No manage externals

[mnlevy1981]

Remove manage_externals and add ADF and mom6-tools as git submodules instead

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[mnlevy1981]

Once the NCAR super computers are back up and running, I'd like to test this out... but I suspect everything will work because I made sure ADF was pinned to the correct hash and the submodules are in the same directory that manage_externals was using.

[TeaganKing]

Thanks for putting this together! This PR generally looks good, but yes, let's test it out once machines are back up!

[mnlevy1981]

Looks like everything is working as expected. I did have some issues running the coupled_model example, because mom6-tools relies on some matplotlib calls that have been deprecated:

AttributeError                            Traceback (most recent call last)
Cell In[2], line 8
      6 import intake
      7 from mom6_tools.MOM6grid import MOM6grid
----> 8 from mom6_tools.surface import get_MLD, get_BLD
      9 import xarray as xr
     11 warnings.filterwarnings("ignore")

File /glade/work/mlevy/codes/CUPiD/externals/mom6-tools/mom6_tools/surface.py:14
     12 from mom6_tools.DiagsCase import DiagsCase
     13 from mom6_tools.m6toolbox import add_global_attrs
---> 14 from mom6_tools.m6plot import xycompare, xyplot
     15 from mom6_tools.MOM6grid import MOM6grid
     16 from distributed import Client

File /glade/work/mlevy/codes/CUPiD/externals/mom6-tools/mom6_tools/m6plot.py:1871
   1868   return lonRange, latRange, hspace, titleOffset
   1870 # Load new named colormaps
-> 1871 c = dunne_rainbow()
   1872 c = dunne_pm()
   1873 c = brownblue_cmap()

File /glade/work/mlevy/codes/CUPiD/externals/mom6-tools/mom6_tools/m6plot.py:1648, in dunne_rainbow(N)
   1646 cmap.set_under([.95*.9,.75*.9,.9]); cmap.set_over([.3,0.,0.])
   1647 #cmap.set_bad('w')
-> 1648 matplotlib.cm.register_cmap(cmap=cmap)
   1649 return cmap

AttributeError: module 'matplotlib.cm' has no attribute 'register_cmap'

The important thing is that mom6-tools was installed in the environment, so dropping manage_externals didn't cause the above error. I opened an issue (https://github.com/NCAR/mom6-tools/issues/48); unless we want to pin matplotlib to 3.8 for now, I think we can proceed with this PR as-is.

[TeaganKing]

Regarding the matplotlib version for mom6-tools, Naoki and I also ran into that issue when working on his PR (without these changes).

As we discussed, given that users could always manually change to an earlier matplotlib version and that this is on the coupled model instead of key metrics example, that seems fine to me to wait to fix until the issue you created in mom6-tools is addressed (rather than pinning version 3.8).