static if isdefined(Base, :get_extension)
-    using NestedSamplers
-else
-    using ..NestedSamplers
-end
+using NestedSamplers
 
 using BAT
 using HeterogeneousComputing

diff --git a/ext/BATOptimExt.jl b/ext/BATOptimExt.jl
@@ -2,11 +2,7 @@
 
 module BATOptimExt
 
-@static if isdefined(Base, :get_extension)
-    import Optim
-else
-    import ..Optim
-end
+import Optim
 
 using BAT
 BAT.pkgext(::Val{:Optim}) = BAT.PackageExtension{:Optim}()

diff --git a/ext/BATOptimizationExt.jl b/ext/BATOptimizationExt.jl
@@ -2,13 +2,7 @@
 
 module BATOptimizationExt
 
-# seems to cause compatibility issues between different Julia versions. 
-# @static if isdefined(Base, :get_extension)
-#     import Optimization
-# else
-#     import ..Optimization
-# end
-import ..Optimization
+import Optimization
 
 using BAT
 BAT.pkgext(::Val{:Optimization}) = BAT.PackageExtension{:Optimization}()

diff --git a/ext/BATPlotsExt.jl b/ext/BATPlotsExt.jl
@@ -1,12 +1,10 @@
 # This file is a part of BAT.jl, licensed under the MIT License (MIT).
 
+# ToDo: Move BAT plotting into BATPlotsExt.
+
 module BATPlotsExt
 
-@static if isdefined(Base, :get_extension)
-    using Plots
-else
-    using ..Plots
-end
+using Plots
 
 using BAT
 

diff --git a/ext/BATUltraNestExt.jl b/ext/BATUltraNestExt.jl
@@ -2,11 +2,7 @@
 
 module BATUltraNestExt
 
-@static if isdefined(Base, :get_extension)
-    using UltraNest
-else
-    using ..UltraNest
-end
+using UltraNest
 
 using BAT
 

diff --git a/src/BAT.jl b/src/BAT.jl
@@ -43,7 +43,6 @@ using Parameters
 using PDMats
 using PositiveFactorizations
 using RecipesBase
-using Requires
 using StaticArrays
 using StatsBase
 using StructArrays
@@ -128,23 +127,4 @@ include("deprecations.jl")
 
 # include("precompile.jl")
 
-
-@static if !isdefined(Base, :get_extension)
-    using Requires
-end
-
-function __init__()
-    @static if !isdefined(Base, :get_extension)
-        @require AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" include("../ext/BATAdvancedHMCExt.jl")
-        @require Folds = "41a02a25-b8f0-4f67-bc48-60067656b558" @require Transducers = "28d57a85-8fef-5791-bfe6-a80928e7c999" include("../ext/BATFoldsExt.jl")
-        @require Cuba = "8a292aeb-7a57-582c-b821-06e4c11590b1" include("../ext/BATCubaExt.jl")
-        @require HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" include("../ext/BATHDF5Ext.jl")
-        @require NestedSamplers = "41ceaf6f-1696-4a54-9b49-2e7a9ec3782e" include("../ext/BATNestedSamplersExt.jl")
-        @require Optim = "429524aa-4258-5aef-a3af-852621145aeb" include("../ext/BATOptimExt.jl")
-        @require Optimization = "429524aa-4258-5aef-a3af-852621145aeb" @require ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" include("../ext/BATOptimizationExt.jl")
-        @require Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" include("../ext/BATPlotsExt.jl")
-        @require UltraNest = "6822f173-b0be-4018-9ee2-28bf56348d09" include("../ext/BATUltraNestExt.jl")
-    end
-end
-
 end # module
diff --git a/src/plotting/recipes_diagnostics.jl b/src/plotting/recipes_diagnostics.jl
@@ -27,7 +27,7 @@
     description ? ndescription = 1 : ndescription = 0
 
     size --> (ndiagnostics*350+100, nparams*nchains*200)
-    layout --> Main.Plots.grid(nparams*nchains, ndiagnostics+ndescription)
+    layout --> _Plots_grid(nparams*nchains, ndiagnostics+ndescription)
 
     ctr = 1
 

diff --git a/src/plotting/vsel_processing.jl b/src/plotting/vsel_processing.jl
@@ -214,7 +214,7 @@ end
 # :a⌞1ˌ3ˌ5⌟ = : a \llcorner 1 \verti 3 \verti 5 \lrcorner
 
 function encode_name(name::Union{Expr, String})
-    # Nested replace to make Julia v1.6 happy:
+    # Nested replace to make Julia v1.6 happy: # ToDo: simplify, now that we require Julia v1.10
     code = replace(replace(replace(replace(replace(
         string(name)," " => ""), "[" => "⌞"), ":" => "ː"), "," => "ˌ"), "]" => "⌟"
     )

diff --git a/test/optimization/test_mode_estimators.jl b/test/optimization/test_mode_estimators.jl
@@ -5,7 +5,6 @@ using LinearAlgebra, Distributions, StatsBase, ValueShapes, Random123, DensityIn
 using UnPack, InverseFunctions
 using AutoDiffOperators, ForwardDiff
 using Optim, OptimizationOptimJL
-include("../../ext/BATOptimizationExt.jl")
 
 @testset "mode_estimators" begin
     prior = NamedTupleDist(

diff --git a/test/samplers/nested_sampling/test_nested_sampling.jl b/test/samplers/nested_sampling/test_nested_sampling.jl
@@ -8,7 +8,7 @@ Test.@testset "nested_sampling" begin
     # Python ultranest package doesn't seem to be available via Conda on
     # 32-bit systems, GLIBCXX version conflicts cause trouble for CI
     # on older Julia versions:
-    if Int == Int64 && VERSION > v"1.8" && ("UltraNest" in keys(Pkg.project().dependencies))
+    if Int == Int64 && ("UltraNest" in keys(Pkg.project().dependencies))
         include("test_ultranest.jl")
     end
     if ("NestedSamplers" in keys(Pkg.project().dependencies))