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Add shell linter Github action for pull requests #1007

Merged
merged 5 commits into from
Aug 31, 2022
Merged

Add shell linter Github action for pull requests #1007

merged 5 commits into from
Aug 31, 2022

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WalterKolczynski-NOAA
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Description
Adds a Github action to apply a shell linter to all pull requests. The linter will identify any deviations from the Google style guide and flag them during the code review.

To begin, only the ush/preamble.sh file is checked. This PR also includes updates to that script to make it compliant with G-Style.

Refs: #397

Type of change

  • New feature (non-breaking change which adds functionality)

How Has This Been Tested?

  • Unit test of preamble script
  • Test PR incorporating the action

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
Adds shellint GitHub action
a8b164f
@WalterKolczynski-NOAA
Update shell linter to diff linter
278e6d1 
Updates the github action to use a differential linter that will annotate
PRs with the warnings and errors. Also restricts the scan to just the
preamble file for now, to prevent a crippling number of errors from being
displayed.

Refs: NOAA-EMC#397
@WalterKolczynski-NOAA
Add shellcheck settings file
e0de360 
Refs: NOAA-EMC#397
@WalterKolczynski-NOAA
Run linter on all PR activity
f8cb9ab 
Refs: NOAA-EMC#397
@WalterKolczynski-NOAA
Make preamble comply with g-style
ee1676d 
Refs: NOAA-EMC#397
@WalterKolczynski-NOAA WalterKolczynski-NOAA added the feature New feature or request label Aug 31, 2022
@WalterKolczynski-NOAA WalterKolczynski-NOAA self-assigned this Aug 31, 2022
@WalterKolczynski-NOAA WalterKolczynski-NOAA changed the title Adds shell linter action for pull requests Add shell linter Github action for pull requests Aug 31, 2022
aerorahul
aerorahul approved these changes Aug 31, 2022
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Looks good to me.
And we now have standards.

@aerorahul aerorahul merged commit 855ee86 into NOAA-EMC:develop Aug 31, 2022
@WalterKolczynski-NOAA WalterKolczynski-NOAA deleted the feature/shell_linter branch August 31, 2022 05:11
jamacku
jamacku reviewed Aug 31, 2022
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.github/workflows/linters.yaml
uses: redhat-plumbers-in-action/differential-shellcheck@latest
with:
token: ${{ secrets.GITHUB_TOKEN }}
shell-scripts: ush/preamble.sh
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Unfortunately, this will not work as you expect. shell-scripts option takes the path to a text file that contains a list of file paths that will be ignored. I know that it is a bit clumsy, and it would deserve to rework on the linter side.

But I think you could be fine by running a linter with default settings. It performs differential scans, so only new changes introduced via PR will be reported.

I'm glad you are using my action. If you have any issues or requests, feel free to reach out to me or create issue on differential-shellcheck.

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Seemed to work when I tested it, but thanks for the information. It was probably just accidental that it did what I expected. I don't know that using a separate file is really all that clumsy at all.

Actually really like your action, thank you for making it available. My only request would be to make a new one that does the same for python linter ;). I'm having trouble finding one quite as well integrated into GitHub actions, to the point I am considering adapting yours for a different linter.

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I'm glad you like it. 👍

We are planning to create also other linters, including differential-cppcheck and differential-pylint. I can't give you any exact release date, but they are coming. They will be available at: @redhat-plumbers-in-action

KateFriedman-NOAA added a commit to KateFriedman-NOAA/global-workflow that referenced this pull request Sep 6, 2022
@KateFriedman-NOAA
Merge branch 'develop' into feature/dev-wcoss2
c11966c 
* develop:
  Add shell linter Github action for pull requests (NOAA-EMC#1007)
  Build updates for WCOSS2 (NOAA-EMC#1002)
  Update checkout.sh to remove git submodule update for upp checkout (NOAA-EMC#768)
  Add 06, 12, and 18 WCOSS2 operational GFS defs
  Add WCOSS2 operational GFS defs files
  Update repository name for EMC_post component to UPP
KateFriedman-NOAA added a commit to KateFriedman-NOAA/global-workflow that referenced this pull request Jan 30, 2023
@KateFriedman-NOAA
Merge branch 'develop' into feature/version-files
e81ed7c 
* 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)
@jamacku jamacku mentioned this pull request Jan 30, 2023
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@aerorahul aerorahul aerorahul approved these changes

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@WalterKolczynski-NOAA WalterKolczynski-NOAA

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