Miscellaneous cleanup of warnings; formatting

.dev/Project.toml

@@ -0,0 +1,5 @@
+[deps]
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+
+[compat]
+JuliaFormatter = "0.3"

.dev/clima_formatter_options.jl

@@ -0,0 +1,8 @@
+clima_formatter_options = (
+    indent = 4,
+    margin = 120,
+    always_for_in = true,
+    whitespace_typedefs = true,
+    whitespace_ops_in_indices = true,
+    remove_extra_newlines = false,
+)

.dev/climaformat.jl

@@ -0,0 +1,85 @@
+#!/usr/bin/env julia
+#
+# This is an adapted version of format.jl from JuliaFormatter with the
+# following license:
+#
+#    MIT License
+#    Copyright (c) 2019 Dominique Luna
+#
+#    Permission is hereby granted, free of charge, to any person obtaining a
+#    copy of this software and associated documentation files (the
+#    "Software"), to deal in the Software without restriction, including
+#    without limitation the rights to use, copy, modify, merge, publish,
+#    distribute, sublicense, and/or sell copies of the Software, and to permit
+#    persons to whom the Software is furnished to do so, subject to the
+#    following conditions:
+#
+#    The above copyright notice and this permission notice shall be included
+#    in all copies or substantial portions of the Software.
+#
+#    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+#    OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+#    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
+#    NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+#    DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+#    OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+#    USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+using Pkg
+Pkg.activate(@__DIR__)
+Pkg.instantiate()
+
+using JuliaFormatter
+
+include("clima_formatter_options.jl")
+
+help = """
+Usage: climaformat.jl [flags] [FILE/PATH]...
+
+Formats the given julia files using the CLIMA formatting options.  If paths
+are given it will format the julia files in the paths. Otherwise, it will
+format all changed julia files.
+
+    -v, --verbose
+        Print the name of the files being formatted with relevant details.
+
+    -h, --help
+        Print this message.
+"""
+
+function parse_opts!(args::Vector{String})
+    i = 1
+    opts = Dict{Symbol, Union{Int, Bool}}()
+    while i ≤ length(args)
+        arg = args[i]
+        if arg[1] != '-'
+            i += 1
+            continue
+        end
+        if arg == "-v" || arg == "--verbose"
+            opt = :verbose
+        elseif arg == "-h" || arg == "--help"
+            opt = :help
+        else
+            error("invalid option $arg")
+        end
+        if opt in (:verbose, :help)
+            opts[opt] = true
+            deleteat!(args, i)
+        end
+    end
+    return opts
+end
+
+opts = parse_opts!(ARGS)
+if haskey(opts, :help)
+    write(stdout, help)
+    exit(0)
+end
+if isempty(ARGS)
+    filenames = readlines(`git ls-files "*.jl"`)
+else
+    filenames = ARGS
+end
+
+format(filenames; clima_formatter_options..., opts...)

.dev/hooks/pre-commit

@@ -0,0 +1,41 @@
+#!/usr/bin/env julia
+#
+# Called by git-commit with no arguments.  This checks to make sure that all
+# .jl files are indented correctly before a commit is made.
+#
+# To enable this hook, make this file executable and copy it in
+# $GIT_DIR/hooks.
+
+toplevel_directory = chomp(read(`git rev-parse --show-toplevel`, String))
+
+using Pkg
+Pkg.activate(joinpath(toplevel_directory, ".dev"))
+Pkg.instantiate()
+
+using JuliaFormatter
+
+include(joinpath(toplevel_directory, ".dev", "clima_formatter_options.jl"))
+
+needs_format = false
+
+for diffoutput in split.(readlines(`git diff --name-status --cached`))
+    status = diffoutput[1]
+    filename = diffoutput[end]
+    (!startswith(status, "D") && endswith(filename, ".jl")) || continue
+
+    a = read(`git show :$filename`, String)
+    b = format_text(a; clima_formatter_options...)
+
+    if a != b
+        fullfilename = joinpath(toplevel_directory, filename)
+
+        @error """File $filename needs to be indented with:
+            julia $(joinpath(toplevel_directory, ".dev", "climaformat.jl")) $fullfilename
+        and added to the git index via
+            git add $fullfilename
+        """
+        global needs_format = true
+    end
+end
+
+exit(needs_format ? 1 : 0)

Manifest.toml

@@ -22,9 +22,9 @@ uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
 
 [[ArrayInterface]]
 deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"]
-git-tree-sha1 = "6e8fada11bb015ecf9263f64b156f98b546918c7"
+git-tree-sha1 = "c933ce606f6535a7c7b98e1d86d5d1014f730596"
 uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
-version = "5.0.5"
+version = "5.0.7"
 
 [[Artifacts]]
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
@@ -50,17 +50,11 @@ git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2"
 uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0"
 version = "1.0.8+0"
 
-[[Calculus]]
-deps = ["LinearAlgebra"]
-git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad"
-uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
-version = "0.5.1"
-
 [[ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra", "SparseArrays"]
-git-tree-sha1 = "c9a6160317d1abe9c44b3beb367fd448117679ca"
+git-tree-sha1 = "9950387274246d08af38f6eef8cb5480862a435f"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "1.13.0"
+version = "1.14.0"
 
 [[ChangesOfVariables]]
 deps = ["ChainRulesCore", "LinearAlgebra", "Test"]
@@ -88,9 +82,9 @@ version = "0.3.0"
 
 [[Compat]]
 deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
-git-tree-sha1 = "96b0bc6c52df76506efc8a441c6cf1adcb1babc4"
+git-tree-sha1 = "b153278a25dd42c65abbf4e62344f9d22e59191b"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "3.42.0"
+version = "3.43.0"
 
 [[CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -114,15 +108,15 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
 version = "4.1.1"
 
 [[DataAPI]]
-git-tree-sha1 = "cc70b17275652eb47bc9e5f81635981f13cea5c8"
+git-tree-sha1 = "fb5f5316dd3fd4c5e7c30a24d50643b73e37cd40"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
-version = "1.9.0"
+version = "1.10.0"
 
 [[DataFrames]]
 deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
-git-tree-sha1 = "ae02104e835f219b8930c7664b8012c93475c340"
+git-tree-sha1 = "6c19003824cbebd804a51211fd3bbd81bf1ecad5"
 uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-version = "1.3.2"
+version = "1.3.3"
 
 [[DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
@@ -151,9 +145,9 @@ version = "1.0.3"
 
 [[DiffRules]]
 deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"]
-git-tree-sha1 = "dd933c4ef7b4c270aacd4eb88fa64c147492acf0"
+git-tree-sha1 = "28d605d9a0ac17118fe2c5e9ce0fbb76c3ceb120"
 uuid = "b552c78f-8df3-52c6-915a-8e097449b14b"
-version = "1.10.0"
+version = "1.11.0"
 
 [[Distances]]
 deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"]
@@ -181,12 +175,6 @@ version = "0.8.6"
 deps = ["ArgTools", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 
-[[DualNumbers]]
-deps = ["Calculus", "NaNMath", "SpecialFunctions"]
-git-tree-sha1 = "90b158083179a6ccbce2c7eb1446d5bf9d7ae571"
-uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74"
-version = "0.6.7"
-
 [[ElasticArrays]]
 deps = ["Adapt"]
 git-tree-sha1 = "a0fcc1bb3c9ceaf07e1d0529c9806ce94be6adf9"
@@ -201,9 +189,9 @@ version = "0.2.2"
 
 [[EnsembleKalmanProcesses]]
 deps = ["Convex", "Distributions", "DocStringExtensions", "LinearAlgebra", "Random", "SCS", "SparseArrays", "Statistics", "StatsBase"]
-git-tree-sha1 = "e0c9d7714fff35dbeaa6bdc7bbaa2d03006bf073"
+git-tree-sha1 = "5e7b26419a9693f8b9223b640f0d8bb08f7432b0"
 uuid = "aa8a2aa5-91d8-4396-bcef-d4f2ec43552d"
-version = "0.5.2"
+version = "0.5.3"
 
 [[FastGaussQuadrature]]
 deps = ["LinearAlgebra", "SpecialFunctions", "StaticArrays"]
@@ -231,9 +219,9 @@ version = "0.4.2"
 
 [[ForwardDiff]]
 deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"]
-git-tree-sha1 = "1bd6fc0c344fc0cbee1f42f8d2e7ec8253dda2d2"
+git-tree-sha1 = "34e6147e7686a101c245f12dba43b743c7afda96"
 uuid = "f6369f11-7733-5829-9624-2563aa707210"
-version = "0.10.25"
+version = "0.10.27"
 
 [[Future]]
 deps = ["Random"]
@@ -245,12 +233,6 @@ git-tree-sha1 = "9cf8ba8037e332b1be14c71e549143e68c42a22d"
 uuid = "891a1506-143c-57d2-908e-e1f8e92e6de9"
 version = "0.12.4"
 
-[[HypergeometricFunctions]]
-deps = ["DualNumbers", "LinearAlgebra", "SpecialFunctions", "Test"]
-git-tree-sha1 = "65e4589030ef3c44d3b90bdc5aac462b4bb05567"
-uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a"
-version = "0.3.8"
-
 [[IfElse]]
 git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1"
 uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
@@ -300,9 +282,9 @@ version = "0.21.3"
 
 [[LDLFactorizations]]
 deps = ["AMD", "LinearAlgebra", "SparseArrays", "Test"]
-git-tree-sha1 = "399bbe845e06e1c2d44ebb241f554d45eaf66788"
+git-tree-sha1 = "736e01b9b2d443c4e3351aebe551b8a374ab9c05"
 uuid = "40e66cde-538c-5869-a4ad-c39174c6795b"
-version = "0.8.1"
+version = "0.8.2"
 
 [[LibCURL]]
 deps = ["LibCURL_jll", "MozillaCACerts_jll"]
@@ -335,9 +317,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[LogExpFunctions]]
 deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"]
-git-tree-sha1 = "58f25e56b706f95125dcb796f39e1fb01d913a71"
+git-tree-sha1 = "44a7b7bb7dd1afe12bac119df6a7e540fa2c96bc"
 uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-version = "0.3.10"
+version = "0.3.13"
 
 [[Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
@@ -433,19 +415,19 @@ version = "0.12.3"
 
 [[Parsers]]
 deps = ["Dates"]
-git-tree-sha1 = "85b5da0fa43588c75bb1ff986493443f821c70b7"
+git-tree-sha1 = "1285416549ccfcdf0c50d4997a94331e88d68413"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.2.3"
+version = "2.3.1"
 
 [[Pkg]]
 deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [[PooledArrays]]
 deps = ["DataAPI", "Future"]
-git-tree-sha1 = "db3a23166af8aebf4db5ef87ac5b00d36eb771e2"
+git-tree-sha1 = "28ef6c7ce353f0b35d0df0d5930e0d072c1f5b9b"
 uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
-version = "1.4.0"
+version = "1.4.1"
 
 [[PositiveFactorizations]]
 deps = ["LinearAlgebra"]
@@ -455,9 +437,9 @@ version = "0.2.4"
 
 [[Preferences]]
 deps = ["TOML"]
-git-tree-sha1 = "d3538e7f8a790dc8903519090857ef8e1283eecd"
+git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d"
 uuid = "21216c6a-2e73-6563-6e65-726566657250"
-version = "1.2.5"
+version = "1.3.0"
 
 [[PrettyTables]]
 deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"]
@@ -475,9 +457,9 @@ uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79"
 
 [[ProgressMeter]]
 deps = ["Distributed", "Printf"]
-git-tree-sha1 = "afadeba63d90ff223a6a48d2009434ecee2ec9e8"
+git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9"
 uuid = "92933f4c-e287-5a05-a399-4b506db050ca"
-version = "1.7.1"
+version = "1.7.2"
 
 [[PyCall]]
 deps = ["Conda", "Dates", "Libdl", "LinearAlgebra", "MacroTools", "Serialization", "VersionParsing"]
@@ -588,25 +570,25 @@ version = "1.8.4"
 
 [[Static]]
 deps = ["IfElse"]
-git-tree-sha1 = "87e9954dfa33fd145694e42337bdd3d5b07021a6"
+git-tree-sha1 = "b1f1f60bf4f25d8b374480fb78c7b9785edf95fd"
 uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
-version = "0.6.0"
+version = "0.6.2"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
-git-tree-sha1 = "74fb527333e72ada2dd9ef77d98e4991fb185f04"
+git-tree-sha1 = "cd56bf18ed715e8b09f06ef8c6b781e6cdc49911"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.4.1"
+version = "1.4.4"
 
 [[Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
 uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [[StatsAPI]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "c3d8ba7f3fa0625b062b82853a7d5229cb728b6b"
+git-tree-sha1 = "c82aaa13b44ea00134f8c9c89819477bd3986ecd"
 uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
-version = "1.2.1"
+version = "1.3.0"
 
 [[StatsBase]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
@@ -615,10 +597,10 @@ uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 version = "0.33.16"
 
 [[StatsFuns]]
-deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
-git-tree-sha1 = "25405d7016a47cf2bd6cd91e66f4de437fd54a07"
+deps = ["ChainRulesCore", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
+git-tree-sha1 = "5950925ff997ed6fb3e985dcce8eb1ba42a0bbe7"
 uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
-version = "0.9.16"
+version = "0.9.18"
 
 [[SuiteSparse]]
 deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]