Merge branch 'main' of https://github.com/CliMA/ParameterEstimocean.jl …

…into ah/calibrate
CliMA · Apr 5, 2022 · 449a72a · 449a72a
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diff --git a/Project.toml b/Project.toml
@@ -1,4 +1,4 @@
-name = "OceanLearning"
+name = "ParameterEstimocean"
 uuid = "eca81dc5-87a6-4430-aec8-c76695404a43"
 license = "MIT"
 authors = ["Adeline Hillier <[email protected]>", "Gregory L. Wagner <[email protected]>", "Navid C. Constantinou <[email protected]>", "and co-contributors"]

diff --git a/README.md b/README.md
@@ -1,14 +1,14 @@
-# OceanLearning.jl
+# ParameterEstimocean.jl
 
 A Julia package that leverages [Oceananigans.jl](http://github.com/CliMA/Oceananigans.jl/) and [EnsembleKalmanProcesses.jl](https://github.com/CliMA/EnsembleKalmanProcesses.jl) to calibrate ocean turbulence parametrizations.
 
-Continuous Integration: [![Build Status](https://github.com/CliMA/OceanLearning.jl/workflows/CI/badge.svg)](https://github.com/CliMA/OceanLearning.jl/actions?query=workflow%3ACI+branch%3Amaster)
+Continuous Integration: [![Build Status](https://github.com/CliMA/ParameterEstimocean.jl/workflows/CI/badge.svg)](https://github.com/CliMA/ParameterEstimocean.jl/actions?query=workflow%3ACI+branch%3Amaster)
 
-Code Coverage: [![codecov](https://codecov.io/gh/CliMA/OceanLearning.jl/branch/main/graph/badge.svg?token=cPeTALmiPU)](https://codecov.io/gh/CliMA/OceanLearning.jl)
+Code Coverage: [![codecov](https://codecov.io/gh/CliMA/ParameterEstimocean.jl/branch/main/graph/badge.svg?token=cPeTALmiPU)](https://codecov.io/gh/CliMA/ParameterEstimocean.jl)
 
-Stable Release Documentation: [![Build Status](https://img.shields.io/badge/documentation-stable%20release-blue)](https://clima.github.io/OceanLearning.jl/stable)
+Stable Release Documentation: [![Build Status](https://img.shields.io/badge/documentation-stable%20release-blue)](https://clima.github.io/ParameterEstimocean.jl/stable)
 
-Latest Documentation: [![Build Status](https://img.shields.io/badge/documentation-in%20development-orange)](https://clima.github.io/OceanLearning.jl/dev)
+Latest Documentation: [![Build Status](https://img.shields.io/badge/documentation-in%20development-orange)](https://clima.github.io/ParameterEstimocean.jl/dev)
 
 Zenodo: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5762810.svg)](https://doi.org/10.5281/zenodo.5762810)
 
@@ -20,7 +20,7 @@ registry so you need to install via Github. To install a tagged version of the p
 
 ```julia
 julia>]
-(v1.6) pkg> add https://github.com/CliMA/OceanLearning.jl#v0.6.0
+(v1.6) pkg> add https://github.com/CliMA/ParameterEstimocean.jl#v0.6.0
 (v1.6) pkg> instantiate
 ```
 
@@ -29,7 +29,7 @@ install the version on the `#main` branch (or any other branch or commit), e.g.
 
 ```julia
 julia>]
-(v1.6) pkg> add https://github.com/CliMA/OceanLearning.jl#main
+(v1.6) pkg> add https://github.com/CliMA/ParameterEstimocean.jl#main
 (v1.6) pkg> instantiate
 ```
 
@@ -38,4 +38,4 @@ julia>]
 
 The code is citable via [zenodo](https://zenodo.org). Please cite as:
 
-> Adeline Hillier, Gregory L. Wagner, and Navid C. Constantinou. (2022). CliMA/OceanLearning.jl: OceanLearning.jl v0.10.2 (Version v0.10.2). Zenodo. [http://doi.org/10.5281/zenodo.5762810](http://doi.org/10.5281/zenodo.5762810)
+> Adeline Hillier, Gregory L. Wagner, and Navid C. Constantinou. (2022). CliMA/ParameterEstimocean.jl: ParameterEstimocean.jl v0.10.2 (Version v0.10.2). Zenodo. [http://doi.org/10.5281/zenodo.5762810](http://doi.org/10.5281/zenodo.5762810)
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,11 +1,11 @@
-pushfirst!(LOAD_PATH, joinpath(@__DIR__, "..")) # add OceanLearning to environment stack
+pushfirst!(LOAD_PATH, joinpath(@__DIR__, "..")) # add ParameterEstimocean to environment stack
 
 using
   Documenter,
   Literate,
   CairoMakie,  # so that Literate.jl does not capture precompilation output or warnings
   Distributions,
-  OceanLearning
+  ParameterEstimocean
 
 # Gotta set this environment variable when using the GR run-time on CI machines.
 # This happens when examples, e.g., use Plots.jl to make plots and movies.
@@ -46,7 +46,7 @@ Timer(t -> println(" "), 0, interval=240)
 format = Documenter.HTML(
   collapselevel = 2,
      prettyurls = get(ENV, "CI", nothing) == "true",
-      canonical = "https://clima.github.io/OceanLearning/dev/",
+      canonical = "https://clima.github.io/ParameterEstimocean/dev/",
 )
 
 pages = [
@@ -73,8 +73,8 @@ pages = [
 ]
 
 makedocs(
-   sitename = "OceanLearning.jl",
-    modules = [OceanLearning],
+   sitename = "ParameterEstimocean.jl",
+    modules = [ParameterEstimocean],
      format = format,
       pages = pages,
     doctest = true,
@@ -83,7 +83,7 @@ makedocs(
   checkdocs = :exports
 )
 
-deploydocs(        repo = "github.com/CliMA/OceanLearning.jl",
+deploydocs(        repo = "github.com/CliMA/ParameterEstimocean.jl",
                versions = ["stable" => "v^", "v#.#.#", "dev" => "dev"],
               forcepush = true,
               devbranch = "main",

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,5 +1,5 @@
-# OceanLearning.jl Documentation
+# ParameterEstimocean.jl Documentation
 
 ## Overview
 
-OceanLearning provides a framework to calibrate turbulence closure parametrizations for ocean models.
+ParameterEstimocean provides a framework to calibrate turbulence closure parametrizations for ocean models.
diff --git a/docs/src/installation_instructions.md b/docs/src/installation_instructions.md
@@ -1,6 +1,6 @@
 # Installation instructions
 
-You can install the latest version of OceanLearning.jl via the built-in
+You can install the latest version of ParameterEstimocean.jl via the built-in
 package manager (by pressing `]` in the Julia REPL command prompt) to add the package and also to 
 instantiate/build all the required dependencies
 
@@ -12,7 +12,7 @@ To install a tagged version of the package, e.g., v0.6.0, use
 
 ```julia
 julia>]
-(v1.6) pkg> add https://github.com/CliMA/OceanLearning.jl#v0.6.0
+(v1.6) pkg> add https://github.com/CliMA/ParameterEstimocean.jl#v0.6.0
 (v1.6) pkg> instantiate
 ```
 
@@ -21,6 +21,6 @@ install the version on the `#main` branch (or any other branch or commit), e.g.
 
 ```julia
 julia>]
-(v1.6) pkg> add https://github.com/CliMA/OceanLearning.jl#main
+(v1.6) pkg> add https://github.com/CliMA/ParameterEstimocean.jl#main
 (v1.6) pkg> instantiate
 ```
diff --git a/docs/src/library/internals.md b/docs/src/library/internals.md
@@ -1,54 +1,54 @@
 # Private types and functions
 
-Documentation for `OceanLearning.jl`'s internal interface.
+Documentation for `ParameterEstimocean.jl`'s internal interface.
 
-## OceanLearning
+## ParameterEstimocean
 
 ```@autodocs
-Modules = [OceanLearning]
+Modules = [ParameterEstimocean]
 Public = false
-Pages   = ["OceanLearning.jl"]
+Pages   = ["ParameterEstimocean.jl"]
 ```
 
 ## Transformations
 
 ```@autodocs
-Modules = [OceanLearning.Transformations]
+Modules = [ParameterEstimocean.Transformations]
 Public = false
 Pages   = ["Transformations.jl"]
 ```
 
 ## Observations
 
 ```@autodocs
-Modules = [OceanLearning.Observations]
+Modules = [ParameterEstimocean.Observations]
 Public = false
 ```
 
 ## Ensemble Simulations
 
 ```@autodocs
-Modules = [OceanLearning.EnsembleSimulations]
+Modules = [ParameterEstimocean.EnsembleSimulations]
 Public = false
 ```
 
 ## Parameters
 
 ```@autodocs
-Modules = [OceanLearning.Parameters]
+Modules = [ParameterEstimocean.Parameters]
 Public = false
 ```
 
 ## Inverse Problems
 
 ```@autodocs
-Modules = [OceanLearning.InverseProblems]
+Modules = [ParameterEstimocean.InverseProblems]
 Public = false
 ```
 
 ## EnsembleKalmanInversions
 
 ```@autodocs
-Modules = [OceanLearning.EnsembleKalmanInversions]
+Modules = [ParameterEstimocean.EnsembleKalmanInversions]
 Public = false
 ```
diff --git a/docs/src/library/public.md b/docs/src/library/public.md
@@ -1,54 +1,54 @@
 # Public Documentation
 
-Documentation for `OceanLearning.jl`'s public interface.
+Documentation for `ParameterEstimocean.jl`'s public interface.
 
 See the Internals section of the manual for internal package docs covering all submodules.
 
-## OceanLearning
+## ParameterEstimocean
 
 ```@autodocs
-Modules = [OceanLearning]
+Modules = [ParameterEstimocean]
 Private = false
 ```
 
 ## Transformations
 
 ```@autodocs
-Modules = [OceanLearning.Transformations]
+Modules = [ParameterEstimocean.Transformations]
 Private = false
 ```
 
 ## Observations
 
 ```@autodocs
-Modules = [OceanLearning.Observations]
+Modules = [ParameterEstimocean.Observations]
 Private = false
 ```
 
 ## Ensemble Simulations
 
 ```@autodocs
-Modules = [OceanLearning.EnsembleSimulations]
+Modules = [ParameterEstimocean.EnsembleSimulations]
 Private = false
 ```
 
 ## Parameters
 
 ```@autodocs
-Modules = [OceanLearning.Parameters]
+Modules = [ParameterEstimocean.Parameters]
 Private = false
 ```
 
 ## Inverse Problems
 
 ```@autodocs
-Modules = [OceanLearning.InverseProblems]
+Modules = [ParameterEstimocean.InverseProblems]
 Private = false
 ```
 
 ## EnsembleKalmanInversions
 
 ```@autodocs
-Modules = [OceanLearning.EnsembleKalmanInversions]
+Modules = [ParameterEstimocean.EnsembleKalmanInversions]
 Private = false
 ```
diff --git a/examples/calibrate_zonally_averaged_baroclinic_adjustment.jl b/examples/calibrate_zonally_averaged_baroclinic_adjustment.jl
@@ -1,7 +1,7 @@
 # Calibration of Gent-McWilliams to a baroclinic adjustment problem
 pushfirst!(LOAD_PATH, joinpath(@__DIR__, ".."))
 
-using OceanLearning
+using ParameterEstimocean
 using Oceananigans
 using Oceananigans.Units
 using Oceananigans.Models.HydrostaticFreeSurfaceModels: SliceEnsembleSize
@@ -37,7 +37,7 @@ close(file)
 field_names = (:b, :c, :u, :v)
 forward_map_names = (:b, :c)
 
-using OceanLearning.Transformations: Transformation
+using ParameterEstimocean.Transformations: Transformation
 
 transformation = (b = ZScore(),
                   c = ZScore(),
@@ -108,10 +108,10 @@ priors = (
 
 free_parameters = FreeParameters(priors)
 
-using OceanLearning.Observations: FieldTimeSeriesCollector
+using ParameterEstimocean.Observations: FieldTimeSeriesCollector
 
 simulation_fields = fields(simulation.model)
-collected_fields = NamedTuple(name => simulation_fields[name] for name in OceanLearning.Observations.forward_map_names(observations))
+collected_fields = NamedTuple(name => simulation_fields[name] for name in ParameterEstimocean.Observations.forward_map_names(observations))
 time_series_collector = FieldTimeSeriesCollector(collected_fields, observation_times(observations), architecture=CPU())
 
 calibration = InverseProblem(observations, simulation, free_parameters; time_series_collector)

diff --git a/examples/calibrate_zonally_averaged_channel.jl b/examples/calibrate_zonally_averaged_channel.jl
@@ -4,11 +4,11 @@
 
 # ```julia
 # using Pkg
-# pkg"add OceanLearning, Oceananigans, Distributions, CairoMakie"
+# pkg"add ParameterEstimocean, Oceananigans, Distributions, CairoMakie"
 # ```
 
-using OceanLearning
-using OceanLearning.Observations: FieldTimeSeriesCollector
+using ParameterEstimocean
+using ParameterEstimocean.Observations: FieldTimeSeriesCollector
 
 using Oceananigans
 using Oceananigans.Units

diff --git a/examples/exploring_priors.jl b/examples/exploring_priors.jl
@@ -1,6 +1,6 @@
 # # Specifying and fine-tuning prior distributions
 #
-# This example shows how to specify priors in `OceanLearning`
+# This example shows how to specify priors in `ParameterEstimocean`
 # and illustrates some of their properties.
 #
 # ## Install dependencies
@@ -9,12 +9,12 @@
 
 # ```julia
 # using Pkg
-# pkg"add OceanLearning, Oceananigans, Distributions, CairoMakie"
+# pkg"add ParameterEstimocean, Oceananigans, Distributions, CairoMakie"
 # ```
 #
 # Then we import packages
 
-using OceanLearning
+using ParameterEstimocean
 using CairoMakie
 using Distributions
 
@@ -31,7 +31,7 @@ using Distributions
 #
 # # Prior flavors
 #
-# `OceanLearning` supports three types of prior
+# `ParameterEstimocean` supports three types of prior
 # distributions. The normal prior distribution is provided by `Distributions.jl`,
 
 normal_prior = Normal(0.1, 0.1)

diff --git a/examples/intro_to_inverse_problems.jl b/examples/intro_to_inverse_problems.jl
@@ -11,12 +11,12 @@
 
 # ```julia
 # using Pkg
-# pkg"add OceanLearning, Oceananigans, Distributions, CairoMakie"
+# pkg"add ParameterEstimocean, Oceananigans, Distributions, CairoMakie"
 # ```
 
 # First we load few things
 
-using OceanLearning
+using ParameterEstimocean
 
 using Oceananigans
 using Oceananigans.Architectures: arch_array
@@ -30,7 +30,7 @@ using JLD2
 
 # We reuse some utilities from a previous example to build observations:
 
-examples_path = joinpath(pathof(OceanLearning), "..", "..", "examples")
+examples_path = joinpath(pathof(ParameterEstimocean), "..", "..", "examples")
 include(joinpath(examples_path, "intro_to_observations.jl"))
 data_path = generate_synthetic_observations()
 observations = SyntheticObservations(data_path, field_names=:b, transformation=ZScore())
@@ -137,7 +137,7 @@ free_parameters = FreeParameters(priors)
 # We visualize our prior distributions by plotting a huge number
 # of samples:
 
-using OceanLearning.Parameters: unconstrained_prior, transform_to_constrained
+using ParameterEstimocean.Parameters: unconstrained_prior, transform_to_constrained
 
 Nsamples = 50000000
 

diff --git a/examples/intro_to_observations.jl b/examples/intro_to_observations.jl
@@ -9,12 +9,12 @@
 
 # ```julia
 # using Pkg
-# pkg"add OceanLearning, Oceananigans, CairoMakie"
+# pkg"add ParameterEstimocean, Oceananigans, CairoMakie"
 # ```
 
 # First we load few things
 
-using OceanLearning
+using ParameterEstimocean
 using Oceananigans
 using Oceananigans.Units
 using Oceananigans.TurbulenceClosures: ConvectiveAdjustmentVerticalDiffusivity