JOSS paper (#87)

* JOSS paper * Fix tests (updated WOA API) * Fix SciML API (no Val{:jac}) * Fix #88
JuliaOcean · Dec 10, 2021 · 382b4dd · 382b4dd · briochemc · Dec 10, 2021
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diff --git a/Project.toml b/Project.toml
@@ -1,15 +1,14 @@
 name = "AIBECS"
 uuid = "ace601d6-714c-11e9-04e5-89b7fad23838"
 authors = ["Benoit Pasquier <[email protected]>"]
-version = "0.11.0"
+version = "0.11.1"
 
 [deps]
 Bijectors = "76274a88-744f-5084-9051-94815aaf08c4"
 CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
 DataDeps = "124859b0-ceae-595e-8997-d05f6a7a8dfe"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
-DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
@@ -27,6 +26,7 @@ OceanGrids = "cfe838f4-859f-11e9-2ea1-df7d4e7c3537"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
+SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 Shapefile = "8e980c4a-a4fe-5da2-b3a7-4b4b0353a2f4"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StringDistances = "88034a9c-02f8-509d-84a9-84ec65e18404"
@@ -40,7 +40,6 @@ Bijectors = "0.8, 0.9"
 CodecZlib = "0.7"
 DataDeps = "0.7"
 DataFrames = "0.20, 0.21, 0.22, 1.0"
-DiffEqBase = "6"
 Distances = "0.9, 0.10"
 Distributions = "0.23, 0.24, 0.25"
 FieldMetadata = "0.3"
@@ -55,6 +54,7 @@ NearestNeighbors = "0.4"
 OceanGrids = "0.4"
 RecipesBase = "1"
 Reexport = "0.2, 1.0"
+SciMLBase = "1"
 Shapefile = "0.6, 0.7"
 StringDistances = "0.10, 0.11"
 UnPack = "1"

diff --git a/docs/lit/howtos/1_parameters.jl b/docs/lit/howtos/1_parameters.jl
@@ -5,6 +5,11 @@
 #md # [![](https://mybinder.org/badge_logo.svg)](@__BINDER_ROOT_URL__/notebooks/1_parameters.ipynb)
 #md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/notebooks/1_parameters.ipynb)
 
+#md # !!! note
+#md #     All the AIBECS tutorials and how-to guides are available as Jupyter notebooks.
+#md #     You can view them with [nbviewer](https://nbviewer.jupyter.org/)or execute them online with [binder](https://mybinder.org/) by clicking on the badges above!
+#md #     (Note that binder can be slow to launch and its memory caps can be a problem when running.)
+
 # Here we will describe the AIBECS interface.
 # This guide will take you through some examples of setting up model parameters.
 

diff --git a/docs/lit/howtos/2_plot.jl b/docs/lit/howtos/2_plot.jl
@@ -6,6 +6,10 @@
 #md # [![](https://mybinder.org/badge_logo.svg)](@__BINDER_ROOT_URL__/notebooks/2_plot.ipynb)
 #md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/notebooks/2_plot.ipynb)
 
+#md # !!! note
+#md #     All the AIBECS tutorials and how-to guides are available as Jupyter notebooks.
+#md #     You can view them with [nbviewer](https://nbviewer.jupyter.org/)or execute them online with [binder](https://mybinder.org/) by clicking on the badges above!
+#md #     (Note that binder can be slow to launch and its memory caps can be a problem when running.)
 
 # This guide is organized as follows
 # - [Horizontal maps](@ref horizontal-plots)

diff --git a/docs/lit/howtos/3_cruiseplot.jl b/docs/lit/howtos/3_cruiseplot.jl
@@ -5,6 +5,10 @@
 #md # [![](https://mybinder.org/badge_logo.svg)](@__BINDER_ROOT_URL__/notebooks/3_cruiseplot.ipynb)
 #md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/notebooks/3_cruiseplot.ipynb)
 
+#md # !!! note
+#md #     All the AIBECS tutorials and how-to guides are available as Jupyter notebooks.
+#md #     You can view them with [nbviewer](https://nbviewer.jupyter.org/)or execute them online with [binder](https://mybinder.org/) by clicking on the badges above!
+#md #     (Note that binder can be slow to launch and its memory caps can be a problem when running.)
 
 # This guide follows the [basic plotting guide](@ref plots) and its goal is to plot data related to oceanographic observations from cruise expeditions.
 # In this walkthrough, we will

diff --git a/docs/lit/howtos/4_fluxes.jl b/docs/lit/howtos/4_fluxes.jl
@@ -5,6 +5,11 @@
 #md # [![](https://mybinder.org/badge_logo.svg)](@__BINDER_ROOT_URL__/notebooks/4_fluxes.ipynb)
 #md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/notebooks/4_fluxes.ipynb)
 
+#md # !!! note
+#md #     All the AIBECS tutorials and how-to guides are available as Jupyter notebooks.
+#md #     You can view them with [nbviewer](https://nbviewer.jupyter.org/)or execute them online with [binder](https://mybinder.org/) by clicking on the badges above!
+#md #     (Note that binder can be slow to launch and its memory caps can be a problem when running.)
+
 # This will take you through the process of extracting flux information from a given transport operator.
 # It is split into 3 parts
 # 1. [Figure out the stencil of the operator](@ref operatorstencil)

diff --git a/docs/lit/tutorials/1_ideal_age.jl b/docs/lit/tutorials/1_ideal_age.jl
@@ -8,7 +8,8 @@
 
 #md # !!! note
 #md #     All the AIBECS tutorials and how-to guides are available as Jupyter notebooks.
-#md #     You can execute them online with [binder](https://mybinder.org/) or just view them with [nbviewer](https://nbviewer.jupyter.org/) by clicking on the badges above!
+#md #     You can view them with [nbviewer](https://nbviewer.jupyter.org/)or execute them online with [binder](https://mybinder.org/) by clicking on the badges above!
+#md #     (Note that binder can be slow to launch and its memory caps can be a problem when running.)
 
 # The tracer equation for the ideal age is
 #
@@ -86,7 +87,7 @@ F = AIBECSFunction(TOCIM2, 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.
-# (`SteadyStateProblem` comes from [DiffEqBase](https://github.com/JuliaDiffEq/DiffEqBase.jl).)
+# (`SteadyStateProblem` comes from [SciMLBase](https://github.com/JuliaDiffEq/SciMLBase.jl).)
 
 # Let's make a vector of 0's for our initial guess.
 

diff --git a/docs/lit/tutorials/2_radiocarbon.jl b/docs/lit/tutorials/2_radiocarbon.jl
@@ -6,6 +6,11 @@
 #md # [![](https://mybinder.org/badge_logo.svg)](@__BINDER_ROOT_URL__/notebooks/2_radiocarbon.ipynb)
 #md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/notebooks/2_radiocarbon.ipynb)
 
+#md # !!! note
+#md #     All the AIBECS tutorials and how-to guides are available as Jupyter notebooks.
+#md #     You can view them with [nbviewer](https://nbviewer.jupyter.org/)or execute them online with [binder](https://mybinder.org/) by clicking on the badges above!
+#md #     (Note that binder can be slow to launch and its memory caps can be a problem when running.)
+
 # In this tutorial, we will simulate the radiocarbon age using the AIBECS by
 # 1. defining the transport `T(p)` and the sources and sinks `G(x,p)`,
 # 1. defining the parameters `p`,

diff --git a/docs/lit/tutorials/3_Pmodel.jl b/docs/lit/tutorials/3_Pmodel.jl
@@ -6,6 +6,11 @@
 #md # [![](https://mybinder.org/badge_logo.svg)](@__BINDER_ROOT_URL__/notebooks/3_Pmodel.ipynb)
 #md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/notebooks/3_Pmodel.ipynb)
 
+#md # !!! note
+#md #     All the AIBECS tutorials and how-to guides are available as Jupyter notebooks.
+#md #     You can view them with [nbviewer](https://nbviewer.jupyter.org/)or execute them online with [binder](https://mybinder.org/) by clicking on the badges above!
+#md #     (Note that binder can be slow to launch and its memory caps can be a problem when running.)
+
 # In this tutorial we will explicitly simulate 2 tracers whose distributions control and feed back on each other.
 
 # We consider a simple model for the cycling of phosphorus with 2 state variables consisting of phosphate (PO₄) AKA dissolved inorganic phosphorus (DIP) and particulate organic phosphorus (POP).

diff --git a/docs/lit/tutorials/4_dustmodel.jl b/docs/lit/tutorials/4_dustmodel.jl
@@ -6,6 +6,11 @@
 #md # [![](https://mybinder.org/badge_logo.svg)](@__BINDER_ROOT_URL__/notebooks/4_dustmodel.ipynb)
 #md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/notebooks/4_dustmodel.ipynb)
 
+#md # !!! note
+#md #     All the AIBECS tutorials and how-to guides are available as Jupyter notebooks.
+#md #     You can view them with [nbviewer](https://nbviewer.jupyter.org/)or execute them online with [binder](https://mybinder.org/) by clicking on the badges above!
+#md #     (Note that binder can be slow to launch and its memory caps can be a problem when running.)
+
 # In this tutorial we will simulate particles of dust that graviationally settle.
 # 2D maps of dust deposition are available from within the AIBECS.
 # To use these, we will convert them into sources in the top layer of the model grid.

diff --git a/docs/lit/tutorials/5_river_discharge.jl b/docs/lit/tutorials/5_river_discharge.jl
@@ -6,6 +6,11 @@
 #md # [![](https://mybinder.org/badge_logo.svg)](@__BINDER_ROOT_URL__/notebooks/5_river_discharge.ipynb)
 #md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/notebooks/5_river_discharge.ipynb)
 
+#md # !!! note
+#md #     All the AIBECS tutorials and how-to guides are available as Jupyter notebooks.
+#md #     You can view them with [nbviewer](https://nbviewer.jupyter.org/)or execute them online with [binder](https://mybinder.org/) by clicking on the badges above!
+#md #     (Note that binder can be slow to launch and its memory caps can be a problem when running.)
+
 # In this tutorial we will simulate a fictitious radioactive tracer that is injected into the ocean by the 200 largest rivers (by estimated discharge).
 # The 200 major rivers dataset from [*Dai and Trenberth* (2002)](https://rda.ucar.edu/datasets/ds551.0/) is available from within the AIBECS.
 # Once "born", our ficitious tracer decays with a parameter timescale $\tau$ as it flows through ocean basins.

diff --git a/docs/lit/tutorials/6_groundwater_discharge.jl b/docs/lit/tutorials/6_groundwater_discharge.jl
@@ -6,6 +6,11 @@
 #md # [![](https://mybinder.org/badge_logo.svg)](@__BINDER_ROOT_URL__/notebooks/6_groundwater_discharge.ipynb)
 #md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/notebooks/6_groundwater_discharge.ipynb)
 
+#md # !!! note
+#md #     All the AIBECS tutorials and how-to guides are available as Jupyter notebooks.
+#md #     You can view them with [nbviewer](https://nbviewer.jupyter.org/)or execute them online with [binder](https://mybinder.org/) by clicking on the badges above!
+#md #     (Note that binder can be slow to launch and its memory caps can be a problem when running.)
+
 #md # !!! note
 #md #     This tutorial is very similar to the [river discharge notebook](@id river-discharge)