Merge pull request #56 from euroargodev/v0p1p20b

add extensions

Project.toml

@@ -22,8 +22,19 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 
+[weakdeps]
+Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
+
+[extensions]
+ArgoDataCondaExt = ["Conda"]
+ArgoDataMakieExt = ["Makie"]
+ArgoDataPyCallExt = ["PyCall"]
+
 [compat]
 CSV = "0.10"
+Conda = "1"
 Bootstrap = "2"
 Climatology = "0.5"
 DataFrames = "1"
@@ -32,9 +43,11 @@ FTPClient = "1"
 Glob = "1"
 Interpolations = "0.13, 0.14, 0.15"
 JLD2 = "0.4"
+Makie = "0.21"
 MeshArrays = "0.3"
 NCDatasets = "0.12, 0.13, 0.14"
 OrderedCollections = "1"
+PyCall = "1"
 Statistics = "1"
 YAML = "0.4"
 julia = "1.9"

docs/make.jl

@@ -2,7 +2,8 @@ using Documenter, ArgoData, PlutoSliderServer
 
 using Climatology, MITgcm
 ENV["DATADEPS_ALWAYS_ACCEPT"]=true
-Climatology.MITPROFclim_download()
+pth=Climatology.MITPROFclim_download()
+println(pth)
 
 #python dependencies
 if false

examples/ArgoToMITprof.jl

@@ -137,9 +137,7 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
 ArgoData = "~0.1.14"
-NCDatasets = "~0.12.9"
 PlutoUI = "~0.7.49"
-PrettyTables = "~2.2.2"
 """
 
 # ╔═╡ 00000000-0000-0000-0000-000000000002
@@ -148,7 +146,7 @@ PLUTO_MANIFEST_TOML_CONTENTS = """
 
 julia_version = "1.10.4"
 manifest_format = "2.0"
-project_hash = "d748463479da7e14a46705f43e52d07311b3262c"
+project_hash = "3370e2e0eba24bed5740ba91ea4ed9bc2381501c"
 
 [[deps.AbstractPlutoDingetjes]]
 deps = ["Pkg"]
@@ -193,6 +191,12 @@ git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d"
 uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
 version = "0.1.9"
 
+[[deps.Blosc_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Lz4_jll", "Zlib_jll", "Zstd_jll"]
+git-tree-sha1 = "19b98ee7e3db3b4eff74c5c9c72bf32144e24f10"
+uuid = "0b7ba130-8d10-5ba8-a3d6-c5182647fed9"
+version = "1.21.5+0"
+
 [[deps.Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd"
@@ -240,10 +244,10 @@ uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
 version = "0.11.5"
 
 [[deps.CommonDataModel]]
-deps = ["CFTime", "DataStructures", "Dates", "Preferences", "Printf"]
-git-tree-sha1 = "7f5717cbb2c1ce650cfd454451f282df33103596"
+deps = ["CFTime", "DataStructures", "Dates", "Preferences", "Printf", "Statistics"]
+git-tree-sha1 = "d6fb5bf939a2753c74984b11434ea25d6c397a58"
 uuid = "1fbeeb36-5f17-413c-809b-666fb144f157"
-version = "0.2.5"
+version = "0.3.6"
 
 [[deps.Compat]]
 deps = ["TOML", "UUIDs"]
@@ -317,6 +321,12 @@ version = "0.2.5"
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 
+[[deps.DiskArrays]]
+deps = ["LRUCache", "OffsetArrays"]
+git-tree-sha1 = "ef25c513cad08d7ebbed158c91768ae32f308336"
+uuid = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3"
+version = "0.3.23"
+
 [[deps.Distances]]
 deps = ["LinearAlgebra", "Statistics", "StatsAPI"]
 git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0"
@@ -374,11 +384,22 @@ version = "0.8.5"
 deps = ["Random"]
 uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 
+[[deps.GMP_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "781609d7-10c4-51f6-84f2-b8444358ff6d"
+version = "6.2.1+6"
+
 [[deps.Glob]]
 git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496"
 uuid = "c27321d9-0574-5035-807b-f59d2c89b15c"
 version = "1.3.1"
 
+[[deps.GnuTLS_jll]]
+deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "Nettle_jll", "P11Kit_jll", "Zlib_jll"]
+git-tree-sha1 = "383db7d3f900f4c1f47a8a04115b053c095e48d3"
+uuid = "0951126a-58fd-58f1-b5b3-b08c7c4a876d"
+version = "3.8.4+0"
+
 [[deps.HDF5_jll]]
 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"
@@ -470,6 +491,15 @@ git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a"
 uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 version = "0.21.4"
 
+[[deps.LRUCache]]
+git-tree-sha1 = "b3cc6698599b10e652832c2f23db3cab99d51b59"
+uuid = "8ac3fa9e-de4c-5943-b1dc-09c6b5f20637"
+version = "1.6.1"
+weakdeps = ["Serialization"]
+
+    [deps.LRUCache.extensions]
+    SerializationExt = ["Serialization"]
+
 [[deps.LaTeXStrings]]
 git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec"
 uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
@@ -525,6 +555,12 @@ git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075"
 uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36"
 version = "1.0.3"
 
+[[deps.Lz4_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "7f26c8fc5229e68484e0b3447312c98e16207d11"
+uuid = "5ced341a-0733-55b8-9ab6-a4889d929147"
+version = "1.10.0+0"
+
 [[deps.MIMEs]]
 git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb"
 uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65"
@@ -611,10 +647,10 @@ uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
 version = "2023.1.10"
 
 [[deps.NCDatasets]]
-deps = ["CFTime", "CommonDataModel", "DataStructures", "Dates", "NetCDF_jll", "NetworkOptions", "Printf"]
-git-tree-sha1 = "4263c4220f22e20729329838bf7e94a49d1ac32f"
+deps = ["CFTime", "CommonDataModel", "DataStructures", "Dates", "DiskArrays", "NetCDF_jll", "NetworkOptions", "Printf"]
+git-tree-sha1 = "a640912695952b074672edb5f9aaee2f7f9fd59a"
 uuid = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
-version = "0.12.17"
+version = "0.14.4"
 
 [[deps.NearestNeighbors]]
 deps = ["Distances", "StaticArrays"]
@@ -623,10 +659,16 @@ uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 version = "0.4.18"
 
 [[deps.NetCDF_jll]]
-deps = ["Artifacts", "Bzip2_jll", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "XML2_jll", "Zlib_jll", "Zstd_jll"]
-git-tree-sha1 = "10c612c81eaffdd6b7c28a45a554cdd9d2f40ff1"
+deps = ["Artifacts", "Blosc_jll", "Bzip2_jll", "HDF5_jll", "JLLWrappers", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "TOML", "XML2_jll", "Zlib_jll", "Zstd_jll", "libzip_jll"]
+git-tree-sha1 = "4686378c4ae1d1948cfbe46c002a11a4265dcb07"
 uuid = "7243133f-43d8-5620-bbf4-c2c921802cf3"
-version = "400.902.208+0"
+version = "400.902.211+1"
+
+[[deps.Nettle_jll]]
+deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "eca63e3847dad608cfa6a3329b95ef674c7160b4"
+uuid = "4c82536e-c426-54e4-b420-14f461c4ed8b"
+version = "3.7.2+0"
 
 [[deps.NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
@@ -683,6 +725,12 @@ git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 version = "1.6.3"
 
+[[deps.P11Kit_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "2cd396108e178f3ae8dedbd8e938a18726ab2fbf"
+uuid = "c2071276-7c44-58a7-b746-946036e04d0a"
+version = "0.24.1+0"
+
 [[deps.Parsers]]
 deps = ["Dates", "PrecompileTools", "UUIDs"]
 git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821"
@@ -719,10 +767,10 @@ uuid = "21216c6a-2e73-6563-6e65-726566657250"
 version = "1.4.3"
 
 [[deps.PrettyTables]]
-deps = ["Crayons", "LaTeXStrings", "Markdown", "Printf", "Reexport", "StringManipulation", "Tables"]
-git-tree-sha1 = "6842ce83a836fbbc0cfeca0b5a4de1a4dcbdb8d1"
+deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"]
+git-tree-sha1 = "66b20dd35966a748321d3b2537c4584cf40387c7"
 uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
-version = "2.2.8"
+version = "2.3.2"
 
 [[deps.Printf]]
 deps = ["Unicode"]
@@ -934,6 +982,12 @@ git-tree-sha1 = "d9717ce3518dc68a99e6b96300813760d887a01d"
 uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
 version = "2.13.1+0"
 
+[[deps.XZ_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632"
+uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800"
+version = "5.4.6+0"
+
 [[deps.YAML]]
 deps = ["Base64", "Dates", "Printf", "StringEncodings"]
 git-tree-sha1 = "dea63ff72079443240fbd013ba006bcbc8a9ac00"
@@ -968,6 +1022,12 @@ deps = ["Artifacts", "Libdl"]
 uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
 version = "5.8.0+1"
 
+[[deps.libzip_jll]]
+deps = ["Artifacts", "Bzip2_jll", "GnuTLS_jll", "JLLWrappers", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"]
+git-tree-sha1 = "3282b7d16ae7ac3e57ec2f3fa8fafb564d8f9f7f"
+uuid = "337d8026-41b4-5cde-a456-74a10e5b31d1"
+version = "1.10.1+0"
+
 [[deps.nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"

ext/ArgoDataCondaExt.jl

@@ -0,0 +1,13 @@
+module ArgoDataCondaExt
+
+using Conda, ArgoData
+
+function ArgoData.conda(flag=:argopy)
+    if flag==:argopy
+        Conda.add("argopy")
+#        Conda.pip_interop(true)
+#        Conda.pip("install", "argopy")
+    end
+end
+
+end

ext/ArgoDataMakieExt.jl

@@ -0,0 +1,8 @@
+module ArgoDataMakieExt
+
+using ArgoData, Makie
+
+end
+
+
+

ext/ArgoDataPyCallExt.jl

@@ -0,0 +1,13 @@
+module ArgoDataPyCallExt
+
+using PyCall, ArgoData
+
+function ArgoData.pyimport(flag=:argopy)
+    if flag==:argopy
+        PyCall.pyimport("argopy")
+    else
+        @warn "unknown flag value   "
+    end
+end
+
+end

src/ArgoData.jl

@@ -14,4 +14,7 @@ export GDAC, ArgoTools, GriddedFields
 export MITprof, MITprofAnalysis, MITprofStat
 export ProfileNative, ProfileStandard, MITprofStandard
 
+conda(dev::String) = conda(:pyargo)
+pyimport(dev::String) = pyimport(:pyargo)
+
 end # module

test/Project.toml

@@ -1,7 +1,10 @@
 [deps]
 Climatology = "9e9a4d37-2d2e-41e3-8b85-f7978328d9c7"
+Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
 MITgcm = "dce5fa8e-68ce-4431-a242-9469c69627a0"
 MeshArrays = "cb8c808f-1acf-59a3-9d2b-6e38d009f683"
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

test/runtests.jl

@@ -4,6 +4,21 @@ using Climatology, MITgcm
 ENV["DATADEPS_ALWAYS_ACCEPT"]=true
 Climatology.MITPROFclim_download()
 
+if Sys.ARCH!==:aarch64
+  if false #external python path
+    tmpfile=joinpath(tempdir(),"pythonpath.txt")
+    run(pipeline(`which python`,tmpfile)) 
+    ENV["PYTHON"]=readline(tmpfile)
+  else #internal python path
+    ENV["PYTHON"]=""
+  end
+  using Pkg; Pkg.build("PyCall")
+
+  using PyCall, Conda
+  ArgoData.conda(:argopy)
+  argopy=ArgoData.pyimport(:argopy)
+end
+
 @testset "ArgoData.jl" begin
 
     files_list=GDAC.files_list()