Adding new XML generation tool and example confs. #330
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christinaholtNOAA
requested review from
christopherwharrop-noaa,
danielabdi-noaa and
robgpita
…nity#734) * Updates to port regional workflow to gaea * Temp change with -v as batch option * new fixes for gaea/slurm * Updated time for make lbcs * added TEST data directory path * Update gaea.sh * fixes for PR
…ity#740) ## DESCRIPTION OF CHANGES: The script/function `get_WE2Etest_names_subdirs_descs.sh` (which is called from `run_WE2E_tests.sh` if needed) creates a CSV (Comma-Separated Value) file named `WE2E_test_info.csv` that contains information about the WE2E tests. Currently, this CSV file contains only 3 columns: the test name, the names of any alternate names for the test, and the test description. In order to have a more complete summary of the WE2E tests, this PR modifies `get_WE2Etest_names_subdirs_descs.sh` so that additional information is included in the CSV file. This additional information consists of the values of the following experiment variables for each test: ``` PREDEF_GRID_NAME CCPP_PHYS_SUITE EXTRN_MDL_NAME_ICS EXTRN_MDL_NAME_LBCS DATE_FIRST_CYCL DATE_LAST_CYCL CYCL_HRS INCR_CYCL_FREQ FCST_LEN_HRS LBC_SPEC_INTVL_HRS NUM_ENS_MEMBERS ``` In addition, the script uses this information to calculate the number of times each test calls the forecast model (e.g. if the test uses 3 different cycle dates, then the forecast model will be called 3 times; if it is an ensemble test for a single cycle, the test will call the forecast model as many times as the number of ensemble members). ## TESTS CONDUCTED: The script `run_WE2E_tests.sh` was called that in turn calls `get_WE2Etest_names_subdirs_descs.sh`. This created a new CSV file that contained the new fields (columns). The CSV file was imported into Google Sheets (using "|" as the field/column separator) and looked correct. ## DOCUMENTATION: The documentation is for the most part already within the `get_WE2Etest_names_subdirs_descs.sh`. This PR slightly modifies that documentation to update it.
* update vertical structure of NCO mode * update sample script for nco * Fix typo on write component of new RRFS CONUS
* Updated the default CCPP physics option to FV3_GFS_v16 * Updated the default CCPP physics option to FV3_GFS_v16 in config_defaults.sh Co-authored-by: Natalie Perlin <[email protected]>
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I noticed that generated xml file sometimes escapes ampersand when it is referencing an entity, for example, |
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| yaml.add_constructor('!cycstr', cycstr, Loader=yaml.SafeLoader) | ||
| yaml.add_constructor('!include', include, Loader=yaml.SafeLoader) | ||
| yaml.add_constructor('!startstopfreq', startstopfreq, Loader=yaml.SafeLoader) |
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I had one difficult to track bug with yaml constructors being "global". I belive you had a !join tag defined in set_namelist.py for joining paths and I had the same tag name defined for joining strings (needed that for `config_defaults.yaml) and this resulted in a conflict, adding "/" when my intention was to join strings. I wonder if there is a way to add yaml constructors to be local to avoid such kind of conflicts ...
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That's an interesting namespace issue.
I'm not sure about the globals, but I am kind of curious if it would make sense to have a "unified" yaml parser that we could import/use in any of the tools that are ingesting a YAML. That may make it easier to deal with the conflicts.
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| dependency: | ||
| and: &make_ics_deps | ||
| taskdep_get_extrn: | ||
| attrs: | ||
| task: get_extrn_ics | ||
| or_grid: | ||
| datadep_complete: | ||
| attrs: | ||
| age: 00:00:00:05 | ||
| text: '&LOGDIR;/&MAKE_GRID_TN;_task_complete.txt' | ||
| streq: | ||
| left: '&RUN_TASK_MAKE_GRID;' | ||
| right: 'FALSE' | ||
| or_orog: | ||
| datadep_complete: | ||
| attrs: | ||
| age: 00:00:00:05 | ||
| text: '&LOGDIR;/&MAKE_OROG_TN;_task_complete.txt' | ||
| streq: | ||
| left: '&RUN_TASK_MAKE_OROG;' | ||
| right: 'FALSE' | ||
| or_sfc_climo: | ||
| datadep_complete: | ||
| attrs: | ||
| age: 00:00:00:05 | ||
| text: '&LOGDIR;/&MAKE_SFC_CLIMO_TN;_task_complete.txt' | ||
| streq: | ||
| left: '&RUN_TASK_MAKE_SFC_CLIMO;' | ||
| right: 'FALSE' |
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I think this is neat! If I understand correctly, every tag in the dependency dictionary is accounted for recursively, and is split with the first hyphen to get the corresponding rocoto tag, then form the xml statement using additional attributes.
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That's right.
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| datadep_dyn: | ||
| text: !cycstr {value: '&CYCLE_BASEDIR;/@Y@m@d@H/dynf#fhr#.nc'} | ||
| attrs: | ||
| age: '05:00' | ||
| datadep_phy: | ||
| text: !cycstr {value: '&CYCLE_BASEDIR;/@Y@m@d@H/phyf#fhr#.nc'} | ||
| attrs: | ||
| age: '05:00' |
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Is the second part of datadep_dyn/phys/complete etc parsed and used ? I am assuming reason why it is not just datadep is for the readablity of the yaml file?
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It is not used. It's partially for readability, but also because you can't have repeated keys in the dict.
* Workflow in python starting to work. * Use new python_utils package structure. * Some bug fixes. * Use uppercase TRUE/FALSE in var_dfns * Use config.sh by default. * Minor bug fixes. * Remove config.yaml * Update to the latest develop * Remove quotes from numbers in predef grid. * Minor bug fix. * Move validity checker to the bottom of setup * Add more unit tests. * Update with python_utils changes. * Update to latest develop additions (Need to re-run regression test) * Use set_namelist and fill_jinja_template as python functions. * Replace sed regex searches with python re. * Use python realpath. * Construct settings as dictionary before passing to fill_jinja and set_namelist * Use yaml for setting predefined grid parameters. * Use xml parser for ccpp phys suite definition file. * Remove more run_command calls. * Simplify some func argument processing. * Move different config format parsers to same file. * Use os.path.join for the sake of macosx * Remove remaining func argument processing via os.environ. * Minor bug fix in set_extrn_mdl_params.sh * Add suite defn in test_data. * Minor fixes on unittest on jet. * Simplify boolean condition checks. * Include old in renaming of old directories * Fix conflicting yaml !join tag for paths and strings. * Bug fix with setting sfcperst dict. * Imitate "readlink -m" with os.path.realpath instead of os.readlink * Don't use /tmp as that is shared by multiple users. * Bug fix with cron line, maintain quotes around TRUE/FALSE. * Update to latest develop (untested) * Bug fix with existing cron line and quotes. * Bug fix with case-sensitive MACHINE name, and empty EXPT_DIR. * Update to latest develop * More updates. * Bug fix thanks to @willmayfield! Check both starting/ending characters are brackets for shell variable to be considered an array. * Make empty EXPT_BASEDIR workable. * Update to latest develop * Update in predef grid. * Check f90nml as well. Co-authored-by: Daniel Abdi <[email protected]>
…fs-community#750) * Fix typo and failure on wcoss * fix new line issue on wcoss dell * remove capture_output * Get USER from environment Co-authored-by: Daniel Abdi <[email protected]>
## DESCRIPTION OF CHANGES: Added two new WE2E config files for the Sub-CONUS Indianapolis domain to support the upcoming SRW release. In addition, modified the external data used in the `config.specify_EXTRN_MDL_SYSBASEDIR_ICS_LBCS.sh` to match more common datasets used in the WE2E testing process. ## TESTS CONDUCTED: Successfully ran the new WE2E tests (`config.SUBCONUS_Ind_3km_ics_HRRR_lbcs_RAP_suite_HRRR.sh`, `config.SUBCONUS_Ind_3km_ics_HRRR_lbcs_RAP_suite_RRFS_v1beta.sh`) and `config.specify_EXTRN_MDL_SYSBASEDIR_ICS_LBCS.sh` on NOAA Parallel Works AWS instance. ## DEPENDENCIES: None. ## DOCUMENTATION: No documentation changes are required.
…ponent parameters (ufs-community#733) * Added a fixed WoF grid and the python tool to determine the write component parameters * Update set_predef_grid_params.sh * Renamed file as recommended and removed unused lines * Modified comment Co-authored-by: JeffBeck-NOAA <[email protected]> Co-authored-by: WYH@MBP <[email protected]>
* change env to mod * update we2e script
## DESCRIPTION OF CHANGES: * Modifications to `run_WE2E_tests.sh`: * Add examples to help/usage statement * Modifications to `check_expts_status.sh`: * Add arguments list that can be processed by `process_args` * Add new optional arguments: `num_log_lines`, `verbose` * Include a help/usage message ## TESTS CONDUCTED: * Ran `run_WE2E_tests.sh --help` from the command line and got the expected help message. * Ran `check_expts_status.sh --help` from the command line and got the expected help message. * Used `run_WE2E_tests.sh` to run a set of 2 WE2E tests -- works as expected. * Used `check_expts_status` to check on the status of the 2 tests run above and got the expected status message. ## DEPENDENCIES: PR #[241](ufs-community/ufs-srweather-app#241) ## DOCUMENTATION: A lot of this PR is documentation in the scripts. There is an accompanying documentation PR #[241](ufs-community/ufs-srweather-app#241) into ufs-srweather-app.
…nd LBC data retrieval (ufs-community#744)
…community#756) ## DESCRIPTION OF CHANGES: 1) Adjust y-direction size of write-component grid of `SUBCONUS_Ind_3km` predefined grid from 195 to 197 (this was just an oversight in PR ufs-community#725 ). 2) Redirect output of module load in launch script (`launch_FV3LAM_wflow.sh`) to `/dev/null` to avoid unwanted screen output (which was introduced in PR #[238](ufs-community/ufs-srweather-app#238) in ufs-srweather-app and is about how to load the `regional_workflow` environment and is not relevant in this context). ## TESTS CONDUCTED: 1) Plotted the `SUBCONUS_Ind_3km` grid to ensure it has correct size (it does). 2) Manually ran `launch_FV3LAM_wflow.sh` from the command line to verify that screen output is suppressed (it is).
…lues (ufs-community#759) * Modify RRFS North America 3- and 13-km domain configuration and WE2E test. * Modify default ISEED values for SPP * Fix grid in WE2E test
* update python scripts
…ity#758) * change output file name * change variable name * update python script * remove duplicates * add a check for empty variables * move variable to common area * clean up unnecessary comments * update scripts * remove duplicate * update python scripts * fix user-staged dir path issue in python script
…y#763) * Add new var to we2e tests for new grids * rename we2e tests for custom grid * remove unnecessary $
* Add @gspetro-NOAA, @natalie-perlin, and @EdwardSnyder-NOAA to CODEOWNERS so they are notified of all PRs and can review them. * Remove duplicates in CODEOWNERS; remove users who will no longer be working with the repo.
Adds a utility that summarizes Rocoto database computational usage information.
* Add github actions for python unittests. * Include all python script in ush * Skip defining QUILTING params when it is set to False * Update py_workflow * Update unittest for set_extrn_mdl_params. * Updates from develop. Co-authored-by: Daniel Shawul <[email protected]>
* update config.nco.sh * Add comment
* updates for noaacloud * working version * fixes for noaacloud * added extra modules for post
Pin down the version of miniconda3 on Hera, and do not append to the module path.
…unity#766) * update IC/LBC file paths to match new IC/LBC file structure * change forecast length * Update config.community.sh These changes reflects the SRW team's preference for a 12-hours forecast. The gfs.t18z.pgrb2.0p25.f012 file will need to be added to all Level 1 systems. Co-authored-by: Gillian Petro <[email protected]>
Co-authored-by: Natalie Perlin <[email protected]>
…2E test info (ufs-community#776) ## DESCRIPTION OF CHANGES: This PR modifies the script `get_WE2Etest_names_subdirs_descs.sh` that creates the CSV file containing test information the columns for relative cost and time step (`DT_ATMOS`). This allows users to have a better idea of what the cost of each test is (the relative cost is defined such that 1 unit represents the cost of running a single 6-hour forecast on the `RRFS_CONUS_25km` grid). Other related changes: * Add the flag `generate_csv_file` to the `run_WE2E_tests.sh` script to allow users to skip the CSV file generation step (since it can take a while). * Use arguments for the function `set_predef_grid_params()` so that it can be called not just from the experiment generation scripts but also others (in this case from `get_WE2Etest_names_subdirs_descs.sh`). Necessary for this PR. * Move some constants (`NH0`, `NH3`, `NH4`) from `config_defaults.sh` to `constants.sh` to make it easier to access them. * Place the contents of `constants.sh` at the start of each experiment's `var_defns.sh` so that these constants are available to the j-jobs and ex-scripts when `var_defns.sh` is sourced. * Use variable `valid_vals_BOOLEAN` in many more places (which allows many other `valid_vals_...` variables in `valid_param_vals.sh` and `setup.sh` to be removed). * Several other bug fixes. ## TESTS CONDUCTED: The following tests (with results) were conducted on Hera. There were only three (previously existing) failures. ``` * grid_CONUS_25km_GFDLgrid_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16: SUCCESS * grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_2017_gfdlmp: SUCCESS * grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_2017_gfdlmp_regional: SUCCESS * grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v15p2: SUCCESS * grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16: SUCCESS * grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_RAP_suite_HRRR: SUCCESS * grid_RRFS_CONUS_25km_ics_GSMGFS_lbcs_GSMGFS_suite_GFS_2017_gfdlmp: SUCCESS * grid_RRFS_CONUS_25km_ics_GSMGFS_lbcs_GSMGFS_suite_GFS_v15p2: SUCCESS * grid_RRFS_CONUS_25km_ics_GSMGFS_lbcs_GSMGFS_suite_GFS_v16: FAILURE * grid_RRFS_CONUS_25km_ics_NAM_lbcs_NAM_suite_HRRR: SUCCESS * grid_RRFS_CONUS_25km_ics_NAM_lbcs_NAM_suite_RRFS_v1beta: SUCCESS * grid_RRFS_CONUScompact_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16: SUCCESS * grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_HRRR_suite_HRRR: SUCCESS * grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_HRRR_suite_RRFS_v1beta: SUCCESS * grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_RAP_suite_HRRR: SUCCESS * grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_RAP_suite_RRFS_v1alpha: SUCCESS * grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_RAP_suite_RRFS_v1beta: SUCCESS * grid_SUBCONUS_Ind_3km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16: SUCCESS * grid_SUBCONUS_Ind_3km_ics_HRRR_lbcs_RAP_suite_HRRR: SUCCESS * grid_SUBCONUS_Ind_3km_ics_HRRR_lbcs_RAP_suite_RRFS_v1beta: SUCCESS * GST_release_public_v1: SUCCESS * MET_ensemble_verification: SUCCESS * MET_verification: SUCCESS * community_ensemble_008mems: SUCCESS * community_ensemble_2mems: SUCCESS * custom_ESGgrid: SUCCESS * custom_GFDLgrid: SUCCESS * custom_GFDLgrid__GFDLgrid_USE_GFDLgrid_RES_IN_FILENAMES_eq_FALSE: SUCCESS * custom_GFDLgrid__GFDLgrid_USE_GFDLgrid_RES_IN_FILENAMES_eq_TRUE: SUCCESS * deactivate_tasks: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_grib2_2019061200: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_grib2_2019101818: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_grib2_2020022518: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_grib2_2020022600: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_grib2_2021010100: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_nemsio: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_nemsio_2019061200: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_nemsio_2019101818: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_nemsio_2020022518: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_nemsio_2020022600: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_nemsio_2021010100: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_netcdf_2021062000: SUCCESS * get_from_HPSS_ics_GSMGFS_lbcs_GSMGFS: SUCCESS * get_from_HPSS_ics_HRRR_lbcs_RAP: SUCCESS * get_from_HPSS_ics_RAP_lbcs_RAP: SUCCESS * get_from_NOMADS_ics_FV3GFS_lbcs_FV3GFS_fmt_nemsio: SUCCESS * inline_post: SUCCESS * nco_ensemble: SUCCESS * nco_inline_post: SUCCESS * pregen_grid_orog_sfc_climo: SUCCESS * specify_DOT_OR_USCORE: SUCCESS * specify_DT_ATMOS_LAYOUT_XY_BLOCKSIZE: SUCCESS * specify_EXTRN_MDL_SYSBASEDIR_ICS_LBCS: SUCCESS * specify_RESTART_INTERVAL: SUCCESS * specify_template_filenames: SUCCESS * subhourly_post: FAILURE * subhourly_post_ensemble_2mems: FAILURE ``` ## DOCUMENTATION: Documentation is updated via PR #[278](ufs-community/ufs-srweather-app#278) in the ``ufs-srweather-app`` repo.
ufs-community#782) ## DESCRIPTION OF CHANGES: This PR fixes a bug in the way the number of time steps (`num_time_steps` in `get_WE2Etest_names_subdirs_descs.sh`) is calculated for each WE2E test when creating the CSV file containing information about the available WE2E tests. ## TESTS CONDUCTED: Reran the `run_WE2E_tests.sh` script (which in turn calls `get_WE2Etest_names_subdirs_descs.sh`), and a CSV file containing the adjusted numbers was successfully created. ## DOCUMENTATION: None needed.
## DESCRIPTION OF CHANGES: PR #[763](ufs-community#763) introduced the experiment variable `POST_OUTPUT_DOMAIN_NAME` and used it to modify the names of the UPP output files. This PR adds `POST_OUTPUT_DOMAIN_NAME` as an argument to the python plotting scripts to enable those scripts to form the proper UPP output file names to read in. It also modifies the batch scripts (`qsub_job.sh`, `qsub_job_diff.sh`, `sq_job.sh`, and `sq_job_diff.sh`) to add the new argument to the calls to the python plotting scripts that are called. ## TESTS CONDUCTED: Both python plotting scripts `plot_allvars.py` and `plot_allvars_diff.py` were run on Hera on preexisting UPP output files and completed successfully. The batch scripts `sq_job.sh` and `sq_job_diff.sh` were also run successfully on Hera (`qsub_job.sh` and `qsub_job_diff.sh` were not run on e.g. Cheyenne). ## DEPENDENCIES: PR # in `ufs-srweather-app`. ## DOCUMENTATION: Modifications to the documentation are in PR #. ## ISSUE: Partially resolves issue ufs-community#781 (still need to introduce tests in `regional_workflow` that run the plotting scripts). ## CONTRIBUTORS: @mark-a-potts pointed out the problem and first made the necessary fixes in the `NOAA-EPIC` fork of `regional_workflow`; @gsketefian introduced those changes to this PR and made edits to the comments and documentation.
…fs-community#775) * update input namelist of chgres_cube * update diag_table templates * update scripts * back to original * specify miniconda version on Jet
…odel (ufs-community#796) * update new variables introduced in uwm * update python script * update template for HRRR suite
…mmunity#779) * remove unused module loads for MET * update met version in machine files * changes to pointstat/pb2nc bufr mapping * add NA to retain bufr variables without qc markers * updated bufr variable list * change bufr var list * Change versions to MET 10.1.1 and METplus 4.1.1
…munity#803) Co-authored-by: Natalie Perlin <[email protected]>
…ity#787) ## DESCRIPTION OF CHANGES: For clarity, rename variables related to GFDLgrid-type grids: 1) Rename `GFDLgrid_RES` to `GFDLgrid_NUM_CELLS`. 2) Rename `GFDLgrid_USE_GFDLgrid_RES_IN_FILENAMES` to `GFDLgrid_USE_NUM_CELLS_IN_FILENAMES`. 3) Rename WE2E tests on GFDLgrid-type custom grids according to variable renaming above. Related improvements: * In `link_fix.sh`, remove creation of unnecessary symlink when using a GFDLgrid-type grid with `GFDLgrid_USE_NUM_CELLS_IN_FILENAMES` is set to `"FALSE"`. * In WE2E test configuration files that use custom grids, move the definition of the variable `POST_OUTPUT_DOMAIN_NAME` to the beginning of the custom grid definition because it is really the name of the custom native grid, and it's most appropriate to place that at the beginning of the grid definition section. * Reduce `WTIME_MAKE_OROG` from 1 hour to 20 minutes since on Hera, 1 hour causes the task to wait quite a while in the queue. This used to be 20 minutes but was changed to 1 hour because 20 minutes was not sufficient to complete the task on `WCOSS_DELL_P3`. Thus, reset it to 1 hour only in the machine file for `WCOSS_DELL_P3`. * Minor fixes to comments in python plotting scripts. * Edits to other comments. ## TESTS CONDUCTED: Ran the four WE2E tests that use custom grids (listed below) on Hera. All were successful. * `custom_ESGgrid` * `custom_GFDLgrid` * `custom_GFDLgrid__GFDLgrid_USE_NUM_CELLS_IN_FILENAMES_eq_FALSE` (previously `custom_GFDLgrid__GFDLgrid_USE_GFDLgrid_RES_IN_FILENAMES_eq_FALSE`) * `custom_GFDLgrid__GFDLgrid_USE_NUM_CELLS_IN_FILENAMES_eq_TRUE` (previously `custom_GFDLgrid__GFDLgrid_USE_GFDLgrid_RES_IN_FILENAMES_eq_TRUE`) ## DEPENDENCIES: PR #[310](ufs-community/ufs-srweather-app#310) in `ufs-srweather-app`. ## DOCUMENTATION: Updates to documentation are in PR #[310](ufs-community/ufs-srweather-app#310) in `ufs-srweather-app`.
This is a bug fix for running the WE2E tests on Hera. The non-existence of this path is causing failures after the path has become unreadable.
* add metplus paths * add run_vx.local for jet Co-authored-by: Edward Snyder <[email protected]>
hu5970
requested review from
AmandaBack-NOAA
and removed request for
robgpita and
AmandaBack-NOAA
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DESCRIPTION OF CHANGES:
Here I've added an xml_generator Python utility that will take in YAML files and write an XML. I have not yet documented the tool thoroughly, but wanted to get a bit of feedback from reviewers on the design ideas/concepts.
TESTS CONDUCTED:
I have run the following command to "eyeball" the output format that it looks as I'd expect.
python xml_creator.py -c ./templates/rrfs_example.yml -o ./example_workflow.xmlDEPENDENCIES:
This will require Python v 3.9 to run. And I can follow up with a conda environment definition if needed to help you run this on your own.
DOCUMENTATION:
TBD