Update test-ModelList.jl #208
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12 errors, 6 warnings, and 1 notice
Julia 1 - ubuntu-latest - x64 - push
Process completed with exit code 1.
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Julia 1.7 - ubuntu-latest - x64 - push
Process completed with exit code 1.
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Documentation:
src/processes/models_inputs_outputs.jl#L119
doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/processes/models_inputs_outputs.jl:119-138
```jldoctest
using PlantSimEngine;
# Load the dummy models given as example in the package:
using PlantSimEngine.Examples;
variables(Process1Model(1.0))
variables(Process1Model(1.0), Process2Model())
# output
5-element Vector{Symbol}:
:var1
:var2
:var3
:var4
:var5
```
Subexpression:
using PlantSimEngine;
# Load the dummy models given as example in the package:
using PlantSimEngine.Examples;
variables(Process1Model(1.0))
variables(Process1Model(1.0), Process2Model())
Evaluated output:
(var1 = -Inf, var2 = -Inf, var3 = -Inf, var4 = -Inf, var5 = -Inf)
Expected output:
5-element Vector{Symbol}:
:var1
:var2
:var3
:var4
:var5
diff =
Warning: Diff output requires color.
5-element Vector{Symbol}:
:var1
:var2
:var3
:var4
:var5(var1 = -Inf, var2 = -Inf, var3 = -Inf, var4 = -Inf, var5 = -Inf)
|
Documentation:
src/mtg/MultiScaleModel.jl#L73
doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/MultiScaleModel.jl:73-76
```jldoctest mylabel
julia> multiscale_model = PlantSimEngine.MultiScaleModel(model, mapping)
MultiScaleModel{ToyCAllocationModel, String}(ToyCAllocationModel(), Pair{Symbol, Union{String, Vector{String}}}[:carbon_allocation => ["Leaf", "Internode"]])
```
Subexpression:
multiscale_model = PlantSimEngine.MultiScaleModel(model, mapping)
Evaluated output:
MultiScaleModel{ToyCAllocationModel, Vector{Pair{Symbol, Union{Pair{String, Symbol}, Vector{Pair{String, Symbol}}}}}}(ToyCAllocationModel(), Pair{Symbol, Union{Pair{String, Symbol}, Vector{Pair{String, Symbol}}}}[:carbon_allocation => ["Leaf" => :carbon_allocation, "Internode" => :carbon_allocation]])
Expected output:
MultiScaleModel{ToyCAllocationModel, String}(ToyCAllocationModel(), Pair{Symbol, Union{String, Vector{String}}}[:carbon_allocation => ["Leaf", "Internode"]])
diff =
Warning: Diff output requires color.
MultiScaleModel{ToyCAllocationModel, String}(ToyCAllocationModel(), Vector{Pair{Symbol, Union{Pair{String, Symbol}, Vector{Pair{String, Symbol}}}}}}(ToyCAllocationModel(), Pair{Symbol, Union{String, Vector{String}}}[:carbon_allocation Union{Pair{String, Symbol}, Vector{Pair{String, Symbol}}}}[:carbon_allocation => ["Leaf", "Internode"]])["Leaf" => :carbon_allocation, "Internode" => :carbon_allocation]])
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Documentation:
src/mtg/MultiScaleModel.jl#L80
doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/MultiScaleModel.jl:80-84
```jldoctest mylabel
julia> PlantSimEngine.mapping_(multiscale_model)
1-element Vector{Pair{Symbol, Union{String, Vector{String}}}}:
:carbon_allocation => ["Leaf", "Internode"]
```
Subexpression:
PlantSimEngine.mapping_(multiscale_model)
Evaluated output:
1-element Vector{Pair{Symbol, Union{Pair{String, Symbol}, Vector{Pair{String, Symbol}}}}}:
:carbon_allocation => ["Leaf" => :carbon_allocation, "Internode" => :carbon_allocation]
Expected output:
1-element Vector{Pair{Symbol, Union{String, Vector{String}}}}:
:carbon_allocation => ["Leaf", "Internode"]
diff =
Warning: Diff output requires color.
1-element Vector{Pair{Symbol, Union{String, Vector{String}}}}:
Union{Pair{String, Symbol}, Vector{Pair{String, Symbol}}}}}:
:carbon_allocation => ["Leaf", "Internode"]["Leaf" => :carbon_allocation, "Internode" => :carbon_allocation]
|
Documentation:
src/mtg/mapping/mapping.jl#L618
doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:618-624
```jldoctest mylabel
julia> PlantSimEngine.reverse_mapping(mapping)
Dict{String, Dict{String, Vector{Pair{Symbol, Symbol}}}} with 3 entries:
"Soil" => Dict("Leaf"=>[:soil_water_content=>:soil_water_content])
"Internode" => Dict("Plant"=>[:carbon_demand=>:carbon_demand, :carbon_allocation=>:carbon_allocation, :Rm=>:Rm_organs])
"Leaf" => Dict("Plant"=>[:carbon_assimilation=>:carbon_assimilation, :carbon_demand=>:carbon_demand, :carbon_allocation=>:carbon_allocation, :Rm=>:Rm_organs])
```
Subexpression:
PlantSimEngine.reverse_mapping(mapping)
Evaluated output:
Dict{String, Dict{String, Dict{Symbol, Any}}} with 3 entries:
"Soil" => Dict("Leaf"=>Dict(:soil_water_content=>:soil_water_content))
"Internode" => Dict("Plant"=>Dict(:carbon_allocation=>:carbon_allocation, :ca…
"Leaf" => Dict("Plant"=>Dict(:carbon_allocation=>:carbon_allocation, :ca…
Expected output:
Dict{String, Dict{String, Vector{Pair{Symbol, Symbol}}}} with 3 entries:
"Soil" => Dict("Leaf"=>[:soil_water_content=>:soil_water_content])
"Internode" => Dict("Plant"=>[:carbon_demand=>:carbon_demand, :carbon_allocation=>:carbon_allocation, :Rm=>:Rm_organs])
"Leaf" => Dict("Plant"=>[:carbon_assimilation=>:carbon_assimilation, :carbon_demand=>:carbon_demand, :carbon_allocation=>:carbon_allocation, :Rm=>:Rm_organs])
diff =
Warning: Diff output requires color.
Dict{String, Dict{String, Vector{Pair{Symbol, Symbol}}}} Dict{Symbol, Any}}} with 3 entries:
"Soil" => Dict("Leaf"=>[:soil_water_content=>:soil_water_content])
Dict("Leaf"=>Dict(:soil_water_content=>:soil_water_content))
"Internode" => Dict("Plant"=>[:carbon_demand=>:carbon_demand, :carbon_allocation=>:carbon_allocation, :Rm=>:Rm_organs])
Dict("Plant"=>Dict(:carbon_allocation=>:carbon_allocation, :ca…
"Leaf" => Dict("Plant"=>[:carbon_assimilation=>:carbon_assimilation, :carbon_demand=>:carbon_demand, :carbon_allocation=>:carbon_allocation, :Rm=>:Rm_organs])Dict("Plant"=>Dict(:carbon_allocation=>:carbon_allocation, :ca…
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Documentation:
src/mtg/mapping/mapping.jl#L415
doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:415-418
```jldoctest
julia> PlantSimEngine.MappedVar("Leaf", :carbon_assimilation, :carbon_assimilation, 1.0, :photosynthesis)
PlantSimEngine.MappedVar{String, Float64}("Leaf", :carbon_assimilation, 1.0)
```
Subexpression:
PlantSimEngine.MappedVar("Leaf", :carbon_assimilation, :carbon_assimilation, 1.0, :photosynthesis)
Evaluated output:
ERROR: MethodError: no method matching PlantSimEngine.MappedVar(::String, ::Symbol, ::Symbol, ::Float64, ::Symbol)
Closest candidates are:
PlantSimEngine.MappedVar(::Any, ::Any, ::Any, ::Any)
@ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:428
PlantSimEngine.MappedVar(!Matched::O, ::Symbol, ::V, ::T, ::Union{Nothing, Symbol}) where {O<:PlantSimEngine.AbstractNodeMapping, V<:(Union{Vector{S}, S} where S<:Symbol), T}
@ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:421
Stacktrace:
[1] top-level scope
@ none:1
Expected output:
PlantSimEngine.MappedVar{String, Float64}("Leaf", :carbon_assimilation, 1.0)
diff =
Warning: Diff output requires color.
PlantSimEngine.MappedVar{String, Float64}("Leaf", :carbon_assimilation, 1.0)ERROR: MethodError: no method matching PlantSimEngine.MappedVar(::String, ::Symbol, ::Symbol, ::Float64, ::Symbol)
Closest candidates are:
PlantSimEngine.MappedVar(::Any, ::Any, ::Any, ::Any)
@ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:428
PlantSimEngine.MappedVar(!Matched::O, ::Symbol, ::V, ::T, ::Union{Nothing, Symbol}) where {O<:PlantSimEngine.AbstractNodeMapping, V<:(Union{Vector{S}, S} where S<:Symbol), T}
@ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:421
Stacktrace:
[1] top-level scope
@ none:1
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Documentation:
src/mtg/save_results.jl#L78
doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/save_results.jl:78-80
```jldoctest mylabel
julia> statuses, = PlantSimEngine.init_statuses(mtg, mapping);
```
Subexpression:
statuses, = PlantSimEngine.init_statuses(mtg, mapping);
Evaluated output:
Issue in function #185 for node #4.
ERROR: Variable `biomass` is not computed by any model, not initialised by the user in the status, and not found in the MTG at scale Internode (checked for MTG node 4).
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] init_node_status!(node::Node{NodeMTG, Dict{Symbol, Any}}, statuses::Dict{String, Vector{Status}}, mapped_vars::Dict{String, Dict{Symbol, Any}}, reverse_multiscale_mapping::Dict{String, Dict{String, Dict{Symbol, Any}}}, vars_need_init::Dict{String, Base.KeySet{Symbol, Dict{Symbol, Any}}}, type_promotion::Nothing; check::Bool)
@ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:111
[3] init_node_status!
@ ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:89 [inlined]
[4] #185
@ ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:47 [inlined]
[5] traverse!_(node::Node{NodeMTG, Dict{Symbol, Any}}, f::PlantSimEngine.var"#185#190"{Nothing, Bool, Dict{String, Vector{Status}}, Dict{String, Base.KeySet{Symbol, Dict{Symbol, Any}}}, Dict{String, Dict{String, Dict{Symbol, Any}}}, Dict{String, Dict{Symbol, Any}}}, scale::Nothing, symbol::Nothing, link::Nothing, filter_fun::Nothing, all::Bool, recursivity_level::Float64)
@ MultiScaleTreeGraph ~/.julia/packages/MultiScaleTreeGraph/WePBo/src/compute_MTG/traverse.jl:72
[6] traverse!_(node::Node{NodeMTG, Dict{Symbol, Any}}, f::PlantSimEngine.var"#185#190"{Nothing, Bool, Dict{String, Vector{Status}}, Dict{String, Base.KeySet{Symbol, Dict{Symbol, Any}}}, Dict{String, Dict{String, Dict{Symbol, Any}}}, Dict{String, Dict{Symbol, Any}}}, scale::Nothing, symbol::Nothing, link::Nothing, filter_fun::Nothing, all::Bool, recursivity_level::Float64) (repeats 2 times)
@ MultiScaleTreeGraph ~/.julia/packages/MultiScaleTreeGraph/WePBo/src/compute_MTG/traverse.jl:83
[7] traverse!(::Node{NodeMTG, Dict{Symbol, Any}}, ::PlantSimEngine.var"#185#190"{Nothing, Bool, Dict{String, Vector{Status}}, Dict{String, Base.KeySet{Symbol, Dict{Symbol, Any}}}, Dict{String, Dict{String, Dict{Symbol, Any}}}, Dict{String, Dict{Symbol, Any}}}; scale::Nothing, symbol::Nothing, link::Nothing, filter_fun::Nothing, all::Bool, recursivity_level::Float64)
@ MultiScaleTreeGraph ~/.julia/packages/MultiScaleTreeGraph/WePBo/src/compute_MTG/traverse.jl:63
[8] traverse!
@ ~/.julia/packages/MultiScaleTreeGraph/WePBo/src/compute_MTG/traverse.jl:47 [inlined]
[9] #traverse!#76
@ ~/.julia/packages/MultiScaleTreeGraph/WePBo/src/compute_MTG/traverse.jl:162 [inlined]
[10] traverse!
@ ~/.julia/packages/MultiScaleTreeGraph/WePBo/src/compute_MTG/traverse.jl:151 [inlined]
[11] init_statuses(mtg::Node{NodeMTG, Dict{Symbol, Any}}, mapping::Dict{String, Tuple{Any, Vararg{Any}}}, dependency_graph::PlantSimEngine.DependencyGraph{Dict{Pair{String, Symbol}, PlantSimEngine.SoftDependencyNode}}; type_promotion::Nothing, verbose::Bool, check::Bool)
@ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:46
[12] init_statuses
@ ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:22 [inlined]
[13] init_statuses(mtg::Node{NodeMTG, Dict{Symbol, Any}}, mapping::Dict{String, Tuple{Any, Vararg{Any}}})
@ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:22
[14] top-level scope
@ none:1
Expected output:
diff =
Warning: Diff output requires color.
Issue in function #185 for node #4.
ERROR: Variable `biomass` is not computed by any model, not initialised by the user in the status, and not found in the MTG at scale Internode (checked for MTG node 4).
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] init_node_status!(node::Node{NodeMTG, Dict{Symbol, Any}}, statuses::D
|
Documentation:
src/mtg/save_results.jl#L88
doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/save_results.jl:88-90
```jldoctest mylabel
julia> preallocated_vars = PlantSimEngine.pre_allocate_outputs(statuses, outs, 2);
```
Subexpression:
preallocated_vars = PlantSimEngine.pre_allocate_outputs(statuses, outs, 2);
Evaluated output:
ERROR: UndefVarError: `statuses` not defined
Stacktrace:
[1] top-level scope
@ none:1
Expected output:
diff =
Warning: Diff output requires color.
ERROR: UndefVarError: `statuses` not defined
Stacktrace:
[1] top-level scope
@ none:1
|
Documentation:
src/mtg/save_results.jl#L94
doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/save_results.jl:94-99
```jldoctest mylabel
julia> collect(keys(preallocated_vars))
2-element Vector{String}:
"Soil"
"Leaf"
```
Subexpression:
collect(keys(preallocated_vars))
Evaluated output:
ERROR: UndefVarError: `preallocated_vars` not defined
Stacktrace:
[1] top-level scope
@ none:1
Expected output:
2-element Vector{String}:
"Soil"
"Leaf"
diff =
Warning: Diff output requires color.
2-element Vector{String}:
"Soil"
"Leaf"ERROR: UndefVarError: `preallocated_vars` not defined
Stacktrace:
[1] top-level scope
@ none:1
|
Documentation:
src/mtg/save_results.jl#L104
doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/save_results.jl:104-110
```jldoctest mylabel
julia> collect(keys(preallocated_vars["Leaf"]))
3-element Vector{Symbol}:
:carbon_assimilation
:node
:carbon_demand
```
Subexpression:
collect(keys(preallocated_vars["Leaf"]))
Evaluated output:
ERROR: UndefVarError: `preallocated_vars` not defined
Stacktrace:
[1] top-level scope
@ none:1
Expected output:
3-element Vector{Symbol}:
:carbon_assimilation
:node
:carbon_demand
diff =
Warning: Diff output requires color.
3-element Vector{Symbol}:
:carbon_assimilation
:node
:carbon_demandERROR: UndefVarError: `preallocated_vars` not defined
Stacktrace:
[1] top-level scope
@ none:1
|
Documentation:
src/mtg/initialisation.jl#L215
doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:215-222
```jldoctest mylabel
julia> organs_statuses = PlantSimEngine.status_template(mapping, nothing)
Dict{String, Dict{Symbol, Any}} with 4 entries:
"Soil" => Dict(:soil_water_content=>RefValue{Float64}(-Inf))
"Internode" => Dict(:carbon_allocation=>-Inf, :TT=>-Inf, :carbon_demand=>-Inf)
"Plant" => Dict(:carbon_allocation=>RefVector{Float64}[], :carbon_assimilation=>RefVector{F…
"Leaf" => Dict(:carbon_allocation=>-Inf, :carbon_assimilation=>-Inf, :TT=>10.0, :aPPFD=>13…
```
Subexpression:
organs_statuses = PlantSimEngine.status_template(mapping, nothing)
Evaluated output:
ERROR: UndefVarError: `find_var_mapped_default` not defined
Stacktrace:
[1] compute_mapping(models::Dict{String, Tuple{Any, Vararg{Any}}}, type_promotion::Nothing)
@ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:234
[2] status_template(mapping::Dict{String, Tuple{Any, Vararg{Any}}}, type_promotion::Nothing)
@ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:233
[3] top-level scope
@ none:1
Expected output:
Dict{String, Dict{Symbol, Any}} with 4 entries:
"Soil" => Dict(:soil_water_content=>RefValue{Float64}(-Inf))
"Internode" => Dict(:carbon_allocation=>-Inf, :TT=>-Inf, :carbon_demand=>-Inf)
"Plant" => Dict(:carbon_allocation=>RefVector{Float64}[], :carbon_assimilation=>RefVector{F…
"Leaf" => Dict(:carbon_allocation=>-Inf, :carbon_assimilation=>-Inf, :TT=>10.0, :aPPFD=>13…
diff =
Warning: Diff output requires color.
Dict{String, Dict{Symbol, Any}} with 4 entries:
"Soil" => Dict(:soil_water_content=>RefValue{Float64}(-Inf))
"Internode" => Dict(:carbon_allocation=>-Inf, :TT=>-Inf, :carbon_demand=>-Inf)
"Plant" => Dict(:carbon_allocation=>RefVector{Float64}[], :carbon_assimilation=>RefVector{F…
"Leaf" => Dict(:carbon_allocation=>-Inf, :carbon_assimilation=>-Inf, :TT=>10.0, :aPPFD=>13…ERROR: UndefVarError: `find_var_mapped_default` not defined
Stacktrace:
[1] compute_mapping(models::Dict{String, Tuple{Any, Vararg{Any}}}, type_promotion::Nothing)
@ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:234
[2] status_template(mapping::Dict{String, Tuple{Any, Vararg{Any}}}, type_promotion::Nothing)
@ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:233
[3] top-level scope
@ none:1
|
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Julia 1 - ubuntu-latest - x64 - push
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Julia 1 - ubuntu-latest - x64 - push
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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Julia 1.7 - ubuntu-latest - x64 - push
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2, julia-actions/setup-julia@v1, actions/cache@4d4ae6ae148a43d0fd1eda1800170683e9882738, pyTooling/Actions/with-post-step@adef08d3bdef092282614f3b683897cefae82ee3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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Julia 1.7 - ubuntu-latest - x64 - push
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
Documentation
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2, julia-actions/setup-julia@v1. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
|
Documentation
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|