diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 59cd6eaa9..19a5f6db2 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -1,6 +1,6 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.3" +julia_version = "1.10.4" manifest_format = "2.0" project_hash = "2d4ae38483c05e04907e6c281e51323f031e5f7e" @@ -9,6 +9,11 @@ git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9" version = "0.0.1" +[[deps.AbstractTrees]] +git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" +uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" +version = "0.4.5" + [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" version = "1.1.1" @@ -27,44 +32,45 @@ version = "0.7.3" [[deps.Blosc_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Lz4_jll", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "6aa2d0b8db41ab860bbbf61b9587e3b957683fd3" +git-tree-sha1 = "19b98ee7e3db3b4eff74c5c9c72bf32144e24f10" uuid = "0b7ba130-8d10-5ba8-a3d6-c5182647fed9" -version = "1.21.4+0" +version = "1.21.5+0" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" +git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+0" - -[[deps.CEnum]] -git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" -uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" -version = "0.4.2" +version = "1.0.8+1" [[deps.CodecBzip2]] deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"] -git-tree-sha1 = "2e62a725210ce3c3c2e1a3080190e7ca491f18d7" +git-tree-sha1 = "9b1ca1aa6ce3f71b3d1840c538a8210a043625eb" uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd" -version = "0.7.2" +version = "0.8.2" [[deps.CodecLz4]] deps = ["Lz4_jll", "TranscodingStreams"] -git-tree-sha1 = "59fe0cb37784288d6b9f1baebddbf75457395d40" +git-tree-sha1 = "b8aecef9f90530cf322a8386630ec18485c17991" uuid = "5ba52731-8f18-5e0d-9241-30f10d1ec561" -version = "0.4.0" +version = "0.4.3" + +[[deps.CodecZlib]] +deps = ["TranscodingStreams", "Zlib_jll"] +git-tree-sha1 = "59939d8a997469ee05c4b4944560a820f9ba0d73" +uuid = "944b1d66-785c-5afd-91f1-9de20f533193" +version = "0.7.4" [[deps.CodecZstd]] -deps = ["CEnum", "TranscodingStreams", "Zstd_jll"] -git-tree-sha1 = "849470b337d0fa8449c21061de922386f32949d9" +deps = ["TranscodingStreams", "Zstd_jll"] +git-tree-sha1 = "0d0612d8646ed6157adaceff420b3bacbc2510a9" uuid = "6b39b394-51ab-5f42-8807-6242bab2b4c2" -version = "0.7.2" +version = "0.8.3" [[deps.Compat]] -deps = ["UUIDs"] -git-tree-sha1 = "e460f044ca8b99be31d35fe54fc33a5c33dd8ed7" +deps = ["TOML", "UUIDs"] +git-tree-sha1 = "b1c55339b7c6c350ee89f2c1604299660525b248" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.9.0" +version = "4.15.0" [deps.Compat.extensions] CompatLinearAlgebraExt = "LinearAlgebra" @@ -76,7 +82,7 @@ version = "4.9.0" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.0.5+0" +version = "1.1.1+0" [[deps.Dates]] deps = ["Printf"] @@ -99,70 +105,99 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" version = "0.9.3" [[deps.Documenter]] -deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] -git-tree-sha1 = "39fd748a73dce4c05a9655475e437170d8fb1b67" +deps = ["ANSIColoredPrinters", "AbstractTrees", "Base64", "CodecZlib", "Dates", "DocStringExtensions", "Downloads", "Git", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "MarkdownAST", "Pkg", "PrecompileTools", "REPL", "RegistryInstances", "SHA", "TOML", "Test", "Unicode"] +git-tree-sha1 = "76deb8c15f37a3853f13ea2226b8f2577652de05" uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -version = "0.27.25" +version = "1.5.0" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" +[[deps.Expat_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7" +uuid = "2e619515-83b5-522b-bb60-26c02a35a201" +version = "2.6.2+0" + [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" +[[deps.Git]] +deps = ["Git_jll"] +git-tree-sha1 = "04eff47b1354d702c3a85e8ab23d539bb7d5957e" +uuid = "d7ba0133-e1db-5d97-8f8c-041e4b3a1eb2" +version = "1.3.1" + +[[deps.Git_jll]] +deps = ["Artifacts", "Expat_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libiconv_jll", "OpenSSL_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "d18fb8a1f3609361ebda9bf029b60fd0f120c809" +uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb" +version = "2.44.0+2" + [[deps.H5Zbitshuffle]] deps = ["HDF5", "bitshuffle_jll"] path = "../filters/H5Zbitshuffle" uuid = "51b4e782-877f-4ccf-958a-27bf628210da" -version = "0.1.2" +version = "0.2.0" [[deps.H5Zblosc]] deps = ["Blosc", "HDF5"] path = "../filters/H5Zblosc" uuid = "c8ec2601-a99c-407f-b158-e79c03c2f5f7" -version = "0.1.2" +version = "0.2.0" [[deps.H5Zbzip2]] deps = ["CodecBzip2", "HDF5"] path = "../filters/H5Zbzip2" uuid = "094576f2-1e46-4c84-8e32-c46c042eaaa2" -version = "0.1.1" +version = "0.2.0" [[deps.H5Zlz4]] deps = ["CodecLz4", "HDF5"] path = "../filters/H5Zlz4" uuid = "eb20ec05-5464-47b5-ba41-098e3c1068a3" -version = "0.1.1" +version = "0.2.0" [[deps.H5Zzstd]] deps = ["CodecZstd", "HDF5"] path = "../filters/H5Zzstd" uuid = "f6f2d980-1ec6-471c-a70d-0270e22f1103" -version = "0.1.1" +version = "0.2.0" [[deps.HDF5]] deps = ["Compat", "HDF5_jll", "Libdl", "MPIPreferences", "Mmap", "Preferences", "Printf", "Random", "Requires", "UUIDs"] path = ".." uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" -version = "0.17.0" -weakdeps = ["MPI"] +version = "0.17.1" +weakdeps = ["Blosc", "CodecBzip2", "CodecLz4", "CodecZstd", "MPI", "bitshuffle_jll"] [deps.HDF5.extensions] + BloscExt = "Blosc" + CodecBzip2Ext = "CodecBzip2" + CodecLz4Ext = "CodecLz4" + CodecZstdExt = "CodecZstd" MPIExt = "MPI" + bitshuffle_jll_ext = "bitshuffle_jll" [[deps.HDF5_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"] -git-tree-sha1 = "38c8874692d48d5440d5752d6c74b0c6b0b60739" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"] +git-tree-sha1 = "82a471768b513dc39e471540fdadc84ff80ff997" uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" -version = "1.14.2+1" +version = "1.14.3+3" + +[[deps.Hwloc_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1d334207121865ac8c1c97eb7f42d0339e4635bf" +uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" +version = "2.11.0+0" [[deps.IOCapture]] deps = ["Logging", "Random"] -git-tree-sha1 = "d75853a0bdbfb1ac815478bacd89cd27b550ace6" +git-tree-sha1 = "b6d6bfdd7ce25b0f9b2f6b3dd56b2673a66c8770" uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" -version = "0.2.3" +version = "0.2.5" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -180,11 +215,10 @@ git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" version = "0.21.4" -[[deps.LLVMOpenMP_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f689897ccbe049adb19a065c495e75f372ecd42b" -uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "15.0.4+0" +[[deps.LazilyInitializedFields]] +git-tree-sha1 = "8f7f3cabab0fd1800699663533b6d5cb3fc0e612" +uuid = "0e77f7df-68c5-4e49-93ce-4cd80f5598bf" +version = "1.2.2" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] @@ -193,25 +227,36 @@ uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" -version = "0.6.3" +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 = "7.84.0+0" +version = "8.4.0+0" [[deps.LibGit2]] -deps = ["Base64", "NetworkOptions", "Printf", "SHA"] +deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" +[[deps.LibGit2_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] +uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" +version = "1.6.4+0" + [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" -version = "1.10.2+0" +version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" +[[deps.Libiconv_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" +uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" +version = "1.17.0+0" + [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -223,9 +268,9 @@ version = "1.9.4+0" [[deps.MPI]] deps = ["Distributed", "DocStringExtensions", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "PkgVersion", "PrecompileTools", "Requires", "Serialization", "Sockets"] -git-tree-sha1 = "df53d0e1e0dbebf2315f4cd35e13e52ad43416c2" +git-tree-sha1 = "14cef41baf5b675b192b02a22c710f725ab333a7" uuid = "da04e1cc-30fd-572f-bb4f-1f8673147195" -version = "0.20.15" +version = "0.20.20" [deps.MPI.extensions] AMDGPUExt = "AMDGPU" @@ -236,44 +281,50 @@ version = "0.20.15" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" [[deps.MPICH_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "8a5b4d2220377d1ece13f49438d71ad20cf1ba83" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "4099bb6809ac109bfc17d521dad33763bcf026b7" uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" -version = "4.1.2+0" +version = "4.2.1+1" [[deps.MPIPreferences]] deps = ["Libdl", "Preferences"] -git-tree-sha1 = "781916a2ebf2841467cda03b6f1af43e23839d85" +git-tree-sha1 = "c105fe467859e7f6e9a852cb15cb4301126fac07" uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267" -version = "0.1.9" +version = "0.1.11" [[deps.MPItrampoline_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "6979eccb6a9edbbb62681e158443e79ecc0d056a" +git-tree-sha1 = "8c35d5420193841b2f367e658540e8d9e0601ed0" uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" -version = "5.3.1+0" +version = "5.4.0+0" [[deps.Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" +[[deps.MarkdownAST]] +deps = ["AbstractTrees", "Markdown"] +git-tree-sha1 = "465a70f0fc7d443a00dcdc3267a497397b8a3899" +uuid = "d0879d2d-cac2-40c8-9cee-1863dc0c7391" +version = "0.1.2" + [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.2+0" +version = "2.28.2+1" [[deps.MicrosoftMPI_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "a8027af3d1743b3bfae34e54872359fdebb31422" +git-tree-sha1 = "f12a29c4400ba812841c6ace3f4efbb6dbb3ba01" uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf" -version = "10.1.3+4" +version = "10.1.4+2" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.10.11" +version = "2023.1.10" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" @@ -281,26 +332,31 @@ version = "1.2.0" [[deps.OpenMPI_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "f3080f4212a8ba2ceb10a34b938601b862094314" +git-tree-sha1 = "e25c1778a98e34219a00455d6e4384e017ea9762" uuid = "fe0851c0-eecd-5654-98d4-656369965a5c" -version = "4.1.5+0" +version = "4.1.6+0" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e78db7bd5c26fc5a6911b50a47ee302219157ea8" +git-tree-sha1 = "a028ee3cb5641cccc4c24e90c36b0a4f7707bdf5" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.10+0" +version = "3.0.14+0" + +[[deps.PCRE2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" +version = "10.42.0+1" [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] -git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851" +git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.7.2" +version = "2.8.1" [[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 = "1.9.2" +version = "1.10.0" [[deps.PkgVersion]] deps = ["Pkg"] @@ -310,15 +366,15 @@ version = "0.3.3" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" +git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.2.0" +version = "1.2.1" [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "7eb1686b4f04b82f96ed7a4ea5890a4f0c7a09f1" +git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.4.0" +version = "1.4.3" [[deps.Printf]] deps = ["Unicode"] @@ -329,9 +385,15 @@ deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" [[deps.Random]] -deps = ["SHA", "Serialization"] +deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +[[deps.RegistryInstances]] +deps = ["LazilyInitializedFields", "Pkg", "TOML", "Tar"] +git-tree-sha1 = "ffd19052caf598b8653b99404058fce14828be51" +uuid = "2792f1a3-b283-48e8-9a74-f99dce5104f3" +version = "0.1.0" + [[deps.Requires]] deps = ["UUIDs"] git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" @@ -363,10 +425,13 @@ deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TranscodingStreams]] -deps = ["Random", "Test"] -git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" +git-tree-sha1 = "d73336d81cafdc277ff45558bb7eaa2b04a8e472" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.13" +version = "0.10.10" +weakdeps = ["Random", "Test"] + + [deps.TranscodingStreams.extensions] + TestExt = ["Test", "Random"] [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -378,32 +443,32 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.13+0" +version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c" +git-tree-sha1 = "e678132f07ddb5bfa46857f0d7620fb9be675d3b" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.5+0" +version = "1.5.6+0" [[deps.bitshuffle_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Lz4_jll", "Pkg", "Zstd_jll"] -git-tree-sha1 = "fc80beaec46263a31471fe2f14f5a0d9bea05c4c" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Lz4_jll", "Zstd_jll"] +git-tree-sha1 = "ff1c6f554744cb0527ed2d932c280f859ad7df17" uuid = "228fe19c-1b83-5282-a626-13744502a320" -version = "0.4.2+0" +version = "0.5.1+0" [[deps.libaec_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "eddd19a8dea6b139ea97bdc8a0e2667d4b661720" +git-tree-sha1 = "46bf7be2917b59b761247be3f317ddf75e50e997" uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0" -version = "1.0.6+1" +version = "1.1.2+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.48.0+0" +version = "1.52.0+1" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+0" +version = "17.4.0+2" diff --git a/docs/make.jl b/docs/make.jl index 286f5f020..e4e8b0b31 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -4,21 +4,34 @@ using H5Zblosc using H5Zbzip2 using H5Zlz4 using H5Zzstd +using H5Zbitshuffle using MPI # needed to generate docs for parallel HDF5 API DocMeta.setdocmeta!(HDF5, :DocTestSetup, :(using HDF5); recursive=true) makedocs(; sitename="HDF5.jl", - modules=[HDF5, H5Zblosc, H5Zbzip2, H5Zlz4, H5Zzstd], + modules=[ + HDF5, + H5Zblosc, + H5Zbzip2, + H5Zlz4, + H5Zzstd, + H5Zbitshuffle, + Base.get_extension(HDF5, :BloscExt), + Base.get_extension(HDF5, :CodecBzip2Ext), + Base.get_extension(HDF5, :CodecLz4Ext), + Base.get_extension(HDF5, :CodecZstdExt), + Base.get_extension(HDF5, :bitshuffle_jll_ext), + ], authors="Mustafa Mohamad and contributors", format=Documenter.HTML(; prettyurls=get(ENV, "CI", "false") == "true", canonical="https://JuliaIO.github.io/HDF5.jl", assets=String[], - sidebar_sitename=false + sidebar_sitename=false, + size_threshold_ignore=["api_bindings.md",] ), - strict=true, pages=[ "Home" => "index.md", "Interface" => [ diff --git a/docs/src/interface/filters.md b/docs/src/interface/filters.md index 99611a677..7367ea177 100644 --- a/docs/src/interface/filters.md +++ b/docs/src/interface/filters.md @@ -39,12 +39,29 @@ Several external Julia packages implement HDF5 filter plugins in Julia. As they are independent of HDF5.jl, they must be installed in order to use their plugins. The +[H5Zbitshuffle.jl](https://github.com/JuliaIO/HDF5.jl/tree/master/filters/H5Zbitshuffle), [H5Zblosc.jl](https://github.com/JuliaIO/HDF5.jl/tree/master/filters/H5Zblosc), [H5Zbzip2.jl](https://github.com/JuliaIO/HDF5.jl/tree/master/filters/H5Zbzip2), [H5Zlz4.jl](https://github.com/JuliaIO/HDF5.jl/tree/master/filters/H5Zlz4), and [H5Zzstd.jl](https://github.com/JuliaIO/HDF5.jl/tree/master/filters/H5Zzstd) packages are maintained as independent subdirectory packages within the HDF5.jl repository. +### Extension packages + +For Julia 1.9 and greater, the external filter packages listed above at version 0.2 and greater are loose wrappers around extension packages. The filter extension packages currently implemented are as follows: +* bitshuffle_jll_ext +* H5Zblosc_ext +* H5Zbzip2_ext +* H5Zlz4_ext +* H5Zzstd_ext + +``` +using HDF5, CodecZstd +const CodecZstdExt = Base.get_extension(HDF5, :CodecZstdExt) +using .CodecZstdExt +filter = ZstdFilter(5) +``` + ### H5Zblosc.jl ```@meta @@ -83,6 +100,19 @@ CurrentModule = H5Zzstd ```@docs ZstdFilter +H5Zzstd +``` + +### H5Zbitshuffle + +```@meta +CurrentModule = H5Zbitshuffle +``` + +```@docs +BitshuffleFilter +H5Zbitshuffle +bitshuffle_jll_ext ``` ## Other External Filters diff --git a/filters/H5Zbitshuffle/src/.H5Zbitshuffle.jl.swp b/filters/H5Zbitshuffle/src/.H5Zbitshuffle.jl.swp deleted file mode 100644 index 36d4c6c5c..000000000 Binary files a/filters/H5Zbitshuffle/src/.H5Zbitshuffle.jl.swp and /dev/null differ diff --git a/filters/H5Zbitshuffle/src/H5Zbitshuffle.jl b/filters/H5Zbitshuffle/src/H5Zbitshuffle.jl index 429c146cf..1d66a9370 100644 --- a/filters/H5Zbitshuffle/src/H5Zbitshuffle.jl +++ b/filters/H5Zbitshuffle/src/H5Zbitshuffle.jl @@ -10,6 +10,7 @@ module H5Zbitshuffle using bitshuffle_jll using HDF5: HDF5 +# The next block of lines can be removed using HDF5.API import HDF5.Filters: Filter, @@ -26,19 +27,19 @@ export BSHUF_H5_COMPRESS_LZ4, const bitshuffle_jll_ext = Base.get_extension(HDF5, :bitshuffle_jll_ext) -const BSHUF_H5_COMPRESS_LZ4 = bitshuffle_jll_ext.BSHUF_H5_COMPRESS_LZ4 -const BSHUF_H5_COMPRESS_ZSTD = bitshuffle_jll_ext.BSHUF_H5_COMPRESS_ZSTD -const BitshuffleFilter = bitshuffle_jll_ext.BitshuffleFilter -const H5Z_filter_bitshuffle = bitshuffle_jll_ext.H5Z_filter_bitshuffle +using .bitshuffle_jll_ext: BSHUF_H5_COMPRESS_LZ4 +using .bitshuffle_jll_ext: BSHUF_H5_COMPRESS_ZSTD +using .bitshuffle_jll_ext: BitshuffleFilter +using .bitshuffle_jll_ext: H5Z_filter_bitshuffle -const BSHUF_H5_COMPRESS_LZ4 = bitshuffle_jll_ext.BSHUF_H5_COMPRESS_LZ4 -const BSHUF_H5_COMPRESS_ZSTD = bitshuffle_jll_ext.BSHUF_H5_COMPRESS_ZSTD -const H5Z_FILTER_BITSHUFFLE = bitshuffle_jll_ext.H5Z_FILTER_BITSHUFFLE +using .bitshuffle_jll_ext: BSHUF_H5_COMPRESS_LZ4 +using .bitshuffle_jll_ext: BSHUF_H5_COMPRESS_ZSTD +using .bitshuffle_jll_ext: H5Z_FILTER_BITSHUFFLE -const BSHUF_VERSION_MAJOR = bitshuffle_jll_ext.BSHUF_VERSION_MAJOR -const BSHUF_VERSION_MINOR = bitshuffle_jll_ext.BSHUF_VERSION_MINOR -const BSHUF_VERSION_POINT = bitshuffle_jll_ext.BSHUF_VERSION_POINT +using .bitshuffle_jll_ext: BSHUF_VERSION_MAJOR +using .bitshuffle_jll_ext: BSHUF_VERSION_MINOR +using .bitshuffle_jll_ext: BSHUF_VERSION_POINT -const bitshuffle_name = bitshuffle_jll_ext.bitshuffle_name +using .bitshuffle_jll_ext: bitshuffle_name end # module diff --git a/filters/H5Zblosc/src/H5Zblosc.jl b/filters/H5Zblosc/src/H5Zblosc.jl index 08c4ff8ac..7cc86f3e3 100644 --- a/filters/H5Zblosc/src/H5Zblosc.jl +++ b/filters/H5Zblosc/src/H5Zblosc.jl @@ -3,6 +3,8 @@ module H5Zblosc import Blosc using HDF5: HDF5 + +# The next block of lines can be removed using HDF5.API import HDF5.Filters: Filter, FilterPipeline import HDF5.Filters: @@ -22,11 +24,11 @@ import Blosc: NOSHUFFLE, SHUFFLE, BITSHUFFLE const BloscExt = Base.get_extension(HDF5, :BloscExt) -const blosc_filter = BloscExt.blosc_filter -const BloscFilter = BloscExt.BloscFilter +using .BloscExt: blosc_filter +using .BloscExt: BloscFilter -const H5Z_FILTER_BLOSC = BloscExt.H5Z_FILTER_BLOSC -const FILTER_BLOSC_VERSION = BloscExt.FILTER_BLOSC_VERSION -const blosc_name = BloscExt.blosc_name +using .BloscExt: H5Z_FILTER_BLOSC +using .BloscExt: FILTER_BLOSC_VERSION +using .BloscExt: blosc_name end # module H5Zblosc diff --git a/filters/H5Zbzip2/src/H5Zbzip2.jl b/filters/H5Zbzip2/src/H5Zbzip2.jl index 458e3af52..b6c898127 100644 --- a/filters/H5Zbzip2/src/H5Zbzip2.jl +++ b/filters/H5Zbzip2/src/H5Zbzip2.jl @@ -6,6 +6,7 @@ module H5Zbzip2 using CodecBzip2: libbzip2 using HDF5: HDF5 +# Remove the next three lines in the future using HDF5.API import HDF5.Filters: Filter, filterid, register_filter, filtername, filter_func, filter_cfunc @@ -14,9 +15,9 @@ export H5Z_FILTER_BZIP2, H5Z_filter_bzip2, Bzip2Filter const CodecBzip2Ext = Base.get_extension(HDF5, :CodecBzip2Ext) -const H5Z_FILTER_BZIP2 = CodecBzip2Ext.H5Z_FILTER_BZIP2 -const H5Z_filter_bzip2 = CodecBzip2Ext.H5Z_filter_bzip2 -const Bzip2Filter = CodecBzip2Ext.Bzip2Filter -const bzip2_name = CodecBzip2Ext.bzip2_name - +using .CodecBzip2Ext: H5Z_FILTER_BZIP2 +using .CodecBzip2Ext: H5Z_filter_bzip2 +using .CodecBzip2Ext: Bzip2Filter +using .CodecBzip2Ext: bzip2_name + end # module H5Zbzip2 diff --git a/filters/H5Zlz4/src/H5Zlz4.jl b/filters/H5Zlz4/src/H5Zlz4.jl index b7060e1f4..158a2726a 100644 --- a/filters/H5Zlz4/src/H5Zlz4.jl +++ b/filters/H5Zlz4/src/H5Zlz4.jl @@ -5,6 +5,8 @@ module H5Zlz4 using CodecLz4 using HDF5: HDF5 + +# The next three lines can be removed using HDF5.API import HDF5.Filters: Filter, filterid, register_filter, filtername, filter_func, filter_cfunc @@ -13,14 +15,14 @@ export H5Z_FILTER_LZ4, H5Z_filter_lz4, Lz4Filter const CodecLz4Ext = Base.get_extension(HDF5, :CodecLz4Ext) -const H5Z_filter_lz4 = CodecLz4Ext.H5Z_filter_lz4 -const Lz4Filter = CodecLz4Ext.Lz4Filter +using .CodecLz4Ext: H5Z_filter_lz4 +using .CodecLz4Ext: Lz4Filter -const H5Z_FILTER_LZ4 = CodecLz4Ext.H5Z_FILTER_LZ4 +using .CodecLz4Ext: H5Z_FILTER_LZ4 -const DEFAULT_BLOCK_SIZE = CodecLz4Ext.DEFAULT_BLOCK_SIZE -const lz4_name = CodecLz4Ext.lz4_name +using .CodecLz4Ext: DEFAULT_BLOCK_SIZE +using .CodecLz4Ext: lz4_name -const LZ4_AGGRESSION = CodecLz4Ext.LZ4_AGGRESSION +using .CodecLz4Ext: LZ4_AGGRESSION end diff --git a/filters/H5Zzstd/src/H5Zzstd.jl b/filters/H5Zzstd/src/H5Zzstd.jl index 94e2335b9..dded8c896 100644 --- a/filters/H5Zzstd/src/H5Zzstd.jl +++ b/filters/H5Zzstd/src/H5Zzstd.jl @@ -12,12 +12,12 @@ using HDF5: HDF5 using CodecZstd: CodecZstd const CodecZstdExt = Base.get_extension(HDF5, :CodecZstdExt) -const H5Z_FILTER_ZSTD = CodecZstdExt.H5Z_FILTER_ZSTD -const zstd_name = CodecZstdExt.zstd_name +using .CodecZstdExt: H5Z_FILTER_ZSTD +using .CodecZstdExt: zstd_name -const H5Z_filter_zstd = CodecZstdExt.H5Z_filter_zstd -const H5Z_FILTER_ZSTD = CodecZstdExt.H5Z_FILTER_ZSTD -const ZstdFilter = CodecZstdExt.ZstdFilter +using .CodecZstdExt: H5Z_filter_zstd +using .CodecZstdExt: H5Z_FILTER_ZSTD +using .CodecZstdExt: ZstdFilter export H5Z_filter_zstd, H5Z_FILTER_ZSTD, ZstdFilter