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increase code coverage #144

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Sep 15, 2024
Merged

increase code coverage #144

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af7fff4
increase codecov
gaelforget Sep 14, 2024
9c47e76
increase codecov
gaelforget Sep 15, 2024
60fefbe
increase codecov
gaelforget Sep 15, 2024
acbf381
add GeoJSON
gaelforget Sep 15, 2024
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2 changes: 1 addition & 1 deletion src/Grids.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down
26 changes: 12 additions & 14 deletions src/Operations.jl
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Expand Up @@ -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

Expand Down Expand Up @@ -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;
Expand All @@ -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)
Expand Down
4 changes: 3 additions & 1 deletion src/Types.jl
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Expand Up @@ -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;
Expand Down
2 changes: 2 additions & 0 deletions test/Project.toml
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Expand Up @@ -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"
70 changes: 61 additions & 9 deletions test/runtests.jl
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Original file line number Diff line number Diff line change
@@ -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()
Expand Down Expand Up @@ -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
Expand All @@ -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);

Expand Down Expand Up @@ -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)
Expand All @@ -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)
Expand Down Expand Up @@ -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()
Expand All @@ -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
Expand Down
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