Reorganized files so that each file is a module

Some files have changed names because there were name conflicts (e.g.,
the module `OutputVar`, the function `OutputVar`, and the struct
`OutputVar`).

NEWS.md

@@ -1,6 +1,10 @@
 ClimaAnalysis.jl Release Notes
 ===============================
 
+v0.5.4
+------
+- Reorganized internal modules so that each file is a module.
+
 v0.5.3
 ------
 - Add `Visualize.contour2D_on_globe!` for discrete contours.

Project.toml

@@ -6,6 +6,7 @@ version = "0.5.3"
 [deps]
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [weakdeps]
@@ -26,6 +27,7 @@ NCDatasets = "0.13.1, 0.14"
 OrderedCollections = "1.3"
 SafeTestsets = "0.1"
 Statistics = "1"
+Reexport = "1"
 Test = "1"
 julia = "1.9"
 

ext/CairoMakieExt.jl

@@ -107,7 +107,7 @@ function _sliced_plot_generic(
     var_sliced = var
 
     for (dim_name, val) in cut
-        var_sliced = ClimaAnalysis._slice_general(var_sliced, val, dim_name)
+        var_sliced = ClimaAnalysis.Var._slice_general(var_sliced, val, dim_name)
     end
 
     func(fig, var_sliced; p_loc, more_kwargs)

src/ClimaAnalysis.jl

@@ -1,13 +1,15 @@
 module ClimaAnalysis
+using Reexport
 
 include("Utils.jl")
 import .Utils
 
-include("OutputVar.jl")
-include("SimDir.jl")
-import .SimDir
+include("Var.jl")
+@reexport using .Var
+include("Sim.jl")
+@reexport using .Sim
 
 include("Visualize.jl")
-import .Visualize
+@reexport using .Visualize
 
 end # module ClimaAnalysis

src/SimDir.jl → src/Sim.jl

@@ -1,7 +1,12 @@
+module Sim
+
 import Base: get
 
 export SimDir, available_vars, available_reductions, available_periods
 
+import ..Utils
+import ..Var: read_var
+
 """
     SimDir(simulation_path::String)
 
@@ -191,3 +196,5 @@ end
 Check if the given SimDir contains OutputVars.
 """
 Base.isempty(simdir::SimDir) = isempty(simdir.vars)
+
+end

src/OutputVar.jl → src/Var.jl

@@ -1,9 +1,11 @@
+module Var
+
 import NCDatasets
 import OrderedCollections: OrderedDict
 
 import Statistics: mean
 
-import .Utils: nearest_index, seconds_to_prettystr
+import ..Utils: nearest_index, seconds_to_prettystr, squeeze
 
 export OutputVar,
     read_var,
@@ -17,7 +19,10 @@ export OutputVar,
     slice,
     window,
     arecompatible,
-    center_longitude!
+    center_longitude!,
+    short_name,
+    long_name,
+    units
 
 """
     Representing an output variable
@@ -184,10 +189,7 @@ function _reduce_over(
     dim_index = var.dim2index[dim]
 
     # squeeze removes the unnecessary singleton dimension
-    data = Utils.squeeze(
-        reduction(var.data, dims = dim_index),
-        dims = (dim_index,),
-    )
+    data = squeeze(reduction(var.data, dims = dim_index), dims = (dim_index,))
 
     # If we reduce over a dimension, we have to remove it
     dims = copy(var.dims)
@@ -518,3 +520,5 @@ end
 @overload_binary_op (-)
 @overload_binary_op (*)
 @overload_binary_op (/)
+
+end

src/Visualize.jl

@@ -1,5 +1,7 @@
 module Visualize
 
+export plot!
+
 function heatmap2D! end
 
 function sliced_heatmap! end

test/runtests.jl

@@ -6,11 +6,11 @@ using Test
 @safetestset "Docstrings" begin @time include("doctest.jl") end
 @safetestset "Format" begin @time include("format.jl") end
 
-@safetestset "Utils" begin @time include("Utils.jl") end
-@safetestset "SimDir" begin @time include("SimDir.jl") end
-@safetestset "OutputVar" begin @time include("OutputVar.jl") end
-@safetestset "CairoMakieExt" begin @time include("CairoMakieExt.jl") end
-@safetestset "GeoMakieExt" begin @time include("GeoMakieExt.jl") end
+@safetestset "Utils" begin @time include("test_Utils.jl") end
+@safetestset "SimDir" begin @time include("test_Sim.jl") end
+@safetestset "OutputVar" begin @time include("test_Var.jl") end
+@safetestset "CairoMakieExt" begin @time include("test_CairoMakieExt.jl") end
+@safetestset "GeoMakieExt" begin @time include("test_GeoMakieExt.jl") end
 #! format: on
 
 nothing