Convert H5Z*.jl packages into package extensions (#1160)

* Convert H5Z*.jl packages into package extensions

* Fix tests for Julia 1.6, set filter pkgs to 0.2.0

* Fix formatting, docs. Import rather than alias symbols.

* Apply formatting

* Update docs for extension packages

* Apply formatter

* Add note in history

HISTORY.md

@@ -4,6 +4,7 @@ Please also see the [release notes](https://github.com/JuliaIO/HDF5.jl/releases)
 
 ## v0.18.0 (in development)
 * Refactor Dataspaces (#1104)
+* Convert filter packages into package extensions (#1160)
 
 ## v0.17.2
 * Fix variable length strings as attributes (#1130)

Project.toml

@@ -6,31 +6,42 @@ version = "0.17.1"
 Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
 HDF5_jll = "0234f1f7-429e-5d53-9886-15a909be8d59"
 Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
+MPIPreferences = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"
 Mmap = "a63ad114-7e13-5084-954f-fe012c677804"
 Preferences = "21216c6a-2e73-6563-6e65-726566657250"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
-MPIPreferences = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"
-
-[weakdeps]
-MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
-
-[extensions]
-MPIExt = "MPI"
 
 [compat]
+Blosc = "0.7.3"
+CodecBzip2 = "0.7, 0.8"
+CodecLz4 = "0.4"
+CodecZstd = "0.7, 0.8"
 Compat = "3.1.0, 4"
 HDF5_jll = "~1.10.5, ~1.12.0, ~1.14.0"
 MPI = "0.20"
 MPIPreferences = "0.1.7"
 Preferences = "1.3"
 Requires = "1.0"
+bitshuffle_jll = "0.4.2, 0.5"
 julia = "1.6"
 
+[extensions]
+BloscExt = "Blosc"
+CodecBzip2Ext = "CodecBzip2"
+CodecLz4Ext = "CodecLz4"
+CodecZstdExt = "CodecZstd"
+MPIExt = "MPI"
+bitshuffle_jll_ext = "bitshuffle_jll"
+
 [extras]
+Blosc = "a74b3585-a348-5f62-a45c-50e91977d574"
 CRC32c = "8bf52ea8-c179-5cab-976a-9e18b702a9bc"
+CodecBzip2 = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd"
+CodecLz4 = "5ba52731-8f18-5e0d-9241-30f10d1ec561"
+CodecZstd = "6b39b394-51ab-5f42-8807-6242bab2b4c2"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 H5Zblosc = "c8ec2601-a99c-407f-b158-e79c03c2f5f7"
@@ -42,6 +53,15 @@ MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+bitshuffle_jll = "228fe19c-1b83-5282-a626-13744502a320"
 
 [targets]
 test = ["Test", "MPI", "Distributed", "LinearAlgebra", "OrderedCollections", "Pkg", "CRC32c", "FileIO"]
+
+[weakdeps]
+Blosc = "a74b3585-a348-5f62-a45c-50e91977d574"
+CodecBzip2 = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd"
+CodecLz4 = "5ba52731-8f18-5e0d-9241-30f10d1ec561"
+CodecZstd = "6b39b394-51ab-5f42-8807-6242bab2b4c2"
+MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
+bitshuffle_jll = "228fe19c-1b83-5282-a626-13744502a320"

docs/Manifest.toml

@@ -145,41 +145,46 @@ version = "2.46.2+0"
 deps = ["HDF5", "bitshuffle_jll"]
 path = "../filters/H5Zbitshuffle"
 uuid = "51b4e782-877f-4ccf-958a-27bf628210da"
-version = "0.1.3"
+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 = "0.1.2"
+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 = "0.1.2"
+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 = "0.17.1"
-weakdeps = ["MPI"]
+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"]

docs/make.jl

@@ -4,13 +4,34 @@ using H5Zblosc
 using H5Zbzip2
 using H5Zlz4
 using H5Zzstd
+using H5Zbitshuffle
 using MPI  # needed to generate docs for parallel HDF5 API
 
+# Load extension packages
+const BloscExt = Base.get_extension(HDF5, :BloscExt)
+const bitshuffle_jll_ext = Base.get_extension(HDF5, :bitshuffle_jll_ext)
+const BloscExt = Base.get_extension(HDF5, :BloscExt)
+const CodecBzip2Ext = Base.get_extension(HDF5, :CodecBzip2Ext)
+const CodecLz4Ext = Base.get_extension(HDF5, :CodecLz4Ext)
+const CodecZstdExt = Base.get_extension(HDF5, :CodecZstdExt)
+
 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,
+        bitshuffle_jll_ext,
+        BloscExt,
+        CodecBzip2Ext,
+        CodecLz4Ext,
+        CodecZstdExt
+    ],
     authors="Mustafa Mohamad <[email protected]> and contributors",
     format=Documenter.HTML(;
         prettyurls=get(ENV, "CI", "false") == "true",

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