Merge branch 'main' into combine_flow_and_control_graphs

.docker/compose.yml

@@ -2,10 +2,10 @@ version: '2'
 
 services:
   qgis:
-    image: qgis/qgis:release-3_30
+    image: qgis/qgis:release-3_28
     container_name: qgis
     volumes:
-      - ../qgis/:/tests_directory/${PLUGIN_NAME}
+      - ../ribasim_qgis/:/tests_directory/${PLUGIN_NAME}
     environment:
       - CI=true
       - DISPLAY=:99

.teamcity/Ribasim_Ribasim/buildTypes/Ribasim_Ribasim_MakeQgisPlugin.xml

@@ -10,7 +10,7 @@
     <build-runners>
       <runner id="RUNNER_2193" name="" type="simpleRunner">
         <parameters>
-          <param name="script.content"><![CDATA[rsync --verbose --recursive --delete qgis/ ribasim_qgis
+          <param name="script.content"><![CDATA[rsync --verbose --recursive --delete ribasim_qgis/ ribasim_qgis
 rm --force ribasim_qgis.zip
 zip -r ribasim_qgis.zip ribasim_qgis]]></param>
           <param name="teamcity.step.mode" value="default" />

build/create_binaries/Project.toml

@@ -13,9 +13,9 @@ TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 TimeZones = "f269a46b-ccf7-5d73-abea-4c690281aa53"
 
 [compat]
-Artifacts = "1"
-LibGit2 = "1"
+Artifacts = "<0.0.1,1"
+LibGit2 = "<0.0.1,1"
 PackageCompiler = "2"
-TOML = "1"
+TOML = "<0.0.1,1"
 TimeZones = "=1.13.0"
 julia = "1.10"

build/libribasim/Project.toml

@@ -12,6 +12,6 @@ TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 
 [compat]
 BasicModelInterface = "0.1"
-Dates = "1"
-TOML = "1"
+Dates = "<0.0.1,1"
+TOML = "<0.0.1,1"
 julia = "1.10"

build/ribasim_cli/Project.toml

@@ -13,9 +13,9 @@ TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 TerminalLoggers = "5d786b92-1e48-4d6f-9151-6b4477ca9bed"
 
 [compat]
-Dates = "1"
-Logging = "1"
+Dates = "<0.0.1,1"
+Logging = "<0.0.1,1"
 SciMLBase = "1.60, 2"
-TOML = "1"
+TOML = "<0.0.1,1"
 TerminalLoggers = "0.1.7"
 julia = "1.10"

core/Project.toml

@@ -41,41 +41,49 @@ TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 
 [compat]
+Aqua = "0.8"
 Arrow = "2.3"
 BasicModelInterface = "0.1"
+CSV = "0.10"
 CodecLz4 = "0.4"
 CodecZstd = "0.7,0.8"
-ComponentArrays = "0.13.14, 0.14, 0.15"
+ComponentArrays = "0.13,0.14,0.15"
 Configurations = "0.17"
 DBInterface = "2.4"
 DataFrames = "1.4"
 DataInterpolations = "4.4"
 DataStructures = "0.18"
-Dates = "1"
+Dates = "<0.0.1,1"
 Dictionaries = "0.3.25"
 DiffEqCallbacks = "2.29.1"
+Documenter = "0.27,1"
 EnumX = "1.0"
 FiniteDiff = "2.21"
 ForwardDiff = "0.10"
 Graphs = "1.9"
 HiGHS = "1.7"
+IOCapture = "0.2"
 IterTools = "1.4"
 JuMP = "1.15"
 Legolas = "0.5"
-Logging = "1"
+Logging = "<0.0.1,1"
 LoggingExtras = "1"
 MetaGraphsNext = "0.6"
 OrdinaryDiffEq = "6.7"
 PreallocationTools = "0.4"
 SQLite = "1.5.1"
+SafeTestsets = "0.1"
 SciMLBase = "1.60, 2"
-SparseArrays = "1"
+SparseArrays = "<0.0.1,1"
 StructArrays = "0.6.13"
+TOML = "<0.0.1,1"
 Tables = "1"
 TerminalLoggers = "0.1.7"
+Test = "<0.0.1,1"
+TestReports = "0.7"
 TimeZones = "=1.13.0"
 TimerOutputs = "0.5"
-TranscodingStreams = "0.9, 0.10"
+TranscodingStreams = "0.9,0.10"
 julia = "1.10"
 
 [extras]

core/test/runtests.jl

@@ -17,5 +17,5 @@ using SafeTestsets: @safetestset
     @safetestset "Docs" include("docs.jl")
     @safetestset "Command Line Interface" include("cli.jl")
     @safetestset "libribasim" include("libribasim.jl")
-    Aqua.test_all(Ribasim; ambiguities = false)
+    Aqua.test_all(Ribasim; ambiguities = false, persistent_tasks = false)
 end

docs/Project.toml

@@ -19,12 +19,12 @@ Ribasim = "aac5e3d9-0b8f-4d4f-8241-b1a7a9632635"
 
 [compat]
 Configurations = "0.17"
-Dates = "1"
-Documenter = "0.27, 1"
+Dates = "<0.0.1,1"
+Documenter = "0.27,1"
 DocumenterMarkdown = "0.2"
-InteractiveUtils = "1"
+InteractiveUtils = "<0.0.1,1"
 JSON3 = "1.12"
 Legolas = "0.5"
-Logging = "1"
+Logging = "<0.0.1,1"
 OrderedCollections = "1.6"
 julia = "1.10"

docs/_quarto.yml

@@ -91,8 +91,3 @@ quartodoc:
         - Terminal
         - DiscreteControl
         - PidControl
-    - title: Utility functions
-      desc: Collection of utility functions.
-      contents:
-        - utils.geometry_from_connectivity
-        - utils.connectivity_from_geometry

docs/contribute/addnode.qmd

@@ -115,6 +115,7 @@ from typing import Optional
 import pandera as pa
 from pandera.engines.pandas_engine import PydanticModel
 from pandera.typing import DataFrame
+from pydantic import ConfigDict
 
 from ribasim import models
 from ribasim.input_base import TableModel
@@ -142,11 +143,10 @@ class NewNodeType(TableModel):
     possible other schemas
     """
 
-    static: Optional[DataFrame[StaticSchema]] = None
+    static: DataFrame[StaticSchema] | None
     # possible other schemas
 
-    class Config:
-        validate_assignment = True
+    model_config = ConfigDict(validate_assignment=True)
 
     def sort(self):
         self.static.sort_values("node_id", ignore_index=True, inplace=True)
@@ -168,7 +168,7 @@ In `python/ribasim/ribasim/geometry/node.py` add a color and shape description i
 
 # QGIS plugin
 
-The script `qgis/core/nodes.py` has to be updated to specify how the new node type is displayed by the QGIS plugin. Specifically:
+The script `ribasim_qgis/core/nodes.py` has to be updated to specify how the new node type is displayed by the QGIS plugin. Specifically:
 
 - Add a color and shape description in the `MARKERS` dictionary in `Node.renderer`,
   consistent with the entries added above;

docs/core/index.qmd

@@ -16,3 +16,68 @@ can be found in the [Ribasim repository](https://github.com/Deltares/Ribasim) un
 %%| file: ../assets/c4_component_ribasim.mmd
 %%| fig-cap: "Component overview of Ribasim"
 ```
+
+# The simulation loop
+
+`Ribasim.jl` in the above figure can be divided into 3 parts:
+
+- Model initialization
+- Running the simulation loop
+- Writing the output files
+
+The figure below gives a more detailed description of the simulation loop in the form of a [sequence diagram](https://en.wikipedia.org/wiki/Sequence_diagram). From top to bottom, it contains the following blocks:
+
+- Allocation optimization; activated when the allocation timestep has been passed;
+- Control actions; activated when some discrete control callback is triggered;
+- Water balance; computing the flows over flow edges happens each timestep;
+- Time integration step; Done by the selected integrator from `OrdinaryDiffEq.jl`.
+
+```{mermaid}
+sequenceDiagram
+    autonumber
+    participant Int as Process: Integrator
+    participant Optim as Process: Allocation optimization
+    participant Param as Data: Parameters
+    participant State as Data: State
+    participant Sim as Process: Water balance
+    loop Simulation loop (OrdinaryDiffEq.jl)
+        activate Int
+        %% Allocation
+        rect rgb(200, 200, 200)
+            opt Allocation optimization, per allocation network (JuMP.jl, HiGHS)
+                activate Optim
+                Int->>Optim: Callback: allocation timestep has passed
+                Param-->>Optim: Input
+                State-->>Optim: Input
+                Optim->>Optim: Optimize Basin allocations if below target level
+                Optim->>Optim: Optimize User allocation, per priority
+                Optim-->>Param: Set allocated flow rates
+                deactivate Optim
+            end
+        end
+        %% Control
+        rect rgb(200, 200, 200)
+            opt Control actions
+                Int->>Int: DiscreteControl callback
+                Int-->>Param: Parameter updates by control
+            end
+        end
+        %% water_balance!
+        rect rgb(200, 200, 200)
+            activate Sim
+            State-->>Sim: Input
+            Param-->>Sim: Input
+            Sim->>Sim: Compute flows over edges per node type
+            Sim-->>Param: Set flows
+            deactivate Sim
+        end
+        %% Time integration
+        rect rgb(200, 200, 200)
+            State-->>Int: Input
+            Param-->>Int: Input
+            Int->>Int: Time integration step
+            Int-->>State: Update state
+        end
+        deactivate Int
+  end
+```

docs/gen_schema.jl

@@ -67,7 +67,7 @@ function gen_root_schema(TT::Vector, prefix = prefix, name = "root")
         "type" => "object",
     )
     for T in TT
-        tname = strip_prefix(T)
+        tname = lowercase(strip_prefix(T))
         schema["properties"][tname] = OrderedDict("\$ref" => "$tname.schema.json")
     end
     open(normpath(@__DIR__, "schema", "$(name).schema.json"), "w") do io