Update docs, examples + Fix intermediate hook (#62)

ARCHITECTURE.md

@@ -0,0 +1,20 @@
+# Architecture
+
+The Simulation Service (soon to be renamed SciML Service) is a REST API that wraps
+specific SciML tasks. The service should match the spec [here](https://github.com/DARPA-ASKEM/simulation-api-spec)
+since PyCIEMSS Service and SciML Service ideally are hot swappable.
+
+The API creates a job using the JobSchedulers.jl library and updates the Terarium Data Service (TDS) with the status 
+of the job throughout its execution. Once the job completes, the results are written to S3. With most of the output artifacts, we do little postprocessing
+after completing the SciML portion.
+
+## Layout
+
+Source is split into 5 major components:
+- `SimulationService.jl`: Contains the start and stop functions for the service
+- `Settings.jl`: Enumerates the environment variables used by the project
+- `service`: Job scheduling, pre/post-processing, endpoints, etc. Handled by TA4. 
+- `contracts`: Location where TA3 and TA4 agree on an interface between the SciML Operations and the rest of the service. 
+  - `Available.jl`: The operations available to the API are here. Generally, the operations just wrap around by the exposed SciML
+                    operations. 
+- `operations`: JuliaHub primarily focuses here.

README.md

@@ -10,12 +10,25 @@ With docker compose:
 docker compose --file docker/docker-compose.yml up --build
 ```
 
-With Julia REPL:
+With Julia REPL assuming you want to run it standalone:
 
 ```
-julia> using SimulationService
+>> export ENABLE_TDS=false # Include if you would like to disable backend services
+>> julia --project --threads 15 # We need multithreading
+julia> using SimulationService, HTTP
+julia> import JSON3 as JSON
 julia> start!()
+julia> model_json = String(read("./examples/BIOMD0000000955_askenet.json"))
+julia> # Let's do a simulate
+julia> operation = "simulate"
+julia> operation_args = Dict(:model=> model_json, :timespan => Dict("start" => 0, "end" => 90)) # should match up to what's in Availble.jl
+julia> simulation = SimulationService.make_deterministic_run(operation_args, operation)
+julia> simulation_id = JSON.read(String(simulation.body)).simulation_id
+julia> status = SimulationService.retrieve_job(nothing, simulation_id, "status") # rerun until complete
+julia> result = SimulationService.retrieve_job(nothing, simulation_id, "result")
 julia> # output of REST API and Scheduler
 julia> stop!()
 julia> # you may safely leave the repl or rerun `start!`
 ````
+
+To check available endpoints, try checking [localhost:8080/docs](localhost:8080/docs)