Merge #22

22: Add Cloudy example to test r=charleskawczynski a=charleskawczynski - Removes "_mb" from filenames - Removes Cloudy dependence from CES.jl by passing objects/emthods as arguments from test I had to remove windows 32-bit build since it was timing out. Opened #25 to track this. Co-authored-by: Charles Kawczynski <kawczynski.charles@gmail.com>
CliMA · Feb 3, 2020 · 59edfb2 · 59edfb2
2 parents b09e88b + a67181a
commit 59edfb2
Show file tree

Hide file tree

Showing 25 changed files with 760 additions and 456 deletions.
diff --git a/.appveyor.yml b/.appveyor.yml
@@ -8,12 +8,17 @@ branches:
     - master
 
 environment:
+  PYTHON: conda
   matrix:
   - julia_version: 1.3
   - julia_version: nightly
 
 platform:
-  - x86 # 32-bit
+  # Currently, the 32-bit build is taking >1hr, which fails
+  # and cannot be increased: https://www.appveyor.com/docs/build-configuration/#build-timeout
+  # TODO: Add 32-bit build back in
+  # This can likely be fixed by reducing the deps
+  # - x86 # 32-bit
   - x64 # 64-bit
 
 # Uncomment the following lines to allow failures on nightly julia
@@ -30,6 +35,8 @@ notifications:
 
 install:
   - ps: iex ((new-object net.webclient).DownloadString("https://raw.githubusercontent.com/JuliaCI/Appveyor.jl/version-1/bin/install.ps1"))
+  - pip install --user -U numpy scipy scikit-learn
+  - C:\julia\bin\julia -e "using Pkg; Pkg.build(\"PyCall\"); Pkg.update()"
 
 build_script:
   - echo "%JL_BUILD_SCRIPT%"

diff --git a/Manifest.toml b/Manifest.toml
@@ -38,16 +38,22 @@ version = "3.5.0+2"
 
 [[ArrayInterface]]
 deps = ["LinearAlgebra", "Requires", "SparseArrays"]
-git-tree-sha1 = "656fd4bcdf204ea96945d9bc1068c0056013438a"
+git-tree-sha1 = "4f1109cf20b2a31b5196f346bba07b2c61587442"
 uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
-version = "2.3.1"
+version = "2.4.1"
 
 [[ArrayLayouts]]
 deps = ["FillArrays", "LinearAlgebra"]
 git-tree-sha1 = "bc779df8d73be70e4e05a63727d3a4dfb4c52b1f"
 uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a"
 version = "0.1.5"
 
+[[AxisAlgorithms]]
+deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"]
+git-tree-sha1 = "a4d07a1c313392a77042855df46c5f534076fab9"
+uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950"
+version = "1.0.0"
+
 [[BandedMatrices]]
 deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"]
 git-tree-sha1 = "03b21fb83f9e0b13f99c407810cd3b6cac293a1d"
@@ -95,9 +101,9 @@ version = "0.2.3"
 
 [[CSV]]
 deps = ["CategoricalArrays", "DataFrames", "Dates", "FilePathsBase", "Mmap", "Parsers", "PooledArrays", "Tables", "Unicode", "WeakRefStrings"]
-git-tree-sha1 = "027b8d04a1983153ecbcf8f905e926bf01c078e8"
+git-tree-sha1 = "fe9b828d5e7b55431d75d6d180ef843d69dea048"
 uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-version = "0.5.22"
+version = "0.5.23"
 
 [[Calculus]]
 deps = ["LinearAlgebra"]
@@ -164,6 +170,12 @@ git-tree-sha1 = "c7559d68defb3708c0e46df1158e21be86e04312"
 uuid = "88353bc9-fd38-507d-a820-d3b43837d6b9"
 version = "0.1.1"
 
+[[Contour]]
+deps = ["LinearAlgebra", "StaticArrays", "Test"]
+git-tree-sha1 = "b974e164358fea753ef853ce7bad97afec15bb80"
+uuid = "d38c429a-6771-53c6-b99e-75d170b6e991"
+version = "0.5.1"
+
 [[DataAPI]]
 git-tree-sha1 = "674b67f344687a88310213ddfa8a2b3c76cc4252"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
@@ -186,6 +198,12 @@ git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
 uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464"
 version = "1.0.0"
 
+[[DataValues]]
+deps = ["DataValueInterfaces", "Dates"]
+git-tree-sha1 = "d88a19299eba280a6d062e135a43f00323ae70bf"
+uuid = "e7dc6d0d-1eca-5fa6-8ad6-5aecde8b7ea5"
+version = "0.4.13"
+
 [[Dates]]
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
@@ -208,9 +226,9 @@ uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 
 [[DiffEqBase]]
 deps = ["ArrayInterface", "ChainRulesCore", "Compat", "DataStructures", "Distributed", "DocStringExtensions", "FunctionWrappers", "IterativeSolvers", "IteratorInterfaceExtensions", "LinearAlgebra", "MuladdMacro", "Parameters", "Printf", "RecipesBase", "RecursiveArrayTools", "RecursiveFactorization", "Requires", "Roots", "SparseArrays", "StaticArrays", "Statistics", "SuiteSparse", "TableTraits", "TreeViews", "ZygoteRules"]
-git-tree-sha1 = "3ef848bc1b8b09ce3cc14b53ddd0b4abec0407ae"
+git-tree-sha1 = "d84f56013dcd658ac725252d24847114c9077f79"
 uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
-version = "6.13.1"
+version = "6.13.2"
 
 [[DiffEqCallbacks]]
 deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "NLsolve", "OrdinaryDiffEq", "RecipesBase", "RecursiveArrayTools", "StaticArrays"]
@@ -296,9 +314,9 @@ version = "0.8.1"
 
 [[Documenter]]
 deps = ["Base64", "Dates", "DocStringExtensions", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
-git-tree-sha1 = "51f0c7df46abb9c07d80e529718951e634670afb"
+git-tree-sha1 = "d497bcc45bb98a1fbe19445a774cfafeabc6c6df"
 uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-version = "0.24.4"
+version = "0.24.5"
 
 [[ElasticArrays]]
 git-tree-sha1 = "5b5b7cb8cba44bcf337b8af0a1f3e57c89468660"
@@ -333,6 +351,12 @@ git-tree-sha1 = "0fa3b52a04a4e210aeb1626def9c90df3ae65268"
 uuid = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
 version = "1.1.0"
 
+[[FFMPEG]]
+deps = ["BinaryProvider", "Libdl"]
+git-tree-sha1 = "9143266ba77d3313a4cf61d8333a1970e8c5d8b6"
+uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a"
+version = "0.2.4"
+
 [[FFTW]]
 deps = ["AbstractFFTs", "FFTW_jll", "IntelOpenMP_jll", "Libdl", "LinearAlgebra", "MKL_jll", "Reexport"]
 git-tree-sha1 = "109d82fa4b00429f9afcce873e9f746f11f018d3"
@@ -396,6 +420,12 @@ version = "1.0.0"
 deps = ["Random"]
 uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 
+[[GR]]
+deps = ["Base64", "DelimitedFiles", "LinearAlgebra", "Printf", "Random", "Serialization", "Sockets", "Test"]
+git-tree-sha1 = "10633436bc2fc836347bda5073b7b6f06dcdc5e6"
+uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"
+version = "0.46.0"
+
 [[GaussianMixtures]]
 deps = ["Clustering", "Compat", "DelimitedFiles", "Distributed", "Distributions", "FileIO", "JLD", "LinearAlgebra", "Logging", "PDMats", "Printf", "Random", "ScikitLearnBase", "SpecialFunctions", "Statistics", "StatsBase"]
 git-tree-sha1 = "9b892cfc95da04ca9eff2387bc66f6baddeed606"
@@ -414,6 +444,12 @@ git-tree-sha1 = "c59a30ef95fa4b5e0567c1911652e0c70a5d055c"
 uuid = "01680d73-4ee2-5a08-a1aa-533608c188bb"
 version = "0.2.2"
 
+[[GeometryTypes]]
+deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "StaticArrays"]
+git-tree-sha1 = "a96baa00f5ac755689c82c29bc3395e161337c69"
+uuid = "4d00f742-c7ba-57c2-abde-4428a4b178cb"
+version = "0.7.7"
+
 [[HDF5]]
 deps = ["BinaryProvider", "Blosc", "CMakeWrapper", "Libdl", "Mmap"]
 git-tree-sha1 = "d3ea5532668bf9bdd5e8d5f16571e0b520cbbb9f"
@@ -442,6 +478,12 @@ version = "2018.0.3+0"
 deps = ["Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
+[[Interpolations]]
+deps = ["AxisAlgorithms", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"]
+git-tree-sha1 = "c7579b2617b513d8e6eb9f4b91837eefe7080af8"
+uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
+version = "0.12.8"
+
 [[InvertedIndices]]
 deps = ["Test"]
 git-tree-sha1 = "15732c475062348b0165684ffe28e85ea8396afc"
@@ -465,17 +507,29 @@ uuid = "82899510-4779-5014-852e-03e436cf321d"
 version = "1.0.0"
 
 [[JLD]]
-deps = ["Compat", "FileIO", "HDF5", "LegacyStrings", "Profile", "Random"]
-git-tree-sha1 = "95fd5d7f129918a75d0535aaaf5b8e235e6e0b0b"
+deps = ["Compat", "FileIO", "HDF5", "LegacyStrings"]
+git-tree-sha1 = "c8c7a9ca4c17a519961a8ec27e508b07ffc9c1a9"
 uuid = "4138dd39-2aa7-5051-a626-17a0bb65d9c8"
-version = "0.9.1"
+version = "0.9.2"
+
+[[JLD2]]
+deps = ["CodecZlib", "DataStructures", "FileIO", "Mmap", "Pkg", "Printf", "UUIDs"]
+git-tree-sha1 = "5deae9f0745ef505ed155a0029629cf08502ccab"
+uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+version = "0.1.11"
 
 [[JSON]]
 deps = ["Dates", "Mmap", "Parsers", "Unicode"]
 git-tree-sha1 = "b34d7cef7b337321e97d22242c3c2b91f476748e"
 uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 version = "0.21.0"
 
+[[KernelDensity]]
+deps = ["Distributions", "FFTW", "Interpolations", "Optim", "StatsBase", "Test"]
+git-tree-sha1 = "c1048817fe5711f699abc8fabd47b1ac6ba4db04"
+uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
+version = "0.5.1"
+
 [[LaTeXStrings]]
 deps = ["Compat"]
 git-tree-sha1 = "7ab9b8788cfab2bdde22adf9004bda7ad9954b6c"
@@ -535,6 +589,11 @@ version = "0.5.3"
 deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
+[[Measures]]
+git-tree-sha1 = "e498ddeee6f9fdb4551ce855a46f54dbd900245f"
+uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e"
+version = "0.3.1"
+
 [[Missings]]
 deps = ["DataAPI"]
 git-tree-sha1 = "de0a5ce9e5289f27df672ffabef4d1e5861247d5"
@@ -569,9 +628,9 @@ version = "2.1.0"
 
 [[NLSolversBase]]
 deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"]
-git-tree-sha1 = "b13b1f97ce88a37dd55ce7ae7e75b81002bf2b9d"
+git-tree-sha1 = "7c4e66c47848562003250f28b579c584e55becc0"
 uuid = "d41bc354-129a-5804-8e4c-c37616107c6c"
-version = "7.6.0"
+version = "7.6.1"
 
 [[NLsolve]]
 deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"]
@@ -602,6 +661,17 @@ git-tree-sha1 = "8bc6180f328f3c0ea2663935db880d34c57d6eae"
 uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 version = "0.4.4"
 
+[[Observables]]
+deps = ["Test"]
+git-tree-sha1 = "dc02cec22747d1d10d9f70d8a1c03432b5bfbcd0"
+uuid = "510215fc-4207-5dde-b226-833fc4488ee2"
+version = "0.2.3"
+
+[[OffsetArrays]]
+git-tree-sha1 = "707e34562700b81e8aa13548eb6b23b18112e49b"
+uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
+version = "1.0.2"
+
 [[OpenBLAS_jll]]
 deps = ["Libdl", "Pkg"]
 git-tree-sha1 = "e2551d7c25d52f35b76d86a50917a3ba8988f519"
@@ -646,14 +716,32 @@ version = "0.12.0"
 
 [[Parsers]]
 deps = ["Dates", "Test"]
-git-tree-sha1 = "0139ba59ce9bc680e2925aec5b7db79065d60556"
+git-tree-sha1 = "d112c19ccca00924d5d3a38b11ae2b4b268dda39"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "0.3.10"
+version = "0.3.11"
 
 [[Pkg]]
 deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Test", "UUIDs"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
+[[PlotThemes]]
+deps = ["PlotUtils", "Requires", "Statistics"]
+git-tree-sha1 = "df772cc7c78862da96af1ee85cd0111c6640e44e"
+uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a"
+version = "1.0.1"
+
+[[PlotUtils]]
+deps = ["Colors", "Dates", "Printf", "Random", "Reexport"]
+git-tree-sha1 = "22bd7d0a1f4665d66317d6c89a57f6bba9f2560d"
+uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043"
+version = "0.6.2"
+
+[[Plots]]
+deps = ["Base64", "Contour", "Dates", "FFMPEG", "FixedPointNumbers", "GR", "GeometryTypes", "JSON", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "Reexport", "Requires", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"]
+git-tree-sha1 = "11c75a31269c1c64790e7cb910346f64cd4440c1"
+uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+version = "0.27.1"
+
 [[PoissonRandom]]
 deps = ["Random", "Statistics", "Test"]
 git-tree-sha1 = "44d018211a56626288b5d3f8c6497d28c26dc850"
@@ -676,10 +764,6 @@ version = "0.2.3"
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
-[[Profile]]
-deps = ["Printf"]
-uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79"
-
 [[ProgressMeter]]
 deps = ["Distributed", "Printf"]
 git-tree-sha1 = "ea1f4fa0ff5e8b771bf130d87af5b7ef400760bd"
@@ -730,6 +814,12 @@ git-tree-sha1 = "441e6fc35597524ada7f85e13df1f4e10137d16f"
 uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143"
 version = "1.4.0"
 
+[[Ratios]]
+deps = ["Compat"]
+git-tree-sha1 = "cdbbe0f350581296f3a2e3e7a91b214121934407"
+uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439"
+version = "0.3.1"
+
 [[RecipesBase]]
 git-tree-sha1 = "7bdce29bc9b2f5660a6e5e64d64d91ec941f6aa2"
 uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
@@ -755,9 +845,9 @@ version = "0.2.0"
 
 [[Requires]]
 deps = ["UUIDs"]
-git-tree-sha1 = "999513b7dea8ac17359ed50ae8ea089e4464e35e"
+git-tree-sha1 = "d37400976e98018ee840e0ca4f9d20baa231dc6b"
 uuid = "ae029012-a4dd-5104-9daa-d747884805df"
-version = "1.0.0"
+version = "1.0.1"
 
 [[ResettableStacks]]
 deps = ["StaticArrays"]
@@ -799,6 +889,12 @@ uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 deps = ["Distributed", "Mmap", "Random", "Serialization"]
 uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
 
+[[Showoff]]
+deps = ["Dates"]
+git-tree-sha1 = "e032c9df551fb23c9f98ae1064de074111b7bc39"
+uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f"
+version = "0.3.1"
+
 [[SimpleTraits]]
 deps = ["InteractiveUtils", "MacroTools"]
 git-tree-sha1 = "2bdf3b6300a9d66fe29ee8bb51ba100c4df9ecbc"
@@ -858,6 +954,12 @@ git-tree-sha1 = "79982835d2ff3970685cb704500909c94189bde9"
 uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
 version = "0.9.3"
 
+[[StatsPlots]]
+deps = ["Clustering", "DataStructures", "DataValues", "Distributions", "Interpolations", "KernelDensity", "Observables", "Plots", "RecipesBase", "Reexport", "StatsBase", "Tables", "Widgets"]
+git-tree-sha1 = "9f3f096a310f25debaca9dbe6b4e0df7bb428fd0"
+uuid = "f3b207a7-027a-5e70-b257-86293d7955fd"
+version = "0.12.0"
+
 [[SteadyStateDiffEq]]
 deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport"]
 git-tree-sha1 = "9a2de84a1618e1702dbb95ebdbb84dbf7f24d1ab"
@@ -866,9 +968,9 @@ version = "1.5.0"
 
 [[StochasticDiffEq]]
 deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "FillArrays", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "Parameters", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays"]
-git-tree-sha1 = "acdb92d3d056cbbfd9c598e9f792eb5c0d21542d"
+git-tree-sha1 = "d7c979f831943fb1d870c862a0d60c5f475c56af"
 uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
-version = "6.18.0"
+version = "6.19.1"
 
 [[SuiteSparse]]
 deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
@@ -950,6 +1052,18 @@ git-tree-sha1 = "28807f85197eaad3cbd2330386fac1dcb9e7e11d"
 uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5"
 version = "0.6.2"
 
+[[Widgets]]
+deps = ["Colors", "Dates", "Observables", "OrderedCollections"]
+git-tree-sha1 = "fc0feda91b3fef7fe6948ee09bb628f882b49ca4"
+uuid = "cc8bc4a8-27d6-5769-a93b-9d913e69aa62"
+version = "0.6.2"
+
+[[WoodburyMatrices]]
+deps = ["LinearAlgebra", "SparseArrays"]
+git-tree-sha1 = "bbb9f7fd6fbdd9582e77c0b698312c543de5eb71"
+uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6"
+version = "0.5.0"
+
 [[XML2_jll]]
 deps = ["Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"]
 git-tree-sha1 = "ed5603a695aefe3e9e404fc7b052e02cc72cfab6"
@@ -970,9 +1084,9 @@ version = "1.2.11+8"
 
 [[Zygote]]
 deps = ["DiffRules", "FFTW", "FillArrays", "ForwardDiff", "IRTools", "InteractiveUtils", "LinearAlgebra", "MacroTools", "NNlib", "NaNMath", "Random", "Requires", "SpecialFunctions", "Statistics", "ZygoteRules"]
-git-tree-sha1 = "ca4dfa4de0a0e2c1da6c8c67d3b9af99645b57fc"
+git-tree-sha1 = "54872ae5411c8795ed52852759796a04fb771f68"
 uuid = "e88e6eb3-aa80-5325-afca-941959d7151f"
-version = "0.4.6"
+version = "0.4.7"
 
 [[ZygoteRules]]
 deps = ["MacroTools"]