Feat: add gamma distribution for roots #371
Annotations
8 errors, 2 warnings, and 1 notice
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/2OZOh/src/utilities/utilities.jl#L44
failed to run `@example` block in src/generated/example-script-01.md:52-92
```@example example-script-01
# Read in providing arguments, requiring less CSVs
model_modified =
loadSPAC(input_path, input_prefix;
simulate_isotopes = true,
Δz_thickness_m = [fill(0.04, 5); # grid spacing (heterogenous), meter (N=21)
fill(0.05, 5); # write Δ in VSCode by typing \Delta and hit shift
fill(0.06, 5);
fill(0.07, 5);
fill(0.10, 1)],
root_distribution = (beta = 0.98, z_rootMax_m=-0.5),
IC_soil = (PSIM_init_kPa = -7.0,
delta18O_init_permil = -9.0,
delta2H_init_permil = -11.0),
canopy_evolution = (DENSEF_rel = 100,
HEIGHT_rel = 100,
SAI_rel = 100,
LAI_rel = (DOY_Bstart = 120,
Bduration = 21,
DOY_Cstart = 270,
Cduration = 60,
LAI_perc_BtoC = 100,
LAI_perc_CtoB = 55)),
storm_durations_h = [5.44, 5.44, 5.44, 5.44, 5.44, 5.44,
5.44, 5.44, 5.44, 5.44, 5.44, 5.44],
IC_scalar = (amount = (u_GWAT_init_mm = 1.,
u_INTS_init_mm = 13.7,
u_INTR_init_mm = 0.,
u_SNOW_init_mm = 22.222,
u_CC_init_MJ_per_m2 = 0.101010,
u_SNOWLQ_init_mm = 0.),
d18O = (u_GWAT_init_permil = -11.111,
u_INTS_init_permil = -12.222,
u_INTR_init_permil = -13.333,
u_SNOW_init_permil = -14.444),
d2H = (u_GWAT_init_permil = -95.111,
u_INTS_init_permil = -95.222,
u_INTR_init_permil = -95.333,
u_SNOW_init_permil = -95.444)));
nothing #hide
```
exception =
MethodError: no method matching sort(::Tuple{Symbol, Symbol})
Closest candidates are:
sort(!Matched::AbstractUnitRange)
@ Base range.jl:1397
sort(!Matched::AbstractRange)
@ Base range.jl:1400
sort(!Matched::OrderedCollections.LittleDict; byvalue, args...)
@ OrderedCollections ~/.julia/packages/OrderedCollections/9C4Uz/src/dict_sorting.jl:38
...
Stacktrace:
[1] overwrite_rootden!(soil_discretization_DF::DataFrames.DataFrame, _to_use_root_distribution::NamedTuple{(:beta, :z_rootMax_m), Tuple{Float64, Float64}}, _to_use_Δz_thickness_m::Vector{Float64})
@ LWFBrook90 ~/work/LWFBrook90.jl/LWFBrook90.jl/src/func_discretize_soil_domain.jl:404
[2] loadSPAC(folder::String, prefix::String; simulate_isotopes::Bool, canopy_evolution::NamedTuple{(:DENSEF_rel, :HEIGHT_rel, :SAI_rel, :LAI_rel), Tuple{Int64, Int64, Int64, NamedTuple{(:DOY_Bstart, :Bduration, :DOY_Cstart, :Cduration, :LAI_perc_BtoC, :LAI_perc_CtoB), NTuple{6, Int64}}}}, Δz_thickness_m::Vector{Float64}, root_distribution::NamedTuple{(:beta, :z_rootMax_m), Tuple{Float64, Float64}}, IC_soil::NamedTuple{(:PSIM_init_kPa, :delta18O_init_permil, :delta2H_init_permil), Tuple{Float64, Float64, Float64}}, IC_scalar::NamedTuple{(:amount, :d18O, :d2H), Tuple{NamedTuple{(:u_GWAT_init_mm, :u_INTS_init_mm, :u_INTR_init_mm, :u_SNOW_init_mm, :u_CC_init_MJ_per_m2, :u_SNOWLQ_init_mm), NTuple{6, Float64}}, NamedTuple{(:u_GWAT_init_permil, :u_INTS_init_permil, :u_INTR_init_permil, :u_SNOW_init_permil), NTuple{4, Float64}}, NamedTuple{(:u_GWAT_init_permil, :u_INTS_init_permil, :u_INTR_init_permil, :u_SNOW_init_permil), NTuple{4, Float64}}}}, storm_durations_h::Vector{Float64})
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/2OZOh/src/utilities/utilities.jl#L44
failed to run `@example` block in src/generated/example-script-01.md:100-111
```@example example-script-01
# Setup and run simulation
simulation = setup(model)
simulation_mod = setup(model_modified)
# Inputs can be checked with:
# `plot_inputs(simulation)`. Note: NOT YET IMPLEMENTED
simulate!(simulation_mod)
simulate!(simulation_mod) # Run it a second time to showcase shorter runtime
# The computed solution is stored within the object.
# When using VSCode a progress bar is shown in the status bar.
```
exception =
UndefVarError: `model_modified` not defined
Stacktrace:
[1] top-level scope
@ example-script-01.md:103
[2] eval
@ ./boot.jl:370 [inlined]
[3] #58
@ ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:514
[8] with_logger
@ ./logging.jl:626 [inlined]
[9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer)
@ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158
[10] runner(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:752
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/2OZOh/src/utilities/utilities.jl#L44
failed to run `@example` block in src/generated/example-script-01.md:120-125
```@example example-script-01
simulation_mod.ODESolution;
simulation_mod.ODESolution_datetime;
typeof(simulation_mod.ODESolution);
# HINT: To get these names, type `simulation_mod.` and wait for the autocomplete!
```
exception =
UndefVarError: `simulation_mod` not defined
Stacktrace:
[1] top-level scope
@ :0
[2] eval
@ ./boot.jl:370 [inlined]
[3] #58
@ ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:514
[8] with_logger
@ ./logging.jl:626 [inlined]
[9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer)
@ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158
[10] runner(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:752
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/2OZOh/src/utilities/utilities.jl#L44
failed to run `@example` block in src/generated/example-script-01.md:142-146
```@example example-script-01
using Plots, Measures; gr();
pl1 = plotamounts(simulation_mod, :above_and_belowground, :showRWUcentroid)
pl1
```
exception =
UndefVarError: `simulation_mod` not defined
Stacktrace:
[1] top-level scope
@ example-script-01.md:144
[2] eval
@ ./boot.jl:370 [inlined]
[3] #58
@ ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:514
[8] with_logger
@ ./logging.jl:626 [inlined]
[9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer)
@ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158
[10] runner(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:752
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/2OZOh/src/utilities/utilities.jl#L44
failed to run `@example` block in src/generated/example-script-01.md:148-151
```@example example-script-01
pl2 = plotisotopes(simulation_mod, :d18O, (d18O = :auto, d2H = :auto), :showRWUcentroid)
pl2
```
exception =
UndefVarError: `simulation_mod` not defined
Stacktrace:
[1] top-level scope
@ example-script-01.md:149
[2] eval
@ ./boot.jl:370 [inlined]
[3] #58
@ ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:514
[8] with_logger
@ ./logging.jl:626 [inlined]
[9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer)
@ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158
[10] runner(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:752
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/2OZOh/src/utilities/utilities.jl#L44
failed to run `@example` block in src/generated/example-script-01.md:153-165
```@example example-script-01
pl3 = plotforcingandstates(simulation_mod)
pl3
# Use of additional arguments to `plotisotopes` is illustrated here.
# Note that typing `?plotisotopes` provides the documentation to the function.
# plotisotopes(simulation_mod, :d2H)
# plotisotopes(simulation_mod, :d18O)
# plotisotopes(simulation_mod;
# xlim = (DateTime("2010-01-01"), DateTime("2010-03-31")))
# plotisotopes(simulation_mod, :d2H, (d18O = :auto, d2H = :auto), :showRWUcentroid;
# xlim = (DateTime("2010-01-01"), DateTime("2010-08-30")))
```
exception =
UndefVarError: `simulation_mod` not defined
Stacktrace:
[1] top-level scope
@ example-script-01.md:154
[2] eval
@ ./boot.jl:370 [inlined]
[3] #58
@ ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:514
[8] with_logger
@ ./logging.jl:626 [inlined]
[9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer)
@ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158
[10] runner(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:752
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|
Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/2OZOh/src/utilities/utilities.jl#L44
failed to run `@example` block in src/generated/example-script-01.md:183-209
```@example example-script-01
using CSV, DataFrames
# How to get θ?
get_soil_(:θ, simulation_mod;
depths_to_read_out_mm = nothing, days_to_read_out_d = nothing)
depth_to_read_out_mm = [10, 150, 500, 1000, 1150]
get_soil_(:θ, simulation_mod;
depths_to_read_out_mm = depth_to_read_out_mm, days_to_read_out_d = nothing)
get_soil_(:θ, simulation_mod;
depths_to_read_out_mm = depth_to_read_out_mm)
# How to export θ as CSV?
# Only every day, provide days_to_read_out
days_to_read_out = range(simulation_mod.ODESolution.prob.tspan...)
dates_to_read_out = LWFBrook90.RelativeDaysFloat2DateTime.(
days_to_read_out, simulation_mod.parametrizedSPAC.reference_date)
df_out_daily = get_soil_(:θ, simulation_mod;
depths_to_read_out_mm = depth_to_read_out_mm, days_to_read_out_d = days_to_read_out)
insertcols!(df_out_daily, 1, :dates => dates_to_read_out);
show(df_out_daily)
##plot(df_out_daily[:,:dates], Matrix(df_out_daily[:,Not([:dates, :time])]))
##CSV.write(
# joinpath(out_dir, fname * "_θ_depths_daily.csv"),
# df_out_daily)
```
exception =
UndefVarError: `simulation_mod` not defined
Stacktrace:
[1] top-level scope
@ example-script-01.md:187
[2] eval
@ ./boot.jl:370 [inlined]
[3] #58
@ ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:514
[8] with_logger
@ ./logging.jl:626 [inlined]
[9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer)
@ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158
[10] runner(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/2OZOh/src/expander_pipeline.jl:752
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Run julia-actions/julia-docdeploy@v1
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Run julia-actions/julia-buildpkg@v1
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