Rename CalibrateAtmos -> ClimaCalibrate

CliMA · May 14, 2024 · 17b790f · 17b790f
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diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml
@@ -13,7 +13,7 @@ steps:
     key: "init_cpu_env"
     command:
       - echo "--- Instantiate SurfaceFluxes calibration project"
-      - julia --project=experiments/surface_fluxes_perfect_model -e 'using Pkg; Pkg.build("CalibrateAtmos"); Pkg.precompile()'
+      - julia --project=experiments/surface_fluxes_perfect_model -e 'using Pkg; Pkg.build("ClimaCalibrate"); Pkg.precompile()'
 
   - wait
   - label: "SurfaceFluxes perfect model calibration"

diff --git a/Project.toml b/Project.toml
@@ -1,4 +1,4 @@
-name = "CalibrateAtmos"
+name = "ClimaCalibrate"
 uuid = "4347a170-ebd6-470c-89d3-5c705c0cacc2"
 authors = ["Climate Modeling Alliance"]
 version = "0.1.0"

diff --git a/README.md b/README.md
@@ -1,11 +1,11 @@
 <!-- Title -->
 <h1 align="center">
-  CalibrateAtmos.jl
+  ClimaCalibrate.jl
 </h1>
 
 <!-- description -->
 <p align="center">
-  <strong>CalibrateAtmos is a toolkit for developing scalable and reproducible 
+  <strong>ClimaCalibrate is a toolkit for developing scalable and reproducible 
 calibration pipelines using with minimal boilerplate.</strong>
 </p>
 
@@ -14,17 +14,17 @@ calibration pipelines using with minimal boilerplate.</strong>
 [![ghaci][gha-ci-img]][gha-ci-url]
 [![codecov][codecov-img]][codecov-url]
 
-[docs-bld-img]: https://github.com/CliMA/CalibrateAtmos.jl/workflows/Documentation/badge.svg
-[docs-bld-url]: https://github.com/CliMA/CalibrateAtmos.jl/actions?query=workflow%3ADocumentation
+[docs-bld-img]: https://github.com/CliMA/ClimaCalibrate.jl/workflows/Documentation/badge.svg
+[docs-bld-url]: https://github.com/CliMA/ClimaCalibrate.jl/actions?query=workflow%3ADocumentation
 
 [docs-dev-img]: https://img.shields.io/badge/docs-dev-blue.svg
-[docs-dev-url]: https://CliMA.github.io/CalibrateAtmos.jl/dev/
+[docs-dev-url]: https://CliMA.github.io/ClimaCalibrate.jl/dev/
 
-[gha-ci-img]: https://github.com/CliMA/CalibrateAtmos.jl/actions/workflows/ci.yml/badge.svg
-[gha-ci-url]: https://github.com/CliMA/CalibrateAtmos.jl/actions/workflows/ci.yml
+[gha-ci-img]: https://github.com/CliMA/ClimaCalibrate.jl/actions/workflows/ci.yml/badge.svg
+[gha-ci-url]: https://github.com/CliMA/ClimaCalibrate.jl/actions/workflows/ci.yml
 
-[codecov-img]: https://codecov.io/gh/CliMA/CalibrateAtmos.jl/branch/main/graph/badge.svg
-[codecov-url]: https://codecov.io/gh/CliMA/CalibrateAtmos.jl
+[codecov-img]: https://codecov.io/gh/CliMA/ClimaCalibrate.jl/branch/main/graph/badge.svg
+[codecov-url]: https://codecov.io/gh/CliMA/ClimaCalibrate.jl
 
 The recommended Julia version is: Stable release v1.10.0
 
@@ -33,6 +33,6 @@ We strive to support flexible and clearly documented calibration experiments.
 
 ## Contributing
 
-If you're interested in contributing to the development of CalibrateAtmos we want your help no matter how big or small a contribution you make! It's always great to have new people look at the code with fresh eyes: you will see errors that other developers have missed.
+If you're interested in contributing to the development of ClimaCalibrate we want your help no matter how big or small a contribution you make! It's always great to have new people look at the code with fresh eyes: you will see errors that other developers have missed.
 
-Let us know by [opening an issue](https://github.com/CliMA/CalibrateAtmos.jl/issues/new) if you'd like to work on a new feature.
+Let us know by [opening an issue](https://github.com/CliMA/ClimaCalibrate.jl/issues/new) if you'd like to work on a new feature.
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,5 +1,5 @@
 [deps]
-CalibrateAtmos = "4347a170-ebd6-470c-89d3-5c705c0cacc2"
+ClimaCalibrate = "4347a170-ebd6-470c-89d3-5c705c0cacc2"
 CalibrateEmulateSample = "95e48a1f-0bec-4818-9538-3db4340308e3"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"

diff --git a/docs/make.jl b/docs/make.jl
@@ -1,19 +1,19 @@
 using Documenter
 using Documenter: doctest
-using CalibrateAtmos
+using ClimaCalibrate
 using Base.CoreLogging
 using DocumenterCitations
 
 disable_logging(Base.CoreLogging.Info) # Hide doctest's `@info` printing
 bib = CitationBibliography(joinpath(@__DIR__, "bibliography.bib"))
 
-doctest(CalibrateAtmos; plugins = [bib])
+doctest(ClimaCalibrate; plugins = [bib])
 disable_logging(Base.CoreLogging.BelowMinLevel) # Re-enable all logging
 
 makedocs(
     plugins = [bib],
-    modules = [CalibrateAtmos],
-    sitename = "CalibrateAtmos.jl",
+    modules = [ClimaCalibrate],
+    sitename = "ClimaCalibrate.jl",
     authors = "Clima",
     checkdocs = :exports,
     format = Documenter.HTML(
@@ -32,7 +32,7 @@ makedocs(
 )
 
 deploydocs(
-    repo = "github.com/CliMA/CalibrateAtmos.jl.git",
+    repo = "github.com/CliMA/ClimaCalibrate.jl.git",
     devbranch = "main",
     push_preview = true,
     forcepush = true,

diff --git a/docs/src/api.md b/docs/src/api.md
@@ -3,27 +3,27 @@
 ## Model Interface
 
 ```@docs
-CalibrateAtmos.get_config
-CalibrateAtmos.run_forward_model
-CalibrateAtmos.get_forward_model
-CalibrateAtmos.observation_map
+ClimaCalibrate.get_config
+ClimaCalibrate.run_forward_model
+ClimaCalibrate.get_forward_model
+ClimaCalibrate.observation_map
 ```
 
 ## Backend Interface
 
 ```@docs
-CalibrateAtmos.calibrate
-CalibrateAtmos.sbatch_model_run
+ClimaCalibrate.calibrate
+ClimaCalibrate.sbatch_model_run
 ```
 
 ## EnsembleKalmanProcesses Interface
 
 ```@docs
-CalibrateAtmos.initialize
-CalibrateAtmos.save_G_ensemble
-CalibrateAtmos.update_ensemble
-CalibrateAtmos.ExperimentConfig
-CalibrateAtmos.get_prior
-CalibrateAtmos.get_param_dict
-CalibrateAtmos.path_to_iteration
+ClimaCalibrate.initialize
+ClimaCalibrate.save_G_ensemble
+ClimaCalibrate.update_ensemble
+ClimaCalibrate.ExperimentConfig
+ClimaCalibrate.get_prior
+ClimaCalibrate.get_param_dict
+ClimaCalibrate.path_to_iteration
 ```
diff --git a/docs/src/emulate_sample.md b/docs/src/emulate_sample.md
@@ -12,7 +12,7 @@ import EnsembleKalmanProcesses as EKP
 using EnsembleKalmanProcesses.ParameterDistributions
 using EnsembleKalmanProcesses.TOMLInterface
 
-import CalibrateAtmos as CAL
+import ClimaCalibrate as CAL
 ```
 
 Next, load in the data, EKP object, and prior distribution. These values are taken

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,6 +1,6 @@
-# CalibrateAtmos.jl
+# ClimaCalibrate.jl
 
-CalibrateAtmos.jl is a toolkit for developing scalable and reproducible model 
+ClimaCalibrate.jl is a toolkit for developing scalable and reproducible model 
 calibration pipelines using CalibrateEmulateSample.jl with minimal boilerplate.
 
 For more information, see our Getting Started page.
diff --git a/docs/src/precompilation.md b/docs/src/precompilation.md
@@ -2,12 +2,12 @@
 
 PrecompileTools.jl enables developers to force the Julia compiler to save more code to disk, preventing re-compilation in the future.
 
-For CalibrateAtmos, this is useful under certain conditions:
+For ClimaCalibrate, this is useful under certain conditions:
 1. **The atmosphere model configuration is set and will not change often**. This is because the model configuration specifies things like the floating-point type and callbacks, which affect the MethodInstances that get precompiled. Generically precompiling ClimaAtmos would take much too long to be useful.
 2. **The model runtime is short compared to the compile time.** If the model runtime is an order of magnitude or more than the compilation time, any benefit from reduced compilation time will be trivial.
 
 # How do I precompile my configuration?
-The easiest way is by copying and pasting the code snippet below into `src/CalibrateAtmos.jl` and replacing the `job_id` with your experiment ID.
+The easiest way is by copying and pasting the code snippet below into `src/ClimaCalibrate.jl` and replacing the `job_id` with your experiment ID.
 This will precompile the model step and all callbacks for the given configuration.
 ```julia
 using PrecompileTools

diff --git a/docs/src/quickstart.md b/docs/src/quickstart.md
@@ -15,7 +15,7 @@ To run the example experiment on your local machine, first open your REPL with t
 
 Next, run the following code:
 ```julia
-import CalibrateAtmos
+import ClimaCalibrate
 
 experiment_dir = dirname(Base.active_project())
 
@@ -24,7 +24,7 @@ include(joinpath(experiment_dir, "generate_data.jl"))
 include(joinpath(experiment_dir, "observation_map.jl"))
 include(joinpath(experiment_dir, "model_interface.jl"))
 
-eki = CalibrateAtmos.calibrate(JuliaBackend, experiment_dir)
+eki = ClimaCalibrate.calibrate(JuliaBackend, experiment_dir)
 include(joinpath(experiment_dir, "postprocessing.jl"))
 ```
 
@@ -33,11 +33,11 @@ This method will queue Julia processes to run on your slurm cluster.
 
 To run this experiment:
 1. Log onto the Caltech HPC
-2. Clone CalibrateAtmos.jl and `cd` into the repository.
+2. Clone ClimaCalibrate.jl and `cd` into the repository.
 3. Start julia: `julia --project=experiments/surace_fluxes_perfect_model`
 4. Run the following:
 ```julia
-import CalibrateAtmos: CaltechHPC, calibrate
+import ClimaCalibrate: CaltechHPC, calibrate
 
 experiment_dir = dirname(Base.active_project())
 
@@ -50,4 +50,4 @@ eki = calibrate(CaltechHPC, experiment_dir;
 include(joinpath(experiment_dir, "postprocessing.jl"))
 ```
 
-New experiments should be defined within the component model repos (in this case, `SurfaceFluxes.jl`), so that the internals of `CalibrateAtmos.jl` do not explicitly depend on component models.
+New experiments should be defined within the component model repos (in this case, `SurfaceFluxes.jl`), so that the internals of `ClimaCalibrate.jl` do not explicitly depend on component models.
diff --git a/experiments/surface_fluxes_perfect_model/Manifest.toml b/experiments/surface_fluxes_perfect_model/Manifest.toml
@@ -2,7 +2,7 @@
 
 julia_version = "1.10.3"
 manifest_format = "2.0"
-project_hash = "ae9cb369c40816d49bb5a565631215d357fe1284"
+project_hash = "c588c67f67784e1b4e65633bdcbfa5bcaa6ddf91"
 
 [[deps.AMD]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"]
@@ -171,18 +171,6 @@ git-tree-sha1 = "a4c43f59baa34011e303e76f5c8c91bf58415aaf"
 uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a"
 version = "1.18.0+1"
 
-[[deps.CalibrateAtmos]]
-deps = ["Distributions", "EnsembleKalmanProcesses", "JLD2", "Random", "TOML", "YAML"]
-path = "../.."
-uuid = "4347a170-ebd6-470c-89d3-5c705c0cacc2"
-version = "0.1.0"
-
-    [deps.CalibrateAtmos.extensions]
-    CESExt = "CalibrateEmulateSample"
-
-    [deps.CalibrateAtmos.weakdeps]
-    CalibrateEmulateSample = "95e48a1f-0bec-4818-9538-3db4340308e3"
-
 [[deps.ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra"]
 git-tree-sha1 = "575cd02e080939a33b6df6c5853d14924c08e35b"
@@ -193,6 +181,18 @@ weakdeps = ["SparseArrays"]
     [deps.ChainRulesCore.extensions]
     ChainRulesCoreSparseArraysExt = "SparseArrays"
 
+[[deps.ClimaCalibrate]]
+deps = ["Distributions", "EnsembleKalmanProcesses", "JLD2", "Random", "TOML", "YAML"]
+path = "../.."
+uuid = "4347a170-ebd6-470c-89d3-5c705c0cacc2"
+version = "0.1.0"
+
+    [deps.ClimaCalibrate.extensions]
+    CESExt = "CalibrateEmulateSample"
+
+    [deps.ClimaCalibrate.weakdeps]
+    CalibrateEmulateSample = "95e48a1f-0bec-4818-9538-3db4340308e3"
+
 [[deps.ClimaParams]]
 deps = ["DocStringExtensions", "TOML", "Test"]
 git-tree-sha1 = "528aadfaae6f447df3879eab224625ecceec5982"

diff --git a/experiments/surface_fluxes_perfect_model/Project.toml b/experiments/surface_fluxes_perfect_model/Project.toml
@@ -1,6 +1,6 @@
 [deps]
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
-CalibrateAtmos = "4347a170-ebd6-470c-89d3-5c705c0cacc2"
+ClimaCalibrate = "4347a170-ebd6-470c-89d3-5c705c0cacc2"
 ClimaParams = "5c42b081-d73a-476f-9059-fd94b934656c"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 EnsembleKalmanProcesses = "aa8a2aa5-91d8-4396-bcef-d4f2ec43552d"

diff --git a/experiments/surface_fluxes_perfect_model/generate_data.jl b/experiments/surface_fluxes_perfect_model/generate_data.jl
@@ -7,9 +7,9 @@ import SurfaceFluxes.UniversalFunctions as UF
 import Thermodynamics as TD
 using YAML
 import SurfaceFluxes.Parameters: SurfaceFluxesParameters
-using CalibrateAtmos
+using ClimaCalibrate
 
-pkg_dir = pkgdir(CalibrateAtmos)
+pkg_dir = pkgdir(ClimaCalibrate)
 experiment_path = "$pkg_dir/experiments/$experiment_id"
 data_path = "$experiment_path/data"
 include(joinpath(experiment_path, "model_interface.jl"))

diff --git a/experiments/surface_fluxes_perfect_model/model_interface.jl b/experiments/surface_fluxes_perfect_model/model_interface.jl
@@ -1,6 +1,6 @@
 import EnsembleKalmanProcesses as EKP
-import CalibrateAtmos
-import CalibrateAtmos:
+using ClimaCalibrate
+import ClimaCalibrate:
     AbstractPhysicalModel,
     get_config,
     run_forward_model,
@@ -35,7 +35,7 @@ We need to follow the following steps for the calibration:
 struct SurfaceFluxModel <: AbstractPhysicalModel end
 
 experiment_dir = joinpath(
-    pkgdir(CalibrateAtmos),
+    pkgdir(ClimaCalibrate),
     "experiments",
     "surface_fluxes_perfect_model",
 )

diff --git a/experiments/surface_fluxes_perfect_model/observation_map.jl b/experiments/surface_fluxes_perfect_model/observation_map.jl
@@ -1,11 +1,11 @@
 using Statistics
 import YAML
 import JLD2
-import CalibrateAtmos:
+import ClimaCalibrate:
     observation_map, ExperimentConfig, path_to_ensemble_member
 
 experiment_dir = joinpath(
-    pkgdir(CalibrateAtmos),
+    pkgdir(ClimaCalibrate),
     "experiments",
     "surface_fluxes_perfect_model",
 )

diff --git a/experiments/surface_fluxes_perfect_model/postprocessing.jl b/experiments/surface_fluxes_perfect_model/postprocessing.jl
@@ -9,10 +9,10 @@ import TOML
 import CairoMakie: Makie
 using Statistics
 
-using CalibrateAtmos
+using ClimaCalibrate
 
 experiment_dir = dirname(Base.active_project())
-experiment_config = CalibrateAtmos.ExperimentConfig(experiment_dir)
+experiment_config = ClimaCalibrate.ExperimentConfig(experiment_dir)
 output_dir = experiment_config.output_dir
 experiment_id = experiment_config.id
 N_iter = experiment_config.n_iterations
@@ -102,13 +102,13 @@ function convergence_plot(
 end
 
 
-pkg_dir = pkgdir(CalibrateAtmos)
+pkg_dir = pkgdir(ClimaCalibrate)
 model_config = YAML.load_file(
     joinpath(pkg_dir, "experiments", experiment_id, "model_config.yml"),
 )
 
 eki_path = joinpath(
-    CalibrateAtmos.path_to_iteration(output_dir, N_iter),
+    ClimaCalibrate.path_to_iteration(output_dir, N_iter),
     "eki_file.jld2",
 );
 eki = JLD2.load_object(eki_path);
@@ -146,7 +146,7 @@ for iter in 0:N_iter
         model_config["toml"] = [
             joinpath(
                 pkg_dir,
-                CalibrateAtmos.path_to_ensemble_member(output_dir, iter, i),
+                ClimaCalibrate.path_to_ensemble_member(output_dir, iter, i),
                 "parameters.toml",
             ),
         ]

diff --git a/ext/CESExt.jl b/ext/CESExt.jl
@@ -9,7 +9,7 @@ using EnsembleKalmanProcesses.ParameterDistributions
 using EnsembleKalmanProcesses.TOMLInterface
 import JLD2
 
-import CalibrateAtmos as CAL
+import ClimaCalibrate as CAL
 
 
 function CAL.get_input_output_pairs(ekp; N_iterations = nothing)

diff --git a/src/CalibrateAtmos.jl → src/ClimaCalibrate.jl b/src/CalibrateAtmos.jl → src/ClimaCalibrate.jl
@@ -1,8 +1,8 @@
-module CalibrateAtmos
+module ClimaCalibrate
 
 include("ekp_interface.jl")
 include("model_interface.jl")
 include("backends.jl")
 include("emulate_sample.jl")
 
-end # module CalibrateAtmos
+end # module ClimaCalibrate