Merge branch 'main' into autodiff_wrt_time

.teamcity/Ribasim_Ribasim/buildTypes/BuildRibasimCliWindows.xml

@@ -6,7 +6,6 @@
     <options>
       <option name="artifactRules" value="ribasim\build/create_binaries/ribasim_cli =&gt; ribasim_cli.zip" />
       <option name="executionTimeoutMin" value="120" />
-      <option name="publishArtifactCondition" value="SUCCESSFUL" />
     </options>
     <parameters>
       <param name="conda_env_path" value="%system.teamcity.build.checkoutDir%/env_build_ribasim_cli" />

.teamcity/Ribasim_Ribasim/buildTypes/Ribasim_Ribasim_TestRibasimCliWindows.xml

@@ -4,7 +4,7 @@
   <description />
   <settings>
     <options>
-      <option name="artifactRules" value="build\ribasim_cli\tests\temp =&gt; test_output.zip" />
+      <option name="artifactRules" value="ribasim\build\ribasim_cli\tests\temp =&gt; test_output.zip" />
     </options>
     <parameters>
       <param name="conda_env_path" value="%system.teamcity.build.checkoutDir%/ribasim_cli_test_env" />

build/create_binaries/Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.9.3"
 manifest_format = "2.0"
-project_hash = "c56985ee841fb30b2cb92ecec4da345315a95306"
+project_hash = "71b2262fd2a2bd6f9c0ade48d4062e051c3f39eb"
 
 [[deps.ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
@@ -14,6 +14,19 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 [[deps.Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
+[[deps.Compat]]
+deps = ["UUIDs"]
+git-tree-sha1 = "8a62af3e248a8c4bad6b32cbbe663ae02275e32c"
+uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
+version = "4.10.0"
+
+    [deps.Compat.extensions]
+    CompatLinearAlgebraExt = "LinearAlgebra"
+
+    [deps.Compat.weakdeps]
+    Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+
 [[deps.Dates]]
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
@@ -23,6 +36,11 @@ deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 version = "1.6.0"
 
+[[deps.ExprTools]]
+git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec"
+uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04"
+version = "0.1.10"
+
 [[deps.FileWatching]]
 uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
 
@@ -31,6 +49,12 @@ git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496"
 uuid = "c27321d9-0574-5035-807b-f59d2c89b15c"
 version = "1.3.1"
 
+[[deps.InlineStrings]]
+deps = ["Parsers"]
+git-tree-sha1 = "9cc2baf75c6d09f9da536ddf58eb2f29dedaf461"
+uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48"
+version = "1.4.0"
+
 [[deps.InteractiveUtils]]
 deps = ["Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
@@ -73,6 +97,12 @@ deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
 version = "2.28.2+0"
 
+[[deps.Mocking]]
+deps = ["Compat", "ExprTools"]
+git-tree-sha1 = "4cc0c5a83933648b615c36c2b956d94fda70641e"
+uuid = "78c3b35d-d492-501b-9361-3d52fe80e533"
+version = "0.7.7"
+
 [[deps.MozillaCACerts_jll]]
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
 version = "2022.10.11"
@@ -87,11 +117,29 @@ git-tree-sha1 = "d24f0920777c64c0265e9725eb4a3ec450bc36dd"
 uuid = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d"
 version = "2.1.10"
 
+[[deps.Parsers]]
+deps = ["Dates", "PrecompileTools", "UUIDs"]
+git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851"
+uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
+version = "2.7.2"
+
 [[deps.Pkg]]
 deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 version = "1.9.2"
 
+[[deps.PrecompileTools]]
+deps = ["Preferences"]
+git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f"
+uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
+version = "1.2.0"
+
+[[deps.Preferences]]
+deps = ["TOML"]
+git-tree-sha1 = "00805cd429dcb4870060ff49ef443486c262e38e"
+uuid = "21216c6a-2e73-6563-6e65-726566657250"
+version = "1.4.1"
+
 [[deps.Printf]]
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
@@ -131,11 +179,29 @@ deps = ["Dates"]
 uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 version = "1.0.3"
 
+[[deps.TZJData]]
+deps = ["Artifacts"]
+git-tree-sha1 = "d39314cdbaf5b90a047db33858626f8d1cc973e1"
+uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7"
+version = "1.0.0+2023c"
+
 [[deps.Tar]]
 deps = ["ArgTools", "SHA"]
 uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
 version = "1.10.0"
 
+[[deps.TimeZones]]
+deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"]
+git-tree-sha1 = "89e64d61ef3cd9e80f7fc12b7d13db2d75a23c03"
+uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53"
+version = "1.13.0"
+
+    [deps.TimeZones.extensions]
+    TimeZonesRecipesBaseExt = "RecipesBase"
+
+    [deps.TimeZones.weakdeps]
+    RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
+
 [[deps.UUIDs]]
 deps = ["Random", "SHA"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"

build/create_binaries/Project.toml

@@ -1,8 +1,11 @@
 [deps]
+Artifacts = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 LibGit2 = "76f85450-5226-5b5a-8eaa-529ad045b433"
 PackageCompiler = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d"
 TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+TimeZones = "f269a46b-ccf7-5d73-abea-4c690281aa53"
 
 [compat]
 PackageCompiler = "2"
+TimeZones = "=1.13.0"
 julia = "1.9"

build/create_binaries/create_app.jl

@@ -2,6 +2,8 @@ using PackageCompiler
 using TOML
 using LibGit2
 
+include("strip_cldr.jl")
+
 # change directory to this script's location
 cd(@__DIR__)
 
@@ -16,7 +18,7 @@ create_app(
     # map from binary name to julia function name
     executables = ["ribasim" => "julia_main"],
     precompile_execution_file = "precompile.jl",
-    filter_stdlibs = false,
+    include_lazy_artifacts = true,
     force = true,
 )
 

build/create_binaries/create_lib.jl

@@ -2,6 +2,8 @@ using PackageCompiler
 using TOML
 using LibGit2
 
+include("strip_cldr.jl")
+
 cd(@__DIR__)
 
 project_dir = "../libribasim"
@@ -14,7 +16,7 @@ create_library(
     output_dir;
     lib_name = "libribasim",
     precompile_execution_file = "precompile.jl",
-    include_lazy_artifacts = false,
+    include_lazy_artifacts = true,
     force = true,
 )
 

build/create_binaries/precompile.jl

@@ -3,5 +3,5 @@
 
 using Ribasim, Dates, TOML
 
-toml_path = normpath(@__DIR__, "../../generated_testmodels/basic/basic.toml")
+toml_path = normpath(@__DIR__, "../../generated_testmodels/basic/ribasim.toml")
 Ribasim.run(toml_path)

build/create_binaries/strip_cldr.jl

@@ -0,0 +1,24 @@
+# The cldr artifact has such long paths that it errors on Windows unless long paths are enabled.
+# Also the artifact has many files and is over 300 MB, while we only need a single small file.
+# This modifies the artifact to remove everything except the file we need.
+# Since the artifact is only used on Windows, only strip do it there.
+# This needs exactly TimeZones 1.13.0, which is fixed in the Project.toml.
+# https://github.com/JuliaTime/TimeZones.jl/issues/373
+
+using Artifacts
+
+if Sys.iswindows()
+    # Get the artifact directory and the file path we need to keep
+    hash = Base.SHA1("40b35727ea0aff9a9f28b7454004b68849caf67b")
+    @assert artifact_exists(hash)
+    artifact_dir = artifact_path(hash)
+    keep_file =
+        normpath(artifact_dir, "cldr-release-43-1/common/supplemental/windowsZones.xml")
+    @assert isfile(keep_file)
+
+    # Read the file into memory, empty the artifact dir, and write the file back
+    keep_file_content = read(keep_file)
+    rm(artifact_dir; recursive = true)
+    mkpath(dirname(keep_file))
+    write(keep_file, keep_file_content)
+end

build/libribasim/Manifest.toml

@@ -979,7 +979,7 @@ uuid = "ae029012-a4dd-5104-9daa-d747884805df"
 version = "1.3.0"
 
 [[deps.Ribasim]]
-deps = ["Arrow", "BasicModelInterface", "CodecLz4", "CodecZstd", "ComponentArrays", "Configurations", "DBInterface", "DataInterpolations", "DataStructures", "Dates", "Dictionaries", "DiffEqCallbacks", "FiniteDiff", "ForwardDiff", "Graphs", "HiGHS", "IterTools", "JuMP", "Legolas", "Logging", "LoggingExtras", "OrdinaryDiffEq", "PreallocationTools", "SQLite", "SciMLBase", "SparseArrays", "StructArrays", "Tables", "TerminalLoggers", "TimeZones", "TimerOutputs", "TranscodingStreams"]
+deps = ["Arrow", "BasicModelInterface", "CodecLz4", "CodecZstd", "ComponentArrays", "Configurations", "DBInterface", "DataInterpolations", "DataStructures", "Dates", "Dictionaries", "DiffEqCallbacks", "FiniteDiff", "ForwardDiff", "Graphs", "HiGHS", "IterTools", "JuMP", "Legolas", "Logging", "LoggingExtras", "OrdinaryDiffEq", "PreallocationTools", "SQLite", "SciMLBase", "SparseArrays", "StructArrays", "Tables", "TerminalLoggers", "TimerOutputs", "TranscodingStreams"]
 path = "../../core"
 uuid = "aac5e3d9-0b8f-4d4f-8241-b1a7a9632635"
 version = "0.3.0"

build/libribasim/README.md

@@ -22,7 +22,7 @@ In [3]: argument = create_string_buffer(0)
    ...: c_dll.init_julia(c_int(0), byref(argument))
 Out[3]: 1
 
-In [4]: config_path = "run.toml"
+In [4]: config_path = "ribasim.toml"
 
 In [5]: c_dll.initialize(c_char_p(config_path.encode()))
 Out[5]: 0

build/ribasim_cli/Manifest.toml

@@ -979,7 +979,7 @@ uuid = "ae029012-a4dd-5104-9daa-d747884805df"
 version = "1.3.0"
 
 [[deps.Ribasim]]
-deps = ["Arrow", "BasicModelInterface", "CodecLz4", "CodecZstd", "ComponentArrays", "Configurations", "DBInterface", "DataInterpolations", "DataStructures", "Dates", "Dictionaries", "DiffEqCallbacks", "FiniteDiff", "ForwardDiff", "Graphs", "HiGHS", "IterTools", "JuMP", "Legolas", "Logging", "LoggingExtras", "OrdinaryDiffEq", "PreallocationTools", "SQLite", "SciMLBase", "SparseArrays", "StructArrays", "Tables", "TerminalLoggers", "TimeZones", "TimerOutputs", "TranscodingStreams"]
+deps = ["Arrow", "BasicModelInterface", "CodecLz4", "CodecZstd", "ComponentArrays", "Configurations", "DBInterface", "DataInterpolations", "DataStructures", "Dates", "Dictionaries", "DiffEqCallbacks", "FiniteDiff", "ForwardDiff", "Graphs", "HiGHS", "IterTools", "JuMP", "Legolas", "Logging", "LoggingExtras", "OrdinaryDiffEq", "PreallocationTools", "SQLite", "SciMLBase", "SparseArrays", "StructArrays", "Tables", "TerminalLoggers", "TimerOutputs", "TranscodingStreams"]
 path = "../../core"
 uuid = "aac5e3d9-0b8f-4d4f-8241-b1a7a9632635"
 version = "0.3.0"

build/ribasim_cli/README.md

@@ -13,11 +13,11 @@ If you have installed Julia and Ribasim, a simulation can also be started from t
 line as follows:
 
 ```
-julia --eval 'using Ribasim; Ribasim.run("path/to/config.toml")'
+julia --eval 'using Ribasim; Ribasim.run("path/to/model/ribasim.toml")'
 ```
 
 With a Ribasim CLI build this becomes:
 
 ```
-ribasim path/to/config.toml
+ribasim path/to/model/ribasim.toml
 ```

build/ribasim_cli/src/ribasim_cli.jl

@@ -7,7 +7,7 @@ using Ribasim
 
 function help(x)::Cint
     println(x)
-    println("Usage: ribasim path/to/config.toml")
+    println("Usage: ribasim path/to/model/ribasim.toml")
     return 1
 end
 

build/ribasim_cli/tests/test_models.py

@@ -7,13 +7,13 @@
 
 
 @pytest.mark.parametrize(
-    "model_constructor",
-    map(ribasim_testmodels.__dict__.get, ribasim_testmodels.__all__),
+    "model_name,model_constructor",
+    ribasim_testmodels.constructors.items(),
 )
-def test_ribasim_cli(model_constructor, tmp_path):
+def test_ribasim_cli(model_name, model_constructor, tmp_path):
     model = model_constructor()
     assert isinstance(model, ribasim.Model)
-    model.write(tmp_path)
+    model.write(tmp_path / model_name)
 
     executable = (
         Path(__file__).parents[2]
@@ -22,10 +22,10 @@ def test_ribasim_cli(model_constructor, tmp_path):
         / "bin"
         / "ribasim.exe"
     )
-    config_file = str(tmp_path / f"{model.modelname}.toml")
+    config_file = str(tmp_path / "ribasim.toml")
     result = subprocess.run([executable, config_file])
 
-    if model.modelname.startswith("invalid"):
+    if model_name.startswith("invalid_"):
         assert result.returncode != 0
     else:
         assert result.returncode == 0

core/Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.9.3"
 manifest_format = "2.0"
-project_hash = "6a00ca0892e2ca78622bd97e6159a398bf80fa0b"
+project_hash = "c63b237aec6a6bf6314284b2b07a94b93a9f0a36"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "5d2e21d7b0d8c22f67483ef95ebdc39c0e6b6003"
@@ -1217,6 +1217,12 @@ deps = ["Dates"]
 uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 version = "1.0.3"
 
+[[deps.TZJData]]
+deps = ["Artifacts"]
+git-tree-sha1 = "d39314cdbaf5b90a047db33858626f8d1cc973e1"
+uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7"
+version = "1.0.0+2023c"
+
 [[deps.TableTraits]]
 deps = ["IteratorInterfaceExtensions"]
 git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39"
@@ -1251,11 +1257,14 @@ uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5"
 version = "0.5.2"
 
 [[deps.TimeZones]]
-deps = ["Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "RecipesBase", "Scratch", "Unicode"]
-git-tree-sha1 = "cdaa0c2a4449724aded839550eca7d7240bb6938"
-pinned = true
+deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"]
+git-tree-sha1 = "89e64d61ef3cd9e80f7fc12b7d13db2d75a23c03"
 uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53"
-version = "1.10.0"
+version = "1.13.0"
+weakdeps = ["RecipesBase"]
+
+    [deps.TimeZones.extensions]
+    TimeZonesRecipesBaseExt = "RecipesBase"
 
 [[deps.TimerOutputs]]
 deps = ["ExprTools", "Printf"]

core/Project.toml

@@ -65,7 +65,7 @@ SciMLBase = "1.60, 2"
 StructArrays = "0.6.13"
 Tables = "1"
 TerminalLoggers = "0.1.7"
-TimeZones = "=1.10.0"
+TimeZones = "=1.13.0"
 TimerOutputs = "0.5"
 TranscodingStreams = "0.9, 0.10"
 julia = "1.9"