Task to allow use of GMAO_perllib for BufrToIoda

[mranst]

Description

@cohen-seth Are you able to change your PR to be a branch of the main swell repository? If so, I will change this PR to merge with your branch to make it easier

This PR adds a task CloneGmaoPerllib, which allows the upcoming convert_bufr suite to use the perl commands acquire and acquire_obsys. It also adds the infrastructure to allow convert_bufr to be created and launched as a swell suite.

Use of the acquire commands through swell will be made possible by extending the PATH of subprocess to include GMAO_perllib in the experiment directory. CloneGmaoPerllib handles placing GMAO_perllib in the experiment directory. On discover, by default this is done by linking to a existing location, /discover/nobackup/projects/gmao/advda/perllib_opt/GMAO_perllib/g1.0.1. If no existing location is specified, it will clone it from github.

I have included a dummy task UseAcquire to demonstrate how acquire can be called from within python using the subprocess.run method. I included a version of the example in (#378), which shows what it would look like translated to python (I'm not sure if it works).

swell/src/swell/tasks/use_acquire.py

Lines 30 to 48 in c02a073

	"""
	Translated c-shell to python:
	satbfrdb = os.path.join(swell_exp_path, "GEOS_mksi", "ObsClass")
	my_exp = "/gpfsm/dnb05/projes/p139/rtodling/TEST/GETBUFR/"
	work = os.path.join(my_exp, "work")
	spool = os.path.join(my_exp, "spool")
	obs_class = "disc_airs_bufr,disc_amsua_bufr,gmao_amsr2_bufr,gmao_gmi_bufr,mls_nrt_nc,ncep_1bamua_bufr,ncep_acftpfl_bufr,ncep_atms_bufr,ncep_aura_omi_bufr,ncep_avcsam_bufr,ncep_avcspm_bufr,ncep_crisfsr_bufr,ncep_goesfv_bufr,ncep_gpsro_bufr,ncep_mhs_bufr,ncep_mtiasi_bufr,ncep_prep_bufr,ncep_satwnd_bufr,ncep_ssmis_bufr,ncep_tcvitals,npp_ompsnm_bufr,r21c_npp_ompslp_nc,m2scr_n21_ompslp_nc,gmao_mlst_bufr"
	nymd = "20231010"
	nhms = "120000"
	nfreq = "060000"
	nstep = "1"
	subprocess.run(["acquire_obsys", "-v", "-d", work, "-s", spool, "strict", "-ssh", nymd, nhms, nfreq, nstep, obs_class])
	"""

To test:

Your experiment.yaml should include the following lines:

# What is the path to where the GMAO_perllib executables, acquire_obsys and acquire, are located?
gmao_perllib_path: /discover/nobackup/projects/gmao/advda/perllib_opt/GMAO_perllib/g1.0.1/

# What is the target tag for GMAO_perllib?
gmao_perllib_tag: g1.0.1

So that running:

swell task CloneGmaoPerllib <your experiment.yaml>
swell task UseAcquire <your experiment.yaml>

will show the help message

Convert_bufr as suite

Running swell create convert_bufr will now automatically create an experiment with the two lines added. (other questions will need to be added). Defaults are populated from src/swell/test/suite_tests/convert_bufr-tier1.yaml. I copied this file from convert_ncdiags, just to see if it works. @cohen-seth Feel free to update the values with the ones you're testing with, but we don't necessarily have to worry about it until after you're done testing your tasks.