Refactor/style guide (#437)

* Add configuration file for Julia Formatter

* Add format on save in vscode settings file

* Remove .vscode from gitignore

* Format all Julia files

* Sync wflow's style guide with ribasim's style guide

* Update formatting

* Update .vscode/settings.json

* Remove outdated comments

* Add workaround for VS Code bugs

.JuliaFormatter.toml

@@ -0,0 +1,12 @@
+# Options for the JuliaFormatter auto syntax formatting tool.
+# https://domluna.github.io/JuliaFormatter.jl/stable/
+# https://docs.sciml.ai/SciMLStyle/stable/
+
+# Based on the default style we do pick these non-default options from SciML style:
+whitespace_ops_in_indices = true
+remove_extra_newlines = true
+always_for_in = true
+whitespace_typedefs = true
+
+# And add other options we like:
+separate_kwargs_with_semicolon = true

.gitignore

@@ -1,9 +1,6 @@
 # General
 .DS_Store
 
-# VS Code stuff
-.vscode
-
 # Packaging stuff
 *.jl.*.cov
 *.jl.cov

.vscode/settings.json

@@ -0,0 +1,9 @@
+{
+    "[julia]": {
+        "editor.formatOnSave": true,
+    },
+    "julia.lint.disabledDirs": [
+        ".pixi"
+    ],
+    "julia.lint.run": true,
+}

build/wflow_cli/test/runtests.jl

@@ -2,7 +2,8 @@ using Test
 using Wflow
 
 extension = Sys.iswindows() ? ".exe" : ""
-wflow_exe = normpath(@__DIR__, "../../create_binaries/wflow_bundle/bin/wflow_cli" * extension)
+wflow_exe =
+    normpath(@__DIR__, "../../create_binaries/wflow_bundle/bin/wflow_cli" * extension)
 
 # this assumes that the Wflow tests have already been run, so the data has been downloaded
 testdir = abspath(dirname(pathof(Wflow)), "..", "test")
@@ -14,15 +15,15 @@ outputdir = joinpath(datadir, "output")
 
 @testset "no_config" begin
     # Clean output directory
-    rm(outputdir; force=true, recursive=true)
+    rm(outputdir; force = true, recursive = true)
     @test_throws ProcessFailedException run(`$wflow_exe`)
     # Check if no files are being created
     @test !(isdir(outputdir))
 end
 
 @testset "wflow_sbm" begin
     # Clean directory
-    rm(outputdir; force=true, recursive=true)
+    rm(outputdir; force = true, recursive = true)
     # Run cli with the toml
     toml = normpath(testdir, "sbm_config.toml")
     run(`$wflow_exe $toml`)
@@ -43,7 +44,7 @@ end
 
 @testset "wflow_sbm-gwf" begin
     # Clean directory
-    rm(outputdir; force=true, recursive=true)
+    rm(outputdir; force = true, recursive = true)
     # Run cli with the toml
     toml = normpath(testdir, "sbm_gwf_config.toml")
     run(`$wflow_exe $toml`)
@@ -63,7 +64,7 @@ end
 
 @testset "wflow_sediment" begin
     # Clean directory
-    rm(outputdir; force=true, recursive=true)
+    rm(outputdir; force = true, recursive = true)
     # Run cli with the toml
     toml = normpath(testdir, "sediment_config.toml")
     run(`$wflow_exe $toml`)
@@ -82,11 +83,12 @@ end
 end
 
 @testset "wflow_sbm_timing" begin
-
     toml = normpath(testdir, "sbm_config.toml")
-    time_sbm_1thread = @elapsed run(Cmd(`$wflow_exe $toml`, env=("JULIA_NUM_THREADS" => "1",)))
+    time_sbm_1thread =
+        @elapsed run(Cmd(`$wflow_exe $toml`; env = ("JULIA_NUM_THREADS" => "1",)))
 
-    time_sbm_4thread = @elapsed run(Cmd(`$wflow_exe $toml`, env=("JULIA_NUM_THREADS" => "4", )))
+    time_sbm_4thread =
+        @elapsed run(Cmd(`$wflow_exe $toml`; env = ("JULIA_NUM_THREADS" => "4",)))
 
     # Test if run with more threads is indeed faster
     @test time_sbm_4thread < time_sbm_1thread

server/src/WflowServer.jl

@@ -1,8 +1,8 @@
 module WflowServer
-import ZMQ
-import JSON3
-import StructTypes
-import Wflow
+using ZMQ: ZMQ
+using JSON3: JSON3
+using StructTypes: StructTypes
+using Wflow: Wflow
 
 include("bmi_service.jl")
 include("server.jl")

server/src/bmi_service.jl

@@ -176,7 +176,7 @@ struct SaveState
     fn::String
 end
 
-function wflow_bmi(m::Initialize, model::Union{Wflow.Model,Nothing})
+function wflow_bmi(m::Initialize, model::Union{Wflow.Model, Nothing})
     model = getfield(Wflow.BMI, Symbol(m.fn))(Wflow.Model, m.config_file)
     return model
 end

server/src/server.jl

@@ -39,28 +39,28 @@ const map_structs = Dict(
 )
 
 mutable struct ModelHandler
-    model::Union{Wflow.Model,Nothing}
+    model::Union{Wflow.Model, Nothing}
 end
 
 "Shutdown ZMQ server"
 function shutdown(s::ZMQ.Socket, ctx::ZMQ.Context)
     @info "Shutting down Wflow ZMQ server on request..."
     ZMQ.close(s)
-    ZMQ.close(ctx)
+    return ZMQ.close(ctx)
 end
 
 "Error response ZMQ server"
 function response(err::AbstractString, s::ZMQ.Socket)
     @info "Send error response"
-    resp = Dict{String,String}("status" => "ERROR", "error" => err)
-    ZMQ.send(s, JSON3.write(resp))
+    resp = Dict{String, String}("status" => "ERROR", "error" => err)
+    return ZMQ.send(s, JSON3.write(resp))
 end
 
 "Status response ZMQ server"
 function response(s::ZMQ.Socket)
     @info "Send status response"
-    resp = Dict{String,String}("status" => "OK")
-    ZMQ.send(s, JSON3.write(resp))
+    resp = Dict{String, String}("status" => "OK")
+    return ZMQ.send(s, JSON3.write(resp))
 end
 
 "Validate JSON request against mapped Struct"
@@ -128,7 +128,7 @@ function main(ARGS::Vector{String})
             ),
         )
     end
-    start(port)
+    return start(port)
 end
 
 """

server/test/client.jl

@@ -52,7 +52,8 @@ vwc_1_size = 0
     @test request((fn = "get_var_itemsize", name = "lateral.subsurface.ssf")) ==
           Dict("var_itemsize" => sizeof(Wflow.Float))
     @test request((fn = "get_var_type", name = "vertical.n"))["status"] == "ERROR"
-    @test request((fn = "get_var_units", name = "vertical.theta_s")) == Dict("var_units" => "-")
+    @test request((fn = "get_var_units", name = "vertical.theta_s")) ==
+          Dict("var_units" => "-")
     @test request((fn = "get_var_location", name = "lateral.river.q")) ==
           Dict("var_location" => "node")
     zi_nbytes = request((fn = "get_var_nbytes", name = "vertical.zi"))["var_nbytes"]

server/test/runtests.jl

@@ -1,12 +1,12 @@
-import ZMQ
-import JSON3
-import StructTypes
-import Wflow
-import WflowServer
+using ZMQ: ZMQ
+using JSON3: JSON3
+using StructTypes: StructTypes
+using Wflow: Wflow
+using WflowServer: WflowServer
 import Statistics: mean
 import Logging: with_logger, NullLogger
 import Test: @testset, @test
-import Downloads
+using Downloads: Downloads
 
 # ensure test data is present
 testdir = @__DIR__

src/Wflow.jl

@@ -26,8 +26,8 @@ using IfElse
 
 const BMI = BasicModelInterface
 const Float = Float64
-const CFDataset = Union{NCDataset,NCDatasets.MFDataset}
-const CFVariable_MF = Union{NCDatasets.CFVariable,NCDatasets.MFCFVariable}
+const CFDataset = Union{NCDataset, NCDatasets.MFDataset}
+const CFVariable_MF = Union{NCDatasets.CFVariable, NCDatasets.MFCFVariable}
 const version =
     VersionNumber(TOML.parsefile(joinpath(@__DIR__, "..", "Project.toml"))["version"])
 
@@ -43,7 +43,7 @@ function Clock(config)
     calendar = get(config, "calendar", "standard")::String
     starttime = cftime(config.starttime, calendar)
     dt = Second(config.timestepsecs)
-    Clock(starttime, 0, dt)
+    return Clock(starttime, 0, dt)
 end
 
 function Clock(config, reader)
@@ -77,7 +77,7 @@ function Clock(config, reader)
     end
     starttime = cftime(config.starttime, calendar)
 
-    Clock(starttime, 0, dt)
+    return Clock(starttime, 0, dt)
 end
 
 include("io.jl")
@@ -88,7 +88,7 @@ include("io.jl")
 Composite type that represents all different aspects of a Wflow Model, such as the
 network, parameters, clock, configuration and input and output.
 """
-struct Model{N,L,V,R,W,T}
+struct Model{N, L, V, R, W, T}
     config::Config  # all configuration options
     network::N  # connectivity information, directed graph
     lateral::L  # lateral model that holds lateral state, moves along network
@@ -184,7 +184,7 @@ function run(config::Config)
         error("unknown model type")
     end
     load_fixed_forcing(model)
-    run(model)
+    return run(model)
 end
 
 function run_timestep(model::Model; update_func = update, write_model_output = true)
@@ -212,7 +212,7 @@ function run(model::Model; close_files = true)
     starttime = clock.time
     dt = clock.dt
     endtime = cftime(config.endtime, calendar)
-    times = range(starttime + dt, endtime, step = dt)
+    times = range(starttime + dt, endtime; step = dt)
 
     @info "Run information" model_type starttime dt endtime nthreads()
     runstart_time = now()
@@ -233,7 +233,7 @@ function run(model::Model; close_files = true)
     # option to support running function twice without re-initializing
     # and thus opening the netCDF files
     if close_files
-        Wflow.close_files(model, delete_output = false)
+        Wflow.close_files(model; delete_output = false)
     end
 
     # copy TOML to dir_output, to archive what settings were used
@@ -242,7 +242,7 @@ function run(model::Model; close_files = true)
         dst = output_path(config, basename(src))
         if src != dst
             @debug "Copying TOML file." src dst
-            cp(src, dst, force = true)
+            cp(src, dst; force = true)
         end
     end
     return model
@@ -258,7 +258,7 @@ function run()
     if !isfile(toml_path)
         throw(ArgumentError("File not found: $(toml_path)\n" * usage))
     end
-    run(toml_path)
+    return run(toml_path)
 end
 
 end # module