fix doc builds

.github/workflows/CI.yml

@@ -40,7 +40,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: julia-actions/setup-julia@v2
         with:
-          version: 'pre'
+          version: '1.10'
       - run: |
           julia --project=docs -e '
             import Pkg; Pkg.add("Documenter")

docs/Manifest.toml

@@ -1,6 +1,6 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.11.0-rc3"
+julia_version = "1.10.5"
 manifest_format = "2.0"
 project_hash = "f24464e24f50c869c4c5b81eaeef23cca078ef04"
 
@@ -32,7 +32,7 @@ version = "1.1.3"
 
 [[deps.ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
-version = "1.1.2"
+version = "1.1.1"
 
 [[deps.ArrayInterface]]
 deps = ["Adapt", "LinearAlgebra"]
@@ -66,17 +66,15 @@ version = "7.16.0"
 
 [[deps.Artifacts]]
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
-version = "1.11.0"
 
 [[deps.AtomsBase]]
 deps = ["LinearAlgebra", "PeriodicTable", "Printf", "Requires", "StaticArrays", "Unitful", "UnitfulAtomic"]
-git-tree-sha1 = "0fa9318ceff45a514bd1dbed7563b32ae2cdb73f"
+git-tree-sha1 = "aab46de4a22e3619fe0167a18019b94a65033bd7"
 uuid = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
-version = "0.4.1"
+version = "0.4.2"
 
 [[deps.Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
-version = "1.11.0"
 
 [[deps.BitFlags]]
 git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d"
@@ -236,7 +234,6 @@ version = "1.0.0"
 [[deps.Dates]]
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
-version = "1.11.0"
 
 [[deps.Dbus_jll]]
 deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"]
@@ -265,7 +262,6 @@ version = "1.15.1"
 [[deps.Distributed]]
 deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
-version = "1.11.0"
 
 [[deps.Distributions]]
 deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
@@ -354,7 +350,6 @@ version = "4.4.4+1"
 
 [[deps.FileWatching]]
 uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
-version = "1.11.0"
 
 [[deps.FillArrays]]
 deps = ["LinearAlgebra"]
@@ -426,7 +421,6 @@ version = "1.0.14+0"
 [[deps.Future]]
 deps = ["Random"]
 uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
-version = "1.11.0"
 
 [[deps.FuzzyCompletions]]
 deps = ["REPL"]
@@ -557,7 +551,6 @@ version = "1.4.2"
 [[deps.InteractiveUtils]]
 deps = ["Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
-version = "1.11.0"
 
 [[deps.InvertedIndices]]
 git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038"
@@ -651,7 +644,6 @@ version = "1.2.2"
 [[deps.LazyArtifacts]]
 deps = ["Artifacts", "Pkg"]
 uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
-version = "1.11.0"
 
 [[deps.LibCURL]]
 deps = ["LibCURL_jll", "MozillaCACerts_jll"]
@@ -661,17 +653,16 @@ version = "0.6.4"
 [[deps.LibCURL_jll]]
 deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
 uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
-version = "8.6.0+0"
+version = "8.4.0+0"
 
 [[deps.LibGit2]]
 deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
-version = "1.11.0"
 
 [[deps.LibGit2_jll]]
 deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"]
 uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5"
-version = "1.7.2+0"
+version = "1.6.4+0"
 
 [[deps.LibSSH2_jll]]
 deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
@@ -680,7 +671,6 @@ version = "1.11.0+1"
 
 [[deps.Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
-version = "1.11.0"
 
 [[deps.Libffi_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -733,7 +723,6 @@ version = "2.40.1+0"
 [[deps.LinearAlgebra]]
 deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
 uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-version = "1.11.0"
 
 [[deps.Literate]]
 deps = ["Base64", "IOCapture", "JSON", "REPL"]
@@ -765,7 +754,6 @@ version = "0.3.28"
 
 [[deps.Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
-version = "1.11.0"
 
 [[deps.LoggingExtras]]
 deps = ["Dates", "Logging"]
@@ -799,7 +787,6 @@ version = "1.1.1"
 [[deps.Markdown]]
 deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
-version = "1.11.0"
 
 [[deps.MarkdownAST]]
 deps = ["AbstractTrees", "Markdown"]
@@ -816,7 +803,7 @@ version = "1.1.9"
 [[deps.MbedTLS_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
-version = "2.28.6+0"
+version = "2.28.2+1"
 
 [[deps.Measures]]
 git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102"
@@ -831,7 +818,6 @@ version = "1.2.0"
 
 [[deps.Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
-version = "1.11.0"
 
 [[deps.MolSimToolkit]]
 deps = ["AtomsBase", "CellListMap", "Chemfiles", "DocStringExtensions", "EasyFit", "LaTeXStrings", "LinearAlgebra", "OffsetArrays", "PDBTools", "ProgressMeter", "ProteinSecondaryStructures", "Reexport", "StaticArrays", "Statistics", "StatsBase", "TestItems"]
@@ -845,7 +831,7 @@ weakdeps = ["Plots"]
 
 [[deps.MozillaCACerts_jll]]
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
-version = "2023.12.12"
+version = "2023.1.10"
 
 [[deps.MsgPack]]
 deps = ["Serialization"]
@@ -887,7 +873,7 @@ version = "1.3.5+1"
 [[deps.OpenBLAS_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
 uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
-version = "0.3.27+1"
+version = "0.3.23+4"
 
 [[deps.OpenLibm_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -976,13 +962,9 @@ uuid = "30392449-352a-5448-841d-b1acce4e97dc"
 version = "0.43.4+0"
 
 [[deps.Pkg]]
-deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "Random", "SHA", "TOML", "Tar", "UUIDs", "p7zip_jll"]
+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 = "1.11.0"
-weakdeps = ["REPL"]
-
-    [deps.Pkg.extensions]
-    REPLExt = "REPL"
+version = "1.10.0"
 
 [[deps.PlotThemes]]
 deps = ["PlotUtils", "Statistics"]
@@ -1066,7 +1048,6 @@ version = "2.3.2"
 [[deps.Printf]]
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
-version = "1.11.0"
 
 [[deps.ProgressMeter]]
 deps = ["Distributed", "Printf"]
@@ -1111,9 +1092,9 @@ version = "6.7.1+1"
 
 [[deps.QuadGK]]
 deps = ["DataStructures", "LinearAlgebra"]
-git-tree-sha1 = "1d587203cf851a51bf1ea31ad7ff89eff8d625ea"
+git-tree-sha1 = "cda3b045cf9ef07a08ad46731f5a3165e56cf3da"
 uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
-version = "2.11.0"
+version = "2.11.1"
 
     [deps.QuadGK.extensions]
     QuadGKEnzymeExt = "Enzyme"
@@ -1122,14 +1103,12 @@ version = "2.11.0"
     Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
 
 [[deps.REPL]]
-deps = ["InteractiveUtils", "Markdown", "Sockets", "StyledStrings", "Unicode"]
+deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
-version = "1.11.0"
 
 [[deps.Random]]
 deps = ["SHA"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-version = "1.11.0"
 
 [[deps.RecipesBase]]
 deps = ["PrecompileTools"]
@@ -1202,7 +1181,6 @@ version = "1.4.5"
 
 [[deps.Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
-version = "1.11.0"
 
 [[deps.Setfield]]
 deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"]
@@ -1217,13 +1195,12 @@ uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f"
 version = "1.0.3"
 
 [[deps.SimpleBufferStream]]
-git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1"
+git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1"
 uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7"
-version = "1.1.0"
+version = "1.2.0"
 
 [[deps.Sockets]]
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
-version = "1.11.0"
 
 [[deps.SortingAlgorithms]]
 deps = ["DataStructures"]
@@ -1234,7 +1211,7 @@ version = "1.2.1"
 [[deps.SparseArrays]]
 deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"]
 uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
-version = "1.11.0"
+version = "1.10.0"
 
 [[deps.SpecialFunctions]]
 deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
@@ -1268,14 +1245,9 @@ uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
 version = "1.4.3"
 
 [[deps.Statistics]]
-deps = ["LinearAlgebra"]
-git-tree-sha1 = "ae3bb1eb3bba077cd276bc5cfc337cc65c3075c0"
+deps = ["LinearAlgebra", "SparseArrays"]
 uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
-version = "1.11.1"
-weakdeps = ["SparseArrays"]
-
-    [deps.Statistics.extensions]
-    SparseArraysExt = ["SparseArrays"]
+version = "1.10.0"
 
 [[deps.StatsAPI]]
 deps = ["LinearAlgebra"]
@@ -1309,18 +1281,14 @@ git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5"
 uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e"
 version = "0.3.4"
 
-[[deps.StyledStrings]]
-uuid = "f489334b-da3d-4c2e-b8f0-e476e12c162b"
-version = "1.11.0"
-
 [[deps.SuiteSparse]]
 deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
 uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
 
 [[deps.SuiteSparse_jll]]
 deps = ["Artifacts", "Libdl", "libblastrampoline_jll"]
 uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
-version = "7.7.0+0"
+version = "7.2.1+1"
 
 [[deps.TOML]]
 deps = ["Dates"]
@@ -1353,7 +1321,6 @@ version = "0.1.1"
 [[deps.Test]]
 deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-version = "1.11.0"
 
 [[deps.TestItems]]
 git-tree-sha1 = "8621ba2637b49748e2dc43ba3d84340be2938022"
@@ -1378,7 +1345,6 @@ version = "1.5.1"
 [[deps.UUIDs]]
 deps = ["Random", "SHA"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
-version = "1.11.0"
 
 [[deps.UnPack]]
 git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b"
@@ -1387,7 +1353,6 @@ version = "1.0.2"
 
 [[deps.Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
-version = "1.11.0"
 
 [[deps.UnicodeFun]]
 deps = ["REPL"]
@@ -1697,7 +1662,7 @@ version = "1.1.6+0"
 [[deps.nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
-version = "1.59.0+0"
+version = "1.52.0+1"
 
 [[deps.p7zip_jll]]
 deps = ["Artifacts", "Libdl"]

docs/make.jl

@@ -30,6 +30,10 @@ makedocs(
     sitename = "PereiraMartinez2024.jl",
     format=Documenter.HTML(;
         mathengine=Documenter.MathJax3(),
+        size_threshold_ignore=[
+            "pluto_notebooks/proteinA_urea.md",
+            "pluto_notebooks/rnaset1_urea.md",
+        ],
     ),
     pages = [
         "Home" => "index.md",