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

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

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

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

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

Process completed with exit code 1.

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/