Update notebooks in extra

[matt-graham]

Updates the Jupyter and Pluto notebooks in extra to be compatible with how ParticleDA now write output files (separate files for simulated observations and filtering estimates, some changes to group names).

Rather than previous approach of storing a HDF5 output file particle_da.h5 in the repository, this is removed in favour of now having a separate Pluto notebook / Julia script llwd_example.jl which will simulated observations from the LLW2d model, run a particle filter and save the simulation and filtering output to HDF5 files.

Two notebooks are shown to illustrate loading the generated HDF5 output data and producing visualizations, one in Python as a Jupyter notebook llw2d_visualizations.ipynb and one in Julia as a Pluto notebook llw2d_visualizations.jl.

EDIT: Now also added a Pluto notebook lorenz63_example.jl showing running filtering with Lorenz 63 model (and producing plots comparable to those in paper).

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.48%. Comparing base (062ff51) to head (97b512d).
Report is 1 commits behind head on master.

❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #251   +/-   ##
=======================================
  Coverage   92.48%   92.48%           
=======================================
  Files           7        7           
  Lines         386      386           
=======================================
  Hits          357      357           
  Misses         29       29           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[matt-graham]

Look at avoiding sidestepping Pluto's dependency management

[matt-graham]

• Remove Manifest.toml and specify dependency on local ParticleDA package in Project.toml using [sources] section
• Use activate notebook environment in Pluto notebook