Merge pull request #58 from gaelforget/v0p2p20

V0p2p20

.github/workflows/ci.yml

@@ -0,0 +1,69 @@
+name: CI
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+    tags: '*'
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.6' # Replace this with the minimum Julia version that your package supports. E.g. if your package requires Julia 1.5 or higher, change this to '1.5'.
+          - '1' # Leave this line unchanged. '1' will automatically expand to the latest stable 1.x release of Julia.
+          - 'nightly'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
+      - run: julia --project=docs docs/make.jl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+          GKSwstype: "100" # https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+

Project.toml

@@ -1,10 +1,11 @@
 name = "MeshArrays"
 uuid = "cb8c808f-1acf-59a3-9d2b-6e38d009f683"
 authors = ["gaelforget <[email protected]>"]
-version = "0.2.19"
+version = "0.2.20"
 
 [deps]
 CatViews = "81a5f4ea-a946-549a-aa7e-2a7f63a27d31"
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"

README.md

@@ -1,7 +1,6 @@
 # MeshArrays.jl
 
-
-[![Travis Build Status](https://travis-ci.com/juliaclimate/MeshArrays.jl.svg?branch=master)](https://travis-ci.com/juliaclimate/MeshArrays.jl)
+[![CI](https://github.com/juliaclimate/MeshArrays.jl/actions/workflows/ci.yml/badge.svg)](https://github.com/juliaclimate/MeshArrays.jl/actions/workflows/ci.yml)
 [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliaclimate.github.io/MeshArrays.jl/stable)
 [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliaclimate.github.io/MeshArrays.jl/dev)
 [![codecov](https://codecov.io/gh/juliaclimate/MeshArrays.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/juliaclimate/MeshArrays.jl)

src/Grids.jl

@@ -35,7 +35,7 @@ function simple_periodic_domain(np::Integer,nq=missing)
     list_p=(pc,pg,pc,pg,pc,pu,pv,pg,pu,pv,pv,pu,pc,fill(0.5,3),[0.,0.5,0.5],[0.5,0.,0.5])
     for ii=1:length(list_n);
         tmp1=fill(1.,np,nq*nFaces);
-        m=varmeta(list_u[ii],list_p[ii],list_n[ii],list_n[ii]);
+        m=varmeta(list_u[ii],list_p[ii],missing,list_n[ii],list_n[ii]);
         tmp1=γ.read(tmp1,MeshArray(γ,Float64;meta=m));
         tmp2=Symbol(list_n[ii]);
         @eval (($tmp2) = ($tmp1))
@@ -164,7 +164,7 @@ function GridLoad(γ::gcmgrid)
     end
 
     for ii=1:length(list_n)
-        m=varmeta(list_u[ii],list_p[ii],list_n[ii],list_n[ii])
+        m=varmeta(list_u[ii],list_p[ii],missing,list_n[ii],list_n[ii])
         tmp1=γ.read(joinpath(γ.path,list_n[ii]*".data"),MeshArray(γ,γ.ioPrec;meta=m))
         tmp2=Symbol(list_n[ii])
         @eval (($tmp2) = ($tmp1))
@@ -196,7 +196,7 @@ function GridLoad(γ::gcmgrid)
     list_p=(fill(0.5,3),[0.,0.5,0.5],[0.5,0.,0.5])
     n3=length(Γ["RC"])
     for ii=1:length(list_n)
-        m=varmeta(list_u[ii],list_p[ii],list_n[ii],list_n[ii]);
+        m=varmeta(list_u[ii],list_p[ii],missing,list_n[ii],list_n[ii]);
         tmp1=γ.read(joinpath(γ.path,list_n[ii]*".data"),MeshArray(γ,γ.ioPrec,n3;meta=m))
         tmp2=Symbol(list_n[ii])
         @eval (($tmp2) = ($tmp1))
@@ -247,7 +247,7 @@ function GridOfOnes(grTp,nF,nP)
     list_p=(pc,pg,pc,pg,pc,pu,pv,pg,pu,pv,pv,pu,pc,fill(0.5,3),[0.,0.5,0.5],[0.5,0.,0.5])
 
     for ii=1:length(list_n);
-        tmp1=fill(1.,nP,nP*nF); m=varmeta(list_u[ii],list_p[ii],list_n[ii],list_n[ii]);
+        tmp1=fill(1.,nP,nP*nF); m=varmeta(list_u[ii],list_p[ii],missing,list_n[ii],list_n[ii]);
         tmp1=γ.read(tmp1,MeshArray(γ,Float64;meta=m));
         tmp2=Symbol(list_n[ii]);
         @eval (($tmp2) = ($tmp1))
@@ -343,10 +343,10 @@ function GridAddWS!(Γ::Dict)
     uX=XC.meta.unit
     uY=YC.meta.unit
 
-    XW=MeshArrays.gcmarray(XC.grid,eltype(XC);meta=varmeta(uX,[0.,0.5],"XW","XW"))
-    YW=MeshArrays.gcmarray(XC.grid,eltype(XC);meta=varmeta(uY,[0.,0.5],"YW","YW"))
-    XS=MeshArrays.gcmarray(XC.grid,eltype(XC);meta=varmeta(uX,[0.5,0.],"XS","XS"))
-    YS=MeshArrays.gcmarray(XC.grid,eltype(XC);meta=varmeta(uY,[0.5,0.],"YS","YS"))
+    XW=MeshArrays.gcmarray(XC.grid,eltype(XC);meta=varmeta(uX,[0.,0.5],missing,"XW","XW"))
+    YW=MeshArrays.gcmarray(XC.grid,eltype(XC);meta=varmeta(uY,[0.,0.5],missing,"YW","YW"))
+    XS=MeshArrays.gcmarray(XC.grid,eltype(XC);meta=varmeta(uX,[0.5,0.],missing,"XS","XS"))
+    YS=MeshArrays.gcmarray(XC.grid,eltype(XC);meta=varmeta(uY,[0.5,0.],missing,"YS","YS"))
 
     for ff=1:nFaces
         tmp1=XC[ff][1:end-2,2:end-1]

src/Type_gcmarray.jl

@@ -19,6 +19,8 @@ gcmarray(grid::gcmgrid)
 gcmarray(grid::gcmgrid,::Type{T})
 gcmarray(grid::gcmgrid,::Type{T},n3::Int)
 gcmarray(grid::gcmgrid,::Type{T},n3::Int,n4::Int)
+
+gcmarray(A::Array{T,N};meta::varmeta=defaultmeta)
 ```
 """
 struct gcmarray{T, N, AT} <: AbstractMeshArray{T, N}
@@ -30,6 +32,21 @@ struct gcmarray{T, N, AT} <: AbstractMeshArray{T, N}
    version::String
 end
 
+function gcmarray(A::Array{T,N};
+  meta::varmeta=defaultmeta) where {T, N}
+  s=size(A)[1:2]
+  fs=Array{NTuple{2, Int},1}(undef,1)
+  fs[1]=s
+  ios=[s[1] s[2]]
+  γ=gcmgrid("","PeriodicDomain",1, fs, ios, T, read, write)
+  if N==2
+    B=γ.read(A,gcmarray(γ,T;meta=meta));
+  else
+    B=γ.read(A,gcmarray(γ,T,size(A)[3];meta=meta));
+  end
+  B
+end
+
 function gcmarray(grid::gcmgrid,f::OuterArray{InnerArray{T,2},N};
                   meta::varmeta=defaultmeta) where {T, N}
   gcmarray{T,N,InnerArray{T,2}}(grid,meta,f,grid.fSize,collect(1:grid.nFaces),thisversion)

src/Types.jl

@@ -1,5 +1,5 @@
 
-using Unitful
+using Unitful, Dates
 
 """
     AbstractMeshArray{T, N}
@@ -36,28 +36,30 @@ end
     varmeta
 
 varmeta data structure. By default, `unit` is `1.0` (non-dimensional), `position`
-is `fill(0.5,3)` (cell center), and `name` / `long_name` is unknown.
+is `fill(0.5,3)` (cell center), time is missing, and `name` / `long_name` is unknown.
 
 Available constructors:
 
 ```
-varmeta(unit::Union{Unitful.AbstractQuantity,Number},position::Array{Float64,1},
-        name::String,long_name::String)
+varmeta(unit::Union{Unitful.Units,Number,Missing},position::Array{Float64,1},
+        time::Union{DateTime,Missing,Array{DateTime,1}},name::String,long_name::String)
 ```
 
 And:
 
-```defaultmeta = varmeta(1.0,fill(0.5,3),"unknown","unknown")```
+```defaultmeta = varmeta(missing,fill(0.5,3),missing,"unknown","unknown")```
 
 """
 struct varmeta
   unit::Union{Unitful.Units,Number,Missing}
   position::Array{Float64,1}
+  time::Union{DateTime,Missing,Array{DateTime,1}}
   name::String
   long_name::String
+  #time? format?
 end
 
-defaultmeta = varmeta(missing,fill(0.5,3),"unknown","unknown")
+defaultmeta = varmeta(missing,fill(0.5,3),missing,"unknown","unknown")
 
 ## concrete types and MeshArray alias: