Pushforwards #682
CI.yml
on: pull_request
Documentation
15m 59s
Matrix: test
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7 errors and 4 warnings
Julia 1.10 - ubuntu-latest - x64 - pull_request x Python 3.8
Process completed with exit code 1.
|
Documentation:
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/literate_tutorials/smoothness_priors.md:15-30
```@example smoothness_priors
rawdata, _, _ = ACEpotentials.example_dataset("Si_tiny")
datakeys = (energy_key = "dft_energy", force_key = "dft_force", virial_key = "dft_virial")
rcut = 6.0 # cut off distance
r_nn = 2.3 # typical nearest neighbour distance
model = ace1_model(elements = [:Si],
order = 3, totaldegree = 12,
rcut = rcut, r0 = r_nn,
Eref = Dict(:Si => -158.54496821))
data = [ AtomsData(at; datakeys..., v_ref = model.model.Vref) for at in rawdata ]
A, Y, W = ACEfit.assemble(data, model);
nothing #hide
```
exception =
BoundsError: attempt to access 0-element StrideArraysCore.PtrArray{Float64, 1, (1,), Tuple{Int64}, Tuple{Nothing}, Tuple{Static.StaticInt{1}}} at index [1]
Stacktrace:
[1] throw_boundserror(A::StrideArraysCore.PtrArray{Float64, 1, (1,), Tuple{Int64}, Tuple{Nothing}, Tuple{Static.StaticInt{1}}}, I::Tuple{Int64})
@ Base ./abstractarray.jl:737
[2] checkbounds
@ ./abstractarray.jl:702 [inlined]
[3] getindex
@ ~/.julia/packages/StrideArraysCore/Yyyvt/src/ptr_array.jl:1039 [inlined]
[4] evaluate_ed_batched!(Rnl::StrideArraysCore.PtrArray{Float64, 2, (1, 2), Tuple{Int64, Int64}, Tuple{Nothing, Nothing}, Tuple{Static.StaticInt{1}, Static.StaticInt{1}}}, Rnl_d::StrideArraysCore.PtrArray{Float64, 2, (1, 2), Tuple{Int64, Int64}, Tuple{Nothing, Nothing}, Tuple{Static.StaticInt{1}, Static.StaticInt{1}}}, basis::ACEpotentials.Models.SplineRnlrzzBasis{1, ACEpotentials.Models.NormalizedTransform{Float64, ACEpotentials.Models.GeneralizedAgnesiTransform{Float64}}, ACEpotentials.Models.PolyEnvelope2sX{Float64}, 52, Float64}, rs::StrideArraysCore.PtrArray{Float64, 1, (1,), Tuple{Int64}, Tuple{Nothing}, Tuple{Static.StaticInt{1}}}, Zi::Int64, Zs::Vector{Int64}, ps::@NamedTuple{}, st::@NamedTuple{})
@ ACEpotentials.Models ~/work/ACEpotentials.jl/ACEpotentials.jl/src/models/Rnl_splines.jl:104
[5] macro expansion
@ ~/.julia/packages/WithAlloc/l9aid/src/WithAlloc.jl:37 [inlined]
[6] macro expansion
@ ./none:0 [inlined]
[7] _genwithalloc
@ ./none:0 [inlined]
[8] withalloc
@ ~/.julia/packages/WithAlloc/l9aid/src/WithAlloc.jl:17 [inlined]
[9] macro expansion
@ ~/.julia/packages/WithAlloc/l9aid/src/WithAlloc.jl:11 [inlined]
[10] macro expansion
@ ~/work/ACEpotentials.jl/ACEpotentials.jl/src/models/ace.jl:670 [inlined]
[11] macro expansion
@ ~/.julia/packages/Bumper/eoK0g/src/internals.jl:74 [inlined]
[12] evaluate_basis_ed(model::ACEpotentials.Models.ACEModel{1, ACEpotentials.Models.SplineRnlrzzBasis{1, ACEpotentials.Models.NormalizedTransform{Float64, ACEpotentials.Models.GeneralizedAgnesiTransform{Float64}}, ACEpotentials.Models.PolyEnvelope2sX{Float64}, 52, Float64}, Polynomials4ML.RealSCWrapper{SpheriCart.SphericalHarmonics{3, :L2, false, Float64}}, ACEpotentials.Models.SparseEquivTensor{Float64, Polynomials4ML.PooledSparseProduct{2}, Polynomials4ML.SparseSymmProdDAG}, ACEpotentials.Models.SplineRnlrzzBasis{1, ACEpotentials.Models.NormalizedTransform{Float64, ACEpotentials.Models.GeneralizedAgnesiTransform{Float64}}, ACEpotentials.Models.ACE1_PolyEnvelope1sR{Float64}, 12, Float64}, ACEpotentials.Models.OneBody{Float64, Unitful.FreeUnits{(), NoDims, nothing}, Unitful.FreeUnits{(Å,), 𝐋, nothing}}}, Rs::Vector{StaticArraysCore.SVector{3, Float64}}, Zs::Vector{Int64}, Z0::Int64, ps::@NamedTuple{WB::Matrix{Float64}, Wpair::Matrix{Float64}, rbasis::@NamedTuple{}, pairbasis::@NamedTuple{}}, st::@NamedTuple{rbasis::@NamedTuple{}, pairbasis::@NamedTuple{}})
@ ACEpotentials.Models ~/work/ACEpotentials.jl/ACEpotentials.jl/src/models/ace.jl:663
[13] energy_forces_virial_basis(at::ExtXYZ.Atoms{@NamedTuple{species::Vector{AtomsBase.ChemicalSpecies}, n_neighb::Vector{Int32}, atomic_number::Vector{Int64}, position::Vector{Vector{Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}}}, map_shif
|
Documentation:
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/literate_tutorials/smoothness_priors.md:53-74
```@example smoothness_priors
priors = Dict("Id" => I, "Algebraic(2)" => Pa2, "Algebraic(4)" => Pa4,"Gaussian" => Pg)
rmse = Dict()
pots = Dict()
for (prior_name, P) in priors
print("Solving with ", prior_name, " prior ... ")
# solve the regularized least squares problem
à = Diagonal(W) * (A / P)
ỹ = Diagonal(W) * Y
c̃ = ACEfit.solve(ACEfit.BLR(; verbose=false), Ã, ỹ)["C"]
_modl = deepcopy(model)
set_parameters!(_modl, P \ c̃)
# compute errors and store them for later use (don't print them here)
errs = linear_errors(rawdata, model; verbose=false, datakeys...)
rmse[prior_name] = errs["rmse"]["set"]["F"]
pots[prior_name] = _modl
println(" force=rmse = ", rmse[prior_name])
end
```
exception =
UndefVarError: `W` not defined
Stacktrace:
[1] top-level scope
@ ./smoothness_priors.md:62
[2] eval
@ ./boot.jl:385 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
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Documentation:
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/literate_tutorials/smoothness_priors.md:82-92
```@example smoothness_priors
labels = sort(collect(keys(priors)))[[4,1,2,3]]
plt_dim = plot(legend = :topright, xlabel = L"r [\AA]", ylabel = "E [eV]",
xlims = (0, rcut), ylims = (-2, 5))
for l in labels
D = ACEpotentials.dimers(pots[l], [:Si,])
plot!(plt_dim, D[(:Si, :Si)]..., label = l, lw=2)
end
vline!([r_nn,], lw=2, ls=:dash, label = L"r_{\rm nn}")
plt_dim
```
exception =
KeyError: key "Id" not found
Stacktrace:
[1] getindex(h::Dict{Any, Any}, key::String)
@ Base ./dict.jl:498
[2] top-level scope
@ ./smoothness_priors.md:87
[3] eval
@ ./boot.jl:385 [inlined]
[4] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[5] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[6] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[7] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[8] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[9] with_logger
@ ./logging.jl:627 [inlined]
[10] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[11] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
|
Documentation:
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/literate_tutorials/smoothness_priors.md:96-105
```@example smoothness_priors
plt_trim = plot(legend = :topright, xlabel = L"\theta", ylabel = "E [eV]",
xlims = (0, pi), ylims = (-0.6, 0.2))
for l in labels
D = ACEpotentials.trimers(pots[l], [:Si,], r_nn*u"Å", r_nn*u"Å")
plot!(plt_trim, D[(:Si, :Si, :Si)]..., label = l, lw=2)
end
vline!(plt_trim, [1.90241,], lw=2, label = "equilibrium angle")
plt_trim
```
exception =
KeyError: key "Id" not found
Stacktrace:
[1] getindex(h::Dict{Any, Any}, key::String)
@ Base ./dict.jl:498
[2] top-level scope
@ ./smoothness_priors.md:100
[3] eval
@ ./boot.jl:385 [inlined]
[4] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[5] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[6] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[7] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[8] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[9] with_logger
@ ./logging.jl:627 [inlined]
[10] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[11] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
|
Documentation:
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/literate_tutorials/smoothness_priors.md:109-120
```@example smoothness_priors
using AtomsBuilder # gives us `bulk`
at0 = bulk(:Si, cubic=true)
plt_dec = plot(legend = :topright, xlabel = L"r [\AA]", ylabel = "strain [eV/Å]",
xlim = (0.0, 5.0))
for l in labels
rr, E, dE = ACEpotentials.decohesion_curve(at0, pots[l])
plot!(plt_dec, ustrip.(rr), ustrip.(dE), label = l, lw=2)
end
plt_dec
```
exception =
KeyError: key "Id" not found
Stacktrace:
[1] getindex(h::Dict{Any, Any}, key::String)
@ Base ./dict.jl:498
[2] top-level scope
@ ./smoothness_priors.md:116
[3] eval
@ ./boot.jl:385 [inlined]
[4] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[5] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[6] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[7] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[8] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[9] with_logger
@ ./logging.jl:627 [inlined]
[10] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[11] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
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Documentation
Process completed with exit code 1.
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Julia 1.10 - ubuntu-latest - x64 - pull_request x Python 3.8
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-python@v2, actions/cache@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
Julia 1.10 - ubuntu-latest - x64 - pull_request x Python 3.8
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2, julia-actions/setup-julia@v1, actions/setup-python@v2, actions/cache@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
|
Documentation
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@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
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
|