rerun advection-diffusion-2d and -1d notebooks; fix hdf5-mpi paths on macOS CI (homebrew); cleanup Trixi comparison notebook; pin CI upper Python version to 3.13.12 (since 3.13.13 errs with a base64 failure)

[AgnieszkaZaba]

No description provided.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.93%. Comparing base (34fe8d8) to head (e490d2f).
⚠️ Report is 6 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #681   +/-   ##
=======================================
  Coverage   92.93%   92.93%           
=======================================
  Files          40       40           
  Lines        1754     1754           
=======================================
  Hits         1630     1630           
  Misses        124      124           

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[AgnieszkaZaba]

Error on Colab:
https://colab.research.google.com/github/open-atmos/PyMPDATA/blob/main/examples/PyMPDATA_examples/advection_diffusion_2d/advection-diffusion-2d.ipynb#

Ok, I found it, it is addressed in this #663

[slayoo]

rerunning as the Trixi issue seems to have been fixed in trixi-framework/Trixi.jl#2976

For the record, this is the error in CI:

ERROR: LoadError: TypeError: non-boolean (Static.True) used in boolean context Stacktrace: [1] _all(f::typeof(identity), itr::NTuple{4, Static.True}, ::Colon) 
@ Base ./anyall.jl:201 [2] all(f::Function, itr::NTuple{4, Static.True}) 
@ Base ./anyall.jl:212 [3] all(itr::NTuple{4, Static.True}) 
@ Base ./anyall.jl:80 [4] _offset_ptr 
@ ~/.julia/packages/StrideArraysCore/t77vK/src/ptr_array.jl:972 [inlined] [5] unsafe_getindex 
@ ~/.julia/packages/StrideArraysCore/t77vK/src/ptr_array.jl:980 [inlined] [6] getindex 
@ ~/.julia/packages/StrideArraysCore/t77vK/src/ptr_array.jl:1015 [inlined] [7] #get_node_vars##0 
@ ~/.julia/packages/Trixi/ZQJee/src/solvers/dg.jl:1066 [inlined] [8] ntuple 
@ ./ntuple.jl:50 [inlined] [9] get_node_vars 
@ ~/.julia/packages/Trixi/ZQJee/src/solvers/dg.jl:1066 [inlined] [10] weak_form_kernel! 
...

[slayoo]

the issue here is that the fix in Trixi was committed after the v0.16.6 release, so we need to wait for v0.16.7...

[JoshuaLampert]

The issue should be fixed upstream. So Trixi.jl v0.16.6 should be fine again.

[slayoo]

@JoshuaLampert, thanks for following up here!

[slayoo]

the base64 issue might be related with changes introduced in Python in 3.13.13: python/cpython#145264

[AgnieszkaZaba]

@JoshuaLampert @slayoo Thank you!