Update jupyter notebooks from the OM2 report

[rbeucher]

Test the jupyter notebooks and make sure that they are working with the current stack of Python packages (available in hh5 or xp65)

[rbeucher]

@max-anu Do you have an update on this?

[max-anu]

I believe i was making changes in this repo: https://github.com/max-anu/ACCESS-OM2-updated/tree/intake
In the cc_updated branch, I was updating recipes to work with the (then) latest version of cosima cookbook.
The intake branch was converting the recipes to use the intake catalog instead of the cosima cookbook.

From my notes at the time (no guarantees), these are the working notebooks:

Using the (then) latest version of cc:

• Age.ipynb
• BarotropicStreamfunction.ipynb
• DynamicTopography.ipynb
• PacificSSHTrends.ipynb
• Equatorial_Pacific.ipynb
• grid.ipynb
• GlobalOverturningStreamfunction.ipynb
• PV_sections.ipynb
• Rayleigh_drag.ipynb
• Southwest_atlantic_analysis_v3.ipynb
• SeaLevelRMS.ipynb
• strait_transports.ipynb
• surface_current.ipynb
• pv.ipynb
• GlobalTimeseries.ipynb
• viscosity.ipynb

Using the intake catalog:

• Age.ipynb
• DynamicTopography.ipynb
• PacificSSHTrends.ipynb
• Equatorial_Pacific.ipynb
• GlobalOverturningStreamfunction.ipynb * partially working or easy to fix
• PV_sections.ipynb
• surface_current.ipynb
• pv.ipynb
• GlobalTimeseries.ipynb

I also matched up the notebooks with the figures in the paper:

• Age.ipynb Not in paper
• BarotropicStreamfunction.ipynb Figs 16, 17, 21, 22,
• bathymetry.ipynb Not in paper
• DynamicTopography.ipynb Figure 05
• PacificSSHTrends.ipynb Not in paper
• Equatorial_Pacific.ipynb Figure 19
• grid.ipynb report: section 3.2.3, figs 3,4,5
• Hovmoller_temp_depth.ipynb Fig 9
• ice_maps.ipynb Not in paper
• ice_timeseries.ipynb Fig 27
• Meridional_Heat_Transport.ipynb Fig 13
• GlobalOverturningStreamfunction.ipynb Fig 7, 8
• PV_sections.ipynb Figure 15
• PV_slices.ipynb Not in paper
• Rayleigh_drag.ipynb Report: section 3.2.7, fig 9
• Southwest_atlantic_analysis_v3.ipynb Figure 24
• spectra.ipynb Not in paper
• SeaLevelRMS.ipynb Fig 6
• strait_transports.ipynb Fig 4
• surface_current.ipynb fig 17-24 in report (not paper)
• pv.ipynb Not in paper
• sss_bias.ipynb Fig 11
• sst_bias.ipynb Fig 10
• zonal_salt_bias.ipynb Not in paper
• zonal_temp_salt_bias.ipynb Fig 12
• GlobalTimeseries.ipynb Figure 3
• viscosity.ipynb report: section 3.2.5, figs 7,8
• vorticity.ipynb Not in paper
• Plot_WOCE_transects.ipynb Figs 14, 20, 23, 25

[rbeucher]

You should move your branch to the access-nri organisation. Thanks!