Code formatting (#56)

* Add JuliaFormatter action and configuration * Reformatted Julia sources From a `format(".")` in the package root * Fix formatting
JuliaHEP · Jun 10, 2024 · 8b5f582 · 8b5f582
1 parent 3c34d06
commit 8b5f582
Show file tree

Hide file tree

Showing 20 changed files with 599 additions and 559 deletions.
diff --git a/.JuliaFormatter.toml b/.JuliaFormatter.toml
@@ -0,0 +1,2 @@
+style = "sciml"
+yas_style_nesting = true
diff --git a/.github/workflows/Format.yml b/.github/workflows/Format.yml
@@ -0,0 +1,13 @@
+name: Format suggestions
+on:
+  pull_request:
+    # this argument is not required if you don't use the `suggestion-label` input
+    types: [ opened, reopened, synchronize, labeled, unlabeled ]
+jobs:
+  code-style:
+    runs-on: ubuntu-latest
+    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')
+          suggestion-label: 'format-suggest' # leave this unset or empty to show suggestions for all PRs
diff --git a/examples/instrumented-jetreco.jl b/examples/instrumented-jetreco.jl
@@ -22,44 +22,39 @@ using JetReconstruction
 # Parsing for algorithm and strategy enums
 include(joinpath(@__DIR__, "parse-options.jl"))
 
-function profile_code(profile, jet_reconstruction, events, niters; R = 0.4, p = -1, strategy = RecoStrategy.N2Tiled)
+function profile_code(profile, jet_reconstruction, events, niters; R = 0.4, p = -1,
+                      strategy = RecoStrategy.N2Tiled)
     Profile.init(n = 5 * 10^6, delay = 0.00001)
     profile_events(events) = begin
         for evt in events
             jet_reconstruction(evt, R = R, p = p, strategy = strategy)
         end
     end
     profile_events(events[1:1])
-    @profile for i ∈ 1:niters
+    @profile for i in 1:niters
         profile_events(events)
     end
     profile_path = joinpath("profile", profile, "profsvg.svg")
     mkpath(dirname(profile_path))
     statprofilehtml(path = dirname(profile_path))
-    fcolor = FlameGraphs.FlameColors(
-        reverse(colormap("Blues", 15))[1:5],
-        colorant"slategray4",
-        colorant"gray95",
-        reverse(colormap("Reds", 15))[1:5],
-        reverse(sequential_palette(39, 10; s = 38, b = 2))[1:5],#brownish pallette
-    )
-    ProfileSVG.save(
-        fcolor,
-        profile_path,
-        combine = true,
-        timeunit = :ms,
-        font = "Arial, Helvetica, sans-serif",
-    )
-    println(
-        "Flame graph from ProfileSVG.jl at file://",
-        abspath(profile_path),
-        "\n",
-        """
-        \tRed tint:          Runtime dispatch
-        \tBrown/yellow tint: Garbage collection
-        \tBlue tint:         OK
-        """,
-    )
+    fcolor = FlameGraphs.FlameColors(reverse(colormap("Blues", 15))[1:5],
+                                     colorant"slategray4",
+                                     colorant"gray95",
+                                     reverse(colormap("Reds", 15))[1:5],
+                                     reverse(sequential_palette(39, 10; s = 38, b = 2))[1:5])
+    ProfileSVG.save(fcolor,
+                    profile_path,
+                    combine = true,
+                    timeunit = :ms,
+                    font = "Arial, Helvetica, sans-serif")
+    println("Flame graph from ProfileSVG.jl at file://",
+            abspath(profile_path),
+            "\n",
+            """
+            \tRed tint:          Runtime dispatch
+            \tBrown/yellow tint: Garbage collection
+            \tBlue tint:         OK
+            """)
 end
 """
 Top level call funtion for demonstrating the use of jet reconstruction
@@ -70,20 +65,18 @@ happens inside the JetReconstruction package itself.
 Some other ustilities are also supported here, such as profiling and
 serialising the reconstructed jet outputs.
 """
-function jet_process(
-    events::Vector{Vector{PseudoJet}};
-    distance::Real = 0.4,
-    algorithm::JetAlgorithm.Algorithm = JetAlgorithm.AntiKt,
-    ptmin::Real = 5.0,
-    dcut = nothing,
-    njets = nothing,
-    strategy::RecoStrategy.Strategy,
-    nsamples::Integer = 1,
-    gcoff::Bool = false,
-    profile = nothing,
-    alloc::Bool = false,
-    dump::Union{String, Nothing} = nothing,
-)
+function jet_process(events::Vector{Vector{PseudoJet}};
+                     distance::Real = 0.4,
+                     algorithm::JetAlgorithm.Algorithm = JetAlgorithm.AntiKt,
+                     ptmin::Real = 5.0,
+                     dcut = nothing,
+                     njets = nothing,
+                     strategy::RecoStrategy.Strategy,
+                     nsamples::Integer = 1,
+                     gcoff::Bool = false,
+                     profile = nothing,
+                     alloc::Bool = false,
+                     dump::Union{String, Nothing} = nothing,)
     @info "Will process $(size(events)[1]) events"
 
     # Map algorithm to power
@@ -98,19 +91,22 @@ function jet_process(
     if nsamples > 1 || !isnothing(profile)
         @info "Doing initial warm-up run"
         for event in events
-            _ = inclusive_jets(jet_reconstruct(event, R = distance, p = power, strategy = strategy), ptmin)
+            _ = inclusive_jets(jet_reconstruct(event, R = distance, p = power,
+                                               strategy = strategy), ptmin)
         end
     end
 
     if !isnothing(profile)
-        profile_code(profile, jet_reconstruct, events, nsamples, R = distance, p = power, strategy = strategy)
+        profile_code(profile, jet_reconstruct, events, nsamples, R = distance, p = power,
+                     strategy = strategy)
         return nothing
     end
 
     if alloc
         println("Memory allocation statistics:")
         @timev for event in events
-            _ = inclusive_jets(jet_reconstruct(event, R = distance, p = power, strategy = strategy), ptmin)
+            _ = inclusive_jets(jet_reconstruct(event, R = distance, p = power,
+                                               strategy = strategy), ptmin)
         end
         return nothing
     end
@@ -120,16 +116,21 @@ function jet_process(
     cummulative_time = 0.0
     cummulative_time2 = 0.0
     lowest_time = typemax(Float64)
-    for irun ∈ 1:nsamples
+    for irun in 1:nsamples
         gcoff && GC.enable(false)
         t_start = time_ns()
         for (ievt, event) in enumerate(events)
             if !isnothing(njets)
-                finaljets = exclusive_jets(jet_reconstruct(event, R = distance, p = power, strategy = strategy), njets = njets)
+                finaljets = exclusive_jets(jet_reconstruct(event, R = distance, p = power,
+                                                           strategy = strategy),
+                                           njets = njets)
             elseif !isnothing(dcut)
-                finaljets = exclusive_jets(jet_reconstruct(event, R = distance, p = power, strategy = strategy), dcut = dcut)
+                finaljets = exclusive_jets(jet_reconstruct(event, R = distance, p = power,
+                                                           strategy = strategy),
+                                           dcut = dcut)
             else
-                finaljets = inclusive_jets(jet_reconstruct(event, R = distance, p = power, strategy = strategy), ptmin)
+                finaljets = inclusive_jets(jet_reconstruct(event, R = distance, p = power,
+                                                           strategy = strategy), ptmin)
             end
             # Only print the jet content once
             if irun == 1
@@ -185,7 +186,7 @@ function jet_process(
     end
 end
 
-parse_command_line(args) = begin
+function parse_command_line(args)
     s = ArgParseSettings(autofix_names = true)
     @add_arg_table! s begin
         "--maxevents", "-n"
@@ -262,7 +263,7 @@ parse_command_line(args) = begin
     return parse_args(args, s; as_symbols = true)
 end
 
-main() = begin
+function main()
     args = parse_command_line(ARGS)
     if args[:debug]
         logger = ConsoleLogger(stdout, Logging.Debug)
@@ -272,12 +273,15 @@ main() = begin
         logger = ConsoleLogger(stdout, Logging.Warn)
     end
     global_logger(logger)
-    events::Vector{Vector{PseudoJet}} =
-        read_final_state_particles(args[:file], maxevents = args[:maxevents], skipevents = args[:skip])
-    jet_process(events, distance = args[:distance], algorithm = args[:algorithm], strategy = args[:strategy],
-        ptmin = args[:ptmin], dcut = args[:exclusive_dcut], njets = args[:exclusive_njets],
-        nsamples = args[:nsamples], gcoff = args[:gcoff], profile = args[:profile],
-        alloc = args[:alloc], dump = args[:dump])
+    events::Vector{Vector{PseudoJet}} = read_final_state_particles(args[:file],
+                                                                   maxevents = args[:maxevents],
+                                                                   skipevents = args[:skip])
+    jet_process(events, distance = args[:distance], algorithm = args[:algorithm],
+                strategy = args[:strategy],
+                ptmin = args[:ptmin], dcut = args[:exclusive_dcut],
+                njets = args[:exclusive_njets],
+                nsamples = args[:nsamples], gcoff = args[:gcoff], profile = args[:profile],
+                alloc = args[:alloc], dump = args[:dump])
     nothing
 end
 

diff --git a/examples/jetreco.jl b/examples/jetreco.jl
@@ -25,16 +25,14 @@ happens inside the JetReconstruction package itself.
 
 Final jets can be serialised if the "dump" option is given
 """
-function jet_process(
-    events::Vector{Vector{PseudoJet}};
-    distance::Real = 0.4,
-    algorithm::JetAlgorithm.Algorithm = JetAlgorithm.AntiKt,
-    ptmin::Real = 5.0,
-    dcut = nothing,
-    njets = nothing,
-    strategy::RecoStrategy.Strategy,
-    dump::Union{String, Nothing} = nothing,
-)
+function jet_process(events::Vector{Vector{PseudoJet}};
+                     distance::Real = 0.4,
+                     algorithm::JetAlgorithm.Algorithm = JetAlgorithm.AntiKt,
+                     ptmin::Real = 5.0,
+                     dcut = nothing,
+                     njets = nothing,
+                     strategy::RecoStrategy.Strategy,
+                     dump::Union{String, Nothing} = nothing,)
     @info "Will process $(size(events)[1]) events"
 
     # If we are dumping the results, setup the JSON structure
@@ -57,11 +55,14 @@ function jet_process(
     # Now run over each event
     for (ievt, event) in enumerate(events)
         if !isnothing(njets)
-            finaljets = exclusive_jets(jet_reconstruct(event, R = distance, p = power, strategy = strategy), njets = njets)
+            finaljets = exclusive_jets(jet_reconstruct(event, R = distance, p = power,
+                                                       strategy = strategy), njets = njets)
         elseif !isnothing(dcut)
-            finaljets = exclusive_jets(jet_reconstruct(event, R = distance, p = power, strategy = strategy), dcut = dcut)
+            finaljets = exclusive_jets(jet_reconstruct(event, R = distance, p = power,
+                                                       strategy = strategy), dcut = dcut)
         else
-            finaljets = inclusive_jets(jet_reconstruct(event, R = distance, p = power, strategy = strategy), ptmin)
+            finaljets = inclusive_jets(jet_reconstruct(event, R = distance, p = power,
+                                                       strategy = strategy), ptmin)
         end
         @info begin
             jet_output = "Event $(ievt)\n"
@@ -83,7 +84,7 @@ function jet_process(
     end
 end
 
-parse_command_line(args) = begin
+function parse_command_line(args)
     s = ArgParseSettings(autofix_names = true)
     @add_arg_table! s begin
         "--maxevents", "-n"
@@ -134,16 +135,18 @@ parse_command_line(args) = begin
     return parse_args(args, s; as_symbols = true)
 end
 
-
-main() = begin
+function main()
     args = parse_command_line(ARGS)
     logger = ConsoleLogger(stdout, Logging.Info)
     global_logger(logger)
-    events::Vector{Vector{PseudoJet}} =
-        read_final_state_particles(args[:file], maxevents = args[:maxevents], skipevents = args[:skip])
-    jet_process(events, distance = args[:distance], algorithm = args[:algorithm], strategy = args[:strategy],
-        ptmin = args[:ptmin], dcut = args[:exclusive_dcut], njets = args[:exclusive_njets],
-        dump = args[:dump])
+    events::Vector{Vector{PseudoJet}} = read_final_state_particles(args[:file],
+                                                                   maxevents = args[:maxevents],
+                                                                   skipevents = args[:skip])
+    jet_process(events, distance = args[:distance], algorithm = args[:algorithm],
+                strategy = args[:strategy],
+                ptmin = args[:ptmin], dcut = args[:exclusive_dcut],
+                njets = args[:exclusive_njets],
+                dump = args[:dump])
     nothing
 end
 

diff --git a/examples/parse-options.jl b/examples/parse-options.jl
@@ -4,17 +4,17 @@ from the command line.
 """
 
 function ArgParse.parse_item(::Type{RecoStrategy.Strategy}, x::AbstractString)
-	s = tryparse(RecoStrategy.Strategy, x)
-	if s === nothing
-		throw(ErrorException("Invalid value for strategy: $(x)"))
-	end
-	s
+    s = tryparse(RecoStrategy.Strategy, x)
+    if s === nothing
+        throw(ErrorException("Invalid value for strategy: $(x)"))
+    end
+    s
 end
 
 function ArgParse.parse_item(::Type{JetAlgorithm.Algorithm}, x::AbstractString)
-	s = tryparse(JetAlgorithm.Algorithm, x)
-	if s === nothing
-		throw(ErrorException("Invalid value for algorithm: $(x)"))
-	end
-	s
-end
+    s = tryparse(JetAlgorithm.Algorithm, x)
+    if s === nothing
+        throw(ErrorException("Invalid value for algorithm: $(x)"))
+    end
+    s
+end
diff --git a/examples/visualise-jets.jl b/examples/visualise-jets.jl
@@ -11,7 +11,6 @@ using JetReconstruction
 include(joinpath(@__DIR__, "parse-options.jl"))
 
 function main()
-
     s = ArgParseSettings(autofix_names = true)
     @add_arg_table s begin
         "--event", "-e"
@@ -57,15 +56,16 @@ function main()
     end
     args = parse_args(ARGS, s; as_symbols = true)
 
-
     logger = ConsoleLogger(stdout, Logging.Info)
     global_logger(logger)
 
-    events::Vector{Vector{PseudoJet}} =
-        read_final_state_particles(args[:file], maxevents = args[:event], skipevents = args[:event])
+    events::Vector{Vector{PseudoJet}} = read_final_state_particles(args[:file],
+                                                                   maxevents = args[:event],
+                                                                   skipevents = args[:event])
 
     power = JetReconstruction.algorithm2power[args[:algorithm]]
-    cs = jet_reconstruct(events[1], R = args[:distance], p = power, strategy = args[:strategy])
+    cs = jet_reconstruct(events[1], R = args[:distance], p = power,
+                         strategy = args[:strategy])
 
     plt = jetsplot(events[1], cs; Module = CairoMakie)
     save(args[:output], plt)