import specific ufsda stage functions in ufsda atm prep script

[RussTreadon-NOAA]

Description
Specify the functions to import from ufsda.stage in UFS-DA atmospheric prep script.

Requirements
GDASApp PR #278 removes stage from ufsda/__init__.py. As a result, global-workflow scripts/exgdas_global_atmos_analysis_prep.py must specify the specific stage functions it uses. GDASApp includes the option to run ctests with g-w. Test test_gdasapp_atm_jjob_var_prep fails without updating exgdas_global_atmos_analysis_prep.py.

Acceptance Criteria (Definition of Done)
GDASApp g-w ctest test_gdasapp_atm_jjob_var_prep should pass.

Dependencies
Closure of this issue requires GDASApp PR #278 to be merged into GDASApp develop. Once this is done, the GDASApp has in g-w sorc/checkout.sh and Externals.cfg should be updated along with the change to scripts/exgdas_global_atmos_analysis_prep.py.

[RussTreadon-NOAA]

Work for this development will be done in RussTreadon-NOAA/global-workflow branch feature/ufsda_stage.

[RussTreadon-NOAA]

@WalterKolczynski-NOAA and @KateFriedman-NOAA , not sure why automated test Install pygw and run tests with pytests (3.7) failed with a9c3d0e.

The log file shows the following test failing with two tests skipped.

src/tests/test_configuration.py::test_configuration_config_files FAILED
src/tests/test_configuration.py::test_parse_config1 SKIPPED (fails i...) [ 37%]
src/tests/test_configuration.py::test_parse_config2 SKIPPED (fails i...) [ 41%]

The log file contains

src/tests/test_configuration.py:149: AssertionError
=========================== short test summary info ============================
FAILED src/tests/test_configuration.py::test_configuration_config_files - AssertionError: assert ['/tmp/pytest...config.file1'] == ['/tmp/pytest...config.file0']

[RussTreadon-NOAA]

@CoryMartin-NOAA 's PR #1106 has a similar failure in the automated pytests (see here).

[WalterKolczynski-NOAA]

The pytests are just failing in general for everyone. Started a couple weeks ago. We're not sure why and may have to turn them off until we figure it out.

[RussTreadon-NOAA]

Thank you, @WalterKolczynski-NOAA . I'll hit pause on digging into what's going on.