bring in (and clean up) notebooks from cesm2-marbl repo

[mnlevy1981]

We want to make sure that all the notebooks from the cesm2-marbl repo that generate the Figures and Tables from the paper are included in this book. Here's a list of those notebooks (using the order of the Figures and Tables as of the version of the paper @matt-long put in dropbox and emailed about on June 2nd)

Figure / Table	notebook
Table 1	MARBL settings table.ipynb
Table 2	MARBL settings table.ipynb
Table 3	Global Flux Table.ipynb
Figure 1	mld.ipynb
Figure 2	ventilation.ipynb
Figure 3	ventilation.ipynb
Figure 4	ventilation.ipynb
Figure 5	nutrient-plots.ipynb
Figure 6	nutrient-plots.ipynb
Figure 7	nutrient-plots.ipynb
Figure 8	nutrient-plots.ipynb
Figure 9	nutrient-limitation.ipynb
Figure 10	chlorophyll-plots.ipynb
Figure 11	biological-pump.ipynb
Figure 12	biological-pump.ipynb
Figure 13	co2-flux.ipynb
Figure 14	DOM-comparison.ipynb
Figure 15	DOM-comparison.ipynb
Figure 16	Ncycle-plots.ipynb
Figure 17	dFe-comparison.ipynb
Figure 18	dFe-comparison.ipynb
Figure 19	dFe-comparison.ipynb
Figure 20	transient-fgco2.ipynb
Figure 21	transient-biological-pump.ipynb
Figure 22	transient-biological-pump.ipynb

[mgrover1]

Alright - I put together a list with the status of each notebook - there are still quite a few notebooks (10) that need to be updated to use funnel + make sure the functionality is there... for now, I can move all these notebooks into this repo.

MARBLE TOC

MARBL Settings Table

• Need funnel?
  • No
• Additional edits
  • Add in how to softlink MARBL directory

Global Flux Table

• Need funnel?
  • Yes
• Additional edits
  • Add in funnelification, see how to incorporate this

MLD (mixed layer depth)

• Figure 1
• Needs funnel?
  • Yes
• Additional edits
  • Add MLD calc to funnel

Ventilation

• Figures 2-4
• Needs funnel?
  • Yes
• Additional edits
  • Figure out how to get zonal average into funnel

Nutrient Plots

• Figures 5-8
• Needs funnel?
  • Yes
• Additional edits
  • Condense data notebook (_nutrient...) into this via funnel
  • Figure out zonal average in funnel

Nutrient Limitation

• Figure 9
• Needs funnel?
  • Yes
• Additional edits
  • Condense data notebook (_data-nutrient-plots)

Biological pump

• Figure 11-12
• Needs funnel?
  • Yes
• Additional edits

CO2 flux

• Figure 13
• Needs funnel?
  • Yes

DOM-comparison

• Figures 14-15
• Needs funnel?
  • Yes
• Additional edits
  • Figuring out dealing with observational data
    • discrete obs

Ncycle-plots

• Figure 16
• Needs funnel?
  • Yes - uses data written out in _data_ncycle
• Additional edits
  • None

dFe-comparison

• Figures 17-19
• Needs funnel?
  • Yes

Transient fgco2

• Figure 20
• Nees funnel?
  • No

Transient Biological Pump

• Figures 21-22
• Needs funnel?
  • No

We also need to consider adding the observation pre-processing notebooks in here.