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Implement fix reorg and remove gfs-utils code #1009

Merged
merged 22 commits into from
Oct 4, 2022
Merged

Implement fix reorg and remove gfs-utils code #1009

merged 22 commits into from
Oct 4, 2022

Commits on Oct 4, 2022

  1. Update fix subfolders to ignore in .gitignore 

    Refs: NOAA-EMC#966
    @KateFriedman-NOAA @WalterKolczynski-NOAA
    KateFriedman-NOAA authored and WalterKolczynski-NOAA committed Oct 4, 2022
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  2. Update link_workflow.sh for fix set reorg 

    - Source new fix.ver file to get fix subfolder version values for setting up fix folder symlinks.
- Change "fix_NEW" to "fix" for FIX_DIR paths: use newly reorganized and versioning fix set.
- Remove "fix_" from /fix folder symlink names.
- Update /fix folder symlink creation to use version variables from fix.ver.
- Update GSI and GDAS fix symlinks.

Refs: NOAA-EMC#966
    @KateFriedman-NOAA @WalterKolczynski-NOAA
    KateFriedman-NOAA authored and WalterKolczynski-NOAA committed Oct 4, 2022
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  3. Update JEDI fix subfolder path name in configs 

    - Change FV3JEDI_FIX in related configs to change the path subfolder from
"fix_jedi" to "gdas".

Refs: NOAA-EMC#966
    @KateFriedman-NOAA @WalterKolczynski-NOAA
    KateFriedman-NOAA authored and WalterKolczynski-NOAA committed Oct 4, 2022
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  4. Update fix subfolders in configs to remove "fix_" 

    - Remove "fix_" text from fix file paths in several configs.

Refs: NOAA-EMC#966
    @KateFriedman-NOAA @WalterKolczynski-NOAA
    KateFriedman-NOAA authored and WalterKolczynski-NOAA committed Oct 4, 2022
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  5. Remove "fix_" from fix subfolder paths in scripts 

    - Update /scripts and /ush scripts to remove the "fix_" text
from fix subfolder paths.

Refs: NOAA-EMC#966
    @KateFriedman-NOAA @WalterKolczynski-NOAA
    KateFriedman-NOAA authored and WalterKolczynski-NOAA committed Oct 4, 2022
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  6. Create versions folder and fix.ver 

    - Create a new version folder to hold version files.
- Create a new fix.ver to hold fix file versions.

Refs: NOAA-EMC#966
    @KateFriedman-NOAA @WalterKolczynski-NOAA
    KateFriedman-NOAA authored and WalterKolczynski-NOAA committed Oct 4, 2022
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  7. Remove gfs-utils code and update for new fix 

    Removes all of the code and scripts that were moved to the new gfs-utils
repo and adjusts workflow scripts to build and use them from the new
location.

Some of the build scripts had unnecessary calls to machine-setup that are
removed because the lower-level script already has the same functionality.

This PR also includes updates to use the new fix organization. This includes
the addition of a fix versions file, updates to the link script, and some
changes in the fix directories used by scripts to account for files that
have been relocated. The versions file sets the version number for each
component of fix, so that fix can be more easily maintained and documented.
The initial versions are all the same, and correspond to the old fix_NEW
directory (other than some directories have been renamed or reorganizated).

Finally, the link script has been updated to match the syntax of the rest
of the build system (`checkout.sh` and `build_all.sh`). `link_workflow.sh`
now detects the machine automatically instead of requiring an argument, and
dev mode, which used to be set using `emc` as an argument, is now assumed.
To run in ops mode (copy instead of link), the `-o` option is used. The
full syntax is now simply:
```
./link_workflow.sh [-o]

-o: Run in operations (NCO) mode (copy instead of link)
```

This commit uses a temporary clone of the UFS_UTILS repo pending the merger
of ufs-community/UFS_UTILS#688.

Fixes NOAA-EMC#356
    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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  8. Correct merge error in link script 

    An incorrect resolution of a merge conflict resulted in an undefined
variable in the link script.

Refs: NOAA-EMC#356
    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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  9. Update gfs utils to pick up Orion gempak fix 

    Updates the gfs utils version to pick up a fix for an incorrect gempak
module version on Orion.
    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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  10. Update to new UFS_UTILS hash

    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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  11. Revert change to checkout for GSI-adjacent repos 

    An earlier change had inadvertently stopped checking out GSI Monitor,
GSI Utils, and GLDAS when GDAS is used instead of GSI.

Refs: NOAA-EMC#966
    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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  12. Add gfs-utils to manage externals config 

    Refs: NOAA-EMC#966
    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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  13. First wave of linter fixes 

    First wave of linter fixes for removing gfs-utils code/fix reorg.

Refs: NOAA-EMC#966
    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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  14. Linter fixes for fix dir reorg 

    Second wave of linter fixes for removing gfs-utils code/fix reorg.

Refs: NOAA-EMC#966
    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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  15. Wave 3 of linter fixes for fix update 

    Wave 3 of linter fixes for removing gfs-utils code/fix reorg.

Refs: NOAA-EMC#966
    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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  16. Wave 4 linter fixes for fix update 

    Wave 4 of linter fixes for removing gfs-utils code/fix reorg.

Refs: NOAA-EMC#966
    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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  17. Fix minor syntax error in link script 

    The last merge from develop introduced a minor syntax error in the
link script due to a bad conflict resolution. The issue is now
corrected.

Refs: NOAA-EMC#966
    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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  18. Update new GLDAS scripts for new fix pattern 

    GLDAS scripts were recent moved into the workflow repo and need to
be updated for the new fix structure like other components.

Refs: NOAA-EMC#622, NOAA-EMC#966
    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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  19. Fix default missing var syntax error 

    Corrects a `:-?` to `:?`.

Refs: NOAA-EMC#356
    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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  20. Move root fixdir setting higher in link script 

    Moved the setting of FIXDIR higher so it errors on an unknown machine
sooner. Also removed redundant version file load.

Refs: NOAA-EMC#966
    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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  21. Fix erronous CR in log directory 

    The closing quotation mark when making the logdir in checkout was
erroneously split into a new line.
    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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  22. Merge branch 'develop' into feature/use_gw_utils

    @WalterKolczynski-NOAA
    WalterKolczynski-NOAA committed Oct 4, 2022
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