Merge pull request #10 from gaelforget/gf-morePOnotebooks-02

Re-organize, update, and add MOC notebook

01_types.jl → DataStructures/01_types.jl

@@ -23,11 +23,13 @@ using MeshArrays, Plots
 
 # #### Select a pre-defined grid such as `LLC90`
 
-mygrid=GridSpec("LLC90")
+mygrid=GridSpec("LLC90","../inputs/")
 
 # And download the pre-defined grid if needed
 
-!isdir("GRID_LLC90") ? run(`git clone https://github.com/gaelforget/GRID_LLC90`) : nothing
+if !isdir("../inputs/GRID_LLC90")
+    run(`git clone https://github.com/gaelforget/GRID_LLC90 ../inputs/GRID_LLC90`)
+end
 
 # #### Read a MeshArray from file
 #

02_exchanges.jl → DataStructures/02_exchanges.jl

@@ -23,13 +23,13 @@ using MeshArrays, Plots
 
 # Download the pre-defined grid if needed
 
-if !isdir("GRID_CS32") 
-    run(`git clone https://github.com/gaelforget/GRID_CS32`)
+if !isdir("../inputs/GRID_CS32") 
+    run(`git clone https://github.com/gaelforget/GRID_CS32 ../inputs/GRID_CS32`)
 end
 
 # Select `cube sphere` grid and read `ocean depth` variable
 
-mygrid=GridSpec("CS32")
+mygrid=GridSpec("CS32","../inputs/")
 D=mygrid.read(mygrid.path*"Depth.data",MeshArray(mygrid,Float32))
 show(D)
 

06_nctiles.ipynb → DataStructures/06_nctiles.ipynb

@@ -35,7 +35,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!isdir(\"nctiles-testcases\") ? run(`git clone https://github.com/gaelforget/nctiles-testcases`) : nothing\n",
+    "if !isdir(\"../inputs/nctiles-testcases\")\n",
+    "    run(`git clone https://github.com/gaelforget/nctiles-testcases ../inputs/nctiles-testcases`)\n",
+    "end\n",
     "#run(`gunzip nctiles-testcases/diags/trsp_3d_set1.0000000732.data.gz`)"
    ]
   },
@@ -55,22 +57,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\u001b[32m\u001b[1m  Updating\u001b[22m\u001b[39m registry at `~/.julia/registries/General`\n",
-      "\u001b[32m\u001b[1m  Updating\u001b[22m\u001b[39m git-repo `https://github.com/JuliaRegistries/General.git`\n",
-      "\u001b[?25l\u001b[2K\u001b[?25h\u001b[32m\u001b[1m Resolving\u001b[22m\u001b[39m package versions...\n",
-      "\u001b[32m\u001b[1m  Updating\u001b[22m\u001b[39m `~/mywork/projects_major/2019-jlpkgs/JuliaCon2018Notebooks/Project.toml`\n",
-      "\u001b[90m [no changes]\u001b[39m\n",
-      "\u001b[32m\u001b[1m  Updating\u001b[22m\u001b[39m `~/mywork/projects_major/2019-jlpkgs/JuliaCon2018Notebooks/Manifest.toml`\n",
-      "\u001b[90m [no changes]\u001b[39m\n"
-     ]
-    },
     {
      "data": {
       "text/plain": [
@@ -80,24 +69,24 @@
        " \"and contact point for user support.\"                    "
       ]
      },
-     "execution_count": 2,
+     "execution_count": 18,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "using Pkg; Pkg.add([\"NCTiles\",\"NCDatasets\",\"NetCDF\"])\n",
+    "#using Pkg; Pkg.add([\"NCTiles\",\"NCDatasets\",\"NetCDF\"])\n",
     "using NCTiles,NCDatasets,NetCDF,MeshArrays\n",
     "\n",
     "# Set Paths\n",
-    "datadir = \"nctiles-testcases/\"\n",
+    "datadir = \"../inputs/nctiles-testcases/\"\n",
     "availdiagsfile = joinpath(datadir,\"available_diagnostics.log\")\n",
     "readmefile = joinpath(datadir,\"README\")\n",
     "griddir = joinpath(datadir,\"grid_float32/\")\n",
     "nativedir = joinpath(datadir,\"diags/\")\n",
     "interpdir = joinpath(datadir,\"diags_interp/\")\n",
     "\n",
-    "resultsdir = \"nctiles-newfiles/\"\n",
+    "resultsdir = \"../outputs/nctiles-newfiles/\"\n",
     "if ~ispath(resultsdir); mkpath(resultsdir); end\n",
     "\n",
     "# Dimensions\n",
@@ -185,7 +174,18 @@
    "cell_type": "code",
    "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "\"../outputs/nctiles-newfiles/interp\""
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "writedir = joinpath(resultsdir,\"interp\")\n",
     "if ~ispath(writedir); mkpath(writedir); end"
@@ -251,7 +251,7 @@
     {
      "data": {
       "text/plain": [
-       "NCvar(\"ETAN\", \"m\", NCvar[NCvar(\"lon_c\", \"degrees_east\", (720,), -179.75:0.5:179.75, Dict(\"long_name\"=>\"longitude\"), NCDatasets), NCvar(\"lat_c\", \"degrees_north\", (360,), -89.75:0.5:89.75, Dict(\"long_name\"=>\"longitude\"), NCDatasets), NCvar(\"tim\", \"days since 1992-01-01 0:0:0\", Inf, 1.5:3.0:718.5, Dict(\"long_name\"=>\"time\",\"standard_name\"=>\"time\"), NCDatasets)], BinData([\"nctiles-testcases/diags_interp/ETAN/ETAN.0000000732.data\", \"nctiles-testcases/diags_interp/ETAN/ETAN.0000001428.data\", \"nctiles-testcases/diags_interp/ETAN/ETAN.0000002172.data\"], Float32, (720, 360), 1), Dict(\"long_name\"=>\"Surface Height Anomaly\"), NCDatasets)"
+       "NCvar(\"ETAN\", \"m\", NCvar[NCvar(\"lon_c\", \"degrees_east\", (720,), -179.75:0.5:179.75, Dict(\"long_name\"=>\"longitude\"), NCDatasets), NCvar(\"lat_c\", \"degrees_north\", (360,), -89.75:0.5:89.75, Dict(\"long_name\"=>\"longitude\"), NCDatasets), NCvar(\"tim\", \"days since 1992-01-01 0:0:0\", Inf, 1.5:3.0:718.5, Dict(\"long_name\"=>\"time\",\"standard_name\"=>\"time\"), NCDatasets)], BinData([\"../inputs/nctiles-testcases/diags_interp/ETAN/ETAN.0000000732.data\", \"../inputs/nctiles-testcases/diags_interp/ETAN/ETAN.0000001428.data\", \"../inputs/nctiles-testcases/diags_interp/ETAN/ETAN.0000002172.data\"], Float32, (720, 360), 1), Dict(\"long_name\"=>\"Surface Height Anomaly\"), NCDatasets)"
       ]
      },
      "execution_count": 6,

06_nctiles.jl → DataStructures/06_nctiles.jl

@@ -32,26 +32,28 @@
 # gunzip nctiles-testcases/diags/*.gz
 # ```
 
-!isdir("nctiles-testcases") ? run(`git clone https://github.com/gaelforget/nctiles-testcases`) : nothing
+if !isdir("../inputs/nctiles-testcases")
+    run(`git clone https://github.com/gaelforget/nctiles-testcases ../inputs/nctiles-testcases`)
+end
 #run(`gunzip nctiles-testcases/diags/trsp_3d_set1.0000000732.data.gz`)
 
 # # Setup
 
 # Setting the paths and dimensions that will be used throughout this notebook.
 
 # +
-using Pkg; Pkg.add(["NCTiles","NCDatasets","NetCDF"])
+#using Pkg; Pkg.add(["NCTiles","NCDatasets","NetCDF"])
 using NCTiles,NCDatasets,NetCDF,MeshArrays
 
 # Set Paths
-datadir = "nctiles-testcases/"
+datadir = "../inputs/nctiles-testcases/"
 availdiagsfile = joinpath(datadir,"available_diagnostics.log")
 readmefile = joinpath(datadir,"README")
 griddir = joinpath(datadir,"grid_float32/")
 nativedir = joinpath(datadir,"diags/")
 interpdir = joinpath(datadir,"diags_interp/")
 
-resultsdir = "nctiles-newfiles/"
+resultsdir = "../outputs/nctiles-newfiles/"
 if ~ispath(resultsdir); mkpath(resultsdir); end
 
 # Dimensions

Manifest.toml

@@ -3,12 +3,24 @@
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
+[[BinDeps]]
+deps = ["Compat", "Libdl", "SHA", "URIParser"]
+git-tree-sha1 = "12093ca6cdd0ee547c39b1870e0c9c3f154d9ca9"
+uuid = "9e28174c-4ba2-5203-b857-d8d62c4213ee"
+version = "0.8.10"
+
 [[BinaryProvider]]
 deps = ["Libdl", "SHA"]
 git-tree-sha1 = "5b08ed6036d9d3f0ee6369410b830f8873d4024c"
 uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
 version = "0.5.8"
 
+[[CFTime]]
+deps = ["Dates", "Printf"]
+git-tree-sha1 = "90eddf050a4d4b35520f87b9ba82302643706a1e"
+uuid = "179af706-886a-5703-950a-314cd64e0468"
+version = "0.0.3"
+
 [[CatViews]]
 deps = ["Random", "Test"]
 git-tree-sha1 = "23d1f1e10d4e24374112fcf800ac981d14a54b24"
@@ -27,6 +39,24 @@ git-tree-sha1 = "177d8b959d3c103a6d57574c38ee79c81059c31b"
 uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
 version = "0.11.2"
 
+[[Compat]]
+deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
+git-tree-sha1 = "ed2c4abadf84c53d9e58510b5fc48912c2336fbb"
+uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
+version = "2.2.0"
+
+[[Conda]]
+deps = ["JSON", "VersionParsing"]
+git-tree-sha1 = "9a11d428dcdc425072af4aea19ab1e8c3e01c032"
+uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d"
+version = "1.3.0"
+
+[[CondaBinDeps]]
+deps = ["BinDeps", "Compat", "Conda", "Libdl"]
+git-tree-sha1 = "3b868935adf4ce2115f5487e789553507739014c"
+uuid = "a9693cdc-2bc8-5703-a9cd-1da358117377"
+version = "0.1.0"
+
 [[Contour]]
 deps = ["LinearAlgebra", "StaticArrays", "Test"]
 git-tree-sha1 = "b974e164358fea753ef853ce7bad97afec15bb80"
@@ -40,9 +70,9 @@ version = "1.1.0"
 
 [[DataStructures]]
 deps = ["InteractiveUtils", "OrderedCollections"]
-git-tree-sha1 = "f784254f428fb8fd7ac15982e5862a38a44523d3"
+git-tree-sha1 = "b7720de347734f4716d1815b00ce5664ed6bbfd4"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.17.7"
+version = "0.17.9"
 
 [[Dates]]
 deps = ["Printf"]
@@ -67,6 +97,18 @@ git-tree-sha1 = "d14a6fa5890ea3a7e5dcab6811114f132fec2b4b"
 uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
 version = "0.6.1"
 
+[[Formatting]]
+deps = ["Printf"]
+git-tree-sha1 = "a0c901c29c0e7c763342751c0a94211d56c0de5c"
+uuid = "59287772-0a20-5a39-b81b-1366585eb4c0"
+version = "0.4.1"
+
+[[FortranFiles]]
+deps = ["Compat"]
+git-tree-sha1 = "261d0569724da4c9bd906586880a2ad0cc29c2a4"
+uuid = "c58ffaec-ab22-586d-bfc5-781a99fd0b10"
+version = "0.5.0"
+
 [[GR]]
 deps = ["Base64", "DelimitedFiles", "LinearAlgebra", "Printf", "Random", "Serialization", "Sockets", "Test"]
 git-tree-sha1 = "c690c2ab22ac9ee323d9966deae61a089362b25c"
@@ -126,11 +168,29 @@ version = "0.4.3"
 [[Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
+[[NCDatasets]]
+deps = ["BinDeps", "CFTime", "Compat", "CondaBinDeps", "DataStructures", "Dates", "Libdl", "Missings", "Printf", "Random"]
+git-tree-sha1 = "6c0398c68c2f1957a8368b8cc6c8f9ee98ad5738"
+uuid = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
+version = "0.9.5"
+
+[[NCTiles]]
+deps = ["Dates", "MeshArrays", "NCDatasets", "NetCDF", "Printf"]
+git-tree-sha1 = "61acfd5c356703132faa7ace9f4191829edfc4ca"
+uuid = "4c1fdd90-559f-11e9-1abf-07ceafc4ffc0"
+version = "0.1.5"
+
 [[NaNMath]]
 git-tree-sha1 = "928b8ca9b2791081dc71a51c55347c27c618760f"
 uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
 version = "0.3.3"
 
+[[NetCDF]]
+deps = ["BinDeps", "CondaBinDeps", "Formatting", "Libdl"]
+git-tree-sha1 = "df78e4daf6148d9ca4657bfd44cb2c14d5cf7b05"
+uuid = "30363a11-5582-574a-97bb-aa9a979735b9"
+version = "0.8.2"
+
 [[OrderedCollections]]
 deps = ["Random", "Serialization", "Test"]
 git-tree-sha1 = "c4c13474d23c60d20a67b217f1d7f22a40edf8f1"
@@ -144,7 +204,7 @@ uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
 version = "0.3.10"
 
 [[Pkg]]
-deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [[PlotThemes]]
@@ -200,6 +260,10 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 [[Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 
+[[SharedArrays]]
+deps = ["Distributed", "Mmap", "Random", "Serialization"]
+uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
+
 [[Showoff]]
 deps = ["Dates"]
 git-tree-sha1 = "e032c9df551fb23c9f98ae1064de074111b7bc39"
@@ -239,9 +303,20 @@ version = "0.32.0"
 deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
+[[URIParser]]
+deps = ["Test", "Unicode"]
+git-tree-sha1 = "6ddf8244220dfda2f17539fa8c9de20d6c575b69"
+uuid = "30578b45-9adc-5946-b283-645ec420af67"
+version = "0.4.0"
+
 [[UUIDs]]
 deps = ["Random", "SHA"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [[Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
+
+[[VersionParsing]]
+git-tree-sha1 = "80229be1f670524750d905f8fc8148e5a8c4537f"
+uuid = "81def892-9a0e-5fdd-b105-ffc91e053289"
+version = "1.2.0"