From b86a66af69e66f921b22e6aceef506124b3ce864 Mon Sep 17 00:00:00 2001 From: nefrathenrici Date: Fri, 10 Jul 2026 13:50:09 -0700 Subject: [PATCH] Update JuliaFormatter to v2.10.1 --- .github/workflows/julia_formatter.yml | 2 +- ext/observation_recipe.jl | 49 +++--- src/ekp_interface.jl | 2 +- test/ensemble_builder.jl | 27 ++- test/observation_recipe.jl | 226 +++++++++++--------------- test/svd_analysis.jl | 9 +- 6 files changed, 135 insertions(+), 180 deletions(-) diff --git a/.github/workflows/julia_formatter.yml b/.github/workflows/julia_formatter.yml index 45acee9806..b60e0823e8 100644 --- a/.github/workflows/julia_formatter.yml +++ b/.github/workflows/julia_formatter.yml @@ -12,5 +12,5 @@ jobs: steps: - uses: julia-actions/julia-format@v3 with: - version: '1' # Set `version` to '1.0.54' if you need to use JuliaFormatter.jl v1.0.54 (default: '1') + version: '2.10.1' suggestion-label: 'format-suggest' # leave this unset or empty to show suggestions for all PRs diff --git a/ext/observation_recipe.jl b/ext/observation_recipe.jl index f79e034ebf..bbbdd7999f 100644 --- a/ext/observation_recipe.jl +++ b/ext/observation_recipe.jl @@ -93,14 +93,13 @@ function _covariance( diag_cov .*= covar_estimator.scalar if covar_estimator.use_latitude_weights - flattened_lat_weights = - ClimaAnalysis.flatten( - _lat_weights_var( - var, - min_cosd_lat = covar_estimator.min_cosd_lat, - ); - dims, - ).data + flattened_lat_weights = ClimaAnalysis.flatten( + _lat_weights_var( + var, + min_cosd_lat = covar_estimator.min_cosd_lat, + ); + dims, + ).data diag_cov .*= flattened_lat_weights end diag_cov @@ -195,14 +194,13 @@ function ObservationRecipe.covariance( # Add latitude weights if covar_estimator.use_latitude_weights - flattened_lat_weights = - ClimaAnalysis.flatten( - _lat_weights_var( - seasonal_variance_var, - min_cosd_lat = covar_estimator.min_cosd_lat, - ); - dims, - ).data + flattened_lat_weights = ClimaAnalysis.flatten( + _lat_weights_var( + seasonal_variance_var, + min_cosd_lat = covar_estimator.min_cosd_lat, + ); + dims, + ).data diag_cov .*= flattened_lat_weights end diag_cov @@ -667,16 +665,15 @@ function _metadata_for_stacked_sample(vars, sample_date_ranges, dims) sample_start_date, sample_end_date = first(sample_date_ranges) metadata = [] for var in vars - md = - ClimaAnalysis.flatten( - ClimaAnalysis.window( - var, - "time", - left = sample_start_date, - right = sample_end_date, - ); - dims, - ).metadata + md = ClimaAnalysis.flatten( + ClimaAnalysis.window( + var, + "time", + left = sample_start_date, + right = sample_end_date, + ); + dims, + ).metadata push!(metadata, md) end return metadata diff --git a/src/ekp_interface.jl b/src/ekp_interface.jl index 1f40aa7090..c531641b92 100644 --- a/src/ekp_interface.jl +++ b/src/ekp_interface.jl @@ -290,7 +290,7 @@ If no iteration has been completed yet, return 0. function last_completed_iteration(output_dir) last_completed_iter = 0 while isfile(path_to_G_ensemble(output_dir, last_completed_iter + 1)) && - isfile(ekp_path(output_dir, last_completed_iter + 2)) + isfile(ekp_path(output_dir, last_completed_iter + 2)) last_completed_iter += 1 end return last_completed_iter diff --git a/test/ensemble_builder.jl b/test/ensemble_builder.jl index 7b0d332599..79e0fa9768 100644 --- a/test/ensemble_builder.jl +++ b/test/ensemble_builder.jl @@ -367,11 +367,10 @@ end @testset "Use GEnsembleBuilder for a fake calibration" begin pkgversion(EnsembleKalmanProcesses) > v"2.4.3" || return - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:11], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:11], + ) time_var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -558,11 +557,10 @@ end end @testset "Utilities functions" begin - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:11], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:11], + ) time_var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -631,11 +629,10 @@ end end @testset "Error handling when constructing GEnsembleBuilder" begin - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:4], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:4], + ) time_var = TemplateVar() |> add_dim("time", time, units = "s") |> diff --git a/test/observation_recipe.jl b/test/observation_recipe.jl index f7e49ff43d..74eb899d67 100644 --- a/test/observation_recipe.jl +++ b/test/observation_recipe.jl @@ -33,11 +33,10 @@ import ClimaAnalysis.Template: @testset "Utils" begin @testset "Dates in var" begin - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:3], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:3], + ) var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -102,11 +101,10 @@ import ClimaAnalysis.Template: [Dates.DateTime(2015, 1, 13), Dates.DateTime(2018, 2, 13)], ) - seconds = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2015, 1, 13), - dates, - ) + seconds = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2015, 1, 13), + dates, + ) expected_seconds = [ ClimaAnalysis.Utils.date_to_time.( Dates.DateTime(2015, 1, 13), @@ -157,11 +155,10 @@ import ClimaAnalysis.Template: end @testset "Seasonally aligned year sample dates" begin - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:13], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:13], + ) var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -187,11 +184,10 @@ end ] # Time dimension with a single element - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12)], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12)], + ) var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -211,11 +207,10 @@ end ]] # Error handling - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2008, 12), Dates.DateTime(2007, 12)], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2008, 12), Dates.DateTime(2007, 12)], + ) var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -280,11 +275,10 @@ end # Seasonal averages across time lat = [-90.0, -30.0, 30.0, 90.0] lon = [-60.0, -30.0, 0.0, 30.0, 60.0] - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2008), - [Dates.DateTime(2008, i) for i in 1:12], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2008), + [Dates.DateTime(2008, i) for i in 1:12], + ) var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -329,11 +323,10 @@ end @testset "Stacked samples" begin lat = [-90.0, -45.0, -30.0, 0.0, 30.0, 45.0, 90.0] lon = [-60.0, -30.0, 0.0, 30.0, 60.0] - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:35], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:35], + ) var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -490,11 +483,10 @@ end @testset "ScalarCovariance" begin lat = [-90.0, -30.0, 30.0, 90.0] lon = [-60.0, -30.0, 0.0, 30.0, 60.0] - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:35], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:35], + ) var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -630,20 +622,17 @@ end scalar_covar = ObservationRecipe.covariance(covar_estimator, var) @test scalar_covar == 10.0 .* Diagonal( - ClimaAnalysis.flatten( - ext._lat_weights_var(var, min_cosd_lat = 0.2), - ).data, + ClimaAnalysis.flatten(ext._lat_weights_var(var, min_cosd_lat = 0.2)).data, ) end @testset "Latitude weights to matrix of samples" begin lat = [-90.0, -30.0, 30.0, 90.0] lon = [-60.0, -30.0, 0.0, 30.0, 60.0] - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(i, 12, 1) for i in 2007:2009], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(i, 12, 1) for i in 2007:2009], + ) var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -677,12 +666,11 @@ end min_cosd_lat = 0.15, ) time_slice = ClimaAnalysis.slice(var, time = Dates.DateTime(2007, 12, 1)) - lat_weights_per_column = - sqrt.( - ClimaAnalysis.flatten( - ext._lat_weights_var(time_slice, min_cosd_lat = 0.15), - ).data, - ) + lat_weights_per_column = sqrt.( + ClimaAnalysis.flatten( + ext._lat_weights_var(time_slice, min_cosd_lat = 0.15), + ).data, + ) lat_weights_per_column = reshape(lat_weights_per_column, length(lat_weights_per_column), 1) @test isequal( @@ -694,11 +682,10 @@ end @testset "SVDplusDCovariance" begin lat = [-90.0, -30.0, 30.0, 90.0] lon = [-60.0, -30.0, 0.0, 30.0, 60.0] - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:35], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:35], + ) var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -824,10 +811,7 @@ end return U * Diagonal(S) * V' end @test any( - .!isapprox.( - reconstruct(svd_plus_d_covar_with_lat_weights.svd_cov), - reconstruct(svd_plus_d_covar_with_no_lat_weights.svd_cov), - ), + .!isapprox.(reconstruct(svd_plus_d_covar_with_lat_weights.svd_cov), reconstruct(svd_plus_d_covar_with_no_lat_weights.svd_cov)), ) # Test rank @@ -876,11 +860,10 @@ end end # Error handling - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:2], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:2], + ) var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -962,11 +945,10 @@ end # Single OutputVar lat = [-90.0, -30.0, 30.0, 90.0] lon = [-60.0, -30.0, 0.0, 30.0, 60.0] - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:35], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:35], + ) var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -1110,11 +1092,10 @@ end end @testset "Seasonal diagonal covariance" begin - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:11], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:11], + ) data = [1.0, 2.0, 3.0, 5.0, 8.0, 13.0, 21.0, 34.0, 55.0, 89.0, 144.0, NaN] DJF = [data[i] for i in 1:4:length(data)] MAM = [data[i] for i in 2:4:length(data)] @@ -1184,11 +1165,10 @@ end # Enable lat weights, but use default settings for everything else lats = [-90.0, -85.0, -20.0, 0.0, 20.0, 85.0, 90.0] - time1 = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Year(i) for i in 0:1], - ) + time1 = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Year(i) for i in 0:1], + ) data = ones(Float64, 2, 7) data[2, :] .*= 2 lat_var = @@ -1264,11 +1244,10 @@ end @test eltype(seasonal_covariance) == Float32 # Error handling - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:2], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:2], + ) var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -1310,11 +1289,10 @@ end lon = [-60.0, -30.0, 0.0, 30.0, 60.0] x = [1.0, 2.0] y = [3.0] - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:35], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:35], + ) var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -1369,10 +1347,7 @@ end data1 = ClimaAnalysis.flatten(window_dates(var); dims = ext.FLATTENED_DIMS).data data2 = - ClimaAnalysis.flatten( - window_dates(neg_var); - dims = ext.FLATTENED_DIMS, - ).data + ClimaAnalysis.flatten(window_dates(neg_var); dims = ext.FLATTENED_DIMS).data flattened_data = vcat(data1, data2) @test obs.samples[1] == flattened_data @@ -1493,11 +1468,10 @@ end @testset "Short names of observation" begin if pkgversion(EnsembleKalmanProcesses) > v"2.4.2" - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:2], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:2], + ) var1 = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -1532,11 +1506,10 @@ end @testset "Get information about metadata from nth iteration" begin pkgversion(EnsembleKalmanProcesses) > v"2.4.3" || return - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:47], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:47], + ) time_var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -1649,11 +1622,10 @@ end end @testset "Reconstruct g and g mean" begin - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:47], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:47], + ) time_var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -1684,18 +1656,10 @@ end ClimaAnalysis.window(var, "time", left = start_date, right = end_date) time_var_length = length( - trim_var( - time_var, - Dates.DateTime(2007, 12), - Dates.DateTime(2008, 9), - ).data, + trim_var(time_var, Dates.DateTime(2007, 12), Dates.DateTime(2008, 9)).data, ) lon_var_length = length( - trim_var( - lon_var, - Dates.DateTime(2007, 12), - Dates.DateTime(2008, 9), - ).data, + trim_var(lon_var, Dates.DateTime(2007, 12), Dates.DateTime(2008, 9)).data, ) covar_estimator = ObservationRecipe.ScalarCovariance() @@ -1765,11 +1729,10 @@ end if pkgversion(EnsembleKalmanProcesses) > v"2.4.3" # Test with a two OutputVars and two iterations with a single # observation (no observation series) - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:47], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:47], + ) time_var = TemplateVar() |> add_dim("time", time, units = "s") |> @@ -1984,11 +1947,10 @@ end end @testset "Reconstruct diagonal of covariance and OutputVars from observations" begin - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:47], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(3 * i) for i in 0:47], + ) time_var = TemplateVar() |> add_dim("time", time, units = "s") |> diff --git a/test/svd_analysis.jl b/test/svd_analysis.jl index 395cdfe675..88e4142462 100644 --- a/test/svd_analysis.jl +++ b/test/svd_analysis.jl @@ -156,11 +156,10 @@ end # on an EKP object lat = [-90.0, -30.0, 30.0, 90.0] lon = [-60.0, -30.0, 0.0, 30.0, 60.0] - time = - ClimaAnalysis.Utils.date_to_time.( - Dates.DateTime(2007, 12), - [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:35], - ) + time = ClimaAnalysis.Utils.date_to_time.( + Dates.DateTime(2007, 12), + [Dates.DateTime(2007, 12) + Dates.Month(i) for i in 0:35], + ) var = TemplateVar() |> add_dim("time", time, units = "s") |>