Fix ReadTheDocs build error #250
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@edwardhartnett This is a small PR. Can we merge this next? We can't update the 'readthedocs' documentation until this is fixed. |
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* develop: This commit references #23. Update sfc_climo_gen and chgres_cube programs: For regrid options other than conservative and neighbor, change pole method from NONE to ALLAVG. This prevents interpolation problems near the poles. * release/v1.1.0: This commit references #26. (#28) develop: This commit references issue #26. Merge minor change to fv3gfs_chgres.sh script from 'release/v1.1.0'. * chgres_cube snow fix (#30) develop: This commit references #27. Update chgres_cube - Initialize all surface variables to a missing flag after the FieldCreate step. In routine qc_check explicitly set snow to zero at open water and ice depth to zero at non-ice points. * Feature/chgres ice check (#35) develop: This commit references #32. Updates to chgres_cube: 1) Ensure sea ice fraction does not exceed 1.00. 2) Update 'model_grid.F90' to use separate pointers for the center and corner point lat/lons for gaussian grids. Recycling the same pointer for both could cause problems. * Update for new NCEPLIB library location on Jet (#34 #37) NCEPLIBS were recompiled on Jet and moved to a new location. Update repository accordingly. See issue #34 for more details. * working version * Revert "Merge branch 'working' into develop" This reverts commit 6f17d4f, reversing changes made to 5147e32. * chgres_cube vertical velocity fix Update chgres_cube to zero out vertical velocity when using tiled history files or tile restart files as input. See issue #31 for details. * develop: chgres_cube and sfc_climo_gen programs: Correct pre-processor directives "__line__" and "__file__" to "__LINE__" and "__FILE__" in order to work with compilers other than Intel (which tolerates the lowercase versions). * chgres_cube grib2 GFS data support (#48) Update chgres_cube program to ingest GFS grib2 data. For more details see issue #7 * Account code update for Cray/Dell (#52) Replace obsolete account code 'FV3GFS-T2O' with new code 'GFS-DEV' in all Cray and Dell scripts. * Update fre-nctools build module on Jet Update the fre-nctools build module on Jet to use Intel v18 and impi 2018.4.274. Per request of HAFS team. * Update serial chgres and global cycle to use parallel netcdf 4.7.4 Update the old serial chgres and global_cycle programs to use hdf5_parallel v1.10.6 and netcdf parallel v4.7.4 on Hera and Dell. Supports GFS V16. See issue #26 for more details. Also, fix an out-of-bounds array in serial chgres discovered by Dusan. * Add GRIB2 regression test for CHGRES_CUBE Add GRIB2 regression test for CHGRES_CUBE. See #64 for details. Update ./ush/chgres_cube.sh for GRIB2 option. Fix legacy Fortran extension in 'write_data.F90' that was identified when compiling with gfortran. Dusan opened issue #61 for this fix. For convenience, add the fix here. * Add LGPL license to repository. (#70) NOAA legal approved licenses for our component repositories. For EMC components we are using the LGPL. * GDAS initialization scripts Baseline set of utility scripts to start a GDAS/ENKF cycle using FV3GFS data as input. The scripts pull the needed data from HPSS and run the chgres_cube program for the high-res and ENKF members. chgres_cube - Fix three argument mismatches in call to error handler routine (see #69 for details). Update Cray build module to point to my own copy of the wgrib2 api instead of Dusan's. Point to official version of ESMF v8 on Cray and Dell. This commit references #33. * Update documentation Update/add documentation from v1.0.0 of the public release branch. Update LICENSE.md. Add VERSION file and docs directory. See issue #87 for more details. * CHGRES_CUBE: range check SST when using GFS GRIB2 input data Add range check to remove bad SST values (< 271.2K or > 310K) when using v14, v15.1 and v15.2 GFS GRIB2 data. Bad values are the result of bi-linear interpolation from the gaussian master files to the lat/lon "pgb" files. As a result, coastal points (even those identified as water by the mask) can be a mixture of land and non-land. This also fixes a model failure discovered when testing v1 of the public release. See issue #59 for more details. * chgres_cube - GFS v16 netcdf history file option Update chgres_cube to ingest GFS v16 gaussian netcdf history files. Input type "gaussian_netcdf". Add regression test for new option. For clarity, rename these input types (gaussian -> gaussian_nemsio; gfs_gaussian -> gfs_gaussian_nemsio; gfs_spectral -> gfs_sigio). Update all scripts and the GDAS initialization utility accordingly. * Regression tests for global_cycle, emcsfc and grid programs. New regression tests for global_cycle, emcsfc_ice_blend, emcsfc_snow2mdl and all programs associated with the grid generation. * Update repository to use CMake Build all UFS_UTILS programs using CMake. Update all driver scripts to load the same module file as the build script. This ensures the build and the run scripts use the same compiler version and libraries. Remove all files associated with the old build system. * Update for path changes on Jet On June 1, the directory 'project' was changed to 'HFIP'. And on June 30, the /lfs3 disk will be replaced by /lfs4. The repository was updated accordingly. For details, see issue #107. * Add geo-referencing to 'orography', 'sfc_climo' and 'chgres_cube' files Remove unused lat/lon records from the orography files. And add geo-referencing records and metadata to the 'orography', 'sfc_climo_gen' and 'chgres_cube' output files. For details see #11 and #22 * Define NDATE in GDAS initialization scripts Add module load of 'prod_util' to the Hera, Cray and Dell build/run modules. This will define the NDATE program for the GDAS initialization scripts. This fixes a bug that was added when the CMake version of UFS_UTILS was merged. For details see #115 * Add processing of climatological Thompson MP tracers to chgres_cube Update chgres_cube to optionally process climatological Thompson MP tracers. To process these tracers, the namelist variable "thomp_mp_climo_file" is set to the path/name of the climo file (netcdf). If variable is not set, the tracers will not be processed. For more details see #106. * feature/cmakemod This commit references #122 (#124) Point to develop of the authoritative repo. * Add extended Schmidt gnomonic grid capability Add capability to create regional extended Schmidt gnomonic grids (from Jim Purser). Includes new program to compute the global equivalent resolution for a regional grid (from Gerard). Move programs filter_topo, global_equiv_resol, regional_esg_grid and shave from fre-nctools.fd to its own directory. fre-nctools.fd should only contain the GFDL tools. For details, see #4 and #125 * Port repository to Orion Updates to compile repo on Orion. New scripts to run regression tests on Orion. New script to run the grid creation step on Orion. Update link_fixdirs.sh to link to Orion fixed directories. Remove some references to Tide/Gyre. See #96 and #134 for more details. * Add lake-maker to grid generation process Adding the lake maker from Shan Sun and Ning Wang: generate lake fraction and depth on the FV3 grid and add these records to the orography files. Ensure land fraction and lake fraction are consistent. For details, see issue #111 * Update to use project configs from NCEPLIBS NCEPLIBS was updated to provide a project-config file with its CMake build. Update the UFS_UTILS build to use the imported targets from these NCEPLIBS. * Updates for the Gnu compiler Some updates for the Gnu compiler. Fix argument mismatches in calls to mpi_abort. Fix syntax errors in ./lake.fd/lakefrac.F90. Add compiler flags for Gnu versions >10. See issues #140 #147. * Update NetCDF and HDF5 modules on Hera NCEPLIBS was built on Hera with a different NetCDF and it wasn't updated in the build module. Users could not run the wgrib2 executable with this NetCDF loaded. * Convert all scripts to bash Convert all scripts to bash, which is standard on most machines. See issue #144 for more details. * Add Mark Iredell's vertical coordinate generator Add Mark's program, a 'readme' and some sample scripts to run it. For details see issue #136. * Update make_solo_mosaic to handle longer file names Increase the length of the string "mosaic_name" in make_solo_mosaic.c from 128 to 255 characters. This is needed for the regional workflow where "mosaic_name" includes the absolute path and can exceed 128 characters. In that case, make_solo_mosaic fails without a clear error message. * Use FVCOM lake surface conditions New program fvcom_to_FV3 takes lake surface data generated by FVCOM and replaces the corresponding variables in the surface file created by chgres_cube. Input data to fvcom_to_FV3 needs to be in netcdf format and already horizontally interpolated to the model grid. Some QC is done within the code to create a minimum lake ice value of 15%. The code is strongly based upon work done by Eric James (GSL) and Ming Hu (GSL) to get FVCOM surface conditions into HRRRv4. PR #158. * CHGRES_CUBE GRIB2 Bug Fix Update chgres_cube to create the wgrib2 inventory file on one mpi task, instead of all tasks. When using all tasks, random failures can occur if one task is still writing the file while another is trying to read it. All programs: replace instances of 'include mpif.h' with 'use mpi'. For details, see #157. * Update GDAS initialization utility for ATMOS subdirectory Update GDAS initialization utility for new 'atmos' subfolder. Add load of NDATE utility to ./gdas_init/driver.hera.sh. It was inadvertently removed during a previous merge. Issue #159. * Bug Fix for FVCOM Processing to Allow Adding NetCDF Variables on Hera Small bug fix to ./sorc/fvcom_tools.fd that allows for the addition of new variables on Hera. * GFS v16 NCO standards updates Updates so GFS v16 will conform with the latest NCO standards: Remove '.ecf' extension from the 'emcsfc_global_sfc_prep.sh' script. Update 'link_fixdirs.sh' to open permissions on fixed directories before removing them. For details, see issue #138. * Update chgres_cube to ingest HRRR, RAP, and NAM grib2 files Update chgres_cube to ingest HRRR, RAP and NAM grib2 files. Add UFS_UTILS build modules for machines Cheyenne, Stampede2, and Odin. In the build script and all utility/regression test scripts, do a 'module load' of the machine-specific build modules instead of sourcing them. This is more portable. * Remove landsfcutil library dependency from snow2mdl program Incorporate landsfcutil library routines 'uninterpred' and 'intlon' into the snow2mdl program. The goal is to eventually retire the landsfcutil library. For details, see issue #169. * added README * Add test for GNU compiler on Hera Add option to compile UFS_UTILS with GNU on Hera. Update regression and utility scripts to optionally load the GNU-based build module on Hera. For more details, see issue #151. * Fix bug in chgres_cube that prevents Thompson aerosols from being created The return statement in read_setup_namelist is a few lines too early, and before the if statement that sets use_thomp_mp_climo to true if thomp_mp_climo_file is set in the namelist. This prevents the aerosols from ever being created or written to file, regardless of input data type. Addresses issue #178 * Update the 'chgres_cube.rst' documentation file Update to the version used by the MRW App v1.1.0 Issue #175. * adding docs * added FindESMF.cmake * updates * removed submodule * updated README * Add lake fraction/depth option for GFDL regional grids Expands the lake fraction and depth calculation for GFDL regional grids. As with global uniform grids, the lake fraction and depth are added to the orography files. For details see #173 * removed empty .gitmodules file * ejh_doc_2 Remove empty CMakeModules directory. Package config files are now in ./cmake. Issue #191 * more doxygen work * changed some code files to doxygen comments * doxygen work * Add build of ufs_utils on Gaea Updates to compile ufs_utils on Gaea using the HPC-stack. Issue #152 * Correct some chgres_cube comment documentation Correct prolog comments in chgres_cube module "program_setup.f90". Addresses Issue #193. * Point to new NCEPLIBS location on Jet UFS_UTILS was pointing to Dom's NCEPLIBS on Jet. He recently renamed the directory. Update the build module accordingly. For details, see issue #196 * More doxygen changes More doxygen changes. Fixed Doxyfile.in to find *.f and *.F files. Simplified doc build. Issue #191 * Create workflow for UFS_UTILS Create initial workflow for UFS_UTILS. For details, see #182. * More doxygen changes Add doxygen documentation for more source code files. Issue #191 * More doxygen changes Add doxygen for more source code files. Issue #191. * More doxygen updates Convert more files to doxygen. Issue #191. * Use hpc-stack on Hera Point to the hpc-stack on Hera. Fixes problem with chgres_cube runtime error. Issues #152 and #210 * chgres_cube fix to correctly read vertical coordinate type from GRIB2 data Operational RAP GRIB2 files on the native grid (and possibly other GRIB2 data types) are provided on isobaric coordinates, but contain some data on the 1.0 hybrid coordinate. This fixes an error with chgres_cube proceeding as if all of the data were on hybrid coordinates. Addresses Issue #222 * Use hpc-stack on Orion, Jet and WCOSS-Dell Update build to use the hpc-stack on Orion, Jet and WCOSS-Dell. Issue #152. * Next round of doxygen changes, and fix some comment warnings More doxygen updates. Fixed nested comment warnings. See #191 and #231 for more details. * Various chgres_cube bug fixes and code improvements Updated logic for reading soil type from the geogrid file. If the user provides a geogrid file and any of the calls in this process fail, the code will now fail with an error. Also, added a check to ensure input and geogrid grid sizes match. Add a sanity check to fail if the variable mapping file is empty or improperly formatted such that the code finds no variable entries to read. Bug fix when using HRRR or RAP data with climo surface fields that caused erroneous soil types. Clean up extraneous print statements. Addresses #228 * Doxygen updates to emcsfc_snow2mdl Add doxygen updates to emcsfc_snow2mdl. Issue #233. * Remove unused module files Remove unused module files. Remove ./ush/fv3gfs_chgres.sh, which used these now obsolete module files. This script is itself obsolete and has been replaced by ./util/gdas_init Resolves #235. * Remove nemsio utilities The nemsio_read, nemsio_get, nemsio_chgdate and mkgfsnemsioctl utilities are now part of the hpc-stack version of the nemsio library. So, remove them from UFS_UTILS. Issue #104. * Add doxygen comments to chgres_cube Resolves #191. * Add basic doxygen to remaining repository routines Add basic doxygen to all files under 'fre-nctools.fd' and 'orog.fd'. Removed unused include file - resovod.h - from orog.fd and converted machine.h to a Fortran module. Doxygen works better with module files. Update Doxyfile.in to use full paths for better online display. Issue #191. * updated workflow * now testing esmf cache * trying to fix esmf caching * working on finding esmf * working on finding esmf * working on finding esmf * testing esmf cache * attempted removal of setting ESMF_DIR * starting to use cacheing on jasper build * starting to use cacheing on jasper build * starting to use cacheing on jasper build * new line weirdness * new line weirdness * new line weirdness * cacheing jasper build * cacheing jasper build * cacheing jasper build still * cacheing jasper build still * switched to nceplibs 1.3.0 * adding new workflow * more work on workflows * turning on cache for nceplibs-1.3.0 build * clean up and test caching * Fix problem with orog program when using MacOS Rearrange the allocation of the "hgt_1d" array in mtnlm7_oclsm.f to fix errors on MacOS. Add matching deallocate statement. Fix subroutine name in comment. Fixes #243 #245 #277 * Start to list and describe all utilities in user_guide.md Also include some documentation clean up. Part of #217 Part of #191 Fixes #219 Fixes #214 Fixes #213 Fixes #268 Fixes #254 * Create macOS Action Resolves #243. * Feature/unit tests for chgres_cube.fd/utils.f90 (#276) * Create unit-tests for testing to_upper and to_lower. This commit references issue #257 * Add unit test to_upper_lower into CMake build * Clean up build and push for draft pull request * Making following improvement: - Using env parameter to assign source code - Add auther name - Modify comment - Change test failing procedure - rename directory for unit test * turned on testing in workflows * added test as test in cmake * added test as test in cmake * clean up test cmake file * renamed test * cleanup output * cleanup output * moved to new test directory * added tests subdirectory Co-authored-by: Edward Hartnett <38856240+edwardhartnett@users.noreply.github.com> Co-authored-by: Edward Hartnett <Edward.Hartnett@noaa.gov> * added documentation build to workflows, turned on doxygen warnings for missing documentation (#297) * turning on docs build in existing workflows Also turned on warnings in doxygen. * updated doxygen docs for chgres_cube.fd/input_data.F90 (#285) * updated doxygen docs * update doxygen for chgres_cube/input_data.F90 * fixed doxygen * fixed doxygen Co-authored-by: George Gayno <George.Gayno@noaa.gov> * doxygen for model_grid.F90 (#289) * doxygen for model_grid.F90 * doxygen updates * Update doxygen for each routine in module chgres_cube/model_grid.F90 Co-authored-by: George Gayno <George.Gayno@noaa.gov> * Start of testing for program_setup.F90 (#304) * adding program_setup test * more test on program_setup test * updated readme (#323) * consolidated gitignore files (#322) * consolidated gitignore files * consolidated gitignore files * doxygen for program_setup.f90 (#290) * doxygen for program_setup.f90 * update doxygen for all routines in chgres_cube.fd/program_setup.f90. Remove unused f11 soil variable. Issue #191 * Begin the move of variable definitions out of the prolog. (chgres_cube.fd/program_setup.f90) Co-authored-by: George Gayno <George.Gayno@noaa.gov> * trying to build test for fre-nctools.fd/shared_lib/create_xgrid.c (#301) * trying to build test * adding test * adding test * getting tst_create_xgrid working * improved docs in write_data (#306) * improved docs in write_data * Update author in chgres_cube.fd/write_data.F90 Fixes #305 Part of #191 Co-authored-by: George Gayno <George.Gayno@noaa.gov> * doxygen improvements for chgres_cube.fd/atmosphere.F90 and grib2_util.F90, turn on doxygen cross-references (#287) * doxygen improvements * cleanup * adding comments to grib2_util.F90 * more doxygen fixes * update doxygen for ./chgres_cube.fd/grib2_util.F90 Part of #191 Fixes #288 * Minor doxygen updates to ./chgres_cube.fd/atmosphere.F90 Part of #191 Fixes #288 Co-authored-by: George Gayno <George.Gayno@noaa.gov> * doxygen updates for chgres_cube.fd/search_util.f90 and sfc_climo_gen.fd/interp.F90 (#302) * Create unit-tests for testing to_upper and to_lower. This commit references issue #257 * Add unit test to_upper_lower into CMake build * Clean up build and push for draft pull request * Making following improvement: - Using env parameter to assign source code - Add auther name - Modify comment - Change test failing procedure - rename directory for unit test * turned on testing in workflows * added test as test in cmake * added test as test in cmake * clean up test cmake file * renamed test * cleanup output * cleanup output * moved to new test directory * added tests subdirectory * Convert and add doxygen document to search_util.f90 * Modified doxygen more to have same style with #285 * Update doxygen information * Update more doxygen on file * Update more doxygen on file author tag * Doxygen update for interp.F90 * Update doxygen information Co-authored-by: Edward Hartnett <38856240+edwardhartnett@users.noreply.github.com> Co-authored-by: Edward Hartnett <Edward.Hartnett@noaa.gov> * fixing more doxygen for sorc/chgres_cube.fd/static_data.F90 (#315) * updated doxygen * updated doxygen * Minor updates to ./chgres_cube.fd/static_data.F90 Fixes #314 Part of #191 * Minor doxygen updates to ./chgres_cube.fd/thompson_mp_climo_data.F90 Fixes #314 Part of #191 Co-authored-by: George Gayno <George.Gayno@noaa.gov> * doxygen fixes for sorc/chgres_cube.fd/chgres.F90 (#319) * doxygen fixes * Minor doxygen updates to chgres.F90. Fixes #318 Co-authored-by: George Gayno <George.Gayno@noaa.gov> * updating README (#333) * updating README * update reame.md Fixes #333 Co-authored-by: George Gayno <George.Gayno@noaa.gov> * More chgres_cube doxygen (#329) * more doxygen changes * more doxygen * fixed comment * Minor doxygen updates to ./chgres_cube.fd/input_data.F90 Part of #191 Fixes #327 * More doxygen updates Part of #191 Fixes #327 * More doxygen updates to chgres_cube. Part of #191. Fixes #327. * More doxygen updates to ./chgres_cube.fd/surface.F90 Part of #191 Fixes #327 * Doxygen updates to ./chgres_cube.fd/surface.F90 Part of #191 Fixes #327 * More doxygen update to chgres_cube. Part of #191 Fixes #327 * Doxygen updates to ./chgres_cube.fd/search_util.f90 Part of #191 Fixes of #327 Co-authored-by: George Gayno <George.Gayno@noaa.gov> * fix doxygen for sorc/emcsfc_snow2mdl.fd/grib_utils.f (#346) * fix doxygen * fix doxygen * Fix doxygen for ./emcsfc_snow2mdl.fd/grib_utils.f Fixes #291 Part of #191 Co-authored-by: George Gayno <George.Gayno@noaa.gov> * delete global_chgres (#299) * removed global_chgres * removed global_chgres from docs * removed nemsiogfs and landsfcutil from the build and modulefiles * now pass filename to read_setup_namelist() (#347) * bugfix/docfix - update conf.py for latest version of (#250) Sphinx. Issue #249. Co-authored-by: Edward Hartnett <38856240+edwardhartnett@users.noreply.github.com> * Rename all chgres_cube routines with F90 extension. (#354) Fixes #284 Co-authored-by: Edward Hartnett <38856240+edwardhartnett@users.noreply.github.com> * doxygen for fvcom_tools.fd (#339) * more doxygen work * more doxygen * updated docs * updated docs * updated docs * for chgres_cube - soil parameter references in program_setup.f90, turned on doxygen documentation for private functions (#352) * turned on documentation of private functions * turned on documentation of private functions * documentation cleanup, references for soil params * fixed links * fixed links * undoing * reapplied doc changes * Doxygen updates to chgres_cube.fd/surface.F90 (#359) * Update doxygen for ./chgres_cube.fd/surface.F90 Fixes #281 * Minor doxygen updates to ./chgres_cube.fd/surface.F90 Fixes #281 * Fix segmentation fault in topo filtering code when processing ESG grids (#238) * bugfix/topo_filter Remove seg faulting loop from filter_topo.F90. Instead always compute dy from lat/lon. Issue #236. * bugfix/topo_filter Add quotes to filter topo namelist variables. This fixed a program failure when using the Gnu compiler. Issue #236. * bugfix/topo_filter Add new regression test for regional ESG grid. Update hera grid_gen regression test script accordingly. Issue #236. * bugfix/topo_filter Bug fix to hera grid gen regression test driver script. Issue #236. * bugfix/topo_filter Update Dell grid gen regression test script for new esg regional test. Issue #236. * bugfix/topo_filter Update Jet grid gen regression test script for new ESG regional test. Issue #236. * bugfix/topo_filter Update orion grid gen regression test script for new ESG regional test. Issue #236. * bugfix/topo_filter Update Cray grid generation regression test script for new ESG regional test. Issue #236. Co-authored-by: Edward Hartnett <38856240+edwardhartnett@users.noreply.github.com> * doxygen updates for emcsfc_ice_blend.fd/emcsfc_ice_blend.f90 (#364) * fix doxygen for sorc/emcsfc_ice_blend.fd (#342) * Doxygen update * Update doxygen * Update to doxygen * break the declaration of each var onto it's own line * doxygen update Co-authored-by: Edward Hartnett <38856240+edwardhartnett@users.noreply.github.com> * improving module documentation in chgres_cube (#363) * More testing of chgres_cube.fd/program_setup.F90, with different config files (#360) * adding program_setup test * more program_setup tests * adding new config files * more test of program_setup.f90 * more testing * more tests * more tests * more tests * checking failing read of namelist file * commented out failing namelist * Remove duplicate 'to_upper'. One version was a function (#367) and the other was a subroutine. Only the function was being used by chgres_cube. The unit test was using the subroutine. So the test was updated to use the function. Fixes #303 * PR to add and correct doxygen docblocks to emcsfc_snow2mdl.fd/*.f (#348) * 3 * added a few ineffective doxygen commands to sorc/emcsfc_snow2mdl.fd/grib_utils.f * removed test build files * changes to add documentation to sorc/emcsfc_snow2mdl.fd/grib_utils.f IT'S BROKEN. SUBMITTED FOR INSPECTION ONLY!! gwv 2/22/21 1429EST * added skgb2 docblock into grib_check docblock. This is not permanent but wanted to at least get something. Format remains unacceptably mashed and munged * added formatting changes to grib_utils.f to improve appearnance and add skgb2 docblock to doxygen docblock at head of file. Still problem. subroutine skgb2 does not show up as documented * added repaired grib_utils.f file . This is the good one made by Ed Hartnett * added model_grid.f changes. * moved contains to before docblock, fixed na comments in docblock, removed brief in subroutine docblock * doxygenated snowdat.f * repaired model_grid.f and snowdat.f doxygen blocks to remove generic no information "none" and n/a lines, removed usage, capitalized author and added doxygen blocks for model_grid.f, missed earlier. * added @note to sections of snowdat.f * repaird author tag misformat and removed extraneous documentation spaces * added snow2mdl doxygen, round 1 * corrected multiple consecutive !! space issues, moved @author to bottom of doxygen docblocks, added @Date as needed, added incomplee docblocs for unterpred and interpred with @param of unknown variables inserted 2/25/2021 1104 * removed additional !! subprogram missed in previous proofreading * corrected @Date directives in snowdat.f * added doxygen block to program_setup.f * added SOME documentation to mtnlm7_oclsm.f Most routines remain undocumented and there are no docblocks. A skeletal docblock for two routines is supplied for evaluation * punctuated sentences, removed hyphens, removed double param definitions * added module <-> specification matching docblock to snowdat.f First attempt submitted for review * added complete sentences to documentation. fixed spacing in author statements removed abstract Co-authored-by: Edward Hartnett <38856240+edwardhartnett@users.noreply.github.com> * Doxygen improvements for sorc/grid_tools.fd/shave.fd/shave_nc.F90 (#369) * Doxygen updates for sorc/grid_tools.fd #366 PR for shave_nc.F90 doxygen * add author name as part of Doxygen updates issue 366 * doxygen fixes * doxygen fixes * doxygen fixes * restarting CI Co-authored-by: Edward Hartnett <Edward.Hartnett@noaa.gov> * Doxygen improvements for sorc/grid_tools.fd/regional_esg_grid.fd/psym2.f90 (#370) * Part of Doxygen updates for sorc/grid_tools.fd #366 Doxygen update for regional_esg_grid.fd/psym2.f90 * Part of Doxygen updates for sorc/grid_tools.fd #366 modify grid_tools.fd/regional_esg_grid.fd/psym2.f90 with doxygen improvement * part of Doxygen updates for sorc/grid_tools.fd #366 sorc/grid_tools.fd/regional_esg_grid.fd/psym2.f90 * doxygen fixes Co-authored-by: Edward Hartnett <Edward.Hartnett@noaa.gov> Co-authored-by: Edward Hartnett <38856240+edwardhartnett@users.noreply.github.com> * Rest of doxygen conversion for sorc/fvcom_tools.fd files (#362) * more doxygen for fvcom_tools.fd * more doxygen for fvcom * more doxygen for fvcom * more doxygen for fvcom * Update module_ncio.f90 Additional information and clarification added to description of each subroutine * Update module_nwp.f90 Additional descriptions added for documentation * fixing fvcom_tools doxygen warnings * fixed typo * Update module_nwp.f90 with comments Identified arrays nwp_mask, nwp_sst, nwp_ice, nwp_sfcT, and nwp_iceT with more detailed comments. * more doxygen changes Co-authored-by: David Wright <dmwright526@gmail.com> * Report test coverage using gcovr (#380) Report test coverage using gcovr The workflow uploads test-coverage.html and stores it as an artifact which can be manually downloaded on the Actions page. Fix NCEPLIBS caching in Action * removed nst_tf_chg utility from UFS_UTILS (#385) * removed nst_tf_chg * removed from readme and user_guide * doxygen improvements for sorc/grid_tools.fd/regional_esg_grid.fd/pesg.f90 (#371) * Part of Doxygen updates for sorc/grid_tools.fd #366 doxygen update for pesg.f90 * Part of Doxygen updates for sorc/grid_tools.fd #366 doxygen update for sorc/grid_tools.fd/regional_esg_grid.fd/pesg.f90 * doxygen fixes * more doxygen work * more doxygen Co-authored-by: Edward Hartnett <Edward.Hartnett@noaa.gov> Co-authored-by: Edward Hartnett <38856240+edwardhartnett@users.noreply.github.com> * Create Doxygen documentation for orog_mask_tools.fd/lake.fd/enclosure_cnvx (#376) Create doxygen documentation for enclosure_cnvx * updated readme with authors of each utility (#384) * updated readme with authors * updated * added more authors * added more authors * added more authors * added more authors * other fixes * other fixes * Doxygen improvements for sorc/grid_tools.fd/regional_esg_grid.fd/pmat5.f90 (#372) * part of Doxygen updates for sorc/grid_tools.fd #366 doxygen update for pmat5.f90 * part of Doxygen updates for sorc/grid_tools.fd #366 modify doxygen for grid_tools.fd/regional_esg_grid.fd/pmat5.f90 * part of Doxygen updates for sorc/grid_tools.fd #366 doxygen update for pmat5.f90 * Doxygen improvements for sorc/grid_tools.fd/regional_esg_grid.fd/pmat5.f90 Part of #366 * Doxygen improvements for sorc/grid_tools.fd/regional_esg_grid.fd/pmat5.f90 Part of #366 * doxygen fixes, clearing off doxygen warnings * doxygen fixes, clearing off doxygen warnings Co-authored-by: Edward Hartnett <Edward.Hartnett@noaa.gov> Co-authored-by: Edward Hartnett <38856240+edwardhartnett@users.noreply.github.com> * Doxygen improvements for sorc/grid_tools.fd/regional_esg_grid.fd/pmat4.f90 (#379) * Part of #366 Doxygen improvements for sorc/grid_tools.fd/regional_esg_grid.fd/pmat4.f90 * Doxygen improvements for sorc/grid_tools.fd/regional_esg_grid.fd/pmat4.f90 Part of #366 * doxygen fixes Co-authored-by: Edward Hartnett <Edward.Hartnett@noaa.gov> Co-authored-by: Edward Hartnett <38856240+edwardhartnett@users.noreply.github.com> * Doxygen improvements for sorc/grid_tools.fd/regional_esg_grid.fd/pmat.f90 (#382) * Part of #366 Doxygen improvements for sorc/grid_tools.fd/regional_esg_grid.fd/pmat.f90 * Part of #366 Doxygen improvements for sorc/grid_tools.fd/regional_esg_grid.fd/pmat2.f90 * Doxygen improvements for pmat.f90 * Part of #366 Doxygen improvements for sorc/grid_tools.fd/regional_esg_grid.fd/pmat.f90 * fixed doxygen warnings * punctuation Co-authored-by: Edward Hartnett <Edward.Hartnett@noaa.gov> Co-authored-by: Edward Hartnett <38856240+edwardhartnett@users.noreply.github.com> * Doxygen improvements for sorc/orog_mask_tools/inland (#386) Improve Doxygen documentation for inland executable * fixed doxygen warnings (#390) * more doxygen fixes (#391) * fix rest of doxygen warnings for emcsfc_snow2mdl.fd (#393) * silence rest of doxygen warnings for emcsfc_snow2mdl.fd * silence rest of doxygen warnings for emcsfc_snow2mdl.fd * doxygen updates for emcsfc_snow2mdl files: model_grid.f and snowdat.f Part of #191 Fixes #291 * Doxygen updates to emcsfc_snow2mdl.fd. Part of #191 Fixes #291 Co-authored-by: George Gayno <George.Gayno@noaa.gov> * highlighted doxygen questions for R. J. Purser in sorc/grid_tools.fd/regional_esg_grid.fd code (#387) * highlighted questions * added updates from R. Purser * more doxygen for sorc/grid_tools.fd/regional_esg_grid.fd files pietc.f90 and pietc_s.f90 (#392) * more doxygen * found bug? * fixed typo * more doxygen updates * fixed comments * separate chgres_cube doxygen build from rest of UFS_UTILS, fix remaining chgres_cube doxygen warnings, turn on WARN_AS_ERROR for chgres_cube (#395) * separate chgres_cube doxygen build from rest of UFS_UTILS * adding debugging to workflow * fixed separate build of docs for chgres_cube * now turn on warn_as_error for chgres_cube doxygen * added comment * doxygen updates for sorc/global_cycle.fd (#365) * doxygen work * more doxygen * more doxygen * more doxygen * Minor doxygen updates to ./global_cycle.fd/cycle.f90 Part of #191 Part of #341 * More doxygen updates to ./global_cycle.fd/cycle.f90 Part of #191 Part of #341 * Doxygen updates to ./global_cycle.fd/cycle.f90 Part of #191 Part of #341 * Doxygen updates to ./global_cycle.fd/cycle.f90 Part of #191 Part of #341 * Doxygen updates to ./global_cycle.fd/read_write_data.f90 Part of #191 Part of #341 * Doxygen updates to ./global_cycle.fd/read_write_data.f90 Fixes #191 Fixes #341 * Doxygen updates to ./global_cycle.fd/read_write_data.f90 Fixes #191 Fixes #341 * Doxygen updates to cycle.f90, machine.f90 and num_parthds.f90 Fixes #191 Fixes #341 * Doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * Doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * Doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * More doxygen updates to global_cycle. Fixes #191 Fixes #341 * Doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * Doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * Doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * Doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191. Fixes #341. * More doxygen updates to ./global_cycle.fd/sfcsub.F. Remove unused routine. Fixes #191 Fixes #341 * Doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * Doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * Doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * Doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * Doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * Doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * Doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * doxygen updtes to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * doxygen updates to ./global_cycle.fd/sfcsub.F Fixes #191 Fixes #341 * doxygen updates to ./global_cycle.fd/cycle.f90 Part of #191 Fixes #341 * Doxygen updates to global_cycle.fd Part of #191. Fixes #341. Co-authored-by: George Gayno <George.Gayno@noaa.gov> * splitting doxygen builds so each utility gets its own documentation build (#397) * splitting doxygen builds so each utility gets its own documentation build * stop documenting sorc at top level doxygen build * accomodate parallel builds * Rename emcsfc_snow2mdl.fd programs with .F90 extention. (#399) Remove 'free form' compiler option from CMakeLists.txt. Fixes #394 * cleared doxygen warnings from vcoord_gen utility (#404) * clearing doxygen warnings for sfc_climo_gen (#402) * clearing doxygen warnings for sfc_climo_gen * fixed names * turned on WARN_AS_ERROR on top level, fixed top-level doxygen warning * added comment * doxygen fixes for sorc/grid_tools.fd (#400) * doxygen fixes * fixed more doxygen warnings * changed author to GFDL Programmer * doxygen updates to global_equiv_resol.f90. * changed author name in global_equiv_resolve * doxygen updates to regional_esg_grid.f90. Co-authored-by: George Gayno <George.Gayno@noaa.gov> * Fix doxygen warnings in ./inland.fd/inland.F90 (#407) Part of #191 Fixes #406 * doxygen updates in sorc/grid_tools.fd - applied comments from R. Purser (#409) * applied comments from R. Purser * doxygen fixes * Doxygen updates to global_cycle (#411) Doxygen updates to sfcsub.F and machine.f90. Remove unused variables from machine.f90. Part of #191 Fixes #398 Fixes #412 * improved chgres_cube doxygen docs with info from chgres_cube.rst, added some formatting in other utility user guides (#410) * improved chgres_cube docs with info from chgres_cube.rst * fixed typo * cleanup user guide * clean up user guide * clean up user guide * clean up user guide * clean up surface.f90 * Eliminate doxygen warnings from sfcsub.F of global_cycle (#414) Eliminate remaining warnings from sfcsub.F. Part of #191 Fixes #398 * turn on WARN_AS_ERROR for global_cycle (#416) * turn on WARN_AS_ERROR for global_cycle * turn on WARN_AS_ERROR for global_cycle * trying to get CI unstuck * Bugfix/mpi ci (#427) Fix failing CI by building MPICH on macOS * Use --html-details option in gcovr and upload all html files as artifacts (#428) * Update doxygen for orog_mask_tools.fd. (#421) Clear all doxygen warnings. Fill in missing subroutine and function descriptions. Define all 'params'. Remove unused routine 'machine.f90' from orog.fd program. Part of #191 Fixes #344 Fixes #408 Fixes #413 * Updating Doxyfile.in files due to doxygen warnings (#418) Eliminates doxygen warnings for v1.9.1. Fixes #417 * more comments from Jim Purser (#423) * more comments from Jim Purser * fixed author tag * Cleanup the landing page of each utility's documentation (#429) * cleanup of user_guides * landing page cleanup * fixed some doxygen warnings * added some code authors to the README * fixed driver.f90 reference * added slideshow and reference in README (#432) * GSL orographic drag parameter computation (#273) Add new program to compute parameters needed for the GSL subgrid-scale orographic drag suite. Update the grid generation scripts to make the creation of these parameters an option. Add a regression test for this new option. Fixes #253 * More doxygen updates by Jim Purser for grid_tools.fd (#435) * cleanup of user_guides * landing page cleanup * fixed some doxygen warnings * added some code authors to the README * fixed driver.f90 reference * added slideshow and reference in README * more documentation improvements * adding brew update * Automatic regression tests (#426) Create rt.sh script for automatic regression tests on NOAA HPC systems * Removed unused submission scripts. (#437) These scripts are no longer used by NCEP workflows. Fixes #266. * converted ftst_program_setup to MPI test (#405) * converted to MPI test * MPI test scripts for hera, orion, and jet * Fix syntax * Make scripts executable, pass account to srun * Add qos Co-authored-by: kgerheiser <kgerheiser@icloud.com> Co-authored-by: Kyle Gerheiser <3209794+kgerheiser@users.noreply.github.com> * More doxygen updates for grid_tools.fd/regional_esg_grid.fd from Jim Purser (#439) * added slideshow and reference in README * added Jim Pursers documentation edits for pmat4.f90 * Change "regression test" in our cron script to the more honest "consistency check." (#440) * added slideshow and reference in README * changed regression to the more honest consistency test * changed regression to the more honest consistency test * changed regression to the more honest consistency test * changed regression to the more honest consistency test * more changes of regression to consistency * Minor documentation update in sorc/grid_tools.fd/regional_esg_grid.fd (#444) * added slideshow and reference in README * removed stray question marks * added authors to filter_topo.f90 * added authors to filter_topo.f90 * last edits from Jim Purser * Use correct error messaging in global_cycle.fd (#438) Update error messaging in the global_cycle program to conform to the NCO standard. The standard is to preface all error messages that stop program execution with "FATAL ERROR". Fixes #368. * Unit test and bug fix for chgres_cube.fd/search_util.F90 (#436) Add a unit test for search_util.F90. Two types of search tests were added: First, a missing value is replaced with a valid neighboring value. Second, a missing value is replaced by a default value. Fix bug in sst_guess routine within search_util.F90 which resulted in below freezing default values at points south of 60 degrees south latitude. Fixes #279 Fixes #441 * Make intermediate libraries for executables to facilitate easier testing (#445) Make a library for each utility that includes all the files except the main program. Then, tests can link to that library to access necessary code. * Eliminate compiler warning in chgres_cube (#456) Fix legacy extension warning for write statement in surface.F90. Remove some unused variables that can cause warnings depending on the compiler. Fixes #450 * Define constants in chgres_cube.fd/search_util.f90 (#448) Define all constants as parameters and use uppercase. Add more descriptive prolog. Fixes #278 * fix namelist in ftst_program_setup.F90 and beef up testing of namelist config_fv3_tiled_warm_restart (#457) * added slideshow and reference in README * uncommented failing test code * trying to fix namelist * fixing test * beefed up test * beefed up test * more testing * more testing * added test code * removed incorrect comment * More documentation for soil paramters (#464) * added slideshow and reference in README * improving documentation of soil parameters * Now show errors in build script (#465) * added slideshow and reference in README * show errors * Turn on fortran flag -fallow-argument-mismatch in chgres_cube for gfortran10 (#469) turn on -fallow-argument-mismatch in chgres_cube for gfortran10 * Add version checking for each library (#466) * Add version checking for each library * Improve beta message and remove MODULE from find_package * Relax version restriction on NetCDF to 4.3.3 * Add version to ESMF message * Enforce NetCDF 4.7.4 and switch to it on WCOSS Cray * Relax NetCDF version to 4.3.3 for WCOSS Cray * Feature/gefs soilt fix (#468) * Fix for seg fault in forecast step with GEFS. * chgres_cube: Correct erroneously high soil temperatures at isolated points in GEFS data by replacing it with skin temperature. Addresses Issue #447 * chgres_cube: Move do loop / if statement block for correcting erroneous soil temperatures to its own subroutine. * chgres_cube: Remove commented code that was previously used for the check on soil temperature. * First attempt at creating a test for check_soilt routine. * Bug fix for incorrect index order in check_soilt. Updates to test, which now passes. * Revert "Fix for seg fault in forecast step with GEFS." This will need to be done in a unique subroutine in input_data This reverts commit 0c0ff98. * Updated comments associated with check_soilt and its test to be more accurate. * Changed constant icet_default to be in ALL CAPS Co-authored-by: Christina.Holt <Christina.Holt@noaa.gov> Co-authored-by: Edward Hartnett <38856240+edwardhartnett@users.noreply.github.com> * Re-add NETCDF env variable so CMake can find NetCDF on WCOSS Cray Variable was removed by accident * Update to v1.1.0 of the hpc-stack (#476) Point to the official v1.1.0 of the hpc-stack. Remove references to unused libraries gfsio and w3emc. Fixes #248 Fixes #449 * Fix install of lakefrac and inland * Updated version file to 1.3.0 (#473) * added slideshow and reference in README * changed version * Include utility name in the name of the test in the cmake output (#478) * added slideshow and reference in README * added utility name to test names in cmake output Co-authored-by: GeorgeGayno-NOAA <52789452+GeorgeGayno-NOAA@users.noreply.github.com> Co-authored-by: Mark A Potts <Mark.Potts@noaa.gov> Co-authored-by: DomHeinzeller <58610420+DomHeinzeller@users.noreply.github.com> Co-authored-by: Jili Dong <jili.dong@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: gsketefian <31046882+gsketefian@users.noreply.github.com> Co-authored-by: David Wright <dmwright526@gmail.com> Co-authored-by: JeffBeck-NOAA <55201531+JeffBeck-NOAA@users.noreply.github.com> Co-authored-by: Edward Hartnett <Edward.Hartnett@noaa.gov> Co-authored-by: Larissa Reames <52886575+LarissaReames-NOAA@users.noreply.github.com> Co-authored-by: shansun6 <48043606+shansun6@users.noreply.github.com> Co-authored-by: George Gayno <George.Gayno@noaa.gov> Co-authored-by: Edward Hartnett <38856240+edwardhartnett@users.noreply.github.com> Co-authored-by: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Co-authored-by: GeorgeVandenberghe-NOAA <54996502+GeorgeVandenberghe-NOAA@users.noreply.github.com> Co-authored-by: mdtoy <toym@asme.org> Co-authored-by: Christina.Holt <Christina.Holt@noaa.gov>
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The default version of Sphinx was updated in December. This requires a
fix to the conf.py file.
Resolves #249.