Merge pull request #42 from ggebbie/moreTMIinput

More tm iinput
ggebbie · Nov 3, 2021 · b43ebb5 · b43ebb5
2 parents 2295a0e + db0904a
commit b43ebb5
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diff --git a/Manifest.toml b/Manifest.toml
@@ -39,12 +39,36 @@ git-tree-sha1 = "ecdec412a9abc8db54c0efc5548c64dfce072058"
 uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
 version = "0.5.10"
 
+[[Blosc]]
+deps = ["Blosc_jll"]
+git-tree-sha1 = "84cf7d0f8fd46ca6f1b3e0305b4b4a37afe50fd6"
+uuid = "a74b3585-a348-5f62-a45c-50e91977d574"
+version = "0.7.0"
+
+[[Blosc_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Lz4_jll", "Pkg", "Zlib_jll", "Zstd_jll"]
+git-tree-sha1 = "e747dac84f39c62aff6956651ec359686490134e"
+uuid = "0b7ba130-8d10-5ba8-a3d6-c5182647fed9"
+version = "1.21.0+0"
+
+[[BufferedStreams]]
+deps = ["Compat", "Test"]
+git-tree-sha1 = "5d55b9486590fdda5905c275bb21ce1f0754020f"
+uuid = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"
+version = "1.0.0"
+
 [[Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2"
 uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0"
 version = "1.0.8+0"
 
+[[CFTime]]
+deps = ["Dates", "Printf"]
+git-tree-sha1 = "bca6cb6ee746e6485ca4535f6cc29cf3579a0f20"
+uuid = "179af706-886a-5703-950a-314cd64e0468"
+version = "0.1.1"
+
 [[CSV]]
 deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings"]
 git-tree-sha1 = "c0a735698d1a0a388c5c7ae9c7fb3da72fd5424e"
@@ -299,9 +323,9 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 
 [[GLFW_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"]
-git-tree-sha1 = "dba1e8614e98949abfa60480b13653813d8f0157"
+git-tree-sha1 = "0c603255764a1fa0b61752d2bec14cfbd18f7fe8"
 uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89"
-version = "3.3.5+0"
+version = "3.3.5+1"
 
 [[GR]]
 deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"]
@@ -356,6 +380,12 @@ git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2"
 uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe"
 version = "1.0.2"
 
+[[HDF5]]
+deps = ["Blosc", "Compat", "HDF5_jll", "Libdl", "Mmap", "Random", "Requires"]
+git-tree-sha1 = "83173193dc242ce4b037f0263a7cc45afb5a0b85"
+uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
+version = "0.15.6"
+
 [[HDF5_jll]]
 deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"]
 git-tree-sha1 = "fd83fa0bde42e01952757f01149dd968c06c4dba"
@@ -567,6 +597,18 @@ git-tree-sha1 = "491a883c4fef1103077a7f648961adbf9c8dd933"
 uuid = "6f1432cf-f94c-5a45-995e-cdbf5db27b0b"
 version = "2.1.2"
 
+[[Lz4_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "5d494bc6e85c4c9b626ee0cab05daa4085486ab1"
+uuid = "5ced341a-0733-55b8-9ab6-a4889d929147"
+version = "1.9.3+0"
+
+[[MAT]]
+deps = ["BufferedStreams", "CodecZlib", "HDF5", "SparseArrays"]
+git-tree-sha1 = "5c62992f3d46b8dce69bdd234279bb5a369db7d5"
+uuid = "23992714-dd62-5051-b70f-ba57cb901cac"
+version = "0.10.1"
+
 [[MacroTools]]
 deps = ["Markdown", "Random"]
 git-tree-sha1 = "5a5bc6bf062f0f95e62d0fe0a2d99699fed82dd9"
@@ -604,6 +646,12 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 [[MozillaCACerts_jll]]
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
 
+[[NCDatasets]]
+deps = ["CFTime", "DataStructures", "Dates", "NetCDF_jll", "Printf"]
+git-tree-sha1 = "5da406d9624f25909a6f556bd8d5c1deaa189ee6"
+uuid = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
+version = "0.11.7"
+
 [[NLSolversBase]]
 deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"]
 git-tree-sha1 = "144bab5b1443545bc4e791536c9f1eacb4eed06a"

diff --git a/Project.toml b/Project.toml
@@ -17,6 +17,8 @@ Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 LineSearches = "d3d80556-e9d4-5f37-9878-2ab0fcc64255"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
+NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 NetCDF = "30363a11-5582-574a-97bb-aa9a979735b9"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"

diff --git a/README.md b/README.md
@@ -6,17 +6,14 @@
 [![Coverage](https://codecov.io/gh/ggebbie/TMI.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/ggebbie/TMI.jl)
 
 * Total Matrix Intercomparison codes for Julia\
-G Jake Gebbie, WHOI, ggebbie@whoi.edu 
+Started by G Jake Gebbie, WHOI, ggebbie@whoi.edu 
 
-# References 
-
-Gebbie, G., and P. Huybers:  "Total matrix intercomparison: A method for resolving the geometry of water mass pathways", J. Phys. Oceanogr., 40(8), doi:10.1175/2010JPO4272.1, 1710-1728, 2010. 
-
-Gebbie, G., and P. Huybers. "How is the ocean filled?", Geophys. Res. Lett., 38, L06604, doi:10.1029/2011GL046769, 2011 
+* See the function list in the documentation linked through the badge above
 
-Gebbie, G., and P. Huybers, "The mean age of ocean waters inferred from radiocarbon observations", 2012, JPO.
+* The MATLAB version of the code is in maintenance mode and is available at https://github.com/ggebbie/TMI 
 
-Gebbie, G., "How much did Glacial North Atlantic Water shoal?", 2014, Paleoceanography.
+* After setting up the environment (instructions below), check that all tests pass via the following shell command in the repository base directory:
+`julia --project=@. test/runtests.jl`
 
 # Requirements
 
@@ -34,7 +31,7 @@ Restart the REPL.\
 `Conda.add("shapely",channel="conda-forge")`\
 `Conda.add("cartopy",channel="conda-forge")`\
 
-This should set up cartopy v. 0.20.0 which can download coastlines from Amazon Web Services.
+This should set up cartopy v0.20.0 which can download coastlines from Amazon Web Services.
 
 # Setting up project environment
 
@@ -71,15 +68,23 @@ An example:\
 
 # Data files
 
-The Julia code is designed to download input files from Google Drive and to place them in the `data` directory. If that doesn't work, extract data from Google Drive using your favorite method, such as the script `readTMIfromGoogleDrive.sh` at a bash shell prompt. 
+The Julia code is designed to download input files from Google Drive and to place them in the `data` directory. If that doesn't work, extract data from Google Drive using your favorite method or download manually at: https://drive.google.com/drive/folders/1nFDSINbst84pK68aWwRGBVfYZkfN1mUR?usp=sharing . Available TMI versions include:
 
-`/bin/sh readTMIfromGoogleDrive.sh`
+`modern_90x45x33_GH10_GH12` : TMI version with 4x4 degree horizontal
+                  resolution and 33 levels  (G & H 2010), \
+				  Includes the input data from the WGHC (Gouretski & Koltermann 2005) 
+
+`modern_180x90x33_GH10_GH12` : TMI version with 2x2 degree horizontal
+                  resolution and 33 levels  (G & H 2010), \
+				  Includes the input data from the WGHC (Gouretski & Koltermann 2005) 
 
-Or download manually at: https://drive.google.com/file/d/1Zycnx6_nifRrJo8XWMdlCFv4ODBpi-i7/view?usp=sharing .
+`modern_90x45x33_unpub12` : TMI version with 4x4 degree horizontal
+                  resolution and 33 levels  (unpublished 2012), \
+				  Includes a steady-state climatology of global tracers
 
-TMI_4deg_2010.mat : TMI version with 4x4 degree horizontal
-                  resolution and 33 levels  (G & H 2010), \
-				  Includes TMI climatology of ocean properties 
+`modern_90x45x33_G14` : TMI version with 4x4 degree horizontal
+                  resolution and 33 levels  (Gebbie 2014), \
+				  Doesn't rely upon a bottom spreading parameterization and solves for mixed-layer depth
 
 # Functions
 
@@ -97,9 +102,9 @@ Steps:
 1. Use PkgTemplates to make git repo.\
 	2. new empty repository on GitHub.\
     3. Then push an existing repository from the command line:
-    `git remote add origin git@github.com:ggebbie/TMI.jl.git`
-    `git branch -M main`
-    `git push -u origin main`
+    `git remote add origin git@github.com:ggebbie/TMI.jl.git`\
+    `git branch -M main`\
+    `git push -u origin main`\
 
 4. Run the following Julia code
 
@@ -118,9 +123,9 @@ Steps:
         Documenter{GitHubActions}(),
         Develop(),
     ],
-             )`
+             )`\
 
-`t("TMI.jl")`
+`t("TMI.jl")`\
 
 # MATLAB version of code
 
@@ -141,3 +146,13 @@ Version 6.2, July 2015, added sq.m function,
                         fixed d_all to properly divide Atlantic/Pacific and put White Sea into Arctic.\
 Version 7, Sept. 2016, major improvements to transient run: 2 types of initial conditions and boundary conditions.\
 Version 8, Jan. 2021, bug fixes, especially those found by Elaine McDonagh
+
+# References 
+
+Gebbie, G., and P. Huybers:  "Total matrix intercomparison: A method for resolving the geometry of water mass pathways", J. Phys. Oceanogr., 40(8), doi:10.1175/2010JPO4272.1, 1710-1728, 2010. 
+
+Gebbie, G., and P. Huybers. "How is the ocean filled?", Geophys. Res. Lett., 38, L06604, doi:10.1029/2011GL046769, 2011 
+
+Gebbie, G., and P. Huybers, "The mean age of ocean waters inferred from radiocarbon observations", 2012, JPO.
+
+Gebbie, G., "How much did Glacial North Atlantic Water shoal?", 2014, Paleoceanography.