Merge branch 'main' into persist

.github/workflows/core_testmodels.yml

@@ -29,7 +29,7 @@ jobs:
           - x64
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
         with:
           cache-compiled: "true"
           cache-registries: "true"

.github/workflows/core_tests.yml

@@ -29,7 +29,7 @@ jobs:
           - x64
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
         with:
           cache-compiled: "true"
           cache-registries: "true"

.github/workflows/docs.yml

@@ -20,7 +20,7 @@ jobs:
       contents: write
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
         with:
           cache-compiled: "true"
           cache-registries: "true"
@@ -33,9 +33,6 @@ jobs:
       - name: Check Quarto installation and all engines
         run: pixi run quarto-check
 
-      - name: Generate Julia docs
-        run: pixi run build-julia-docs
-
       - name: Render Quarto Project
         run: pixi run quarto-render
 

.gitignore

@@ -5,10 +5,6 @@
 # Files generated by invoking Julia with --track-allocation
 *.jl.mem
 
-# Build artifacts for creating documentation generated by the Documenter package
-docs/build/
-docs/site/
-
 /generated_testmodels
 build/ribasim/
 build/cli/target

.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimBinaries.xml

@@ -16,8 +16,7 @@
 source /usr/share/Modules/init/bash
 
 module load pixi
-pixi --version
-pixi run install-python]]></param>
+pixi --version]]></param>
           <param name="teamcity.build.workingDir" value="ribasim" />
           <param name="teamcity.step.mode" value="default" />
           <param name="use.custom.script" value="true" />
@@ -30,7 +29,6 @@ pixi run install-python]]></param>
 source /usr/share/Modules/init/bash
 
 module load pixi
-pixi run --environment=dev install
 pixi run test-ribasim-api
 pixi run test-ribasim-cli]]></param>
           <param name="teamcity.build.workingDir" value="ribasim" />

.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_TestRibasimBinaries.xml

@@ -10,16 +10,15 @@
     <build-runners>
       <runner id="RUNNER_1501" name="Set up pixi" type="simpleRunner">
         <parameters>
-          <param name="script.content" value="pixi run install-python" />
+          <param name="script.content" value="pixi --version" />
           <param name="teamcity.build.workingDir" value="ribasim" />
           <param name="teamcity.step.mode" value="default" />
           <param name="use.custom.script" value="true" />
         </parameters>
       </runner>
       <runner id="RUNNER_1503" name="Run tests" type="simpleRunner">
         <parameters>
-          <param name="script.content"><![CDATA[pixi run --environment=dev install
-pixi run test-ribasim-api
+          <param name="script.content"><![CDATA[pixi run test-ribasim-api
 pixi run test-ribasim-cli]]></param>
           <param name="teamcity.build.workingDir" value="ribasim" />
           <param name="teamcity.step.mode" value="default" />

Manifest.toml

@@ -2,18 +2,13 @@
 
 julia_version = "1.10.3"
 manifest_format = "2.0"
-project_hash = "045162196d64ccb59bdab2af0422fde0b0e83c77"
+project_hash = "dc6d536cc58558be9be8b5e2e4d511d0451ed14f"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "016833eb52ba2d6bea9fcb50ca295980e728ee24"
 uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
 version = "0.2.7"
 
-[[deps.ANSIColoredPrinters]]
-git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c"
-uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9"
-version = "0.0.1"
-
 [[deps.AbstractTrees]]
 git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177"
 uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
@@ -438,18 +433,6 @@ git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d"
 uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 version = "0.9.3"
 
-[[deps.Documenter]]
-deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
-git-tree-sha1 = "39fd748a73dce4c05a9655475e437170d8fb1b67"
-uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-version = "0.27.25"
-
-[[deps.DocumenterMarkdown]]
-deps = ["Documenter"]
-git-tree-sha1 = "9af057a98652336e30586d8092fac06f8b28ecdc"
-uuid = "997ab1e6-3595-5248-9280-8efb232c3433"
-version = "0.2.2"
-
 [[deps.Downloads]]
 deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
@@ -498,9 +481,9 @@ version = "0.3.2"
 
 [[deps.FastLapackInterface]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "0a59c7d1002f3131de53dc4568a47d15a44daef7"
+git-tree-sha1 = "f4102aab9c7df8691ed09f9c42e34f5ab5458ab9"
 uuid = "29a986be-02c6-4525-aec4-84b980013641"
-version = "2.0.2"
+version = "2.0.3"
 
 [[deps.FileIO]]
 deps = ["Pkg", "Requires", "UUIDs"]
@@ -626,12 +609,6 @@ git-tree-sha1 = "47ac8cc196b81001a711f4b2c12c97372338f00c"
 uuid = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
 version = "1.24.2"
 
-[[deps.IOCapture]]
-deps = ["Logging", "Random"]
-git-tree-sha1 = "8b72179abc660bfab5e28472e019392b97d0985c"
-uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89"
-version = "0.2.4"
-
 [[deps.IfElse]]
 git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1"
 uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
@@ -753,9 +730,9 @@ version = "0.6.0"
 
 [[deps.Krylov]]
 deps = ["LinearAlgebra", "Printf", "SparseArrays"]
-git-tree-sha1 = "8a6837ec02fe5fb3def1abc907bb802ef11a0729"
+git-tree-sha1 = "267dad6b4b7b5d529c76d40ff48d33f7e94cb834"
 uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
-version = "0.9.5"
+version = "0.9.6"
 
 [[deps.LaTeXStrings]]
 git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec"
@@ -1211,9 +1188,9 @@ version = "1.3.4"
 
 [[deps.RecursiveArrayTools]]
 deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"]
-git-tree-sha1 = "d8f131090f2e44b145084928856a561c83f43b27"
+git-tree-sha1 = "6305b6fe0391eeb4f280a4a403ac0c350b82c718"
 uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
-version = "3.13.0"
+version = "3.15.0"
 
     [deps.RecursiveArrayTools.extensions]
     RecursiveArrayToolsFastBroadcastExt = "FastBroadcast"
@@ -1303,9 +1280,9 @@ version = "3.45.0+0"
 
 [[deps.SciMLBase]]
 deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"]
-git-tree-sha1 = "beb1f94b08c4976ed1db0ca01b9e6bac89706faf"
+git-tree-sha1 = "397367599b9526a49cc06a4db70835807498b561"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "2.35.0"
+version = "2.36.1"
 
     [deps.SciMLBase.extensions]
     SciMLBaseChainRulesCoreExt = "ChainRulesCore"
@@ -1530,10 +1507,10 @@ uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
 version = "7.2.1+1"
 
 [[deps.SymbolicIndexingInterface]]
-deps = ["Accessors", "ArrayInterface", "MacroTools", "RuntimeGeneratedFunctions", "StaticArraysCore"]
-git-tree-sha1 = "7a7be02e16d11c17e2407bab80c2dd1410f774cb"
+deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"]
+git-tree-sha1 = "b479c7a16803f08779ac5b7f9844a42621baeeda"
 uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
-version = "0.3.17"
+version = "0.3.21"
 
 [[deps.TOML]]
 deps = ["Dates"]

Project.toml

@@ -17,8 +17,6 @@ DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Dictionaries = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
-Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-DocumenterMarkdown = "997ab1e6-3595-5248-9280-8efb232c3433"
 EnumX = "4e289a0a-7415-4d19-859d-a7e5c4648b56"
 FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"

core/Project.toml

@@ -56,7 +56,6 @@ DataStructures = "0.18"
 Dates = "<0.0.1,1"
 Dictionaries = "0.3.25, 0.4"
 DiffEqCallbacks = "3.6"
-Documenter = "0.27,1"
 EnumX = "1.0"
 FiniteDiff = "2.21"
 ForwardDiff = "0.10"
@@ -74,7 +73,7 @@ OrdinaryDiffEq = "6.7"
 PreallocationTools = "0.4"
 ReTestItems = "1.20"
 SQLite = "1.5.1"
-SciMLBase = "1.60, 2"
+SciMLBase = "2.36"
 SparseArrays = "<0.0.1,1"
 StructArrays = "0.6.13"
 TOML = "<0.0.1,1"
@@ -89,7 +88,6 @@ julia = "1.10"
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 IOCapture = "b5f81e59-6552-4d32-b1f0-c071b021bf89"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 ReTestItems = "817f1d60-ba6b-4fd5-9520-3cf149f6a823"
@@ -111,4 +109,4 @@ PrecompileNonStiff = false
 PrecompileStiff = false
 
 [targets]
-test = ["Aqua", "CSV", "DataFrames", "Documenter", "IOCapture", "Logging", "ReTestItems", "TerminalLoggers", "Test", "TOML"]
+test = ["Aqua", "CSV", "DataFrames", "IOCapture", "Logging", "ReTestItems", "TerminalLoggers", "Test", "TOML"]

core/src/Ribasim.jl

@@ -55,6 +55,7 @@ using SciMLBase:
     init,
     solve!,
     step!,
+    check_error!,
     SciMLBase,
     ReturnCode,
     successful_retcode,

core/src/model.jl

@@ -229,12 +229,7 @@ function SciMLBase.solve!(model::Model)::Model
             update_allocation!(integrator)
             step!(integrator, timestep, true)
         end
-
-        if integrator.sol.retcode != ReturnCode.Default
-            return model
-        end
-        # TODO replace with `check_error!` https://github.com/SciML/SciMLBase.jl/issues/669
-        integrator.sol = SciMLBase.solution_new_retcode(integrator.sol, ReturnCode.Success)
+        check_error!(integrator)
     else
         solve!(integrator)
     end

core/src/schema.jl

@@ -8,12 +8,17 @@
 @schema "ribasim.basin.profile" BasinProfile
 @schema "ribasim.basin.state" BasinState
 @schema "ribasim.basin.subgrid" BasinSubgrid
+@schema "ribasim.basin.concentration" BasinConcentration
+@schema "ribasim.basin.concentrationexternal" BasinConcentrationExternal
+@schema "ribasim.basin.concentrationstate" BasinConcentrationState
 @schema "ribasim.terminal.static" TerminalStatic
 @schema "ribasim.fractionalflow.static" FractionalFlowStatic
 @schema "ribasim.flowboundary.static" FlowBoundaryStatic
 @schema "ribasim.flowboundary.time" FlowBoundaryTime
+@schema "ribasim.flowboundary.concentration" FlowBoundaryConcentration
 @schema "ribasim.levelboundary.static" LevelBoundaryStatic
 @schema "ribasim.levelboundary.time" LevelBoundaryTime
+@schema "ribasim.levelboundary.concentration" LevelBoundaryConcentration
 @schema "ribasim.linearresistance.static" LinearResistanceStatic
 @schema "ribasim.manningresistance.static" ManningResistanceStatic
 @schema "ribasim.pidcontrol.static" PidControlStatic
@@ -99,6 +104,21 @@ end
     urban_runoff::Union{Missing, Float64}
 end
 
+@version BasinConcentrationV1 begin
+    node_id::Int32
+    time::DateTime
+    substance::String
+    drainage::Union{Missing, Float64}
+    precipitation::Union{Missing, Float64}
+end
+
+@version BasinConcentrationExternalV1 begin
+    node_id::Int32
+    time::DateTime
+    substance::String
+    concentration::Union{Missing, Float64}
+end
+
 @version BasinProfileV1 begin
     node_id::Int32
     area::Float64
@@ -110,6 +130,12 @@ end
     level::Float64
 end
 
+@version BasinConcentrationStateV1 begin
+    node_id::Int32
+    substance::String
+    concentration::Union{Missing, Float64}
+end
+
 @version BasinSubgridV1 begin
     subgrid_id::Int32
     node_id::Int32
@@ -135,6 +161,13 @@ end
     level::Float64
 end
 
+@version LevelBoundaryConcentrationV1 begin
+    node_id::Int32
+    time::DateTime
+    substance::String
+    concentration::Float64
+end
+
 @version FlowBoundaryStaticV1 begin
     node_id::Int32
     active::Union{Missing, Bool}
@@ -147,6 +180,13 @@ end
     flow_rate::Float64
 end
 
+@version FlowBoundaryConcentrationV1 begin
+    node_id::Int32
+    time::DateTime
+    substance::String
+    concentration::Float64
+end
+
 @version LinearResistanceStaticV1 begin
     node_id::Int32
     active::Union{Missing, Bool}

docs/.gitignore

@@ -4,5 +4,4 @@
 python/reference/
 python/data/
 *.html
-/Manifest.toml
 objects.json

docs/_quarto.yml

@@ -32,7 +32,6 @@ website:
         - core/equations.qmd
         - core/allocation.qmd
         - core/numerics.qmd
-        - build/index.md
     - title: "Python tooling"
       contents:
         - python/index.qmd

docs/contribute/core.qmd

@@ -75,11 +75,6 @@ The first run will be slow.
 ## Render documentation
 
 Example models are created and simulated as part of the rendering of the documentation.
-The Julia API reference is created using Documenter.jl by running this command:
-
-```bash
-pixi run build-julia-docs
-```
 
 In order to preview documentation you can run the following command from the `docs/` folder.
 Afterwards, a browser tab will open with the rendered documentation, updating it as you