Pin DiskArrays to 0.4.n DiskArrays to 0.4.9

YAXArrays uses DiskArrays and it is raising an error in its last update.
See JuliaIO/DiskArrays.jl#236 for more details.
To solve the problem we add and pin DiskArrays version to
0.4.9.
It also updates the Manifest and ran tests to check the code is still
working.

Manifest.toml

@@ -2,14 +2,20 @@
 
 julia_version = "1.10.5"
 manifest_format = "2.0"
-project_hash = "27fb80f7cf3feae80cb78f9588336932fd4c23a6"
+project_hash = "053417a9974cc3e664509d876afa8b5246b975dd"
 
 [[deps.ARFFFiles]]
 deps = ["CategoricalArrays", "Dates", "Parsers", "Tables"]
 git-tree-sha1 = "678eb18590a8bc6674363da4d5faa4ac09c40a18"
 uuid = "da404889-ca92-49ff-9e8b-0aa6b4d38dc8"
 version = "1.5.0"
 
+[[deps.ASL_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "6252039f98492252f9e47c312c8ffda0e3b9e78d"
+uuid = "ae81ac8f-d209-56e5-92de-9978fef736f9"
+version = "0.1.3+0"
+
 [[deps.AWS]]
 deps = ["Base64", "Compat", "Dates", "Downloads", "GitHub", "HTTP", "IniFile", "JSON", "MbedTLS", "Mocking", "OrderedCollections", "Random", "SHA", "Sockets", "URIs", "UUIDs", "XMLDict"]
 git-tree-sha1 = "319ade7f8fc88243369e119859a7d3a3e7e7f267"
@@ -205,6 +211,12 @@ git-tree-sha1 = "aebf55e6d7795e02ca500a689d326ac979aaf89e"
 uuid = "9718e550-a3fa-408a-8086-8db961cd8217"
 version = "0.1.1"
 
+[[deps.BenchmarkTools]]
+deps = ["Compat", "JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"]
+git-tree-sha1 = "e38fbc49a620f5d0b660d7f543db1009fe0f8336"
+uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+version = "1.6.0"
+
 [[deps.BitFlags]]
 git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d"
 uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
@@ -261,19 +273,14 @@ deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Un
 git-tree-sha1 = "1568b28f91293458345dabba6a5ea3f183250a61"
 uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597"
 version = "0.10.8"
+weakdeps = ["JSON", "RecipesBase", "SentinelArrays", "StructTypes"]
 
     [deps.CategoricalArrays.extensions]
     CategoricalArraysJSONExt = "JSON"
     CategoricalArraysRecipesBaseExt = "RecipesBase"
     CategoricalArraysSentinelArraysExt = "SentinelArrays"
     CategoricalArraysStructTypesExt = "StructTypes"
 
-    [deps.CategoricalArrays.weakdeps]
-    JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
-    RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
-    SentinelArrays = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
-    StructTypes = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
-
 [[deps.CategoricalDistributions]]
 deps = ["CategoricalArrays", "Distributions", "Missings", "OrderedCollections", "Random", "ScientificTypes"]
 git-tree-sha1 = "926862f549a82d6c3a7145bc7f1adff2a91a39f0"
@@ -308,6 +315,12 @@ git-tree-sha1 = "9ebb045901e9bbf58767a9f34ff89831ed711aae"
 uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
 version = "0.15.7"
 
+[[deps.CodecBzip2]]
+deps = ["Bzip2_jll", "TranscodingStreams"]
+git-tree-sha1 = "84990fa864b7f2b4901901ca12736e45ee79068c"
+uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd"
+version = "0.8.5"
+
 [[deps.CodecInflate64]]
 deps = ["TranscodingStreams"]
 git-tree-sha1 = "d981a6e8656b1e363a2731716f46851a2257deb7"
@@ -443,6 +456,12 @@ git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
 version = "1.16.0"
 
+[[deps.DataEnvelopmentAnalysis]]
+deps = ["Distributed", "Distributions", "GLPK", "InvertedIndices", "Ipopt", "JuMP", "LinearAlgebra", "PrecompileTools", "Printf", "ProgressMeter", "Random", "SharedArrays", "SparseArrays", "Statistics", "StatsAPI", "StatsBase"]
+git-tree-sha1 = "d79c7c880808ca66f24b65d8e064b8eca43c183a"
+uuid = "a100299e-89d6-11e9-0fa0-2daf497e6a05"
+version = "0.9.1"
+
 [[deps.DataFrames]]
 deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
 git-tree-sha1 = "fb61b4812c49343d7ef0b533ba982c46021938a6"
@@ -508,10 +527,10 @@ uuid = "fcd2136c-9f69-4db6-97e5-f31981721d63"
 version = "0.1.10"
 
 [[deps.DiskArrays]]
-deps = ["LRUCache", "OffsetArrays"]
-git-tree-sha1 = "dea23e3d787c25fbf5f879c4501da828bc729472"
+deps = ["LRUCache", "Mmap", "OffsetArrays"]
+git-tree-sha1 = "64650943240652ebedc6c43d03cccda247b327a3"
 uuid = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3"
-version = "0.4.5"
+version = "0.4.9"
 
 [[deps.Distances]]
 deps = ["LinearAlgebra", "Statistics", "StatsAPI"]
@@ -736,6 +755,18 @@ git-tree-sha1 = "273bd1cd30768a2fddfa3fd63bbc746ed7249e5f"
 uuid = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
 version = "1.9.0"
 
+[[deps.GLPK]]
+deps = ["GLPK_jll", "MathOptInterface"]
+git-tree-sha1 = "1d706bd23e5d2d407bfd369499ee6f96afb0c3ad"
+uuid = "60bf3e95-4087-53dc-ae20-288a0d20c6a6"
+version = "1.2.1"
+
+[[deps.GLPK_jll]]
+deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "6aa6294ba949ccfc380463bf50ff988b46de5bc7"
+uuid = "e8aa6df9-e6ca-548a-97ff-1f85fc5b8b98"
+version = "5.0.1+1"
+
 [[deps.GMP_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "781609d7-10c4-51f6-84f2-b8444358ff6d"
@@ -1000,6 +1031,18 @@ git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038"
 uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f"
 version = "1.3.0"
 
+[[deps.Ipopt]]
+deps = ["Ipopt_jll", "LinearAlgebra", "MathOptInterface", "OpenBLAS32_jll", "PrecompileTools"]
+git-tree-sha1 = "edcc4d1ec92e1abb5ebadc81b306c69ed58f53e2"
+uuid = "b6b21f68-93f8-5de0-b562-5493be1d77c9"
+version = "1.7.2"
+
+[[deps.Ipopt_jll]]
+deps = ["ASL_jll", "Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "MUMPS_seq_jll", "SPRAL_jll", "libblastrampoline_jll"]
+git-tree-sha1 = "4f55ad688c698a4f77d892a1cb673f7e8a30f178"
+uuid = "9cc047cb-c261-5740-88fc-0cf96f7bdcc7"
+version = "300.1400.1700+0"
+
 [[deps.IrrationalConstants]]
 git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2"
 uuid = "92d709cd-6900-40b7-9082-c6be49f344b6"
@@ -1045,6 +1088,16 @@ git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a"
 uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 version = "0.21.4"
 
+[[deps.JSON3]]
+deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"]
+git-tree-sha1 = "1d322381ef7b087548321d3f878cb4c9bd8f8f9b"
+uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
+version = "1.14.1"
+weakdeps = ["ArrowTypes"]
+
+    [deps.JSON3.extensions]
+    JSON3ArrowExt = ["ArrowTypes"]
+
 [[deps.JpegTurbo]]
 deps = ["CEnum", "FileIO", "ImageCore", "JpegTurbo_jll", "TOML"]
 git-tree-sha1 = "fa6d0bcff8583bac20f1ffa708c3913ca605c611"
@@ -1057,6 +1110,16 @@ git-tree-sha1 = "25ee0be4d43d0269027024d75a24c24d6c6e590c"
 uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8"
 version = "3.0.4+0"
 
+[[deps.JuMP]]
+deps = ["LinearAlgebra", "MacroTools", "MathOptInterface", "MutableArithmetics", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays"]
+git-tree-sha1 = "cf832644f225dbe721bb9b97bf432007765fc695"
+uuid = "4076af6c-e467-56ae-b986-b466b2749572"
+version = "1.24.0"
+weakdeps = ["DimensionalData"]
+
+    [deps.JuMP.extensions]
+    JuMPDimensionalDataExt = "DimensionalData"
+
 [[deps.JuliaVariables]]
 deps = ["MLStyle", "NameResolution"]
 git-tree-sha1 = "49fb3cb53362ddadb4415e9b73926d6b40709e70"
@@ -1289,6 +1352,12 @@ git-tree-sha1 = "1d2dd9b186742b0f317f2530ddcbf00eebb18e96"
 uuid = "23992714-dd62-5051-b70f-ba57cb901cac"
 version = "0.10.7"
 
+[[deps.METIS_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "1c20a46719c0dc4ec4e7021ca38f53e1ec9268d9"
+uuid = "d00139f3-1899-568f-a2f0-47f597d42d70"
+version = "5.1.2+1"
+
 [[deps.MLFlowClient]]
 deps = ["Dates", "FilePathsBase", "HTTP", "JSON", "ShowCases", "URIs", "UUIDs"]
 git-tree-sha1 = "9abb12b62debc27261c008daa13627255bf79967"
@@ -1388,6 +1457,12 @@ git-tree-sha1 = "70e830dab5d0775183c99fc75e4c24c614ed7142"
 uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748"
 version = "5.5.1+0"
 
+[[deps.MUMPS_seq_jll]]
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "METIS_jll", "libblastrampoline_jll"]
+git-tree-sha1 = "0eab12f94948ca67908aec14b9f2ebefd17463fe"
+uuid = "d7ed1dd3-d0ae-5e8e-bfb4-87a502085b8d"
+version = "500.700.301+0"
+
 [[deps.MacroTools]]
 deps = ["Markdown", "Random"]
 git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df"
@@ -1409,6 +1484,12 @@ version = "0.4.2"
 deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
+[[deps.MathOptInterface]]
+deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON3", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"]
+git-tree-sha1 = "cfc8c22e3b0157430fc80eb6ef46546483356ea9"
+uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
+version = "1.36.0"
+
 [[deps.MbedTLS]]
 deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"]
 git-tree-sha1 = "c067a280ddc25f196b5e7df3877c6b226d390aaf"
@@ -1469,6 +1550,12 @@ version = "0.3.4"
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
 version = "2023.1.10"
 
+[[deps.MutableArithmetics]]
+deps = ["LinearAlgebra", "SparseArrays", "Test"]
+git-tree-sha1 = "491bdcdc943fcbc4c005900d7463c9f216aabf4c"
+uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0"
+version = "1.6.4"
+
 [[deps.NLSolversBase]]
 deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"]
 git-tree-sha1 = "a0b464d183da839699f4c79e7606d9d186ec172c"
@@ -1569,6 +1656,12 @@ git-tree-sha1 = "a5a5a68d079ce531b0220e99789e0c1c8c5ed215"
 uuid = "925886fa-5bf2-5e8e-b522-a9147a512338"
 version = "1.7.1"
 
+[[deps.OpenBLAS32_jll]]
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "6065c4cff8fee6c6770b277af45d5082baacdba1"
+uuid = "656ef2d0-ae68-5445-9ca0-591084a874a2"
+version = "0.3.24+0"
+
 [[deps.OpenBLAS_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
 uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
@@ -1632,13 +1725,11 @@ deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra",
 git-tree-sha1 = "d9b79c4eed437421ac4285148fcadf42e0700e89"
 uuid = "429524aa-4258-5aef-a3af-852621145aeb"
 version = "1.9.4"
+weakdeps = ["MathOptInterface"]
 
     [deps.Optim.extensions]
     OptimMOIExt = "MathOptInterface"
 
-    [deps.Optim.weakdeps]
-    MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
-
 [[deps.OrderedCollections]]
 git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
@@ -1758,6 +1849,10 @@ version = "0.5.6"
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
+[[deps.Profile]]
+deps = ["Printf"]
+uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79"
+
 [[deps.ProgressMeter]]
 deps = ["Distributed", "Printf"]
 git-tree-sha1 = "8f6bc219586aef8baf0ff9a5fe16ee9c70cb65e4"
@@ -1908,6 +2003,12 @@ git-tree-sha1 = "7cf3e4a9432defe1eaa9959c1c82e85485817d07"
 uuid = "cdeec39e-fb35-4959-aadb-a1dd5dede958"
 version = "2.0.1"
 
+[[deps.SPRAL_jll]]
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "Libdl", "METIS_jll", "libblastrampoline_jll"]
+git-tree-sha1 = "11f3da4b25efacd1cec8e263421f2a9003a5e8e0"
+uuid = "319450e9-13b8-58e8-aa9f-8fd1420848ab"
+version = "2024.5.8+0"
+
 [[deps.SQLite_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"]
 git-tree-sha1 = "004fffbe2711abdc7263a980bbb1af9620781dd9"
@@ -2144,6 +2245,12 @@ weakdeps = ["Adapt", "GPUArraysCore", "SparseArrays", "StaticArrays"]
     StructArraysSparseArraysExt = "SparseArrays"
     StructArraysStaticArraysExt = "StaticArrays"
 
+[[deps.StructTypes]]
+deps = ["Dates", "UUIDs"]
+git-tree-sha1 = "159331b30e94d7b11379037feeb9b690950cace8"
+uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
+version = "1.11.0"
+
 [[deps.SuiteSparse]]
 deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
 uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"

Project.toml

@@ -17,6 +17,7 @@ DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
+DiskArrays = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"