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Rename post scripts #1038

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WalterKolczynski-NOAA
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Description
Rename post scripts to remove the unnecessary "ncep" qualifier. Also changes the executable name for upp to be the one produced by upp (upp.x).

The ush/global_nceppost.sh script is removed as it is not used by any job. We may want to rename the gfs_post.sh script (the one that is used) to global_post.sh to be more reflective of its usage.

Type of change

  • Maintenance (alteration that does not change functionality)

How Has This Been Tested?

  • Forecast-only test on Hera
  • Cycled test on Hera

Checklist

  • My code follows the style guidelines of this project
  • I have performed a self-review of my own code
  • I have commented my code, particularly in hard-to-understand areas
  • My changes generate no new warnings
  • New and existing tests pass with my changes

@WalterKolczynski-NOAA WalterKolczynski-NOAA self-assigned this Sep 29, 2022
@WalterKolczynski-NOAA WalterKolczynski-NOAA added the maintenance Regular updates and maintenance work label Sep 29, 2022
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scripts/exgdas_atmos_post.sh Fixed Show fixed Hide fixed
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@KateFriedman-NOAA KateFriedman-NOAA left a comment

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Changes look good! Thanks @WalterKolczynski-NOAA ! Approve pending resolution of linter warnings.

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@aerorahul aerorahul left a comment

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Several comments:

  • Use of (( )) at status checks. See specific comment
  • Use of shellcheck statements. See specific comment
  • Some other, inline.

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done


##########################################
# Source machine runtime environment
##########################################
. $HOMEgfs/env/${machine}.env post
# shellcheck source-path=env
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are we adding this now to every file?
Can this be set in higher level env?

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No, but we may be able to do without it. I was hoping to get fewer other complaints if shellcheck can source the right files, and I'm not sure it is even helping (especially this one, which I don't think is followed).

setpdy.sh
# shellcheck disable=SC1091
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I am not sure littering the code w/ this type of stuff is a good idea.
Its distracting for one, and its hard to know what are we disabling and why specifically here.

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The latter issue can be solved by explaining in comment, but I was trying to make them minimally intrusive. So far, I've only needed shellcheck directives in a couple places per file. We could turn certain warnings off all the time, but, well, then they'd be off all the time.

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shellcheck found more than 10 potential problems in the proposed changes. Check the Files changed tab for more details.

scripts/exgdas_atmos_post.sh Fixed Show fixed Hide fixed
scripts/exgfs_atmos_post.sh Fixed Show fixed Hide fixed
scripts/exgfs_atmos_post.sh Fixed Show fixed Hide fixed
scripts/exgfs_atmos_post.sh Fixed Show fixed Hide fixed
scripts/exgfs_atmos_post.sh Fixed Show fixed Hide fixed
ush/gfs_post.sh Fixed Show fixed Hide fixed
scripts/exgdas_atmos_post.sh Fixed Show fixed Hide fixed
scripts/exgfs_atmos_post.sh Fixed Show fixed Hide fixed
jobs/JGLOBAL_ATMOS_POST Fixed Show fixed Hide fixed
jobs/JGLOBAL_ATMOS_POST Fixed Show fixed Hide fixed
Rename post scripts to remove the unnecessary "ncep" qualifier.
Disables SC2154 (variable assigned but not defined).
With SC2154 turned off, the excessive usage of :? can be removed.
Turns off shellcheck parsing sourced scripts and removes some shellcheck
directives that are no longer necessary.
After linter modifications, a variable was being treated as an octal, resulting
in the wrong result when adding.
@WalterKolczynski-NOAA WalterKolczynski-NOAA merged commit 948f941 into NOAA-EMC:develop Oct 4, 2022
@WalterKolczynski-NOAA WalterKolczynski-NOAA deleted the feature/rename_post branch October 4, 2022 02:56
KateFriedman-NOAA added a commit to KateFriedman-NOAA/global-workflow that referenced this pull request Jan 30, 2023
* develop:
  Correct issue in linking final restart files (NOAA-EMC#1285)
  Remove execute permissions from config files (NOAA-EMC#1281)
  Make needed updates to run forecast from GEFS (NOAA-EMC#1203)
  Remove unnecessary variables which reference to nemsio (NOAA-EMC#1259)
  Create analysis files for early-cycle EnKF by default (NOAA-EMC#1237)
  Don't wipe $DATA before running ocean bmat (NOAA-EMC#1280)
  More marine DA j-jobs (NOAA-EMC#1270)
  Update UFS-DA atmospheric prep script to be consistent with GDASApp update (NOAA-EMC#1265)
  Add new jjob for ocean analysis bmat (NOAA-EMC#1239)
  Retire ecf/versions in develop (NOAA-EMC#1267)
  Deploy documentation to RTD (NOAA-EMC#1264)
  Temporarily disable failing pytest (NOAA-EMC#1263)
  Remove incorrect/misleading comments in config.base (NOAA-EMC#1261)
  Add initial Sphinx documentation (NOAA-EMC#1258)
  Remove nemsio support (NOAA-EMC#1255)
  Increase wallclock for diag jobs (NOAA-EMC#1216)
  Use correct resources for GFS gempak (NOAA-EMC#1214)
  Abstract common j-job tasks (NOAA-EMC#1230)
  Add missing mkgfsawps.x link (NOAA-EMC#1218)
  Fix post sounding job (NOAA-EMC#1212)
  Revert "Use fracoro data for all new UFS applications (NOAA-EMC#1182)" (NOAA-EMC#1240)
  Use fracoro data for all new UFS applications (NOAA-EMC#1182)
  Revert "Merge GFS v16.3 operational GSI changes into develop branch. (NOAA-EMC#1158)" (NOAA-EMC#1238)
  Add more user defined parameters for the marine DA (NOAA-EMC#1235)
  Update pytests action version and run sequentially (NOAA-EMC#1236)
  Add utility to compare Fortran namelists (NOAA-EMC#1234)
  Updates for pygw (NOAA-EMC#1231)
  Merge GFS v16.3 operational GSI changes into develop branch. (NOAA-EMC#1158)
  Move member up in directory hierarchy (NOAA-EMC#1201)
  Enable staging ics for cycled experiments. (NOAA-EMC#1199)
  Add tests for configuration.py (NOAA-EMC#1192)
  Replace ocnanal_${CDATE}} with ${RUN}ocnanal_${cyc} (NOAA-EMC#1191)
  define NET and RUN in the Rocoto XML to accurately mimic the ecf in ecflow (NOAA-EMC#1193)
  Fix checking for restart files (NOAA-EMC#1186)
  Fix 'DEBUG' option in build_ufs.sh (NOAA-EMC#1188)
  Update archive job memory request value for R&Ds (NOAA-EMC#1183)
  Reorder post so all flux files are generated when running offline (NOAA-EMC#1181)
  Stop checking for restarts on non-GFS CDUMPs (NOAA-EMC#1179)
  Add missing jobids in some pre-job scripts (NOAA-EMC#1176)
  Remove existing directory if it exists when getic runs (NOAA-EMC#1165)
  Add logging decorator, test and test for yaml_file (NOAA-EMC#1178)
  fix coding norm check in `hosts.py` (NOAA-EMC#1174)
  Fix some bugs and make other changes so ctest in GDASApp works (NOAA-EMC#1172)
  Support for the GDASApp testing in containers (NOAA-EMC#1151)
  ATM 3DVAR with and without IAU (NOAA-EMC#1113)
  Enable checking for python norms and fix violating code (NOAA-EMC#1168)
  Enforce decimal math in atmos post (NOAA-EMC#1171)
  Update marine DA j-jobs to new format (NOAA-EMC#1149)
  Add utility to manipulate files en masse  (NOAA-EMC#1166)
  add action to run pytests (NOAA-EMC#1167)
  Pin `differential-shellcheck` to `v3` tag (NOAA-EMC#1162)
  Add a task base class and basic logger (NOAA-EMC#1160)
  Recursively convert dict to AttrDict when making an AttrDict (NOAA-EMC#1154)
  move configuration.py to pygw. Use it from there.  return AttrDict after sourcing configs (NOAA-EMC#1153)
  JEDI based Marine DA tasks (NOAA-EMC#1134)
  Allow customizations based on user/configuration (NOAA-EMC#1146)
  First step towards making j-jobs consistent in use from ecflow and rocoto (NOAA-EMC#1120)
  enable APP=S2SWA on WCOSS2 (NOAA-EMC#1142)
  Fix typo in .shellcheckrc
  Remove prod_envir module load from WCOSS2 (NOAA-EMC#1138)
  Link staged GSI fix files instead of cloning them from gerrit (NOAA-EMC#1132)
  Address shellcheck warnings in env files (NOAA-EMC#1136)
  Adds group size and nmem for GEFS (NOAA-EMC#1127)
  Remove unnecessary sCDATE assignment in forecast_predet.sh (NOAA-EMC#1133)
  Convert archive jobs to proper j-jobs (NOAA-EMC#1115)
  Update C48 forecast to run with one thread (NOAA-EMC#1131)
  Improved error messages from atmos analysis (NOAA-EMC#1125)
  Update MODULEPATH for Orion (NOAA-EMC#1126)
  MPMD variable updates and fix (NOAA-EMC#1124)
  Introduce FHMAX_ENKF_GFS to extending ensemble forecast capabilities (NOAA-EMC#1122)
  Update R&D launcher commands for tasks and multi-prog (NOAA-EMC#1112)
  Correct crtm path in UFS DA atmospheric analysis scripts (NOAA-EMC#1111)
  Correct syntax in remaining sorc scripts (NOAA-EMC#1105)
  Add GSI background error covariance as an option for UFS DA variational assimilation (NOAA-EMC#1104)
  Add Early Cycle EnKF workflow (NOAA-EMC#1022)
  Correct errors with gdas and monitoring symlinks (NOAA-EMC#1101)
  Fixed gfs-utils links (NOAA-EMC#1099)
  Fix build scripts and bring into compliance (NOAA-EMC#1096)
  Feature/updates for gdas app (NOAA-EMC#1091)
  Change GLDAS USE_CFP to NO on Hera (NOAA-EMC#1094)
  Resource updates to support WCOSS2 (NOAA-EMC#1070)
  Set COMPILER in link for detect machine (NOAA-EMC#1092)
  gfs utils update (NOAA-EMC#1088)
  GFS-UTILS update for build and ush scripts (NOAA-EMC#1082)
  Update UFS version to 2022 Oct 19 (NOAA-EMC#1083)
  Use more cycledefs for task control (NOAA-EMC#1078)
  removing superfluous EFSOI-specific files from develop (NOAA-EMC#1079)
  Update UFS to Sept 9 version (NOAA-EMC#1073)
  Modify default file location for monitor data when using rocoto (NOAA-EMC#1065)
  Fix companion ocean resolution for C48 (NOAA-EMC#1066)
  Add trailing slash for gldas topo path (NOAA-EMC#1064)
  Limit number of CPU for post (NOAA-EMC#1061)
  Fix eupd trace (NOAA-EMC#1057)
  Port to S4 (NOAA-EMC#1023)
  Update to obsproc.v1.0.2 and prepobs.v1.0.1 (NOAA-EMC#1049)
  Add GDAS to the partial build list (NOAA-EMC#1050)
  Fix group number being treated as octal in gdas arch (NOAA-EMC#1053)
  Remove trace from link script (NOAA-EMC#1046)
  Update gfs-utils hash to 3a609ea (NOAA-EMC#1048)
  Fix link script usage statement (NOAA-EMC#1045)
  Replace preamble variable commands with functions (NOAA-EMC#1012)
  Implement fix reorg and remove gfs-utils code (NOAA-EMC#1009)
  Rename post scripts (NOAA-EMC#1038)
  Fix missing @ symbol with COMINsyn in config.base (NOAA-EMC#1039)
  WCOSS2 run support and script/config updates (NOAA-EMC#1030)
  Remove base_svn from Hera and Orion hosts files (NOAA-EMC#1036)
  initial commit for incoming yaml work (NOAA-EMC#1029)
  Fix radiance verification failing to find diag files (NOAA-EMC#1031)
  Supported resolutions on platforms and defaults for mode (NOAA-EMC#1026)
  Add GLDAS scripts & fix GLDAS job (NOAA-EMC#1018)
  Update GSI Monitor for radmon fix
  Correct shell linter config (NOAA-EMC#1013)
  Correct diagnostic file handling in ush/ozn_xtrct.sh (NOAA-EMC#1016)
  Add shell linter Github action for pull requests (NOAA-EMC#1007)
  Build updates for WCOSS2 (NOAA-EMC#1002)
  Update UFS_UTILS tag to `ufs_utils_1_8_0` (NOAA-EMC#1001)
  Fix preamble id (NOAA-EMC#996)
  Add missing "atmos" into job dependencies (NOAA-EMC#998)
  Bugfix in arch.sh to remove hardwired "htar" (NOAA-EMC#992)
  Add in stubs for aerosol DA tasks + bugfix for setup_expt where cycled and ATMA are used (NOAA-EMC#990)
  Add GSI monitor scripts (NOAA-EMC#969)
  Fix product generation at some fcst hrs (NOAA-EMC#988)
  Add initial config files for global aerosol DA (NOAA-EMC#986)
  Update diag table to remove wav-ocn coupling fields (NOAA-EMC#979)
  use a robust Findwgrib2.cmake to find wgrib2 built w/ native wgrib2 build (NOAA-EMC#970)
  Externals.cfg was stale and had drifted off (NOAA-EMC#965)
  Fix post comparison with zero-padded numbers (NOAA-EMC#964)
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