V0p3p11a

.github/workflows/DeployPage.yml

@@ -3,7 +3,7 @@ on:
   push:
     branches:
       - master
-      - v0p3p10d
+      - v0p3p11a
 jobs:
   build-and-deploy:
     runs-on: ubuntu-latest

.github/workflows/binder.yaml

@@ -3,7 +3,7 @@ on:
   push:
     branches:
       - master
-      - v0p3p10a
+      - v0p3p11a
 jobs:
   binder:
     runs-on: ubuntu-latest

Dockerfile

@@ -11,6 +11,7 @@ USER ${NB_USER}
 
 COPY --chown=${NB_USER}:users ./plutoserver ./plutoserver
 COPY --chown=${NB_USER}:users ./sysimage ./sysimage
+COPY --chown=${NB_USER}:users ./tutorials ./tutorials
 
 RUN cp ./sysimage/environment.yml ./environment.yml
 RUN cp ./sysimage/setup.py ./setup.py

binder/Dockerfile

@@ -1,2 +1,2 @@
 ### DO NOT EDIT THIS FILE! This Is Automatically Generated And Will Be Overwritten ###
-FROM gaelforget/notebooks:1bd00887b14d
+FROM gaelforget/notebooks:d76e1ed15de3

page/index.md

@@ -154,10 +154,10 @@ In this section, we provide additional representative examples that cover common
 
 Notebooks below were presented as part of the JuliaCon 2021 Workshop on `Modeling Marine Ecosystems At Multiple Scales Using Julia`. More detail is available in the [workshop repository](https://github.com/JuliaOcean/MarineEcosystemsJuliaCon2021.jl).
 
-- [AIBECSExample](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/AIBECSExample.html) ([notebook url](https://github.com/JuliaOcean/MarineEcosystemsJuliaCon2021.jl/blob/main/AIBECSExample.jl)) : global steady-state biogeochemistry and gridded transport models that run fast for long time scales (centuries or even millennia).
-- [PlanktonIndividualExample](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/PlanktonIndividualExample.html) ([notebook url](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/PlanktonIndividualExample.jl))  local to global agent-based model, particularly suited to study microbial communities, plankton physiology, and nutrient cycles.
-- [MITgcm\_tutorial\_global\_oce\_biogeo](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/MITgcm_tutorial_global_oce_biogeo.html) ([notebook url](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/MITgcm_tutorial_global_oce_biogeo.jl)) : interface to full-featured, Fortran-based, general circulation model and its output (transports, chemistry, ecology, ocean, sea-ice, atmosphere, and more).
-- [IndividualDisplacementsExample](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/IndividualDisplacementsExample.html) ([notebook url](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/IndividualDisplacementsExample.jl)) : local to global particle tracking, for simulating dispersion, connectivity, transports in the ocean or atmosphere, etc.
+- [AIBECS](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/AIBECSExample.html) ([notebook url](https://raw.githubusercontent.com/JuliaOcean/MarineEcosystemsJuliaCon2021.jl/main/src/AIBECSExample.jl)) : global steady-state biogeochemistry and gridded transport models that run fast for long time scales (centuries or even millennia).
+- [PlanktonIndividuals](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/PlanktonIndividualExample.html) ([notebook url](https://raw.githubusercontent.com/JuliaOcean/MarineEcosystemsJuliaCon2021.jl/main/src/PlanktonIndividualExample.jl))  local to global agent-based model, particularly suited to study microbial communities, plankton physiology, and nutrient cycles.
+- [MITgcm global biogeo](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/MITgcm_tutorial_global_oce_biogeo.html) ([notebook url](https://raw.githubusercontent.com/JuliaOcean/MarineEcosystemsJuliaCon2021.jl/main/src/MITgcm_tutorial_global_oce_biogeo.jl)) : interface to full-featured, Fortran-based, general circulation model and its output (transports, chemistry, ecology, ocean, sea-ice, atmosphere, and more).
+- [IndividualDisplacements](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/IndividualDisplacementsExample.html) ([notebook url](https://raw.githubusercontent.com/JuliaOcean/MarineEcosystemsJuliaCon2021.jl/main/src/IndividualDisplacementsExample.jl)) : local to global particle tracking, for simulating dispersion, connectivity, transports in the ocean or atmosphere, etc.
 
 \end{section}
 

sysimage/download_stuff.jl

@@ -11,4 +11,9 @@ OceanStateEstimation.Downloads.download(
   joinpath(OceanStateEstimation.ECCOdiags_path,"interp_coeffs_halfdeg.jld2");
   timeout=60000.0)
 
+include("../tutorials/list_notebooks.jl")
+notebooks=list_notebooks()
+download_notebooks("notebooks",notebooks)
+
+
 

tutorials/list_notebooks.jl

@@ -0,0 +1,46 @@
+
+using DataFrames, Downloads
+
+function list_notebooks()
+    fil=Downloads.download("https://raw.githubusercontent.com/JuliaClimate/Notebooks/master/page/index.md")
+
+    lines=readlines(fil);
+    ii=findall( occursin.("[notebook url]",lines) )
+    lines=lines[ii]
+
+    sources=["gaelforget" "JuliaClimate" "JuliaOcean" "MarineEcosystemsJuliaCon2021.jl"]
+    notebooks=DataFrame("folder" => [], "file" => [], "url" => [])
+
+    for ii in lines
+        tmp1=split(ii,"(")
+        ii=findall( occursin.("[notebook url]",tmp1) )[1]
+        tmp1=tmp1[ii+1]
+        tmp1=split(tmp1,")")[1]
+
+        tmp2=split(tmp1,"/")
+        test=sum(tmp2[4].==sources)
+        if test!==1
+            println("Skipping : ")
+            println(tmp1)
+        end
+
+        push!(notebooks, (tmp2[5], tmp2[end], string(tmp1) ))
+    end
+
+    notebooks
+end
+
+function download_notebooks(path,notebooks)
+    !isdir(path) ? mkdir(path) : nothing
+    for i in 1:size(notebooks,1)
+        tmp1=joinpath(path,notebooks[i,:folder])
+        !isdir(tmp1) ? mkdir(tmp1) : nothing
+        tmp2=joinpath(tmp1,notebooks[i,:file])
+        try
+            Downloads.download(notebooks[i,:url],tmp2)
+        catch e
+            println("Skipping : ")
+            println(tmp2)
+        end
+    end
+end