Use DataFrames instead of MetadataArrays (#17)

* Use DataFrames instead of MetadataArrays

* Update LICENSE.md

LICENSE → LICENSE.md

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2019 Benoit Pasquier
+Copyright (c) 2021 Benoit Pasquier
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Project.toml

@@ -1,12 +1,13 @@
 name = "WorldOceanAtlasTools"
 uuid = "04f20302-f1b9-11e8-29d9-7d841cb0a64a"
 authors = ["Benoit Pasquier <briochemc@gmail.com>"]
-version = "0.4.4"
+version = "0.5.0"
 
 [deps]
 DataDeps = "124859b0-ceae-595e-8997-d05f6a7a8dfe"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 Match = "7eb4fadd-790c-5f42-8a69-bfa0b872bfbf"
-MetadataArrays = "49441bc9-da82-574f-b07c-a0d10dd4ac13"
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 OceanGrids = "cfe838f4-859f-11e9-2ea1-df7d4e7c3537"
@@ -16,11 +17,11 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [compat]
 DataDeps = "0.7"
+DataFrames = "1"
 Match = "1"
-MetadataArrays = "0.1"
 NCDatasets = "0.9, 0.10, 0.11"
 NearestNeighbors = "0.4"
-OceanGrids = "0.1, 0.2, 0.3"
+OceanGrids = "0.1, 0.2, 0.3, 0.4"
 StatsBase = "0.33"
 Unitful = "1"
 julia = "1"

src/WorldOceanAtlasTools.jl

@@ -1,7 +1,15 @@
 module WorldOceanAtlasTools
 
-using DataDeps, NCDatasets, Match, Statistics, StatsBase, Unitful
-using OceanGrids, NearestNeighbors
+using DataDeps
+using Downloads
+using NCDatasets
+using DataFrames
+using Match
+using Statistics
+using StatsBase
+using Unitful
+using OceanGrids
+using NearestNeighbors
 
 include("names.jl")
 include("citations.jl")

src/functions.jl

@@ -161,33 +161,19 @@ end
 
 
 
-#==================================
-More general API functions
-==================================#
-# GEOTRACES.jl inspired functions.
-# Maybe faster that what I previously had.
-# Anyway it would be better to compare interpolated model to obs,
-# rather than interpolated obs to model.
-# So this is the format of obs I should use.
-# obs, MD
-# with obs and units
-# and MD a named tuple with fields Depth, Latitude, and Longitude
-# If MD is used a lot, maybe use depth, lat, lon?
-# TODO make this the basic API and let AIBECS use it
-# TODO push new version with new API
-
-
+#=========================================
+observations function returns a DataFrames
+=========================================#
 
-using MetadataArrays
 
 
 function observations(ds::Dataset, tracer::String; metadatakeys)
     var, v, ikeep = indices_and_var(ds, tracer)
     u = _unit(var)
     WOAmetadatakeys = varname.(metadatakeys)
-    metadata = [metadatakeyvaluepair(ds[k], ikeep) for k in WOAmetadatakeys]
-    metadata = (name="Observed $(WOA_path_varname(tracer))", WOAvarname=name(var), metadata...)
-    return MetadataVector(float.(v[ikeep]) .* u, metadata)
+    metadata = (metadatakeyvaluepair(ds[k], ikeep) for k in WOAmetadatakeys)
+    df = DataFrame(metadata..., Symbol(tracer)=>float.(view(v, ikeep))*u)
+    return df
 end
 """
     observations(tracer::String; metadatakeys=("lat", "lon", "depth"))
@@ -216,9 +202,9 @@ end
 _unit(v) = convert_to_Unitful(get(v.attrib, "units", "nothing"))
 _fillvalue(v) = get(v.attrib, "_FillValue", NaN)
 metadatakeyvaluepair(v, idx) = @match name(v) begin
-    "lon"   => (:lon, float.(v.var[:][[i.I[1] for i in idx]]) * u"°")
-    "lat"   => (:lat, float.(v.var[:][[i.I[2] for i in idx]]) * u"°")
-    "depth" => (:depth, float.(v.var[:][[i.I[3] for i in idx]]) * u"m")
+    "lon"   => (:lon => float.(v.var[:][[i.I[1] for i in idx]]))
+    "lat"   => (:lat => float.(v.var[:][[i.I[2] for i in idx]]))
+    "depth" => (:depth => float.(v.var[:][[i.I[3] for i in idx]]) * u"m")
 end
 
 

src/names.jl

@@ -7,7 +7,7 @@ function fallback_download(remotepath, localdir)
     @assert(isdir(localdir))
     filename = basename(remotepath)  # only works for URLs with filename as last part of name
     localpath = joinpath(localdir, filename)
-    Base.download(remotepath, localpath)
+    Downloads.download(remotepath, localpath)
     return localpath
 end
 

test/test_functions.jl

@@ -54,7 +54,8 @@
     # new functionality
     @testset "observations function" begin
         σSW = 1.035u"kg/L" # approximate mean sea water density to convert mol/kg to mol/m^3
-        PO₄obs = WorldOceanAtlasTools.observations(tracer) * σSW
-        @test 0.1u"μM" < mean(PO₄obs) < 10u"μM"
+        obs = WorldOceanAtlasTools.observations(tracer)
+        obs.value = obs.p .* σSW .|> u"μM"
+        @test 0.1u"μM" < mean(obs.value) < 10u"μM"
     end
 end