Merge pull request #16 from ConnectedSystems/migration

Performance changes and updates for Julia v1.11

Author: ConnectedSystems

.gitignore

@@ -24,3 +24,5 @@ docs/site/
 Manifest.toml
 
 .vscode/
+
+sandbox

Project.toml

@@ -1,7 +1,7 @@
 name = "Streamfall"
 uuid = "09d4d480-e905-4803-959d-af438f1c2811"
 authors = ["ConnectedSystems"]
-version = "0.1.9"
+version = "0.2.0"
 
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
@@ -23,7 +23,6 @@ GR = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"
 GR_jll = "d2c73de3-f751-5644-a686-071e5b155ba9"
 GraphPlot = "a2cc645c-3eea-5389-862e-a155d0052231"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
-Infiltrator = "5903a43b-9cc3-4c30-8d17-598619ec4e9b"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
@@ -34,7 +33,6 @@ OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
-Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
@@ -43,9 +41,8 @@ StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
 StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd"
 Tar = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-Traceur = "37b6cedf-1f77-55f8-9503-c64b63398394"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 ZipFile = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"
 
 [compat]
-ModelParameters = "0.3.0"
+ModelParameters = "0.4.4"

src/Climate.jl

@@ -8,19 +8,50 @@ struct Climate
     # t_id::Union{String, Nothing} = nothing
 end
 
-
 """
-    subcatchment_data(node::NetworkNode, climate::Climate)
+Extract streamflow data from file.
 
-Extract all data for a given node from climate object.
+Streamflow (Q) column is identified the Gauge ID.
+
+Flow data is identified with the suffix `_Q` by default
+e.g., ("000001_Q")
+
+# Arguments
+- `data` : Observation data
+- `gauge_id` : Gauge/Node ID
+- `suffix` : Suffix used to indicate flow data (default: "_Q")
+
+# Returns
+DataFrame of observations for selected gauge.
 """
-function subcatchment_data(node::NetworkNode, climate::Climate)::DataFrame
-    data = climate.climate_data
-    cols = filter(x -> occursin(node.name, string(x)), names(data))
+@inline function extract_flow(
+    data::DataFrame, gauge_id::String, suffix::String="_Q"
+)::DataFrame
+    target = data[:, ["Date", gauge_id * suffix]]
+    rename!(target, gauge_id * suffix => gauge_id)
 
-    return data[:, vcat(["Date"], cols)]
+    return target
 end
 
+"""
+Create a climate dataset of Precipitation (P) and Potential Evapotranspiration (PET).
+Data for multiple gauges may be defined in a single dataset.
+
+P and PET columns are identified by `_P` and `_PET` suffixes by default.
+
+# Arguments
+- `data` : Observation data
+- `P_suffix` : Suffix used to indicate precipitation (default: "_P")
+- `PET_suffix` : Suffix used to indicate Potential Evapotranspiration (default: "_PET")
+
+# Returns
+Climate
+"""
+@inline function extract_climate(
+    data::DataFrame; P_suffix::String="_P", PET_suffix::String="_PET"
+)::Climate
+    return Climate(data, P_suffix, PET_suffix)
+end
 
 """
     rainfall_data(node::NetworkNode, climate::Climate)::DataFrame
@@ -29,27 +60,38 @@ Extract rainfall data for a given node.
 """
 function rainfall_data(node::NetworkNode, climate::Climate)::DataFrame
     data = climate.climate_data
-    rain_col = filter(x -> occursin(node.name, x) 
-                            & occursin(climate.rainfall_id, x), 
+    rain_col = filter(x -> occursin(node.name, x)
+                            & occursin(climate.rainfall_id, x),
                             names(data))[1]
 
     return data[:, rain_col]
 end
 
+"""
+    subcatchment_data(node::NetworkNode, climate::Climate)
+
+Extract all data for a given node from climate object.
+"""
+function subcatchment_data(node::NetworkNode, climate::Climate)::DataFrame
+    data = climate.climate_data
+    cols = filter(x -> occursin(node.name, string(x)), names(data))
+
+    return data[:, vcat(["Date"], cols)]
+end
 
 """
     climate_values(node::NetworkNode, climate::Climate, timestep::Int)
 
 Extract climate related data for a given time step.
 """
-function climate_values(node::NetworkNode, climate::Climate, 
+function climate_values(node::NetworkNode, climate::Climate,
                         timestep::Int)
     node_name::String = node.name
     data::DataFrame = climate.climate_data
 
     # TODO : Catch instances where data is not found (raises BoundsError)
-    rain_col = filter(x -> occursin(node_name, x) 
-                        & occursin(climate.rainfall_id, x), 
+    rain_col = filter(x -> occursin(node_name, x)
+                        & occursin(climate.rainfall_id, x),
                         names(data))[1]
     et_col = filter(x -> occursin(node_name, x)
                         & occursin(climate.et_id, x),
@@ -66,14 +108,14 @@ end
 """
     climate_values(node::NetworkNode, climate::Climate)
 
-Extract climate related data for a given time step.
+Extract climate related data.
 """
 function climate_values(node::NetworkNode, climate::Climate)
     data::DataFrame = climate.climate_data
 
     # TODO : Catch instances where data is not found (raises BoundsError)
-    rain_col = filter(x -> occursin(node.name, x) 
-                            & occursin(climate.rainfall_id, x), 
+    rain_col = filter(x -> occursin(node.name, x)
+                            & occursin(climate.rainfall_id, x),
                             names(data))[1]
     et_col = filter(x -> occursin(node.name, x)
                             & occursin(climate.et_id, x),

src/DamNode.jl

@@ -26,10 +26,11 @@ function c_dam_outflow(discharge, irrigation_extraction)
 end
 
 
-Base.@kwdef mutable struct DamNode{P} <: NetworkNode
-    @network_node
+Base.@kwdef mutable struct DamNode{P, A<:AbstractFloat} <: NetworkNode
+    name::String
+    area::A
 
-    max_storage::Float64
+    max_storage::A
     storage_coef::P = Param(0.5, bounds=(0.00001, 10.0))
 
 
@@ -45,16 +46,16 @@ Base.@kwdef mutable struct DamNode{P} <: NetworkNode
     # Function to calculate outflow from dam
     calc_dam_outflow::Function = c_dam_outflow
 
-    storage::Array{Float64} = [0.0]
+    storage::Array{A} = [0.0]
 
-    effective_rainfall::Array{Float64} = []
-    et::Array{Float64} = []
-    inflow::Array{Float64} = []
-    dam_area::Array{Float64} = []
+    effective_rainfall::Array{A} = []
+    et::Array{A} = []
+    inflow::Array{A} = []
+    dam_area::Array{A} = []
 
-    level::Array{Float64} = []
-    discharge::Array{Float64} = []
-    outflow::Array{Float64} = []
+    level::Array{A} = []
+    discharge::Array{A} = []
+    outflow::Array{A} = []
 
 end
 
@@ -161,25 +162,25 @@ Update dam volume for timestep.
 volume of water stored in dam
 """
 function update_volume(volume, node_inflow, gamma, rain, evap, area, extractions, discharge, max_store)::Float64
-    
+
     vol = volume + (node_inflow + gamma) + (rain - evap) * area - extractions - discharge
 
     return max(0.0, min(max_store, vol))
 end
 
 
-function run_node!(node::DamNode, climate::Climate; 
+function run_node!(node::DamNode, climate::Climate;
                    inflow=nothing, extraction=nothing, exchange=nothing)
     timesteps = sim_length(climate)
     for ts in 1:timesteps
-        run_node!(node, climate, ts; 
+        run_node!(node, climate, ts;
                   inflow=inflow, extraction=extraction, exchange=exchange)
     end
 end
 
 
 """
-    run_node!(node::DamNode, climate::Climate, timestep::Int; 
+    run_node!(node::DamNode, climate::Climate, timestep::Int;
               inflow=nothing, extraction=nothing, exchange=nothing)
 
 Run a specific node for a specified time step.
@@ -192,7 +193,7 @@ Run a specific node for a specified time step.
 - `extraction::DataFrame` : Time series of water orders (expects column of `_releases`)
 - `exchange::DataFrame` : Time series of groundwater flux
 """
-function run_node!(node::DamNode, climate::Climate, timestep::Int; 
+function run_node!(node::DamNode, climate::Climate, timestep::Int;
                    inflow=nothing, extraction=nothing, exchange=nothing)
     ts = timestep
     if checkbounds(Bool, node.outflow, ts)
@@ -220,14 +221,14 @@ Calculate outflow for the dam node for a single time step.
 - node : DamNode
 - rain : rainfall in mm
 - et : evapotranspiration data in mm
-- irrig_ext : irrigation extractions 
+- irrig_ext : irrigation extractions
 - extractions : extraction data in ML
 - gw_flux : groundwater interaction
 
 # Returns
 - outflow from dam
 """
-function run_node!(node::DamNode, 
+function run_node!(node::DamNode,
                    rain::Float64,
                    et::Float64,
                    vol::Float64,

src/EnsembleNode.jl

@@ -6,8 +6,9 @@ using Statistics
 abstract type EnsembleNode <: NetworkNode end
 
 
-Base.@kwdef mutable struct BaseEnsemble{N<:NetworkNode, P, R<:Real} <: EnsembleNode
-    @network_node
+Base.@kwdef mutable struct BaseEnsemble{N<:NetworkNode, P, A<:Real} <: EnsembleNode
+    name::String
+    area::A
 
     instances::Array{N} = []
     weights::Array{P} = [
@@ -17,7 +18,7 @@ Base.@kwdef mutable struct BaseEnsemble{N<:NetworkNode, P, R<:Real} <: EnsembleN
     # Default to weighted sum
     comb_method::Function = (X, weights) -> sum([x * w for (x, w) in zip(X, weights)])
 
-    outflow::Array{R} = []
+    outflow::Array{A} = []
 end