investigate RT for met_help #2

dwfncar · 2009-08-17T22:40:16Z

Randy will check into RT since we may use it for our ticketing system
[MET-2] created by tressa

* testing new anchoring link idea. * testing without the bold asterik * tinkering with the look * another attempt * another attempt #2 * another attempt #3 * another attempt #4 * making sure new anchor works as expected. * seeing if link will save with spaces instead of dashes * need underscores to link * is it fixed? * testing * testing 2 * testing 4 * testing 5 * testing 6 * testing 7 * testing 8 * going back to test original problem * able to link with spaces instead of underscores. Testing if a return is possible to keep under 79 character limit. * double checking everything is still working. * DO NOT break ref lines apart, it won't work. * trying a shorter name. * continuing to add anchors * updating lines 1946 thru 2214 with anchors * updating lines 2214 thru 3371 with anchors * updating lines 3371 to the end with anchors * testing anchor * testing anchor * testing anchor 3 * testing anchor 4 * testing anchor 45 percent * testing anchor final half * fixing typo * numbering fcst, obs_1 and 2 to create different links. * finding more anchors that need numbers to keep them separate. * fixing warnings * fixing warnings * fixing typo

* Start on write netcdf pickle alternative. * Write dataplane array. * Start on read of netcdf as pickle alternative. * Create attribute variables. * Use global attributes for met_info attrs. * Add grid structure. * Read metadata back into met_info.attrs. * Convert grid.nx and grid.ny to int. * Rename _name key to name. * Removed pickle write. * Fixed write_pickle_dataplane to work for both numpy and xarray. * Use items() to iterate of key, value attrs. * Write temporary text file. * Renamed scripts. * Changed script names in Makefile.am. * Replaced pickle with tmp_nc. * Fixed wrapper script names. * Test for attrs in met_in.met_data. * Initial version of read_tmp_point module. * Added read_tmp_point.py to install list. * Start on Python3_Script::read_tmp_point. * Write MPR tmp ascii file. * Renamed to read_tmp_ascii to use for point point and MPR. * Renamed to read_tmp_ascii to use for point point and MPR. * Define Python3_Script::import_read_tmp_ascii_py. * Call Python3_Script::import_read_tmp_ascii_py. * Append MET_BASE/wrappers to sys.path. * Finished implementation of Python3_Script::import_read_tmp_ascii_py. * Call Python3_Script::read_tmp_ascii in python_handler. * Revised python3_script::read_tmp_ascii with call to run, PyRun_String. * Return PyObject* from Python3_Script::run. * Restored call to run_python_string for now. * Per #1429, enhance error message from DataLine::get_item(). (#1682) * Feature 1429 tc_log second try (#1686) * Per #1429, enhance error message from DataLine::get_item(). * Per #1429, I realize that the line number actually is readily available in the DataLine class... so include it in the error message. * Feature 1588 ps_log (#1687) * Per #1588, updated pair_data_point.h/.cc to add detailed Debug(4) log messages, as specified in the GitHub issue. Do still need to test each of these cases to confirm that the log messages look good. * Per #1588, switch very detailed interpolation details from debug level 4 to 5. * Per #1588, remove the Debug(4) log message about duplicate obs since it's been moved up to a higher level. * Per #1588, add/update detailed log messages when processing point observations for bad data, off the grid, bad topo, big topo diffs, bad fcst value, and duplicate obs. * #1454 Disabled plot_data_plane_CESM_SSMI_microwave and plot_data_plane_CESM_sea_ice_nc becaues of not evenly spaced * #1454 Moved NC attribute name to nc_utils.h * #1454 Corrected sanity checking for lat/lon projection based on the percentage of the delta instead of fixed tolerance * #1454 Corrected sanity checking for lat/lon projection based on the percentage of the delta instead of fixed tolerance * #1454 Corrected data.delta_lon * #1454 Change bact to use diff instead of absolute value of diff * 454 Deleted instea dof commenting out * 454 Deleted instea dof commenting out * Feature 1684 bss and 1685 single reference model (#1689) * Per #1684, move an instance of the ClimoCDFInfo class into PairBase. Also define derive_climo_vals() and derive_climo_prob() utility functions. * Add to VxPairDataPoint and VxPairDataEnsemble functions to set the ClimoCDFInfo class. * Per #1684, update ensemble_stat and point_stat to set the ClimoCDFInfo object based on the contents of the config file. * Per #1684, update the vx_statistics library and stat_analysis to make calls to the new derive_climo_vals() and derive_climo_prob() functions. * Per #1684, since cdf_info is a member of PairBase class, need to handle it in the PairDataPoint and PairDataEnsemble assignment and subsetting logic. * Per #1684, during development, I ran across and then updated this log message. * Per #1684, working on log messages and figured that the regridding climo data should be moved from Debug(1) to at least Debug(2). * Per #1684 and #1685, update the logic for the derive_climo_vals() utility function. If only a single climo bin is requested, just return the climo mean. Otherwise, sample the requested number of values. * Per #1684, just fixing the format of this log message. * Per #1684, add a STATLine::get_offset() member function. * Per #1684, update parse_orank_line() logic. Rather than calling NumArray::clear() call NumArray::erase() to preserve allocated memory. Also, instead of parsing ensemble member values by column name, parse them by offset number. * Per #1684, call EnsemblePairData::extend() when parsing ORANK data to allocate one block of memory instead of bunches of litte ones. * Per #1684 and #1685, add another call to Ensemble-Stat to test computing the CRPSCL_EMP from a single climo mean instead of using the full climo distribution. * Per #1684 and #1685, update ensemble-stat docs about computing CRPSS_EMP relative to a single reference model. * Per #1684, need to update Grid-Stat to store the climo cdf info in the PairDataPoint objects. * Per #1684, remove debug print statements. * Per #1684, need to set cdf_info when aggregating MPR lines in Stat-Analysis. * Per #1684 and #1685, update PairDataEnsemble::compute_pair_vals() to print a log message indicating the climo data being used as reference: For a climo distribution defined by mean and stdev: DEBUG 3: Computing ensemble statistics relative to a 9-member climatological ensemble. For a single deterministic reference: DEBUG 3: Computing ensemble statistics relative to the climatological mean. * Per #1691, add met-10.0.0-beta4 release notes. (#1692) * Updated Python documentation * Per #1694, add VarInfo::magic_str_attr() to construct a field summary string from the name_attr() and level_attr() functions. * Per #1694, fixing 2 issues here. There was a bug in the computation of the max value. Had a less-than sign that should have been greater-than. Also, switch from tracking data by it's magic_str() to simply using VAR_i and VAR_j strings. We *could* have just used the i, j integers directly, but constructing the ij joint histogram integer could have been tricky since we start numbering with 0 instead of 1. i=0, j=1 would result in 01 which is the same as integer of 1. If we do want to switch to integers, we just need to make them 1-based and add +1 all over the place. * Per #1694, just switching to consistent variable name. * Just consistent spacing. * Added python3_script::import_read_tmp_ascii. * Restored read_tmp_ascii call. * Added lookup into ascii module. * Adding files for ReadTheDocs * Adding .yaml file for ReadTheDocs * Updated path to requirements.txt file * Updated path to conf.py file * Removing ReadTheDocs files and working in separate branch * Return PyObject* from read_tmp_ascii. * Put point_data in global namespace. * Remove temporary ascii file. * Added tmp_ascii_path. * Removed read_obs_from_pickle. * Trying different options for formats (#1702) * Per #1706, add bugfix to the develop branch. Also add a new job to unit_stat_analysis.xml to test out the aggregation of the ECNT line type. This will add new unit test output and cause the NB to fail. (#1708) * Feature 1471 python_grid (#1704) * Per #1471, defined a parse_grid_string() function in the vx_statistics library and then updated vx_data2d_python to call that function. However, this creates a circular dependency because vx_data2d_python now depends on vx_statistics. * Per #1471, because of the change in dependencies, I had to modify many, many Makefile.am files to link to the -lvx_statistics after -lvx_data2d_python. This is not great, but I didn't find a better solution. * Per #1471, add a sanity check to make sure the grid and data dimensions actually match. * Per #1471, add 3 new unit tests to demonstrate setting the python grid as a named grid, grid specification string, or a gridded data file. * Per #1471, document python grid changes in appendix F. * Per #1471, just spacing. * Per #1471, lots of Makefile.am changes to get this code to compile on kiowa. Worringly, it compiled and linked fine on my Mac laptop but not on kiowa. Must be some large differences in the linker logic. Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> * Committing a fix for unit_python.xml directly to the develop branch. We referenced in a place where it's not defined. * Add *.dSYM to the .gitignore files in the src and internal_tests directories. * Replaced tmp netcdf _name attribute with name_str. * Append user script path to system path. * Revert "Feature 1319 no pickle" (#1717) * Fixed typos, added content, and modified release date format * #1715 Initial release * #1715 Do not combined if there are no overlapping beteewn TQZ and UV records * #1715 Added pb2nc_compute_pbl_cape * #1715 Added pb2nc_compute_pbl_cape * #1715 Reduced obs_bufr_var. Removed pb_report_type * #1715 Added a blank line for Error/Warning * Per #1725, return good status from TrackInfoArray::add() when using an ATCF line to create a new track. (#1726) * Per #1705, update the threshold node heirarchy by adding a climo_prob() function to determine the climatological probability of a CDP-type threshold. Also update derive_climo_prob() in pair_base.cc to call the new climo_prob() function. (#1724) * Bugfix 1716 develop perc_thresh (#1722) * Per #1716, committing changes from Randy Bullock to support floating point percentile thresholds. * Per #1716, no code changes, just consistent formatting. * Per #1716, change SFP50 example to SFP33.3 to show an example of using floating point percentile values. * Update pull_request_template.md * Feature 1733 exc (#1734) * Per #1733, add column_exc_name, column_exc_val, init_exc_name, and init_exc_val options to the TCStat config files. * Per #1733, enhance tc_stat to support the column_exc and init_exc config file and job command filtering options. * Per #1733, update stat_analysis to support the -column_exc job filtering option. Still need to update docuementation and add unit tests. * Per #1773, update the user's guide with the new config and job command options. * Per #1733, add call to stat_analysis to exercise -column_str and -column_exc options. * Per #1733, I ran into a namespace conflict in tc_stat where -init_exc was used for to filter by time AND my string value. So I switched to using -init_str_exc instead. And made the corresponding change to -column_str_exc in stat_analysis and tc_stat. Also changed internal variable names to use IncMap and ExcMap to keep the logic clear. * Per #1733, tc_stat config file updates to switch from column_exc and init_exc to column_str_exc and init_str_exc. * Per #1733, add tc_stat and stat_analysis jobs to exercise the string filtering options. * Bugfix 1737 develop little_r (#1739) * Per #1737, migrate the same fix from main_v9.1 over to the develop branch. * Per #1737, add another unit test for running ascii2nc with corrupt littl_r records. * Feature GitHub actions (#1742) * Adding files to build documenation via GitHub Actions * Removing html_theme_options * Removed warnings.log from help section * Feature 1575 large_diffs (#1741) * Per #1575, add mpr_column and mpr_thresh entries to all of the Grid-Stat and Point-Stat config files. * Per #1575, define config strings to be parsed from the config files. * Per #1575, store col_name_ptr and col_thresh_ptr in PairBase. They are being used for PairDataPoint to do MPR filtering in Grid-Stat and Point-Stat. But they could be eventually be extended to filter ORANK columns for Ensemble-Stat. * Per #1575, add MPR filtering logic to pair_data_point.cc. Include filtering logic in PairDataPoint instead of VxPairDataPoint since Grid-Stat uses PairDataPoint. * Per #1575, update point_stat to parse the mpr_column and mpr_thresh config file options. Include the MPR rejection reason code counts in the log output. * Per #1575, updated Grid-Stat to parse mpr_column and mpr_thresh options. * Per #1575, update Point-Stat to store mpr_sa and mpr_ta locally and then call set_mpr_filt() after the VxPairDataPoint object has been sized and allocated. * Per #1575, renamed PairDataEnsemble::subset_pairs() to subset_pairs_obs_thresh() to be a little more explicit about things. I'll do the same for PairDataPoint using names subset_pairs_cnt_thresh() and subset_pairs_mpr_thresh(). * Per #1575, some cleanup, moving check_fo_thresh() utility function from vx_config to vx_statistics library. * Per #1575, when implementing this for Grid-Stat, I realized that there isn't much benefit in storing col_name_ptr and col_name_thresh in PairBase. These changes remove that. * Per #1575, updating pair_data_point.h/.cc to handle the subsetting of data based on the MPR thresh. * Per #1575, rename subset_pairs() to subset_pairs_cnt_thresh() to be a bit more explicit with the naming conventions. * Per #1575, no real changes here. Just reorganizing the location of the mpr_sa and mpr_ta members. * Per #1575, make the subset_pairs() utility function a member function of the PairDataPoint class named subset_pairs_cnt_thresh() and update the application code to call it. * Per #1575, need to actually set the mpr_thresh! * Per #1575, update subset_pairs_mpr_thresh() to make sure the StringArray and ThreshArray lengths are the same. * Per #1575, replace PairDataPoint::subset_pairs_mpr_thresh() with a utility function named apply_mpr_thresh_mask(). This is for Grid-Stat to apply the mpr_thresh settings after the DataPlane pairs have been created but prior to applying any smoothing operations. * Per #1575, add documentation about mpr_column and mpr_thresh. * Per #1575, mpr_columns can also include CLIMO_CDF. * Per #1575, add tests for Grid-Stat and Point-Stat to exercise the mpr_column and mpr_thresh config file options. * Feature 1319 no pickle (#1720) * Try path insert. * sys.path insert. * Per #1319, adding David's changes back into the feature_1319_no_pickle branch. It compiles but TEST: python_numpy_plot_data_plane_pickle fails when testing on my Mac. Comitting now to test on kiowa. * Per #1319, small updated to write_tmp_dataplane.py script. Had a couple of if statements that should really be elif. Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Feature 1736 out_stat (#1744) * Per #1736, if -out_stat was used for aggregate or aggregate_stat jobs, do not write output to the -out or log output. * Per #1736, clarify stat_analysis documentation for -out_stat option. * Per #1736, for jobs which can write .stat output, don't waste time populating the output AsciiTable unless it's actually going to be written. Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> * Per #1319, this is a hotfix to the develop branch. While running unit_python.xml works via the command line, it fails when run through cron. The problem is the PATH setting. Need to have the anaconda bin directory in the path for it to succeeed. Adding that for the single test. * Just lining up a log message in the output of gen_vx_mask. * Per #1319, setting PATH as an envvar might cause problems. All variables set prior to the test are unset afterwards! So we'd run all the rest of the tests after unit_python.xml with an empty path. That would likely cause any subsequent call to Rscript to fail. Recommend tightening up this logic when we move these tests to GHA. * Trying to get the PATH setting correct for unit_python.xml. * Changed weblink for METplus documentation * per #1319 added netCDF4 python package to MET docker image so it is available for python embedding cases that use MET_PYTHON_EXE * Feature 1747 pylonglong (#1748) * Per #1747, update MET to interpret longlong values as integers. NetCDF file attributes that have an LL suffix are read into python as numpy.int64 objects. Right now MET fails when trying to read those as integers. Update the parsing logic to interpret those as ints. * Per #1747, since MET can now interpret both long and longlong's as ints, there's no need to cast nx and ny to ints in the read_tmp_dataplane.py script anymore. * Per #1747, this is slightly unrelated. But after installing the netCDF4 module on kiowa for /usr/local/met-python3/bin/python3, we should no longer need a custom PATH setting to get unit_python.xml to work. Reverting the change I made to it a couple of days ago to get it working. * Hotfix for the develop branch in tc_pairs.cc. The METplus unit tests kept failing through GHA with a divide by zero error. It occurs in compute_track_err() but only for a very specific set of data. The bdeck valid increment evaluates to 0 which causes the divide by 0 error. It also can evaluate to bad data (e.g. -9999). The fix is to check for 0 and bad data. If found, use the constant best_track_time_step value instead. * Turned specific section numbers into linked sections because section numbers can change * Removed hard-coded references to section numbers * Feature 1714 tc_gen (#1750) * Per #1714, add tc_gen genesis_match_window configuration option to define a search window relative to the forecast genesis time. * Per #1714, clarify docs to state the genesis_match_window.end = 12 allows for matches for early forecasts. Also add an example of this option to the tc_gen unit test. * Per #1714, switch ops_hit_tdiff to ops_hit_window. * Per #1714, skip genesis events for tracks where the cyclone number is > 50. * Per #1714, only discard cyclone numbers > 50 from the Best track, not the forecast tracks. * Per #1716, add note to the tc_gen chapter about skipping Best tracks with cyclone number > 50. * Per #1714, adding genesis_match_point_to_track config file option for TC-Gen. Note that this version of the code is close but doesn't actually compile yet. I still need to figure out exactly how to process the operational tracks. Should this logic also apply to the matching for those tracks? * Per #1714, the logic for checking the operational tracks is pretty simple. We only store/check operational track points for lead time = 0. So applying the genesis_match_point_to_track boolean config option does not make sense. * Per #1714, update the tc-gen user's guide chapter to describe the updated logic and new config file option. * Per #1714, fix the logic of the is_match() function. * Per #1714, reconfigure the call to tc_gen to exercise the new genesis_match_track_to_point option. * Per #1714, just fixing spacing in source code. * Committing 2 small changes not specifically related to #1714, but related the processing of genesis tracks. When getting items from ATCFGenLines, the columns to be shifted are off by one. We had been shifting offset 2 up to 3, but it should have remained at 2. Also when initializing a TrackInfo object, set the StormID by calling ATCFLineBase::storm_id() instead of constructing it from BASIN:CYCLONE:YYYY. For ATCFGenLines we want to set the Storm ID equal to the 3rd column rather than constructing it! * Per #1714, fix an error in the logic of GenesisInfo::is_match(const GenesisInfo &,...). I was using the index of the current GenesisInfo object instead of the one from the input argument. Fix this by adding GenesisInfo::genesis() member function to return a reference the TrackPoint for Genesis. * Per #1714, correcting logic for parsing the storm_id and warning_time columns for ATCFGen and regular ATCF line types. For ATCFGen line types, the code was incorrectly using the 3rd column when it should have used the 4th column! Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> * feature_1552_gcc_10 (#1752) * Cleaned bash comparison operators; Made changes for MET to compile using GNU 10.1.0 compilers * Updated documentation for new flag for BUFRLIB compilation * #1755 Support time string for slicing at MetNcCFDataFile::collect_time_offsets * #1755 Support time string for slicing at MetNcCFDataFile::collect_time_offsets * Feature 1735 stat_analysis (#1754) * Per #1735, enhance Stat-Analysis to support multiple -out_thresh settings when processing aggregate_stat jobs for MPR line types. This applies to output for FHO, CTC, CTS, ECLV, CNT, SL1L2, and SAL1L2. * Per #1735, since we are writing multiple output line types to the same .stat file, adding stat_row counter to the job class. This way all functions that write to it can increment that row counter when needed. * Per #1735, lots of little changes here to enable the aggregate_stat job type to write multiple output line types.g * Per #1735, update documentation for stat_analysis. * Per #1735, add AsciiTable::expand() function to increase the AsciiTable dimensions and also update the Stat-Analysis handling of the output .stat file it writes. * Per #1735, fix bug in the write_job_aggr_ssvar where I was using the wrong row counter when writing .stat outptu. * Per #1735, print a warning message is the continuous filtering logic results in 0 matched pairs. Also, match existing logic to NOT WRITE any output, not even header rows, when the output AsciiTable contains no results. * Per #1735, update unit_stat_analysis.xml to consolidate jobs stat_analysis_AGG_STAT_ORANK_RHIST and stat_analysis_AGG_STAT_ORANK_PHIST down into 1 job with 2 output line types. Rename the output files accordingly. * Per #1735, update the STATAnalysis config file for processing MPR data by tweaking the jobs to write multiple output line types and/or apply multiple output thresholds. * Per #1753, this one change to write_tmp_data.py solves this problem. When creating the variable to write the temp NetCDF file, we just need to pass through the fill value for the data. Also, make the script less verbose. * Per #1753, make the read_tmp_dataplane.py script less verbose. * Per #1753, there are 3 calls to the user's python version throughout MET. Update all 3 to print consistent log message when writing/reading the temp file. In particular, print the system command that is being executed at Debug(4) to make it easier to replicate python embedding problems that may arise. * Per #1753, wrap the call to get_fill_value() in a try block in case the input in a regular numpy array instead of a masked array. * Per #1620, correct bug in read_ascii_mpr.py script. The MPR line type has 37 columns in it, not 36! (#1760) * Feature 1700 python (#1765) * Per #1700, no real change, removing extra newline. * Per #1700, move global_python.h from vx_data2d_python over to the vx_python3_utils library where it belongs better. * Per #1700, no code changes. Just removing commented out code. * Per #1700, lots of little changes to make the python scripts consistent, updating the write*.py functions to add the user script directory to the system path, and remove extraneous log messages. * Per #1700, rename generic_python.py to set_python_env.py. Still actually need to change the source code to handle this change! * Per #1700 remove the pickle import. * Per #1700, work in progress. Replaced pickle file with tmp file. * Per #1700, work in progress. Replaced pickle file with tmp file. * Per #1700, update read_tmp_ascii.py to work for both ascii2nc and stat_analysis. Just create an object named ascii_data and have both instances read it. * Per #1700, getting closer. Work in progress. Just need to get user-python embedding working for stat-analysis. * Per #1700, removing extraneous cout. * Per #1700, fix logic in PyLineDataFile::do_tmp_ascii() to get stat_analysis python embedding working again. * Per #1700, just comments. * Per #1700, replace references to pickle with user_python * Per #1700, update documentation to replace pickle with temp files. * Feature 1766 v10.0.0_beta5 (#1767) * Per #1766, udpate the release date and add release notes for v10.0.0-beta5. * Per #1766 and #1728, update the copyright notice year to 2021. * Bugfix 1768 edeck (#1769) * Per #1768, update logic in ATCFProbLine::read_line(). If read_line() from the base class returns bad status, have this one return bad status as well. But do NOT for unsupported line types. Just print a Debug(4) log message instead. * Per #1768, update the probability line types to match those listed in https://www.nrlmry.navy.mil/atcf_web/docs/database/new/edeck.txt. That documentation was last updated in 11/2020, so presumably these reflect NHC's latest changes. * Per #1768, renaming enumerated value from ATCFLineType_ProbRIRW to ATCFLineType_ProbRI since there are now separated ATCF line type for rapid intensitifcation (RI) and weakening (RW). Will work more with this data in future issues to verify more of these probability types. * Feature 1771 release_notes (#1772) * Per #1771, draft version of combined met-10.0.0 release notes. * Per #1771, add bolding to indicate emphasis. * Per #1771, add bolding to indicate emphasis. * Per #1771, add bolding to indicate emphasis. * Per #1771, add bolding to indicate emphasis. * Per #1771, add bolding to indicate emphasis. * Per #1771, add bolding to indicate emphasis. * Per #1771, add bolding to indicate emphasis. * Per #1771, add bolding to indicate emphasis. * Per #1771, also update the flowchart for met-10.0.0. * Per #1771, update flowchart to indicate that tc_gen now has netcdf output. * Per #1771, rotate the authorship list for met-10.0.0, shifting Barb from first author down to the end. * Committing hotfix to the develop branch to fix a bad merge that caused the MET compilation to fail. * Update compile_MET_all.sh Added "-L${LIB_LIBPNG}" to rpath to fix problem on WCOSS" * Update pull_request_template.md Added entry for completion date of pull request review. * Per #1731, add ioda2nc documentation. * Changes to make the authorship list consistent with METplus. * Rename CIR to CIRA. * Per #1731, fix alignment issued caused by tabs vs spaces. * Per #1777, fixing memory management in DbfHeader::set_subrecords(). It is dynamically allocating a buffer based on the record_legnth (e.g. 5) but then reading 32 characters into it! Deleting the dynamically allocated buf variable causes it to abort. Since we always read 32 bytes here, switch to a static buffer of that size rather than dynamically allocating. (#1779) Co-authored-by: John.H.Gotway@noaa.gov <John.H.Gotway@v72a1.ncep.noaa.gov> * Feature 1731 authorship (#1776) * Per #1731, add ioda2nc documentation. * Changes to make the authorship list consistent with METplus. * Rename CIR to CIRA. * Per #1731, fix alignment issued caused by tabs vs spaces. * Updated input sources to include newly acceptable data formats * Per #1731, add more details about the grid-diag bin definition. * Per #1731, clarify wording. * Update met/docs/Users_Guide/tc-pairs.rst Co-authored-by: johnhg <johnhg@ucar.edu> * Changes to align Xarray language with that used in Xarray documentation, to clarify only DataArray Xarray structures are supported and not Xarray Dataset structures, and an example of how to quickly create a DataArray for MET from a Dataset. * Corrects plural of DataArray. * Aligns references to NumPy arrays with NumPy docs to refer to them as ndarrays. * Fixes formatting of note for Xarray. * Update met/docs/Users_Guide/tc-pairs.rst Co-authored-by: johnhg <johnhg@ucar.edu> * Fixes hyperlink reference. * Fixes line spacing in note directive. * Changes to reference again. * #1782 Set the time offset to 0 if the time dimension does not exist at the data variable * Updates to link and note directive. * Corrects plural of DataArray once more. * Adds more clarity to NumPy heading. * Adds bold for emphasis. * Removes bold in note directive. * Feature 1778 debug (#1785) * Per #1778, please see #1778 (comment) for details. Basically, when doing development, compile with the -g debug option. Otherwise, remove it by default. * Per #1778, update stale URL's in the README and configure.ac file. Also, change the default MET version from 8.1 to development. * Made suggested changes by Tara Jensen * Update python embedding docs to list required packages for the base python version. * Feature 1786 v10.0.0 (#1787) * Per #1786, updates for the v10.0.0 release. Note that no changes were needed in conf.py. It had already been updated. * Added update MET to compile using GNU version 10 compilers and PGI version 20 compilers * Made updates to improve compilation * Per #1768, added a couple more 10.0.0 release notes. * Adding pgi config file from cheyenne Co-authored-by: Julie.Prestopnik <jpresto@ucar.edu> * Per #1789, remove duplicate plot_point_obs configuration section. (#1791) * Update the version of Fortify on kiowa from 19.2.0 to 20.2.1. * #1795 Release memory at time_values * Bugfix 1798 develop py_grid_string (#1800) * Per #1798, fix up the read_tmpe_dataplane.py script to handle a grid string or dictionary. * Per #1798, add a test to unit_python.xml to exercise this bugfix. * #1794 Corrected the offset for Filter * Github Issue #1801: Comment out code that checks for BEST track to support extra-tropical cyclone tracks not verified against BEST tracks. * #1795 Cleanup * #1795 Create DataCube for 2D or 3D only, not both to avoid memory leak * Bugfix 1395 develop comp script (#1804) * Updated compile script and added assocaited config files * Added jet config file * Updated orion file * Added new stampede config file and modulefiles for various machines * Gitub Issue #1801 Remove code that checks for -bmodel filter to support plotting of extra-tropical cyclone tracks that aren't verified against BEST tracks. * Migrate issue and PR template changes from PR #1803 into the develop branch so that they'll be available for future releases. * Per met-help question (https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=99964) clarify the description of the obs_thresh option. * Update README.md Adding GitHub Discussions information * changed non-unicode apostrophe and fixed typo in URL * Feature 1581 api point obs (#1812) * #1581 Initial release * #1581 Added met_nc_point_obs.cc met_nc_point_obs.h * Removed nc_ in function names and moved them to the struct members * #1581 Added HDR_TYPE_ARR_LEN * #1581 Changed API calls (API names) * #1581 Cleanup * #1581 Removed duplicated definitions:hdr_arr_len, hdr_typ_arr_len, and obs_arr_len * #1581 Removed duplicated definitions:hdr_arr_len and obs_arr_len * #1581 Removed duplicated definitions: str_len, hdr_arr_len, and obs_arr_len * Added vx_nc_obs library * #1581 Using common APIs * #1581 Corrected API calls because of renaming for common APIs * #1581 Moved function from nc_obs_util to nc_point_obs2 * #1581renamed met_nc_point_obs to nc_point_obs * #1581 API ica changed from obs_vars to nc_point_obs * #1581 Initial release * #1581 Renamed from met_nc_point_obs to nc_point_obs * 1581 Renamed met_nc_point_obs to nc_point_obs * Per #1581, update the Makefile.am for lidar2nc to fix a linker error. Unfortunatley, the vx_config library now depends on the vx_gsl_prob library. threshold.cc in vx_config includes a call to normal_cdf_inv(double, double, double) which is defined in vx_gsl_prob. This adds to the complexity of dependencies for MET's libraries. Just linking to -lvx_gsl_prob one more time does fix the linker problem but doesn't solve the messy dependencies. * #1581 Added method for NcDataBuffer * Cleanup * #1581 Cleanup * #1581 Cleanup * #1591 Cleanup * #1591 Corrected API * #1581 Avoid reading PB header twice * #1581 Warning if PB header is not defined but read_pb_hdr_data is called * #1581 Cleanup libraries * 1581 cleanup * 1581 cleanup * 1581 cleanup * #1581 Cleanup for Fortify (removed unused variables) * #1581 Cleanup * #1581 Cleanup * #1581 Use MetNcPointObsIn instead of MetNcPointObs * #1581 Use MetNcPointObsOut instead of MetNcPointObs2Write * #1581 Separated nc_point_obs2.cc to nc_point_obs_in.cc and nc_point_obs_out.cc * #1581 Renamed nc_point_obs2.cc to nc_point_obs_in.cc And added add nc_point_obs_in.h nc_point_obs_out.h nc_point_obs_out.cc * #1581 Removed APIs related with writing point obs * #1581 Changed copyright years * #1581 Cleanup * #1581 Updated copyright year * #1581 Cleanup * #1581 Reanmed read_obs_data_strings to read_obs_data_table_lookups * #1581 Reanmed read_obs_data_strings to read_obs_data_table_lookups * #1581 Added more APIs Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> * Feature 1792 gen_vx_mask (#1816) * Per issue #1792, Change -type from optional to required. Set default_mask_type to MaskType_None. Added a check on mask_type to see if it's set and print error message accordingly. * Update test_gen_vx_mask.sh * For the first test, added -type poly, since the masking type is now required. SL * For all of the Poly unit tests added -type poly to the command line. The mask type is now required. SL * Modified document to indicate that -type string (masking type) is now required on the command line for gen_vx_mask. SL * Update met/docs/Users_Guide/masking.rst Co-authored-by: johnhg <johnhg@ucar.edu> * Update met/src/tools/other/gen_vx_mask/gen_vx_mask.cc Co-authored-by: johnhg <johnhg@ucar.edu> Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: johnhg <johnhg@ucar.edu> * Fix 2 minor formatting errors in the release notes. * PR #1816 for issue #1792 unexpectedly caused the NB to fail on 20210605. We changed -type from optional to required, but missed adding the -type option in unit_met_test_scripts.xml and unit_ref_config.xml. This is a hotfix to resolve that. * Feature 1811 anchor links (#1822) * testing new anchoring link idea. * testing without the bold asterik * tinkering with the look * another attempt * another attempt #2 * another attempt #3 * another attempt #4 * making sure new anchor works as expected. * seeing if link will save with spaces instead of dashes * need underscores to link * is it fixed? * testing * testing 2 * testing 4 * testing 5 * testing 6 * testing 7 * testing 8 * going back to test original problem * able to link with spaces instead of underscores. Testing if a return is possible to keep under 79 character limit. * double checking everything is still working. * DO NOT break ref lines apart, it won't work. * trying a shorter name. * continuing to add anchors * updating lines 1946 thru 2214 with anchors * updating lines 2214 thru 3371 with anchors * updating lines 3371 to the end with anchors * testing anchor * testing anchor * testing anchor 3 * testing anchor 4 * testing anchor 45 percent * testing anchor final half * fixing typo * numbering fcst, obs_1 and 2 to create different links. * finding more anchors that need numbers to keep them separate. * fixing warnings * fixing warnings * fixing typo * Feature 1749 hss (#1825) * Per #1749, updating the MET version number from 10.0 to 10.1 prior to adding new columns of output to existing line types. * Per #1749, adding 10.1 columns to the Makefile.am * Per #1749, changes for the mechanics of adding the HSS_EC statistic to the MCTS line type. Still need to acutally compute it and make the expected correct value configurable. * Per #1749, add hss_ec_value as a configurable option for Point-Stat and Grid-Stat. Still need to actually compute it correctly, add it to other test config files, add support to series_analysis/stat_analysis, update the docs, and make writeup corresponding issues for other METplus components. * Per #1749, fix the column offsets for the HSS_EC columns. * Per #1749, add correct definition of HSS_EC. * Per #1749, pass hss_ec_value from the config file into the computation of the MCTS statistics. * Per #1749, add hss_ec_value entry to all the Grid-Stat config files. * Per #1749, update the documentation about the HSS_EC statistic. * Per #1749, add the -hss_ec_value job command option to Stat-Analysis. * Per #1749, no real code changes here. Just changing to consistent ordering with hss_ec_value preceeding rank_corr_flag. * Per #1749, update docs for stat_analysis supporting hss_ec_value. * Per #1749, add HSS_EC to Series-Analysis, but only with a constant hss_ec_value for now. * Per #1749, add EC_VALUE to the MCTC line type definition. * Per #1749, move ECvalue from the MCTSInfo class into the ContingencyTable class so that it's available to be included in the MCTC output line type. * Per #1749, update point_stat, grid_stat, and series_analysis to accomodate the move of ECvalue from the MCTSInfo class to the ContingencyTable class. * Per #1749, update library code to write EC_VALUE to the MCTC line type and update the User's Guide docs. * Per #1749, update stat_analysis code for the addition of EC_VALUE in the MCTC line type. * Per #1749, write EC_VALUE to the MCTC output line type. * Per #1749, store the ec_value that was actually used to compute the stats. * Per #1749, parsing EC_VALUE from the MCTC line type. * Per #1749, move the MCTC EC_VALUE column to the end of the line, as requested by METdatadb. * Per #932, need to write MCTS HSS_EC value to temp file during the bootstrapping process. * Added new reference for Ou 2016 * Layout correction * Added generalized HSS, removed word from HSS_EC * Per #1749, change the hss_ec_value config entry to match new conventions. Co-authored-by: j-opatz <59586397+j-opatz@users.noreply.github.com> * Feature 1826 v10.1.0_beta1 (#1828) * Per #1826, add update the version in the docs to 10.1.0-beta1 and add release notes for this development version. * Per #1826, change the beta1 release date to 6/11 so that I can do it today. * Revoming Randy and David from the email notification list for nightly run scripts. Co-authored-by: David Fillmore <fillmore.winslow.david@gmail.com> Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> Co-authored-by: hsoh-u <hsoh@ucar.edu> Co-authored-by: Julie.Prestopnik <jpresto@ucar.edu> Co-authored-by: David Fillmore <davidfillmore@users.noreply.github.com> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@kiowa.rap.ucar.edu> Co-authored-by: George McCabe <mccabe@ucar.edu> Co-authored-by: John.H.Gotway@noaa.gov <John.H.Gotway@v72a1.ncep.noaa.gov> Co-authored-by: j-opatz <59586397+j-opatz@users.noreply.github.com> Co-authored-by: Daniel Adriaansen <dadriaan@ucar.edu> Co-authored-by: bikegeek <minnawin@ucar.edu> Co-authored-by: bikegeek <3753118+bikegeek@users.noreply.github.com> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: Seth Linden <linden@ucar.edu> Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com>

* testing possible new drop-down menus for FAQ * adding sphinx-panels to extensions to be able to use drop down menus in appendixA * Per #1834, adding sphinx-panels to requirements.txt to see if that fixes the error * Per #1834, added sphinx.ext to beginning of sphinx_panels to see if that fixes the error * Per #1834, remove sphinx.ext and add trailing comma to end of extensions to see if that fixed the error * Per #1834, added sphinx-panels to pip install command to see if that fixes the error * Per #1834, added extra space in comment to get docs to build to see if change to documentation.yml will fix an error * Per #1834, added return character to get rid of warning * testing dropdown menus #1 * testing dropdown menus #2 removing lines and dotted lines * testing #3 * testing 4 * fixing numbering, removing 2nd pulldown menu, trying to fix box width * adding code block in dropdown * trying to fix width * trying to fix width with spacing * trying to fix width with spacing 2nd dropdown * removing panels * solved problem, just use dropdown no panels * adding second dropdown menu * removing the dropdown menus and fixing the spacing. * fixing typos * adding in matched pairs * adding in formating files for NetCDF and making FILE_IO a header * fixing spacing * time slice * fixing spacing * UNIX time conversion * fixing spacing * fixed-width * scientific notation * removing which per Julie P * adding Gen_Vx_Mask section * fixing formatting * changing to numbers * complex masking region * neighborhood methods boundaries * Neighborhood Methods to Compute Fraction * adding Grid_Stat - How do I use Config File Setup to Read a NetCDF file * using backticks with asterics * one more backtick with asterics * Grid_Stat - What would be an example of Verifying Probabilities * fixing typos * What is an example of using Grid-Stat with Regridding and Masking Turned On * fixing typos * Grid_Stat - What would be an example of Verifying Probabilities Example2 * trying to fix typos * trying to fix code-block spacing * Per #1834, attempting to fix warning. * How do I use different masks in MET tools using MODE as an example * trying to fix bullet list * trying to fix bullet list 2 * trying to fix bullet list 2 * trying to fix bullet list 3 * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, modified formatting, including adding backslashes and removing extra returns in command line calls, and adding indentation for config file notation, and adding a return after each 'A.' * Per #1834, changed code-block from ini to none to fix formatting * *Pcp-Combine - What are some examples using -add * Pcp-Combine - How do I add and subtract with Pcp-Combine * Pcp-Combine - How do I Combine 12-hour Accumulated Precipitation from Two Different Initialization Times * Pcp-Combine - How Do I Correct a Precipitation Time Range * Pcp-Combine - What Data Formats does MET Read * Pcp-Combine - How does pass through work * Pcp_Combine - How do I use -pcprx to run a project faster * Pcp-Combine - How Do I Enter the Time Format Correctly * Pcp-Combine - How do I use -subtract * fixing formatting * Pcp_Combine - How Do I Use -sum, -add, and -subtract to Achieve Same Accumulation Interval * Pcp-Combine - What is the difference between -sum vs. -add * Pcp-Combine - How Do I Select a Specific GRIB Record to Use * fixing spacing for original text * Plot-Data-Plane - How Do I Inspect Gen_Vx_Mask Output * fixing typo * Plot-Data-Plane - How Do I Specify GRIB Version * Plot-Data-Plane - last 2 entries * 2 misc. entries * fixing typo * Stat_Analysis - How does -aggregate_stat work * Stat_Analysis - remaining entries * fixing typo * tc-pairs * tc-stat * troubleshooting area * another stat-analysis * another stat-analysis * utilities * fixing dashes * Per #1834, trying out syntax * Per #1834, removing added syntax * fixing returns with bolding * Per #1834, modified formatting * adding italics for directories #1834 * replacing code-block ini with none to remove red lettering * fixing questions to lower case #1834 * linking to section using numref #1834 * linking to section using numref #1834 attempt 2 * linking to section using numref #1834 attempt 3 * linking to section using numref #1834 attempt 4 * linking to section using numref #1834 attempt 5 * linking to section using numref #1834 attempt 6 * linking to section using numref #1834 attempt 7 * linking to section using numref #1834 attempt 8 * linking to anothre section #1834 * linking to another section #1834 * removing old info #1834 * grammar updates #1834 * grammar updates #1834 * fixing typos #1834 * email changes with Julie #1834 * trying to fix warning #1834 * changes #1834 * Per #1834, updating question titles and answers * Per #1834, made updates to the content. * Per #1834, made updates to the content * Per #1834, made updates to the content * Per #1834, made some major changes to the first 3 FAQ's. I don't have the time/bandwidth to review these completely at this time, but wanted to include at least these updates. * testing some of the updates John O. suggested. * updates John O. suggested take 2 #1834. * updates John O. suggested take 3 #1834. * updates John O. suggested take 4 #1834. * updates John O. suggested take 5 #1834. * updates John O. suggested. Some didn't show up even though they've been removed #1834. * trying to fix numbered list indenting #1834 * fixing numbered list indenting #1834 * cleaning up formatting #1834 * fixing broken links #1834 Co-authored-by: Julie.Prestopnik <jpresto@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu>

@ericgilleland

* Update install_met_env.kiowa Commented out items and added text to description * #1817 Added to_north argument at two_to_one() * #1817 Calls two_to_one() with false for the third argument, to_north, if latitude moves north to south * Feature 1819 automation doc warnings (#1836) * Removing "/lib" that should not be there. * #1508 checking stat() methoid returns no error before looking at FILE flag * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * #1838 Added log message for lat/lon values * #1838 Give warning if the first and lat lat/lon is same * #1838 Support the double data type variable on reading float type values * Feature 1833 develop discussions (#1849) * Per #1833, changed references to met_help to Discussions. * Per #1833, fixed typo and removed an unnecessary word * #1852 Removed unused nc_buf_size. Make cur and dim to the same size (called API handles 2D or 3D) * #1852 Check the start and count before calling NetCDF API * Feature 1746 wavelet stat (#1851) * For issue #1746 modified code to allow users to pass in an empty list (or NA) for forecast and observation thresholds in order to skip applying the threhsolds, but it will still compute stats with the raw fields. SL * For issue #1746, added new unit test that uses a config file that has empty lists for the forecast and observation thresholds. SL * For issue #1746 Added some content related to allowing users to set forecast and observation cat thresholds to an empty list in order to skip the binary masking (and consider all grid-points for stats). SL * Per #1746, cleaning up for consistent indentation. * Per #1746, cleaning up for consistent indentation. * Per #1746, add a revision history note, update the plotting range in the postscript output to be [-n,n] where n is the maximum value of the maximum absolute difference and 1.0, and also fix a bug. When the NA threshold comes AFTER a real threshold, the resulting data and difference values were not being updated. * Per #1746, change the Wavelet-Stat config file values in the the wvlt_plot dictionary by setting plot_min = plot_max = 0.0. That enables the default logic of the tool to take effect. Choose the plotting range of the wavelet plots as [-n,n], where n is the maximum of 1.0 and the maximum absolute difference. * Per #1746, used apply_fcst_thresh where it should have been apply_obs_thresh. * Per issue #1746, modified some content related to users being able to skip applying the categorical threhsolds by putting an empty list or NA in the configuration file. SL * Per issue #1746 Added some warnings if the forecast threshold is set to NA but the observation threshold is not NA (a numeric threshold) and vice versa. SL * Per #1746, fix a couple of typos and tweak wording in the wavelet-stat chapter. * Per #1746, loop over each pair of fcst/obs thresholds to check for inconsistent use of the NA threshold type. * Per #1746, a bit of code cleanup replacing calls to n_elements() with n() to make the code more concise. * Per #1746, need to reinitialize apply_fcst_thresh and apply_obs_thresh to true inside the loop since the NA threshold can appear anywhere in the list of thresholds. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Update README.md * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py * #1852 get_string_val: check if 2D variable. Also checking if the variable does not have dimension (#1860) Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> * Feature 1453 create pdf user guide (#1859) * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Feature 1853 rps doc (#1861) * Per #1853, adding RPS docs from Eric. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, adding a manual page break after the ROC image to get it to stay in the right spot. * Per #1853, backing out last change which didn't make the ROC image stay in the right spot. * #1855 Removed break after return (SobarQube) * #1855 Removed break after exit * 1855 Added return at MetNcPointObsOut::write_to_netcdf * #1855 Avoid releasing memory twice * #1855 Removed unused code * #1855 Corrected syntax error * #1855 Changed the second call of close() to release _ncFile * #1855 Deleted break after exit * #1855 Chamnged while to if * #1855 Added constructor TCLineCounts and initialized the members * #1855 Added break statement back for case '-' * #1855 Check the new size before extending to avoid thereference of the null pointer * #1855 Changed count to processed_count for log messages. Initialized variables at get_filtered_nc_data\*() * #1855 Corected the number of memory copy * #1855 Exit with an error message if both fgi & bgi are null * #1855 Clear Lead_Times before extening. Formatting for error messages * Add definition for the compilation environment on seneca. * #1855 Extend Lead_Times for new times * #1855 Removed break after exit * #1855 define "c" dynamically * #1855 Move the log message within if statement to avoid dereferencing a null pointer * Feature 1843 scatter index (#1863) * Added scatter index variables: SI, SI_BCL, SI_BCU to cnt columns. SL * Per issue #1843 Added Scatter Index variables (SI, SI_BCL, SI_BCU) to the CNT stat type. SL * Added Scatter Index (SI, SI_BCL, SI_BCU) to cnt stat type header. SL * Per issue #1843, added Scatter Index variables to write_cnt_cols(). SL * Per issue #1843 added Scatter Index (si) to CNTinfo class. SL * Per issue #1843 added Scatter Index (SI, si) to CNTInfo::get_stat(). SL * Per issue #1843 added Scatter Index (SI, si) calculation to both versions of compute_cntinfo(). SL * Per issue #1843, forgot semi-colon after SI calculation, fixed. SL * Added Scatter Index (si) to some of the clear() and allocate() functions. SL * Per issue #1843, added Scatter Index (si) to compute_cnt_mean(). SL * Per issue #1843, added Scatter Index (si) to bootstrap interval calculation and to the CNT write function. SL * Per issue #1843 added Scatter Index (SI, SI_BCL, SI_BCU) to store_stat_cnt(). SL * Per issue #1843, in get_stat() moved Scatterd Index (SI) line to be below RMSE for consitency. SL * Added Scatter Index (SI) to the CNT output format table. SL * Added Scatter Index (SI) to CNT statistics definitions. SL * Update appendixC.rst * Update stat_columns.cc * Update compute_ci.cc * Update met_stats.cc * Per #1843, update write_cntinfo() function. Since we're READING the SI value immediately after the RMSE value when computing CI's, we also need to write SI immediately after RMSE. Otherwise, we'll be computing CI's using the wrong statistics replicates. * Per #1843, check for divide by zero when computing SI... this could happen if comparing the same input file to itself with Grid-Stat. * Per #1843, correct definition of SI from RMSE/ME to RMSE/OBAR. * Per #1843, updated the SI definition to divide by OBAR instead of ME, but forgot to update the divide-by-zero check. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: johnhg <johnhg@ucar.edu> * #1855 Corected typo - compare the numnber of U and V * #1855 Check if var_info is hull * #1855 Avoid un-initialized variables: dt at open(), v at lat() & lon(), and local variables at data() * #1855 Check if ldf is null pointer * #1855 Removed break after exit * #1855 Removed break after exit * Update pcp_combine.cc * Feature 1864 config urls (#1868) * Per #1864, remove stale GitHub pages URL for the MET User's Guide. * Per #1864, found stale GitHub IO links in the issue templates. Should make this same fix in the develop and default branches for all the METplus repos. * Per #1864, fix stale GitHub IO link in the PR template. * Move ROC curve in Appendix C * Crop ROC image for better PDF formatting * Shrink ROC image for better PDF formatting * Modify figure alignment in conf.py * Change text placement for ROC curve figure * Feature 1834 faq (#1867) * testing possible new drop-down menus for FAQ * adding sphinx-panels to extensions to be able to use drop down menus in appendixA * Per #1834, adding sphinx-panels to requirements.txt to see if that fixes the error * Per #1834, added sphinx.ext to beginning of sphinx_panels to see if that fixes the error * Per #1834, remove sphinx.ext and add trailing comma to end of extensions to see if that fixed the error * Per #1834, added sphinx-panels to pip install command to see if that fixes the error * Per #1834, added extra space in comment to get docs to build to see if change to documentation.yml will fix an error * Per #1834, added return character to get rid of warning * testing dropdown menus #1 * testing dropdown menus #2 removing lines and dotted lines * testing #3 * testing 4 * fixing numbering, removing 2nd pulldown menu, trying to fix box width * adding code block in dropdown * trying to fix width * trying to fix width with spacing * trying to fix width with spacing 2nd dropdown * removing panels * solved problem, just use dropdown no panels * adding second dropdown menu * removing the dropdown menus and fixing the spacing. * fixing typos * adding in matched pairs * adding in formating files for NetCDF and making FILE_IO a header * fixing spacing * time slice * fixing spacing * UNIX time conversion * fixing spacing * fixed-width * scientific notation * removing which per Julie P * adding Gen_Vx_Mask section * fixing formatting * changing to numbers * complex masking region * neighborhood methods boundaries * Neighborhood Methods to Compute Fraction * adding Grid_Stat - How do I use Config File Setup to Read a NetCDF file * using backticks with asterics * one more backtick with asterics * Grid_Stat - What would be an example of Verifying Probabilities * fixing typos * What is an example of using Grid-Stat with Regridding and Masking Turned On * fixing typos * Grid_Stat - What would be an example of Verifying Probabilities Example2 * trying to fix typos * trying to fix code-block spacing * Per #1834, attempting to fix warning. * How do I use different masks in MET tools using MODE as an example * trying to fix bullet list * trying to fix bullet list 2 * trying to fix bullet list 2 * trying to fix bullet list 3 * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, modified formatting, including adding backslashes and removing extra returns in command line calls, and adding indentation for config file notation, and adding a return after each 'A.' * Per #1834, changed code-block from ini to none to fix formatting * *Pcp-Combine - What are some examples using -add * Pcp-Combine - How do I add and subtract with Pcp-Combine * Pcp-Combine - How do I Combine 12-hour Accumulated Precipitation from Two Different Initialization Times * Pcp-Combine - How Do I Correct a Precipitation Time Range * Pcp-Combine - What Data Formats does MET Read * Pcp-Combine - How does pass through work * Pcp_Combine - How do I use -pcprx to run a project faster * Pcp-Combine - How Do I Enter the Time Format Correctly * Pcp-Combine - How do I use -subtract * fixing formatting * Pcp_Combine - How Do I Use -sum, -add, and -subtract to Achieve Same Accumulation Interval * Pcp-Combine - What is the difference between -sum vs. -add * Pcp-Combine - How Do I Select a Specific GRIB Record to Use * fixing spacing for original text * Plot-Data-Plane - How Do I Inspect Gen_Vx_Mask Output * fixing typo * Plot-Data-Plane - How Do I Specify GRIB Version * Plot-Data-Plane - last 2 entries * 2 misc. entries * fixing typo * Stat_Analysis - How does -aggregate_stat work * Stat_Analysis - remaining entries * fixing typo * tc-pairs * tc-stat * troubleshooting area * another stat-analysis * another stat-analysis * utilities * fixing dashes * Per #1834, trying out syntax * Per #1834, removing added syntax * fixing returns with bolding * Per #1834, modified formatting * adding italics for directories #1834 * replacing code-block ini with none to remove red lettering * fixing questions to lower case #1834 * linking to section using numref #1834 * linking to section using numref #1834 attempt 2 * linking to section using numref #1834 attempt 3 * linking to section using numref #1834 attempt 4 * linking to section using numref #1834 attempt 5 * linking to section using numref #1834 attempt 6 * linking to section using numref #1834 attempt 7 * linking to section using numref #1834 attempt 8 * linking to anothre section #1834 * linking to another section #1834 * removing old info #1834 * grammar updates #1834 * grammar updates #1834 * fixing typos #1834 * email changes with Julie #1834 * trying to fix warning #1834 * changes #1834 * Per #1834, updating question titles and answers * Per #1834, made updates to the content. * Per #1834, made updates to the content * Per #1834, made updates to the content * Per #1834, made some major changes to the first 3 FAQ's. I don't have the time/bandwidth to review these completely at this time, but wanted to include at least these updates. * testing some of the updates John O. suggested. * updates John O. suggested take 2 #1834. * updates John O. suggested take 3 #1834. * updates John O. suggested take 4 #1834. * updates John O. suggested take 5 #1834. * updates John O. suggested. Some didn't show up even though they've been removed #1834. * trying to fix numbered list indenting #1834 * fixing numbered list indenting #1834 * cleaning up formatting #1834 * fixing broken links #1834 Co-authored-by: Julie.Prestopnik <jpresto@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * bugfix 1872 plot_tcmpr.R -lookin directory (develop) (#1874) * Bugfix 1875 develop memory (#1877) * Per #1875, fix set_cdf_ta() to initialize cdf_ta prior to populating it. * Per #1875, add debug(4) log messages whenever defining a new aggregation case in stat-analysis. * Per #1875, switch log messages about new cases from Debug(4) to Debug(3). * Per #1879, porting the same changes over to the develop branch. (#1881) * Feature 1673 gbeta (#1857) * Per #1673, add a distance_map.beta_value entry to all the Grid-Stat config files. * Per #1673, enhance Grid-Stat to parse the new beta_value option and set its value in the library code. * Per #1673, set the user-defined beta_value when processing the distance map scores. * Per #1673, add 4 new DMAP columns write them. Just writing bad data values right now, still need to actually compute them! Also need to update Stat-Analysis to update the parsing/aggregation of these new values. * Per #1673, enable beta_value to be set to a default bad data value. * Per #1673 and @ericgilleland instruction (#1673 (comment)), strip asymmetric G-Beta (AGBETA) from the output. * Per #1673, fix typo that was causing the code not to compile. * Per #1673, update MET User's Guide about G/GBETA. * Per #1673, report BETA_VALUE = TOTAL / 2 in the output instead of NA, as directed by Eric. * Per #1673, remove descriptions of Grid-Stat-specific config options for nbrhd, fourier, gradient, and distance_map from the overview section since they belong in the Grid-Stat chapter. Also add direct links for them in the Grid-Stat chapter. * Per #1673, do not reset the beta_value in DMAP::clear(). * Per #1673, log the DMAP options only after the beta_value has been determined. * Per #1673, correct the default beta_value setting as N*N / 2.0. * Per #1673, trying to format G-beta well. * Per #1673, trying to format G-beta well. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, switch to defining beta_value as a function of the input grid size. * Per #1673, push initial appendix C updates for GBETA. * Per #1673, working on G and GBETA equations. * Per #1673, working on G and GBETA equations. * Per 1673, update GBETA details in appendix C. * Per #1673, add Eric's info about selecting beta. * Per #1673, update reference for Gilleland-2019 to Gilleland_PartI-2020 and Gilleland_PartII-2020. * Per 1673, fix typo. * Per #1673, making changes requested by Eric. * Per #1673, making changes requested by Eric. * Per #1673, update references based on Eric's feedback. * Update appendixD.rst (#1869) Updated this appendix. * Update appendixD.rst * Per #1673, making the formatting of Gilleland-2020 part I and II references consistent. * Per #1673, update Grid-Stat docs to clarify that GBETA is only computed on the FULL verification domain and not any masking regions. * Per #1673, add DataPlane::n_good_data() function to return a count valid data values. * Per #1673, update vx_statistics library code to only set gbeta/beta_value to bad data for sub-domains. * Per #1673, update grid_stat to mask out bad data between the fcst/obs fields before computing distance maps. This will change existing unit test results! Also store the count of valid data values in the full verification domain. * Per #1673, since GBETA is only reported when VX_MASK = FULL, updating GridStatConfig_all to include the FULL masking region to make this example more meaningful. Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com> Co-authored-by: jprestop <jpresto@ucar.edu> Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> Co-authored-by: hsoh-u <hsoh@ucar.edu> Co-authored-by: Keith Searight <keith.searight@noaa.gov> Co-authored-by: Seth Linden <linden@ucar.edu> Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@seneca.rap.ucar.edu> Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com>

@ericgilleland

* Update install_met_env.kiowa Commented out items and added text to description * #1817 Added to_north argument at two_to_one() * #1817 Calls two_to_one() with false for the third argument, to_north, if latitude moves north to south * Feature 1819 automation doc warnings (#1836) * Removing "/lib" that should not be there. * #1508 checking stat() methoid returns no error before looking at FILE flag * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * #1838 Added log message for lat/lon values * #1838 Give warning if the first and lat lat/lon is same * #1838 Support the double data type variable on reading float type values * Feature 1833 develop discussions (#1849) * Per #1833, changed references to met_help to Discussions. * Per #1833, fixed typo and removed an unnecessary word * #1852 Removed unused nc_buf_size. Make cur and dim to the same size (called API handles 2D or 3D) * #1852 Check the start and count before calling NetCDF API * Feature 1746 wavelet stat (#1851) * For issue #1746 modified code to allow users to pass in an empty list (or NA) for forecast and observation thresholds in order to skip applying the threhsolds, but it will still compute stats with the raw fields. SL * For issue #1746, added new unit test that uses a config file that has empty lists for the forecast and observation thresholds. SL * For issue #1746 Added some content related to allowing users to set forecast and observation cat thresholds to an empty list in order to skip the binary masking (and consider all grid-points for stats). SL * Per #1746, cleaning up for consistent indentation. * Per #1746, cleaning up for consistent indentation. * Per #1746, add a revision history note, update the plotting range in the postscript output to be [-n,n] where n is the maximum value of the maximum absolute difference and 1.0, and also fix a bug. When the NA threshold comes AFTER a real threshold, the resulting data and difference values were not being updated. * Per #1746, change the Wavelet-Stat config file values in the the wvlt_plot dictionary by setting plot_min = plot_max = 0.0. That enables the default logic of the tool to take effect. Choose the plotting range of the wavelet plots as [-n,n], where n is the maximum of 1.0 and the maximum absolute difference. * Per #1746, used apply_fcst_thresh where it should have been apply_obs_thresh. * Per issue #1746, modified some content related to users being able to skip applying the categorical threhsolds by putting an empty list or NA in the configuration file. SL * Per issue #1746 Added some warnings if the forecast threshold is set to NA but the observation threshold is not NA (a numeric threshold) and vice versa. SL * Per #1746, fix a couple of typos and tweak wording in the wavelet-stat chapter. * Per #1746, loop over each pair of fcst/obs thresholds to check for inconsistent use of the NA threshold type. * Per #1746, a bit of code cleanup replacing calls to n_elements() with n() to make the code more concise. * Per #1746, need to reinitialize apply_fcst_thresh and apply_obs_thresh to true inside the loop since the NA threshold can appear anywhere in the list of thresholds. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Update README.md * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py * #1852 get_string_val: check if 2D variable. Also checking if the variable does not have dimension (#1860) Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> * Feature 1453 create pdf user guide (#1859) * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Feature 1853 rps doc (#1861) * Per #1853, adding RPS docs from Eric. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, adding a manual page break after the ROC image to get it to stay in the right spot. * Per #1853, backing out last change which didn't make the ROC image stay in the right spot. * #1855 Removed break after return (SobarQube) * #1855 Removed break after exit * 1855 Added return at MetNcPointObsOut::write_to_netcdf * #1855 Avoid releasing memory twice * #1855 Removed unused code * #1855 Corrected syntax error * #1855 Changed the second call of close() to release _ncFile * #1855 Deleted break after exit * #1855 Chamnged while to if * #1855 Added constructor TCLineCounts and initialized the members * #1855 Added break statement back for case '-' * #1855 Check the new size before extending to avoid thereference of the null pointer * #1855 Changed count to processed_count for log messages. Initialized variables at get_filtered_nc_data\*() * #1855 Corected the number of memory copy * #1855 Exit with an error message if both fgi & bgi are null * #1855 Clear Lead_Times before extening. Formatting for error messages * Add definition for the compilation environment on seneca. * #1855 Extend Lead_Times for new times * #1855 Removed break after exit * #1855 define "c" dynamically * #1855 Move the log message within if statement to avoid dereferencing a null pointer * Feature 1843 scatter index (#1863) * Added scatter index variables: SI, SI_BCL, SI_BCU to cnt columns. SL * Per issue #1843 Added Scatter Index variables (SI, SI_BCL, SI_BCU) to the CNT stat type. SL * Added Scatter Index (SI, SI_BCL, SI_BCU) to cnt stat type header. SL * Per issue #1843, added Scatter Index variables to write_cnt_cols(). SL * Per issue #1843 added Scatter Index (si) to CNTinfo class. SL * Per issue #1843 added Scatter Index (SI, si) to CNTInfo::get_stat(). SL * Per issue #1843 added Scatter Index (SI, si) calculation to both versions of compute_cntinfo(). SL * Per issue #1843, forgot semi-colon after SI calculation, fixed. SL * Added Scatter Index (si) to some of the clear() and allocate() functions. SL * Per issue #1843, added Scatter Index (si) to compute_cnt_mean(). SL * Per issue #1843, added Scatter Index (si) to bootstrap interval calculation and to the CNT write function. SL * Per issue #1843 added Scatter Index (SI, SI_BCL, SI_BCU) to store_stat_cnt(). SL * Per issue #1843, in get_stat() moved Scatterd Index (SI) line to be below RMSE for consitency. SL * Added Scatter Index (SI) to the CNT output format table. SL * Added Scatter Index (SI) to CNT statistics definitions. SL * Update appendixC.rst * Update stat_columns.cc * Update compute_ci.cc * Update met_stats.cc * Per #1843, update write_cntinfo() function. Since we're READING the SI value immediately after the RMSE value when computing CI's, we also need to write SI immediately after RMSE. Otherwise, we'll be computing CI's using the wrong statistics replicates. * Per #1843, check for divide by zero when computing SI... this could happen if comparing the same input file to itself with Grid-Stat. * Per #1843, correct definition of SI from RMSE/ME to RMSE/OBAR. * Per #1843, updated the SI definition to divide by OBAR instead of ME, but forgot to update the divide-by-zero check. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: johnhg <johnhg@ucar.edu> * #1855 Corected typo - compare the numnber of U and V * #1855 Check if var_info is hull * #1855 Avoid un-initialized variables: dt at open(), v at lat() & lon(), and local variables at data() * #1855 Check if ldf is null pointer * #1855 Removed break after exit * #1855 Removed break after exit * Update pcp_combine.cc * Feature 1864 config urls (#1868) * Per #1864, remove stale GitHub pages URL for the MET User's Guide. * Per #1864, found stale GitHub IO links in the issue templates. Should make this same fix in the develop and default branches for all the METplus repos. * Per #1864, fix stale GitHub IO link in the PR template. * Move ROC curve in Appendix C * Crop ROC image for better PDF formatting * Shrink ROC image for better PDF formatting * Modify figure alignment in conf.py * Change text placement for ROC curve figure * Feature 1834 faq (#1867) * testing possible new drop-down menus for FAQ * adding sphinx-panels to extensions to be able to use drop down menus in appendixA * Per #1834, adding sphinx-panels to requirements.txt to see if that fixes the error * Per #1834, added sphinx.ext to beginning of sphinx_panels to see if that fixes the error * Per #1834, remove sphinx.ext and add trailing comma to end of extensions to see if that fixed the error * Per #1834, added sphinx-panels to pip install command to see if that fixes the error * Per #1834, added extra space in comment to get docs to build to see if change to documentation.yml will fix an error * Per #1834, added return character to get rid of warning * testing dropdown menus #1 * testing dropdown menus #2 removing lines and dotted lines * testing #3 * testing 4 * fixing numbering, removing 2nd pulldown menu, trying to fix box width * adding code block in dropdown * trying to fix width * trying to fix width with spacing * trying to fix width with spacing 2nd dropdown * removing panels * solved problem, just use dropdown no panels * adding second dropdown menu * removing the dropdown menus and fixing the spacing. * fixing typos * adding in matched pairs * adding in formating files for NetCDF and making FILE_IO a header * fixing spacing * time slice * fixing spacing * UNIX time conversion * fixing spacing * fixed-width * scientific notation * removing which per Julie P * adding Gen_Vx_Mask section * fixing formatting * changing to numbers * complex masking region * neighborhood methods boundaries * Neighborhood Methods to Compute Fraction * adding Grid_Stat - How do I use Config File Setup to Read a NetCDF file * using backticks with asterics * one more backtick with asterics * Grid_Stat - What would be an example of Verifying Probabilities * fixing typos * What is an example of using Grid-Stat with Regridding and Masking Turned On * fixing typos * Grid_Stat - What would be an example of Verifying Probabilities Example2 * trying to fix typos * trying to fix code-block spacing * Per #1834, attempting to fix warning. * How do I use different masks in MET tools using MODE as an example * trying to fix bullet list * trying to fix bullet list 2 * trying to fix bullet list 2 * trying to fix bullet list 3 * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, modified formatting, including adding backslashes and removing extra returns in command line calls, and adding indentation for config file notation, and adding a return after each 'A.' * Per #1834, changed code-block from ini to none to fix formatting * *Pcp-Combine - What are some examples using -add * Pcp-Combine - How do I add and subtract with Pcp-Combine * Pcp-Combine - How do I Combine 12-hour Accumulated Precipitation from Two Different Initialization Times * Pcp-Combine - How Do I Correct a Precipitation Time Range * Pcp-Combine - What Data Formats does MET Read * Pcp-Combine - How does pass through work * Pcp_Combine - How do I use -pcprx to run a project faster * Pcp-Combine - How Do I Enter the Time Format Correctly * Pcp-Combine - How do I use -subtract * fixing formatting * Pcp_Combine - How Do I Use -sum, -add, and -subtract to Achieve Same Accumulation Interval * Pcp-Combine - What is the difference between -sum vs. -add * Pcp-Combine - How Do I Select a Specific GRIB Record to Use * fixing spacing for original text * Plot-Data-Plane - How Do I Inspect Gen_Vx_Mask Output * fixing typo * Plot-Data-Plane - How Do I Specify GRIB Version * Plot-Data-Plane - last 2 entries * 2 misc. entries * fixing typo * Stat_Analysis - How does -aggregate_stat work * Stat_Analysis - remaining entries * fixing typo * tc-pairs * tc-stat * troubleshooting area * another stat-analysis * another stat-analysis * utilities * fixing dashes * Per #1834, trying out syntax * Per #1834, removing added syntax * fixing returns with bolding * Per #1834, modified formatting * adding italics for directories #1834 * replacing code-block ini with none to remove red lettering * fixing questions to lower case #1834 * linking to section using numref #1834 * linking to section using numref #1834 attempt 2 * linking to section using numref #1834 attempt 3 * linking to section using numref #1834 attempt 4 * linking to section using numref #1834 attempt 5 * linking to section using numref #1834 attempt 6 * linking to section using numref #1834 attempt 7 * linking to section using numref #1834 attempt 8 * linking to anothre section #1834 * linking to another section #1834 * removing old info #1834 * grammar updates #1834 * grammar updates #1834 * fixing typos #1834 * email changes with Julie #1834 * trying to fix warning #1834 * changes #1834 * Per #1834, updating question titles and answers * Per #1834, made updates to the content. * Per #1834, made updates to the content * Per #1834, made updates to the content * Per #1834, made some major changes to the first 3 FAQ's. I don't have the time/bandwidth to review these completely at this time, but wanted to include at least these updates. * testing some of the updates John O. suggested. * updates John O. suggested take 2 #1834. * updates John O. suggested take 3 #1834. * updates John O. suggested take 4 #1834. * updates John O. suggested take 5 #1834. * updates John O. suggested. Some didn't show up even though they've been removed #1834. * trying to fix numbered list indenting #1834 * fixing numbered list indenting #1834 * cleaning up formatting #1834 * fixing broken links #1834 Co-authored-by: Julie.Prestopnik <jpresto@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * bugfix 1872 plot_tcmpr.R -lookin directory (develop) (#1874) * Bugfix 1875 develop memory (#1877) * Per #1875, fix set_cdf_ta() to initialize cdf_ta prior to populating it. * Per #1875, add debug(4) log messages whenever defining a new aggregation case in stat-analysis. * Per #1875, switch log messages about new cases from Debug(4) to Debug(3). * Per #1879, porting the same changes over to the develop branch. (#1881) * Feature 1673 gbeta (#1857) * Per #1673, add a distance_map.beta_value entry to all the Grid-Stat config files. * Per #1673, enhance Grid-Stat to parse the new beta_value option and set its value in the library code. * Per #1673, set the user-defined beta_value when processing the distance map scores. * Per #1673, add 4 new DMAP columns write them. Just writing bad data values right now, still need to actually compute them! Also need to update Stat-Analysis to update the parsing/aggregation of these new values. * Per #1673, enable beta_value to be set to a default bad data value. * Per #1673 and @ericgilleland instruction (#1673 (comment)), strip asymmetric G-Beta (AGBETA) from the output. * Per #1673, fix typo that was causing the code not to compile. * Per #1673, update MET User's Guide about G/GBETA. * Per #1673, report BETA_VALUE = TOTAL / 2 in the output instead of NA, as directed by Eric. * Per #1673, remove descriptions of Grid-Stat-specific config options for nbrhd, fourier, gradient, and distance_map from the overview section since they belong in the Grid-Stat chapter. Also add direct links for them in the Grid-Stat chapter. * Per #1673, do not reset the beta_value in DMAP::clear(). * Per #1673, log the DMAP options only after the beta_value has been determined. * Per #1673, correct the default beta_value setting as N*N / 2.0. * Per #1673, trying to format G-beta well. * Per #1673, trying to format G-beta well. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, switch to defining beta_value as a function of the input grid size. * Per #1673, push initial appendix C updates for GBETA. * Per #1673, working on G and GBETA equations. * Per #1673, working on G and GBETA equations. * Per 1673, update GBETA details in appendix C. * Per #1673, add Eric's info about selecting beta. * Per #1673, update reference for Gilleland-2019 to Gilleland_PartI-2020 and Gilleland_PartII-2020. * Per 1673, fix typo. * Per #1673, making changes requested by Eric. * Per #1673, making changes requested by Eric. * Per #1673, update references based on Eric's feedback. * Update appendixD.rst (#1869) Updated this appendix. * Update appendixD.rst * Per #1673, making the formatting of Gilleland-2020 part I and II references consistent. * Per #1673, update Grid-Stat docs to clarify that GBETA is only computed on the FULL verification domain and not any masking regions. * Per #1673, add DataPlane::n_good_data() function to return a count valid data values. * Per #1673, update vx_statistics library code to only set gbeta/beta_value to bad data for sub-domains. * Per #1673, update grid_stat to mask out bad data between the fcst/obs fields before computing distance maps. This will change existing unit test results! Also store the count of valid data values in the full verification domain. * Per #1673, since GBETA is only reported when VX_MASK = FULL, updating GridStatConfig_all to include the FULL masking region to make this example more meaningful. Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com> * Feature 1764 point stat (#1885) * Per #1764 added write_orank_row() to do_hera_ens(). SL * Per issue #1764, added orank stat type for ensemble output. SL * Per issue #1764, added code to setup_txt_files() for ORANK output. SL * Added some comments for debuging. SL * Per #1764, add orank to the list of outputs created by point_stat. * Per #1764, add functions to compute the number of requested HiRA probabilities and ensemble members. Also update n_txt_row() to keep track of the number of ORANK rows to be written. Not totally sure if I'm counting these ORANK output lines correctly though. * Per #1764, update logic in setup_txt_files() to call get_max_n_hira_prob() and get_max_n_hira_ens() functions. * Per #1764, no real changes. Just fixing spacing. * Per issue #1764, cleaned up print (cout) debug statements. SL * Per issue #1764 added 'orank = NONE' to the config files for compatibility with changes to point_stat for calculating ORANK. SL * Per issue #1764 added 'orank = STAT' to config file to produce ORANK output lines in point_stat. SL * Per issue #1764 added content in all relevant sections for ORANK: observation rank statistic. SL * Added 'orank = NONE' to config file for compatibility with changes to point_stant for ORANK. SL * Added 'orank = NONE' to config file for compatibility with changes to point_stant for ORANK. SL * Apply suggestions from code review Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Per #1764, no real changes, just fixing indents. * Per #1764, no real changes, just fixing indents. * Per #1764, no real changes, just fixing indents. * Per #1764, putting the docs for VCNT back into its logical order with the other vector line types. The order that they're listed here does not need to match their order in the enumeration in the code. * Per #1764, fixing a vcnt typo I found in the grid-stat chapter... and making them consistent. * Per issue #1764: After the call to write_orank_row, added lines to reset the observation begin and end times. SL * Per #1764, no code changes, just fixing indents. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Adding Seth to the NB notification list. Co-authored-by: jprestop <jpresto@ucar.edu> Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> Co-authored-by: hsoh-u <hsoh@ucar.edu> Co-authored-by: Keith Searight <keith.searight@noaa.gov> Co-authored-by: Seth Linden <linden@ucar.edu> Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@seneca.rap.ucar.edu> Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@kiowa.rap.ucar.edu>

@ericgilleland

* Update install_met_env.kiowa Commented out items and added text to description * #1817 Added to_north argument at two_to_one() * #1817 Calls two_to_one() with false for the third argument, to_north, if latitude moves north to south * Feature 1819 automation doc warnings (#1836) * Removing "/lib" that should not be there. * #1508 checking stat() methoid returns no error before looking at FILE flag * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * #1838 Added log message for lat/lon values * #1838 Give warning if the first and lat lat/lon is same * #1838 Support the double data type variable on reading float type values * Feature 1833 develop discussions (#1849) * Per #1833, changed references to met_help to Discussions. * Per #1833, fixed typo and removed an unnecessary word * #1852 Removed unused nc_buf_size. Make cur and dim to the same size (called API handles 2D or 3D) * #1852 Check the start and count before calling NetCDF API * Feature 1746 wavelet stat (#1851) * For issue #1746 modified code to allow users to pass in an empty list (or NA) for forecast and observation thresholds in order to skip applying the threhsolds, but it will still compute stats with the raw fields. SL * For issue #1746, added new unit test that uses a config file that has empty lists for the forecast and observation thresholds. SL * For issue #1746 Added some content related to allowing users to set forecast and observation cat thresholds to an empty list in order to skip the binary masking (and consider all grid-points for stats). SL * Per #1746, cleaning up for consistent indentation. * Per #1746, cleaning up for consistent indentation. * Per #1746, add a revision history note, update the plotting range in the postscript output to be [-n,n] where n is the maximum value of the maximum absolute difference and 1.0, and also fix a bug. When the NA threshold comes AFTER a real threshold, the resulting data and difference values were not being updated. * Per #1746, change the Wavelet-Stat config file values in the the wvlt_plot dictionary by setting plot_min = plot_max = 0.0. That enables the default logic of the tool to take effect. Choose the plotting range of the wavelet plots as [-n,n], where n is the maximum of 1.0 and the maximum absolute difference. * Per #1746, used apply_fcst_thresh where it should have been apply_obs_thresh. * Per issue #1746, modified some content related to users being able to skip applying the categorical threhsolds by putting an empty list or NA in the configuration file. SL * Per issue #1746 Added some warnings if the forecast threshold is set to NA but the observation threshold is not NA (a numeric threshold) and vice versa. SL * Per #1746, fix a couple of typos and tweak wording in the wavelet-stat chapter. * Per #1746, loop over each pair of fcst/obs thresholds to check for inconsistent use of the NA threshold type. * Per #1746, a bit of code cleanup replacing calls to n_elements() with n() to make the code more concise. * Per #1746, need to reinitialize apply_fcst_thresh and apply_obs_thresh to true inside the loop since the NA threshold can appear anywhere in the list of thresholds. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Update README.md * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py * #1852 get_string_val: check if 2D variable. Also checking if the variable does not have dimension (#1860) Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> * Feature 1453 create pdf user guide (#1859) * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Feature 1853 rps doc (#1861) * Per #1853, adding RPS docs from Eric. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, adding a manual page break after the ROC image to get it to stay in the right spot. * Per #1853, backing out last change which didn't make the ROC image stay in the right spot. * #1855 Removed break after return (SobarQube) * #1855 Removed break after exit * 1855 Added return at MetNcPointObsOut::write_to_netcdf * #1855 Avoid releasing memory twice * #1855 Removed unused code * #1855 Corrected syntax error * #1855 Changed the second call of close() to release _ncFile * #1855 Deleted break after exit * #1855 Chamnged while to if * #1855 Added constructor TCLineCounts and initialized the members * #1855 Added break statement back for case '-' * #1855 Check the new size before extending to avoid thereference of the null pointer * #1855 Changed count to processed_count for log messages. Initialized variables at get_filtered_nc_data\*() * #1855 Corected the number of memory copy * #1855 Exit with an error message if both fgi & bgi are null * #1855 Clear Lead_Times before extening. Formatting for error messages * Add definition for the compilation environment on seneca. * #1855 Extend Lead_Times for new times * #1855 Removed break after exit * #1855 define "c" dynamically * #1855 Move the log message within if statement to avoid dereferencing a null pointer * Feature 1843 scatter index (#1863) * Added scatter index variables: SI, SI_BCL, SI_BCU to cnt columns. SL * Per issue #1843 Added Scatter Index variables (SI, SI_BCL, SI_BCU) to the CNT stat type. SL * Added Scatter Index (SI, SI_BCL, SI_BCU) to cnt stat type header. SL * Per issue #1843, added Scatter Index variables to write_cnt_cols(). SL * Per issue #1843 added Scatter Index (si) to CNTinfo class. SL * Per issue #1843 added Scatter Index (SI, si) to CNTInfo::get_stat(). SL * Per issue #1843 added Scatter Index (SI, si) calculation to both versions of compute_cntinfo(). SL * Per issue #1843, forgot semi-colon after SI calculation, fixed. SL * Added Scatter Index (si) to some of the clear() and allocate() functions. SL * Per issue #1843, added Scatter Index (si) to compute_cnt_mean(). SL * Per issue #1843, added Scatter Index (si) to bootstrap interval calculation and to the CNT write function. SL * Per issue #1843 added Scatter Index (SI, SI_BCL, SI_BCU) to store_stat_cnt(). SL * Per issue #1843, in get_stat() moved Scatterd Index (SI) line to be below RMSE for consitency. SL * Added Scatter Index (SI) to the CNT output format table. SL * Added Scatter Index (SI) to CNT statistics definitions. SL * Update appendixC.rst * Update stat_columns.cc * Update compute_ci.cc * Update met_stats.cc * Per #1843, update write_cntinfo() function. Since we're READING the SI value immediately after the RMSE value when computing CI's, we also need to write SI immediately after RMSE. Otherwise, we'll be computing CI's using the wrong statistics replicates. * Per #1843, check for divide by zero when computing SI... this could happen if comparing the same input file to itself with Grid-Stat. * Per #1843, correct definition of SI from RMSE/ME to RMSE/OBAR. * Per #1843, updated the SI definition to divide by OBAR instead of ME, but forgot to update the divide-by-zero check. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: johnhg <johnhg@ucar.edu> * #1855 Corected typo - compare the numnber of U and V * #1855 Check if var_info is hull * #1855 Avoid un-initialized variables: dt at open(), v at lat() & lon(), and local variables at data() * #1855 Check if ldf is null pointer * #1855 Removed break after exit * #1855 Removed break after exit * Update pcp_combine.cc * Feature 1864 config urls (#1868) * Per #1864, remove stale GitHub pages URL for the MET User's Guide. * Per #1864, found stale GitHub IO links in the issue templates. Should make this same fix in the develop and default branches for all the METplus repos. * Per #1864, fix stale GitHub IO link in the PR template. * Move ROC curve in Appendix C * Crop ROC image for better PDF formatting * Shrink ROC image for better PDF formatting * Modify figure alignment in conf.py * Change text placement for ROC curve figure * Feature 1834 faq (#1867) * testing possible new drop-down menus for FAQ * adding sphinx-panels to extensions to be able to use drop down menus in appendixA * Per #1834, adding sphinx-panels to requirements.txt to see if that fixes the error * Per #1834, added sphinx.ext to beginning of sphinx_panels to see if that fixes the error * Per #1834, remove sphinx.ext and add trailing comma to end of extensions to see if that fixed the error * Per #1834, added sphinx-panels to pip install command to see if that fixes the error * Per #1834, added extra space in comment to get docs to build to see if change to documentation.yml will fix an error * Per #1834, added return character to get rid of warning * testing dropdown menus #1 * testing dropdown menus #2 removing lines and dotted lines * testing #3 * testing 4 * fixing numbering, removing 2nd pulldown menu, trying to fix box width * adding code block in dropdown * trying to fix width * trying to fix width with spacing * trying to fix width with spacing 2nd dropdown * removing panels * solved problem, just use dropdown no panels * adding second dropdown menu * removing the dropdown menus and fixing the spacing. * fixing typos * adding in matched pairs * adding in formating files for NetCDF and making FILE_IO a header * fixing spacing * time slice * fixing spacing * UNIX time conversion * fixing spacing * fixed-width * scientific notation * removing which per Julie P * adding Gen_Vx_Mask section * fixing formatting * changing to numbers * complex masking region * neighborhood methods boundaries * Neighborhood Methods to Compute Fraction * adding Grid_Stat - How do I use Config File Setup to Read a NetCDF file * using backticks with asterics * one more backtick with asterics * Grid_Stat - What would be an example of Verifying Probabilities * fixing typos * What is an example of using Grid-Stat with Regridding and Masking Turned On * fixing typos * Grid_Stat - What would be an example of Verifying Probabilities Example2 * trying to fix typos * trying to fix code-block spacing * Per #1834, attempting to fix warning. * How do I use different masks in MET tools using MODE as an example * trying to fix bullet list * trying to fix bullet list 2 * trying to fix bullet list 2 * trying to fix bullet list 3 * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, modified formatting, including adding backslashes and removing extra returns in command line calls, and adding indentation for config file notation, and adding a return after each 'A.' * Per #1834, changed code-block from ini to none to fix formatting * *Pcp-Combine - What are some examples using -add * Pcp-Combine - How do I add and subtract with Pcp-Combine * Pcp-Combine - How do I Combine 12-hour Accumulated Precipitation from Two Different Initialization Times * Pcp-Combine - How Do I Correct a Precipitation Time Range * Pcp-Combine - What Data Formats does MET Read * Pcp-Combine - How does pass through work * Pcp_Combine - How do I use -pcprx to run a project faster * Pcp-Combine - How Do I Enter the Time Format Correctly * Pcp-Combine - How do I use -subtract * fixing formatting * Pcp_Combine - How Do I Use -sum, -add, and -subtract to Achieve Same Accumulation Interval * Pcp-Combine - What is the difference between -sum vs. -add * Pcp-Combine - How Do I Select a Specific GRIB Record to Use * fixing spacing for original text * Plot-Data-Plane - How Do I Inspect Gen_Vx_Mask Output * fixing typo * Plot-Data-Plane - How Do I Specify GRIB Version * Plot-Data-Plane - last 2 entries * 2 misc. entries * fixing typo * Stat_Analysis - How does -aggregate_stat work * Stat_Analysis - remaining entries * fixing typo * tc-pairs * tc-stat * troubleshooting area * another stat-analysis * another stat-analysis * utilities * fixing dashes * Per #1834, trying out syntax * Per #1834, removing added syntax * fixing returns with bolding * Per #1834, modified formatting * adding italics for directories #1834 * replacing code-block ini with none to remove red lettering * fixing questions to lower case #1834 * linking to section using numref #1834 * linking to section using numref #1834 attempt 2 * linking to section using numref #1834 attempt 3 * linking to section using numref #1834 attempt 4 * linking to section using numref #1834 attempt 5 * linking to section using numref #1834 attempt 6 * linking to section using numref #1834 attempt 7 * linking to section using numref #1834 attempt 8 * linking to anothre section #1834 * linking to another section #1834 * removing old info #1834 * grammar updates #1834 * grammar updates #1834 * fixing typos #1834 * email changes with Julie #1834 * trying to fix warning #1834 * changes #1834 * Per #1834, updating question titles and answers * Per #1834, made updates to the content. * Per #1834, made updates to the content * Per #1834, made updates to the content * Per #1834, made some major changes to the first 3 FAQ's. I don't have the time/bandwidth to review these completely at this time, but wanted to include at least these updates. * testing some of the updates John O. suggested. * updates John O. suggested take 2 #1834. * updates John O. suggested take 3 #1834. * updates John O. suggested take 4 #1834. * updates John O. suggested take 5 #1834. * updates John O. suggested. Some didn't show up even though they've been removed #1834. * trying to fix numbered list indenting #1834 * fixing numbered list indenting #1834 * cleaning up formatting #1834 * fixing broken links #1834 Co-authored-by: Julie.Prestopnik <jpresto@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * bugfix 1872 plot_tcmpr.R -lookin directory (develop) (#1874) * Bugfix 1875 develop memory (#1877) * Per #1875, fix set_cdf_ta() to initialize cdf_ta prior to populating it. * Per #1875, add debug(4) log messages whenever defining a new aggregation case in stat-analysis. * Per #1875, switch log messages about new cases from Debug(4) to Debug(3). * Per #1879, porting the same changes over to the develop branch. (#1881) * Feature 1673 gbeta (#1857) * Per #1673, add a distance_map.beta_value entry to all the Grid-Stat config files. * Per #1673, enhance Grid-Stat to parse the new beta_value option and set its value in the library code. * Per #1673, set the user-defined beta_value when processing the distance map scores. * Per #1673, add 4 new DMAP columns write them. Just writing bad data values right now, still need to actually compute them! Also need to update Stat-Analysis to update the parsing/aggregation of these new values. * Per #1673, enable beta_value to be set to a default bad data value. * Per #1673 and @ericgilleland instruction (#1673 (comment)), strip asymmetric G-Beta (AGBETA) from the output. * Per #1673, fix typo that was causing the code not to compile. * Per #1673, update MET User's Guide about G/GBETA. * Per #1673, report BETA_VALUE = TOTAL / 2 in the output instead of NA, as directed by Eric. * Per #1673, remove descriptions of Grid-Stat-specific config options for nbrhd, fourier, gradient, and distance_map from the overview section since they belong in the Grid-Stat chapter. Also add direct links for them in the Grid-Stat chapter. * Per #1673, do not reset the beta_value in DMAP::clear(). * Per #1673, log the DMAP options only after the beta_value has been determined. * Per #1673, correct the default beta_value setting as N*N / 2.0. * Per #1673, trying to format G-beta well. * Per #1673, trying to format G-beta well. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, switch to defining beta_value as a function of the input grid size. * Per #1673, push initial appendix C updates for GBETA. * Per #1673, working on G and GBETA equations. * Per #1673, working on G and GBETA equations. * Per 1673, update GBETA details in appendix C. * Per #1673, add Eric's info about selecting beta. * Per #1673, update reference for Gilleland-2019 to Gilleland_PartI-2020 and Gilleland_PartII-2020. * Per 1673, fix typo. * Per #1673, making changes requested by Eric. * Per #1673, making changes requested by Eric. * Per #1673, update references based on Eric's feedback. * Update appendixD.rst (#1869) Updated this appendix. * Update appendixD.rst * Per #1673, making the formatting of Gilleland-2020 part I and II references consistent. * Per #1673, update Grid-Stat docs to clarify that GBETA is only computed on the FULL verification domain and not any masking regions. * Per #1673, add DataPlane::n_good_data() function to return a count valid data values. * Per #1673, update vx_statistics library code to only set gbeta/beta_value to bad data for sub-domains. * Per #1673, update grid_stat to mask out bad data between the fcst/obs fields before computing distance maps. This will change existing unit test results! Also store the count of valid data values in the full verification domain. * Per #1673, since GBETA is only reported when VX_MASK = FULL, updating GridStatConfig_all to include the FULL masking region to make this example more meaningful. Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com> * Feature 1764 point stat (#1885) * Per #1764 added write_orank_row() to do_hera_ens(). SL * Per issue #1764, added orank stat type for ensemble output. SL * Per issue #1764, added code to setup_txt_files() for ORANK output. SL * Added some comments for debuging. SL * Per #1764, add orank to the list of outputs created by point_stat. * Per #1764, add functions to compute the number of requested HiRA probabilities and ensemble members. Also update n_txt_row() to keep track of the number of ORANK rows to be written. Not totally sure if I'm counting these ORANK output lines correctly though. * Per #1764, update logic in setup_txt_files() to call get_max_n_hira_prob() and get_max_n_hira_ens() functions. * Per #1764, no real changes. Just fixing spacing. * Per issue #1764, cleaned up print (cout) debug statements. SL * Per issue #1764 added 'orank = NONE' to the config files for compatibility with changes to point_stat for calculating ORANK. SL * Per issue #1764 added 'orank = STAT' to config file to produce ORANK output lines in point_stat. SL * Per issue #1764 added content in all relevant sections for ORANK: observation rank statistic. SL * Added 'orank = NONE' to config file for compatibility with changes to point_stant for ORANK. SL * Added 'orank = NONE' to config file for compatibility with changes to point_stant for ORANK. SL * Apply suggestions from code review Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Per #1764, no real changes, just fixing indents. * Per #1764, no real changes, just fixing indents. * Per #1764, no real changes, just fixing indents. * Per #1764, putting the docs for VCNT back into its logical order with the other vector line types. The order that they're listed here does not need to match their order in the enumeration in the code. * Per #1764, fixing a vcnt typo I found in the grid-stat chapter... and making them consistent. * Per issue #1764: After the call to write_orank_row, added lines to reset the observation begin and end times. SL * Per #1764, no code changes, just fixing indents. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Adding Seth to the NB notification list. * Bugfix 1886 develop grid_diag (#1888) * Per #1886, port over the bugfixes from main_v10.0 to develop. * Per #1886, make grid_diag error out if to_grid is set to FCST or OBS. Co-authored-by: jprestop <jpresto@ucar.edu> Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> Co-authored-by: hsoh-u <hsoh@ucar.edu> Co-authored-by: Keith Searight <keith.searight@noaa.gov> Co-authored-by: Seth Linden <linden@ucar.edu> Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@seneca.rap.ucar.edu> Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@kiowa.rap.ucar.edu>

@ericgilleland

* Update install_met_env.kiowa Commented out items and added text to description * #1817 Added to_north argument at two_to_one() * #1817 Calls two_to_one() with false for the third argument, to_north, if latitude moves north to south * Feature 1819 automation doc warnings (#1836) * Removing "/lib" that should not be there. * #1508 checking stat() methoid returns no error before looking at FILE flag * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * #1838 Added log message for lat/lon values * #1838 Give warning if the first and lat lat/lon is same * #1838 Support the double data type variable on reading float type values * Feature 1833 develop discussions (#1849) * Per #1833, changed references to met_help to Discussions. * Per #1833, fixed typo and removed an unnecessary word * #1852 Removed unused nc_buf_size. Make cur and dim to the same size (called API handles 2D or 3D) * #1852 Check the start and count before calling NetCDF API * Feature 1746 wavelet stat (#1851) * For issue #1746 modified code to allow users to pass in an empty list (or NA) for forecast and observation thresholds in order to skip applying the threhsolds, but it will still compute stats with the raw fields. SL * For issue #1746, added new unit test that uses a config file that has empty lists for the forecast and observation thresholds. SL * For issue #1746 Added some content related to allowing users to set forecast and observation cat thresholds to an empty list in order to skip the binary masking (and consider all grid-points for stats). SL * Per #1746, cleaning up for consistent indentation. * Per #1746, cleaning up for consistent indentation. * Per #1746, add a revision history note, update the plotting range in the postscript output to be [-n,n] where n is the maximum value of the maximum absolute difference and 1.0, and also fix a bug. When the NA threshold comes AFTER a real threshold, the resulting data and difference values were not being updated. * Per #1746, change the Wavelet-Stat config file values in the the wvlt_plot dictionary by setting plot_min = plot_max = 0.0. That enables the default logic of the tool to take effect. Choose the plotting range of the wavelet plots as [-n,n], where n is the maximum of 1.0 and the maximum absolute difference. * Per #1746, used apply_fcst_thresh where it should have been apply_obs_thresh. * Per issue #1746, modified some content related to users being able to skip applying the categorical threhsolds by putting an empty list or NA in the configuration file. SL * Per issue #1746 Added some warnings if the forecast threshold is set to NA but the observation threshold is not NA (a numeric threshold) and vice versa. SL * Per #1746, fix a couple of typos and tweak wording in the wavelet-stat chapter. * Per #1746, loop over each pair of fcst/obs thresholds to check for inconsistent use of the NA threshold type. * Per #1746, a bit of code cleanup replacing calls to n_elements() with n() to make the code more concise. * Per #1746, need to reinitialize apply_fcst_thresh and apply_obs_thresh to true inside the loop since the NA threshold can appear anywhere in the list of thresholds. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Update README.md * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py * #1852 get_string_val: check if 2D variable. Also checking if the variable does not have dimension (#1860) Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> * Feature 1453 create pdf user guide (#1859) * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Feature 1853 rps doc (#1861) * Per #1853, adding RPS docs from Eric. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, adding a manual page break after the ROC image to get it to stay in the right spot. * Per #1853, backing out last change which didn't make the ROC image stay in the right spot. * #1855 Removed break after return (SobarQube) * #1855 Removed break after exit * 1855 Added return at MetNcPointObsOut::write_to_netcdf * #1855 Avoid releasing memory twice * #1855 Removed unused code * #1855 Corrected syntax error * #1855 Changed the second call of close() to release _ncFile * #1855 Deleted break after exit * #1855 Chamnged while to if * #1855 Added constructor TCLineCounts and initialized the members * #1855 Added break statement back for case '-' * #1855 Check the new size before extending to avoid thereference of the null pointer * #1855 Changed count to processed_count for log messages. Initialized variables at get_filtered_nc_data\*() * #1855 Corected the number of memory copy * #1855 Exit with an error message if both fgi & bgi are null * #1855 Clear Lead_Times before extening. Formatting for error messages * Add definition for the compilation environment on seneca. * #1855 Extend Lead_Times for new times * #1855 Removed break after exit * #1855 define "c" dynamically * #1855 Move the log message within if statement to avoid dereferencing a null pointer * Feature 1843 scatter index (#1863) * Added scatter index variables: SI, SI_BCL, SI_BCU to cnt columns. SL * Per issue #1843 Added Scatter Index variables (SI, SI_BCL, SI_BCU) to the CNT stat type. SL * Added Scatter Index (SI, SI_BCL, SI_BCU) to cnt stat type header. SL * Per issue #1843, added Scatter Index variables to write_cnt_cols(). SL * Per issue #1843 added Scatter Index (si) to CNTinfo class. SL * Per issue #1843 added Scatter Index (SI, si) to CNTInfo::get_stat(). SL * Per issue #1843 added Scatter Index (SI, si) calculation to both versions of compute_cntinfo(). SL * Per issue #1843, forgot semi-colon after SI calculation, fixed. SL * Added Scatter Index (si) to some of the clear() and allocate() functions. SL * Per issue #1843, added Scatter Index (si) to compute_cnt_mean(). SL * Per issue #1843, added Scatter Index (si) to bootstrap interval calculation and to the CNT write function. SL * Per issue #1843 added Scatter Index (SI, SI_BCL, SI_BCU) to store_stat_cnt(). SL * Per issue #1843, in get_stat() moved Scatterd Index (SI) line to be below RMSE for consitency. SL * Added Scatter Index (SI) to the CNT output format table. SL * Added Scatter Index (SI) to CNT statistics definitions. SL * Update appendixC.rst * Update stat_columns.cc * Update compute_ci.cc * Update met_stats.cc * Per #1843, update write_cntinfo() function. Since we're READING the SI value immediately after the RMSE value when computing CI's, we also need to write SI immediately after RMSE. Otherwise, we'll be computing CI's using the wrong statistics replicates. * Per #1843, check for divide by zero when computing SI... this could happen if comparing the same input file to itself with Grid-Stat. * Per #1843, correct definition of SI from RMSE/ME to RMSE/OBAR. * Per #1843, updated the SI definition to divide by OBAR instead of ME, but forgot to update the divide-by-zero check. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: johnhg <johnhg@ucar.edu> * #1855 Corected typo - compare the numnber of U and V * #1855 Check if var_info is hull * #1855 Avoid un-initialized variables: dt at open(), v at lat() & lon(), and local variables at data() * #1855 Check if ldf is null pointer * #1855 Removed break after exit * #1855 Removed break after exit * Update pcp_combine.cc * Feature 1864 config urls (#1868) * Per #1864, remove stale GitHub pages URL for the MET User's Guide. * Per #1864, found stale GitHub IO links in the issue templates. Should make this same fix in the develop and default branches for all the METplus repos. * Per #1864, fix stale GitHub IO link in the PR template. * Move ROC curve in Appendix C * Crop ROC image for better PDF formatting * Shrink ROC image for better PDF formatting * Modify figure alignment in conf.py * Change text placement for ROC curve figure * Feature 1834 faq (#1867) * testing possible new drop-down menus for FAQ * adding sphinx-panels to extensions to be able to use drop down menus in appendixA * Per #1834, adding sphinx-panels to requirements.txt to see if that fixes the error * Per #1834, added sphinx.ext to beginning of sphinx_panels to see if that fixes the error * Per #1834, remove sphinx.ext and add trailing comma to end of extensions to see if that fixed the error * Per #1834, added sphinx-panels to pip install command to see if that fixes the error * Per #1834, added extra space in comment to get docs to build to see if change to documentation.yml will fix an error * Per #1834, added return character to get rid of warning * testing dropdown menus #1 * testing dropdown menus #2 removing lines and dotted lines * testing #3 * testing 4 * fixing numbering, removing 2nd pulldown menu, trying to fix box width * adding code block in dropdown * trying to fix width * trying to fix width with spacing * trying to fix width with spacing 2nd dropdown * removing panels * solved problem, just use dropdown no panels * adding second dropdown menu * removing the dropdown menus and fixing the spacing. * fixing typos * adding in matched pairs * adding in formating files for NetCDF and making FILE_IO a header * fixing spacing * time slice * fixing spacing * UNIX time conversion * fixing spacing * fixed-width * scientific notation * removing which per Julie P * adding Gen_Vx_Mask section * fixing formatting * changing to numbers * complex masking region * neighborhood methods boundaries * Neighborhood Methods to Compute Fraction * adding Grid_Stat - How do I use Config File Setup to Read a NetCDF file * using backticks with asterics * one more backtick with asterics * Grid_Stat - What would be an example of Verifying Probabilities * fixing typos * What is an example of using Grid-Stat with Regridding and Masking Turned On * fixing typos * Grid_Stat - What would be an example of Verifying Probabilities Example2 * trying to fix typos * trying to fix code-block spacing * Per #1834, attempting to fix warning. * How do I use different masks in MET tools using MODE as an example * trying to fix bullet list * trying to fix bullet list 2 * trying to fix bullet list 2 * trying to fix bullet list 3 * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, modified formatting, including adding backslashes and removing extra returns in command line calls, and adding indentation for config file notation, and adding a return after each 'A.' * Per #1834, changed code-block from ini to none to fix formatting * *Pcp-Combine - What are some examples using -add * Pcp-Combine - How do I add and subtract with Pcp-Combine * Pcp-Combine - How do I Combine 12-hour Accumulated Precipitation from Two Different Initialization Times * Pcp-Combine - How Do I Correct a Precipitation Time Range * Pcp-Combine - What Data Formats does MET Read * Pcp-Combine - How does pass through work * Pcp_Combine - How do I use -pcprx to run a project faster * Pcp-Combine - How Do I Enter the Time Format Correctly * Pcp-Combine - How do I use -subtract * fixing formatting * Pcp_Combine - How Do I Use -sum, -add, and -subtract to Achieve Same Accumulation Interval * Pcp-Combine - What is the difference between -sum vs. -add * Pcp-Combine - How Do I Select a Specific GRIB Record to Use * fixing spacing for original text * Plot-Data-Plane - How Do I Inspect Gen_Vx_Mask Output * fixing typo * Plot-Data-Plane - How Do I Specify GRIB Version * Plot-Data-Plane - last 2 entries * 2 misc. entries * fixing typo * Stat_Analysis - How does -aggregate_stat work * Stat_Analysis - remaining entries * fixing typo * tc-pairs * tc-stat * troubleshooting area * another stat-analysis * another stat-analysis * utilities * fixing dashes * Per #1834, trying out syntax * Per #1834, removing added syntax * fixing returns with bolding * Per #1834, modified formatting * adding italics for directories #1834 * replacing code-block ini with none to remove red lettering * fixing questions to lower case #1834 * linking to section using numref #1834 * linking to section using numref #1834 attempt 2 * linking to section using numref #1834 attempt 3 * linking to section using numref #1834 attempt 4 * linking to section using numref #1834 attempt 5 * linking to section using numref #1834 attempt 6 * linking to section using numref #1834 attempt 7 * linking to section using numref #1834 attempt 8 * linking to anothre section #1834 * linking to another section #1834 * removing old info #1834 * grammar updates #1834 * grammar updates #1834 * fixing typos #1834 * email changes with Julie #1834 * trying to fix warning #1834 * changes #1834 * Per #1834, updating question titles and answers * Per #1834, made updates to the content. * Per #1834, made updates to the content * Per #1834, made updates to the content * Per #1834, made some major changes to the first 3 FAQ's. I don't have the time/bandwidth to review these completely at this time, but wanted to include at least these updates. * testing some of the updates John O. suggested. * updates John O. suggested take 2 #1834. * updates John O. suggested take 3 #1834. * updates John O. suggested take 4 #1834. * updates John O. suggested take 5 #1834. * updates John O. suggested. Some didn't show up even though they've been removed #1834. * trying to fix numbered list indenting #1834 * fixing numbered list indenting #1834 * cleaning up formatting #1834 * fixing broken links #1834 Co-authored-by: Julie.Prestopnik <jpresto@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * bugfix 1872 plot_tcmpr.R -lookin directory (develop) (#1874) * Bugfix 1875 develop memory (#1877) * Per #1875, fix set_cdf_ta() to initialize cdf_ta prior to populating it. * Per #1875, add debug(4) log messages whenever defining a new aggregation case in stat-analysis. * Per #1875, switch log messages about new cases from Debug(4) to Debug(3). * Per #1879, porting the same changes over to the develop branch. (#1881) * Feature 1673 gbeta (#1857) * Per #1673, add a distance_map.beta_value entry to all the Grid-Stat config files. * Per #1673, enhance Grid-Stat to parse the new beta_value option and set its value in the library code. * Per #1673, set the user-defined beta_value when processing the distance map scores. * Per #1673, add 4 new DMAP columns write them. Just writing bad data values right now, still need to actually compute them! Also need to update Stat-Analysis to update the parsing/aggregation of these new values. * Per #1673, enable beta_value to be set to a default bad data value. * Per #1673 and @ericgilleland instruction (#1673 (comment)), strip asymmetric G-Beta (AGBETA) from the output. * Per #1673, fix typo that was causing the code not to compile. * Per #1673, update MET User's Guide about G/GBETA. * Per #1673, report BETA_VALUE = TOTAL / 2 in the output instead of NA, as directed by Eric. * Per #1673, remove descriptions of Grid-Stat-specific config options for nbrhd, fourier, gradient, and distance_map from the overview section since they belong in the Grid-Stat chapter. Also add direct links for them in the Grid-Stat chapter. * Per #1673, do not reset the beta_value in DMAP::clear(). * Per #1673, log the DMAP options only after the beta_value has been determined. * Per #1673, correct the default beta_value setting as N*N / 2.0. * Per #1673, trying to format G-beta well. * Per #1673, trying to format G-beta well. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, switch to defining beta_value as a function of the input grid size. * Per #1673, push initial appendix C updates for GBETA. * Per #1673, working on G and GBETA equations. * Per #1673, working on G and GBETA equations. * Per 1673, update GBETA details in appendix C. * Per #1673, add Eric's info about selecting beta. * Per #1673, update reference for Gilleland-2019 to Gilleland_PartI-2020 and Gilleland_PartII-2020. * Per 1673, fix typo. * Per #1673, making changes requested by Eric. * Per #1673, making changes requested by Eric. * Per #1673, update references based on Eric's feedback. * Update appendixD.rst (#1869) Updated this appendix. * Update appendixD.rst * Per #1673, making the formatting of Gilleland-2020 part I and II references consistent. * Per #1673, update Grid-Stat docs to clarify that GBETA is only computed on the FULL verification domain and not any masking regions. * Per #1673, add DataPlane::n_good_data() function to return a count valid data values. * Per #1673, update vx_statistics library code to only set gbeta/beta_value to bad data for sub-domains. * Per #1673, update grid_stat to mask out bad data between the fcst/obs fields before computing distance maps. This will change existing unit test results! Also store the count of valid data values in the full verification domain. * Per #1673, since GBETA is only reported when VX_MASK = FULL, updating GridStatConfig_all to include the FULL masking region to make this example more meaningful. Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com> * Feature 1764 point stat (#1885) * Per #1764 added write_orank_row() to do_hera_ens(). SL * Per issue #1764, added orank stat type for ensemble output. SL * Per issue #1764, added code to setup_txt_files() for ORANK output. SL * Added some comments for debuging. SL * Per #1764, add orank to the list of outputs created by point_stat. * Per #1764, add functions to compute the number of requested HiRA probabilities and ensemble members. Also update n_txt_row() to keep track of the number of ORANK rows to be written. Not totally sure if I'm counting these ORANK output lines correctly though. * Per #1764, update logic in setup_txt_files() to call get_max_n_hira_prob() and get_max_n_hira_ens() functions. * Per #1764, no real changes. Just fixing spacing. * Per issue #1764, cleaned up print (cout) debug statements. SL * Per issue #1764 added 'orank = NONE' to the config files for compatibility with changes to point_stat for calculating ORANK. SL * Per issue #1764 added 'orank = STAT' to config file to produce ORANK output lines in point_stat. SL * Per issue #1764 added content in all relevant sections for ORANK: observation rank statistic. SL * Added 'orank = NONE' to config file for compatibility with changes to point_stant for ORANK. SL * Added 'orank = NONE' to config file for compatibility with changes to point_stant for ORANK. SL * Apply suggestions from code review Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Per #1764, no real changes, just fixing indents. * Per #1764, no real changes, just fixing indents. * Per #1764, no real changes, just fixing indents. * Per #1764, putting the docs for VCNT back into its logical order with the other vector line types. The order that they're listed here does not need to match their order in the enumeration in the code. * Per #1764, fixing a vcnt typo I found in the grid-stat chapter... and making them consistent. * Per issue #1764: After the call to write_orank_row, added lines to reset the observation begin and end times. SL * Per #1764, no code changes, just fixing indents. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Adding Seth to the NB notification list. * Bugfix 1886 develop grid_diag (#1888) * Per #1886, port over the bugfixes from main_v10.0 to develop. * Per #1886, make grid_diag error out if to_grid is set to FCST or OBS. * Added additional default labels * Feature 1870 realtime (#1893) * Per #1870. add TCPairs config entries for valid_inc, valid_exc, and write_valid. * Per #1870, removing 2 files I accidentally added. * Per #1870, add code to parse the new tc_pairs config options. * Per #1870, unrelated... just fixing spacing. * Per #1870, update TrackPairInfo/Array classes and tc_pairs application code to use the write_valid option to subset the tracks by requested valid time before writing them. * Per #1870, update the User's Guide with the new config options. Document valid_inc/valid_exc in the common TC config section and add write_valid to the TC-Pairs chapter. * Per #1870, move the subset_write_valid() functionality to the library code and support it for both track and probability arrays. * Per #1870, update unit_tc_pairs.xml with 2 new calls to exercise the new write_valid functionality for both tracks and probabilities. * Per #1870, correct some typos in the docs... PROBRI and probri should be PROBRIRW and probrirw, resp. * Per #1870, switching match_points from TRUE back to FALSE after I acciedentally committed that change. * Per #1870, just fixing indent. Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: jprestop <jpresto@ucar.edu> Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> Co-authored-by: hsoh-u <hsoh@ucar.edu> Co-authored-by: Keith Searight <keith.searight@noaa.gov> Co-authored-by: Seth Linden <linden@ucar.edu> Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@seneca.rap.ucar.edu> Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@kiowa.rap.ucar.edu> Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>

@ericgilleland

* Update install_met_env.kiowa Commented out items and added text to description * #1817 Added to_north argument at two_to_one() * #1817 Calls two_to_one() with false for the third argument, to_north, if latitude moves north to south * Feature 1819 automation doc warnings (#1836) * Removing "/lib" that should not be there. * #1508 checking stat() methoid returns no error before looking at FILE flag * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * #1838 Added log message for lat/lon values * #1838 Give warning if the first and lat lat/lon is same * #1838 Support the double data type variable on reading float type values * Feature 1833 develop discussions (#1849) * Per #1833, changed references to met_help to Discussions. * Per #1833, fixed typo and removed an unnecessary word * #1852 Removed unused nc_buf_size. Make cur and dim to the same size (called API handles 2D or 3D) * #1852 Check the start and count before calling NetCDF API * Feature 1746 wavelet stat (#1851) * For issue #1746 modified code to allow users to pass in an empty list (or NA) for forecast and observation thresholds in order to skip applying the threhsolds, but it will still compute stats with the raw fields. SL * For issue #1746, added new unit test that uses a config file that has empty lists for the forecast and observation thresholds. SL * For issue #1746 Added some content related to allowing users to set forecast and observation cat thresholds to an empty list in order to skip the binary masking (and consider all grid-points for stats). SL * Per #1746, cleaning up for consistent indentation. * Per #1746, cleaning up for consistent indentation. * Per #1746, add a revision history note, update the plotting range in the postscript output to be [-n,n] where n is the maximum value of the maximum absolute difference and 1.0, and also fix a bug. When the NA threshold comes AFTER a real threshold, the resulting data and difference values were not being updated. * Per #1746, change the Wavelet-Stat config file values in the the wvlt_plot dictionary by setting plot_min = plot_max = 0.0. That enables the default logic of the tool to take effect. Choose the plotting range of the wavelet plots as [-n,n], where n is the maximum of 1.0 and the maximum absolute difference. * Per #1746, used apply_fcst_thresh where it should have been apply_obs_thresh. * Per issue #1746, modified some content related to users being able to skip applying the categorical threhsolds by putting an empty list or NA in the configuration file. SL * Per issue #1746 Added some warnings if the forecast threshold is set to NA but the observation threshold is not NA (a numeric threshold) and vice versa. SL * Per #1746, fix a couple of typos and tweak wording in the wavelet-stat chapter. * Per #1746, loop over each pair of fcst/obs thresholds to check for inconsistent use of the NA threshold type. * Per #1746, a bit of code cleanup replacing calls to n_elements() with n() to make the code more concise. * Per #1746, need to reinitialize apply_fcst_thresh and apply_obs_thresh to true inside the loop since the NA threshold can appear anywhere in the list of thresholds. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Update README.md * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py * #1852 get_string_val: check if 2D variable. Also checking if the variable does not have dimension (#1860) Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> * Feature 1453 create pdf user guide (#1859) * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Feature 1853 rps doc (#1861) * Per #1853, adding RPS docs from Eric. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, adding a manual page break after the ROC image to get it to stay in the right spot. * Per #1853, backing out last change which didn't make the ROC image stay in the right spot. * #1855 Removed break after return (SobarQube) * #1855 Removed break after exit * 1855 Added return at MetNcPointObsOut::write_to_netcdf * #1855 Avoid releasing memory twice * #1855 Removed unused code * #1855 Corrected syntax error * #1855 Changed the second call of close() to release _ncFile * #1855 Deleted break after exit * #1855 Chamnged while to if * #1855 Added constructor TCLineCounts and initialized the members * #1855 Added break statement back for case '-' * #1855 Check the new size before extending to avoid thereference of the null pointer * #1855 Changed count to processed_count for log messages. Initialized variables at get_filtered_nc_data\*() * #1855 Corected the number of memory copy * #1855 Exit with an error message if both fgi & bgi are null * #1855 Clear Lead_Times before extening. Formatting for error messages * Add definition for the compilation environment on seneca. * #1855 Extend Lead_Times for new times * #1855 Removed break after exit * #1855 define "c" dynamically * #1855 Move the log message within if statement to avoid dereferencing a null pointer * Feature 1843 scatter index (#1863) * Added scatter index variables: SI, SI_BCL, SI_BCU to cnt columns. SL * Per issue #1843 Added Scatter Index variables (SI, SI_BCL, SI_BCU) to the CNT stat type. SL * Added Scatter Index (SI, SI_BCL, SI_BCU) to cnt stat type header. SL * Per issue #1843, added Scatter Index variables to write_cnt_cols(). SL * Per issue #1843 added Scatter Index (si) to CNTinfo class. SL * Per issue #1843 added Scatter Index (SI, si) to CNTInfo::get_stat(). SL * Per issue #1843 added Scatter Index (SI, si) calculation to both versions of compute_cntinfo(). SL * Per issue #1843, forgot semi-colon after SI calculation, fixed. SL * Added Scatter Index (si) to some of the clear() and allocate() functions. SL * Per issue #1843, added Scatter Index (si) to compute_cnt_mean(). SL * Per issue #1843, added Scatter Index (si) to bootstrap interval calculation and to the CNT write function. SL * Per issue #1843 added Scatter Index (SI, SI_BCL, SI_BCU) to store_stat_cnt(). SL * Per issue #1843, in get_stat() moved Scatterd Index (SI) line to be below RMSE for consitency. SL * Added Scatter Index (SI) to the CNT output format table. SL * Added Scatter Index (SI) to CNT statistics definitions. SL * Update appendixC.rst * Update stat_columns.cc * Update compute_ci.cc * Update met_stats.cc * Per #1843, update write_cntinfo() function. Since we're READING the SI value immediately after the RMSE value when computing CI's, we also need to write SI immediately after RMSE. Otherwise, we'll be computing CI's using the wrong statistics replicates. * Per #1843, check for divide by zero when computing SI... this could happen if comparing the same input file to itself with Grid-Stat. * Per #1843, correct definition of SI from RMSE/ME to RMSE/OBAR. * Per #1843, updated the SI definition to divide by OBAR instead of ME, but forgot to update the divide-by-zero check. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: johnhg <johnhg@ucar.edu> * #1855 Corected typo - compare the numnber of U and V * #1855 Check if var_info is hull * #1855 Avoid un-initialized variables: dt at open(), v at lat() & lon(), and local variables at data() * #1855 Check if ldf is null pointer * #1855 Removed break after exit * #1855 Removed break after exit * Update pcp_combine.cc * Feature 1864 config urls (#1868) * Per #1864, remove stale GitHub pages URL for the MET User's Guide. * Per #1864, found stale GitHub IO links in the issue templates. Should make this same fix in the develop and default branches for all the METplus repos. * Per #1864, fix stale GitHub IO link in the PR template. * Move ROC curve in Appendix C * Crop ROC image for better PDF formatting * Shrink ROC image for better PDF formatting * Modify figure alignment in conf.py * Change text placement for ROC curve figure * Feature 1834 faq (#1867) * testing possible new drop-down menus for FAQ * adding sphinx-panels to extensions to be able to use drop down menus in appendixA * Per #1834, adding sphinx-panels to requirements.txt to see if that fixes the error * Per #1834, added sphinx.ext to beginning of sphinx_panels to see if that fixes the error * Per #1834, remove sphinx.ext and add trailing comma to end of extensions to see if that fixed the error * Per #1834, added sphinx-panels to pip install command to see if that fixes the error * Per #1834, added extra space in comment to get docs to build to see if change to documentation.yml will fix an error * Per #1834, added return character to get rid of warning * testing dropdown menus #1 * testing dropdown menus #2 removing lines and dotted lines * testing #3 * testing 4 * fixing numbering, removing 2nd pulldown menu, trying to fix box width * adding code block in dropdown * trying to fix width * trying to fix width with spacing * trying to fix width with spacing 2nd dropdown * removing panels * solved problem, just use dropdown no panels * adding second dropdown menu * removing the dropdown menus and fixing the spacing. * fixing typos * adding in matched pairs * adding in formating files for NetCDF and making FILE_IO a header * fixing spacing * time slice * fixing spacing * UNIX time conversion * fixing spacing * fixed-width * scientific notation * removing which per Julie P * adding Gen_Vx_Mask section * fixing formatting * changing to numbers * complex masking region * neighborhood methods boundaries * Neighborhood Methods to Compute Fraction * adding Grid_Stat - How do I use Config File Setup to Read a NetCDF file * using backticks with asterics * one more backtick with asterics * Grid_Stat - What would be an example of Verifying Probabilities * fixing typos * What is an example of using Grid-Stat with Regridding and Masking Turned On * fixing typos * Grid_Stat - What would be an example of Verifying Probabilities Example2 * trying to fix typos * trying to fix code-block spacing * Per #1834, attempting to fix warning. * How do I use different masks in MET tools using MODE as an example * trying to fix bullet list * trying to fix bullet list 2 * trying to fix bullet list 2 * trying to fix bullet list 3 * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, modified formatting, including adding backslashes and removing extra returns in command line calls, and adding indentation for config file notation, and adding a return after each 'A.' * Per #1834, changed code-block from ini to none to fix formatting * *Pcp-Combine - What are some examples using -add * Pcp-Combine - How do I add and subtract with Pcp-Combine * Pcp-Combine - How do I Combine 12-hour Accumulated Precipitation from Two Different Initialization Times * Pcp-Combine - How Do I Correct a Precipitation Time Range * Pcp-Combine - What Data Formats does MET Read * Pcp-Combine - How does pass through work * Pcp_Combine - How do I use -pcprx to run a project faster * Pcp-Combine - How Do I Enter the Time Format Correctly * Pcp-Combine - How do I use -subtract * fixing formatting * Pcp_Combine - How Do I Use -sum, -add, and -subtract to Achieve Same Accumulation Interval * Pcp-Combine - What is the difference between -sum vs. -add * Pcp-Combine - How Do I Select a Specific GRIB Record to Use * fixing spacing for original text * Plot-Data-Plane - How Do I Inspect Gen_Vx_Mask Output * fixing typo * Plot-Data-Plane - How Do I Specify GRIB Version * Plot-Data-Plane - last 2 entries * 2 misc. entries * fixing typo * Stat_Analysis - How does -aggregate_stat work * Stat_Analysis - remaining entries * fixing typo * tc-pairs * tc-stat * troubleshooting area * another stat-analysis * another stat-analysis * utilities * fixing dashes * Per #1834, trying out syntax * Per #1834, removing added syntax * fixing returns with bolding * Per #1834, modified formatting * adding italics for directories #1834 * replacing code-block ini with none to remove red lettering * fixing questions to lower case #1834 * linking to section using numref #1834 * linking to section using numref #1834 attempt 2 * linking to section using numref #1834 attempt 3 * linking to section using numref #1834 attempt 4 * linking to section using numref #1834 attempt 5 * linking to section using numref #1834 attempt 6 * linking to section using numref #1834 attempt 7 * linking to section using numref #1834 attempt 8 * linking to anothre section #1834 * linking to another section #1834 * removing old info #1834 * grammar updates #1834 * grammar updates #1834 * fixing typos #1834 * email changes with Julie #1834 * trying to fix warning #1834 * changes #1834 * Per #1834, updating question titles and answers * Per #1834, made updates to the content. * Per #1834, made updates to the content * Per #1834, made updates to the content * Per #1834, made some major changes to the first 3 FAQ's. I don't have the time/bandwidth to review these completely at this time, but wanted to include at least these updates. * testing some of the updates John O. suggested. * updates John O. suggested take 2 #1834. * updates John O. suggested take 3 #1834. * updates John O. suggested take 4 #1834. * updates John O. suggested take 5 #1834. * updates John O. suggested. Some didn't show up even though they've been removed #1834. * trying to fix numbered list indenting #1834 * fixing numbered list indenting #1834 * cleaning up formatting #1834 * fixing broken links #1834 Co-authored-by: Julie.Prestopnik <jpresto@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * bugfix 1872 plot_tcmpr.R -lookin directory (develop) (#1874) * Bugfix 1875 develop memory (#1877) * Per #1875, fix set_cdf_ta() to initialize cdf_ta prior to populating it. * Per #1875, add debug(4) log messages whenever defining a new aggregation case in stat-analysis. * Per #1875, switch log messages about new cases from Debug(4) to Debug(3). * Per #1879, porting the same changes over to the develop branch. (#1881) * Feature 1673 gbeta (#1857) * Per #1673, add a distance_map.beta_value entry to all the Grid-Stat config files. * Per #1673, enhance Grid-Stat to parse the new beta_value option and set its value in the library code. * Per #1673, set the user-defined beta_value when processing the distance map scores. * Per #1673, add 4 new DMAP columns write them. Just writing bad data values right now, still need to actually compute them! Also need to update Stat-Analysis to update the parsing/aggregation of these new values. * Per #1673, enable beta_value to be set to a default bad data value. * Per #1673 and @ericgilleland instruction (#1673 (comment)), strip asymmetric G-Beta (AGBETA) from the output. * Per #1673, fix typo that was causing the code not to compile. * Per #1673, update MET User's Guide about G/GBETA. * Per #1673, report BETA_VALUE = TOTAL / 2 in the output instead of NA, as directed by Eric. * Per #1673, remove descriptions of Grid-Stat-specific config options for nbrhd, fourier, gradient, and distance_map from the overview section since they belong in the Grid-Stat chapter. Also add direct links for them in the Grid-Stat chapter. * Per #1673, do not reset the beta_value in DMAP::clear(). * Per #1673, log the DMAP options only after the beta_value has been determined. * Per #1673, correct the default beta_value setting as N*N / 2.0. * Per #1673, trying to format G-beta well. * Per #1673, trying to format G-beta well. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, switch to defining beta_value as a function of the input grid size. * Per #1673, push initial appendix C updates for GBETA. * Per #1673, working on G and GBETA equations. * Per #1673, working on G and GBETA equations. * Per 1673, update GBETA details in appendix C. * Per #1673, add Eric's info about selecting beta. * Per #1673, update reference for Gilleland-2019 to Gilleland_PartI-2020 and Gilleland_PartII-2020. * Per 1673, fix typo. * Per #1673, making changes requested by Eric. * Per #1673, making changes requested by Eric. * Per #1673, update references based on Eric's feedback. * Update appendixD.rst (#1869) Updated this appendix. * Update appendixD.rst * Per #1673, making the formatting of Gilleland-2020 part I and II references consistent. * Per #1673, update Grid-Stat docs to clarify that GBETA is only computed on the FULL verification domain and not any masking regions. * Per #1673, add DataPlane::n_good_data() function to return a count valid data values. * Per #1673, update vx_statistics library code to only set gbeta/beta_value to bad data for sub-domains. * Per #1673, update grid_stat to mask out bad data between the fcst/obs fields before computing distance maps. This will change existing unit test results! Also store the count of valid data values in the full verification domain. * Per #1673, since GBETA is only reported when VX_MASK = FULL, updating GridStatConfig_all to include the FULL masking region to make this example more meaningful. Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com> * Feature 1764 point stat (#1885) * Per #1764 added write_orank_row() to do_hera_ens(). SL * Per issue #1764, added orank stat type for ensemble output. SL * Per issue #1764, added code to setup_txt_files() for ORANK output. SL * Added some comments for debuging. SL * Per #1764, add orank to the list of outputs created by point_stat. * Per #1764, add functions to compute the number of requested HiRA probabilities and ensemble members. Also update n_txt_row() to keep track of the number of ORANK rows to be written. Not totally sure if I'm counting these ORANK output lines correctly though. * Per #1764, update logic in setup_txt_files() to call get_max_n_hira_prob() and get_max_n_hira_ens() functions. * Per #1764, no real changes. Just fixing spacing. * Per issue #1764, cleaned up print (cout) debug statements. SL * Per issue #1764 added 'orank = NONE' to the config files for compatibility with changes to point_stat for calculating ORANK. SL * Per issue #1764 added 'orank = STAT' to config file to produce ORANK output lines in point_stat. SL * Per issue #1764 added content in all relevant sections for ORANK: observation rank statistic. SL * Added 'orank = NONE' to config file for compatibility with changes to point_stant for ORANK. SL * Added 'orank = NONE' to config file for compatibility with changes to point_stant for ORANK. SL * Apply suggestions from code review Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Per #1764, no real changes, just fixing indents. * Per #1764, no real changes, just fixing indents. * Per #1764, no real changes, just fixing indents. * Per #1764, putting the docs for VCNT back into its logical order with the other vector line types. The order that they're listed here does not need to match their order in the enumeration in the code. * Per #1764, fixing a vcnt typo I found in the grid-stat chapter... and making them consistent. * Per issue #1764: After the call to write_orank_row, added lines to reset the observation begin and end times. SL * Per #1764, no code changes, just fixing indents. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Adding Seth to the NB notification list. * Bugfix 1886 develop grid_diag (#1888) * Per #1886, port over the bugfixes from main_v10.0 to develop. * Per #1886, make grid_diag error out if to_grid is set to FCST or OBS. * Added additional default labels * Feature 1870 realtime (#1893) * Per #1870. add TCPairs config entries for valid_inc, valid_exc, and write_valid. * Per #1870, removing 2 files I accidentally added. * Per #1870, add code to parse the new tc_pairs config options. * Per #1870, unrelated... just fixing spacing. * Per #1870, update TrackPairInfo/Array classes and tc_pairs application code to use the write_valid option to subset the tracks by requested valid time before writing them. * Per #1870, update the User's Guide with the new config options. Document valid_inc/valid_exc in the common TC config section and add write_valid to the TC-Pairs chapter. * Per #1870, move the subset_write_valid() functionality to the library code and support it for both track and probability arrays. * Per #1870, update unit_tc_pairs.xml with 2 new calls to exercise the new write_valid functionality for both tracks and probabilities. * Per #1870, correct some typos in the docs... PROBRI and probri should be PROBRIRW and probrirw, resp. * Per #1870, switching match_points from TRUE back to FALSE after I acciedentally committed that change. * Per #1870, just fixing indent. Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> * Feature 1788 ssidx (#1892) * Per #1788, add initial definition of the SSIDX line type. * Per #1788, add a STAT-Analysis config file for computing the CBS Score. This is currently just a copy of the GO Index. * Per #1788, add hooks for computing -job cbs_score. * Per #1788, since we're adding a new SSIDX line type, the columns for that line type replace the job_ss_columns and job_go_columns arrays. * Per #1788, rename cbs_score to cbs_index per UK Met Office instruction on 7/22/21. This convention is also consistent with the existing go_index and ss_index jobs. * Per #1788 rename STATAnalysisConfig_CBS_Score to STATAnalysisConfig_CBS_Index * Per #1788, update Makefile to handle name change. * Per #1788, add support for SSIDX stat line type. * Per #1788, define 4 output SSIDX columns. * Per #1788, define an SSIndexInfo struct for stashing/writing SS Index values. * Per #1788, write the SSIDX columns. However we don't need to function to write the whole row since it's only written by Stat-Analysis. * Per #1788, create an AggrSSIndexInfo struct to keep track of unique stat header column input values. * Per #1788, update the stat-analysis job code to make use of the new structs. * Per #1788 fix typo. * Per #1788, remove GO Index defintion from the code comments. That detail belongs elsewhere. * Per #1788, since coding up the GO Index several CNT and CTC columns have been added. Adding them here to let them be included as part of the Skill Score index computations. * Per #1788, update check_hdr_str() to print the name of the problematic header columns. * Per #1788, add a set(one) member function to multiple array classes. This calls clear or erase on the array prior to adding a single element. Add this for StringArray, NumArray, and ThreshArray, and CRCArray. * Per #1788, update the compute_ss_index() function in stat_analysis to make the code more concise by calling the newly adding singular set functions for arrays. * Per #1788, add FCST_MODEL and REF_MODEL output columns to the SSIDX line type. * Per #1788, add a new N_INIT column to the SSIDX line type to report the number of initialization times represented by this skill score. Also define the SSIDXData struct to store the skill score index job output. * Per #1788, update STATAnalysisJob to explicitly set the job type directly rather than parsing a string. * Per #1788, major change here adding skill_score_index_job.h/.cc to handle the computation of the skill score indices. * Per #1788, update stat_analysis source code to make use of the new classes in skill_score_index_job.h/.cc. * Per #1788, write a log message listing the model initialization times over which the skill score index is computed. * Per #1788, tweak log message. * Per #1788, compute n_term as the max lenght of the required arrays. * Per #1788, drop in the ACTUAL definition of the GO index provide by the DTC AF project team. Also simplify the existing arrays down to lenght one if the value remains constant. * Per #1788, correct CBS Index config file. Some parameters had 40 elements while others only had 32. * Per #1788, do not write SSIDX output if there are no valid terms found. * Per #1788, format the values in the skill score index log messages, replacing -9999 with NA. * Per #1788, update the get_stat() member functions. For 0 pairs, return bad data for all statistics other than TOTAL. * Per #1788, working on readability of the warning and error messages. * Per #1788, define the ss_index_name directly in the STATAnalysis config file to make it really easy to modify. * Per #1788, store the ss_index_name configuration option in the StatJob class. Also support a command line -ss_index_name option to override the config file value. * Per #1788, change from name to ss_index_name variable to be a bit more descriptive in the variable names. * Per #1788, since ss_index_name is in the StatJob class we no longer need to pass it around as an argument. * Per #1788, simply the skill score index job handling logic a bit. We only need to update the default job once, not twice.: * Revert "Per #1788, since ss_index_name is in the StatJob class we no longer need to pass it around as an argument." This reverts commit cde0be0. * Revert "Revert "Per #1788, since ss_index_name is in the StatJob class we no longer need to pass it around as an argument."" This reverts commit bbfd838. * Per #1788, I'd pruned too much code from stat_analysis.cc which caused the processing of config file jobs to fail. Fixing that here. * Per #1788, switch Z0 to L0 to match the sample data for computing CBS Index. * Per #1788, make it so that cbs_index and go_index work from config file. * Per #1788, update the documentation for the skill score index changes. * Per #1788, just move some variable definitions further down since they're only used sometimes. * Per #1788, make job output description into a numbered section. * Per #1788, little tweak. * Per #1788, update the STATAnalysisConfig files to add ss_index_name and hss_ec_value, as needed. * Per #1788, add new unit tests to exercise recent ss_index changes and update the Stat-Analysis documentation. * Update met/docs/Users_Guide/stat-analysis.rst Co-authored-by: jprestop <jpresto@ucar.edu> * Update met/docs/Users_Guide/stat-analysis.rst Sorry for the typos! Thanks for catching them. Co-authored-by: jprestop <jpresto@ucar.edu> * Update met/docs/Users_Guide/stat-analysis.rst Co-authored-by: jprestop <jpresto@ucar.edu> * Per #1788, fix typo in error message. * Per #1788, fix a bug for ss_index... changing 'add' to 'set'. Also set the line_type seperately for each term, if requested. * Per #1788, tweak the ss_index logic slightly to make it more efficient. For each input STATLine, instead of checking all the index terms, stop searching after the first match. This assumes that each input line should be used for only one of the terms... and I think that's a pretty reasonable assumption. * Per #1788, minor tweaks to the STAT-Analysis docs. * Per #1788, add ss_index_vld_thresh option to existing STAT-Analysis config files. * Per #1788, add StatAnalysisJob ss_index_vld_thresh entry and parse it from the STAT-Analysis config file. * Per #1788, update stat_analysis code to check ss_index_vld_thresh setting when computing the skill score index. Also update the Stat-Analysis chapter of the User's Guide. * Per #1788, tweak one test to exercise a non-default ss_index_vld_thresh value. Co-authored-by: jprestop <jpresto@ucar.edu> Co-authored-by: jprestop <jpresto@ucar.edu> Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> Co-authored-by: hsoh-u <hsoh@ucar.edu> Co-authored-by: Keith Searight <keith.searight@noaa.gov> Co-authored-by: Seth Linden <linden@ucar.edu> Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@seneca.rap.ucar.edu> Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@kiowa.rap.ucar.edu> Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>

@ericgilleland

* Update install_met_env.kiowa Commented out items and added text to description * #1817 Added to_north argument at two_to_one() * #1817 Calls two_to_one() with false for the third argument, to_north, if latitude moves north to south * Feature 1819 automation doc warnings (#1836) * Removing "/lib" that should not be there. * #1508 checking stat() methoid returns no error before looking at FILE flag * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * #1838 Added log message for lat/lon values * #1838 Give warning if the first and lat lat/lon is same * #1838 Support the double data type variable on reading float type values * Feature 1833 develop discussions (#1849) * Per #1833, changed references to met_help to Discussions. * Per #1833, fixed typo and removed an unnecessary word * #1852 Removed unused nc_buf_size. Make cur and dim to the same size (called API handles 2D or 3D) * #1852 Check the start and count before calling NetCDF API * Feature 1746 wavelet stat (#1851) * For issue #1746 modified code to allow users to pass in an empty list (or NA) for forecast and observation thresholds in order to skip applying the threhsolds, but it will still compute stats with the raw fields. SL * For issue #1746, added new unit test that uses a config file that has empty lists for the forecast and observation thresholds. SL * For issue #1746 Added some content related to allowing users to set forecast and observation cat thresholds to an empty list in order to skip the binary masking (and consider all grid-points for stats). SL * Per #1746, cleaning up for consistent indentation. * Per #1746, cleaning up for consistent indentation. * Per #1746, add a revision history note, update the plotting range in the postscript output to be [-n,n] where n is the maximum value of the maximum absolute difference and 1.0, and also fix a bug. When the NA threshold comes AFTER a real threshold, the resulting data and difference values were not being updated. * Per #1746, change the Wavelet-Stat config file values in the the wvlt_plot dictionary by setting plot_min = plot_max = 0.0. That enables the default logic of the tool to take effect. Choose the plotting range of the wavelet plots as [-n,n], where n is the maximum of 1.0 and the maximum absolute difference. * Per #1746, used apply_fcst_thresh where it should have been apply_obs_thresh. * Per issue #1746, modified some content related to users being able to skip applying the categorical threhsolds by putting an empty list or NA in the configuration file. SL * Per issue #1746 Added some warnings if the forecast threshold is set to NA but the observation threshold is not NA (a numeric threshold) and vice versa. SL * Per #1746, fix a couple of typos and tweak wording in the wavelet-stat chapter. * Per #1746, loop over each pair of fcst/obs thresholds to check for inconsistent use of the NA threshold type. * Per #1746, a bit of code cleanup replacing calls to n_elements() with n() to make the code more concise. * Per #1746, need to reinitialize apply_fcst_thresh and apply_obs_thresh to true inside the loop since the NA threshold can appear anywhere in the list of thresholds. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Update README.md * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py * #1852 get_string_val: check if 2D variable. Also checking if the variable does not have dimension (#1860) Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> * Feature 1453 create pdf user guide (#1859) * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Feature 1853 rps doc (#1861) * Per #1853, adding RPS docs from Eric. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, adding a manual page break after the ROC image to get it to stay in the right spot. * Per #1853, backing out last change which didn't make the ROC image stay in the right spot. * #1855 Removed break after return (SobarQube) * #1855 Removed break after exit * 1855 Added return at MetNcPointObsOut::write_to_netcdf * #1855 Avoid releasing memory twice * #1855 Removed unused code * #1855 Corrected syntax error * #1855 Changed the second call of close() to release _ncFile * #1855 Deleted break after exit * #1855 Chamnged while to if * #1855 Added constructor TCLineCounts and initialized the members * #1855 Added break statement back for case '-' * #1855 Check the new size before extending to avoid thereference of the null pointer * #1855 Changed count to processed_count for log messages. Initialized variables at get_filtered_nc_data\*() * #1855 Corected the number of memory copy * #1855 Exit with an error message if both fgi & bgi are null * #1855 Clear Lead_Times before extening. Formatting for error messages * Add definition for the compilation environment on seneca. * #1855 Extend Lead_Times for new times * #1855 Removed break after exit * #1855 define "c" dynamically * #1855 Move the log message within if statement to avoid dereferencing a null pointer * Feature 1843 scatter index (#1863) * Added scatter index variables: SI, SI_BCL, SI_BCU to cnt columns. SL * Per issue #1843 Added Scatter Index variables (SI, SI_BCL, SI_BCU) to the CNT stat type. SL * Added Scatter Index (SI, SI_BCL, SI_BCU) to cnt stat type header. SL * Per issue #1843, added Scatter Index variables to write_cnt_cols(). SL * Per issue #1843 added Scatter Index (si) to CNTinfo class. SL * Per issue #1843 added Scatter Index (SI, si) to CNTInfo::get_stat(). SL * Per issue #1843 added Scatter Index (SI, si) calculation to both versions of compute_cntinfo(). SL * Per issue #1843, forgot semi-colon after SI calculation, fixed. SL * Added Scatter Index (si) to some of the clear() and allocate() functions. SL * Per issue #1843, added Scatter Index (si) to compute_cnt_mean(). SL * Per issue #1843, added Scatter Index (si) to bootstrap interval calculation and to the CNT write function. SL * Per issue #1843 added Scatter Index (SI, SI_BCL, SI_BCU) to store_stat_cnt(). SL * Per issue #1843, in get_stat() moved Scatterd Index (SI) line to be below RMSE for consitency. SL * Added Scatter Index (SI) to the CNT output format table. SL * Added Scatter Index (SI) to CNT statistics definitions. SL * Update appendixC.rst * Update stat_columns.cc * Update compute_ci.cc * Update met_stats.cc * Per #1843, update write_cntinfo() function. Since we're READING the SI value immediately after the RMSE value when computing CI's, we also need to write SI immediately after RMSE. Otherwise, we'll be computing CI's using the wrong statistics replicates. * Per #1843, check for divide by zero when computing SI... this could happen if comparing the same input file to itself with Grid-Stat. * Per #1843, correct definition of SI from RMSE/ME to RMSE/OBAR. * Per #1843, updated the SI definition to divide by OBAR instead of ME, but forgot to update the divide-by-zero check. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: johnhg <johnhg@ucar.edu> * #1855 Corected typo - compare the numnber of U and V * #1855 Check if var_info is hull * #1855 Avoid un-initialized variables: dt at open(), v at lat() & lon(), and local variables at data() * #1855 Check if ldf is null pointer * #1855 Removed break after exit * #1855 Removed break after exit * Update pcp_combine.cc * Feature 1864 config urls (#1868) * Per #1864, remove stale GitHub pages URL for the MET User's Guide. * Per #1864, found stale GitHub IO links in the issue templates. Should make this same fix in the develop and default branches for all the METplus repos. * Per #1864, fix stale GitHub IO link in the PR template. * Move ROC curve in Appendix C * Crop ROC image for better PDF formatting * Shrink ROC image for better PDF formatting * Modify figure alignment in conf.py * Change text placement for ROC curve figure * Feature 1834 faq (#1867) * testing possible new drop-down menus for FAQ * adding sphinx-panels to extensions to be able to use drop down menus in appendixA * Per #1834, adding sphinx-panels to requirements.txt to see if that fixes the error * Per #1834, added sphinx.ext to beginning of sphinx_panels to see if that fixes the error * Per #1834, remove sphinx.ext and add trailing comma to end of extensions to see if that fixed the error * Per #1834, added sphinx-panels to pip install command to see if that fixes the error * Per #1834, added extra space in comment to get docs to build to see if change to documentation.yml will fix an error * Per #1834, added return character to get rid of warning * testing dropdown menus #1 * testing dropdown menus #2 removing lines and dotted lines * testing #3 * testing 4 * fixing numbering, removing 2nd pulldown menu, trying to fix box width * adding code block in dropdown * trying to fix width * trying to fix width with spacing * trying to fix width with spacing 2nd dropdown * removing panels * solved problem, just use dropdown no panels * adding second dropdown menu * removing the dropdown menus and fixing the spacing. * fixing typos * adding in matched pairs * adding in formating files for NetCDF and making FILE_IO a header * fixing spacing * time slice * fixing spacing * UNIX time conversion * fixing spacing * fixed-width * scientific notation * removing which per Julie P * adding Gen_Vx_Mask section * fixing formatting * changing to numbers * complex masking region * neighborhood methods boundaries * Neighborhood Methods to Compute Fraction * adding Grid_Stat - How do I use Config File Setup to Read a NetCDF file * using backticks with asterics * one more backtick with asterics * Grid_Stat - What would be an example of Verifying Probabilities * fixing typos * What is an example of using Grid-Stat with Regridding and Masking Turned On * fixing typos * Grid_Stat - What would be an example of Verifying Probabilities Example2 * trying to fix typos * trying to fix code-block spacing * Per #1834, attempting to fix warning. * How do I use different masks in MET tools using MODE as an example * trying to fix bullet list * trying to fix bullet list 2 * trying to fix bullet list 2 * trying to fix bullet list 3 * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, modified formatting, including adding backslashes and removing extra returns in command line calls, and adding indentation for config file notation, and adding a return after each 'A.' * Per #1834, changed code-block from ini to none to fix formatting * *Pcp-Combine - What are some examples using -add * Pcp-Combine - How do I add and subtract with Pcp-Combine * Pcp-Combine - How do I Combine 12-hour Accumulated Precipitation from Two Different Initialization Times * Pcp-Combine - How Do I Correct a Precipitation Time Range * Pcp-Combine - What Data Formats does MET Read * Pcp-Combine - How does pass through work * Pcp_Combine - How do I use -pcprx to run a project faster * Pcp-Combine - How Do I Enter the Time Format Correctly * Pcp-Combine - How do I use -subtract * fixing formatting * Pcp_Combine - How Do I Use -sum, -add, and -subtract to Achieve Same Accumulation Interval * Pcp-Combine - What is the difference between -sum vs. -add * Pcp-Combine - How Do I Select a Specific GRIB Record to Use * fixing spacing for original text * Plot-Data-Plane - How Do I Inspect Gen_Vx_Mask Output * fixing typo * Plot-Data-Plane - How Do I Specify GRIB Version * Plot-Data-Plane - last 2 entries * 2 misc. entries * fixing typo * Stat_Analysis - How does -aggregate_stat work * Stat_Analysis - remaining entries * fixing typo * tc-pairs * tc-stat * troubleshooting area * another stat-analysis * another stat-analysis * utilities * fixing dashes * Per #1834, trying out syntax * Per #1834, removing added syntax * fixing returns with bolding * Per #1834, modified formatting * adding italics for directories #1834 * replacing code-block ini with none to remove red lettering * fixing questions to lower case #1834 * linking to section using numref #1834 * linking to section using numref #1834 attempt 2 * linking to section using numref #1834 attempt 3 * linking to section using numref #1834 attempt 4 * linking to section using numref #1834 attempt 5 * linking to section using numref #1834 attempt 6 * linking to section using numref #1834 attempt 7 * linking to section using numref #1834 attempt 8 * linking to anothre section #1834 * linking to another section #1834 * removing old info #1834 * grammar updates #1834 * grammar updates #1834 * fixing typos #1834 * email changes with Julie #1834 * trying to fix warning #1834 * changes #1834 * Per #1834, updating question titles and answers * Per #1834, made updates to the content. * Per #1834, made updates to the content * Per #1834, made updates to the content * Per #1834, made some major changes to the first 3 FAQ's. I don't have the time/bandwidth to review these completely at this time, but wanted to include at least these updates. * testing some of the updates John O. suggested. * updates John O. suggested take 2 #1834. * updates John O. suggested take 3 #1834. * updates John O. suggested take 4 #1834. * updates John O. suggested take 5 #1834. * updates John O. suggested. Some didn't show up even though they've been removed #1834. * trying to fix numbered list indenting #1834 * fixing numbered list indenting #1834 * cleaning up formatting #1834 * fixing broken links #1834 Co-authored-by: Julie.Prestopnik <jpresto@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * bugfix 1872 plot_tcmpr.R -lookin directory (develop) (#1874) * Bugfix 1875 develop memory (#1877) * Per #1875, fix set_cdf_ta() to initialize cdf_ta prior to populating it. * Per #1875, add debug(4) log messages whenever defining a new aggregation case in stat-analysis. * Per #1875, switch log messages about new cases from Debug(4) to Debug(3). * Per #1879, porting the same changes over to the develop branch. (#1881) * Feature 1673 gbeta (#1857) * Per #1673, add a distance_map.beta_value entry to all the Grid-Stat config files. * Per #1673, enhance Grid-Stat to parse the new beta_value option and set its value in the library code. * Per #1673, set the user-defined beta_value when processing the distance map scores. * Per #1673, add 4 new DMAP columns write them. Just writing bad data values right now, still need to actually compute them! Also need to update Stat-Analysis to update the parsing/aggregation of these new values. * Per #1673, enable beta_value to be set to a default bad data value. * Per #1673 and @ericgilleland instruction (#1673 (comment)), strip asymmetric G-Beta (AGBETA) from the output. * Per #1673, fix typo that was causing the code not to compile. * Per #1673, update MET User's Guide about G/GBETA. * Per #1673, report BETA_VALUE = TOTAL / 2 in the output instead of NA, as directed by Eric. * Per #1673, remove descriptions of Grid-Stat-specific config options for nbrhd, fourier, gradient, and distance_map from the overview section since they belong in the Grid-Stat chapter. Also add direct links for them in the Grid-Stat chapter. * Per #1673, do not reset the beta_value in DMAP::clear(). * Per #1673, log the DMAP options only after the beta_value has been determined. * Per #1673, correct the default beta_value setting as N*N / 2.0. * Per #1673, trying to format G-beta well. * Per #1673, trying to format G-beta well. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, switch to defining beta_value as a function of the input grid size. * Per #1673, push initial appendix C updates for GBETA. * Per #1673, working on G and GBETA equations. * Per #1673, working on G and GBETA equations. * Per 1673, update GBETA details in appendix C. * Per #1673, add Eric's info about selecting beta. * Per #1673, update reference for Gilleland-2019 to Gilleland_PartI-2020 and Gilleland_PartII-2020. * Per 1673, fix typo. * Per #1673, making changes requested by Eric. * Per #1673, making changes requested by Eric. * Per #1673, update references based on Eric's feedback. * Update appendixD.rst (#1869) Updated this appendix. * Update appendixD.rst * Per #1673, making the formatting of Gilleland-2020 part I and II references consistent. * Per #1673, update Grid-Stat docs to clarify that GBETA is only computed on the FULL verification domain and not any masking regions. * Per #1673, add DataPlane::n_good_data() function to return a count valid data values. * Per #1673, update vx_statistics library code to only set gbeta/beta_value to bad data for sub-domains. * Per #1673, update grid_stat to mask out bad data between the fcst/obs fields before computing distance maps. This will change existing unit test results! Also store the count of valid data values in the full verification domain. * Per #1673, since GBETA is only reported when VX_MASK = FULL, updating GridStatConfig_all to include the FULL masking region to make this example more meaningful. Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com> * Feature 1764 point stat (#1885) * Per #1764 added write_orank_row() to do_hera_ens(). SL * Per issue #1764, added orank stat type for ensemble output. SL * Per issue #1764, added code to setup_txt_files() for ORANK output. SL * Added some comments for debuging. SL * Per #1764, add orank to the list of outputs created by point_stat. * Per #1764, add functions to compute the number of requested HiRA probabilities and ensemble members. Also update n_txt_row() to keep track of the number of ORANK rows to be written. Not totally sure if I'm counting these ORANK output lines correctly though. * Per #1764, update logic in setup_txt_files() to call get_max_n_hira_prob() and get_max_n_hira_ens() functions. * Per #1764, no real changes. Just fixing spacing. * Per issue #1764, cleaned up print (cout) debug statements. SL * Per issue #1764 added 'orank = NONE' to the config files for compatibility with changes to point_stat for calculating ORANK. SL * Per issue #1764 added 'orank = STAT' to config file to produce ORANK output lines in point_stat. SL * Per issue #1764 added content in all relevant sections for ORANK: observation rank statistic. SL * Added 'orank = NONE' to config file for compatibility with changes to point_stant for ORANK. SL * Added 'orank = NONE' to config file for compatibility with changes to point_stant for ORANK. SL * Apply suggestions from code review Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Per #1764, no real changes, just fixing indents. * Per #1764, no real changes, just fixing indents. * Per #1764, no real changes, just fixing indents. * Per #1764, putting the docs for VCNT back into its logical order with the other vector line types. The order that they're listed here does not need to match their order in the enumeration in the code. * Per #1764, fixing a vcnt typo I found in the grid-stat chapter... and making them consistent. * Per issue #1764: After the call to write_orank_row, added lines to reset the observation begin and end times. SL * Per #1764, no code changes, just fixing indents. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Adding Seth to the NB notification list. * Bugfix 1886 develop grid_diag (#1888) * Per #1886, port over the bugfixes from main_v10.0 to develop. * Per #1886, make grid_diag error out if to_grid is set to FCST or OBS. * Added additional default labels * Feature 1870 realtime (#1893) * Per #1870. add TCPairs config entries for valid_inc, valid_exc, and write_valid. * Per #1870, removing 2 files I accidentally added. * Per #1870, add code to parse the new tc_pairs config options. * Per #1870, unrelated... just fixing spacing. * Per #1870, update TrackPairInfo/Array classes and tc_pairs application code to use the write_valid option to subset the tracks by requested valid time before writing them. * Per #1870, update the User's Guide with the new config options. Document valid_inc/valid_exc in the common TC config section and add write_valid to the TC-Pairs chapter. * Per #1870, move the subset_write_valid() functionality to the library code and support it for both track and probability arrays. * Per #1870, update unit_tc_pairs.xml with 2 new calls to exercise the new write_valid functionality for both tracks and probabilities. * Per #1870, correct some typos in the docs... PROBRI and probri should be PROBRIRW and probrirw, resp. * Per #1870, switching match_points from TRUE back to FALSE after I acciedentally committed that change. * Per #1870, just fixing indent. Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> * Feature 1788 ssidx (#1892) * Per #1788, add initial definition of the SSIDX line type. * Per #1788, add a STAT-Analysis config file for computing the CBS Score. This is currently just a copy of the GO Index. * Per #1788, add hooks for computing -job cbs_score. * Per #1788, since we're adding a new SSIDX line type, the columns for that line type replace the job_ss_columns and job_go_columns arrays. * Per #1788, rename cbs_score to cbs_index per UK Met Office instruction on 7/22/21. This convention is also consistent with the existing go_index and ss_index jobs. * Per #1788 rename STATAnalysisConfig_CBS_Score to STATAnalysisConfig_CBS_Index * Per #1788, update Makefile to handle name change. * Per #1788, add support for SSIDX stat line type. * Per #1788, define 4 output SSIDX columns. * Per #1788, define an SSIndexInfo struct for stashing/writing SS Index values. * Per #1788, write the SSIDX columns. However we don't need to function to write the whole row since it's only written by Stat-Analysis. * Per #1788, create an AggrSSIndexInfo struct to keep track of unique stat header column input values. * Per #1788, update the stat-analysis job code to make use of the new structs. * Per #1788 fix typo. * Per #1788, remove GO Index defintion from the code comments. That detail belongs elsewhere. * Per #1788, since coding up the GO Index several CNT and CTC columns have been added. Adding them here to let them be included as part of the Skill Score index computations. * Per #1788, update check_hdr_str() to print the name of the problematic header columns. * Per #1788, add a set(one) member function to multiple array classes. This calls clear or erase on the array prior to adding a single element. Add this for StringArray, NumArray, and ThreshArray, and CRCArray. * Per #1788, update the compute_ss_index() function in stat_analysis to make the code more concise by calling the newly adding singular set functions for arrays. * Per #1788, add FCST_MODEL and REF_MODEL output columns to the SSIDX line type. * Per #1788, add a new N_INIT column to the SSIDX line type to report the number of initialization times represented by this skill score. Also define the SSIDXData struct to store the skill score index job output. * Per #1788, update STATAnalysisJob to explicitly set the job type directly rather than parsing a string. * Per #1788, major change here adding skill_score_index_job.h/.cc to handle the computation of the skill score indices. * Per #1788, update stat_analysis source code to make use of the new classes in skill_score_index_job.h/.cc. * Per #1788, write a log message listing the model initialization times over which the skill score index is computed. * Per #1788, tweak log message. * Per #1788, compute n_term as the max lenght of the required arrays. * Per #1788, drop in the ACTUAL definition of the GO index provide by the DTC AF project team. Also simplify the existing arrays down to lenght one if the value remains constant. * Per #1788, correct CBS Index config file. Some parameters had 40 elements while others only had 32. * Per #1788, do not write SSIDX output if there are no valid terms found. * Per #1788, format the values in the skill score index log messages, replacing -9999 with NA. * Per #1788, update the get_stat() member functions. For 0 pairs, return bad data for all statistics other than TOTAL. * Per #1788, working on readability of the warning and error messages. * Per #1788, define the ss_index_name directly in the STATAnalysis config file to make it really easy to modify. * Per #1788, store the ss_index_name configuration option in the StatJob class. Also support a command line -ss_index_name option to override the config file value. * Per #1788, change from name to ss_index_name variable to be a bit more descriptive in the variable names. * Per #1788, since ss_index_name is in the StatJob class we no longer need to pass it around as an argument. * Per #1788, simply the skill score index job handling logic a bit. We only need to update the default job once, not twice.: * Revert "Per #1788, since ss_index_name is in the StatJob class we no longer need to pass it around as an argument." This reverts commit cde0be0. * Revert "Revert "Per #1788, since ss_index_name is in the StatJob class we no longer need to pass it around as an argument."" This reverts commit bbfd838. * Per #1788, I'd pruned too much code from stat_analysis.cc which caused the processing of config file jobs to fail. Fixing that here. * Per #1788, switch Z0 to L0 to match the sample data for computing CBS Index. * Per #1788, make it so that cbs_index and go_index work from config file. * Per #1788, update the documentation for the skill score index changes. * Per #1788, just move some variable definitions further down since they're only used sometimes. * Per #1788, make job output description into a numbered section. * Per #1788, little tweak. * Per #1788, update the STATAnalysisConfig files to add ss_index_name and hss_ec_value, as needed. * Per #1788, add new unit tests to exercise recent ss_index changes and update the Stat-Analysis documentation. * Update met/docs/Users_Guide/stat-analysis.rst Co-authored-by: jprestop <jpresto@ucar.edu> * Update met/docs/Users_Guide/stat-analysis.rst Sorry for the typos! Thanks for catching them. Co-authored-by: jprestop <jpresto@ucar.edu> * Update met/docs/Users_Guide/stat-analysis.rst Co-authored-by: jprestop <jpresto@ucar.edu> * Per #1788, fix typo in error message. * Per #1788, fix a bug for ss_index... changing 'add' to 'set'. Also set the line_type seperately for each term, if requested. * Per #1788, tweak the ss_index logic slightly to make it more efficient. For each input STATLine, instead of checking all the index terms, stop searching after the first match. This assumes that each input line should be used for only one of the terms... and I think that's a pretty reasonable assumption. * Per #1788, minor tweaks to the STAT-Analysis docs. * Per #1788, add ss_index_vld_thresh option to existing STAT-Analysis config files. * Per #1788, add StatAnalysisJob ss_index_vld_thresh entry and parse it from the STAT-Analysis config file. * Per #1788, update stat_analysis code to check ss_index_vld_thresh setting when computing the skill score index. Also update the Stat-Analysis chapter of the User's Guide. * Per #1788, tweak one test to exercise a non-default ss_index_vld_thresh value. Co-authored-by: jprestop <jpresto@ucar.edu> * Bugfix 1891 gen_vx_mask (#1895) * Per #1891, tighten up the gen_vx_mask logic a bit. Use a global config for the default NC compression level. Then read the input and mask fields using local variables instead of the global one to ensure they don't affect eachother. Also took the opportunity to refine the logic so that we only create a mtddf object in one spot, in the get_data_plane() function. * Per #1891, add a new test in unit_gen_vx_mask.xml that fails prior to #1891 and succeeds with these changes. * Per #1891, file name typo in unit_gen_vx_mask.xml. Co-authored-by: jprestop <jpresto@ucar.edu> Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> Co-authored-by: hsoh-u <hsoh@ucar.edu> Co-authored-by: Keith Searight <keith.searight@noaa.gov> Co-authored-by: Seth Linden <linden@ucar.edu> Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@seneca.rap.ucar.edu> Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@kiowa.rap.ucar.edu> Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>

@ericgilleland

* Update install_met_env.kiowa Commented out items and added text to description * #1817 Added to_north argument at two_to_one() * #1817 Calls two_to_one() with false for the third argument, to_north, if latitude moves north to south * Feature 1819 automation doc warnings (#1836) * Removing "/lib" that should not be there. * #1508 checking stat() methoid returns no error before looking at FILE flag * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * #1838 Added log message for lat/lon values * #1838 Give warning if the first and lat lat/lon is same * #1838 Support the double data type variable on reading float type values * Feature 1833 develop discussions (#1849) * Per #1833, changed references to met_help to Discussions. * Per #1833, fixed typo and removed an unnecessary word * #1852 Removed unused nc_buf_size. Make cur and dim to the same size (called API handles 2D or 3D) * #1852 Check the start and count before calling NetCDF API * Feature 1746 wavelet stat (#1851) * For issue #1746 modified code to allow users to pass in an empty list (or NA) for forecast and observation thresholds in order to skip applying the threhsolds, but it will still compute stats with the raw fields. SL * For issue #1746, added new unit test that uses a config file that has empty lists for the forecast and observation thresholds. SL * For issue #1746 Added some content related to allowing users to set forecast and observation cat thresholds to an empty list in order to skip the binary masking (and consider all grid-points for stats). SL * Per #1746, cleaning up for consistent indentation. * Per #1746, cleaning up for consistent indentation. * Per #1746, add a revision history note, update the plotting range in the postscript output to be [-n,n] where n is the maximum value of the maximum absolute difference and 1.0, and also fix a bug. When the NA threshold comes AFTER a real threshold, the resulting data and difference values were not being updated. * Per #1746, change the Wavelet-Stat config file values in the the wvlt_plot dictionary by setting plot_min = plot_max = 0.0. That enables the default logic of the tool to take effect. Choose the plotting range of the wavelet plots as [-n,n], where n is the maximum of 1.0 and the maximum absolute difference. * Per #1746, used apply_fcst_thresh where it should have been apply_obs_thresh. * Per issue #1746, modified some content related to users being able to skip applying the categorical threhsolds by putting an empty list or NA in the configuration file. SL * Per issue #1746 Added some warnings if the forecast threshold is set to NA but the observation threshold is not NA (a numeric threshold) and vice versa. SL * Per #1746, fix a couple of typos and tweak wording in the wavelet-stat chapter. * Per #1746, loop over each pair of fcst/obs thresholds to check for inconsistent use of the NA threshold type. * Per #1746, a bit of code cleanup replacing calls to n_elements() with n() to make the code more concise. * Per #1746, need to reinitialize apply_fcst_thresh and apply_obs_thresh to true inside the loop since the NA threshold can appear anywhere in the list of thresholds. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Update README.md * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py * #1852 get_string_val: check if 2D variable. Also checking if the variable does not have dimension (#1860) Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> * Feature 1453 create pdf user guide (#1859) * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Feature 1853 rps doc (#1861) * Per #1853, adding RPS docs from Eric. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, adding a manual page break after the ROC image to get it to stay in the right spot. * Per #1853, backing out last change which didn't make the ROC image stay in the right spot. * #1855 Removed break after return (SobarQube) * #1855 Removed break after exit * 1855 Added return at MetNcPointObsOut::write_to_netcdf * #1855 Avoid releasing memory twice * #1855 Removed unused code * #1855 Corrected syntax error * #1855 Changed the second call of close() to release _ncFile * #1855 Deleted break after exit * #1855 Chamnged while to if * #1855 Added constructor TCLineCounts and initialized the members * #1855 Added break statement back for case '-' * #1855 Check the new size before extending to avoid thereference of the null pointer * #1855 Changed count to processed_count for log messages. Initialized variables at get_filtered_nc_data\*() * #1855 Corected the number of memory copy * #1855 Exit with an error message if both fgi & bgi are null * #1855 Clear Lead_Times before extening. Formatting for error messages * Add definition for the compilation environment on seneca. * #1855 Extend Lead_Times for new times * #1855 Removed break after exit * #1855 define "c" dynamically * #1855 Move the log message within if statement to avoid dereferencing a null pointer * Feature 1843 scatter index (#1863) * Added scatter index variables: SI, SI_BCL, SI_BCU to cnt columns. SL * Per issue #1843 Added Scatter Index variables (SI, SI_BCL, SI_BCU) to the CNT stat type. SL * Added Scatter Index (SI, SI_BCL, SI_BCU) to cnt stat type header. SL * Per issue #1843, added Scatter Index variables to write_cnt_cols(). SL * Per issue #1843 added Scatter Index (si) to CNTinfo class. SL * Per issue #1843 added Scatter Index (SI, si) to CNTInfo::get_stat(). SL * Per issue #1843 added Scatter Index (SI, si) calculation to both versions of compute_cntinfo(). SL * Per issue #1843, forgot semi-colon after SI calculation, fixed. SL * Added Scatter Index (si) to some of the clear() and allocate() functions. SL * Per issue #1843, added Scatter Index (si) to compute_cnt_mean(). SL * Per issue #1843, added Scatter Index (si) to bootstrap interval calculation and to the CNT write function. SL * Per issue #1843 added Scatter Index (SI, SI_BCL, SI_BCU) to store_stat_cnt(). SL * Per issue #1843, in get_stat() moved Scatterd Index (SI) line to be below RMSE for consitency. SL * Added Scatter Index (SI) to the CNT output format table. SL * Added Scatter Index (SI) to CNT statistics definitions. SL * Update appendixC.rst * Update stat_columns.cc * Update compute_ci.cc * Update met_stats.cc * Per #1843, update write_cntinfo() function. Since we're READING the SI value immediately after the RMSE value when computing CI's, we also need to write SI immediately after RMSE. Otherwise, we'll be computing CI's using the wrong statistics replicates. * Per #1843, check for divide by zero when computing SI... this could happen if comparing the same input file to itself with Grid-Stat. * Per #1843, correct definition of SI from RMSE/ME to RMSE/OBAR. * Per #1843, updated the SI definition to divide by OBAR instead of ME, but forgot to update the divide-by-zero check. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: johnhg <johnhg@ucar.edu> * #1855 Corected typo - compare the numnber of U and V * #1855 Check if var_info is hull * #1855 Avoid un-initialized variables: dt at open(), v at lat() & lon(), and local variables at data() * #1855 Check if ldf is null pointer * #1855 Removed break after exit * #1855 Removed break after exit * Update pcp_combine.cc * Feature 1864 config urls (#1868) * Per #1864, remove stale GitHub pages URL for the MET User's Guide. * Per #1864, found stale GitHub IO links in the issue templates. Should make this same fix in the develop and default branches for all the METplus repos. * Per #1864, fix stale GitHub IO link in the PR template. * Move ROC curve in Appendix C * Crop ROC image for better PDF formatting * Shrink ROC image for better PDF formatting * Modify figure alignment in conf.py * Change text placement for ROC curve figure * Feature 1834 faq (#1867) * testing possible new drop-down menus for FAQ * adding sphinx-panels to extensions to be able to use drop down menus in appendixA * Per #1834, adding sphinx-panels to requirements.txt to see if that fixes the error * Per #1834, added sphinx.ext to beginning of sphinx_panels to see if that fixes the error * Per #1834, remove sphinx.ext and add trailing comma to end of extensions to see if that fixed the error * Per #1834, added sphinx-panels to pip install command to see if that fixes the error * Per #1834, added extra space in comment to get docs to build to see if change to documentation.yml will fix an error * Per #1834, added return character to get rid of warning * testing dropdown menus #1 * testing dropdown menus #2 removing lines and dotted lines * testing #3 * testing 4 * fixing numbering, removing 2nd pulldown menu, trying to fix box width * adding code block in dropdown * trying to fix width * trying to fix width with spacing * trying to fix width with spacing 2nd dropdown * removing panels * solved problem, just use dropdown no panels * adding second dropdown menu * removing the dropdown menus and fixing the spacing. * fixing typos * adding in matched pairs * adding in formating files for NetCDF and making FILE_IO a header * fixing spacing * time slice * fixing spacing * UNIX time conversion * fixing spacing * fixed-width * scientific notation * removing which per Julie P * adding Gen_Vx_Mask section * fixing formatting * changing to numbers * complex masking region * neighborhood methods boundaries * Neighborhood Methods to Compute Fraction * adding Grid_Stat - How do I use Config File Setup to Read a NetCDF file * using backticks with asterics * one more backtick with asterics * Grid_Stat - What would be an example of Verifying Probabilities * fixing typos * What is an example of using Grid-Stat with Regridding and Masking Turned On * fixing typos * Grid_Stat - What would be an example of Verifying Probabilities Example2 * trying to fix typos * trying to fix code-block spacing * Per #1834, attempting to fix warning. * How do I use different masks in MET tools using MODE as an example * trying to fix bullet list * trying to fix bullet list 2 * trying to fix bullet list 2 * trying to fix bullet list 3 * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, modified formatting, including adding backslashes and removing extra returns in command line calls, and adding indentation for config file notation, and adding a return after each 'A.' * Per #1834, changed code-block from ini to none to fix formatting * *Pcp-Combine - What are some examples using -add * Pcp-Combine - How do I add and subtract with Pcp-Combine * Pcp-Combine - How do I Combine 12-hour Accumulated Precipitation from Two Different Initialization Times * Pcp-Combine - How Do I Correct a Precipitation Time Range * Pcp-Combine - What Data Formats does MET Read * Pcp-Combine - How does pass through work * Pcp_Combine - How do I use -pcprx to run a project faster * Pcp-Combine - How Do I Enter the Time Format Correctly * Pcp-Combine - How do I use -subtract * fixing formatting * Pcp_Combine - How Do I Use -sum, -add, and -subtract to Achieve Same Accumulation Interval * Pcp-Combine - What is the difference between -sum vs. -add * Pcp-Combine - How Do I Select a Specific GRIB Record to Use * fixing spacing for original text * Plot-Data-Plane - How Do I Inspect Gen_Vx_Mask Output * fixing typo * Plot-Data-Plane - How Do I Specify GRIB Version * Plot-Data-Plane - last 2 entries * 2 misc. entries * fixing typo * Stat_Analysis - How does -aggregate_stat work * Stat_Analysis - remaining entries * fixing typo * tc-pairs * tc-stat * troubleshooting area * another stat-analysis * another stat-analysis * utilities * fixing dashes * Per #1834, trying out syntax * Per #1834, removing added syntax * fixing returns with bolding * Per #1834, modified formatting * adding italics for directories #1834 * replacing code-block ini with none to remove red lettering * fixing questions to lower case #1834 * linking to section using numref #1834 * linking to section using numref #1834 attempt 2 * linking to section using numref #1834 attempt 3 * linking to section using numref #1834 attempt 4 * linking to section using numref #1834 attempt 5 * linking to section using numref #1834 attempt 6 * linking to section using numref #1834 attempt 7 * linking to section using numref #1834 attempt 8 * linking to anothre section #1834 * linking to another section #1834 * removing old info #1834 * grammar updates #1834 * grammar updates #1834 * fixing typos #1834 * email changes with Julie #1834 * trying to fix warning #1834 * changes #1834 * Per #1834, updating question titles and answers * Per #1834, made updates to the content. * Per #1834, made updates to the content * Per #1834, made updates to the content * Per #1834, made some major changes to the first 3 FAQ's. I don't have the time/bandwidth to review these completely at this time, but wanted to include at least these updates. * testing some of the updates John O. suggested. * updates John O. suggested take 2 #1834. * updates John O. suggested take 3 #1834. * updates John O. suggested take 4 #1834. * updates John O. suggested take 5 #1834. * updates John O. suggested. Some didn't show up even though they've been removed #1834. * trying to fix numbered list indenting #1834 * fixing numbered list indenting #1834 * cleaning up formatting #1834 * fixing broken links #1834 Co-authored-by: Julie.Prestopnik <jpresto@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * bugfix 1872 plot_tcmpr.R -lookin directory (develop) (#1874) * Bugfix 1875 develop memory (#1877) * Per #1875, fix set_cdf_ta() to initialize cdf_ta prior to populating it. * Per #1875, add debug(4) log messages whenever defining a new aggregation case in stat-analysis. * Per #1875, switch log messages about new cases from Debug(4) to Debug(3). * Per #1879, porting the same changes over to the develop branch. (#1881) * Feature 1673 gbeta (#1857) * Per #1673, add a distance_map.beta_value entry to all the Grid-Stat config files. * Per #1673, enhance Grid-Stat to parse the new beta_value option and set its value in the library code. * Per #1673, set the user-defined beta_value when processing the distance map scores. * Per #1673, add 4 new DMAP columns write them. Just writing bad data values right now, still need to actually compute them! Also need to update Stat-Analysis to update the parsing/aggregation of these new values. * Per #1673, enable beta_value to be set to a default bad data value. * Per #1673 and @ericgilleland instruction (#1673 (comment)), strip asymmetric G-Beta (AGBETA) from the output. * Per #1673, fix typo that was causing the code not to compile. * Per #1673, update MET User's Guide about G/GBETA. * Per #1673, report BETA_VALUE = TOTAL / 2 in the output instead of NA, as directed by Eric. * Per #1673, remove descriptions of Grid-Stat-specific config options for nbrhd, fourier, gradient, and distance_map from the overview section since they belong in the Grid-Stat chapter. Also add direct links for them in the Grid-Stat chapter. * Per #1673, do not reset the beta_value in DMAP::clear(). * Per #1673, log the DMAP options only after the beta_value has been determined. * Per #1673, correct the default beta_value setting as N*N / 2.0. * Per #1673, trying to format G-beta well. * Per #1673, trying to format G-beta well. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, switch to defining beta_value as a function of the input grid size. * Per #1673, push initial appendix C updates for GBETA. * Per #1673, working on G and GBETA equations. * Per #1673, working on G and GBETA equations. * Per 1673, update GBETA details in appendix C. * Per #1673, add Eric's info about selecting beta. * Per #1673, update reference for Gilleland-2019 to Gilleland_PartI-2020 and Gilleland_PartII-2020. * Per 1673, fix typo. * Per #1673, making changes requested by Eric. * Per #1673, making changes requested by Eric. * Per #1673, update references based on Eric's feedback. * Update appendixD.rst (#1869) Updated this appendix. * Update appendixD.rst * Per #1673, making the formatting of Gilleland-2020 part I and II references consistent. * Per #1673, update Grid-Stat docs to clarify that GBETA is only computed on the FULL verification domain and not any masking regions. * Per #1673, add DataPlane::n_good_data() function to return a count valid data values. * Per #1673, update vx_statistics library code to only set gbeta/beta_value to bad data for sub-domains. * Per #1673, update grid_stat to mask out bad data between the fcst/obs fields before computing distance maps. This will change existing unit test results! Also store the count of valid data values in the full verification domain. * Per #1673, since GBETA is only reported when VX_MASK = FULL, updating GridStatConfig_all to include the FULL masking region to make this example more meaningful. Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com> * Feature 1764 point stat (#1885) * Per #1764 added write_orank_row() to do_hera_ens(). SL * Per issue #1764, added orank stat type for ensemble output. SL * Per issue #1764, added code to setup_txt_files() for ORANK output. SL * Added some comments for debuging. SL * Per #1764, add orank to the list of outputs created by point_stat. * Per #1764, add functions to compute the number of requested HiRA probabilities and ensemble members. Also update n_txt_row() to keep track of the number of ORANK rows to be written. Not totally sure if I'm counting these ORANK output lines correctly though. * Per #1764, update logic in setup_txt_files() to call get_max_n_hira_prob() and get_max_n_hira_ens() functions. * Per #1764, no real changes. Just fixing spacing. * Per issue #1764, cleaned up print (cout) debug statements. SL * Per issue #1764 added 'orank = NONE' to the config files for compatibility with changes to point_stat for calculating ORANK. SL * Per issue #1764 added 'orank = STAT' to config file to produce ORANK output lines in point_stat. SL * Per issue #1764 added content in all relevant sections for ORANK: observation rank statistic. SL * Added 'orank = NONE' to config file for compatibility with changes to point_stant for ORANK. SL * Added 'orank = NONE' to config file for compatibility with changes to point_stant for ORANK. SL * Apply suggestions from code review Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Per #1764, no real changes, just fixing indents. * Per #1764, no real changes, just fixing indents. * Per #1764, no real changes, just fixing indents. * Per #1764, putting the docs for VCNT back into its logical order with the other vector line types. The order that they're listed here does not need to match their order in the enumeration in the code. * Per #1764, fixing a vcnt typo I found in the grid-stat chapter... and making them consistent. * Per issue #1764: After the call to write_orank_row, added lines to reset the observation begin and end times. SL * Per #1764, no code changes, just fixing indents. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Adding Seth to the NB notification list. * Bugfix 1886 develop grid_diag (#1888) * Per #1886, port over the bugfixes from main_v10.0 to develop. * Per #1886, make grid_diag error out if to_grid is set to FCST or OBS. * Added additional default labels * Feature 1870 realtime (#1893) * Per #1870. add TCPairs config entries for valid_inc, valid_exc, and write_valid. * Per #1870, removing 2 files I accidentally added. * Per #1870, add code to parse the new tc_pairs config options. * Per #1870, unrelated... just fixing spacing. * Per #1870, update TrackPairInfo/Array classes and tc_pairs application code to use the write_valid option to subset the tracks by requested valid time before writing them. * Per #1870, update the User's Guide with the new config options. Document valid_inc/valid_exc in the common TC config section and add write_valid to the TC-Pairs chapter. * Per #1870, move the subset_write_valid() functionality to the library code and support it for both track and probability arrays. * Per #1870, update unit_tc_pairs.xml with 2 new calls to exercise the new write_valid functionality for both tracks and probabilities. * Per #1870, correct some typos in the docs... PROBRI and probri should be PROBRIRW and probrirw, resp. * Per #1870, switching match_points from TRUE back to FALSE after I acciedentally committed that change. * Per #1870, just fixing indent. Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> * Feature 1788 ssidx (#1892) * Per #1788, add initial definition of the SSIDX line type. * Per #1788, add a STAT-Analysis config file for computing the CBS Score. This is currently just a copy of the GO Index. * Per #1788, add hooks for computing -job cbs_score. * Per #1788, since we're adding a new SSIDX line type, the columns for that line type replace the job_ss_columns and job_go_columns arrays. * Per #1788, rename cbs_score to cbs_index per UK Met Office instruction on 7/22/21. This convention is also consistent with the existing go_index and ss_index jobs. * Per #1788 rename STATAnalysisConfig_CBS_Score to STATAnalysisConfig_CBS_Index * Per #1788, update Makefile to handle name change. * Per #1788, add support for SSIDX stat line type. * Per #1788, define 4 output SSIDX columns. * Per #1788, define an SSIndexInfo struct for stashing/writing SS Index values. * Per #1788, write the SSIDX columns. However we don't need to function to write the whole row since it's only written by Stat-Analysis. * Per #1788, create an AggrSSIndexInfo struct to keep track of unique stat header column input values. * Per #1788, update the stat-analysis job code to make use of the new structs. * Per #1788 fix typo. * Per #1788, remove GO Index defintion from the code comments. That detail belongs elsewhere. * Per #1788, since coding up the GO Index several CNT and CTC columns have been added. Adding them here to let them be included as part of the Skill Score index computations. * Per #1788, update check_hdr_str() to print the name of the problematic header columns. * Per #1788, add a set(one) member function to multiple array classes. This calls clear or erase on the array prior to adding a single element. Add this for StringArray, NumArray, and ThreshArray, and CRCArray. * Per #1788, update the compute_ss_index() function in stat_analysis to make the code more concise by calling the newly adding singular set functions for arrays. * Per #1788, add FCST_MODEL and REF_MODEL output columns to the SSIDX line type. * Per #1788, add a new N_INIT column to the SSIDX line type to report the number of initialization times represented by this skill score. Also define the SSIDXData struct to store the skill score index job output. * Per #1788, update STATAnalysisJob to explicitly set the job type directly rather than parsing a string. * Per #1788, major change here adding skill_score_index_job.h/.cc to handle the computation of the skill score indices. * Per #1788, update stat_analysis source code to make use of the new classes in skill_score_index_job.h/.cc. * Per #1788, write a log message listing the model initialization times over which the skill score index is computed. * Per #1788, tweak log message. * Per #1788, compute n_term as the max lenght of the required arrays. * Per #1788, drop in the ACTUAL definition of the GO index provide by the DTC AF project team. Also simplify the existing arrays down to lenght one if the value remains constant. * Per #1788, correct CBS Index config file. Some parameters had 40 elements while others only had 32. * Per #1788, do not write SSIDX output if there are no valid terms found. * Per #1788, format the values in the skill score index log messages, replacing -9999 with NA. * Per #1788, update the get_stat() member functions. For 0 pairs, return bad data for all statistics other than TOTAL. * Per #1788, working on readability of the warning and error messages. * Per #1788, define the ss_index_name directly in the STATAnalysis config file to make it really easy to modify. * Per #1788, store the ss_index_name configuration option in the StatJob class. Also support a command line -ss_index_name option to override the config file value. * Per #1788, change from name to ss_index_name variable to be a bit more descriptive in the variable names. * Per #1788, since ss_index_name is in the StatJob class we no longer need to pass it around as an argument. * Per #1788, simply the skill score index job handling logic a bit. We only need to update the default job once, not twice.: * Revert "Per #1788, since ss_index_name is in the StatJob class we no longer need to pass it around as an argument." This reverts commit cde0be0. * Revert "Revert "Per #1788, since ss_index_name is in the StatJob class we no longer need to pass it around as an argument."" This reverts commit bbfd838. * Per #1788, I'd pruned too much code from stat_analysis.cc which caused the processing of config file jobs to fail. Fixing that here. * Per #1788, switch Z0 to L0 to match the sample data for computing CBS Index. * Per #1788, make it so that cbs_index and go_index work from config file. * Per #1788, update the documentation for the skill score index changes. * Per #1788, just move some variable definitions further down since they're only used sometimes. * Per #1788, make job output description into a numbered section. * Per #1788, little tweak. * Per #1788, update the STATAnalysisConfig files to add ss_index_name and hss_ec_value, as needed. * Per #1788, add new unit tests to exercise recent ss_index changes and update the Stat-Analysis documentation. * Update met/docs/Users_Guide/stat-analysis.rst Co-authored-by: jprestop <jpresto@ucar.edu> * Update met/docs/Users_Guide/stat-analysis.rst Sorry for the typos! Thanks for catching them. Co-authored-by: jprestop <jpresto@ucar.edu> * Update met/docs/Users_Guide/stat-analysis.rst Co-authored-by: jprestop <jpresto@ucar.edu> * Per #1788, fix typo in error message. * Per #1788, fix a bug for ss_index... changing 'add' to 'set'. Also set the line_type seperately for each term, if requested. * Per #1788, tweak the ss_index logic slightly to make it more efficient. For each input STATLine, instead of checking all the index terms, stop searching after the first match. This assumes that each input line should be used for only one of the terms... and I think that's a pretty reasonable assumption. * Per #1788, minor tweaks to the STAT-Analysis docs. * Per #1788, add ss_index_vld_thresh option to existing STAT-Analysis config files. * Per #1788, add StatAnalysisJob ss_index_vld_thresh entry and parse it from the STAT-Analysis config file. * Per #1788, update stat_analysis code to check ss_index_vld_thresh setting when computing the skill score index. Also update the Stat-Analysis chapter of the User's Guide. * Per #1788, tweak one test to exercise a non-default ss_index_vld_thresh value. Co-authored-by: jprestop <jpresto@ucar.edu> * #1855 Initialize AllocInc * 855 call snprintf instead of sprintf * Avoid the same for loops (SobarQube warns this) * #1855 Checking the minimum rows (3) for formatting. Initialize left & right array * #1855 Removed the unreachable return statement * #1855 Avoide out of index for v_miss * #1855 Keep buf_size for for-loop (avoid changing it in for loop). The buffer size for strncpy is decided by the targetbuffer size or the input length, not the existing data at the target buffer. The size of existing data at the target buffer is used to erase the previous data * #1855 Make sure the variuble c has enough data to avoid out of index error * #1855 nake sure the index is in range (avoid out of index error) * #1855 Make sure no negative offset for s array * #1855 Allocated line before calling getline'. Simplify the code to check the first level only. Check pbl_level before provcessing * #1855 Added m_strlen, m_strcpy, m_strcpy2, and m_strncpy * #1855 Added m_strlen, m_strcpy, m_strcpy2, and m_strncpy> Check if null pointer * #1855 Calls m_strcpy intead of strcpy * #1855 Calls m_strcpy2 intead of strcpy * #1855 Calls m_strcpy intead of strcpy * #1855 Removed spaces at the empty line * Bugfix 1891 gen_vx_mask (#1895) * Per #1891, tighten up the gen_vx_mask logic a bit. Use a global config for the default NC compression level. Then read the input and mask fields using local variables instead of the global one to ensure they don't affect eachother. Also took the opportunity to refine the logic so that we only create a mtddf object in one spot, in the get_data_plane() function. * Per #1891, add a new test in unit_gen_vx_mask.xml that fails prior to #1891 and succeeds with these changes. * Per #1891, file name typo in unit_gen_vx_mask.xml. * #1855 sonarqube: replaced strlen to m_strlen * #1855 sonarqube: replaced strcpy to m_strcpy * #1855 sonarqube: replaced strlen to m_strlen * #1855 sonarqube: replaced strlen to m_strlen * #1855 sonarqube: replaced strlen to m_strlen * #1855 Replaced strncpy to m_strncpy and enhance m_strcpy & m_strncpy (#1901) Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> * #1855 Turn off new strcpy functions * #1855 Corretced typo (arguments were swapped at MetPythonDataFile::open) * #1855 Make sure the to_str is null terminated after strncpy * Feature 1827 v10.1.0 beta2 (#1902) * Per #1827, updated release notes * Per #1827, Added extra ~ under header * Update met/docs/Users_Guide/release-notes.rst Co-authored-by: johnhg <johnhg@ucar.edu> * Update met/docs/Users_Guide/release-notes.rst Co-authored-by: johnhg <johnhg@ucar.edu> * Update met/docs/Users_Guide/release-notes.rst Co-authored-by: johnhg <johnhg@ucar.edu> * Per #1827, rereferenced GitHub issue number Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu> Co-authored-by: johnhg <johnhg@ucar.edu> * #1903 Added str_wrappers.cc & str_wrappers.h. They are moved from string_fxns * #1903 Added enum_to_string.h. They are moved from enum_to_string.cc * #1903 Moved include statements to the top. Included enum_to_string.h & str_wrappers.h. Changed 0 to NULL to reset the pointer * #1903 Moved m_strXXX to str_wrappers. Includes str_wrappers.h instead of string_fxns.h * #1903 Changed strXXX to m_strXXX * #1903 Chaged dst_info to const * #1903 Separated two || conditions to avoid potential side effect * #1903 Avoid the negative offset if the string length is 0 * #1903 make sure the pointer is not NULL before releasing * #1903 Replaced strXXX to m_strXXX. Separated two || conditions to avoid the potential side effects * #1903 Allow to truncate the string on calling m_strncpy * #1903 Replaced strXXX calls to m_strXXX * #1903 Avoid the negative offset if the string length is 0 * Separated third AND condition to avoid a possible side effect (assigned lead) * #1903 Renamed import (which is a keyword) to import_image) * Initialize data at get_filtered_nc_data_2d * #1903 Initialize r, g, b at dhsv_to_drgb * Modified to avoid unreachable return statement * #1903 Separated the second AND condition to avoid a potential side effect (assignment at the second condition) * #1903 Removed unreachable break (after exit) * #1903 Removed a unused offset variable * #1903 Initialize fcst variable * Renamed module (keyword) to py_module * Removed the second argument at m_strlen * #1903 Deleted extra two empty lines * #1903 Formatting (tab to spaces) * #1903 mstcpy is changed to m_strcpy2 * Deleted the commented out code * #1903 Calls sizeof instead of m_strlen at m_strcpy * #1903 Calls m_strncpy instead of m_strcpy * #1903 Replaced m_strcpy to m_strncpy * #1903 Do not use sizeof * Feature 1912 missing (#1915) * Per #1912, update logic of Met2dDataFile::process_data_plane(). Rather than returning bad status for a field of all bad data, print a warning message and continue processing. * Per #1912, fixing typo in error message that I ran into. Doesn't actually apply to this issue. * Per #1912, making an unrelated change here to fix up the MODE-Analysis log output. It was reporting (nul) for the number of lines being read/kept. Simplify the log messages to print the correct numbers. * Testing RTD updates * Added sphinx-panels * Testing double hyphen change to code-block * Testing double hyphen change to code-block * Changed bolding of options to code-blocks * Feature 1858 obs quality (#1919) * Per issue #1858: changed parse_conf_obs_qty to parse_conf_obs_qty_inc. Added new function parse_conf_obs_qty_exc. SL * Per issue #1858: changed conf_key_obs_qty to conf_key_obs_qty_inc. Added conf_key_obs_qty_exc. SL * Per issue #1858: modified vx_pd.set_obs_qty_filt() to use parse_conf_obs_qty_inc() instead of parse_conf_obs_qty(). SL * Per issue #1858: added back the original parse_conf_obs_qty() function for backward compatibility. SL * Per issue #1858: added back config_constants.h for backwards compatibility. SL * Per issue #1858: added code to read in obs_qty_inc instead of obs_qty. Also added in code for backwards compatibility to check for obs_qty (obs_quality) and use that for obs_qty_inc. SL * Changed obs_qty_filt to obs_qty_inc_filt. Added obs_qty_exc_filt, including relevant function. SL * Per issue #1858 added vx_pd.set_obs_qty_exc_filt. SL * In add_point_obs() added if block to apply obs_qty_exc_filt. SL * Per issue #1858, in add_point_obs(), cleaned up sections that apply obs_qty_inc and obs_qty_exc filters. Fixed spacing issue. SL * Per issue #1858 in process_config(), cleaned up sections that set obs_qty_inc_filt and obs_qty_exc_filt. Fixed spacing issue. SL * Per issue #1858 in process_obs_file() cleaned up code. SL * Per issue #1858: changed obs_qty_filt to obs_qty_inc_filt. Added obs_qty_exc_filt. Modified add_point_obs() to use obs_qty_exc_filt. SL * Per issue #1858: in process_config(): added code to set_obs_qty_inc_filt and set_obs_qty_exc_filt. Also added code to check if old obs_quality is being used, if so, set it to obs_qty_inc_filt. SL * Per issue #1858: in add_point_obs() modified section that applies the obs_qty_inc and obs_qty_exc filters. Combined the if-blocks into one concise if-block that applies both filters. SL * Per issue #1858: replaced obs_quality with obs_quality_inc and added obs_quality_inc. SL * Per issue #1858: replaced obs_quality with obs_quality_inc and added obs_quality_exc. SL * Per issue #1858: For both the point_stat and ensemble_stat tests: modified tests that use OBS_QTY to use OBS_QTY_INC. Added unit test for OBS_QTY_EXC (obs_quality_exclude). SL * Per issue #1858: just added comment at top of file indicating what changed. SL * Per issue #1858: just added comment at top of file indicating what changed. SL * Per issue #1858: removed parse_conf_obs_qty. Modified parse_conf_obs_qty_inc to check for old 'obs_quality' entry. SL * Per issue #1858: in process_config(), modified section that calls set_obs_qty_inc_filt...this new function can now handle old 'obs_quality' entry as well as the new 'obs_quality_inc'. SL * Modified parse_conf_obs_qty_inc and parse_conf_obs_qty_exc. SL * Per issue #1858: re-updated parse_conf_obs_qty_exc and reverted back to the simplier version of this function. SL * Per issue #1858: replaced obs_quality with obs_quality_inc and added obs_quality_exc. SL * Per issue #1858: replaced obs_quality with obs_quality_inc and added obs_quality_exc. SL * Per issue #1858: replaced obs_quality with obs_quality_inc and added obs_quality_exc. SL * Per issue #1858: replaced obs_quality with obs_quality_inc and added obs_quality_exc. SL * Per issue #1858: replaced obs_quality with obs_quality_inc and added obs_quality_inc. SL * Per issue #1858: replaced obs_quality with obs_quality_inc. Added documentation for obs_quality_exc. SL * Per issue #1858: checking in latest version. Modified section that calls set_obs_qty_inc_filt...this new function can now handle old 'obs_quality' entry as well as the new 'obs_quality_inc'. SL * Per issue #1858: cleaned up some extra line spaces. SL * Per #1858, removed the deprecated obs_quality configuration entry from 3 EnsembleStat and 5 PointStat configuration files. * Per issue #1858: duplicated fcst/obs fields to run/test with both obs_quality_inc and obs_quality_exc. SL * Per issue #1858: duplicated fcst/obs fields to run/test with both obs_quality_inc and obs_quality_exc. SL * Per issue #1858. Deleted these files git repository. These were replaced with: PointStatConfig_qty_inc_exc. SL * Per issue #1858. Deleted these files from the git repository. These were replaced with: EnsembleStatConfig_qty_inc_exc. SL * Per issue #1858. Deleted these files from the git repository. These were replaced with: PointStatConfig_qty_inc_exc. SL * Per issue #1858: Modified: Don't need to run separate tests for obs_quality_inc and obs_quality_exc, these are now combined into one test via the updated config files: PointStatConfig_qty_inc_exc and EnsembleStatConfig_qty_inc_exc. SL * Per #1858, update the logic in parse_conf_obs_qty_inc() to use last_lookup_status(). See forthcoming GitHub issue comment about this. * Per #1858, tweak the warning message. * Per #1858, made the existing unit_quality_filter.xml tests a bit more concise. Call Point-Stat and Ensemble-Stat only once each time. But for each, test 3 things: all qty, obs_quality_inc, and obs_quality_exc. * Per #1858, remove the _ON from the job name since the _OFF has been included in the same configuration. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> * Feature 1894 pb2nc var all (#1917) * #1894 Added station ID 14008 to pb2nc_NDAS_var_all unit test * #1894 Check the existance of the valid data up to 16 levels Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> * Feature 1913 MAX_PBL (#1916) * #1913 Changed MAX_PBL to 10000. Filter out if the PBL input data is invalid * #1912 Replaced is_eq to is_bad_data * #1913 Changed is_eq to is_bad_data Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> * Add bolding the MET version 10.1.0 beta2 release notes to indicate emphasis prior to the METplus Governance meeting. Co-authored-by: jprestop <jpresto@ucar.edu> Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> Co-authored-by: hsoh-u <hsoh@ucar.edu> Co-authored-by: Keith Searight <keith.searight@noaa.gov> Co-authored-by: Seth Linden <linden@ucar.edu> Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@seneca.rap.ucar.edu> Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@kiowa.rap.ucar.edu> Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>

@ericgilleland

* Update install_met_env.kiowa Commented out items and added text to description * #1817 Added to_north argument at two_to_one() * #1817 Calls two_to_one() with false for the third argument, to_north, if latitude moves north to south * Feature 1819 automation doc warnings (#1836) * Removing "/lib" that should not be there. * #1508 checking stat() methoid returns no error before looking at FILE flag * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * #1838 Added log message for lat/lon values * #1838 Give warning if the first and lat lat/lon is same * #1838 Support the double data type variable on reading float type values * Feature 1833 develop discussions (#1849) * Per #1833, changed references to met_help to Discussions. * Per #1833, fixed typo and removed an unnecessary word * #1852 Removed unused nc_buf_size. Make cur and dim to the same size (called API handles 2D or 3D) * #1852 Check the start and count before calling NetCDF API * Feature 1746 wavelet stat (#1851) * For issue #1746 modified code to allow users to pass in an empty list (or NA) for forecast and observation thresholds in order to skip applying the threhsolds, but it will still compute stats with the raw fields. SL * For issue #1746, added new unit test that uses a config file that has empty lists for the forecast and observation thresholds. SL * For issue #1746 Added some content related to allowing users to set forecast and observation cat thresholds to an empty list in order to skip the binary masking (and consider all grid-points for stats). SL * Per #1746, cleaning up for consistent indentation. * Per #1746, cleaning up for consistent indentation. * Per #1746, add a revision history note, update the plotting range in the postscript output to be [-n,n] where n is the maximum value of the maximum absolute difference and 1.0, and also fix a bug. When the NA threshold comes AFTER a real threshold, the resulting data and difference values were not being updated. * Per #1746, change the Wavelet-Stat config file values in the the wvlt_plot dictionary by setting plot_min = plot_max = 0.0. That enables the default logic of the tool to take effect. Choose the plotting range of the wavelet plots as [-n,n], where n is the maximum of 1.0 and the maximum absolute difference. * Per #1746, used apply_fcst_thresh where it should have been apply_obs_thresh. * Per issue #1746, modified some content related to users being able to skip applying the categorical threhsolds by putting an empty list or NA in the configuration file. SL * Per issue #1746 Added some warnings if the forecast threshold is set to NA but the observation threshold is not NA (a numeric threshold) and vice versa. SL * Per #1746, fix a couple of typos and tweak wording in the wavelet-stat chapter. * Per #1746, loop over each pair of fcst/obs thresholds to check for inconsistent use of the NA threshold type. * Per #1746, a bit of code cleanup replacing calls to n_elements() with n() to make the code more concise. * Per #1746, need to reinitialize apply_fcst_thresh and apply_obs_thresh to true inside the loop since the NA threshold can appear anywhere in the list of thresholds. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Update README.md * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py * #1852 get_string_val: check if 2D variable. Also checking if the variable does not have dimension (#1860) Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> * Feature 1453 create pdf user guide (#1859) * Enable PDF creation * Modify inputenc, fontenc latex_elements * Fix typo in conf.py * Replace unicode with ascii * Replace unicode exponent with math mode * Change eqnarray to align * Replace gif images with png for PDF * Fix png file names * Escape underscore in variable name in math mode * Escape underscore in variable name in math mode * Remove underscores from variables in math mode * Replace bar with overline in some equations * Test derefencing underscores in tables * Test math changes in grid stat * Test math formatting * Test math formatting * Add sphinx.ext.pngmath to conf.py * Fix typo in conf.py * Add sphinx.ext.mathjax to conf.py * Add sphinx.ext.imgmath to conf.py * Fix typo in conf.py * Change math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Add sphinx.ext.imgmath to conf.py * Modify math formatting in Appendix C * Temporarily disable equations with errors in Appendix C * Remove sphinx.ext.imgmath in conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Temporarily disable equations with errors * Modify math formatting in Appendix C * Add usepackage{amssymb} to conf.py * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Modify math formatting in Appendix C * Fix warnings in wavelet-stat.rst * Omit Indices and tables in PDF version of User Guide * Modify math formatting in Appendix G * Modify math formatting in Appendix E * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Modify math formatting in Appendix G * Change release date in conf.py Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * Feature 1853 rps doc (#1861) * Per #1853, adding RPS docs from Eric. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, work in progress getting the formatting correct. * Per #1853, adding a manual page break after the ROC image to get it to stay in the right spot. * Per #1853, backing out last change which didn't make the ROC image stay in the right spot. * #1855 Removed break after return (SobarQube) * #1855 Removed break after exit * 1855 Added return at MetNcPointObsOut::write_to_netcdf * #1855 Avoid releasing memory twice * #1855 Removed unused code * #1855 Corrected syntax error * #1855 Changed the second call of close() to release _ncFile * #1855 Deleted break after exit * #1855 Chamnged while to if * #1855 Added constructor TCLineCounts and initialized the members * #1855 Added break statement back for case '-' * #1855 Check the new size before extending to avoid thereference of the null pointer * #1855 Changed count to processed_count for log messages. Initialized variables at get_filtered_nc_data\*() * #1855 Corected the number of memory copy * #1855 Exit with an error message if both fgi & bgi are null * #1855 Clear Lead_Times before extening. Formatting for error messages * Add definition for the compilation environment on seneca. * #1855 Extend Lead_Times for new times * #1855 Removed break after exit * #1855 define "c" dynamically * #1855 Move the log message within if statement to avoid dereferencing a null pointer * Feature 1843 scatter index (#1863) * Added scatter index variables: SI, SI_BCL, SI_BCU to cnt columns. SL * Per issue #1843 Added Scatter Index variables (SI, SI_BCL, SI_BCU) to the CNT stat type. SL * Added Scatter Index (SI, SI_BCL, SI_BCU) to cnt stat type header. SL * Per issue #1843, added Scatter Index variables to write_cnt_cols(). SL * Per issue #1843 added Scatter Index (si) to CNTinfo class. SL * Per issue #1843 added Scatter Index (SI, si) to CNTInfo::get_stat(). SL * Per issue #1843 added Scatter Index (SI, si) calculation to both versions of compute_cntinfo(). SL * Per issue #1843, forgot semi-colon after SI calculation, fixed. SL * Added Scatter Index (si) to some of the clear() and allocate() functions. SL * Per issue #1843, added Scatter Index (si) to compute_cnt_mean(). SL * Per issue #1843, added Scatter Index (si) to bootstrap interval calculation and to the CNT write function. SL * Per issue #1843 added Scatter Index (SI, SI_BCL, SI_BCU) to store_stat_cnt(). SL * Per issue #1843, in get_stat() moved Scatterd Index (SI) line to be below RMSE for consitency. SL * Added Scatter Index (SI) to the CNT output format table. SL * Added Scatter Index (SI) to CNT statistics definitions. SL * Update appendixC.rst * Update stat_columns.cc * Update compute_ci.cc * Update met_stats.cc * Per #1843, update write_cntinfo() function. Since we're READING the SI value immediately after the RMSE value when computing CI's, we also need to write SI immediately after RMSE. Otherwise, we'll be computing CI's using the wrong statistics replicates. * Per #1843, check for divide by zero when computing SI... this could happen if comparing the same input file to itself with Grid-Stat. * Per #1843, correct definition of SI from RMSE/ME to RMSE/OBAR. * Per #1843, updated the SI definition to divide by OBAR instead of ME, but forgot to update the divide-by-zero check. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: johnhg <johnhg@ucar.edu> * #1855 Corected typo - compare the numnber of U and V * #1855 Check if var_info is hull * #1855 Avoid un-initialized variables: dt at open(), v at lat() & lon(), and local variables at data() * #1855 Check if ldf is null pointer * #1855 Removed break after exit * #1855 Removed break after exit * Update pcp_combine.cc * Feature 1864 config urls (#1868) * Per #1864, remove stale GitHub pages URL for the MET User's Guide. * Per #1864, found stale GitHub IO links in the issue templates. Should make this same fix in the develop and default branches for all the METplus repos. * Per #1864, fix stale GitHub IO link in the PR template. * Move ROC curve in Appendix C * Crop ROC image for better PDF formatting * Shrink ROC image for better PDF formatting * Modify figure alignment in conf.py * Change text placement for ROC curve figure * Feature 1834 faq (#1867) * testing possible new drop-down menus for FAQ * adding sphinx-panels to extensions to be able to use drop down menus in appendixA * Per #1834, adding sphinx-panels to requirements.txt to see if that fixes the error * Per #1834, added sphinx.ext to beginning of sphinx_panels to see if that fixes the error * Per #1834, remove sphinx.ext and add trailing comma to end of extensions to see if that fixed the error * Per #1834, added sphinx-panels to pip install command to see if that fixes the error * Per #1834, added extra space in comment to get docs to build to see if change to documentation.yml will fix an error * Per #1834, added return character to get rid of warning * testing dropdown menus #1 * testing dropdown menus #2 removing lines and dotted lines * testing #3 * testing 4 * fixing numbering, removing 2nd pulldown menu, trying to fix box width * adding code block in dropdown * trying to fix width * trying to fix width with spacing * trying to fix width with spacing 2nd dropdown * removing panels * solved problem, just use dropdown no panels * adding second dropdown menu * removing the dropdown menus and fixing the spacing. * fixing typos * adding in matched pairs * adding in formating files for NetCDF and making FILE_IO a header * fixing spacing * time slice * fixing spacing * UNIX time conversion * fixing spacing * fixed-width * scientific notation * removing which per Julie P * adding Gen_Vx_Mask section * fixing formatting * changing to numbers * complex masking region * neighborhood methods boundaries * Neighborhood Methods to Compute Fraction * adding Grid_Stat - How do I use Config File Setup to Read a NetCDF file * using backticks with asterics * one more backtick with asterics * Grid_Stat - What would be an example of Verifying Probabilities * fixing typos * What is an example of using Grid-Stat with Regridding and Masking Turned On * fixing typos * Grid_Stat - What would be an example of Verifying Probabilities Example2 * trying to fix typos * trying to fix code-block spacing * Per #1834, attempting to fix warning. * How do I use different masks in MET tools using MODE as an example * trying to fix bullet list * trying to fix bullet list 2 * trying to fix bullet list 2 * trying to fix bullet list 3 * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, attempting formatting changes * Per #1834, modified formatting, including adding backslashes and removing extra returns in command line calls, and adding indentation for config file notation, and adding a return after each 'A.' * Per #1834, changed code-block from ini to none to fix formatting * *Pcp-Combine - What are some examples using -add * Pcp-Combine - How do I add and subtract with Pcp-Combine * Pcp-Combine - How do I Combine 12-hour Accumulated Precipitation from Two Different Initialization Times * Pcp-Combine - How Do I Correct a Precipitation Time Range * Pcp-Combine - What Data Formats does MET Read * Pcp-Combine - How does pass through work * Pcp_Combine - How do I use -pcprx to run a project faster * Pcp-Combine - How Do I Enter the Time Format Correctly * Pcp-Combine - How do I use -subtract * fixing formatting * Pcp_Combine - How Do I Use -sum, -add, and -subtract to Achieve Same Accumulation Interval * Pcp-Combine - What is the difference between -sum vs. -add * Pcp-Combine - How Do I Select a Specific GRIB Record to Use * fixing spacing for original text * Plot-Data-Plane - How Do I Inspect Gen_Vx_Mask Output * fixing typo * Plot-Data-Plane - How Do I Specify GRIB Version * Plot-Data-Plane - last 2 entries * 2 misc. entries * fixing typo * Stat_Analysis - How does -aggregate_stat work * Stat_Analysis - remaining entries * fixing typo * tc-pairs * tc-stat * troubleshooting area * another stat-analysis * another stat-analysis * utilities * fixing dashes * Per #1834, trying out syntax * Per #1834, removing added syntax * fixing returns with bolding * Per #1834, modified formatting * adding italics for directories #1834 * replacing code-block ini with none to remove red lettering * fixing questions to lower case #1834 * linking to section using numref #1834 * linking to section using numref #1834 attempt 2 * linking to section using numref #1834 attempt 3 * linking to section using numref #1834 attempt 4 * linking to section using numref #1834 attempt 5 * linking to section using numref #1834 attempt 6 * linking to section using numref #1834 attempt 7 * linking to section using numref #1834 attempt 8 * linking to anothre section #1834 * linking to another section #1834 * removing old info #1834 * grammar updates #1834 * grammar updates #1834 * fixing typos #1834 * email changes with Julie #1834 * trying to fix warning #1834 * changes #1834 * Per #1834, updating question titles and answers * Per #1834, made updates to the content. * Per #1834, made updates to the content * Per #1834, made updates to the content * Per #1834, made some major changes to the first 3 FAQ's. I don't have the time/bandwidth to review these completely at this time, but wanted to include at least these updates. * testing some of the updates John O. suggested. * updates John O. suggested take 2 #1834. * updates John O. suggested take 3 #1834. * updates John O. suggested take 4 #1834. * updates John O. suggested take 5 #1834. * updates John O. suggested. Some didn't show up even though they've been removed #1834. * trying to fix numbered list indenting #1834 * fixing numbered list indenting #1834 * cleaning up formatting #1834 * fixing broken links #1834 Co-authored-by: Julie.Prestopnik <jpresto@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> * bugfix 1872 plot_tcmpr.R -lookin directory (develop) (#1874) * Bugfix 1875 develop memory (#1877) * Per #1875, fix set_cdf_ta() to initialize cdf_ta prior to populating it. * Per #1875, add debug(4) log messages whenever defining a new aggregation case in stat-analysis. * Per #1875, switch log messages about new cases from Debug(4) to Debug(3). * Per #1879, porting the same changes over to the develop branch. (#1881) * Feature 1673 gbeta (#1857) * Per #1673, add a distance_map.beta_value entry to all the Grid-Stat config files. * Per #1673, enhance Grid-Stat to parse the new beta_value option and set its value in the library code. * Per #1673, set the user-defined beta_value when processing the distance map scores. * Per #1673, add 4 new DMAP columns write them. Just writing bad data values right now, still need to actually compute them! Also need to update Stat-Analysis to update the parsing/aggregation of these new values. * Per #1673, enable beta_value to be set to a default bad data value. * Per #1673 and @ericgilleland instruction (#1673 (comment)), strip asymmetric G-Beta (AGBETA) from the output. * Per #1673, fix typo that was causing the code not to compile. * Per #1673, update MET User's Guide about G/GBETA. * Per #1673, report BETA_VALUE = TOTAL / 2 in the output instead of NA, as directed by Eric. * Per #1673, remove descriptions of Grid-Stat-specific config options for nbrhd, fourier, gradient, and distance_map from the overview section since they belong in the Grid-Stat chapter. Also add direct links for them in the Grid-Stat chapter. * Per #1673, do not reset the beta_value in DMAP::clear(). * Per #1673, log the DMAP options only after the beta_value has been determined. * Per #1673, correct the default beta_value setting as N*N / 2.0. * Per #1673, trying to format G-beta well. * Per #1673, trying to format G-beta well. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, beta is formatted as \beta and not \Beta in latex. * Per #1673, switch to defining beta_value as a function of the input grid size. * Per #1673, push initial appendix C updates for GBETA. * Per #1673, working on G and GBETA equations. * Per #1673, working on G and GBETA equations. * Per 1673, update GBETA details in appendix C. * Per #1673, add Eric's info about selecting beta. * Per #1673, update reference for Gilleland-2019 to Gilleland_PartI-2020 and Gilleland_PartII-2020. * Per 1673, fix typo. * Per #1673, making changes requested by Eric. * Per #1673, making changes requested by Eric. * Per #1673, update references based on Eric's feedback. * Update appendixD.rst (#1869) Updated this appendix. * Update appendixD.rst * Per #1673, making the formatting of Gilleland-2020 part I and II references consistent. * Per #1673, update Grid-Stat docs to clarify that GBETA is only computed on the FULL verification domain and not any masking regions. * Per #1673, add DataPlane::n_good_data() function to return a count valid data values. * Per #1673, update vx_statistics library code to only set gbeta/beta_value to bad data for sub-domains. * Per #1673, update grid_stat to mask out bad data between the fcst/obs fields before computing distance maps. This will change existing unit test results! Also store the count of valid data values in the full verification domain. * Per #1673, since GBETA is only reported when VX_MASK = FULL, updating GridStatConfig_all to include the FULL masking region to make this example more meaningful. Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com> * Feature 1764 point stat (#1885) * Per #1764 added write_orank_row() to do_hera_ens(). SL * Per issue #1764, added orank stat type for ensemble output. SL * Per issue #1764, added code to setup_txt_files() for ORANK output. SL * Added some comments for debuging. SL * Per #1764, add orank to the list of outputs created by point_stat. * Per #1764, add functions to compute the number of requested HiRA probabilities and ensemble members. Also update n_txt_row() to keep track of the number of ORANK rows to be written. Not totally sure if I'm counting these ORANK output lines correctly though. * Per #1764, update logic in setup_txt_files() to call get_max_n_hira_prob() and get_max_n_hira_ens() functions. * Per #1764, no real changes. Just fixing spacing. * Per issue #1764, cleaned up print (cout) debug statements. SL * Per issue #1764 added 'orank = NONE' to the config files for compatibility with changes to point_stat for calculating ORANK. SL * Per issue #1764 added 'orank = STAT' to config file to produce ORANK output lines in point_stat. SL * Per issue #1764 added content in all relevant sections for ORANK: observation rank statistic. SL * Added 'orank = NONE' to config file for compatibility with changes to point_stant for ORANK. SL * Added 'orank = NONE' to config file for compatibility with changes to point_stant for ORANK. SL * Apply suggestions from code review Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Per #1764, no real changes, just fixing indents. * Per #1764, no real changes, just fixing indents. * Per #1764, no real changes, just fixing indents. * Per #1764, putting the docs for VCNT back into its logical order with the other vector line types. The order that they're listed here does not need to match their order in the enumeration in the code. * Per #1764, fixing a vcnt typo I found in the grid-stat chapter... and making them consistent. * Per issue #1764: After the call to write_orank_row, added lines to reset the observation begin and end times. SL * Per #1764, no code changes, just fixing indents. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Adding Seth to the NB notification list. * Bugfix 1886 develop grid_diag (#1888) * Per #1886, port over the bugfixes from main_v10.0 to develop. * Per #1886, make grid_diag error out if to_grid is set to FCST or OBS. * Added additional default labels * Feature 1870 realtime (#1893) * Per #1870. add TCPairs config entries for valid_inc, valid_exc, and write_valid. * Per #1870, removing 2 files I accidentally added. * Per #1870, add code to parse the new tc_pairs config options. * Per #1870, unrelated... just fixing spacing. * Per #1870, update TrackPairInfo/Array classes and tc_pairs application code to use the write_valid option to subset the tracks by requested valid time before writing them. * Per #1870, update the User's Guide with the new config options. Document valid_inc/valid_exc in the common TC config section and add write_valid to the TC-Pairs chapter. * Per #1870, move the subset_write_valid() functionality to the library code and support it for both track and probability arrays. * Per #1870, update unit_tc_pairs.xml with 2 new calls to exercise the new write_valid functionality for both tracks and probabilities. * Per #1870, correct some typos in the docs... PROBRI and probri should be PROBRIRW and probrirw, resp. * Per #1870, switching match_points from TRUE back to FALSE after I acciedentally committed that change. * Per #1870, just fixing indent. Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> * Feature 1788 ssidx (#1892) * Per #1788, add initial definition of the SSIDX line type. * Per #1788, add a STAT-Analysis config file for computing the CBS Score. This is currently just a copy of the GO Index. * Per #1788, add hooks for computing -job cbs_score. * Per #1788, since we're adding a new SSIDX line type, the columns for that line type replace the job_ss_columns and job_go_columns arrays. * Per #1788, rename cbs_score to cbs_index per UK Met Office instruction on 7/22/21. This convention is also consistent with the existing go_index and ss_index jobs. * Per #1788 rename STATAnalysisConfig_CBS_Score to STATAnalysisConfig_CBS_Index * Per #1788, update Makefile to handle name change. * Per #1788, add support for SSIDX stat line type. * Per #1788, define 4 output SSIDX columns. * Per #1788, define an SSIndexInfo struct for stashing/writing SS Index values. * Per #1788, write the SSIDX columns. However we don't need to function to write the whole row since it's only written by Stat-Analysis. * Per #1788, create an AggrSSIndexInfo struct to keep track of unique stat header column input values. * Per #1788, update the stat-analysis job code to make use of the new structs. * Per #1788 fix typo. * Per #1788, remove GO Index defintion from the code comments. That detail belongs elsewhere. * Per #1788, since coding up the GO Index several CNT and CTC columns have been added. Adding them here to let them be included as part of the Skill Score index computations. * Per #1788, update check_hdr_str() to print the name of the problematic header columns. * Per #1788, add a set(one) member function to multiple array classes. This calls clear or erase on the array prior to adding a single element. Add this for StringArray, NumArray, and ThreshArray, and CRCArray. * Per #1788, update the compute_ss_index() function in stat_analysis to make the code more concise by calling the newly adding singular set functions for arrays. * Per #1788, add FCST_MODEL and REF_MODEL output columns to the SSIDX line type. * Per #1788, add a new N_INIT column to the SSIDX line type to report the number of initialization times represented by this skill score. Also define the SSIDXData struct to store the skill score index job output. * Per #1788, update STATAnalysisJob to explicitly set the job type directly rather than parsing a string. * Per #1788, major change here adding skill_score_index_job.h/.cc to handle the computation of the skill score indices. * Per #1788, update stat_analysis source code to make use of the new classes in skill_score_index_job.h/.cc. * Per #1788, write a log message listing the model initialization times over which the skill score index is computed. * Per #1788, tweak log message. * Per #1788, compute n_term as the max lenght of the required arrays. * Per #1788, drop in the ACTUAL definition of the GO index provide by the DTC AF project team. Also simplify the existing arrays down to lenght one if the value remains constant. * Per #1788, correct CBS Index config file. Some parameters had 40 elements while others only had 32. * Per #1788, do not write SSIDX output if there are no valid terms found. * Per #1788, format the values in the skill score index log messages, replacing -9999 with NA. * Per #1788, update the get_stat() member functions. For 0 pairs, return bad data for all statistics other than TOTAL. * Per #1788, working on readability of the warning and error messages. * Per #1788, define the ss_index_name directly in the STATAnalysis config file to make it really easy to modify. * Per #1788, store the ss_index_name configuration option in the StatJob class. Also support a command line -ss_index_name option to override the config file value. * Per #1788, change from name to ss_index_name variable to be a bit more descriptive in the variable names. * Per #1788, since ss_index_name is in the StatJob class we no longer need to pass it around as an argument. * Per #1788, simply the skill score index job handling logic a bit. We only need to update the default job once, not twice.: * Revert "Per #1788, since ss_index_name is in the StatJob class we no longer need to pass it around as an argument." This reverts commit cde0be0. * Revert "Revert "Per #1788, since ss_index_name is in the StatJob class we no longer need to pass it around as an argument."" This reverts commit bbfd838. * Per #1788, I'd pruned too much code from stat_analysis.cc which caused the processing of config file jobs to fail. Fixing that here. * Per #1788, switch Z0 to L0 to match the sample data for computing CBS Index. * Per #1788, make it so that cbs_index and go_index work from config file. * Per #1788, update the documentation for the skill score index changes. * Per #1788, just move some variable definitions further down since they're only used sometimes. * Per #1788, make job output description into a numbered section. * Per #1788, little tweak. * Per #1788, update the STATAnalysisConfig files to add ss_index_name and hss_ec_value, as needed. * Per #1788, add new unit tests to exercise recent ss_index changes and update the Stat-Analysis documentation. * Update met/docs/Users_Guide/stat-analysis.rst Co-authored-by: jprestop <jpresto@ucar.edu> * Update met/docs/Users_Guide/stat-analysis.rst Sorry for the typos! Thanks for catching them. Co-authored-by: jprestop <jpresto@ucar.edu> * Update met/docs/Users_Guide/stat-analysis.rst Co-authored-by: jprestop <jpresto@ucar.edu> * Per #1788, fix typo in error message. * Per #1788, fix a bug for ss_index... changing 'add' to 'set'. Also set the line_type seperately for each term, if requested. * Per #1788, tweak the ss_index logic slightly to make it more efficient. For each input STATLine, instead of checking all the index terms, stop searching after the first match. This assumes that each input line should be used for only one of the terms... and I think that's a pretty reasonable assumption. * Per #1788, minor tweaks to the STAT-Analysis docs. * Per #1788, add ss_index_vld_thresh option to existing STAT-Analysis config files. * Per #1788, add StatAnalysisJob ss_index_vld_thresh entry and parse it from the STAT-Analysis config file. * Per #1788, update stat_analysis code to check ss_index_vld_thresh setting when computing the skill score index. Also update the Stat-Analysis chapter of the User's Guide. * Per #1788, tweak one test to exercise a non-default ss_index_vld_thresh value. Co-authored-by: jprestop <jpresto@ucar.edu> * #1855 Initialize AllocInc * 855 call snprintf instead of sprintf * Avoid the same for loops (SobarQube warns this) * #1855 Checking the minimum rows (3) for formatting. Initialize left & right array * #1855 Removed the unreachable return statement * #1855 Avoide out of index for v_miss * #1855 Keep buf_size for for-loop (avoid changing it in for loop). The buffer size for strncpy is decided by the targetbuffer size or the input length, not the existing data at the target buffer. The size of existing data at the target buffer is used to erase the previous data * #1855 Make sure the variuble c has enough data to avoid out of index error * #1855 nake sure the index is in range (avoid out of index error) * #1855 Make sure no negative offset for s array * #1855 Allocated line before calling getline'. Simplify the code to check the first level only. Check pbl_level before provcessing * #1855 Added m_strlen, m_strcpy, m_strcpy2, and m_strncpy * #1855 Added m_strlen, m_strcpy, m_strcpy2, and m_strncpy> Check if null pointer * #1855 Calls m_strcpy intead of strcpy * #1855 Calls m_strcpy2 intead of strcpy * #1855 Calls m_strcpy intead of strcpy * #1855 Removed spaces at the empty line * Bugfix 1891 gen_vx_mask (#1895) * Per #1891, tighten up the gen_vx_mask logic a bit. Use a global config for the default NC compression level. Then read the input and mask fields using local variables instead of the global one to ensure they don't affect eachother. Also took the opportunity to refine the logic so that we only create a mtddf object in one spot, in the get_data_plane() function. * Per #1891, add a new test in unit_gen_vx_mask.xml that fails prior to #1891 and succeeds with these changes. * Per #1891, file name typo in unit_gen_vx_mask.xml. * #1855 sonarqube: replaced strlen to m_strlen * #1855 sonarqube: replaced strcpy to m_strcpy * #1855 sonarqube: replaced strlen to m_strlen * #1855 sonarqube: replaced strlen to m_strlen * #1855 sonarqube: replaced strlen to m_strlen * #1855 Replaced strncpy to m_strncpy and enhance m_strcpy & m_strncpy (#1901) Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> * #1855 Turn off new strcpy functions * #1855 Corretced typo (arguments were swapped at MetPythonDataFile::open) * #1855 Make sure the to_str is null terminated after strncpy * Feature 1827 v10.1.0 beta2 (#1902) * Per #1827, updated release notes * Per #1827, Added extra ~ under header * Update met/docs/Users_Guide/release-notes.rst Co-authored-by: johnhg <johnhg@ucar.edu> * Update met/docs/Users_Guide/release-notes.rst Co-authored-by: johnhg <johnhg@ucar.edu> * Update met/docs/Users_Guide/release-notes.rst Co-authored-by: johnhg <johnhg@ucar.edu> * Per #1827, rereferenced GitHub issue number Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu> Co-authored-by: johnhg <johnhg@ucar.edu> * #1903 Added str_wrappers.cc & str_wrappers.h. They are moved from string_fxns * #1903 Added enum_to_string.h. They are moved from enum_to_string.cc * #1903 Moved include statements to the top. Included enum_to_string.h & str_wrappers.h. Changed 0 to NULL to reset the pointer * #1903 Moved m_strXXX to str_wrappers. Includes str_wrappers.h instead of string_fxns.h * #1903 Changed strXXX to m_strXXX * #1903 Chaged dst_info to const * #1903 Separated two || conditions to avoid potential side effect * #1903 Avoid the negative offset if the string length is 0 * #1903 make sure the pointer is not NULL before releasing * #1903 Replaced strXXX to m_strXXX. Separated two || conditions to avoid the potential side effects * #1903 Allow to truncate the string on calling m_strncpy * #1903 Replaced strXXX calls to m_strXXX * #1903 Avoid the negative offset if the string length is 0 * Separated third AND condition to avoid a possible side effect (assigned lead) * #1903 Renamed import (which is a keyword) to import_image) * Initialize data at get_filtered_nc_data_2d * #1903 Initialize r, g, b at dhsv_to_drgb * Modified to avoid unreachable return statement * #1903 Separated the second AND condition to avoid a potential side effect (assignment at the second condition) * #1903 Removed unreachable break (after exit) * #1903 Removed a unused offset variable * #1903 Initialize fcst variable * Renamed module (keyword) to py_module * Removed the second argument at m_strlen * #1903 Deleted extra two empty lines * #1903 Formatting (tab to spaces) * #1903 mstcpy is changed to m_strcpy2 * Deleted the commented out code * #1903 Calls sizeof instead of m_strlen at m_strcpy * #1903 Calls m_strncpy instead of m_strcpy * #1903 Replaced m_strcpy to m_strncpy * #1903 Do not use sizeof * Feature 1912 missing (#1915) * Per #1912, update logic of Met2dDataFile::process_data_plane(). Rather than returning bad status for a field of all bad data, print a warning message and continue processing. * Per #1912, fixing typo in error message that I ran into. Doesn't actually apply to this issue. * Per #1912, making an unrelated change here to fix up the MODE-Analysis log output. It was reporting (nul) for the number of lines being read/kept. Simplify the log messages to print the correct numbers. * Testing RTD updates * Added sphinx-panels * Testing double hyphen change to code-block * Testing double hyphen change to code-block * Changed bolding of options to code-blocks * Feature 1858 obs quality (#1919) * Per issue #1858: changed parse_conf_obs_qty to parse_conf_obs_qty_inc. Added new function parse_conf_obs_qty_exc. SL * Per issue #1858: changed conf_key_obs_qty to conf_key_obs_qty_inc. Added conf_key_obs_qty_exc. SL * Per issue #1858: modified vx_pd.set_obs_qty_filt() to use parse_conf_obs_qty_inc() instead of parse_conf_obs_qty(). SL * Per issue #1858: added back the original parse_conf_obs_qty() function for backward compatibility. SL * Per issue #1858: added back config_constants.h for backwards compatibility. SL * Per issue #1858: added code to read in obs_qty_inc instead of obs_qty. Also added in code for backwards compatibility to check for obs_qty (obs_quality) and use that for obs_qty_inc. SL * Changed obs_qty_filt to obs_qty_inc_filt. Added obs_qty_exc_filt, including relevant function. SL * Per issue #1858 added vx_pd.set_obs_qty_exc_filt. SL * In add_point_obs() added if block to apply obs_qty_exc_filt. SL * Per issue #1858, in add_point_obs(), cleaned up sections that apply obs_qty_inc and obs_qty_exc filters. Fixed spacing issue. SL * Per issue #1858 in process_config(), cleaned up sections that set obs_qty_inc_filt and obs_qty_exc_filt. Fixed spacing issue. SL * Per issue #1858 in process_obs_file() cleaned up code. SL * Per issue #1858: changed obs_qty_filt to obs_qty_inc_filt. Added obs_qty_exc_filt. Modified add_point_obs() to use obs_qty_exc_filt. SL * Per issue #1858: in process_config(): added code to set_obs_qty_inc_filt and set_obs_qty_exc_filt. Also added code to check if old obs_quality is being used, if so, set it to obs_qty_inc_filt. SL * Per issue #1858: in add_point_obs() modified section that applies the obs_qty_inc and obs_qty_exc filters. Combined the if-blocks into one concise if-block that applies both filters. SL * Per issue #1858: replaced obs_quality with obs_quality_inc and added obs_quality_inc. SL * Per issue #1858: replaced obs_quality with obs_quality_inc and added obs_quality_exc. SL * Per issue #1858: For both the point_stat and ensemble_stat tests: modified tests that use OBS_QTY to use OBS_QTY_INC. Added unit test for OBS_QTY_EXC (obs_quality_exclude). SL * Per issue #1858: just added comment at top of file indicating what changed. SL * Per issue #1858: just added comment at top of file indicating what changed. SL * Per issue #1858: removed parse_conf_obs_qty. Modified parse_conf_obs_qty_inc to check for old 'obs_quality' entry. SL * Per issue #1858: in process_config(), modified section that calls set_obs_qty_inc_filt...this new function can now handle old 'obs_quality' entry as well as the new 'obs_quality_inc'. SL * Modified parse_conf_obs_qty_inc and parse_conf_obs_qty_exc. SL * Per issue #1858: re-updated parse_conf_obs_qty_exc and reverted back to the simplier version of this function. SL * Per issue #1858: replaced obs_quality with obs_quality_inc and added obs_quality_exc. SL * Per issue #1858: replaced obs_quality with obs_quality_inc and added obs_quality_exc. SL * Per issue #1858: replaced obs_quality with obs_quality_inc and added obs_quality_exc. SL * Per issue #1858: replaced obs_quality with obs_quality_inc and added obs_quality_exc. SL * Per issue #1858: replaced obs_quality with obs_quality_inc and added obs_quality_inc. SL * Per issue #1858: replaced obs_quality with obs_quality_inc. Added documentation for obs_quality_exc. SL * Per issue #1858: checking in latest version. Modified section that calls set_obs_qty_inc_filt...this new function can now handle old 'obs_quality' entry as well as the new 'obs_quality_inc'. SL * Per issue #1858: cleaned up some extra line spaces. SL * Per #1858, removed the deprecated obs_quality configuration entry from 3 EnsembleStat and 5 PointStat configuration files. * Per issue #1858: duplicated fcst/obs fields to run/test with both obs_quality_inc and obs_quality_exc. SL * Per issue #1858: duplicated fcst/obs fields to run/test with both obs_quality_inc and obs_quality_exc. SL * Per issue #1858. Deleted these files git repository. These were replaced with: PointStatConfig_qty_inc_exc. SL * Per issue #1858. Deleted these files from the git repository. These were replaced with: EnsembleStatConfig_qty_inc_exc. SL * Per issue #1858. Deleted these files from the git repository. These were replaced with: PointStatConfig_qty_inc_exc. SL * Per issue #1858: Modified: Don't need to run separate tests for obs_quality_inc and obs_quality_exc, these are now combined into one test via the updated config files: PointStatConfig_qty_inc_exc and EnsembleStatConfig_qty_inc_exc. SL * Per #1858, update the logic in parse_conf_obs_qty_inc() to use last_lookup_status(). See forthcoming GitHub issue comment about this. * Per #1858, tweak the warning message. * Per #1858, made the existing unit_quality_filter.xml tests a bit more concise. Call Point-Stat and Ensemble-Stat only once each time. But for each, test 3 things: all qty, obs_quality_inc, and obs_quality_exc. * Per #1858, remove the _ON from the job name since the _OFF has been included in the same configuration. Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> * Feature 1894 pb2nc var all (#1917) * #1894 Added station ID 14008 to pb2nc_NDAS_var_all unit test * #1894 Check the existance of the valid data up to 16 levels Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> * Feature 1913 MAX_PBL (#1916) * #1913 Changed MAX_PBL to 10000. Filter out if the PBL input data is invalid * #1912 Replaced is_eq to is_bad_data * #1913 Changed is_eq to is_bad_data Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> * Add bolding the MET version 10.1.0 beta2 release notes to indicate emphasis prior to the METplus Governance meeting. * feature 1922 iodas2nc - Removed trailing spaces based on the string length (#1923) * #1922 Removed trailing spaces based on the string lenth than buffer length * #1922 Renamed cleanup_hdr_bfr to m_rstrip and moved to str_wrappers.cc Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> Co-authored-by: jprestop <jpresto@ucar.edu> Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu> Co-authored-by: hsoh-u <hsoh@ucar.edu> Co-authored-by: Keith Searight <keith.searight@noaa.gov> Co-authored-by: Seth Linden <linden@ucar.edu> Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@seneca.rap.ucar.edu> Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: ericgilleland <34106925+ericgilleland@users.noreply.github.com> Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu> Co-authored-by: MET Tools Test Account <met_test@kiowa.rap.ucar.edu> Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>

dwfncar closed this as completed Feb 18, 2011

dwfncar added the Library Code label Apr 30, 2019

dwfncar added this to the MET 2.0 and prior milestone Apr 30, 2019

dwfncar mentioned this issue Mar 24, 2020

MODE-Multivar boolean logic from config file #1282

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lisagoodrich added a commit that referenced this issue May 25, 2021

another attempt #2

0ab9b5e

JohnHalleyGotway added MET: Library Code and removed component: library code labels Jun 10, 2021

JohnHalleyGotway mentioned this issue Jun 11, 2021

Enhance TC-Gen to verify NHC tropical weather outlook shapefiles. Refine logic to prevent rounding shapefile points to the nearest grid point. #1810

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lisagoodrich added a commit that referenced this issue Jun 28, 2021

testing dropdown menus #2 removing lines and dotted lines

77d5bce

georgemccabe mentioned this issue Jun 6, 2022

Documentation: Improve clarity of which config variables are supported in each tool #2172

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PerryShafran-NOAA mentioned this issue Aug 31, 2022

Add support for EPA AirNow ASCII data in ASCII2NC #2142

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hertneky mentioned this issue Apr 11, 2023

Enhance Multivariate MODE to generate object statistics for each input field requested by the user. #1283

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jvigh mentioned this issue Oct 13, 2023

Enhance TC-Diag to actually compute and write diagnostics #2550

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hertneky mentioned this issue Nov 17, 2023

Feature 2706 mvmode obs fcst input size #2742

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investigate RT for met_help #2

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dwfncar commented Aug 17, 2009

investigate RT for met_help #2

investigate RT for met_help #2

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dwfncar commented Aug 17, 2009