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* Store change of sonar.login to sonar.token. * Hotfix to develop, updating aclocal.m4 and config.h.in to what is created when running bootstrap inside the dtcenter/met-base:v3.1 Docker image. Updates autoconf 2.69 output to 2.71. * Adding -lnetcdf to configure_lib_args for NetCDF-CXX compilation * Added eckit and atlas loads and paths * Added atlas and eckit loads and paths * Changing -j to "-j 5" as the recommended value * Update ensemble-stat.rst Fixed incorrect path to obs error table * Updated values for GRIB2CLIB_NAME and BUFRLIB_NAME * Updated for proj, eckit, and atlas * Feature #2761 develop seneca (#2762) * Per #2761, define runtime python version for testing rather than using the default version which no longer exists in /usr/local * Per #2761, fix setting ci-skip-all * Per #2761, patching test_util.R to use the -C command line option for ncdiff. I did test running comp_dir.sh with this change and confirmed that it now runs to completion. * #2652 Added find_var_by_standard_name and separated common codes to find_xy_vars * #2757 Get the email list from the environment variable MET_CRON_EMAIL_LIST__MET (or MET_CRON_EMAIL_LIST_) * #2757 THe SonarQube token and URL are replaced by ujsing the environment variable SONAR_TOKEN_VALUE and SONAR_SERVER_URL * #2757 The SonarQube token and URL are replaced with the pre-defined strings, SONAR_TOKEN_VALUE and SONAR_SERVER_URL * Bugfix #2670 develop --enable-python (#2768) * Update install_met_env.acorn_py3.10 * Update install_met_env.wcoss2_py3.10 * Feature #2776 cleanup (#2777) * Per #2776, delete stale prob_pair_info.h/.cc, wwmca_utils.h/.cc, and rmw_analysis_utils.h/.cc files that were not being compiled by their Makefiles. * Per #2776, update Makefile to compile the test_read_rmw utility. * Per #2776, add Makefile for the vx_python3_utils test utility directory. * add rpath for atlas and eckit lib dirs so dynamic libraries can be found when running on seneca * only set -L and -I arguments for atlas and eckit if the appropriate environment variable is set -- this matches how it is handled for other external library dependencies * Per #2776, just whitespace and capitalization --------- Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Bugfix #2782 develop MASSDEN (#2783) * Per #2782, port over fixes from the bugfix_2782_main_v11.1_MASSDEN branch over to the bugfix branch for develop. Will also add new GRIB2 filtering options in this branch. * Per #2782, add support for 4 new GRIB2 filtering options for GRIB2_aerosol_type, GRIB2_aerosol_interval_type, GRIB2_aerosol_size_lower, and GRIB2_aerosol_size_upper. These are useful in filtering the MASSDEN records in the RRFS smoke output files. * Per #2782, fix aerosol_size_lower() and aersol_size_upper() inline definitions. * Per #2782, add a unit test for GRIB2 table 4.48. * Per #2782, switch from strict equality to using the is_eq() function when checking the GRIB2_aerosol_size_lower and upper values since they're doubles and not ints. * Feature #2701 ismn (#2758) * Add support for ISMN soil moisture data * Per #2701, update ascii2nc.cc with the ismn file option. * Per #2701, update ascii2nc docs * Per #2701, store the depth for precip as 0. * Per #2701, parse the ISMN observation value from the correct column. * Per #2701, every time I run ascii2nc to I see a log message for 'DEBUG 1: Number of NDBC skipped files due to no lookup 0'. This is printed by the NdbcHandler destructor. Update the logic to only print a debug level 3 log message when the number of missing locations is greater than 0, 'DEBUG 3: Skipped 5 NDBC files whose locations are not defined in 'MET_BASE/table_files/ndbc_stations.xml'. Set the MET_NDBC_STATIONS environment variable to override this file.' * Per #2701, as instructed by @anewman89, store the average of the depth values rather than the maximum value. * Per #2701, add a test of processing the ISMN data through ascii2nc. * Per #2701, fix parsing of year and month to subtract 1900 and 1, respectively. * Per #2701, set use_var_id to true for ISMN inputs * Per #2701, even though we're mapping obs data to GRIB code names and units, we want to encode them with use_var_id = true and so we need to keep track of those var_id values. * Per #2701, fix typo in the name of the ascii2nc netcdf output file. --------- Co-authored-by: MET Tools Test Account <met_test@seneca.rap.ucar.edu> * Feature 2753 comp script config (#2771) * set dynamic library file extension to .dylib if running on MacOS and .so otherwise * Added disabling of jasper documentation for compiliation on Hera * Updated * remove extra export of compiler env vars * include full path to log file so it is easier to file the log file to examine when a command fails * send cmake output to a log file * remove redundant semi-colon * use full path to log file so it is easier to examine on failure * use run_cmd to catch if rm command fails * Modifications for compilation on hera, gaea, and orion * Updating * fixed variable name * clean up if/else statements * set TIFF_LIBRARY_RELEASE argument to use full path to dynamic library file to prevent failure installing proj library * set LDFLAGS so that LDFLAGS value set in the user's environment will also be used * Updated based on gaea, orion, and hera installs * Updated * change extension of dynamic library files only if architecture is arm64 because older Macs still use .so * added netcdf library to args to prevent error installing NetCDF-CXX when PROJ has been installed in the same run of the script -- PATH is set in the COMPILE_PROJ if block that causes this flag from being added automatically * clean up how rpath and -L are added to LDFLAGS so that each entry is separate -- prevents errors installing on Mac arm64 because multiple rpath values aren't read using :. Also use MET_PROJLIB * Updated * removed -ltiff from MET libs * only add path to rpath and -L arguments if they are not already included in LDFLAGS * changed from using LIB_TIFF (full path to tiff lib file) to use TIFF_LIB_DIR (dir containing tiff lib file). Added TIFF_INCLUDE_DIR to proj compilation and -DJAS_ENABLE_DOC to jasper compliation taken from @jprestop branch * update comments * ensure all MET_* and MET_*LIB variables are added to the rpath for consistency * remove unnecessary if block and only export LDFLAGS at the end of setting locally * Updated * Added section for adding <VALUE>/lib64 and rearranged placement of ADDTL_DIR * Commenting out the running of the Jasper lib tests * Updating and/or removing files * Updating and/or removing files * Latest udpates which include the addition of the tiff library for proj * Remove commented out line. Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Make indentation consistent. Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Make indentation consistent. Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Make indentation consistent. Co-authored-by: John Halley Gotway <johnhg@ucar.edu> --------- Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Removing ${MAKE_ARGS} in some locations Removing ${MAKE_ARGS} from "make install" and "make test" for MET. Removing "met" prefix from met.configure.log because we really need config.log for any detail. It is confusing to have met.configure.log when that does not contain useful information. * Feature #2547 Read WRF output files natively (#2790) * Per #2547, add the file_type = NETCDF_WRF configuration option. * Per #2547, rename vx_data2d_nc_interp as vx_data2d_nc_wrf and vx_data2d_nccf as vx_data2d_nc_cf. * Per #2547, rename nccf files as nc_cf for consistency throughout * Per #2547, rename Pinterp classes as Wrf * only set -L and -I arguments for atlas and eckit if the appropriate environment variable is set -- this matches how it is handled for other external library dependencies * add rpath for atlas and eckit lib dirs so dynamic libraries can be found when running on seneca * ignore directory automatically created by CLion * rename pinterp variables and classes to Wrf * more rename and fix typos * per #2547, add support for reading WRF files by adding support for different X/Y/Z dimensions, read X/Y/Z dimension names when reading a field instead of storing them per file, track if data is staggered in X/Y/Z dimension (still need to add DataPlane function to destagger data), handle pressure field that also includes time dimension * per #2547, add DataPlane function to handle staggering of grid * per #2547, change file type returned from pinterp to wrf * per #2547, call function to stagger DataPlane if necessary * per #2547, keep store if variable is on pressure levels and only read pressure field if it is * ignore cmake directory * per #2547, support U_PL, U_ZL, U, and U<x> where <x> is an integer in is_u_wind and the same for is_v_wind * change regex to match zero or more instances of a number after U or V instead of 1 or more to include the fields named U and V * error and exit if var with unsupported subgrid dimension is processed * clean up logging * only destagger Z dimension for bottom_top_stag because other _stag Z dimensions don't need to be destaggered, clean up logic to read X/Y/Z dimension info * Per #2547, instead of checking dimensions of all vars in file, check dimensions for the var that is being read. Only read pressure var if the z dimension matches the var to read. Set class variable DimNames instead of local gDimNames so dump function will work as expected * per #2547, support reading variable that corresponds to dimension with different name as dimension and includes a time dimension, e.g. P_PL(Time, num_press_levels_stag) * per #2547, added unit tests to process WRF out data with plot_data_plane and grid_stat * merged develop and resolved conflicts * rename lib from pinterp to wrf * rename lib * fixed incorrect merge changes * fixed broken unit test format * Per #2547, restore the mention of NAK.poly to Appendix B. * Change model to WRF Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * change obtype to WRF Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * plot higher vertical level to get non-zero output Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * indentation Co-authored-by: John Halley Gotway <johnhg@ucar.edu> --------- Co-authored-by: John Halley Gotway <johnhg@ucar.edu> --------- Co-authored-by: MET Tools Test Account <met_test@seneca.rap.ucar.edu> Co-authored-by: root <root@83062d57c5dd> Co-authored-by: Julie Prestopnik <jpresto@ucar.edu> Co-authored-by: Christina Kalb <kalb@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> Co-authored-by: Howard Soh <hsoh@seneca.rap.ucar.edu> Co-authored-by: Howard Soh <hsoh@ucar.edu> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: metplus-bot <97135045+metplus-bot@users.noreply.github.com>
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