Merge pull request #18 from gaelforget/Climatology_plus_cmake_bis

Climatology plus cmake bis

.github/workflows/binder.yaml

@@ -3,7 +3,7 @@ on:
   push:
     branches:
       - main
-      - v0p2p2c
+      - Climatology_plus_cmake_bis
 jobs:
   binder:
     runs-on: ubuntu-latest

Dockerfile

@@ -2,7 +2,7 @@ FROM jupyter/base-notebook:latest
 
 USER root
 
-ENV mainpath ./
+ENV mainpath /home/jovyan/
 RUN mkdir -p ${mainpath}
 
 RUN apt-get update
@@ -44,17 +44,14 @@ RUN echo 'alias julia="${mainpath}/.juliaup/bin/julia --project=${mainpath}"' >>
 
 RUN conda config --env --add channels conda-forge
 RUN conda config --env --add channels r
-RUN conda install numpy xarray
-RUN conda install dask pandas
+RUN conda install numpy xarray pandas
 RUN conda install octave_kernel texinfo r-irkernel
 
 RUN curl -fsSL https://install.julialang.org | sh -s -- --yes
 
 RUN ${mainpath}/.juliaup/bin/julia --project=${mainpath} -e "import Pkg; Pkg.instantiate();"
 RUN ${mainpath}/.juliaup/bin/julia --project=${mainpath} ${mainpath}/src/warmup.jl
 
-ENV MPI_INC_DIR /usr/lib/x86_64-linux-gnu/openmpi/include
-
 RUN jupyter lab build && \
     jupyter lab clean && \
     pip install ${mainpath} --no-cache-dir && \

binder/Dockerfile

@@ -1,2 +1,2 @@
 ### DO NOT EDIT THIS FILE! This Is Automatically Generated And Will Be Overwritten ###
-FROM gaelforget/ecco-docker:a2bcb0725279
+FROM gaelforget/ecco-docker:f8dc82b8e5d3

src/warmup.jl

@@ -1,23 +1,27 @@
 using Pluto, CairoMakie, Downloads, IJulia, Pkg
 
-import MITgcm, OceanStateEstimation
-import MITgcm.ClimateModels
-import MITgcm.MeshArrays
-using MITgcm.ClimateModels.Git
+import MITgcm, Climatology
+import MITgcm.ClimateModels, MITgcm.MeshArrays
+import MITgcm.ClimateModels.git
+
+ENV["DATADEPS_ALWAYS_ACCEPT"]=true
+MITgcm.set_environment_variables_to_default()
 
 ##
 
 p0=pathof(MITgcm)
 fil=joinpath(dirname(p0),"..","examples","configurations","OCCA2.toml")
 MC=MITgcm.MITgcm_config(inputs=MITgcm.read_toml(fil))
+push!(MC.inputs[:setup][:main],(:input_folder => tempname()))
 ClimateModels.setup(MC)
 ClimateModels.build(MC)
 
 cp(joinpath(dirname(p0),"..","examples","configurations","ECCO4.toml"),"src/ECCO4.toml")
 cp(joinpath(dirname(p0),"..","examples","configurations","OCCA2.toml"),"src/OCCA2.toml")
 cp(joinpath(MC,"MITgcm/mysetups/ECCOv4/input/download_files.jl"),"src/download_files.jl")
 
-mv(joinpath(MC,"MITgcm/mysetups/ECCOv4/build/mitgcmuv"),"src/mitgcmuv")
+f=joinpath(MC,"MITgcm/mysetups/ECCOv4/build/mitgcmuv")
+isfile(f) ? mv(f,"src/mitgcmuv") : println("mitgcmuv not found")
 rm(pathof(MC),recursive=true)
 
 ##
@@ -29,18 +33,19 @@ ClimateModels.launch(tmp)
 ##
 
 MeshArrays.GRID_LLC90_download()
-OceanStateEstimation.ECCOdiags_add("release2")
-OceanStateEstimation.ECCOdiags_add("release4")
+
+Climatology.ECCOdiags_add("release2")
+#Climatology.ECCOdiags_add("release4")
 
 Downloads.download(
   "https://zenodo.org/record/5784905/files/interp_coeffs_halfdeg.jld2",
-  joinpath(OceanStateEstimation.ScratchSpaces.ECCO,"interp_coeffs_halfdeg.jld2");
+  joinpath(Climatology.ScratchSpaces.ECCO,"interp_coeffs_halfdeg.jld2");
   timeout=60000.0)
 
 ##
 
-pth=joinpath(ENV["HOME"],"src","OceanStateEstimation.jl")
-run(`$(git()) clone https://github.com/gaelforget/OceanStateEstimation.jl $pth`)
+pth=joinpath(ENV["HOME"],"src","Climatology.jl")
+run(`$(git()) clone https://github.com/JuliaOcean/Climatology.jl $pth`)
 nb=joinpath(pth,"examples/ECCO/ECCO_standard_plots.jl")
 Pluto.activate_notebook_environment(nb)
 Pkg.instantiate()