Merge branch 'main' into partition_basin_struct

build/README.md

@@ -7,3 +7,38 @@ pixi run build
 ```
 
 > :warning: If the build is failing, because it cannot find certain files, chances are high that you need to enable long paths in Windows.
+
+## Ribasim CLI
+
+In order to find out about it's usage call `ribasim --help`
+
+## Libribasim
+
+Libribasim is a shared library that exposes Ribasim functionality to external (non-Julian)
+programs. It can be compiled using [PackageCompiler's
+create_lib](https://julialang.github.io/PackageCompiler.jl/stable/libs.html), which is set
+up in this directory. The C API that is offered to control Ribasim is the C API of the
+[Basic Model Interface](https://bmi.readthedocs.io/en/latest/), also known as BMI.
+
+Not all BMI functions are implemented yet.
+Couplings to other models are implemented in [`imod_coupler`](https://github.com/Deltares/imod_coupler).
+
+Here is an example of using libribasim from Python:
+
+```python
+In [1]: from ctypes import CDLL, c_int, c_char_p, create_string_buffer, byref
+
+In [2]: c_dll = CDLL("libribasim", winmode=0x08)  # winmode for Windows
+
+In [3]: argument = create_string_buffer(0)
+   ...: c_dll.init_julia(c_int(0), byref(argument))
+Out[3]: 1
+
+In [4]: config_path = "ribasim.toml"
+
+In [5]: c_dll.initialize(c_char_p(config_path.encode()))
+Out[5]: 0
+
+In [6]: c_dll.update()
+Out[6]: 0
+```

build/build.jl

@@ -3,44 +3,6 @@ using PackageCompiler
 using TOML
 using LibGit2
 
-"""
-# Ribasim CLI
-
-In order to find out about it's usage call `ribasim --help`
-
-# Libribasim
-
-Libribasim is a shared library that exposes Ribasim functionality to external (non-Julian)
-programs. It can be compiled using [PackageCompiler's
-create_lib](https://julialang.github.io/PackageCompiler.jl/stable/libs.html), which is set
-up in this directory. The C API that is offered to control Ribasim is the C API of the
-[Basic Model Interface](https://bmi.readthedocs.io/en/latest/), also known as BMI.
-
-Not all BMI functions are implemented yet, this has been set up as a proof of concept to
-demonstrate that we can use other software such as
-[`imod_coupler`](https://github.com/Deltares/imod_coupler) to control Ribasim and couple it to
-other models.
-
-Here is an example of using libribasim from Python:
-
-```python
-In [1]: from ctypes import CDLL, c_int, c_char_p, create_string_buffer, byref
-
-In [2]: c_dll = CDLL("libribasim", winmode=0x08)  # winmode for Windows
-
-In [3]: argument = create_string_buffer(0)
-   ...: c_dll.init_julia(c_int(0), byref(argument))
-Out[3]: 1
-
-In [4]: config_path = "ribasim.toml"
-
-In [5]: c_dll.initialize(c_char_p(config_path.encode()))
-Out[5]: 0
-
-In [6]: c_dll.update()
-Out[6]: 0
-```
-"""
 function main()
     project_dir = "../core"
     license_file = "../LICENSE"
@@ -61,13 +23,22 @@ function main()
         force = true,
     )
 
-    readme = @doc(build_app)
-    add_metadata(project_dir, license_file, output_dir, git_repo, readme)
+    add_metadata(project_dir, license_file, output_dir, git_repo, readme_start)
     run(Cmd(`cargo build --release`; dir = "cli"))
     ribasim = Sys.iswindows() ? "ribasim.exe" : "ribasim"
     cp("cli/target/release/$ribasim", "ribasim/$ribasim"; force = true)
 end
 
+readme_start = """
+# Ribasim
+
+Ribasim is a water resources model to simulate the physical behavior of a managed open water system
+based on a set of control rules and a prioritized water allocation strategy.
+
+Usage: `ribasim path/to/model/ribasim.toml`
+Documentation: https://ribasim.org/
+"""
+
 function set_version(filename, version; group = nothing)
     data = TOML.parsefile(filename)
     if !isnothing(group)

core/src/parameter.jl

@@ -266,10 +266,6 @@ for discrete control
     itp_update::Vector{ParameterUpdate{ScalarInterpolation}} = []
 end
 
-abstract type AbstractParameterNode end
-
-abstract type AbstractDemandNode <: AbstractParameterNode end
-
 """
 In-memory storage of saved mean flows for writing to results.
 
@@ -307,6 +303,10 @@ In-memory storage of saved instantaneous storages and levels for writing to resu
     t::Float64
 end
 
+abstract type AbstractParameterNode end
+
+abstract type AbstractDemandNode <: AbstractParameterNode end
+
 """
 Caches of current basin properties
 """

core/src/util.jl

@@ -359,6 +359,7 @@ function FlatVector(saveval::Vector{<:SavedFlow}, sym::Symbol)
     v = isempty(saveval) ? Vector{Float64}[] : getfield.(saveval, sym)
     FlatVector(v)
 end
+FlatVector(v::Vector{Matrix{Float64}}) = FlatVector(vec.(v))
 
 """
 Function that goes smoothly from 0 to 1 in the interval [0,threshold],

core/src/write.jl

@@ -276,18 +276,9 @@ function concentration_table(
     ntsteps = length(data.time) - 1
     nbasin = length(data.node_id)
     nsubstance = length(basin.concentration_data.substances)
-    nrows = ntsteps * nbasin * nsubstance
 
     substances = String.(basin.concentration_data.substances)
-    concentration = zeros(nrows)
-
-    idx_row = 0
-    for cvec in saved.flow.saveval
-        for concentration_ in vec(cvec.concentration)
-            idx_row += 1
-            concentration[idx_row] = concentration_
-        end
-    end
+    concentration = FlatVector(saved.flow.saveval, :concentration)
 
     time = repeat(data.time[begin:(end - 1)]; inner = nbasin * nsubstance)
     substance = repeat(substances; inner = nbasin, outer = ntsteps)

core/test/run_models_test.jl

@@ -229,6 +229,11 @@ end
 
     # flows are recorded at the end of each period, and are undefined at the start
     @test unique(table.time) == Ribasim.datetimes(model)[1:(end - 1)]
+
+    @test isfile(joinpath(dirname(toml_path), "results/concentration.arrow"))
+    table = Ribasim.concentration_table(model)
+    @test "Continuity" in table.substance
+    @test all(isapprox.(table.concentration[table.substance .== "Continuity"], 1.0))
 end
 
 @testitem "basic arrow model" begin

python/ribasim_testmodels/ribasim_testmodels/basic.py

@@ -5,7 +5,7 @@
 import numpy as np
 import pandas as pd
 import ribasim
-from ribasim.config import Node
+from ribasim.config import Experimental, Node
 from ribasim.input_base import TableModel
 from ribasim.nodes import (
     basin,
@@ -26,6 +26,7 @@ def basic_model() -> ribasim.Model:
         starttime="2020-01-01",
         endtime="2021-01-01",
         crs="EPSG:28992",
+        experimental=Experimental(concentration=True),
     )
     model.logging = ribasim.Logging(verbosity="debug")
 

python/ribasim_testmodels/ribasim_testmodels/discrete_control.py

@@ -1,6 +1,6 @@
 import numpy as np
 import pandas as pd
-from ribasim.config import Node
+from ribasim.config import Experimental, Node
 from ribasim.model import Model, Solver
 from ribasim.nodes import (
     basin,
@@ -604,6 +604,7 @@ def continuous_concentration_condition_model() -> Model:
         endtime="2020-02-01",
         crs="EPSG:28992",
         solver=Solver(saveat=86400 / 8),
+        experimental=Experimental(concentration=True),
     )
 
     basi = model.basin.add(