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import specific ufsda stage functions in ufsda atm prep script #1262

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RussTreadon-NOAA opened this issue Jan 20, 2023 · 5 comments · Fixed by #1265
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import specific ufsda stage functions in ufsda atm prep script #1262

RussTreadon-NOAA opened this issue Jan 20, 2023 · 5 comments · Fixed by #1265
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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
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Work for this development will be done in RussTreadon-NOAA/global-workflow branch feature/ufsda_stage.

RussTreadon-NOAA added a commit to RussTreadon-NOAA/global-workflow that referenced this issue Jan 20, 2023
@RussTreadon-NOAA
import ufsda stage functions atm_obs and bias_obs in ufsda atm analys…
a9c3d0e 
…is prep script (NOAA-EMC#1262)
@RussTreadon-NOAA
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@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
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@CoryMartin-NOAA 's PR #1106 has a similar failure in the automated pytests (see here).

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

@RussTreadon-NOAA RussTreadon-NOAA mentioned this issue Jan 21, 2023
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@RussTreadon-NOAA RussTreadon-NOAA self-assigned this Jan 21, 2023
RussTreadon-NOAA added a commit to RussTreadon-NOAA/global-workflow that referenced this issue Jan 24, 2023
@RussTreadon-NOAA
Update GDASApp hash (NOAA-EMC#1262)
0744e22
WalterKolczynski-NOAA pushed a commit that referenced this issue Jan 25, 2023
@RussTreadon-NOAA
Update UFS-DA atmospheric prep script to be consistent with GDASApp u…
fb54bb6 
…pdate (#1265)

Updates the GDAS App version to incorporate the changes of NOAA-EMC/GDASApp#278, which restores the ability of `run_jedi_exe.py` to execute UFS-DA applications, specifically `fv3jedi_var.x`. Included in NOAA-EMC/GDASApp#278 is the removal of entry `ufsda.stage` from `ush/ufsda/__init__.py`.  Scripts which simply `import ufsda` must now specify the functions to from `ufsda.stage`. 

g-w issue #1262 documents the addition of the `ufsda.stage` line to `scripts/exgdas_global_atmos_analysis_prep.py`.  This change is required for g-w to successfully stage files used by the var and ensemble UFS-DA applications.

Fixes #1262
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