Insitu temp and salt

[guillaumevernieres]

Mostly Shastri's work.

This will need a companion pr in the global-workflow.

[emcbot]

Automated Global-Workflow GDASApp Testing Results: Machine: orion

Start: Thu May 30 16:50:49 CDT 2024 on Orion-login-1.HPC.MsState.Edu
---------------------------------------------------
Build:                                 *SUCCESS*
Build: Completed at Thu May 30 17:35:24 CDT 2024
---------------------------------------------------
Tests:                                  *Failed*
Tests: Failed at Thu May 30 17:55:31 CDT 2024
Tests: 83% tests passed, 8 tests failed out of 47
    1775 - test_gdasapp_atm_jjob_var_init (Failed)
    1776 - test_gdasapp_atm_jjob_var_run (Failed)
    1777 - test_gdasapp_atm_jjob_var_inc (Failed)
    1778 - test_gdasapp_atm_jjob_var_final (Failed)
    1779 - test_gdasapp_atm_jjob_ens_init (Failed)
    1780 - test_gdasapp_atm_jjob_ens_run (Failed)
    1781 - test_gdasapp_atm_jjob_ens_inc (Failed)
    1782 - test_gdasapp_atm_jjob_ens_final (Failed)
Tests: see output at /work2/noaa/stmp/cmartin/CI/GDASApp/workflow/PR/1135/global-workflow/sorc/gdas.cd/build/log.ctest

[emcbot]

Automated Global-Workflow GDASApp Testing Results: Machine: hera

Start: Thu May 30 21:57:25 UTC 2024 on hfe12
---------------------------------------------------
Build:                                 *SUCCESS*
Build: Completed at Thu May 30 22:42:49 UTC 2024
---------------------------------------------------
Tests:                                  *Failed*
Tests: Failed at Thu May 30 23:05:25 UTC 2024
Tests: 83% tests passed, 8 tests failed out of 47
    1774 - test_gdasapp_atm_jjob_var_init (Failed)
    1775 - test_gdasapp_atm_jjob_var_run (Failed)
    1776 - test_gdasapp_atm_jjob_var_inc (Failed)
    1777 - test_gdasapp_atm_jjob_var_final (Failed)
    1778 - test_gdasapp_atm_jjob_ens_init (Failed)
    1779 - test_gdasapp_atm_jjob_ens_run (Failed)
    1780 - test_gdasapp_atm_jjob_ens_inc (Failed)
    1781 - test_gdasapp_atm_jjob_ens_final (Failed)
Tests: see output at /scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/workflow/PR/1135/global-workflow/sorc/gdas.cd/build/log.ctest

[guillaumevernieres]

I only looked at the hera log:

[[38;5;39m2024-05-30 22:58:33,149 - DEBUG    - atm_analysis: ( <pygfs.task.atm_analysis.AtmAnalysis object at 0x148ad883fdc0> )^[[0m                                                                                      
^[[38;21m2024-05-30 22:58:33,149 - INFO     - analysis    : BEGIN: pygfs.task.analysis.get_jedi_config^[[0m                                                                                                                
^[[38;5;39m2024-05-30 22:58:33,149 - DEBUG    - analysis    : ( <pygfs.task.atm_analysis.AtmAnalysis object at 0x148ad883fdc0> )^[[0m                                                                                      
^[[38;21m2024-05-30 22:58:33,149 - INFO     - analysis    : Generate JEDI YAML config: /scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/workflow/PR/1135/global-workflow/sorc/gdas.cd/build/gdas/test/atm/global-workflow/tes\
trun/RUNDIRS/gdas_test/gdasatmanl_18/gdas.t18z.atmvar.yaml^[[0m                                                                                                                                                            
Traceback (most recent call last):                                                                                                                                                                                         
  File "/scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/workflow/PR/1135/global-workflow/scripts/exglobal_atm_analysis_initialize.py", line 24, in <module>                                                                  
    AtmAnl.initialize()                                                                                                                                                                                                    
  File "/scratch1/NCEPDEV/da/python/gdasapp/wxflow/20240307/src/wxflow/logger.py", line 266, in wrapper                                                                                                                    
    retval = func(*args, **kwargs)                                                                                                                                                                                         
  File "/scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/workflow/PR/1135/global-workflow/ush/python/pygfs/task/atm_analysis.py", line 74, in initialize                                                                      
    super().initialize()                                                                                                                                                                                                   
  File "/scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/workflow/PR/1135/global-workflow/ush/python/pygfs/task/analysis.py", line 36, in initialize                                                                          
    self.task_config.jedi_config = self.get_jedi_config()                                                                                                                                                                  
  File "/scratch1/NCEPDEV/da/python/gdasapp/wxflow/20240307/src/wxflow/logger.py", line 266, in wrapper                                                                                                                    
    retval = func(*args, **kwargs)                                                                                                                                                                                         
  File "/scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/workflow/PR/1135/global-workflow/ush/python/pygfs/task/analysis.py", line 82, in get_jedi_config                                                                     
    jedi_config = render(jcb_config)                                                                                                                                                                                       
  File "/scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/workflow/PR/1135/global-workflow/ush/python/jcb/renderer.py", line 265, in render                                                                                    
    return jcb_object.render(algorithm)                                                                                                                                                                                    
  File "/scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/workflow/PR/1135/global-workflow/ush/python/jcb/renderer.py", line 221, in render                                                                                    
    for observer in observers['observers']:                                                                                                                                                                                
TypeError: list indices must be integers or slices, not str 

is this expected @RussTreadon-NOAA ?

[guillaumevernieres]

@RussTreadon-NOAA , @CoryMartin-NOAA , @danholdaway Once this is merged, I'm going to build from scratch and run the ctest after updating the jcb and gdas.cd # in the companion g-w PR https://github.com/NOAA-EMC/global-workflow/pull/2644 @danholdaway , is the HEAD of jcb develop OK as the new #?