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reapply formatter #88

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3 changes: 2 additions & 1 deletion .JuliaFormatter.toml
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@@ -1,2 +1,3 @@
style = "sciml"
format_markdown = true
format_markdown = true
format_docstrings = true
16 changes: 8 additions & 8 deletions docs/make.jl
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Expand Up @@ -6,13 +6,13 @@ cp("./docs/Project.toml", "./docs/src/assets/Project.toml", force = true)
include("pages.jl")

makedocs(sitename = "MultiScaleArrays.jl",
authors = "Chris Rackauckas",
modules = [MultiScaleArrays],
clean = true, doctest = false, linkcheck = true,
warnonly = [:missing_docs],
format = Documenter.HTML(assets = ["assets/favicon.ico"],
canonical = "https://docs.sciml.ai/MultiScaleArrays/stable/"),
pages = pages)
authors = "Chris Rackauckas",
modules = [MultiScaleArrays],
clean = true, doctest = false, linkcheck = true,
warnonly = [:missing_docs],
format = Documenter.HTML(assets = ["assets/favicon.ico"],
canonical = "https://docs.sciml.ai/MultiScaleArrays/stable/"),
pages = pages)

deploydocs(repo = "github.com/SciML/MultiScaleArrays.jl.git";
push_preview = true)
push_preview = true)
2 changes: 1 addition & 1 deletion docs/pages.jl
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Expand Up @@ -2,5 +2,5 @@

pages = [
"Home" => "index.md",
"multiscalearray.md",
"multiscalearray.md"
]
2 changes: 1 addition & 1 deletion docs/src/index.md
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Expand Up @@ -165,4 +165,4 @@ file and the
[project]($link_project)
file.
""")
```
```
2 changes: 1 addition & 1 deletion src/MultiScaleArrays.jl
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Expand Up @@ -160,7 +160,7 @@ organ3 = Organ([1.2, 2.2, 3.2], :Shoot, OrganParams(true))
organ4 = Organ([4.2, 5.2, 6.2], :Root, OrganParams(1 // 3))
plant1 = construct(Plant, (deepcopy(organ1), deepcopy(organ2)), Float64[], PlantSettings(1))
plant2 = construct(Plant, (deepcopy(organ3), deepcopy(organ4)), Float64[],
PlantSettings(1.0))
PlantSettings(1.0))
community = construct(Community, (deepcopy(plant1), deepcopy(plant2)))
scenario = construct(Scenario, (deepcopy(community),))
```
Expand Down
4 changes: 2 additions & 2 deletions src/addition_deletion.jl
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Expand Up @@ -18,7 +18,7 @@ function __add_node!(m::AbstractMultiScaleArray, node::AbstractMultiScaleArray,
end

function __add_node!(m::AbstractMultiScaleArray, node::AbstractMultiScaleArray, i,
I::Int...)
I::Int...)
__add_node!(m.nodes[i], node, I...)
__update_lengths(m, i, length(node))
end
Expand All @@ -32,7 +32,7 @@ function add_node!(m::AbstractMultiScaleArrayHead, node::AbstractMultiScaleArray
end

function add_node!(m::AbstractMultiScaleArrayHead, node::AbstractMultiScaleArray, i,
I::Int...)
I::Int...)
__add_node!(m, node, i, I...)
end

Expand Down
72 changes: 36 additions & 36 deletions src/diffeq.jl
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Expand Up @@ -49,40 +49,40 @@ end
reshape(m::AbstractMultiScaleArray, i::Int...) = m

function remove_node_non_user_cache!(integrator::DiffEqBase.AbstractODEIntegrator, idxs,
node...)
node...)
remove_node_non_user_cache!(integrator, integrator.cache, node...)
end

function remove_node_non_user_cache!(integrator::DiffEqBase.AbstractODEIntegrator,
cache::OrdinaryDiffEq.OrdinaryDiffEqCache, idxs,
node...)
cache::OrdinaryDiffEq.OrdinaryDiffEqCache, idxs,
node...)
nothing
end

function add_node_non_user_cache!(integrator::DiffEqBase.AbstractODEIntegrator, idxs,
x::AbstractArray)
x::AbstractArray)
add_node_non_user_cache!(integrator, integrator.cache, x)
end

function add_node_non_user_cache!(integrator::DiffEqBase.AbstractODEIntegrator, idxs,
x::AbstractArray, node...)
x::AbstractArray, node...)
add_node_non_user_cache!(integrator, integrator.cache, x, node...)
end

function add_node_non_user_cache!(integrator::DiffEqBase.AbstractODEIntegrator,
cache::OrdinaryDiffEq.OrdinaryDiffEqCache,
x::AbstractArray)
cache::OrdinaryDiffEq.OrdinaryDiffEqCache,
x::AbstractArray)
nothing
end
function add_node_non_user_cache!(integrator::DiffEqBase.AbstractODEIntegrator,
cache::OrdinaryDiffEq.OrdinaryDiffEqCache,
x::AbstractArray, node...)
cache::OrdinaryDiffEq.OrdinaryDiffEqCache,
x::AbstractArray, node...)
nothing
end

function add_node_non_user_cache!(integrator::DiffEqBase.AbstractODEIntegrator,
cache::OrdinaryDiffEq.RosenbrockMutableCache,
x::AbstractArray)
cache::OrdinaryDiffEq.RosenbrockMutableCache,
x::AbstractArray)
i = length(integrator.u)
cache.J = similar(cache.J, i, i)
cache.W = similar(cache.W, i, i)
Expand All @@ -92,8 +92,8 @@ function add_node_non_user_cache!(integrator::DiffEqBase.AbstractODEIntegrator,
end

function add_node_non_user_cache!(integrator::DiffEqBase.AbstractODEIntegrator,
cache::OrdinaryDiffEq.RosenbrockMutableCache,
x::AbstractArray, node...)
cache::OrdinaryDiffEq.RosenbrockMutableCache,
x::AbstractArray, node...)
i = length(integrator.u)
cache.J = similar(cache.J, i, i)
cache.W = similar(cache.W, i, i)
Expand All @@ -103,8 +103,8 @@ function add_node_non_user_cache!(integrator::DiffEqBase.AbstractODEIntegrator,
end

function remove_node_non_user_cache!(integrator::DiffEqBase.AbstractODEIntegrator,
cache::OrdinaryDiffEq.RosenbrockMutableCache,
node...)
cache::OrdinaryDiffEq.RosenbrockMutableCache,
node...)
i = length(integrator.u)
cache.J = similar(cache.J, i, i)
cache.W = similar(cache.W, i, i)
Expand All @@ -114,32 +114,32 @@ function remove_node_non_user_cache!(integrator::DiffEqBase.AbstractODEIntegrato
end

function add_node_jac_config!(cache, config::SparseDiffTools.ForwardColorJacCache, i, x,
node...)
node...)
@assert cache.jac_config.colorvec isa UnitRange
cache.jac_config = SparseDiffTools.ForwardColorJacCache(cache.uf, cache.uprev,
config.chunksize)
config.chunksize)
nothing
end

function add_node_jac_config!(cache, config::SparseDiffTools.ForwardColorJacCache, i, x)
@assert cache.jac_config.colorvec isa UnitRange
cache.jac_config = SparseDiffTools.ForwardColorJacCache(cache.uf, cache.uprev,
config.chunksize)
config.chunksize)
nothing
end

function remove_node_jac_config!(cache, config::SparseDiffTools.ForwardColorJacCache, i, x,
node...)
node...)
@assert cache.jac_config.colorvec isa UnitRange
cache.jac_config = SparseDiffTools.ForwardColorJacCache(cache.uf, cache.uprev,
config.chunksize)
config.chunksize)
nothing
end

function remove_node_jac_config!(cache, config::SparseDiffTools.ForwardColorJacCache, i, x)
@assert cache.jac_config.colorvec isa UnitRange
cache.jac_config = SparseDiffTools.ForwardColorJacCache(cache.uf, cache.uprev,
config.chunksize)
config.chunksize)
nothing
end

Expand Down Expand Up @@ -183,40 +183,40 @@ function remove_node_grad_config!(cache, grad_config::ForwardDiff.DerivativeConf
end

function remove_node_grad_config!(cache, grad_config::ForwardDiff.DerivativeConfig, i, x,
I...)
I...)
cache.grad_config = ForwardDiff.DerivativeConfig(cache.tf, cache.du1, cache.uf.t)
nothing
end

function add_node_grad_config!(cache, grad_config::AbstractArray, i, x)
cache.grad_config = ForwardDiff.Dual{
typeof(ForwardDiff.Tag(cache.tf,
eltype(cache.du1)))
}.(cache.du1, cache.du1)
typeof(ForwardDiff.Tag(cache.tf,
eltype(cache.du1)))
}.(cache.du1, cache.du1)
nothing
end

function add_node_grad_config!(cache, grad_config::AbstractArray, i, x, I...)
cache.grad_config = ForwardDiff.Dual{
typeof(ForwardDiff.Tag(cache.tf,
eltype(cache.du1)))
}.(cache.du1, cache.du1)
typeof(ForwardDiff.Tag(cache.tf,
eltype(cache.du1)))
}.(cache.du1, cache.du1)
nothing
end

function remove_node_grad_config!(cache, grad_config::AbstractArray, i, x)
cache.grad_config = ForwardDiff.Dual{
typeof(ForwardDiff.Tag(cache.tf,
eltype(cache.du1)))
}.(cache.du1, cache.du1)
typeof(ForwardDiff.Tag(cache.tf,
eltype(cache.du1)))
}.(cache.du1, cache.du1)
nothing
end

function remove_node_grad_config!(cache, grad_config::AbstractArray, i, x, I...)
cache.grad_config = ForwardDiff.Dual{
typeof(ForwardDiff.Tag(cache.tf,
eltype(cache.du1)))
}.(cache.du1, cache.du1)
typeof(ForwardDiff.Tag(cache.tf,
eltype(cache.du1)))
}.(cache.du1, cache.du1)
nothing
end

Expand All @@ -242,7 +242,7 @@ function remove_node_grad_config!(cache, grad_config::FiniteDiff.GradientCache,
end

function add_node_non_user_cache!(integrator::DiffEqBase.AbstractSDEIntegrator, idxs, x,
node...)
node...)
#addat_non_user_cache!(integrator, idxs)
if DiffEqBase.is_diagonal_noise(integrator.sol.prob)
add_node_noise!(integrator, idxs, x, node...)
Expand All @@ -263,7 +263,7 @@ function add_node_non_user_cache!(integrator::DiffEqBase.AbstractSDEIntegrator,
end

function remove_node_non_user_cache!(integrator::DiffEqBase.AbstractSDEIntegrator, idxs,
node...)
node...)
#deleteat_non_user_cache!(integrator, idxs)
if DiffEqBase.is_diagonal_noise(integrator.sol.prob)
remove_node_noise!(integrator, node...)
Expand Down
6 changes: 3 additions & 3 deletions src/indexing.jl
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Expand Up @@ -91,9 +91,9 @@ end

function getindices(m::AbstractMultiScaleArray, bot_idx, top_idx, i, I::Int...)
getindices(m.nodes[i],
bot_idx + ((i > 1) ? m.end_idxs[i - 1] : 0),
top_idx + m.end_idxs[i] - length(m),
I...)
bot_idx + ((i > 1) ? m.end_idxs[i - 1] : 0),
top_idx + m.end_idxs[i] - length(m),
I...)
end

function getindices(m::AbstractMultiScaleArrayLeaf, bot_idx, top_idx, i::Int)
Expand Down
2 changes: 1 addition & 1 deletion src/math.jl
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Expand Up @@ -41,7 +41,7 @@ end
end

@inline function Base.copyto!(dest::AbstractMultiScaleArrayLeaf,
bc::Broadcast.Broadcasted{<:AMSAStyle})
bc::Broadcast.Broadcasted{<:AMSAStyle})
copyto!(dest.values, unpack(bc, nothing))
dest
end
Expand Down
46 changes: 24 additions & 22 deletions src/print_human_readable.jl
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Expand Up @@ -11,7 +11,7 @@ function take_first_char(s::Union{String, SubString{String}}, N::Int64)
end

function toprint_AbstractMultiScaleArray!(toprint, X::AbstractMultiScaleArray, fields,
levelmax, n_char_per_name, level = 1)
levelmax, n_char_per_name, level = 1)
if length(toprint) < level
push!(toprint, Vector{String}())
end
Expand All @@ -20,28 +20,30 @@ function toprint_AbstractMultiScaleArray!(toprint, X::AbstractMultiScaleArray, f
for x in X.nodes
if fieldname(typeof(x), 1) == :nodes
push!(toprint[level],
"|" *
take_first_char(split(string(typeof(x)), "{")[1], n_char_per_name))
"|" *
take_first_char(split(string(typeof(x)), "{")[1], n_char_per_name))
first_element = add_separator!(first_element, toprint, level)
toprint_AbstractMultiScaleArray!(toprint, x, fields, levelmax,
n_char_per_name, level + 1)
n_char_per_name, level + 1)
else
if fields == nothing
push!(toprint[level],
take_first_char(split(string(typeof(x)), "{")[1],
n_char_per_name))
take_first_char(split(string(typeof(x)), "{")[1],
n_char_per_name))
first_element = add_separator!(first_element, toprint, level)
else
if !(x isa AbstractMultiScaleArrayLeaf)
push!(toprint[level],
take_first_char(split(string(typeof(x)), "{")[1],
n_char_per_name))
take_first_char(split(string(typeof(x)), "{")[1],
n_char_per_name))
first_element = add_separator!(first_element, toprint, level)
else
push!(toprint[level],
join([take_first_char(string(field), n_char_per_name) * ": " *
string(getfield(x, Symbol(field)))
for field in collect(fields)], ", "))
join(
[take_first_char(string(field), n_char_per_name) * ": " *
string(getfield(x, Symbol(field)))
for field in collect(fields)],
", "))
first_element = add_separator!(first_element, toprint, level)
end
end
Expand Down Expand Up @@ -80,7 +82,7 @@ print_human_readable(embryo.nodes[1].nodes[1]; fields = [:values])
```
"""
function print_human_readable(X::AbstractMultiScaleArray; n_char_per_name = 6,
fields = nothing, levelmax = Inf, n_item_max_per_levels = Inf) # fields = nothing OR [field1,field2,...]
fields = nothing, levelmax = Inf, n_item_max_per_levels = Inf) # fields = nothing OR [field1,field2,...]
# if X isa AbstractMultiScaleArrayLeaf
# println(X)
# else
Expand Down Expand Up @@ -119,18 +121,18 @@ function print_human_readable(X::AbstractMultiScaleArray; n_char_per_name = 6,
Move = findfirst("+ ", toprint[level])[1]
To = findnext(" |", toprint[level], Move[end])[1]
toprint[level] = join([
toprint[level][1:(Move - 1)],
toprint[level][(Move + 1):To],
toprint[level][Move],
toprint[level][(To + 1):end],
])
toprint[level][1:(Move - 1)],
toprint[level][(Move + 1):To],
toprint[level][Move],
toprint[level][(To + 1):end]
])
for level_ in 1:(level - 1)
toprint[level_] = join([
toprint[level_][1:(Move - 1)],
toprint[level_][(To + 1):(To + To - Move)],
toprint[level_][Move:To],
toprint[level_][(To + To - Move + 1):end],
])
toprint[level_][1:(Move - 1)],
toprint[level_][(To + 1):(To + To - Move)],
toprint[level_][Move:To],
toprint[level_][(To + To - Move + 1):end]
])
end
end
end
Expand Down
2 changes: 1 addition & 1 deletion src/shape_construction.jl
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Expand Up @@ -23,7 +23,7 @@ end
(sq = Meta.quot(s); :(deepcopy(getfield(m, $sq))))
for s in fieldnames(m)[4:end]] # 1:3 is nodes,values,end_idxs
:(construct(parameterless_type(m), recursive_similar(m.nodes, T), similar(m.values, T),
$(assignments...)))
$(assignments...)))
end

Base.zero(A::AbstractMultiScaleArray) = fill!(similar(A), 0)
Expand Down
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