Quality of life improvements

Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.10.5"
 manifest_format = "2.0"
-project_hash = "acf9296ffbaffd3f335bdb6005badef66b3e10fe"
+project_hash = "986b47155507036c06218d23750fe8de28eb001a"
 
 [[deps.AbstractTrees]]
 git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177"
@@ -11,9 +11,9 @@ version = "0.4.5"
 
 [[deps.Adapt]]
 deps = ["LinearAlgebra", "Requires"]
-git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099"
+git-tree-sha1 = "d80af0733c99ea80575f612813fa6aa71022d33a"
 uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
-version = "4.0.4"
+version = "4.1.0"
 weakdeps = ["StaticArrays"]
 
     [deps.Adapt.extensions]
@@ -78,15 +78,15 @@ version = "0.1.6"
 
 [[deps.Blosc_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Lz4_jll", "Zlib_jll", "Zstd_jll"]
-git-tree-sha1 = "19b98ee7e3db3b4eff74c5c9c72bf32144e24f10"
+git-tree-sha1 = "ef12cdd1c7fb7e1dfd6fa8fd60d4db6bc61d2f23"
 uuid = "0b7ba130-8d10-5ba8-a3d6-c5182647fed9"
-version = "1.21.5+0"
+version = "1.21.6+0"
 
 [[deps.Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd"
+git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1"
 uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0"
-version = "1.0.8+1"
+version = "1.0.8+2"
 
 [[deps.CFTime]]
 deps = ["Dates", "Printf"]
@@ -239,9 +239,9 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
 [[deps.JLLWrappers]]
 deps = ["Artifacts", "Preferences"]
-git-tree-sha1 = "f389674c99bfcde17dc57454011aa44d5a260a40"
+git-tree-sha1 = "be3dc50a92e5a386872a493a10050136d4703f9b"
 uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
-version = "1.6.0"
+version = "1.6.1"
 
 [[deps.LRUCache]]
 git-tree-sha1 = "b3cc6698599b10e652832c2f23db3cab99d51b59"
@@ -337,9 +337,9 @@ version = "1.10.0+1"
 
 [[deps.MPICH_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
-git-tree-sha1 = "19d4bd098928a3263693991500d05d74dbdc2004"
+git-tree-sha1 = "7715e65c47ba3941c502bffb7f266a41a7f54423"
 uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4"
-version = "4.2.2+0"
+version = "4.2.3+0"
 
 [[deps.MPIPreferences]]
 deps = ["Libdl", "Preferences"]
@@ -349,9 +349,9 @@ version = "0.1.11"
 
 [[deps.MPItrampoline_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
-git-tree-sha1 = "fde81c9f9c94fe5fbeaed7b3f1330305cf9a327c"
+git-tree-sha1 = "70e830dab5d0775183c99fc75e4c24c614ed7142"
 uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748"
-version = "5.5.0+0"
+version = "5.5.1+0"
 
 [[deps.MacroTools]]
 deps = ["Markdown", "Random"]
@@ -559,9 +559,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"]
 
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
-git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50"
+git-tree-sha1 = "777657803913ffc7e8cc20f0fd04b634f871af8f"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.9.7"
+version = "1.9.8"
 
     [deps.StaticArrays.extensions]
     StaticArraysChainRulesCoreExt = "ChainRulesCore"
@@ -668,9 +668,9 @@ version = "5.11.0+0"
 
 [[deps.libzip_jll]]
 deps = ["Artifacts", "Bzip2_jll", "GnuTLS_jll", "JLLWrappers", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"]
-git-tree-sha1 = "3282b7d16ae7ac3e57ec2f3fa8fafb564d8f9f7f"
+git-tree-sha1 = "668ac0297e6bd8f4d53dfdcd3ace71f2e00f4a35"
 uuid = "337d8026-41b4-5cde-a456-74a10e5b31d1"
-version = "1.10.1+0"
+version = "1.11.1+0"
 
 [[deps.nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]

Project.toml

@@ -18,12 +18,10 @@ NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588"
 ProgressLogging = "33c8b6b6-d38a-422a-b730-caa89a2f386c"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 TerminalLoggers = "5d786b92-1e48-4d6f-9151-6b4477ca9bed"
-UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 
 [compat]
 Aqua = "0.8"
@@ -50,15 +48,15 @@ Statistics = "1"
 TOML = "1"
 TerminalLoggers = "0.1.5"
 Test = "1"
-UnPack = "1"
 julia = "1.6"
 
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 Polynomials = "f27b6e38-b328-58d1-80ce-0feddd5e7a45"
 QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Aqua", "Downloads", "Polynomials", "QuadGK", "Test"]
+test = ["Aqua", "Downloads", "Polynomials", "QuadGK", "Test", "Random"]

src/Wflow.jl

@@ -1,34 +1,32 @@
 module Wflow
 
-using Dates
-using TOML
-using Graphs
-using NCDatasets
-using StaticArrays
-using Statistics
-using UnPack
-using Random
-using BasicModelInterface
-using FieldMetadata
-using Parameters
-using DelimitedFiles
-using ProgressLogging
+import BasicModelInterface as BMI
+
+using Base.Threads: nthreads
+using CFTime: CFTime, monthday, dayofyear
+using Dates: Dates, Second, Minute, Hour, Day, Month, year, TimeType, DatePeriod, TimePeriod, Date, DateTime, now, isleapyear, datetime2unix
+using DelimitedFiles: readdlm
+using FieldMetadata: @metadata
+using Glob: glob
+using Graphs: Graphs, Graph, DiGraph, add_edge!, is_cyclic, inneighbors, outneighbors, edges, topological_sort_by_dfs, src, dst, vertices, nv, ne, induced_subgraph, add_vertex!
+using IfElse: IfElse
 using LoggingExtras
+using LoopVectorization: @tturbo
+using NCDatasets: NCDatasets, NCDataset, dimnames, dimsize, nomissing, defDim, defVar
+using Parameters: @with_kw
+using Polyester: @batch
+using ProgressLogging: @progress
+using StaticArrays: SVector, pushfirst, setindex
+using Statistics: mean, median, quantile!
 using TerminalLoggers
-using CFTime
-using Base.Threads
-using Glob
-using Polyester
-using LoopVectorization
-using IfElse
+using TOML: TOML
 
 @metadata get_units "mm dt-1" String
 # metadata for BMI grid
 @metadata exchange 1 Integer
 @metadata grid_type "unstructured" String
 @metadata grid_location "node" String
 
-const BMI = BasicModelInterface
 const Float = Float64
 const CFDataset = Union{NCDataset,NCDatasets.MFDataset}
 const CFVariable_MF = Union{NCDatasets.CFVariable,NCDatasets.MFCFVariable}
@@ -213,7 +211,7 @@ function run_timestep(model::Model; update_func = update, write_model_output = t
 end
 
 function run(model::Model; close_files = true)
-    @unpack network, config, writer, clock = model
+    (; config, writer, clock) = model
 
     model_type = config.model.type::String
 

src/bmi.jl

@@ -48,7 +48,6 @@ Update the model for a single timestep.
 - `run = nothing`: to update a model partially.
 """
 function BMI.update(model::Model; run = nothing)
-    @unpack clock, network, config = model
     if isnothing(run)
         model = run_timestep(model)
     elseif run == "sbm_until_recharge"
@@ -64,7 +63,6 @@ function BMI.update(model::Model; run = nothing)
 end
 
 function BMI.update_until(model::Model, time::Float64)
-    @unpack clock, network, config = model
     t = BMI.get_current_time(model)
     _div, _rem = divrem(time - t, model.clock.dt.value)
     steps = Int(_div)
@@ -85,7 +83,7 @@ end
 
 "Write state output to netCDF and close files."
 function BMI.finalize(model::Model)
-    @unpack config, writer, clock = model
+    (; config, writer) = model
     # it is possible that the state dataset has been closed by `save_state`
     if !isnothing(writer.state_dataset) && isopen(writer.state_dataset)
         write_netcdf_timestep(model, writer.state_dataset, writer.state_parameters)
@@ -95,8 +93,7 @@ function BMI.finalize(model::Model)
 end
 
 function BMI.get_component_name(model::Model)
-    @unpack config = model
-    return config.model.type
+    return model.config.model.type
 end
 
 function BMI.get_input_item_count(model::Model)
@@ -115,7 +112,7 @@ This `API` sections contains a list of `Model` components for which variables ca
 exchanged.
 """
 function BMI.get_input_var_names(model::Model)
-    @unpack config = model
+    (; config) = model
     if haskey(config, "API")
         var_names = Vector{String}()
         for c in config.API.components
@@ -211,7 +208,7 @@ function BMI.get_var_location(model::Model, name::String)
 end
 
 function BMI.get_current_time(model::Model)
-    @unpack config = model
+    (; config) = model
     calendar = get(config, "calendar", "standard")::String
     starttime = cftime(config.starttime, calendar)
     return 0.001 * Dates.value(model.clock.time - starttime)
@@ -222,7 +219,7 @@ function BMI.get_start_time(model::Model)
 end
 
 function BMI.get_end_time(model::Model)
-    @unpack config = model
+    (; config) = model
     calendar = get(config, "calendar", "standard")::String
     starttime = cftime(config.starttime, calendar)
     endtime = cftime(config.endtime, calendar)
@@ -243,7 +240,7 @@ function BMI.get_value(model::Model, name::String, dest::Vector{T}) where {T<:Ab
 end
 
 function BMI.get_value_ptr(model::Model, name::String)
-    @unpack network = model
+    (; network) = model
     s = split(name, "[")
     key = symbols(first(s))
     if exchange(param(model, key[1:end-1]), key[end]) == 1
@@ -322,19 +319,19 @@ function BMI.get_grid_rank(model::Model, grid::Int)
 end
 
 function BMI.get_grid_x(model::Model, grid::Int, x::Vector{T}) where {T<:AbstractFloat}
-    @unpack reader, config = model
-    @unpack dataset = reader
-    sel = active_indices(model.network, grids[grid])
+    (; reader, network) = model
+    (; dataset) = reader
+    sel = active_indices(network, grids[grid])
     inds = [sel[i][1] for i in eachindex(sel)]
     x_nc = read_x_axis(dataset)
     x .= x_nc[inds]
     return x
 end
 
 function BMI.get_grid_y(model::Model, grid::Int, y::Vector{T}) where {T<:AbstractFloat}
-    @unpack reader, config = model
-    @unpack dataset = reader
-    sel = active_indices(model.network, grids[grid])
+    (; reader, network) = model
+    (; dataset) = reader
+    sel = active_indices(network, grids[grid])
     inds = [sel[i][2] for i in eachindex(sel)]
     y_nc = read_y_axis(dataset)
     y .= y_nc[inds]
@@ -350,7 +347,7 @@ function BMI.get_grid_size(model::Model, grid::Int)
 end
 
 function BMI.get_grid_edge_count(model::Model, grid::Int)
-    @unpack network = model
+    (; network) = model
     if grid == 3
         return ne(network.river.graph)
     elseif grid == 4
@@ -365,7 +362,7 @@ function BMI.get_grid_edge_count(model::Model, grid::Int)
 end
 
 function BMI.get_grid_edge_nodes(model::Model, grid::Int, edge_nodes::Vector{Int})
-    @unpack network = model
+    (; network) = model
     n = length(edge_nodes)
     m = div(n, 2)
     # inactive nodes (boundary/ghost points) are set at -999
@@ -402,7 +399,7 @@ function load_state(model::Model)
 end
 
 function save_state(model::Model)
-    @unpack config, writer, clock = model
+    (; config, writer) = model
     if haskey(config, "state") && haskey(config.state, "path_output")
         @info "Write output states to netCDF file `$(model.writer.state_nc_path)`."
     end

src/flextopo_model.jl

@@ -665,7 +665,7 @@ function initialize_flextopo_model(config::Config)
 end
 
 function update(model::Model{N,L,V,R,W,T}) where {N,L,V,R,W,T<:FlextopoModel}
-    @unpack lateral, vertical, network, clock, config = model
+    (; lateral, vertical, network, config) = model
 
     inds_riv = network.index_river
 
@@ -716,7 +716,7 @@ function update(model::Model{N,L,V,R,W,T}) where {N,L,V,R,W,T<:FlextopoModel}
 end
 
 function set_states(model::Model{N,L,V,R,W,T}) where {N,L,V,R,W,T<:FlextopoModel}
-    @unpack lateral, config = model
+    (; lateral, config) = model
     reinit = get(config.model, "reinit", true)::Bool
     # read and set states in model object if reinit=true
     if reinit == false