streamlining streamlining

.gitignore

@@ -3,7 +3,7 @@
 /.quarto/
 /Manifest.toml
 /replicated/
-**/.CondaPkg/
+**/.CondaPkg
 /dev/rebuttal/www
 
 # Tex

README.md

@@ -39,8 +39,7 @@ The `experiments/` folder contains separate Julia scripts for each dataset and a
 To run the experiment for a single dataset, (e.g. `linearly_separable`) simply run the following command:
 
 ```shell
-DATANAME=linearly_separable
-julia experiments/run_experiments.jl
+julia experiments/run_experiments.jl -- data=linearly_separable
 ```
 
 We use the following identifiers:
@@ -51,14 +50,17 @@ We use the following identifiers:
 - `mnist` (*MNIST* data)
 - `gmsc` (*GMSC* data)
 
-To run all experiments at once you can instead just specify `DATANAME=all`.
+To run all experiments at once you can instead run
+
+```shell
+julia experiments/run_experiments.jl -- run-all
+```
 
-Pre-trained versions of all of our black-box models have been archived as `Pkg` [artifacts](https://pkgdocs.julialang.org/v1/artifacts/) and are used by default. Should you wish to retrain the models as well, simply run the following command:
+Pre-trained versions of all of our black-box models have been archived as `Pkg` [artifacts](https://pkgdocs.julialang.org/v1/artifacts/) and are used by default. Should you wish to retrain the models as well, simply use the `retrain` flag as follows:
 
 ```shell
 DATANAME=linearly_separable
-RETRAIN=true
-julia experiments/run_experiments.jl
+julia experiments/run_experiments.jl -- retrain
 ```
 
 When running the experiments from the command line, the parameter choices used in the main paper are applied by default. To have control over these choices, we recommend you instead rely on the notebooks.

experiments/run_experiments.jl

@@ -1,11 +1,12 @@
 include("setup.jl")
 
 # User inputs:
-if ENV["DATANAME"] == "all"
+if "run-all" in ARGS
     datanames = ["linearly_separable", "moons", "circles", "mnist", "gmsc"]
 else
-    datanames = [ENV["DATANAME"]]
+    datanames = [ARGS[findall(contains.(ARGS, "data="))] |> x -> replace(x, "data=" => "")]
 end
+datanames = ["linearly_separable", "moons", "circles", "mnist", "gmsc"]
 
 # Linearly Separable
 if "linearly_separable" in datanames

experiments/setup.jl

@@ -10,11 +10,7 @@ isdir(params_path) || mkdir(params_path)
 test_size = 0.2
 
 # Constants:
-if ENV["RETRAIN"] == "true"
-    const RETRAIN = true
-else
-    const RETRAIN = false
-end
+const RETRAIN = "retrain" ∈ ARGS ? true : false
 
 # Artifacts:
 using LazyArtifacts

notebooks/Manifest.toml

@@ -1,8 +1,8 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.9.0"
+julia_version = "1.9.2"
 manifest_format = "2.0"
-project_hash = "5dac8702e1bf52ac1887686257c409c28f8872ae"
+project_hash = "8709f4905068b3fffb11e99abcb4fafbd6d48a97"
 
 [[deps.ANSIColoredPrinters]]
 git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c"
@@ -122,6 +122,12 @@ git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be"
 uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458"
 version = "0.1.0"
 
+[[deps.AtomsBase]]
+deps = ["LinearAlgebra", "PeriodicTable", "Printf", "Requires", "StaticArrays", "Unitful", "UnitfulAtomic"]
+git-tree-sha1 = "c9804781ca49261c8eb6ce4b62f171cfa3d900f0"
+uuid = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
+version = "0.3.4"
+
 [[deps.Automa]]
 deps = ["TranscodingStreams"]
 git-tree-sha1 = "ef9997b3d5547c48b41c7bd8899e812a917b409d"
@@ -265,9 +271,9 @@ version = "0.6.0+0"
 
 [[deps.CUDNN_jll]]
 deps = ["Artifacts", "CUDA_Runtime_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"]
-git-tree-sha1 = "c30b29597102341a1ea4c2175c4acae9ae522c9d"
+git-tree-sha1 = "75923dce4275ead3799b238e10178a68c07dbd3b"
 uuid = "62b44479-cb7b-5706-934f-f13b2eb2e645"
-version = "8.9.2+0"
+version = "8.9.4+0"
 
 [[deps.Cairo]]
 deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"]
@@ -342,10 +348,10 @@ uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 version = "1.16.0"
 
 [[deps.Chemfiles]]
-deps = ["Chemfiles_jll", "DocStringExtensions"]
-git-tree-sha1 = "6951fe6a535a07041122a3a6860a63a7a83e081e"
+deps = ["AtomsBase", "Chemfiles_jll", "DocStringExtensions", "PeriodicTable", "Unitful", "UnitfulAtomic"]
+git-tree-sha1 = "82fe5e341c793cb51149d993307da9543824b206"
 uuid = "46823bd8-5fb3-5f92-9aa0-96921f3dd015"
-version = "0.10.40"
+version = "0.10.41"
 
 [[deps.Chemfiles_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -443,7 +449,7 @@ weakdeps = ["Dates", "LinearAlgebra"]
 [[deps.CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "1.0.2+0"
+version = "1.0.5+0"
 
 [[deps.CompositionsBase]]
 git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad"
@@ -480,7 +486,7 @@ uuid = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
 version = "0.2.18"
 
 [[deps.ConformalPrediction]]
-deps = ["CategoricalArrays", "ChainRules", "ComputationalResources", "Flux", "LazyArtifacts", "LinearAlgebra", "MLJBase", "MLJEnsembles", "MLJFlux", "MLJModelInterface", "MLUtils", "NaturalSort", "Plots", "ProgressMeter", "Random", "Serialization", "StatsBase", "Tables"]
+deps = ["CategoricalArrays", "ChainRules", "Flux", "LazyArtifacts", "LinearAlgebra", "MLJBase", "MLJEnsembles", "MLJFlux", "MLJModelInterface", "MLUtils", "NaturalSort", "Plots", "Serialization", "StatsBase"]
 path = "../../ConformalPrediction.jl"
 uuid = "98bfc277-1877-43dc-819b-a3e38c30242f"
 version = "0.1.8"
@@ -693,9 +699,9 @@ version = "0.5.2"
 
 [[deps.EvoTrees]]
 deps = ["BSON", "CUDA", "CategoricalArrays", "Distributions", "MLJModelInterface", "NetworkLayout", "Random", "RecipesBase", "Statistics", "StatsBase", "Tables"]
-git-tree-sha1 = "5023442c1f797c0fd6677b1a1886ab44f43f3378"
+git-tree-sha1 = "a1fa1d1743478394a0a7188d054b67546e4ca143"
 uuid = "f6006082-12f8-11e9-0c9c-0d5d367ab1e5"
-version = "0.16.0"
+version = "0.16.1"
 
 [[deps.ExactPredicates]]
 deps = ["IntervalArithmetic", "Random", "StaticArraysCore", "Test"]
@@ -1292,9 +1298,9 @@ version = "0.1.5"
 
 [[deps.JLLWrappers]]
 deps = ["Artifacts", "Preferences"]
-git-tree-sha1 = "a7e91ef94114d5bc8952bcaa8d6ff952cf709808"
+git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca"
 uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
-version = "1.4.2"
+version = "1.5.0"
 
 [[deps.JSON]]
 deps = ["Dates", "Mmap", "Parsers", "Unicode"]
@@ -1403,8 +1409,8 @@ uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 version = "1.3.0"
 
 [[deps.LaplaceRedux]]
-deps = ["CSV", "Compat", "ComputationalResources", "DataFrames", "Flux", "LinearAlgebra", "MLJ", "MLJBase", "MLJFlux", "MLJModelInterface", "MLUtils", "Parameters", "Plots", "ProgressMeter", "Random", "Serialization", "Statistics", "Tables", "Tullio", "Zygote"]
-path = "../../LaplaceRedux.jl"
+deps = ["Flux", "LinearAlgebra", "Parameters", "Plots", "Zygote"]
+git-tree-sha1 = "a4adebbeafb96d0864b4833c254013f66dc6e0ee"
 uuid = "c52c1a26-f7c5-402b-80be-ba1e638ad478"
 version = "0.1.2"
 
@@ -1555,9 +1561,9 @@ version = "0.6.1"
 
 [[deps.LogExpFunctions]]
 deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
-git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f"
+git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d"
 uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-version = "0.3.24"
+version = "0.3.25"
 
     [deps.LogExpFunctions.extensions]
     LogExpFunctionsChainRulesCoreExt = "ChainRulesCore"
@@ -1631,9 +1637,9 @@ version = "0.19.2"
 
 [[deps.MLJBase]]
 deps = ["CategoricalArrays", "CategoricalDistributions", "ComputationalResources", "Dates", "DelimitedFiles", "Distributed", "Distributions", "InteractiveUtils", "InvertedIndices", "LinearAlgebra", "LossFunctions", "MLJModelInterface", "Missings", "OrderedCollections", "Parameters", "PrettyTables", "ProgressMeter", "Random", "ScientificTypes", "Serialization", "StatisticalTraits", "Statistics", "StatsBase", "Tables"]
-git-tree-sha1 = "2c9d6b9c627a80f6e6acbc6193026f455581fd04"
+git-tree-sha1 = "0b7307d1a7214ec3c0ba305571e713f9492ea984"
 uuid = "a7f614a8-145f-11e9-1d2a-a57a1082229d"
-version = "0.21.13"
+version = "0.21.14"
 
 [[deps.MLJDecisionTreeInterface]]
 deps = ["CategoricalArrays", "DecisionTree", "MLJModelInterface", "Random", "Tables"]
@@ -1661,9 +1667,9 @@ version = "0.5.1"
 
 [[deps.MLJModelInterface]]
 deps = ["Random", "ScientificTypesBase", "StatisticalTraits"]
-git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9"
+git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5"
 uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea"
-version = "1.9.1"
+version = "1.9.2"
 
 [[deps.MLJModels]]
 deps = ["CategoricalArrays", "CategoricalDistributions", "Combinatorics", "Dates", "Distances", "Distributions", "InteractiveUtils", "LinearAlgebra", "MLJModelInterface", "Markdown", "OrderedCollections", "Parameters", "Pkg", "PrettyPrinting", "REPL", "Random", "RelocatableFolders", "ScientificTypes", "StatisticalTraits", "Statistics", "StatsBase", "Tables"]
@@ -1690,9 +1696,9 @@ version = "0.4.3"
 
 [[deps.MacroTools]]
 deps = ["Markdown", "Random"]
-git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2"
+git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48"
 uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
-version = "0.5.10"
+version = "0.5.11"
 
 [[deps.Makie]]
 deps = ["Animations", "Base64", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG", "FileIO", "FixedPointNumbers", "Formatting", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "InteractiveUtils", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "Match", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Setfield", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "StableHashTraits", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun"]
@@ -1999,9 +2005,9 @@ version = "2.0.2"
 
 [[deps.Optimisers]]
 deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"]
-git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e"
+git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b"
 uuid = "3bd65402-5787-11e9-1adc-39752487f4e2"
-version = "0.2.19"
+version = "0.2.20"
 
 [[deps.Opus_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -2067,6 +2073,12 @@ git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
 version = "2.7.2"
 
+[[deps.PeriodicTable]]
+deps = ["Base64", "Test", "Unitful"]
+git-tree-sha1 = "9a9731f346797126271405971dfdf4709947718b"
+uuid = "7b2266bf-644c-5ea3-82d8-af4bbd25a884"
+version = "1.1.4"
+
 [[deps.Permutations]]
 deps = ["Combinatorics", "LinearAlgebra", "Random"]
 git-tree-sha1 = "6e6cab1c54ae2382bcc48866b91cf949cea703a1"
@@ -2099,7 +2111,7 @@ version = "0.42.2+0"
 [[deps.Pkg]]
 deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
-version = "1.9.0"
+version = "1.9.2"
 
 [[deps.PkgTemplates]]
 deps = ["Dates", "InteractiveUtils", "LibGit2", "Mocking", "Mustache", "Parameters", "Pkg", "REPL", "UUIDs"]
@@ -2851,12 +2863,6 @@ git-tree-sha1 = "4d4ed7f294cda19382ff7de4c137d24d16adc89b"
 uuid = "981d1d27-644d-49a2-9326-4793e63143c3"
 version = "0.1.0"
 
-[[deps.Tullio]]
-deps = ["ChainRulesCore", "DiffRules", "LinearAlgebra", "Requires"]
-git-tree-sha1 = "7871a39eac745697ee512a87eeff06a048a7905b"
-uuid = "bc48ee85-29a4-5162-ae0b-a64e1601d4bc"
-version = "0.3.5"
-
 [[deps.TupleTools]]
 git-tree-sha1 = "3c712976c47707ff893cf6ba4354aa14db1d8938"
 uuid = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6"
@@ -2905,6 +2911,12 @@ version = "1.16.3"
     ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
     InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112"
 
+[[deps.UnitfulAtomic]]
+deps = ["Unitful"]
+git-tree-sha1 = "903be579194534af1c4b4778d1ace676ca042238"
+uuid = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
+version = "1.0.0"
+
 [[deps.UnitfulLatexify]]
 deps = ["LaTeXStrings", "Latexify", "Unitful"]
 git-tree-sha1 = "e2d817cc500e960fdbafcf988ac8436ba3208bfd"
@@ -3189,7 +3201,7 @@ version = "0.15.1+0"
 [[deps.libblastrampoline_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
-version = "5.7.0+0"
+version = "5.8.0+0"
 
 [[deps.libfdk_aac_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]

notebooks/Project.toml

@@ -16,7 +16,6 @@ ECCCo = "0232c203-4013-4b0d-ad96-43e3e11ac3bf"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
 JointEnergyModels = "48c56d24-211d-4463-bbc0-7a701b291131"
-LaplaceRedux = "c52c1a26-f7c5-402b-80be-ba1e638ad478"
 LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
 MLDatasets = "eb30cadb-4394-5ae3-aed4-317e484a6458"
 MLJ = "add582a8-e3ab-11e8-2d5e-e98b27df1bc7"