add infrastructure for running as electron app

.gitignore

@@ -29,3 +29,13 @@ JuliaLocalPreferences.toml
 
 # icloud/finder specific files on macOS.
 *.DS_Store
+
+# Electron app
+GUI/electron/node_modules/
+GUI/electron/dist/
+
+# Julia compiled app output (large binary, built locally)
+GUI/backend/julia-app/
+
+# Julia build environment manifest (resolved locally)
+GUI/backend/build/Manifest.toml

GUI/backend/Project.toml

@@ -5,7 +5,6 @@ authors = ["Helmut Strey <Helmut.Strey@stonybrook.edu>"]
 
 [deps]
 Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
-DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"

GUI/backend/build.jl

@@ -0,0 +1,40 @@
+"""
+Build script for NT Cycling Model – compiles the Julia backend into a
+standalone executable using PackageCompiler.jl.
+
+Usage (from repo root):
+    julia --project=GUI/backend/build GUI/backend/build.jl
+
+Prerequisites:
+  1. Julia 1.10+ installed and on PATH.
+  2. Backend dependencies resolved:
+       julia --project=GUI/backend -e 'using Pkg; Pkg.instantiate()'
+  3. PackageCompiler installed in the build env:
+       julia --project=GUI/backend/build -e 'using Pkg; Pkg.instantiate()'
+
+Output: GUI/backend/julia-app/
+  bin/server        – compiled executable
+  lib/              – Julia runtime + precompiled sysimage
+  share/            – Julia standard library sources
+
+The julia-app/ directory is then bundled by electron-builder as an
+extraResource inside the Electron app (see GUI/electron/package.json).
+"""
+
+using PackageCompiler
+
+backend_dir = joinpath(@__DIR__)          # GUI/backend/
+output_dir  = joinpath(@__DIR__, "julia-app")
+precompile  = joinpath(@__DIR__, "precompile_app.jl")
+
+@info "Building NT Cycling app..." backend_dir output_dir
+
+create_app(
+    backend_dir,
+    output_dir;
+    precompile_execution_file = precompile,
+    force = true,
+    include_lazy_artifacts = true,
+)
+
+@info "Build complete." output_dir

GUI/backend/build/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+PackageCompiler = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d"

GUI/backend/precompile_app.jl

@@ -0,0 +1,56 @@
+# Precompile workload for PackageCompiler.
+# This script exercises key code paths so the compiled sysimage covers them,
+# resulting in faster startup and response times.
+
+using Catalyst
+using HTTP
+using Oxygen
+using OrdinaryDiffEqTsit5
+using JSON3
+using XLSX
+
+include(joinpath(@__DIR__, "src", "NTModelModule.jl"))
+using .NTModelModule
+
+# Exercise model construction and simulation
+model = NTModel()
+sol = simulate(model; tspan=(0.0, 600.0))
+
+# Exercise result extraction (both absolute and percentage modes)
+results = extract_results(sol, ["GLU_e", "GABA_i", "GLN_a", "GLN_e", "GLU_i", "GABA_v", "GLN_i", "GLU_a", "KET_b"], false)
+results_pct = extract_results(sol, ["GLU_e", "GABA_i"], true)
+
+# Exercise defaults serialisation
+defaults = get_defaults(model)
+
+# Exercise JSON round-trip
+json_str = JSON3.write(results)
+JSON3.read(json_str)
+json_str2 = JSON3.write(defaults)
+JSON3.read(json_str2)
+
+# Exercise a second simulation with modified parameters (mirrors /api/simulate usage)
+model2 = NTModel()
+model2.ps[:KET_p] = 3.9
+sol2 = simulate(model2; tspan=(0.0, 90.0))
+extract_results(sol2, ["GLU_e", "GABA_i"], true)
+
+# Exercise Oxygen route registration — this is the critical step that ensures
+# Oxygen's router, @get/@post macro expansions, and handler dispatch are all
+# compiled into the sysimage.  (serve() itself cannot be called here because
+# it blocks, but registering routes + invoking handlers covers all hot paths.)
+using NTCycling
+NTCycling.register_routes!()
+
+# Exercise handler functions directly to precompile the full request/response
+# dispatch path for each endpoint.
+NTCycling._handle_defaults(HTTP.Request("GET", "/api/defaults"))
+
+simulate_body = """{"simLength":60,"selectedStates":["GLU_e","GABA_i"],"percentageChange":false}"""
+NTCycling._handle_simulate(
+    HTTP.Request("POST", "/api/simulate",
+        ["Content-Type" => "application/json"],
+        simulate_body)
+)
+
+println("Precompile workload complete")

GUI/backend/src/NTCycling.jl

@@ -1,4 +1,17 @@
 module NTCycling
-println("Hello")
-# does nothing
+
+include("server.jl")
+
+Base.@ccallable function julia_main()::Cint
+    try
+        port = parse(Int, get(ENV, "NT_PORT", "8090"))
+        host = get(ENV, "NT_HOST", "127.0.0.1")
+        start_server(; host=host, port=port)
+    catch e
+        println(stderr, "Error starting server: ", e)
+        return 1
+    end
+    return 0
+end
+
 end

GUI/backend/src/NTModelModule.jl

@@ -2,9 +2,8 @@ module NTModelModule
 
 using Catalyst
 using OrdinaryDiffEqTsit5
-using DataFrames
 
-export NTModel, simulate, get_timeseries, get_defaults, extract_results
+export NTModel, simulate, get_defaults, extract_results
 export unknowns
 
 mutable struct NTModel
@@ -262,24 +261,24 @@ function extract_results(sol, selected_states::Vector{String}, percentage_change
     )
 end
 
-"""
-    get_timeseries(sol; selected_states=["GLN_e(t)"], percentage_change=false)
-
-Returns time series as DataFrame for selected states.
-"""
-function get_timeseries(sol; selected_states=["GLN_e(t)"], percentage_change=false)
-    timeseries = []
-    for state in selected_states
-        state_symbol = Symbol(replace(state, "(t)" => ""))
-        if percentage_change
-            push!(timeseries, round.(100 .* sol[state_symbol]./(sol[state_symbol][1]) .- 100, digits=1))
-        else
-            push!(timeseries, sol[state_symbol])
-        end
-    end
-
-    df = DataFrame([sol.t, timeseries...], Symbol.(["time", selected_states...]))
-    return df
-end
+#"""
+#    get_timeseries(sol; selected_states=["GLN_e(t)"], percentage_change=false)
+#
+#Returns time series as DataFrame for selected states.
+#"""
+#function get_timeseries(sol; selected_states=["GLN_e(t)"], percentage_change=false)
+#    timeseries = []
+#    for state in selected_states
+#        state_symbol = Symbol(replace(state, "(t)" => ""))
+#        if percentage_change
+#            push!(timeseries, round.(100 .* sol[state_symbol]./(sol[state_symbol][1]) .- 100, digits=1))
+#        else
+#            push!(timeseries, sol[state_symbol])
+#        end
+#    end
+#
+#    df = DataFrame([sol.t, timeseries...], Symbol.(["time", selected_states...]))
+#    return df
+#end
 
 end

GUI/backend/src/api/defaults.jl

@@ -1,7 +1,11 @@
 # GET /api/defaults - Returns default parameters, states, units, descriptions
 
-@get "/api/defaults" function(req::HTTP.Request)
+function _handle_defaults(req::HTTP.Request)
     model = NTModel()
     defaults = get_defaults(model)
     return JSON3.write(defaults)
 end
+
+function register_defaults_routes!()
+    @get "/api/defaults" _handle_defaults
+end

GUI/backend/src/api/examples.jl

@@ -1,4 +1,4 @@
-# GET /api/examples - List available examples
+# GET /api/examples  - List available examples
 # GET /api/example/:id - Get specific example configuration
 
 const EXAMPLES = Dict(
@@ -50,7 +50,7 @@ const EXAMPLES = Dict(
     )
 )
 
-@get "/api/examples" function(req::HTTP.Request)
+function _handle_examples(req::HTTP.Request)
     examples_list = [
         Dict(
             "id" => id,
@@ -62,10 +62,15 @@ const EXAMPLES = Dict(
     return JSON3.write(examples_list)
 end
 
-@get "/api/example/{id}" function(req::HTTP.Request, id::String)
+function _handle_example_by_id(req::HTTP.Request, id::String)
     if haskey(EXAMPLES, id)
         return JSON3.write(EXAMPLES[id])
     else
         return HTTP.Response(404, JSON3.write(Dict("error" => "Example not found")))
     end
 end
+
+function register_examples_routes!()
+    @get "/api/examples" _handle_examples
+    @get "/api/example/{id}" _handle_example_by_id
+end

GUI/backend/src/api/export.jl

@@ -1,9 +1,6 @@
 # POST /api/export - Generate XLSX file
 
-using XLSX
-using DataFrames
-
-@post "/api/export" function(req::HTTP.Request)
+function _handle_export(req::HTTP.Request)
     body = JSON3.read(String(req.body))
 
     # Create a temporary file for the XLSX
@@ -97,3 +94,7 @@ using DataFrames
     ]
     return HTTP.Response(200, headers, xlsx_data)
 end
+
+function register_export_routes!()
+    @post "/api/export" _handle_export
+end

GUI/backend/src/api/simulation.jl

@@ -1,6 +1,6 @@
 # POST /api/simulate - Run simulation for both conditions
 
-@post "/api/simulate" function(req::HTTP.Request)
+function _handle_simulate(req::HTTP.Request)
     body = JSON3.read(String(req.body))
 
     # Create models for each condition
@@ -59,3 +59,7 @@
         "condition2" => results2
     ))
 end
+
+function register_simulation_routes!()
+    @post "/api/simulate" _handle_simulate
+end

GUI/backend/src/server.jl

@@ -1,64 +1,77 @@
 using Oxygen
 using HTTP
 using JSON3
+using XLSX
 
 # Include the model
 include("NTModelModule.jl")
 using .NTModelModule
 
 # Serve static files from public directory
-const PUBLIC_DIR = joinpath(@__DIR__, "..", "public")
+const PUBLIC_DIR = get(ENV, "NT_PUBLIC_DIR", joinpath(@__DIR__, "..", "public"))
 
-# Main page
-@get "/" function(req::HTTP.Request)
-    html_content = read(joinpath(PUBLIC_DIR, "index.html"), String)
-    return HTTP.Response(200, ["Content-Type" => "text/html"], html_content)
-end
+# Include API files at module load time so handler functions are compiled into the sysimage.
+# Route *registration* (@get/@post calls) happens inside register_routes!() at runtime,
+# because Oxygen's HTTP router state does not survive sysimage serialisation.
+include("api/defaults.jl")
+include("api/simulation.jl")
+include("api/examples.jl")
+include("api/export.jl")
+
+function register_routes!()
 
-# Documentation page
-@get "/documentation" function(req::HTTP.Request)
-    filepath = joinpath(PUBLIC_DIR, "docs.html")
-    if isfile(filepath)
-        html_content = read(filepath, String)
+    # Main page
+    @get "/" function(req::HTTP.Request)
+        html_content = read(joinpath(PUBLIC_DIR, "index.html"), String)
         return HTTP.Response(200, ["Content-Type" => "text/html"], html_content)
-    else
-        return HTTP.Response(404, "Documentation page not found")
     end
-end
 
-# Serve static files (CSS, images, etc.)
-@get "/css/{filename}" function(req::HTTP.Request, filename::String)
-    filepath = joinpath(PUBLIC_DIR, "css", filename)
-    if isfile(filepath)
-        content = read(filepath, String)
-        return HTTP.Response(200, ["Content-Type" => "text/css"], content)
-    else
-        return HTTP.Response(404, "File not found")
+    # Documentation page
+    @get "/documentation" function(req::HTTP.Request)
+        filepath = joinpath(PUBLIC_DIR, "docs.html")
+        if isfile(filepath)
+            html_content = read(filepath, String)
+            return HTTP.Response(200, ["Content-Type" => "text/html"], html_content)
+        else
+            return HTTP.Response(404, "Documentation page not found")
+        end
     end
-end
 
-@get "/images/{filename}" function(req::HTTP.Request, filename::String)
-    filepath = joinpath(PUBLIC_DIR, "images", filename)
-    if isfile(filepath)
-        content = read(filepath)
-        content_type = endswith(filename, ".png") ? "image/png" : "image/jpeg"
-        return HTTP.Response(200, ["Content-Type" => content_type], content)
-    else
-        return HTTP.Response(404, "File not found")
+    # Serve static files (CSS, images, etc.)
+    @get "/css/{filename}" function(req::HTTP.Request, filename::String)
+        filepath = joinpath(PUBLIC_DIR, "css", filename)
+        if isfile(filepath)
+            content = read(filepath, String)
+            return HTTP.Response(200, ["Content-Type" => "text/css"], content)
+        else
+            return HTTP.Response(404, "File not found")
+        end
     end
-end
 
-# Include API endpoints
-include("api/defaults.jl")
-include("api/simulation.jl")
-include("api/examples.jl")
-include("api/export.jl")
+    @get "/images/{filename}" function(req::HTTP.Request, filename::String)
+        filepath = joinpath(PUBLIC_DIR, "images", filename)
+        if isfile(filepath)
+            content = read(filepath)
+            content_type = endswith(filename, ".png") ? "image/png" : "image/jpeg"
+            return HTTP.Response(200, ["Content-Type" => content_type], content)
+        else
+            return HTTP.Response(404, "File not found")
+        end
+    end
+
+    # API routes
+    register_defaults_routes!()
+    register_simulation_routes!()
+    register_examples_routes!()
+    register_export_routes!()
+end
 
 # Start server
 function start_server(; host="127.0.0.1", port::Int=8090)
+    register_routes!()
     println("Starting NT Cycling Model server on http://localhost:$port")
     println("Press Ctrl+C to stop the server")
-    serve(; host=host,port=port)
+    serve(; host=host, port=port)
 end
 
 # Run if executed directly