[WIP]: NEON Wrapper for batch running neon single point runs

[negin513]

Description of changes

This python script is a wrapper for running CTSM simulations for one or more neon sites.

This script first makes sure:

• CIME and other dependencies are checked out.
• Downloads and parses neon listing file for the available neon data :
  https://neon-ncar.s3.data.neonscience.org/listing.csv

Please note that this is still a work in progress and will be updated frequently.

Specific notes

Contributors other than yourself, if any:

CTSM Issues Fixed (include github issue #): #1354

Are answers expected to change (and if so in what way)?

Any User Interface Changes (namelist or namelist defaults changes)?
./run_neon.py has the following interface:

|------------------------------------------------------------------|
|---------------------  Instructions  -----------------------------|
|------------------------------------------------------------------|
This is a wrapper script for running CTSM simulation for one or more
neon sites. 

This script will do the following:
    1) Make sure CIME and other dependencies is checked out.
    2) Make the case for the specific neon site(s).
    3) Make changes to the case, for:
        a. AD spinup
        b. SASU spinup
    4) Build and submit the case.

-------------------------------------------------------------------
Instructions for running on Cheyenne/Casper:

load the following into your local environment
    module load python
    ncar_pylib

To remove NPL from your environment on Cheyenne/Casper:
    deactivate

-------------------------------------------------------------------
To see the available options:
    ./run_neon.py --help
-------------------------------------------------------------------

optional arguments:
  -h, --help            show this help message and exit
  --neon_site {ABBY,BARR,BART,BLAN,BONA,CLBJ,CPER,DCFS,DEJU,DELA,DSNY,GRSM,GUAN,HARV,HEAL,JERC,JORN,KONA,KONZ,LAJA,LENO,MLBS,MOAB,NIWO,NOGP,OAES,ONAQ,ORNL,OSBS,PUUM,RMNP,SCBI,SERC,SJER,SOAP,SRER,STEI,STER,TALL,TEAK,TOOL,TREE,UKFS,UNDE,WOOD,WREF,YELL} [{ABBY,BARR,BART,BLAN,BONA,CLBJ,CPER,DCFS,DEJU,DELA,DSNY,GRSM,GUAN,HARV,HEAL,JERC,JORN,KONA,KONZ,LAJA,LENO,MLBS,MOAB,NIWO,NOGP,OAES,ONAQ,ORNL,OSBS,PUUM,RMNP,SCBI,SERC,SJER,SOAP,SRER,STEI,STER,TALL,TEAK,TOOL,TREE,UKFS,UNDE,WOOD,WREF,YELL} ...]
                        4-letter neon site code.
  --surf_dir SURF_DIR   Directory of single point surface dataset. [default:
                        /glade/scratch/negins/single_point/]
  --out_dir OUT_DIR     Directory to write updated single point surface
                        dataset. [default: /glade/scratch/negins/neon_sims/]
  -a, --all             Flag for running all neon sites, instead of selected
                        few sites. [default: False]
  --start_date START_DATE
                        Start date for running CTSM simulation. [default:
                        2018]
  --end_year END_YEAR   End year for running CTSM simulation. [default: 2020]
  --spinup              AD spin-up [default: True]
  --sasu, --matrix      Matrix (SASU) spin-up [default: False]
  -d, --debug           Debug mode will print more information.

[jedwards4b]

• A case object should be used
• This should optionally invoke tests instead of cases
• All of the cases can (and should) use a single executable (case clone and keepexe)
• I think that if RUN_STARTDATE and RUN_REFDATE were 2018 not 0018 it would be less confusing to users.
• DATM_YR_END should be based on the available data.

[jedwards4b]

Rather than calling execute you should use a case object and the cime api here to call the case create directly. There should also be an option to submit tests instead of cases.

[negin513]

Based on the feedback received, I rewrote this code using CIME case object and the PR is in #1444.
So I am closing this issue.