Add ClimaOceanCopernicusMarineExt (#661)

* add ClimaOceanCopernicusMarineExt

* tests use CopernicusMarine

* nuke ClimaOceanPythonCallExt

* Bump version from 0.8.6 to 0.8.7

* Update citation for ClimaOcean version to v0.8.7

* use CopernicusMarine.pylist

* Update Project.toml

* drop PythonCall/CondaPkg

* nuke CondaPkg

* global_barrier -> barrier

Author: navidcy

Project.toml

@@ -2,7 +2,7 @@ name = "ClimaOcean"
 uuid = "0376089a-ecfe-4b0e-a64f-9c555d74d754"
 license = "MIT"
 authors = ["Climate Modeling Alliance and contributors"]
-version = "0.8.6"
+version = "0.8.7"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
@@ -33,20 +33,19 @@ Thermodynamics = "b60c26fb-14c3-4610-9d3e-2d17fe7ff00c"
 ZipFile = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"
 
 [weakdeps]
-CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
-PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
+CopernicusMarine = "cd43e856-93a3-40c8-bc9e-6146cdce14fa"
 Reactant = "3c362404-f566-11ee-1572-e11a4b42c853"
 
 [extensions]
-ClimaOceanPythonCallExt = ["PythonCall", "CondaPkg"]
+ClimaOceanCopernicusMarineExt = "CopernicusMarine"
 ClimaOceanReactantExt = "Reactant"
 
 [compat]
 Adapt = "4"
 CFTime = "0.1, 0.2"
 CUDA = "4, 5"
 ClimaSeaIce = "0.3.9"
-CondaPkg = "0.2.28"
+CopernicusMarine = "0.1.1"
 CubicSplines = "0.2"
 DataDeps = "0.7"
 DocStringExtensions = "0.9"
@@ -58,10 +57,9 @@ KernelAbstractions = "0.9"
 MPI = "0.20"
 MeshArrays = "0.3"
 NCDatasets = "0.12, 0.13, 0.14"
-Oceananigans = "0.100.3"
+Oceananigans = "0.100.4"
 OffsetArrays = "1.14"
 PrecompileTools = "1"
-PythonCall = "0.9"
 Reactant = "0.2.45"
 Scratch = "1"
 SeawaterPolynomials = "0.3.5"
@@ -78,4 +76,4 @@ MPIPreferences = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Coverage", "Test", "MPIPreferences", "CUDA_Runtime_jll", "Reactant", "PythonCall", "CondaPkg"]
+test = ["Coverage", "Test", "MPIPreferences", "CUDA_Runtime_jll", "Reactant", "CopernicusMarine"]

README.md

@@ -105,7 +105,7 @@ Note that though ClimaOcean is currently focused on hydrostatic modeling with `O
 If you use ClimaOcean for your research, teaching, or fun 🤩, everyone in our community will be grateful
 if you give credit by citing the corresponding Zenodo record, e.g.,
 
-> Wagner, G. L. et al. (2025). CliMA/ClimaOcean.jl: v0.8.1 (v0.8.1). Zenodo. https://doi.org/10.5281/zenodo.7677442
+> Wagner, G. L. et al. (2025). CliMA/ClimaOcean.jl: v0.8.7 (v0.8.7). Zenodo. https://doi.org/10.5281/zenodo.7677442
 
 and also the recent [preprint submitted to the Journal of Advances in Modeling Earth Systems](https://arxiv.org/abs/2502.14148) that presents an overview of all the things that make Oceananigans unique:
 

examples/download_glorys_data.jl

@@ -1,6 +1,6 @@
 using ClimaOcean
 using Oceananigans
-using PythonCall
+using CopernicusMarine
 
 arch = CPU()
 Nx = 20 * 12

ext/ClimaOceanPythonCallExt.jl renamed to ext/ClimaOceanCopernicusMarineExt.jl

@@ -1,8 +1,8 @@
-module ClimaOceanPythonCallExt
+module ClimaOceanCopernicusMarineExt
 
 using ClimaOcean
-using CondaPkg
-using PythonCall
+using CopernicusMarine
+
 using Oceananigans
 using Oceananigans.DistributedComputations: @root
 
@@ -11,19 +11,6 @@ using ClimaOcean.DataWrangling.Copernicus: CopernicusMetadata, CopernicusMetadat
 
 import ClimaOcean.DataWrangling: download_dataset
 
-"""
-    install_copernicusmarine()
-
-Install the Copernicus Marine CLI using CondaPkg.
-Returns a NamedTuple containing package information if successful.
-"""
-function install_copernicusmarine()
-    @info "Installing the copernicusmarine CLI..."
-    CondaPkg.add("copernicusmarine"; channel = "conda-forge")
-    cli = CondaPkg.which("copernicusmarine")
-    @info "... the copernicusmarine CLI has been installed at $(cli)."
-    return cli
-end
 
 # Download each date individually, instead of downloading the entire dataset at once.
 # This is useful for a possible extension of the temporal horizon of the dataset.
@@ -35,8 +22,8 @@ function download_dataset(metadata::CopernicusMetadata; kwargs...)
     return paths
 end
 
-function download_dataset(meta::CopernicusMetadatum; 
-                          skip_existing=true, 
+function download_dataset(meta::CopernicusMetadatum;
+                          skip_existing=true,
                           username=get(ENV, "COPERNICUS_USERNAME", nothing),
                           password=get(ENV, "COPERNICUS_PASSWORD", nothing),
                           additional_kw...)
@@ -46,15 +33,10 @@ function download_dataset(meta::CopernicusMetadatum;
     output_path = joinpath(output_directory, output_filename)
     isfile(output_path) && return output_path
 
-    toolbox = try
-        pyimport("copernicusmarine")
-    catch
-        install_copernicusmarine()
-        pyimport("copernicusmarine")
-    end
+    toolbox = CopernicusMarine.copernicusmarine
 
     variable_name = ClimaOcean.DataWrangling.Copernicus.copernicus_dataset_variable_names[meta.name]
-    variables = PythonCall.pylist([variable_name])
+    variables = CopernicusMarine.pylist([variable_name])
 
     dataset_id = ClimaOcean.DataWrangling.Copernicus.copernicusmarine_dataset_id(meta.dataset)
     datetime_kw = if meta.dataset isa ClimaOcean.DataWrangling.Copernicus.GLORYSStatic
@@ -79,8 +61,8 @@ function download_dataset(meta::CopernicusMetadatum;
     if !isnothing(username) && !isnothing(password)
         kw = merge(kw, (; username, password))
     else
-        @warn "No Copernicus credentials found. \\ 
-        Set the COPERNICUS_USERNAME and COPERNICUS_PASSWORD environment variables to download data from the Copernicus Marine Service. \\
+        @warn "No Copernicus credentials found.
+        Set the COPERNICUS_USERNAME and COPERNICUS_PASSWORD environment variables to download data from the Copernicus Marine Service.
         You can sign up for free at: https://data.marine.copernicus.eu/register."
     end
 
@@ -120,4 +102,4 @@ function depth_bounds_kw(z)
     return (; minimum_depth, maximum_depth)
 end
 
-end # module ClimaOceanPythonCallExt
+end # module ClimaOceanCopernicusMarineExt

src/Bathymetry.jl

@@ -176,7 +176,7 @@ function regrid_bathymetry(target_grid::DistributedGrid, metadata;
     end
 
     # Synchronize
-    Oceananigans.DistributedComputations.global_barrier(arch.communicator)
+    Oceananigans.DistributedComputations.barrier(arch.communicator)
 
     # Share the result (can we share SubArrays?)
     bottom_height = all_reduce(+, bottom_height, arch)

test/runtests.jl

@@ -2,8 +2,6 @@
 include("runtests_setup.jl")
 
 using CUDA
-using PythonCall
-using CondaPkg
 using Scratch
 
 test_group = get(ENV, "TEST_GROUP", :all)

test/test_copernicus_downloading.jl

@@ -1,7 +1,6 @@
 include("runtests_setup.jl")
 
-using PythonCall
-using CondaPkg
+using CopernicusMarine
 
 @testset "Downloading Copernicus data" begin
     variables = (:temperature, :salinity, :u_velocity, :v_velocity)