Merge pull request #93 from JuliaOcean/v0p2p4a

V0p2p4a
JuliaOcean · Sep 3, 2024 · 6dd5e1e · 6dd5e1e
2 parents 896c3ea + d40c27e
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diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "OceanRobots"
 uuid = "0b51df41-3294-4961-8d23-db645e32016d"
 authors = ["gaelforget <[email protected]>"]
-version = "0.2.3"
+version = "0.2.4"
 
 [deps]
 CFTime = "179af706-886a-5703-950a-314cd64e0468"

diff --git a/README.md b/README.md
@@ -32,7 +32,7 @@ Global Data Coverage | Individual Data Platforms
  <summary> Research Vessels & Ships </summary>
 <p>
 
-👉 [CTD Profiles notebook](https://juliaocean.github.io/OceanRobots.jl/dev/examples/OceanExpedition_CCHDO.html) 👈
+👉 [CTD Profiles notebook](https://juliaocean.github.io/OceanRobots.jl/dev/examples/ShipCruise_CCHDO.html) 👈
 
 </p>
 </details>

diff --git a/docs/make.jl b/docs/make.jl
@@ -28,7 +28,7 @@ makedocs(;
 GliderFiles.check_for_file_Spray("GulfStream.nc")
 GliderFiles.check_for_file_Spray("CUGN_along.nc")
 
-lst=("OceanExpedition_CCHDO.jl","Drifter_CloudDrift.jl","SatelliteAltimetry.jl",
+lst=("ShipCruise_CCHDO.jl","Drifter_CloudDrift.jl","SatelliteAltimetry.jl",
   "Buoy_NWP_NOAA_monthly.jl","Glider_Spray.jl","OceanOPS.jl",
   "Buoy_NWP_NOAA.jl","Mooring_WHOTS.jl","Drifter_GDP.jl","Float_Argo.jl")
 for i in lst

diff --git a/docs/src/examples.md b/docs/src/examples.md
@@ -3,19 +3,17 @@
 !!! note
     The static `html` rendering of the notebooks (this website) lack the interactivity that comes from [Running Examples](@ref) yourself.
 
-## List of Notebooks
-
-The suite of examples includes :
+## Included Notebooks
 
 - [OceanOPS.jl](OceanOPS.html) (➭ [code link](https://raw.githubusercontent.com/JuliaOcean/OceanRobots.jl/master/examples/OceanOPS.jl)) : global ocean observing systems
-- [Buoy\_NWP\_NOAA.jl](Buoy_NWP_NOAA.html) (➭ [code link](https://raw.githubusercontent.com/JuliaOcean/OceanRobots.jl/master/examples/Buoy_NWP_NOAA.jl)) : NOAA [station](https://www.ndbc.noaa.gov/) data (a few days)
-- [Buoy\_NWP\_NOAA\_monthly.jl](Buoy_NWP_NOAA_monthly.html) (➭ [code link](https://raw.githubusercontent.com/JuliaOcean/OceanRobots.jl/master/examples/Buoy_NWP_NOAA_monthly.jl)) : NOAA [station](https://www.ndbc.noaa.gov/) data (monthly means) 
-- [Mooring\_WHOTS.jl](Mooring_WHOTS.html) (➭ [code link](https://raw.githubusercontent.com/JuliaOcean/OceanRobots.jl/master/examples/Mooring_WHOTS.jl)) : WHOTS [mooring](http://www.soest.hawaii.edu/whots/wh_data.html) data
+- [ShipCruise\_CCHDO.jl](ShipCruise_CCHDO.html) (➭ [code link](https://raw.githubusercontent.com/JuliaOcean/OceanRobots.jl/master/examples/ShipCruise_CCHDO.jl)) : [ship](https://cchdo.ucsd.edu) CTD and other data
+- [Float\_Argo.jl](Float_Argo.html) (➭ [code link](https://raw.githubusercontent.com/JuliaOcean/OceanRobots.jl/master/examples/Float_Argo.jl)) : Argo profiling [float](https://argo.ucsd.edu) data
 - [Drifter\_GDP.jl](Drifter_GDP.html) (➭ [code link](https://raw.githubusercontent.com/JuliaOcean/OceanRobots.jl/master/examples/Drifter_GDP.jl)) : [drifter](https://www.aoml.noaa.gov/phod/gdp/hourly_data.php) time series
 - [Drifter\_CloudDrift.jl](Drifter_CloudDrift.html) (➭ [code link](https://github.com/JuliaOcean/OceanRobots.jl/blob/master/examples/Drifter_CloudDrift.jl)) : drifter statistics
-- [Float\_Argo.jl](Float_Argo.html) (➭ [code link](https://raw.githubusercontent.com/JuliaOcean/OceanRobots.jl/master/examples/Float_Argo.jl)) : Argo profiling [float](https://argo.ucsd.edu) data
-- [OceanExpedition\_CCHDO.jl](OceanExpedition_CCHDO.html) (➭ [code link](https://raw.githubusercontent.com/JuliaOcean/OceanRobots.jl/master/examples/OceanExpedition_CCHDO.jl)) : [ship](https://cchdo.ucsd.edu) CTD and other data
 - [Glider\_Spray.jl](Glider_Spray.html) (➭ [code link](https://raw.githubusercontent.com/JuliaOcean/OceanRobots.jl/master/examples/Glider_Spray.jl)) : underwater [glider](http://spraydata.ucsd.edu/projects/) data
+- [Buoy\_NWP\_NOAA.jl](Buoy_NWP_NOAA.html) (➭ [code link](https://raw.githubusercontent.com/JuliaOcean/OceanRobots.jl/master/examples/Buoy_NWP_NOAA.jl)) : NOAA [station](https://www.ndbc.noaa.gov/) data (a few days)
+- [Buoy\_NWP\_NOAA\_monthly.jl](Buoy_NWP_NOAA_monthly.html) (➭ [code link](https://raw.githubusercontent.com/JuliaOcean/OceanRobots.jl/master/examples/Buoy_NWP_NOAA_monthly.jl)) : NOAA [station](https://www.ndbc.noaa.gov/) data (monthly means) 
+- [Mooring\_WHOTS.jl](Mooring_WHOTS.html) (➭ [code link](https://raw.githubusercontent.com/JuliaOcean/OceanRobots.jl/master/examples/Mooring_WHOTS.jl)) : WHOTS [mooring](http://www.soest.hawaii.edu/whots/wh_data.html) data
 - [SatelliteAltimetry.jl](SatelliteAltimetry.html) (➭ [code link](https://raw.githubusercontent.com/JuliaOcean/OceanRobots.jl/master/examples/SatelliteAltimetry.jl)) : gridded satellite data
 
 ## More Notebooks

diff --git a/docs/src/reference.md b/docs/src/reference.md
@@ -34,7 +34,7 @@ plot(argo,pol=pol)
 
 ```@example ex1
 using OceanRobots, CairoMakie
-cruise=OceanExpedition("33RR20160208")
+cruise=ShipCruise("33RR20160208")
 plot(cruise,variable="salinity",colorrange=(33.5,35.0))
 ```
 

diff --git a/examples/Drifter_GDP.jl b/examples/Drifter_GDP.jl
@@ -331,14 +331,14 @@ uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb"
 version = "2.4.2"
 
 [[deps.ConstructionBase]]
-deps = ["LinearAlgebra"]
-git-tree-sha1 = "a33b7ced222c6165f624a3f2b55945fac5a598d9"
+git-tree-sha1 = "76219f1ed5771adbb096743bff43fb5fdd4c1157"
 uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
-version = "1.5.7"
-weakdeps = ["IntervalSets", "StaticArrays"]
+version = "1.5.8"
+weakdeps = ["IntervalSets", "LinearAlgebra", "StaticArrays"]
 
     [deps.ConstructionBase.extensions]
     ConstructionBaseIntervalSetsExt = "IntervalSets"
+    ConstructionBaseLinearAlgebraExt = "LinearAlgebra"
     ConstructionBaseStaticArraysExt = "StaticArrays"
 
 [[deps.Contour]]
@@ -1153,9 +1153,9 @@ version = "0.5.5"
 
 [[deps.OceanRobots]]
 deps = ["CFTime", "CSV", "DataFrames", "DataStructures", "Dataverse", "Dates", "Downloads", "FTPClient", "Glob", "HTTP", "Interpolations", "JSON3", "LightXML", "NCDatasets", "Printf", "Statistics", "URIs"]
-git-tree-sha1 = "cc465516ec877501c515bf04429cec576e0102f2"
+git-tree-sha1 = "70e15a9c6fe33aaf969f91b986dce3383a94c3c2"
 uuid = "0b51df41-3294-4961-8d23-db645e32016d"
-version = "0.2.2"
+version = "0.2.3"
 
     [deps.OceanRobots.extensions]
     OceanRobotsArgoDataExt = ["ArgoData"]

diff --git a/examples/OceanExpedition_CCHDO.jl → examples/ShipCruise_CCHDO.jl b/examples/OceanExpedition_CCHDO.jl → examples/ShipCruise_CCHDO.jl
diff --git a/ext/OceanRobotsMakieExt.jl b/ext/OceanRobotsMakieExt.jl
@@ -316,25 +316,25 @@ function plot_standard(wmo,arr,spd,T_std,S_std; markersize=2,pol=Any[],size=(900
 end
 
 """
-    plot(x::OceanExpedition; 
+    plot(x::ShipCruise; 
 	markersize=6,pol=Any[],colorrange=(2,20),
 	size=(900,600),variable="temperature")
 
 ```
 using OceanRobots, CairoMakie
-x=OceanExpedition("33RR20160208")
+x=ShipCruise("33RR20160208")
 plot(x)
 ```
 """
-function plot(x::OceanExpedition; 
+function plot(x::ShipCruise; 
 	markersize=6,pol=Any[],colorrange=(2,20),
 	size=(900,600),variable="temperature")
 
 	fig=Figure(size=size); ax=Axis(fig[1,1],title="$(variable) from cruise $(x.ID)")
 	if variable=="temperature"||variable=="salinity"
-		list1=findall(occursin.(Ref("_ctd.nc"),x.list_files[:,"filename"]))
-		for f in x.list_files[list1,"filename"]
-			ds=CCHDO.read(f)
+		list1=CCHDO.list_CTD_files(x)		
+		for f in list1
+			ds=CCHDO.NCDatasets.Dataset(f)
 			tim=fill(ds["time"][1],ds.dim["pressure"])
 			depth=-ds["pressure"][:]
 			scatter!(tim,depth,color=ds[variable][:],markersize=markersize,colorrange=colorrange)
@@ -347,10 +347,7 @@ function plot(x::OceanExpedition;
 end
 
 function plot_chi!(x;variable="chi_up",colorrange=(-12.0,-10.0),markersize=3)
-	fil0=basename(CCHDO.ancillary_files(x.ID).chipod)
-	ii=findall(occursin.(Ref(fil0),x.list_files[:,"filename"]))[1]
-	fil1=x.list_files[ii,"filename"]
-	ds=CCHDO.read(fil1)
+	ds=CCHDO.open_chipod_file(x)
 
 	time=permutedims(repeat(ds["time"][:],1,ds.dim["pressure"]))
 	pressure=permutedims(repeat(ds["pressure"][:]',ds.dim["station"],1))

diff --git a/src/OceanRobots.jl b/src/OceanRobots.jl
@@ -16,6 +16,6 @@ include("gridded_data.jl")
 export cmems_sla, podaac_sla
 
 export NOAAbuoy, NOAAbuoy_monthly, ArgoFloat, SurfaceDrifter, Gliders
-export OceanSite, CloudDrift, SeaLevelAnomaly, OceanExpedition
+export OceanSite, CloudDrift, SeaLevelAnomaly, ShipCruise
 
 end # module
diff --git a/src/files.jl b/src/files.jl
@@ -1,7 +1,7 @@
 
 module CCHDO
 
-import Downloads, Dataverse, NCDatasets
+import Downloads, Dataverse, NCDatasets, Glob
 import NCDatasets: Dataset
 
 """
@@ -103,10 +103,14 @@ function ancillary_files(cruise::Union{Symbol,String})
     end
 end
 
-function read(fil)
-    ds=Dataset(fil)
+open_chipod_file(x) = begin
+	fil0=basename(CCHDO.ancillary_files(x.ID).chipod)
+	fil1=joinpath(x.path,fil0)
+	Dataset(fil1)
 end
 
+list_CTD_files(x) = Glob.glob(x.ID*"*_ctd.nc",x.path)
+
 end
 
 

diff --git a/src/types.jl b/src/types.jl
@@ -71,15 +71,13 @@ end
 
 SeaLevelAnomaly() = SeaLevelAnomaly(:unknown,[],"")
 
-Base.@kwdef struct OceanExpedition <: AbstractOceanRobotData
+Base.@kwdef struct ShipCruise <: AbstractOceanRobotData
     ID::String
     data::Union{Array,Dataset}
-    list_files::DataFrame
+    path::String
 end
 
-OceanExpedition(ID::String)=begin
+ShipCruise(ID::String)=begin
     path=CCHDO.download(ID)
-    filenames=joinpath.(Ref(path),readdir(path))
-    list1=DataFrames.DataFrame(:filename=>filenames)
-    OceanExpedition(ID,[],list1)
+    ShipCruise(ID,[],path)
 end
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -113,8 +113,8 @@ using Test
     path=CCHDO.download(ID)
     @test ispath(path)
 
-    cruise=OceanExpedition(ID)
-    @test isa(cruise,OceanExpedition)
+    cruise=ShipCruise(ID)
+    @test isa(cruise,ShipCruise)
 
     fig=plot(cruise)
     @test isa(fig,Figure)