From 5298058ba2c23a8a739fac203dc419bca905f577 Mon Sep 17 00:00:00 2001
From: Samuel-AMAP <samuel.mackeown@cirad.fr>
Date: Fri, 22 Nov 2024 15:25:48 +0100
Subject: [PATCH 1/7] Add == method on statuses for easy comparison in tests

---
 src/component_models/Status.jl | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/component_models/Status.jl b/src/component_models/Status.jl
index debca9d2..eed425a4 100644
--- a/src/component_models/Status.jl
+++ b/src/component_models/Status.jl
@@ -126,6 +126,12 @@ function Base.indexed_iterate(mnt::Status, i::Int, state=1)
     Base.indexed_iterate(NamedTuple(mnt), i, state)
 end
 
+function Base.:(==)(s1::Status, s2::Status)
+    return (length(s1) == length(s2)) && 
+    (propertynames(s1) == propertynames(s2)) && 
+    (values(s1) == values(s2))
+end
+
 
 """
     propagate_values!(status1::Dict, status2::Dict, vars_not_propagated::Set)

From b65f733c50572a8c5d89fd3d677c69d908d3d31b Mon Sep 17 00:00:00 2001
From: Samuel-AMAP <samuel.mackeown@cirad.fr>
Date: Fri, 22 Nov 2024 15:26:14 +0100
Subject: [PATCH 2/7] Remove type instability accidentally introduced a little
 while ago

---
 src/dependencies/hard_dependencies.jl | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/src/dependencies/hard_dependencies.jl b/src/dependencies/hard_dependencies.jl
index a40ed307..4728b102 100644
--- a/src/dependencies/hard_dependencies.jl
+++ b/src/dependencies/hard_dependencies.jl
@@ -126,11 +126,7 @@ function hard_dependencies(mapping::Dict{String,T}; verbose::Bool=true) where {T
     # so keep tabs on them during initialisation until they're no longer needed
     hard_dependency_dict = Dict{Pair{Symbol, String}, HardDependencyNode}()
     
-    hard_deps = Dict()
-    
-    for (organ, mods_scale) in mods
-         hard_deps[organ] = hard_dependencies(mods_scale, scale=organ, verbose=false)
-    end
+    hard_deps = Dict(organ => hard_dependencies(mods_scale, scale=organ, verbose=false) for (organ, mods_scale) in mods)
 
     # Compute the inputs and outputs of all "root" node of the hard dependencies, so the root 
     # node that takes control over other models appears to have the union of its own inputs (resp. outputs)

From 71183c3d45720ec0ed6b0c77c95907c883bdec07 Mon Sep 17 00:00:00 2001
From: Samuel-AMAP <samuel.mackeown@cirad.fr>
Date: Fri, 22 Nov 2024 16:29:32 +0100
Subject: [PATCH 3/7] Simple multithreading test (will fail without changes to
 CI) + model generating many organs in an mtg

---
 test/test-performance.jl | 174 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 174 insertions(+)
 create mode 100644 test/test-performance.jl

diff --git a/test/test-performance.jl b/test/test-performance.jl
new file mode 100644
index 00000000..781a27ac
--- /dev/null
+++ b/test/test-performance.jl
@@ -0,0 +1,174 @@
+ 
+using BenchmarkTools
+using Dates
+
+PlantSimEngine.@process "sleep" verbose = false
+
+struct ToySleepModel <: AbstractSleepModel   
+end
+
+PlantSimEngine.inputs_(::ToySleepModel) = (a = -Inf,)
+PlantSimEngine.outputs_(::ToySleepModel) = NamedTuple()
+
+function PlantSimEngine.run!(m::ToySleepModel, models, status, meteo, constants=nothing, extra=nothing)
+    # sleep for 0.01 seconds (not going to be perfectly accurate)
+    Base.sleep(0.001)
+end
+
+PlantSimEngine.TimeStepDependencyTrait(::Type{<:ToySleepModel}) = PlantSimEngine.IsTimeStepIndependent()
+
+@testset begin "Check number of threads"
+    nthr = Threads.nthreads()
+    @test nthr == 4
+    
+    meteo_day = read_weather(joinpath(pkgdir(PlantSimEngine), "examples/meteo_day.csv"), duration=Day)
+    nrows = nrow(meteo_day)
+    
+    vc = [0 for i in 1:nrows]
+
+    models1 = ModelList(process1=ToySleepModel(), status=(a=vc,))
+    models2 = ModelList(process1=ToySleepModel(), status=(a=vc,))
+
+    t_seq = @benchmark run!(models1, meteo_day; executor = SequentialEx())
+    #t_seq = run!(models1, meteo_day; executor = SequentialEx())
+    min_time_seq = minimum(t_seq).time 
+
+    #time is in nanoseconds
+    @test min_time_seq > nrows * 1000000
+
+    t_mt = @benchmark run!(models2, meteo_day; executor = ThreadedEx())
+    #t_mt = run!(models2, meteo_day; executor = ThreadedEx())
+    min_time_mt = minimum(t_mt).time 
+
+    @test min_time_mt > nrows * 1000000 / nthr
+
+    # expecting mt to have some overhead
+    @test nthr * min_time_mt > min_time_seq
+
+    # todo DataFrame equals
+    @test status(models1) == status(models2)
+end
+
+
+#############################################
+### Simulation with many organs in the MTG (but only a few different types of organs)
+
+
+PlantSimEngine.@process "organ_crazy_emergence" verbose = false
+
+"""
+    ToyInternodeCrazyEmergence(;init_TT=0.0, TT_emergence = 300)
+
+Computes the organ emergence based on cumulated thermal time since last event.
+"""
+struct ToyInternodeCrazyEmergence <: AbstractOrgan_Crazy_EmergenceModel
+    TT_emergence::Float64
+end
+
+ToyInternodeCrazyEmergence(; TT_emergence=300.0) = ToyInternodeCrazyEmergence(TT_emergence)
+
+PlantSimEngine.inputs_(m::ToyInternodeCrazyEmergence) = (TT_cu=-Inf,)
+PlantSimEngine.outputs_(m::ToyInternodeCrazyEmergence) = (TT_cu_emergence=0.0,)
+
+function PlantSimEngine.run!(m::ToyInternodeCrazyEmergence, models, status, meteo, constants=nothing, sim_object=nothing)
+
+    #root = get_root(status.node)
+
+    #if nleaves(root) > 10000
+    #    return nothing
+    #end
+
+    if length(MultiScaleTreeGraph.children(status.node)) == 1 && status.TT_cu - status.TT_cu_emergence >= m.TT_emergence 
+       
+        status_new_internode = add_organ!(status.node, sim_object, "<", "Internode", 2, index=1)
+        add_organ!(status_new_internode.node, sim_object, "+", "Leaf", 2, index=1)
+        status_new_internode.TT_cu_emergence = status.TT_cu   
+    elseif (length(MultiScaleTreeGraph.children(status.node)) >= 2 && length(MultiScaleTreeGraph.children(status.node)) < 7) && status.TT_cu - status.TT_cu_emergence >= m.TT_emergence 
+        status_new_internode = add_organ!(status.node, sim_object, "<", "Internode", 2, index=1)
+        add_organ!(status.node, sim_object, "+", "Leaf", 2, index=4)
+        add_organ!(status.node, sim_object, "+", "Leaf", 2, index=5)
+        status_new_internode.TT_cu_emergence = status.TT_cu
+    elseif (length(MultiScaleTreeGraph.children(status.node)) >= 7 && length(MultiScaleTreeGraph.children(status.node)) < 30) && status.TT_cu - status.TT_cu_emergence >= m.TT_emergence 
+        add_organ!(status.node, sim_object, "+", "Leaf", 2, index=6)
+        add_organ!(status.node, sim_object, "+", "Leaf", 2, index=7)
+        add_organ!(status.node, sim_object, "+", "Leaf", 2, index=8)
+        add_organ!(status.node, sim_object, "+", "Leaf", 2, index=9)
+        add_organ!(status.node, sim_object, "+", "Leaf", 2, index=10)
+        add_organ!(status.node, sim_object, "+", "Leaf", 2, index=11)
+
+    end
+
+    return nothing
+end
+
+
+# Wrapped this into a function so that it doesn't plague the benchmark with variables on a global scope
+#@check_allocs
+function do_benchmark_on_heavier_mtg()
+    mtg = import_mtg_example();
+
+    # Example meteo, 365 timesteps :
+    meteo_day = read_weather(joinpath(pkgdir(PlantSimEngine), "examples/meteo_day.csv"), duration=Day)
+    
+    #similar to the mtg growth test but with a much lower emergence threshold
+    mapping = Dict(
+        "Scene" => ToyDegreeDaysCumulModel(),
+        "Plant" => (
+            MultiScaleModel(
+                model=ToyLAIModel(),
+                mapping=[
+                    :TT_cu => "Scene",
+                ],
+            ),
+            Beer(0.6),
+            MultiScaleModel(
+                model=ToyCAllocationModel(),
+                mapping=[
+                    :carbon_assimilation => ["Leaf"],
+                    :carbon_demand => ["Leaf", "Internode"],
+                    :carbon_allocation => ["Leaf", "Internode"]
+                ],
+            ),
+            MultiScaleModel(
+                model=ToyPlantRmModel(),
+                mapping=[:Rm_organs => ["Leaf" => :Rm, "Internode" => :Rm],],
+            ),
+        ),
+        "Internode" => (
+            MultiScaleModel(
+                model=ToyCDemandModel(optimal_biomass=10.0, development_duration=200.0),
+                mapping=[:TT => "Scene",],
+            ),
+            MultiScaleModel(
+                model=ToyInternodeCrazyEmergence(TT_emergence=1.0),
+                mapping=[:TT_cu => "Scene"],
+            ),
+            ToyMaintenanceRespirationModel(1.5, 0.06, 25.0, 0.6, 0.004),
+            Status(carbon_biomass=1.0)
+        ),
+        "Leaf" => (
+            MultiScaleModel(
+                model=ToyAssimModel(),
+                mapping=[:soil_water_content => "Soil", :aPPFD => "Plant"],
+            ),
+            MultiScaleModel(
+                model=ToyCDemandModel(optimal_biomass=10.0, development_duration=200.0),
+                mapping=[:TT => "Scene",],
+            ),
+            ToyMaintenanceRespirationModel(2.1, 0.06, 25.0, 1.0, 0.025),
+            Status(carbon_biomass=1.0)
+        ),
+        "Soil" => (
+            ToySoilWaterModel(),
+        ),
+    )
+    
+    out_vars = Dict(
+        "Leaf" => (:carbon_assimilation, :carbon_demand, :soil_water_content, :carbon_allocation),
+        "Internode" => (:carbon_allocation, :TT_cu_emergence),
+        "Plant" => (:carbon_allocation,),
+        "Soil" => (:soil_water_content,),
+    )
+    
+    out = run!(mtg, mapping, meteo_day, outputs=out_vars, executor=SequentialEx());
+end

From 9ea77e5854a317f64321395da2ea93a626eff1a9 Mon Sep 17 00:00:00 2001
From: Samuel-AMAP <samuel.mackeown@cirad.fr>
Date: Wed, 27 Nov 2024 17:17:57 +0100
Subject: [PATCH 4/7] PlantBioPhysics integration tentative commit, see what is
 broken

---
 test/downstream/Manifest.toml           | 1153 +++++++++++++++++++++++
 test/downstream/Project.toml            |    9 +
 test/downstream/test-plantbiophysics.jl |  146 +++
 test/downstream/test-xpalm.jl           |    5 +
 4 files changed, 1313 insertions(+)
 create mode 100644 test/downstream/Manifest.toml
 create mode 100644 test/downstream/Project.toml
 create mode 100644 test/downstream/test-plantbiophysics.jl
 create mode 100644 test/downstream/test-xpalm.jl

diff --git a/test/downstream/Manifest.toml b/test/downstream/Manifest.toml
new file mode 100644
index 00000000..a90d7a7c
--- /dev/null
+++ b/test/downstream/Manifest.toml
@@ -0,0 +1,1153 @@
+# This file is machine-generated - editing it directly is not advised
+
+julia_version = "1.11.1"
+manifest_format = "2.0"
+project_hash = "48c0cf248125af237657d8187328ec0ddef91af0"
+
+[[deps.AbstractTrees]]
+git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177"
+uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
+version = "0.4.5"
+
+[[deps.Accessors]]
+deps = ["CompositionsBase", "ConstructionBase", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown"]
+git-tree-sha1 = "b392ede862e506d451fc1616e79aa6f4c673dab8"
+uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
+version = "0.1.38"
+
+    [deps.Accessors.extensions]
+    AccessorsAxisKeysExt = "AxisKeys"
+    AccessorsDatesExt = "Dates"
+    AccessorsIntervalSetsExt = "IntervalSets"
+    AccessorsStaticArraysExt = "StaticArrays"
+    AccessorsStructArraysExt = "StructArrays"
+    AccessorsTestExt = "Test"
+    AccessorsUnitfulExt = "Unitful"
+
+    [deps.Accessors.weakdeps]
+    AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5"
+    Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+    IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
+    Requires = "ae029012-a4dd-5104-9daa-d747884805df"
+    StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+    StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
+    Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+    Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+
+[[deps.Adapt]]
+deps = ["LinearAlgebra", "Requires"]
+git-tree-sha1 = "50c3c56a52972d78e8be9fd135bfb91c9574c140"
+uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
+version = "4.1.1"
+weakdeps = ["StaticArrays"]
+
+    [deps.Adapt.extensions]
+    AdaptStaticArraysExt = "StaticArrays"
+
+[[deps.AliasTables]]
+deps = ["PtrArrays", "Random"]
+git-tree-sha1 = "9876e1e164b144ca45e9e3198d0b689cadfed9ff"
+uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8"
+version = "1.1.3"
+
+[[deps.ArgCheck]]
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+
+[[deps.ArgTools]]
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+
+[[deps.ArnoldiMethod]]
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+git-tree-sha1 = "d57bd3762d308bded22c3b82d033bff85f6195c6"
+uuid = "ec485272-7323-5ecc-a04f-4719b315124d"
+version = "0.4.0"
+
+[[deps.ArrayInterface]]
+deps = ["Adapt", "LinearAlgebra"]
+git-tree-sha1 = "d5140b60b87473df18cf4fe66382b7c3596df047"
+uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
+version = "7.17.1"
+
+    [deps.ArrayInterface.extensions]
+    ArrayInterfaceBandedMatricesExt = "BandedMatrices"
+    ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices"
+    ArrayInterfaceCUDAExt = "CUDA"
+    ArrayInterfaceCUDSSExt = "CUDSS"
+    ArrayInterfaceChainRulesCoreExt = "ChainRulesCore"
+    ArrayInterfaceChainRulesExt = "ChainRules"
+    ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore"
+    ArrayInterfaceReverseDiffExt = "ReverseDiff"
+    ArrayInterfaceSparseArraysExt = "SparseArrays"
+    ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore"
+    ArrayInterfaceTrackerExt = "Tracker"
+
+    [deps.ArrayInterface.weakdeps]
+    BandedMatrices = "aae01518-5342-5314-be14-df237901396f"
+    BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0"
+    CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
+    CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e"
+    ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2"
+    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+    GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
+    ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
+    SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+    StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
+    Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
+
+[[deps.Artifacts]]
+uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
+version = "1.11.0"
+
+[[deps.BangBang]]
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+version = "0.4.3"
+
+    [deps.BangBang.extensions]
+    BangBangChainRulesCoreExt = "ChainRulesCore"
+    BangBangDataFramesExt = "DataFrames"
+    BangBangStaticArraysExt = "StaticArrays"
+    BangBangStructArraysExt = "StructArrays"
+    BangBangTablesExt = "Tables"
+    BangBangTypedTablesExt = "TypedTables"
+
+    [deps.BangBang.weakdeps]
+    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+    DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
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+    Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
+    TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9"
+
+[[deps.Base64]]
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+
+[[deps.BenchmarkTools]]
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+
+[[deps.CSV]]
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+weakdeps = ["Dates", "LinearAlgebra"]
+
+    [deps.Compat.extensions]
+    CompatLinearAlgebraExt = "LinearAlgebra"
+
+[[deps.CompilerSupportLibraries_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
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+
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+weakdeps = ["InverseFunctions"]
+
+    [deps.CompositionsBase.extensions]
+    CompositionsBaseInverseFunctionsExt = "InverseFunctions"
+
+[[deps.ConcurrentUtilities]]
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+git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1"
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+
+    [deps.ConstructionBase.extensions]
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+    ConstructionBaseLinearAlgebraExt = "LinearAlgebra"
+    ConstructionBaseStaticArraysExt = "StaticArrays"
+
+    [deps.ConstructionBase.weakdeps]
+    IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
+    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+    StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+
+[[deps.ContextVariablesX]]
+deps = ["Compat", "Logging", "UUIDs"]
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+
+[[deps.XML2_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
+git-tree-sha1 = "a2fccc6559132927d4c5dc183e3e01048c6dcbd6"
+uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
+version = "2.13.5+0"
+
+[[deps.YAML]]
+deps = ["Base64", "Dates", "Printf", "StringEncodings"]
+git-tree-sha1 = "dea63ff72079443240fbd013ba006bcbc8a9ac00"
+uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
+version = "0.4.12"
+
+[[deps.ZipArchives]]
+deps = ["ArgCheck", "CodecInflate64", "CodecZlib", "InputBuffers", "PrecompileTools", "TranscodingStreams", "Zlib_jll"]
+git-tree-sha1 = "f7fd93aa03f519c25b8b328693f2d36ce01220a9"
+uuid = "49080126-0e18-4c2a-b176-c102e4b3760c"
+version = "2.4.0"
+
+[[deps.ZipFile]]
+deps = ["Libdl", "Printf", "Zlib_jll"]
+git-tree-sha1 = "f492b7fe1698e623024e873244f10d89c95c340a"
+uuid = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"
+version = "0.10.1"
+
+[[deps.Zlib_jll]]
+deps = ["Libdl"]
+uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
+version = "1.2.13+1"
+
+[[deps.libblastrampoline_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
+version = "5.11.0+0"
+
+[[deps.nghttp2_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
+version = "1.59.0+0"
+
+[[deps.p7zip_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
+version = "17.4.0+2"
diff --git a/test/downstream/Project.toml b/test/downstream/Project.toml
new file mode 100644
index 00000000..f3acf78c
--- /dev/null
+++ b/test/downstream/Project.toml
@@ -0,0 +1,9 @@
+[deps]
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+PlantBiophysics = "7ae8fcfa-76ad-4ec6-9ea7-5f8f5e2d6ec9"
+PlantMeteo = "4630fe09-e0fb-4da5-a846-781cb73437b6"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
diff --git a/test/downstream/test-plantbiophysics.jl b/test/downstream/test-plantbiophysics.jl
new file mode 100644
index 00000000..7f3a495e
--- /dev/null
+++ b/test/downstream/test-plantbiophysics.jl
@@ -0,0 +1,146 @@
+#TODO REMOVE SOME OF THOSE BITS
+using Pkg
+#Pkg.develop("PlantSimEngine")
+using PlantSimEngine
+using Statistics
+using DataFrames
+using CSV
+using Random
+using PlantBiophysics
+using BenchmarkTools
+using Test
+
+function benchmark_plantbiophysics()
+
+    Random.seed!(1) # Set random seed
+    microbenchmark_steps = 100 # Number of times the microbenchmark is run
+    microbenchmark_evals = 1 # N. times each sample is run to be sure of the output
+    N = 100 # Number of timesteps simulated for each microbenchmark step
+
+    length_range = 10000
+    Rs = range(10, 500, length=length_range)
+    Ta = range(18, 40, length=length_range)
+    Wind = range(0.5, 20, length=length_range)
+    P = range(90, 101, length=length_range)
+    Rh = range(0.1, 0.98, length=length_range)
+    Ca = range(360, 900, length=length_range)
+    skyF = range(0.0, 1.0, length=length_range)
+    d = range(0.001, 0.5, length=length_range)
+    Jmax = range(200.0, 300.0, length=length_range)
+    Vmax = range(150.0, 250.0, length=length_range)
+    Rd = range(0.3, 2.0, length=length_range)
+    TPU = range(5.0, 20.0, length=length_range)
+    g0 = range(0.001, 2.0, length=length_range)
+    g1 = range(0.5, 15.0, length=length_range)
+    vars = hcat([Ta, Wind, P, Rh, Ca, Jmax, Vmax, Rd, Rs, skyF, d, TPU, g0, g1])
+
+    set = [rand.(vars) for i = 1:N]
+    set = reshape(vcat(set...), (length(set[1]), length(set)))'
+    name = [
+        "T",
+        "Wind",
+        "P",
+        "Rh",
+        "Ca",
+        "JMaxRef",
+        "VcMaxRef",
+        "RdRef",
+        "Rs",
+        "sky_fraction",
+        "d",
+        "TPURef",
+        "g0",
+        "g1",
+    ]
+    set = DataFrame(set, name)
+    @. set[!, :vpd] = e_sat(set.T) - vapor_pressure(set.T, set.Rh)
+    @. set[!, :PPFD] = set.Rs * 0.48 * 4.57
+    set
+
+
+    constants = Constants()
+    time_PB = []
+    for i = 1:N
+        leaf = ModelList(
+            energy_balance=Monteith(),
+            photosynthesis=Fvcb(
+                VcMaxRef=set.VcMaxRef[i],
+                JMaxRef=set.JMaxRef[i],
+                RdRef=set.RdRef[i],
+                TPURef=set.TPURef[i],
+            ),
+            stomatal_conductance=Medlyn(set.g0[i], set.g1[i]),
+            status=(
+                Rₛ=set.Rs[i],
+                sky_fraction=set.sky_fraction[i],
+                PPFD=set.PPFD[i],
+                d=set.d[i],
+            ),
+        )
+        deps = PlantSimEngine.dep(leaf)
+        meteo = Atmosphere(T=set.T[i], Wind=set.Wind[i], P=set.P[i], Rh=set.Rh[i], Cₐ=set.Ca[i])
+        st = PlantMeteo.row_struct(leaf.status[1])
+        b_PB = @benchmark run!($leaf, $deps, 1, $st, $meteo, $constants, nothing; executor = ThreadedEx()) evals = microbenchmark_evals samples = microbenchmark_steps
+        append!(time_PB, b_PB.times .* 1e-9) # transform in seconds
+    end
+    return time_PB
+end
+
+@testset "PlantBiophysics benchmark" begin
+
+    time_PB = benchmark_plantbiophysics()
+    
+    #statsPB = (mean(time_PB), median(time_PB), Statistics.std(time_PB), findmin(time_PB), findmax(time_PB))
+    mean(time_PB)
+    @test mean(time_PB) > 1000000000000000
+    #TODO deal with results
+end
+
+
+#=
+function run_plantbiophysics()
+
+
+    Rs = 10.0
+    Ta = 18.0
+    Wind = 0.5
+    P = 90.0
+    Rh = 0.1
+    Ca = 360.0
+    skyF = 0.0
+    d = 0.001
+    Jmax = 200.0
+    Vmax = 150.0
+    Rd = 0.3
+    TPU = 5.0
+    g0 = 0.001
+    g1 = 0.5
+    vpd = e_sat(Ta) - vapor_pressure(Ta, Rh)
+    PPFD = Rs*0.48*4.57
+
+    constants = Constants()
+
+        leaf = ModelList(
+            energy_balance=Monteith(),
+            photosynthesis=Fvcb(
+                VcMaxRef=Vmax,
+                JMaxRef=Jmax,
+                RdRef=Rd,
+                TPURef=TPU,
+            ),
+            stomatal_conductance=Medlyn(g0, g1),
+            status=(
+                Rₛ=Rs,
+                sky_fraction=skyF,
+                PPFD=PPFD,
+                d=d,
+            ),
+        )
+        deps = PlantSimEngine.dep(leaf)
+        meteo = Atmosphere(T=Ta, Wind=Wind, P=P, Rh=Rh, Cₐ=Ca)
+        st = PlantMeteo.row_struct(leaf.status[1])
+        run!(leaf, deps, 1, st, meteo, constants, nothing) 
+end
+
+run_plantbiophysics()
+=#
\ No newline at end of file
diff --git a/test/downstream/test-xpalm.jl b/test/downstream/test-xpalm.jl
new file mode 100644
index 00000000..5e199e39
--- /dev/null
+++ b/test/downstream/test-xpalm.jl
@@ -0,0 +1,5 @@
+using Test
+
+@testset "XPalm dummy test TODO" begin
+    @test true
+end 
\ No newline at end of file

From 3685b9db366145c4e140ef891c404d7f640c40cb Mon Sep 17 00:00:00 2001
From: Samuel-AMAP <samuel.mackeown@cirad.fr>
Date: Wed, 27 Nov 2024 17:29:01 +0100
Subject: [PATCH 5/7] PlantBioPhysics integration : oops, forgot the yml file
 in the previous commit

---
 .github/workflows/Integration.yml | 69 +++++++++++++++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100644 .github/workflows/Integration.yml

diff --git a/.github/workflows/Integration.yml b/.github/workflows/Integration.yml
new file mode 100644
index 00000000..d4573d09
--- /dev/null
+++ b/.github/workflows/Integration.yml
@@ -0,0 +1,69 @@
+name: Integration
+on:
+  push:
+    branches:
+      - main
+    tags: "*"
+  pull_request:
+  workflow_dispatch:
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      actions: write
+      contents: read
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - "1.9"
+          - "1"
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+        package:
+        - {user: PalmStudio, repo: XPalm.jl}
+        - {user: VEZY, repo: PlantBioPhysics.jl}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/julia-buildpkg@v1
+      - name: Clone Downstream
+        uses: actions/checkout@v4
+        with:
+          repository: ${{ matrix.package.user }}/${{ matrix.package.repo }}
+          path: downstream
+      - name: Load this and run the downstream tests
+        shell: julia --threads 4 --color=yes --project=downstream --depwarn=yes {0}
+        run: |
+          using Pkg
+          try
+            # force it to use this PR's version of the package
+            Pkg.develop(PackageSpec(path="."))  # resolver may fail with main deps
+            Pkg.update()
+            Pkg.test()  # resolver may fail with test time deps
+          catch err
+            err isa Pkg.Resolve.ResolverError || rethrow()
+            # If we can't resolve that means this is incompatible by SemVer and this is fine
+            # It means we marked this as a breaking change, so we don't need to worry about
+            # Mistakenly introducing a breaking change, as we have intentionally made one
+            @info "Testing with an incompatible downstream release as a breaking change was introduced. Expected failure." exception=err
+            exit(0)  # Exit immediately, as a success
+          end
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v5
+        with:
+          files: lcov.info
\ No newline at end of file

From 4fd15ad8bca489a8bad339ff1dd55c9ef1965222 Mon Sep 17 00:00:00 2001
From: Samuel-AMAP <samuel.mackeown@cirad.fr>
Date: Thu, 28 Nov 2024 14:29:31 +0100
Subject: [PATCH 6/7] Slight changes to the PBP benchmark, preallocating
 outputs

---
 test/downstream/test-plantbiophysics.jl | 28 ++++++++++++++++---------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/test/downstream/test-plantbiophysics.jl b/test/downstream/test-plantbiophysics.jl
index 7f3a495e..f8c1dd47 100644
--- a/test/downstream/test-plantbiophysics.jl
+++ b/test/downstream/test-plantbiophysics.jl
@@ -1,7 +1,7 @@
-#TODO REMOVE SOME OF THOSE BITS
-using Pkg
+#TODO Cleanup
+#using Pkg
 #Pkg.develop("PlantSimEngine")
-using PlantSimEngine
+#using PlantSimEngine
 using Statistics
 using DataFrames
 using CSV
@@ -9,6 +9,7 @@ using Random
 using PlantBiophysics
 using BenchmarkTools
 using Test
+using PlantMeteo
 
 function benchmark_plantbiophysics()
 
@@ -59,7 +60,7 @@ function benchmark_plantbiophysics()
 
 
     constants = Constants()
-    time_PB = []
+    time_PB = Vector{Float64}(undef, N*microbenchmark_steps)
     for i = 1:N
         leaf = ModelList(
             energy_balance=Monteith(),
@@ -81,7 +82,11 @@ function benchmark_plantbiophysics()
         meteo = Atmosphere(T=set.T[i], Wind=set.Wind[i], P=set.P[i], Rh=set.Rh[i], Cₐ=set.Ca[i])
         st = PlantMeteo.row_struct(leaf.status[1])
         b_PB = @benchmark run!($leaf, $deps, 1, $st, $meteo, $constants, nothing; executor = ThreadedEx()) evals = microbenchmark_evals samples = microbenchmark_steps
-        append!(time_PB, b_PB.times .* 1e-9) # transform in seconds
+        
+        # transform in seconds        
+        for j in 1:microbenchmark_steps
+            time_PB[microbenchmark_steps*(i-1) + j] = b_PB.times[j]*1e-9
+        end
     end
     return time_PB
 end
@@ -89,14 +94,17 @@ end
 @testset "PlantBiophysics benchmark" begin
 
     time_PB = benchmark_plantbiophysics()
-    
+    N = length(time_PB)
     #statsPB = (mean(time_PB), median(time_PB), Statistics.std(time_PB), findmin(time_PB), findmax(time_PB))
-    mean(time_PB)
-    @test mean(time_PB) > 1000000000000000
-    #TODO deal with results
+    min__ = findmin(time_PB)[1]
+    max__ = findmin(time_PB)[1]
+    @test min__ > 1e-7
+    @test max__ < 1e-5
+    @test mean(time_PB) > 5e-7
+    @test mean(time_PB) < 5e-6
+    #TODO
 end
 
-
 #=
 function run_plantbiophysics()
 

From 736afdf9ae4f43841565b8a2ec75692629223e24 Mon Sep 17 00:00:00 2001
From: Samuel-AMAP <samuel.mackeown@cirad.fr>
Date: Wed, 11 Dec 2024 10:39:51 +0100
Subject: [PATCH 7/7] Remove XPalm (temporarily) from downstream tests

---
 .github/workflows/Integration.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/Integration.yml b/.github/workflows/Integration.yml
index d4573d09..05f3d0a8 100644
--- a/.github/workflows/Integration.yml
+++ b/.github/workflows/Integration.yml
@@ -32,7 +32,7 @@ jobs:
         arch:
           - x64
         package:
-        - {user: PalmStudio, repo: XPalm.jl}
+        #- {user: PalmStudio, repo: XPalm.jl}
         - {user: VEZY, repo: PlantBioPhysics.jl}
     steps:
       - uses: actions/checkout@v4