Improve setup of examples (#125)

* Update configuration documentation and example

* Update package versions

* Update docs/literate.jl

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* Fix the documentation

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Author: devmotion

.github/workflows/CompatHelper.yml

@@ -1,16 +1,38 @@
 name: CompatHelper
 on:
   schedule:
-    - cron: '00 00 * * *'
+    - cron: 0 0 * * *
   workflow_dispatch:
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main()
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          subdirs = ["", "docs", "test/gpu"]
+          for f in readdir("examples"; join=true)
+              if isdir(f)
+                  push!(subdirs, joinpath("examples", basename(f)))
+              end
+          end
+          @info "CompatHelper directories" subdirs
+          CompatHelper.main(; subdirs=subdirs, bump_version=true)
+        shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-        run: julia -e 'using CompatHelper; CompatHelper.main(; subdirs = ["", "docs", "docs/gpu", "examples/basic"])'

.github/workflows/Documentation.yml

@@ -23,14 +23,15 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1'
-      - name: Install dependencies, build and deploy
+      - name: Install dependencies
         run: |
           using Pkg: Pkg
-          Pkg.develop(Pkg.PackageSpec(path=pwd()))
           Pkg.instantiate()
-          include(joinpath(pwd(), "docs", "make.jl"))
+        shell: julia --color=yes --project=docs/ {0}
+      - name: Build and deploy
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
           GKSwstype: nul # avoid (irrelevant) error messages from GR
-        shell: julia --color=yes --project=docs/ {0}
+          JULIA_DEBUG: Documenter # Print `@debug` statements (https://github.com/JuliaDocs/Documenter.jl/issues/955)
+        run: julia --color=yes --project=docs/ docs/make.jl

docs/Manifest.toml

@@ -1,5 +1,16 @@
 # This file is machine-generated - editing it directly is not advised
 
+[[ANSIColoredPrinters]]
+git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c"
+uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9"
+version = "0.0.1"
+
+[[Adapt]]
+deps = ["LinearAlgebra"]
+git-tree-sha1 = "84918055d15b3114ede17ac6a7182f68870c16f7"
+uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
+version = "3.3.1"
+
 [[ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
 
@@ -11,9 +22,9 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
 [[BenchmarkTools]]
 deps = ["JSON", "Logging", "Printf", "Statistics", "UUIDs"]
-git-tree-sha1 = "01ca3823217f474243cc2c8e6e1d1f45956fe872"
+git-tree-sha1 = "42ac5e523869a84eac9669eaceed9e4aa0e1587b"
 uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
-version = "1.0.0"
+version = "1.1.4"
 
 [[Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -23,9 +34,9 @@ version = "1.0.8+0"
 
 [[ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra", "SparseArrays"]
-git-tree-sha1 = "8b31cc69cbc38c5c826aaa1c890c694be3622d99"
+git-tree-sha1 = "bdc0937269321858ab2a4f288486cb258b9a0af7"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "0.10.3"
+version = "1.3.0"
 
 [[CodecBzip2]]
 deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"]
@@ -41,24 +52,24 @@ version = "0.7.0"
 
 [[Compat]]
 deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
-git-tree-sha1 = "e4e2b39db08f967cc1360951f01e8a75ec441cab"
+git-tree-sha1 = "727e463cfebd0c7b999bbf3e9e7e16f254b94193"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "3.30.0"
+version = "3.34.0"
 
 [[CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
 
 [[DataAPI]]
-git-tree-sha1 = "dfb3b7e89e395be1e25c2ad6d7690dc29cc53b1d"
+git-tree-sha1 = "ee400abb2298bd13bfc3df1c412ed228061a2385"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
-version = "1.6.0"
+version = "1.7.0"
 
 [[DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
-git-tree-sha1 = "4437b64df1e0adccc3e5d1adbc3ac741095e4677"
+git-tree-sha1 = "7d9d316f04214f7efdbb6398d545446e246eff02"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.18.9"
+version = "0.18.10"
 
 [[Dates]]
 deps = ["Printf"]
@@ -80,9 +91,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[Distributions]]
 deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "013020ec9a5cdf1dd454eba3704dbffa69d3047e"
+git-tree-sha1 = "f389cb8974e02d7eaa6ae2ccedbbfb43174cd8e8"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.25.3"
+version = "0.25.14"
 
 [[DocStringExtensions]]
 deps = ["LibGit2"]
@@ -91,32 +102,32 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 version = "0.8.5"
 
 [[Documenter]]
-deps = ["Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
-git-tree-sha1 = "5acbebf1be22db43589bc5aa1bb5fcc378b17780"
+deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
+git-tree-sha1 = "350dced36c11f794c6c4da5dc6493ec894e50c16"
 uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-version = "0.27.0"
+version = "0.27.5"
 
 [[Downloads]]
 deps = ["ArgTools", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 
 [[FillArrays]]
-deps = ["LinearAlgebra", "Random", "SparseArrays"]
-git-tree-sha1 = "31939159aeb8ffad1d4d8ee44d07f8558273120a"
+deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"]
+git-tree-sha1 = "7c365bdef6380b29cfc5caaf99688cd7489f9b87"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "0.11.7"
+version = "0.12.2"
 
 [[HTTP]]
-deps = ["Base64", "Dates", "IniFile", "MbedTLS", "NetworkOptions", "Sockets", "URIs"]
-git-tree-sha1 = "86ed84701fbfd1142c9786f8e53c595ff5a4def9"
+deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"]
+git-tree-sha1 = "44e3b40da000eab4ccb1aecdc4801c040026aeb5"
 uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-version = "0.9.10"
+version = "0.9.13"
 
 [[IOCapture]]
-deps = ["Logging"]
-git-tree-sha1 = "1868e4e7ad2f93d8de0904d89368c527b46aa6a1"
+deps = ["Logging", "Random"]
+git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a"
 uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89"
-version = "0.2.1"
+version = "0.2.2"
 
 [[IniFile]]
 deps = ["Test"]
@@ -128,6 +139,11 @@ version = "0.5.0"
 deps = ["Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
+[[IrrationalConstants]]
+git-tree-sha1 = "f76424439413893a832026ca355fe273e93bce94"
+uuid = "92d709cd-6900-40b7-9082-c6be49f344b6"
+version = "0.1.0"
+
 [[IterativeSolvers]]
 deps = ["LinearAlgebra", "Printf", "Random", "RecipesBase", "SparseArrays"]
 git-tree-sha1 = "1a8c6237e78b714e901e406c096fc8a65528af7d"
@@ -142,9 +158,9 @@ version = "1.3.0"
 
 [[JSON]]
 deps = ["Dates", "Mmap", "Parsers", "Unicode"]
-git-tree-sha1 = "81690084b6198a2e1da36fcfda16eeca9f9f24e4"
+git-tree-sha1 = "8076680b162ada2a031f707ac7b4953e30667a37"
 uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
-version = "0.21.1"
+version = "0.21.2"
 
 [[JSONSchema]]
 deps = ["HTTP", "JSON", "ZipFile"]
@@ -175,17 +191,11 @@ uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 deps = ["Libdl"]
 uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
-[[Literate]]
-deps = ["Base64", "IOCapture", "JSON", "REPL"]
-git-tree-sha1 = "501a1a74a0c825037860d36d87d703e987d39dbc"
-uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
-version = "2.8.1"
-
 [[LogExpFunctions]]
-deps = ["DocStringExtensions", "LinearAlgebra"]
-git-tree-sha1 = "1ba664552f1ef15325e68dc4c05c3ef8c2d5d885"
+deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
+git-tree-sha1 = "3d682c07e6dd250ed082f883dc88aee7996bf2cc"
 uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-version = "0.2.4"
+version = "0.3.0"
 
 [[Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
@@ -212,9 +222,9 @@ uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
 
 [[Missings]]
 deps = ["DataAPI"]
-git-tree-sha1 = "4ea90bd5d3985ae1f9a908bd4500ae88921c5ce7"
+git-tree-sha1 = "2ca267b08821e86c5ef4376cffed98a46c2cb205"
 uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
-version = "1.0.0"
+version = "1.0.1"
 
 [[Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
@@ -224,9 +234,15 @@ uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
 
 [[MutableArithmetics]]
 deps = ["LinearAlgebra", "SparseArrays", "Test"]
-git-tree-sha1 = "ad9b2bce6021631e0e20706d361972343a03e642"
+git-tree-sha1 = "3927848ccebcc165952dc0d9ac9aa274a87bfe01"
 uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0"
-version = "0.2.19"
+version = "0.2.20"
+
+[[NNlib]]
+deps = ["Adapt", "ChainRulesCore", "Compat", "LinearAlgebra", "Pkg", "Requires", "Statistics"]
+git-tree-sha1 = "3bc876dbff74cc9c4ece84ef9326da8ccd71c98f"
+uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
+version = "0.7.28"
 
 [[NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
@@ -238,10 +254,10 @@ uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
 version = "0.5.5+0"
 
 [[OptimalTransport]]
-deps = ["Distances", "Distributions", "IterativeSolvers", "LinearAlgebra", "LogExpFunctions", "MathOptInterface", "PDMats", "QuadGK", "SparseArrays", "StatsBase"]
+deps = ["Distances", "Distributions", "IterativeSolvers", "LinearAlgebra", "LogExpFunctions", "MathOptInterface", "NNlib", "PDMats", "QuadGK", "SparseArrays", "StatsBase"]
 path = ".."
 uuid = "7e02d93a-ae51-4f58-b602-d97af76e3b33"
-version = "0.3.11"
+version = "0.3.15"
 
 [[OrderedCollections]]
 git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c"
@@ -250,15 +266,15 @@ version = "1.4.1"
 
 [[PDMats]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
-git-tree-sha1 = "f82a0e71f222199de8e9eb9a09977bd0767d52a0"
+git-tree-sha1 = "4dd403333bcf0909341cfe57ec115152f937d7d8"
 uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
-version = "0.11.0"
+version = "0.11.1"
 
 [[Parsers]]
 deps = ["Dates"]
-git-tree-sha1 = "c8abc88faa3f7a3950832ac5d6e690881590d6dc"
+git-tree-sha1 = "438d35d2d95ae2c5e8780b330592b6de8494e779"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "1.1.0"
+version = "2.0.3"
 
 [[Pkg]]
 deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
@@ -289,9 +305,20 @@ deps = ["Serialization"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [[RecipesBase]]
-git-tree-sha1 = "b3fb709f3c97bfc6e948be68beeecb55a0b340ae"
+git-tree-sha1 = "44a75aa7a527910ee3d1751d1f0e4148698add9e"
 uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
-version = "1.1.1"
+version = "1.1.2"
+
+[[Reexport]]
+git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b"
+uuid = "189a3867-3050-52da-a836-e630ba90ab69"
+version = "1.2.2"
+
+[[Requires]]
+deps = ["UUIDs"]
+git-tree-sha1 = "4036a3bd08ac7e968e27c203d45f5fff15020621"
+uuid = "ae029012-a4dd-5104-9daa-d747884805df"
+version = "1.1.3"
 
 [[Rmath]]
 deps = ["Random", "Rmath_jll"]
@@ -320,19 +347,19 @@ uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 
 [[SortingAlgorithms]]
 deps = ["DataStructures"]
-git-tree-sha1 = "2ec1962eba973f383239da22e75218565c390a96"
+git-tree-sha1 = "b3363d7460f7d098ca0912c69b082f75625d7508"
 uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
-version = "1.0.0"
+version = "1.0.1"
 
 [[SparseArrays]]
 deps = ["LinearAlgebra", "Random"]
 uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[SpecialFunctions]]
 deps = ["ChainRulesCore", "LogExpFunctions", "OpenSpecFun_jll"]
-git-tree-sha1 = "a50550fa3164a8c46747e62063b4d774ac1bcf49"
+git-tree-sha1 = "a322a9493e49c5f3a10b50df3aedaf1cdb3244b7"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "1.5.1"
+version = "1.6.1"
 
 [[Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
@@ -345,15 +372,15 @@ version = "1.0.0"
 
 [[StatsBase]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
-git-tree-sha1 = "2f6792d523d7448bbe2fec99eca9218f06cc746d"
+git-tree-sha1 = "fed1ec1e65749c4d96fc20dd13bea72b55457e62"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.33.8"
+version = "0.33.9"
 
 [[StatsFuns]]
-deps = ["LogExpFunctions", "Rmath", "SpecialFunctions"]
-git-tree-sha1 = "30cd8c360c54081f806b1ee14d2eecbef3c04c49"
+deps = ["IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
+git-tree-sha1 = "20d1bb720b9b27636280f751746ba4abb465f19d"
 uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
-version = "0.9.8"
+version = "0.9.9"
 
 [[SuiteSparse]]
 deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
@@ -373,9 +400,9 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[TranscodingStreams]]
 deps = ["Random", "Test"]
-git-tree-sha1 = "7c53c35547de1c5b9d46a4797cf6d8253807108c"
+git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
-version = "0.9.5"
+version = "0.9.6"
 
 [[URIs]]
 git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355"

docs/Project.toml

@@ -1,12 +1,7 @@
 [deps]
-Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 OptimalTransport = "7e02d93a-ae51-4f58-b602-d97af76e3b33"
 
 [compat]
-Distributions = "0.25"
 Documenter = "0.27"
-Literate = "2.8"
 OptimalTransport = "0.3"
-julia = "1"