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NQCD / NQCDynamics.jl

Fast and flexible nonadiabatic molecular dynamics in Julia!
https://nqcd.github.io/NQCDynamics.jl/stable
MIT License
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Update documenter to v1 and add docs profiling info #312

Closed jamesgardner1421 closed 12 months ago

jamesgardner1421 commented 12 months ago

I tried to update the documenter version but the build kept crashing. It turned out this was an error with one of the examples in the ase.md file. I've changed this example a little to get it to work.

To help identify this kind of thing in future I've added profiling information to the start and end of each .md file. Now we know which part of the docs build is in progress and how long each markdown file takes, this is very useful for #274 as there are a few examples that are taking a long time to run.

jamesgardner1421 commented 12 months ago

I also turned off the doctests as I think it's easiest to run these for the separate packages, this should be enabled for all of the separate packages. An upstream change seems to have caused the symbolics output in the NQCModels docstrings to have changed a little. Since this is in a separate package it's easiest to have the issue identified there instead.

jamesgardner1421 commented 12 months ago

The modified ase example is broken, probably should change back to PyCall:


ERROR: MethodError: no method matching *(::PythonCall.Py, ::Unitful.FreeUnits{(eV,), 𝐋^2 𝐌 𝐓^-2, nothing})

Closest candidates are:
  *(::Any, ::Any, ::Any, ::Any...)
   @ Base operators.jl:578
  *(::Union{Dates.Day, Dates.Hour, Dates.Microsecond, Dates.Millisecond, Dates.Minute, Dates.Nanosecond, Dates.Second, Dates.Week}, ::Unitful.Units)
   @ Unitful ~/.julia/packages/Unitful/J4AJj/src/dates.jl:90
  *(::Union{InitialValues.NonspecificInitialValue, InitialValues.SpecificInitialValue{typeof(*)}}, ::Any)
   @ InitialValues ~/.julia/packages/InitialValues/OWP8V/src/InitialValues.jl:154
  ...

julia> derivative(model, rand(3, 2))
ERROR: MethodError: no method matching adjoint(::PythonCall.Py)

Closest candidates are:
  adjoint(::Union{LinearAlgebra.QR, LinearAlgebra.QRCompactWY, LinearAlgebra.QRPivoted})
   @ LinearAlgebra /opt/hostedtoolcache/julia/1.9.3/x64/share/julia/stdlib/v1.9/LinearAlgebra/src/qr.jl:517
  adjoint(::Union{LinearAlgebra.Cholesky, LinearAlgebra.CholeskyPivoted})
   @ LinearAlgebra /opt/hostedtoolcache/julia/1.9.3/x64/share/julia/stdlib/v1.9/LinearAlgebra/src/cholesky.jl:556
  adjoint(::Union{FillArrays.AbstractOnes{T, 2} where T, FillArrays.AbstractZeros{T, 2} where T})
   @ FillArrays ~/.julia/packages/FillArrays/p9YG6/src/fillalgebra.jl:10
  ...
Alexsp32 commented 12 months ago

Failing dynamics_cme test is a separate issue #313 unrelated to documentation changes.