Keep only the root and core project (#1021)

This attempts to simplifiy our Julia project and build setup.

Where possible, existing projects are moved into the root project like
in #1014. All core dependencies are now also direct root dependencies to
make using the root project more convenient for development.

While working on this I realized that we can remove the `libribasim` and
`ribasim_cli` projects entirely. `libribasim` is now a module of the
Ribasim package, and `ribasim_cli` already was just a tiny wrapper
around `Ribasim.main`. The content of the README.md files from those two
folders now reside in the `build_lib` and `build_app` docstring.

Since that left only the `create_binaries` folder under `/build`, I
collapsed that level out. `create_binaries` is no longer a package, but
the code is still used, but now simply directly included in `build.jl`.

.github/workflows/core_compat_helper.yml

@@ -38,11 +38,8 @@ jobs:
         run: |
           import CompatHelper
           CompatHelper.main(; subdirs=[
+              ".",
               "core",
-              "docs",
-              "build/create_binaries",
-              "build/libribasim",
-              "build/ribasim_cli"
           ])
         shell: julia --color=yes {0}
         env:

.gitignore

@@ -10,8 +10,8 @@ docs/build/
 docs/site/
 
 /generated_testmodels
-build/create_binaries/ribasim_cli/
-build/create_binaries/libribasim/
+build/ribasim_cli/
+build/libribasim/
 
 JuliaSysimage.dll
 LocalPreferences.toml
@@ -147,7 +147,7 @@ dmypy.json
 .pyre/
 
 /.luarc.json
-build/ribasim_cli/tests/temp/
+build/tests/temp/
 python/ribasim_api/tests/temp/
 report.xml
 /utils/juliaup

.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_BuildLibribasim.xml

@@ -4,7 +4,7 @@
   <description />
   <settings>
     <options>
-      <option name="artifactRules" value="ribasim\build\create_binaries\libribasim =&gt; libribasim.zip" />
+      <option name="artifactRules" value="ribasim\build\libribasim =&gt; libribasim.zip" />
       <option name="cleanBuild" value="true" />
       <option name="executionTimeoutMin" value="120" />
       <option name="publishArtifactCondition" value="SUCCESSFUL" />

.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_BuildRibasimCli.xml

@@ -4,7 +4,7 @@
   <description />
   <settings>
     <options>
-      <option name="artifactRules" value="ribasim\build/create_binaries/ribasim_cli =&gt; ribasim_cli_linux.zip" />
+      <option name="artifactRules" value="ribasim\build/ribasim_cli =&gt; ribasim_cli_linux.zip" />
       <option name="cleanBuild" value="true" />
       <option name="executionTimeoutMin" value="120" />
     </options>
@@ -42,7 +42,7 @@ pixi run build-ribasim-cli]]></param>
       <runner id="RUNNER_1932" name="Get version from Ribasim" type="simpleRunner">
         <parameters>
           <param name="script.content" value="./ribasim --version" />
-          <param name="teamcity.build.workingDir" value="ribasim/build/create_binaries/ribasim_cli/bin" />
+          <param name="teamcity.build.workingDir" value="ribasim/build/ribasim_cli/bin" />
           <param name="teamcity.step.mode" value="default" />
           <param name="use.custom.script" value="true" />
         </parameters>

.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimApi.xml

@@ -93,7 +93,7 @@ pixi run test-ribasim-api]]></param>
     <artifact-dependencies>
       <dependency id="ARTIFACT_DEPENDENCY_570" sourceBuildTypeId="Ribasim_Linux_BuildLibribasim" cleanDestination="true">
         <revisionRule name="sameChainOrLastFinished" revision="latest.sameChainOrLastFinished" />
-        <artifact sourcePath="libribasim.zip!** =&gt; ribasim/build/create_binaries/libribasim&#xD;&#xA;" />
+        <artifact sourcePath="libribasim.zip!** =&gt; ribasim/build/libribasim&#xD;&#xA;" />
       </dependency>
     </artifact-dependencies>
     <dependencies>

.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimCli.xml

@@ -4,7 +4,7 @@
   <description />
   <settings>
     <options>
-      <option name="artifactRules" value="ribasim\build\ribasim_cli\tests\temp =&gt; test_output.zip" />
+      <option name="artifactRules" value="ribasim\build\tests\temp =&gt; test_output.zip" />
       <option name="cleanBuild" value="true" />
     </options>
     <parameters>
@@ -93,7 +93,7 @@ pixi run test-ribasim-cli]]></param>
     <artifact-dependencies>
       <dependency id="ARTIFACT_DEPENDENCY_570" sourceBuildTypeId="Ribasim_Linux_BuildRibasimCli" cleanDestination="true">
         <revisionRule name="sameChainOrLastFinished" revision="latest.sameChainOrLastFinished" />
-        <artifact sourcePath="ribasim_cli_linux.zip!** =&gt; ribasim/build/create_binaries/ribasim_cli&#xD;&#xA;" />
+        <artifact sourcePath="ribasim_cli_linux.zip!** =&gt; ribasim/build/ribasim_cli&#xD;&#xA;" />
       </dependency>
     </artifact-dependencies>
     <dependencies>

.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_BuildLibribasim.xml

@@ -4,7 +4,7 @@
   <description />
   <settings>
     <options>
-      <option name="artifactRules" value="ribasim\build\create_binaries\libribasim =&gt; libribasim.zip" />
+      <option name="artifactRules" value="ribasim\build\libribasim =&gt; libribasim.zip" />
       <option name="cleanBuild" value="true" />
       <option name="executionTimeoutMin" value="120" />
       <option name="publishArtifactCondition" value="SUCCESSFUL" />

.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_BuildRibasimCli.xml

@@ -4,7 +4,7 @@
   <description />
   <settings>
     <options>
-      <option name="artifactRules" value="ribasim\build/create_binaries/ribasim_cli =&gt; ribasim_cli_windows.zip" />
+      <option name="artifactRules" value="ribasim\build/ribasim_cli =&gt; ribasim_cli_windows.zip" />
       <option name="cleanBuild" value="true" />
       <option name="executionTimeoutMin" value="120" />
     </options>
@@ -30,7 +30,7 @@ pixi run build-ribasim-cli]]></param>
       <runner id="RUNNER_1932" name="Get version from Ribasim" type="simpleRunner">
         <parameters>
           <param name="script.content" value="ribasim --version" />
-          <param name="teamcity.build.workingDir" value="ribasim/build/create_binaries/ribasim_cli" />
+          <param name="teamcity.build.workingDir" value="ribasim/build/ribasim_cli" />
           <param name="teamcity.step.mode" value="default" />
           <param name="use.custom.script" value="true" />
         </parameters>

.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_TestRibasimApi.xml

@@ -82,7 +82,7 @@
     <artifact-dependencies>
       <dependency id="ARTIFACT_DEPENDENCY_570" sourceBuildTypeId="Ribasim_Windows_BuildLibribasim" cleanDestination="true">
         <revisionRule name="sameChainOrLastFinished" revision="latest.sameChainOrLastFinished" />
-        <artifact sourcePath="libribasim.zip!** =&gt; ribasim/build/create_binaries/libribasim&#xD;&#xA;" />
+        <artifact sourcePath="libribasim.zip!** =&gt; ribasim/build/libribasim&#xD;&#xA;" />
       </dependency>
     </artifact-dependencies>
     <dependencies>

.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_TestRibasimCli.xml

@@ -4,7 +4,7 @@
   <description />
   <settings>
     <options>
-      <option name="artifactRules" value="ribasim\build\ribasim_cli\tests\temp =&gt; test_output.zip" />
+      <option name="artifactRules" value="ribasim\build\tests\temp =&gt; test_output.zip" />
       <option name="cleanBuild" value="true" />
     </options>
     <parameters>
@@ -82,7 +82,7 @@
     <artifact-dependencies>
       <dependency id="ARTIFACT_DEPENDENCY_570" sourceBuildTypeId="Ribasim_Windows_BuildRibasimCli" cleanDestination="true">
         <revisionRule name="sameChainOrLastFinished" revision="latest.sameChainOrLastFinished" />
-        <artifact sourcePath="ribasim_cli_windows.zip!** =&gt; ribasim/build/create_binaries/ribasim_cli&#xD;&#xA;" />
+        <artifact sourcePath="ribasim_cli_windows.zip!** =&gt; ribasim/build/ribasim_cli&#xD;&#xA;" />
       </dependency>
     </artifact-dependencies>
     <dependencies>

Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.10.0"
 manifest_format = "2.0"
-project_hash = "1a68754569dae741c9232c9ae2db3512f52c2b80"
+project_hash = "7e18cea33bf679231c5c94c6b99a1b635f9a1b61"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "41c37aa88889c171f1300ceac1313c06e891d245"
@@ -150,9 +150,9 @@ version = "0.2.4"
 
 [[deps.ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra"]
-git-tree-sha1 = "c1deebd76f7a443d527fc0430d5758b8b2112ed8"
+git-tree-sha1 = "1287e3872d646eed95198457873249bd9f0caed2"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "1.19.1"
+version = "1.20.1"
 weakdeps = ["SparseArrays"]
 
     [deps.ChainRulesCore.extensions]
@@ -172,9 +172,9 @@ version = "1.3.5"
 
 [[deps.CodecBzip2]]
 deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"]
-git-tree-sha1 = "c0ae2a86b162fb5d7acc65269b469ff5b8a73594"
+git-tree-sha1 = "9b1ca1aa6ce3f71b3d1840c538a8210a043625eb"
 uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd"
-version = "0.8.1"
+version = "0.8.2"
 
 [[deps.CodecLz4]]
 deps = ["Lz4_jll", "TranscodingStreams"]
@@ -184,9 +184,9 @@ version = "0.4.1"
 
 [[deps.CodecZlib]]
 deps = ["TranscodingStreams", "Zlib_jll"]
-git-tree-sha1 = "cd67fc487743b2f0fd4380d4cbd3a24660d0eec8"
+git-tree-sha1 = "59939d8a997469ee05c4b4944560a820f9ba0d73"
 uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
-version = "0.7.3"
+version = "0.7.4"
 
 [[deps.CodecZstd]]
 deps = ["TranscodingStreams", "Zstd_jll"]
@@ -355,9 +355,9 @@ uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 
 [[deps.Dictionaries]]
 deps = ["Indexing", "Random", "Serialization"]
-git-tree-sha1 = "5bde104a45593207307e1481a58e0339d4643fca"
+git-tree-sha1 = "8b73c5a704d74e78a114b785d648ceba1e5790a9"
 uuid = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4"
-version = "0.3.26"
+version = "0.4.0"
 
 [[deps.DiffEqBase]]
 deps = ["ArrayInterface", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"]
@@ -497,9 +497,9 @@ version = "0.3.2"
 
 [[deps.FastLapackInterface]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "b12f05108e405dadcc2aff0008db7f831374e051"
+git-tree-sha1 = "d576a29bf8bcabf4b1deb9abe88a3d7f78306ab5"
 uuid = "29a986be-02c6-4525-aec4-84b980013641"
-version = "2.0.0"
+version = "2.0.1"
 
 [[deps.FileIO]]
 deps = ["Pkg", "Requires", "UUIDs"]
@@ -939,9 +939,9 @@ version = "1.1.0"
 
 [[deps.MathOptInterface]]
 deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"]
-git-tree-sha1 = "e2ae8cf5ac6daf5a3959f7f6ded9c2028b61d09d"
+git-tree-sha1 = "8b40681684df46785a0012d352982e22ac3be59e"
 uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
-version = "1.25.1"
+version = "1.25.2"
 
 [[deps.MatrixFactorizations]]
 deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"]
@@ -1026,9 +1026,9 @@ version = "1.2.0"
 
 [[deps.NonlinearSolve]]
 deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "TimerOutputs"]
-git-tree-sha1 = "78bdd3a4a62865cf43c53d63783b0cbfddcdbbe6"
+git-tree-sha1 = "323d2a61f4adc4dfe404bf332b59690253b4f4f2"
 uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
-version = "3.5.0"
+version = "3.5.3"
 
     [deps.NonlinearSolve.extensions]
     NonlinearSolveBandedMatricesExt = "BandedMatrices"
@@ -1086,9 +1086,9 @@ version = "1.6.3"
 
 [[deps.OrdinaryDiffEq]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
-git-tree-sha1 = "7c6738f21fba2ccd07b7eaa9d23b437a8a97f1a1"
+git-tree-sha1 = "c971a69e5eea2eba435b55e962c283f15502a0c8"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.69.0"
+version = "6.70.0"
 
 [[deps.PackageCompiler]]
 deps = ["Artifacts", "Glob", "LazyArtifacts", "Libdl", "Pkg", "Printf", "RelocatableFolders", "TOML", "UUIDs", "p7zip_jll"]
@@ -1191,9 +1191,9 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [[deps.ReTestItems]]
 deps = ["Dates", "Logging", "LoggingExtras", "Pkg", "Serialization", "Sockets", "Test", "TestEnv"]
-git-tree-sha1 = "68a7d4fd86f12c2fc6dec60d566f033a10ffb5fb"
+git-tree-sha1 = "32138ef9f7205330693b0e8e366370c470b2285d"
 uuid = "817f1d60-ba6b-4fd5-9520-3cf149f6a823"
-version = "1.23.0"
+version = "1.23.1"
 
 [[deps.RecipesBase]]
 deps = ["PrecompileTools"]
@@ -1203,21 +1203,23 @@ version = "1.3.4"
 
 [[deps.RecursiveArrayTools]]
 deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"]
-git-tree-sha1 = "dd7fc1923fde0cc6cdff451352d17924b0704ca1"
+git-tree-sha1 = "5a904ad526cc9a2c5b464f6642ce9dd230fd69b6"
 uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
-version = "3.5.4"
+version = "3.7.0"
 
     [deps.RecursiveArrayTools.extensions]
     RecursiveArrayToolsFastBroadcastExt = "FastBroadcast"
     RecursiveArrayToolsMeasurementsExt = "Measurements"
     RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements"
+    RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"]
     RecursiveArrayToolsTrackerExt = "Tracker"
     RecursiveArrayToolsZygoteExt = "Zygote"
 
     [deps.RecursiveArrayTools.weakdeps]
     FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
     Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"
     MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca"
+    ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
     Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
     Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
@@ -1285,15 +1287,15 @@ version = "1.6.0"
 
 [[deps.SQLite_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"]
-git-tree-sha1 = "81f7d934b52b2441f7b44520bd982fdb3607b0da"
+git-tree-sha1 = "75e28667a36b5650b5cc4baa266c5760c3672275"
 uuid = "76ed43ae-9a5d-5a62-8c75-30186b810ce8"
-version = "3.43.0+0"
+version = "3.45.0+0"
 
 [[deps.SciMLBase]]
 deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"]
-git-tree-sha1 = "de41474ac529bf81598e064587421cc5ebc28fa0"
+git-tree-sha1 = "e4344257d8a9dfc92e0fc113f0a5bababa8d2082"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "2.20.0"
+version = "2.22.0"
 
     [deps.SciMLBase.extensions]
     SciMLBaseChainRulesCoreExt = "ChainRulesCore"
@@ -1441,9 +1443,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"]
 
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
-git-tree-sha1 = "f68dd04d131d9a8a8eb836173ee8f105c360b0c5"
+git-tree-sha1 = "7b0e9c14c624e435076d19aea1e5cbdec2b9ca37"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.9.1"
+version = "1.9.2"
 weakdeps = ["ChainRulesCore", "Statistics"]
 
     [deps.StaticArrays.extensions]
@@ -1500,9 +1502,9 @@ uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
 version = "7.2.1+1"
 
 [[deps.SymbolicIndexingInterface]]
-git-tree-sha1 = "74502f408d99fc217a9d7cd901d9ffe45af892b1"
+git-tree-sha1 = "b3103f4f50a3843e66297a2456921377c78f5e31"
 uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
-version = "0.3.3"
+version = "0.3.5"
 
 [[deps.TOML]]
 deps = ["Dates"]
@@ -1511,9 +1513,9 @@ version = "1.0.3"
 
 [[deps.TZJData]]
 deps = ["Artifacts"]
-git-tree-sha1 = "d39314cdbaf5b90a047db33858626f8d1cc973e1"
+git-tree-sha1 = "b69f8338df046774bd975b13be9d297eca5efacb"
 uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7"
-version = "1.0.0+2023c"
+version = "1.1.0+2023d"
 
 [[deps.TableTraits]]
 deps = ["IteratorInterfaceExtensions"]
@@ -1656,23 +1658,11 @@ git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c"
 uuid = "3161d3a3-bdf6-5164-811a-617609db77b4"
 version = "1.5.5+0"
 
-[[deps.create_binaries]]
-deps = ["Artifacts", "LibGit2", "PackageCompiler", "TOML", "TimeZones"]
-path = "build/create_binaries"
-uuid = "3cfb6a46-05f0-43df-bb16-bf763deb14b4"
-version = "0.1.0"
-
 [[deps.libblastrampoline_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
 version = "5.8.0+1"
 
-[[deps.libribasim]]
-deps = ["BasicModelInterface", "Dates", "Ribasim", "TOML"]
-path = "build/libribasim"
-uuid = "f319f290-633d-4573-adfe-d6d5548b6388"
-version = "0.1.0"
-
 [[deps.libsodium_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "848ab3d00fe39d6fbc2a8641048f8f272af1c51e"
@@ -1688,9 +1678,3 @@ version = "1.52.0+1"
 deps = ["Artifacts", "Libdl"]
 uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
 version = "17.4.0+2"
-
-[[deps.ribasim_cli]]
-deps = ["Dates", "Logging", "Ribasim", "SciMLBase", "TOML", "TerminalLoggers"]
-path = "build/ribasim_cli"
-uuid = "e45c999e-e944-4589-a8e6-7d0b7a60140a"
-version = "0.1.0"