Merge pull request #144 from gaelforget/codecov01

increase code coverage

src/Grids.jl

@@ -286,7 +286,7 @@ function GridLoad(γ=GridSpec(); ID=:default, option=:minimal)
     end
 
     [Γ[ii]=GridLoadVar(ii,gr) for ii in list_n]
-    option=="full"||option=="light" ? GridAddWS!(Γ) : nothing
+    op=="full"||op=="light" ? GridAddWS!(Γ) : nothing
     return Dict_to_NamedTuple(Γ)
 end
 

src/Operations.jl

@@ -483,20 +483,18 @@ function UVtoUEVN(u::MeshArray,v::MeshArray,G::NamedTuple)
     return uC.*G.AngleCS-vC.*G.AngleSN, uC.*G.AngleSN+vC.*G.AngleCS
 end
 
-function UVtoSpeed!(u::MeshArray,v::MeshArray,G::NamedTuple,dD)
-  (u,v)=exch_UV(u,v)
+function UVtoSpeed!(uC::MeshArray,vC::MeshArray,G::NamedTuple,dD)
+  (u,v)=exch_UV(uC,vC)
   for iF=1:u.grid.nFaces
-      for i in 1:size(vC[iF],1)
+    for i in 1:size(vC[iF],1)
       for j in 1:size(vC[iF],2)
-      u0=nanmean(u[iF][i,j],u[iF][i+1,j])
-      v0=nanmean(v[iF][i,j],v[iF][i,j+1])
-      u1=u0*G.AngleCS[iF][i,j]-v0*G.AngleSN[iF][i,j]
-      v1=u0*G.AngleSN[iF][i,j]+v0*G.AngleCS[iF][i,j]
-      dD[iF][i,j]=sqrt(u1^2 + v1^2)
-      #uC[iF][i,j]=u0*G.AngleCS[iF][i,j]-v0*G.AngleSN[iF][i,j]
-      #vC[iF][i,j]=u0*G.AngleSN[iF][i,j]+v0*G.AngleCS[iF][i,j]
-      end
+        u0=nanmean(u[iF][i,j],u[iF][i+1,j])
+        v0=nanmean(v[iF][i,j],v[iF][i,j+1])
+        u1=u0*G.AngleCS[iF][i,j]-v0*G.AngleSN[iF][i,j]
+        v1=u0*G.AngleSN[iF][i,j]+v0*G.AngleCS[iF][i,j]
+        dD[iF][i,j]=sqrt(u1^2 + v1^2)
       end
+    end
   end
 end
 
@@ -553,8 +551,8 @@ function calc_bolus(GM_PsiX,GM_PsiY, Γ)
         bolusU.f[:,k].=(GM_PsiX.f[:,k+1].-GM_PsiX.f[:,k])/Γ.DRF[k];
         bolusV.f[:,k].=(GM_PsiY.f[:,k+1].-GM_PsiY.f[:,k])/Γ.DRF[k];
     end;
-    bolusU.f[:, nr] .= 0. -GM_PsiX.f[:,nr]./Γ.DRF[nr];
-    bolusV.f[:, nr] .= 0. -GM_PsiY.f[:,nr]./Γ.DRF[nr];
+    bolusU.f[:, nr] .= 0*GM_PsiX.f[:,nr] .-GM_PsiX.f[:,nr]./Γ.DRF[nr];
+    bolusV.f[:, nr] .= 0*GM_PsiY.f[:,nr] .-GM_PsiY.f[:,nr]./Γ.DRF[nr];
 
     bolusU=bolusU.*mskW;
     bolusV=bolusV.*mskS;
@@ -568,7 +566,7 @@ function calc_bolus(GM_PsiX,GM_PsiY, Γ)
     for k in 1:nr
         (tmpU,tmpV)=exch_UV(tmp_x[:, k],tmp_y[:, k])
         for a=1:tmpU.grid.nFaces
-            (s1,s2)=size(tmpU.f[a])
+            (s1,s2)=size(tmp_x.f[a])
             tmpU1=view(tmpU.f[a],1:s1,1:s2)
             tmpU2=view(tmpU.f[a],2:s1+1,1:s2)
             tmpV1=view(tmpV.f[a],1:s1,1:s2)

src/Types.jl

@@ -97,7 +97,9 @@ MeshArray=gcmarray
 
 ## Methods that apply to all AbstractMeshArray types
 
-import Base: maximum, minimum, sum, fill, fill!
+import Base: maximum, minimum, extrema, sum, fill, fill!
+
+extrema(a::AbstractMeshArray) = [minimum(a) maximum(a)]
 
 function maximum(a::AbstractMeshArray)
   c=-Inf;

test/Project.toml

@@ -2,7 +2,9 @@
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 DataDeps = "124859b0-ceae-595e-8997-d05f6a7a8dfe"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+GeoJSON = "61d90e0f-e114-555e-ac52-39dfb47a3ef9"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 Proj = "c94c279d-25a6-4763-9509-64d165bea63e"
 Shapefile = "8e980c4a-a4fe-5da2-b3a7-4b4b0353a2f4"
+Suppressor = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

test/runtests.jl

@@ -1,5 +1,5 @@
-using Test, Documenter
-using MeshArrays, DataDeps, CairoMakie, JLD2, Shapefile, Proj
+using Test, Documenter, Suppressor, MeshArrays, CairoMakie
+import DataDeps, JLD2, Shapefile, GeoJSON, Proj
 
 MeshArrays.GRID_LL360_download()
 MeshArrays.GRID_LLC90_download()
@@ -54,12 +54,14 @@ end
     γ=GridSpec("LatLonCap",MeshArrays.GRID_LLC90)
     Tx=γ.read(MeshArrays.GRID_LLC90*"TrspX.bin",MeshArray(γ,Float32))
     Ty=γ.read(MeshArrays.GRID_LLC90*"TrspY.bin",MeshArray(γ,Float32))
-    Γ=GridLoad(γ;option="light")
-
+    Γ=GridLoad(γ;option=:full)
+    plot(Γ.XC)
+
     hFacC=GridLoadVar("hFacC",γ)
     μ=land_mask(hFacC[:,1])
 
     lons=[-68 -63]; lats=[-54 -66]; name="Drake Passage"
+    Trsct=Transect(name,lons,lats,Γ,segment=:long,format=:NamedTuple)
     Trsct=Transect(name,lons,lats,Γ)
 
     #Various vector operations
@@ -71,13 +73,32 @@ end
     UVtoTransport(U,V,Γ)
     UVtoUEVN(U[:,1],V[:,1],Γ)
     curl(U[:,1],V[:,1], merge(Γ,(hFacW=hFacW,hFacS=hFacS,RAZ=RAZ,)) )
+    dD=zeros(γ)
+    MeshArrays.UVtoSpeed!(U[:,1],V[:,1],Γ,dD)
 
     #Meridional transport integral
     uv=Dict("U"=>Tx,"V"=>Ty,"dimensions"=>["x","y"])
     L=-85.0:5.0:85.0; LC=LatitudeCircles(L,Γ,format=:gridpath)
     T=Array{Float64,1}(undef,length(LC))
     [T[i]=1e-6*ThroughFlow(uv,LC[i],Γ) for i=1:length(LC)]
-
+    plot(LC)
+    plot(LC[1])
+
+    x=zeros(γ)
+    fill!(x,1.0)
+    y=fill(-1.0,γ)
+    extrema(y)
+    @test minimum(y)<minimum(x)
+
+    y*ones(3,2)
+    ones(γ)
+    ones(y)
+    zeros(y)
+
+    GM_PsiX=read(randn(90,1170,50),Γ.hFacW)
+    GM_PsiY=read(randn(90,1170,50),Γ.hFacS)
+    bolusU, bolusV, bolusW=MeshArrays.calc_bolus(GM_PsiX,GM_PsiY, Γ)
+
     #See: OceanTransports/helper_functions.jl
     #u,v,uC,vC=rotate_uv(uv,Γ);
 
@@ -115,7 +136,7 @@ end
     MeshArrays.fsize(tmp.f,2)
     size(tmp)
     size(tmp,3)
-    show(tmp)
+    @suppress show(tmp)
 
     x=tmp[1:10,1,1:2]; y=x[2]; x[3]=1.0
     view(x,1:3,:,1)
@@ -136,11 +157,11 @@ end
     size(tmp1)
     tmp1[2]
     view(tmp1,:)
-    show(tmp1)
+    @suppress show(tmp1)
     similar(tmp1)
     #tmp[tmp1]
 
-    show(tmp)
+    @suppress show(tmp)
     MeshArrays.getindexetc(tmp,2)
     MeshArray(γ,tmp.f,meta=tmp.meta)
     MeshArray(γ,meta=tmp.meta)
@@ -197,8 +218,10 @@ end
 	proj=Proj.Transformation(MA_preset=2,lon0=lon0)
     Dint=reshape(Interpolate(D,λ.f,λ.i,λ.j,λ.w),size(λ.lon))
 
-    fil=demo.download_polygons("ne_110m_admin_0_countries.shp")
 #    fil=demo.download_polygons("countries.geojson")
+#    pol=MeshArrays.read_polygons(fil)
+
+    fil=demo.download_polygons("ne_110m_admin_0_countries.shp")
     pol=MeshArrays.read_polygons(fil)
 
     f = Figure()
@@ -210,6 +233,35 @@ end
 	MeshArrays.grid_lines!(pr_ax;color=:lightgreen,linewidth=0.5)
 	f
 
+	meta=(colorrange=(0.0,6000.0),cmap=:BrBG_10,ttl="Ocean Depth (m)",lon0=lon0)
+	data=(lon=λ.lon,lat=λ.lat,var=Dint,meta=meta) #,polygons=pol)
+    plot_examples(:projmap,data,lon0,proj)
+
+end
+
+@testset "nanmath" begin
+    x=[NaN 1 2]
+    nansum(x)
+    nansum(x,1)
+    nanmax(x,2)
+    nanmin(x,2)
+
+    nanmean(NaN,1)
+    nanmean(1,NaN)
+    nanmean(2,1)
+    nanmean(NaN,NaN)
+end
+
+@testset "plotting" begin
+    lon,lat,earth_img=demo.get_basemap()
+    plot_examples(:basemap,lon,lat,earth_img)
+
+    pol_file=demo.download_polygons("ne_110m_admin_0_countries.shp")
+    pol=MeshArrays.read_polygons(pol_file)
+
+    lon0=-160
+    proj=Proj.Transformation(MA_preset=2,lon0=lon0)
+    plot_examples(:baseproj,proj,lon0,pol=pol)
 end
 
 @testset "doctests" begin