Cleanup PR #1

[TeaganKing]

Description of changes:

Address #151 by moving nblibrary out of examples and cleaning up the names of output directories. This PR also updates documentation to point to key_metrics example.

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[TeaganKing]

Note: In addition to the items mentioned in the related issue, I am updating our documentation to use the key_metrics example instead of the coupled_model example.

[TeaganKing]

For the key_metrics example, the rof notebooks seem to be failing for some reason, but the other notebooks work as expected with these changes and cupid-run and cupid-build both complete successfully with output looking as expected in the resulting website.

The ADF link in external_diag_packages seems to be working but the actual in-line plots are not showing up, so this needs to be further tested. Is this possibly related to the change @mnlevy1981 made in #154?

[mnlevy1981]

The ADF link in external_diag_packages seems to be working but the actual in-line plots are not showing up, so this needs to be further tested. Is this possibly related to the change @mnlevy1981 made in #154?

In the external_diag_packages directory, you'll need to modifyconfig.yml so adf_root points to the right place:

- adf_root: ../../external_diag_packages/ADF/
+ adf_root: ../../externals/external_diag_packages/ADF/

adf_root is relative to where the notebook is run, which used to be ${CUPID_ROOT}/externals/nblibrary/atm but is now ${CUPID_ROOT}/nblibrary/atm

[mnlevy1981]

The ADF link in external_diag_packages seems to be working but the actual in-line plots are not showing up, so this needs to be further tested. Is this possibly related to the change @mnlevy1981 made in #154?

In the external_diag_packages directory, you'll need to modifyconfig.yml so adf_root points to the right place:

- adf_root: ../../external_diag_packages/ADF/
+ adf_root: ../../externals/external_diag_packages/ADF/

adf_root is relative to where the notebook is run, which used to be ${CUPID_ROOT}/externals/nblibrary/atm but is now ${CUPID_ROOT}/nblibrary/atm

Actually, you want

- adf_root: ../../external_diag_packages/ADF/
+ adf_root: ../../externals/external_diag_packages/ADF_output/

(In #141 I changed the location of the ADF output in build.py, and I guess I never deleted externals/external_diag_packages/ADF so my testing didn't catch the change in adf_root until I started working on #154)

[TeaganKing]

I fixed the ADF path by setting the adf_root to ../../examples/external_diag_packages/ADF_output/.

I'll work on the rof notebooks outside this PR.

This is ready for review.

[mnlevy1981]

This looks great! I'm baffled by the ROF issue, especially because it looks like the notebook actually ran fine despite throwing a bunch of cryptic errors

[mnlevy1981]

FYI, it looks like we never added the runoff notebooks to the Jupyter Book... config.yml will need

    - caption: River Runoff
      chapters:
        - file: rof/global_discharge_gauge_compare_obs
        - file: rof/global_discharge_ocean_compare_obs

Where the rest of the chapters are defined

[TeaganKing]

FYI, it looks like we never added the runoff notebooks to the Jupyter Book... config.yml will need

    - caption: River Runoff
      chapters:
        - file: rof/global_discharge_gauge_compare_obs
        - file: rof/global_discharge_ocean_compare_obs

Where the rest of the chapters are defined

Ack, thanks for catching that! I remember looking at it so must have updated this in my own version somewhere... I'll follow up on that outside this PR.