Add JRA55 references + fix Edson stability function latex rendering in docstring (#536)

* add ETOPO

* better latex rendering

* add JRA55 refs

Author: navidcy

docs/climaocean.bib

@@ -29,3 +29,23 @@ @article{nishizawa2018surface
   doi = {10.1029/2018MS001534},
   year = {2018}
 }
+
+@article{stewart2020jra55,
+  title={{JRA55-do-based} repeat year forcing datasets for driving ocean--sea-ice models},
+  author={Stewart, K D and Kim, W M and Urakawa, S and Hogg, A McC and Yeager, S and Tsujino, H and Nakano, H and Kiss, A E and Danabasoglu, G},
+  journal={Ocean Modelling},
+  volume={147},
+  pages={101557},
+  year={2020},
+  doi={10.1016/j.ocemod.2019.101557}
+}
+
+@article{tsujino2018jra,
+  title={JRA-55 based surface dataset for driving ocean--sea-ice models (JRA55-do)},
+  author={Tsujino, H and Urakawa, S and Nakano, H and Small, R J and Kim, W M and Yeager, S G and Danabasoglu, G and Suzuki, T and Bamber, J L and Bentsen, M and and B{\"o}ning, C and Bozec, A and Chassignet, E and Curchitser, E and Dias, F and Durack, P J and Griffies, S M and Harada, Y and Ilicak, M and Josey, S A and Kobayashi, C and Kobayashi, S and Komuro, Y and Large, W G and Sommer, J and Marsland, S J and Masina, S and Scheinert, M and Tomita, H and ValRdivieso, M and Yamazaki, D},
+  journal={Ocean Modelling},
+  volume={130},
+  pages={79--139},
+  year={2018},
+  doi={10.1016/j.ocemod.2018.07.002}
+}

src/DataWrangling/DataWrangling.jl

@@ -140,7 +140,7 @@ Note: if called by multiple processes via MPI, `download_dataset` should only ru
 Arguments
 =========
 - `metadata`: The metadata specifying the dataset to be downloaded. Available options are metadata for
-              ECCO4, ECCO2, EN4, and JRA55 datasets.
+              ETOPO, ECCO4, ECCO2, EN4, and JRA55 datasets.
 
 !!! info "Credential setup requirements for ECCO datasets"
 

src/DataWrangling/JRA55/JRA55_field_time_series.jl

@@ -81,7 +81,7 @@ Adapt.adapt_structure(to, b::JRA55NetCDFBackend) = JRA55NetCDFBackend(b.start, b
 """
     JRA55NetCDFBackend(length)
 
-Represents a JRA55 FieldTimeSeries backed by JRA55 native .nc files.
+Represents a JRA55 FieldTimeSeries backed by JRA55 native netCDF files.
 """
 JRA55NetCDFBackend(length, metadata::Metadata) = JRA55NetCDFBackend(1, length, metadata)
 JRA55NetCDFBackend(start::Integer, length::Integer) = JRA55NetCDFBackend(start, length, nothing)
@@ -235,9 +235,7 @@ new_backend(b::JRA55NetCDFBackend, start, length) = JRA55NetCDFBackend(start, le
 
 Return a `FieldTimeSeries` containing atmospheric reanalysis data for `variable_name`,
 which describes one of the variables from the Japanese 55-year atmospheric reanalysis
-for driving ocean-sea ice models (JRA55-do). The JRA55-do dataset is described by:
-
-> Tsujino et al. (2018). JRA-55 based surface dataset for driving ocean-sea-ice models (JRA55-do), _Ocean Modelling_, **130(1)**, 79-139
+for driving ocean-sea ice models (JRA55-do). The JRA55-do dataset is described by [tsujino2018jra](@citet).
 
 The `variable_name`s (and their `shortname`s used in the netCDF files) available from the JRA55-do are:
 - `:river_freshwater_flux`              ("friver")
@@ -264,9 +262,7 @@ Keyword arguments
 
   !!! info "Repeat-year forcing"
 
-  For more information about the derivation of the repeat-year forcing dataset, see:
-
-  > Stewart et al. (2020). JRA55-do-based repeat year forcing datasets for driving ocean–sea-ice models, _Ocean Modelling_, **147**, 101557, https://doi.org/10.1016/j.ocemod.2019.101557.
+      For more information about the derivation of the repeat-year forcing dataset, see [stewart2020jra55](@citet).
 
   The repeat year in `RepeatYearJRA55()` corresponds to May 1st, 1990 - April 30th, 1991. However, the
   returned dataset has dates that range from January 1st to December 31st. This implies
@@ -292,7 +288,14 @@ Keyword arguments
 - `backend`: Backend for the `FieldTimeSeries`. The two options are:
   * `InMemory()`: the whole time series is loaded into memory.
   * `JRA55NetCDFBackend(total_time_instances_in_memory)`: only a subset of the time series
-  is loaded into memory. Default: `InMemory()`.
+                                                          is loaded into memory. Default: `InMemory()`.
+
+References
+==========
+
+- Tsujino et al. (2018). JRA-55 based surface dataset for driving ocean-sea-ice models (JRA55-do), _Ocean Modelling_, **130(1)**, 79-139.
+
+- Stewart et al. (2020). JRA55-do-based repeat year forcing datasets for driving ocean–sea-ice models, _Ocean Modelling_, **147**, 101557.
 """
 function JRA55FieldTimeSeries(variable_name::Symbol, architecture=CPU(), FT=Float32;
                               dataset = RepeatYearJRA55(),

src/OceanSeaIceModels/InterfaceComputations/similarity_theory_turbulent_fluxes.jl

@@ -304,25 +304,29 @@ These stability functions are obtained by regression to experimental data.
 
 The stability parameter for stable atmospheric conditions is defined as
 ```math
-dζ = min(ζmax, Aˢζ)
-ψₛ = - Bˢ * ζ⁺ - Cˢ * (ζ⁺ - Dˢ) * exp(- dζ) - Cˢ * Dˢ
+\\begin{align*}
+dζ &= \\min(ζ_{\\max}, A⁺ ζ) \\\\
+ψ⁺ &= - B⁺ ζ⁺ - C⁺ (ζ⁺ - D⁺) \\exp(- dζ) - C⁺ D⁺
+\\end{align*}
 ```
 
 While the stability parameter for unstable atmospheric conditions is calculated
 as a function of the two individual stability functions as follows
 
 ```math
-fᵤ₁ = √√(1 - Aᵘζ)
-ψᵤ₁ = Bᵘ / 2 ⋅ log((1 + fᵤ₁ + fᵤ₁² + fᵤ₁³) / Bᵘ) - √Bᵘ atan(fᵤ₁) - Cᵘ
-
-fᵤ₂ = ∛(1 - Dᵘζ)
-ψᵤ₂ = Eᵘ / 2 ⋅ log((1 + fᵤ₂ + fᵤ₂²) / Eᵘ) - √Eᵘ atan( (1 + 2fᵤ₂) / √Eᵘ) + Fᵘ
-
-f  = ζ² / (1 + ζ²)
-ψᵤ = (1 - f) ψᵤ₁ + f ψᵤ₂
+\\begin{align*}
+f⁻₁ &= (1 - A⁻ζ)^{1/4} \\\\
+ψ⁻₁ &= (B⁻ / 2) \\log[(1 + f⁻₁ + f⁻₁² + f⁻₁³) / B⁻] - √B⁻ \\mathrm{atan}(f⁻₁) - C⁻ \\\\
+\\\\
+f⁻₂ &= ∛(1 - D⁻ζ) \\\\
+ψ⁻₂ &= (E⁻ / 2) \\log[(1 + f⁻₂ + f⁻₂²) / E⁻]- √E⁻ \\mathrm{atan}[(1 + 2f⁻₂) / √E⁻] + F⁻ \\\\
+\\\\
+f   &= ζ² / (1 + ζ²) \\\\
+ψ⁻  &= (1 - f) ψ⁻₁ + f ψ⁻₂
+\\end{align*}
 ```
 
-The superscripts ``ˢ`` and ``ᵘ`` indicate if the parameter applies to the
+The superscripts ``+`` and ``-`` indicate if the parameter applies to the
 stability function for _stable_ or _unstable_ atmospheric conditions, respectively.
 """
 @kwdef struct EdsonMomentumStabilityFunction{FT} <: AbstractStabilityFunction
@@ -385,24 +389,28 @@ These stability functions are obtained by regression to experimental data.
 The stability parameter for stable atmospheric conditions is defined as
 
 ```math
-dζ = min(ζmax, A⁺ζ)
-ψ⁺ = - (1 + B⁺ ζ) ^ C⁺ - B⁺ ( ζ - D⁺ ) * exp( - dζ) - E⁺
+\\begin{align*}
+dζ &= \\min(ζ_{\\max}, A⁺ζ) \\\\
+ψ⁺ &= - (1 + B⁺ ζ)^{C⁺} - B⁺ (ζ - D⁺) \\exp( - dζ) - E⁺
+\\end{align*}
 ```
 
 While the stability parameter for unstable atmospheric conditions is calculated
 as a function of the two individual stability functions as follows
 ```math
-f⁻₁ = √(1 - A⁻ζ)
-ψ⁻₁ = B⁻ ⋅ log((1 + f⁻₁) / B⁻) + C⁻
-
-f⁻₂ = ∛(1 - D⁻ζ)
-ψ⁻₂ = E⁻ / 2 ⋅ log((1 + f⁻₂ + f⁻₂²) / E⁻) - √E⁻ atan( (1 + 2f⁻₂) / √E⁻) + F⁻
-
-f  = ζ² / (1 + ζ²)
-ψ⁻ = (1 - f) ψ⁻₁ + f ψ⁻₂
+\\begin{align*}
+f⁻₁ &= √(1 - A⁻ζ) \\\\
+ψ⁻₁ &= B⁻ \\log[(1 + f⁻₁) / B⁻] + C⁻ \\\\
+\\\\
+f⁻₂ &= ∛(1 - D⁻ζ) \\\\
+ψ⁻₂ &= (E⁻ / 2) \\log[(1 + f⁻₂ + f⁻₂²) / E⁻] - √E⁻ \\mathrm{atan}[(1 + 2f⁻₂) / √E⁻] + F⁻ \\\\
+\\\\
+f   &= ζ² / (1 + ζ²) \\\\
+ψ⁻  &= (1 - f) ψ⁻₁ + f ψ⁻₂
+\\end{align*}
 ```
 
-The superscripts ``⁺`` and ``⁻`` indicate if the parameter applies to the
+The superscripts ``+`` and ``-`` indicate if the parameter applies to the
 stability function for _stable_ or _unstable_ atmospheric conditions, respectively.
 """
 @kwdef struct EdsonScalarStabilityFunction{FT} <: AbstractStabilityFunction