From 274e8526fd7a5e79f8e4e4820d140b9388d6a848 Mon Sep 17 00:00:00 2001
From: Benoit Pasquier <briochemc@gmail.com>
Date: Tue, 25 Jun 2024 15:05:23 +1000
Subject: [PATCH] fix #97

---
 Project.toml                      |  2 +-
 docs/lit/tutorials/1_ideal_age.jl |  6 +++---
 src/OCIM2_48L.jl                  | 18 +++++++++---------
 test/runtests.jl                  |  2 +-
 4 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/Project.toml b/Project.toml
index 7cd8d42b..3d889c46 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "AIBECS"
 uuid = "ace601d6-714c-11e9-04e5-89b7fad23838"
 authors = ["Benoit Pasquier <briochemc@gmail.com>"]
-version = "0.13.3"
+version = "0.13.4"
 
 [deps]
 Bijectors = "76274a88-744f-5084-9051-94815aaf08c4"
diff --git a/docs/lit/tutorials/1_ideal_age.jl b/docs/lit/tutorials/1_ideal_age.jl
index 2e72107e..48141d58 100644
--- a/docs/lit/tutorials/1_ideal_age.jl
+++ b/docs/lit/tutorials/1_ideal_age.jl
@@ -33,7 +33,7 @@
 #md #     DeVries, T., & Holzer, M. (2019). Radiocarbon and helium isotope constraints on deep ocean ventilation and mantle‐³He sources. Journal of Geophysical Research: Oceans, 124, 3036–3057. doi:[10.1029/2018JC014716](https://doi.org/10.1029/2018JC014716)
 
 using AIBECS
-grd, TOCIM2 = OCIM2.load()
+grd, TOCIM2_48L = OCIM2_48L.load()
 
 #md # !!! note
 #md #     If it's your first time, Julia will ask you to download the OCIM2, in which case you should accept (i.e., type `y` and "return").
@@ -42,7 +42,7 @@ grd, TOCIM2 = OCIM2.load()
 #nb # > If it's your first time, Julia will ask you to download the OCIM2, in which case you should accept (i.e., type `y` and "return").
 #nb # > Once downloaded, AIBECS will remember where it downloaded the file and it will only load it from your laptop.
 
-# `grd` is an `OceanGrid` object containing information about the 3D grid of the OCIM2 circulation and `TOCIM2` is the transport matrix representing advection and diffusion.
+# `grd` is an `OceanGrid` object containing information about the 3D grid of the OCIM2 circulation and `TOCIM2_48L` is the transport matrix representing advection and diffusion.
 
 # The local sources and sinks for the age take the form
 
@@ -75,7 +75,7 @@ p = IdealAgeParameters(1.0, 30.0)
 
 # We now use the AIBECS to generate the state function $\boldsymbol{F}$ (and its Jacobian) via
 
-F = AIBECSFunction(TOCIM2, G)
+F = AIBECSFunction(TOCIM2_48L, G)
 
 # Now that `F` and `p` are defined, we are going to solve for the steady-state.
 # But first, we must create a `SteadyStateProblem` object that contains `F`, `p`, and an initial guess `x_init` for the age.
diff --git a/src/OCIM2_48L.jl b/src/OCIM2_48L.jl
index 927dc71b..762d476f 100644
--- a/src/OCIM2_48L.jl
+++ b/src/OCIM2_48L.jl
@@ -94,17 +94,17 @@ function load()
     # Create grid object from NetCDF file variables
     # TODO: Add Hyrothermal He fluxes as for the OCIM2 load function
     grid = Dataset(joinpath(files_path, "OCIM2_48L_base_data.nc"), "r") do ds
-        wet3D = ds["ocnmask"][:] .== 1
+        wet3D = Array(ds["ocnmask"]) .== 1
         nlat, nlon, ndepth = size(wet3D)
-        lat_3D = ds["tlat"][:]°
-        lon_3D = ds["tlon"][:]°
-        depth_3D = ds["tz"][:]m
+        lat_3D = Array(ds["tlat"])°
+        lon_3D = Array(ds["tlon"])°
+        depth_3D = Array(ds["tz"])m
         lat = unique(lat_3D)
         lon = unique(lon_3D)
         depth = unique(depth_3D)
-        ulat = unique(ds["ulon"][:])° # ulat↔ulon in OCIM2-48L original files
-        ulon = unique(ds["ulat"][:])° # ulat↔ulon in OCIM2-48L original files
-        depth_top_3D = ds["wz"][:]m
+        ulat = unique(Array(ds["ulon"]))° # ulat↔ulon in OCIM2-48L original files
+        ulon = unique(Array(ds["ulat"]))° # ulat↔ulon in OCIM2-48L original files
+        depth_top_3D = Array(ds["wz"])m
         depth_top = unique(depth_top_3D)
         δlat = 2(ulat - lat)
         δlon = 2(ulon - lon)
@@ -112,9 +112,9 @@ function load()
         R = 6371.0km
         δy = R * δlat ./ 360°
         δy_3D = repeat(reshape(δy, (nlat,1,1)), outer=(1,nlon,ndepth))
-        A_3D = ds["area"][:]m^2
+        A_3D = Array(ds["area"])m^2
         δx_3D = A_3D ./ δy_3D
-        volume_3D = ds["vol"]m^3
+        volume_3D = Array(ds["vol"])m^3
         δz_3D = volume_3D ./ A_3D
         A_2D = A_3D[:,:,1]
         nboxes = count(wet3D)
diff --git a/test/runtests.jl b/test/runtests.jl
index 5451f44c..06778fbd 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -16,7 +16,7 @@ using Plots
 # For CI, make sure the downloads do not hang
 ENV["DATADEPS_ALWAYS_ACCEPT"] = true
 
-test_setup_only = [:OCIM1, :OCIM0, :OCCA]
+test_setup_only = [:OCIM2_48L, :OCIM1, :OCIM0, :OCCA]
 # Using `include` evaluates at global scope,
 # so `Circulation` must be changed at the global scope too.
 # This is why there is an `eval` in the for loop(s) below