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Feature 1809 gen prob #1967

Merged
merged 28 commits into from
Nov 16, 2021
Merged

Feature 1809 gen prob #1967

merged 28 commits into from
Nov 16, 2021

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JohnHalleyGotway
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@JohnHalleyGotway JohnHalleyGotway commented Nov 14, 2021

Pull Request Testing

@georgemccabe we'll likely need updates the tc-gen METplus wrapper to supply the new -edeck command line option and configure the new prob_genesis_thresh option. I'd recommend holding off until #1810 is done, which will also change the inputs/configuration options.

@halperin-erau please review the config file changes and doc updates, if possible:
https://met.readthedocs.io/en/feature_1809_gen_prob/Users_Guide/tc-gen.html
You can try out the actual code in the docker container for the MET-10.1.0-beta4 development release, once that's ready.

  • Describe testing already performed for these changes:

    Manual testing of new functionality using sample files provided by @halperin-erau. During the beta5 development cycle, @KathrynNewman will be adding a METplus use case demonstrating this new functionality with a much larger sample of data. Recommend revisiting the existing tests in unit_tc_gen.xml and consider making them more robust once that larger dataset if available.

  • Recommend testing for the reviewer(s) to perform, including the location of input datasets, and any additional instructions:

    Review the regression test output in kiowa:/d1/projects/MET/MET_pull_requests/met-10.1.0/met-10.1.0_beta4/feature_1809

  • Do these changes include sufficient documentation updates, ensuring that no errors or warnings exist in the build of the documentation? [Yes]

Still working on the doc updates. Once they're complete I'll change this from a draft PR to one that's ready for review.
See doc updates here:
https://met.readthedocs.io/en/feature_1809_gen_prob/Users_Guide/tc-gen.html

  • Do these changes include sufficient testing updates? [Yes]

Add a new call to tc_gen in unit_tc_gen.xml.

  • Will this PR result in changes to the test suite? [Yes]

    If yes, describe the new output and/or changes to the existing output:

Expected changes are:
In kiowa:/d1/projects/MET/MET_pull_requests/met-10.1.0/met-10.1.0_beta4/feature_1809/test_regression.log

  • new tc_gen probabilistic output files
ERROR: folder MET-develop/test_output missing 6 files
    tc_gen/tc_gen_prob_genmpr.txt 
    tc_gen/tc_gen_prob_pct.txt 
    tc_gen/tc_gen_prob_pjc.txt 
    tc_gen/tc_gen_prob_prc.txt 
    tc_gen/tc_gen_prob_pstd.txt 
    tc_gen/tc_gen_prob.stat 
  • modification to the contents of existing GENMPR line type
file1: MET-feature_1809_gen_prob/test_output/tc_gen/tc_gen_2016_genmpr.txt
ERROR: compareStat() failed
--
file1: MET-feature_1809_gen_prob/test_output/tc_gen/tc_gen_2016.stat
ERROR: compareStat() failed
  • Please complete this pull request review by [Monday 11/15/21].

Pull Request Checklist

See the METplus Workflow for details.

  • Complete the PR definition above.
  • Ensure the PR title matches the feature or bugfix branch name.
  • Define the PR metadata, as permissions allow.
    Select: Reviewer(s)
    Select: Organization level software support Project or Repository level development cycle Project
    Select: Milestone as the version that will include these changes
  • After submitting the PR, select Linked issues with the original issue number.
  • After the PR is approved, merge your changes. If permissions do not allow this, request that the reviewer do the merge.
  • Close the linked issue and delete your feature or bugfix branch from GitHub.

…mpile it. Define ATCF offsets specific to ATCF EDECK GN lines. Update the is_match() logic slightly by moving the checking for consistent valid times from the base class to the ProbRIRWInfo class. That way we can store all probabilities for the same genesis event (across multiple lead times) in the same object.
…esis, update it to only process RIRW probabilities from the ProbInfoArray class rather than all of them.
…enesis probability forecasts and now needs to be enhanced to actually verify them.
…pdate the other classes accordingly to set it. Also, update tc_pairs to only process ATCF EDECK probability of RI lines.
…n evaluating the genesis probability forecasts.
…bility of genesis as ProbGen rather than mixing it with GenProb, for consistency. Also define ProbGenPCTInfo class for storing PCTInfo.
…ing with changes to simplify the matching logic.
…hat the tc-gen application can modify their contents.
…rifying genesis probabilities. Still need to add a probgen_mpr line type, a unit test, and documentaiton.
…ched pair objects. This is cleaner than the last kludgy solution.
@JohnHalleyGotway JohnHalleyGotway marked this pull request as ready for review November 15, 2021 02:48
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Quick question on consistency before I approve: I see PROB_GENESIS for the fcst_var and obs_var in the output files, which is consistent with the genesis methodology listed in the UG (GENESIS_DEV, GENESIS_OPS, or GENESIS_PROB). But in the TCGenConfig_prob the dev and ops scoring method flags appear (which I believe is what we want). How are these differentiated?

@JohnHalleyGotway
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@KathrynNewman you are correct that these flags are listed in TCGenConfig_prob:

dev_method_flag = TRUE;
ops_method_flag = TRUE;

However, these currently have no effect on the probability of genesis verification! These is only one set of vx logic defined for this data, as described in the Scoring Logic section.

So we do NOT have different "development" and "operational" scoring logic. That was a detail that was a bit murky for me. Should we support 2 types of scoring logic for this input? If so, is it crystal clear to you what they should be and how they should differ?

@KathrynNewman
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I'm sorry for the stupid question, John! I was recalling that you listed both DEV and OPS in the meeting notes from 11/11, but now that I look back at the issue, I see I somehow missed the entire discussion between you and Dan on only using OPS=PROBGENESIS. This all sounds good!

@georgemccabe
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I created 2 METplus issues that are related to this work:
Enhance TCGen wrapper to add support for new configurations: dtcenter/METplus#1273
New Use Case: TCGen Verify Genesis Probabilities from ATCF e-deck files: dtcenter/METplus#1274

JohnHalleyGotway added a commit that referenced this pull request Nov 16, 2021
Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>
Co-authored-by: johnhg <johnhg@ucar.edu>
Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu>
Co-authored-by: John Halley Gotway <johnhg@ucar.edu>
Co-authored-by: j-opatz <59586397+j-opatz@users.noreply.github.com>
Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu>
Co-authored-by: jprestop <jpresto@ucar.edu>
Co-authored-by: Seth Linden <linden@ucar.edu>
Co-authored-by: hsoh-u <hsoh@ucar.edu>
georgemccabe added a commit to dtcenter/METplus that referenced this pull request Nov 19, 2021
Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>
Co-authored-by: TaraJensen <jensen@ucar.edu>
Co-authored-by: bikegeek <3753118+bikegeek@users.noreply.github.com>
Co-authored-by: bikegeek <minnawin@ucar.edu>
Co-authored-by: johnhg <johnhg@ucar.edu>
Co-authored-by: Christina Kalb <kalb@ucar.edu>
Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com>
Co-authored-by: jprestop <jpresto@ucar.edu>
JohnHalleyGotway added a commit that referenced this pull request Feb 3, 2022
* Per #1906, modify code to pass entire path to make_temp_file_name instead of only the filename so that the function can tell whether or not the file exists. (#1952)

Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>

* Feature 1761 percent thresh (#1956)

* Per issue #1761 in set_perc() adding code to get FBIAS numeric value, like 1.0 or 0.9, etc. SL

* Per issue #1761: in set_perc(), modified actual percentile calculation at end to use the extracted FBIAS numeric value (float). SL

* Per issue #1761: modified the check on the perc_thresh_freq_bias, just has to be > 0 now. SL

* Per issue #1761: cleaned up code in set_perc(). SL

* Per #1761, updates to Simple_Node::set_perc() to handle variable frequency bias amounts.
Changes include:
- Reverting the formatting of this back to how it originally was in the develop branch. In general, just match the formatting of the existing file, so as the minimize the number of difference lines.
- Add logic to adjust the percentile to be found based on the requested FBIAS value. Multiplying or dividing the percentile by the FBIAS value depends on the inequality type and whether we're bias adjusting the forecast or observation data.
- Adjust the log messages slightly.

Please be aware that I'm not totally confident in these changes. They warrant much more testing. This logic is very, very confusing.

* Per #1761, call compute_percentile() when double-checking the percentile values.

* Per #1761, remove unused variable.

* Per #1761, add warning for percentiles > 100.

* Per #1761. In set_perc(), after testing cleaned up code. SL

* Per issue #1761: adding new config file for testing dynamic FBIAS values. SL

* Per issue #1761: added new unit test for dynamic FBIAS values when running grid_stat. SL

* Per issue #1761, modified FBIAS section to indicated that the user can use dynamic values that are not 1.0. SL

* Update met/docs/Users_Guide/config_options.rst

Co-authored-by: johnhg <johnhg@ucar.edu>

* Update met/docs/Users_Guide/config_options.rst

Co-authored-by: johnhg <johnhg@ucar.edu>

* Update met/docs/Users_Guide/config_options.rst

Co-authored-by: johnhg <johnhg@ucar.edu>

* Update test/config/GridStatConfig_fbias_perc_thresh

Co-authored-by: johnhg <johnhg@ucar.edu>

* Update test/config/GridStatConfig_fbias_perc_thresh

Co-authored-by: johnhg <johnhg@ucar.edu>

* Update test/config/GridStatConfig_fbias_perc_thresh

Co-authored-by: johnhg <johnhg@ucar.edu>

* Update test/config/GridStatConfig_fbias_perc_thresh

Co-authored-by: johnhg <johnhg@ucar.edu>

* Per issue #1761, set nc_pairs_flag = FALSE. SL

Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu>
Co-authored-by: John Halley Gotway <johnhg@ucar.edu>

* Feature 1905 ens_ctrl (#1955)

Co-authored-by: j-opatz <59586397+j-opatz@users.noreply.github.com>

* Hotfix after merging changing for #1761. Updating the list of expected output files.

* Per #1905, committing a hotfix directly to the develop branch. Reverting the logic for computing the ensemble range back to what it was previously. The new version produced very slight differences in the 6-th or 7-th decimal place when compared to previous results. There's not good reason for these changes which were caused by the order of operations in casting from doubles to floats. Reverting back to the old logic prevents diffs for anyone else downstream and is the prudent choice.

* Feature 1957 ascii2nc_python (#1958)

* Feature 1949 cf netcdf documentaton (#1951)

* #1949 Added CF compliant NetCDF into data IO

* #1949 Added commas

* #1948 Some corrections for typo and added the links for CF attributes

* #1948 Added Performance with NetCDF input data

* #1949 Corrected tyoe and applied Juloie's suggestions

Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu>

* Feature 1968 ens_ctrl (#1969)

* Feature 1809 gen prob (#1967)

* Feature 1970 v10.1.0-beta4 (#1973)

* Fix tiny typo in plot_data_plane usage statement.

* Hotfix for the develop branch to get met-10.1.0-beta4 compiling on WCOSS. The intel compiler does not allow adjacent >> characters when defining maps.

* Updating the beta4 release date from 11/16 to 11/17 since the beta4 release needs to be recreated.

* Update the MET PR template to list expected changes up front.

* Bugfix 1976 develop cdist (#1979)

* #1936 Excludes precip3hr, precip6hr, precip12hr, and precip10min from required variables for MESONET

* Per #1985, correcting typo found while creating V10.0.1 in the develop branch as well.

* Per #1985, VERY minor change to fix alignment of titles in Point-Stat... updating the develop branch.

* #1936 Added an unit test for newer MESONET file

* Feature 1989 sort (#1990)

* Feature 1991 VCNT (#1992)

* Feature 1993 grid_mask (#1994)

* #1844 Added vx_pointdata_python

* #1844 Added vx_pointdata_python to PYTHON_LIBS & make file for vx_pointdata_python

* #1844 Added vx_pointdata_python to SUBDIRS

* #1844 Initial release

* #1844 Added met_point_data.cc & met_point_data.h

* #1844 NcHeaderData is renamed to MetPointHeader and moved to met_point_dataq.h

* #1844 NcPointObsData is derived from MetPointObsData. Many methods are moved to the base class MetPointObsData

* #1844 Moved varianbles and methods to the base class MetPointData

* #1844 override the obs_data pointer to the derived class

* #1844 Added pyobject_as_bool & pyobject_as_string_array

* #1844 Cleanup include statements and addpointdata_python.h if python is enabled

* #18443 Support python embedding

* #1844 Initial release

* #1844 Make buf_size const

* Add GitHub Actions workflow to trigger METplus testing workflow (#2002)

* changed names of inputs to send to METplus to match changes to METplus repo

* #1965 Excludes the duplicated variable names from multiple input files

* #1965 Processed with the raw variable names and update them when the output is saved.

* #1965 Added unit test ioda2nc_same_input

* #1965 Processed with the raw variable names and update them when the output is saved.

* #1965 Added unit test ioda2nc_same_input

* #1965 initialize var_idx

* Update the development environment for seneca to add /usr/local/nco/bin and /usr/local/netcdf/bin to the path. Also define MET_TEST_RSCRIPT to point to a new enough version of RSCRIPT that has the ncdf4 package 1.17 or later.

* send email address of user who triggered event to METplus workflow as input

* Fixup the Rscript diffing logic to support running the nightly build on seneca. The problem here is that the ncdiff -x -v command line options that worked in version 4.7.0 NO LONGER work in 4.9.2. Added a check to skip over the time_bounds variable when processing the ncdiff output.

* No real changes here. Just formatting

* Feature 1974 message_type_group_map (#1999)

Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu>
Co-authored-by: John Halley Gotway <johnhg@ucar.edu>

* Feature 1996 uninitialized variables (#2004)

Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu>
Co-authored-by: John Halley Gotway <johnhg@ucar.edu>

* Feature 1695 ensemble single file (gen_ens_prod) (#2001)

Co-authored-by: johnhg <johnhg@ucar.edu>

* Feature 1965 NB faile with time summary by ioda2nc (#2008)

Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu>

* Feature 1810 shapes (#2005)

* #1844 Added log message for use_var_id

* #1844 Get use_var_id for python embedding

* #1844 Initial release

* #1844 Added met_point_obs.py and read_met_point_obs.py

* #1844 Added 4 unit test for python embedding of MET point data

* More changes to test_util.R to account for differences between 4.7.0 and 4.9.2 of ncdiff. The earlier version reported 0 diffs for the time_bounds, lat, lon, latitude, and longitude variables while the newer version reports their raw values. Simply ignore these variables for now. This isn't a great solution but when we reimplement this testing logic in python, we can address this issue then.

* #1844 Added python embedding for point observation data

* Feature 1926 gridstat openmp (#1977)

Co-authored-by: johnhg <johnhg@ucar.edu>
Co-authored-by: John Halley Gotway <johnhg@ucar.edu>
Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>

* feature 1695 ensemble single file (ensemble_stat) (#2007)

Co-authored-by: johnhg <johnhg@ucar.edu>

* Committing directly to the develop branch. Removing many, many instances of MET_BUILD_BASE and a couple instances of MET_BASE from the examples listed in Appendix A. The inconsistent use of these variables will only cause confusion. Removing them will help avoid that confusion. Big picture... MET_BASE defines the installed 'share/met' directory. It can be used to reference the location of map or polyline files. MET_BUILD_BASE is only used in the context of the test scripts. There, it's defined as the top-level source code directory in which the code was compiled. Its used to reference the location of sample data files or Rscript included in the tarball. I left a couple references to these variables in Appendix A where thier use is not confusing. But I removed all instances which are used to the define the location of the 'bin' directory. Instead, let's just assume the MET binaries are already in their path... or the user knows where to find them.

* feature 2011 v10.1.0-beta5 (#2014)

* feature 1695 fix issues with ensemble changes (#2012)

Co-authored-by: John Halley Gotway <johnhg@ucar.edu>
Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu>

* Hotfix for #1695 committed directly to the develop branch. The new Ensemble-Stat config files added for this issue don't define a random number generator seed. This results in different output for each run and prevents the regression test from producing repeatable results. Defining the seed here to fix that.

* Adding George to email list for the nightly build.

* Fix the links for the met-10.1.0-beta5 release notes.

* #1844 Make met_point_obs as abstract class

* #1844 correctedb for loop end condition on processing obs bdata

* Feature 1546 unit_tests (#2021)

* #2020 Added SonarQube related varibales

* #2020 Initial release

* #2015 Avoid the repeasted debug message if derived varibales are disabled

* #1996 Initialize right and left

* #1966 Call clear() instead of reset memory for Header variable

* #1966 Make sure the levels from variable  does not exceed the maxLevel

* #1966 Removed unreachable codes

* #1966 Do not write into NetcDF if empty data

* #2015 Corrected "retained or derived" count

* Feature 1546 CI testing (#2029)

Co-authored-by: John Halley Gotway <johnhg@ucar.edu>

* fixed broken workflow by setting environment variable expected for docker build script

* add missing docker tag from push command

* added correct docker tag value

* fixed incorrect truth data version for updating -ref reference data

* Updating develop with changes to the unit tests names. Renaming unit_test.yml to a more generic testing.yml name since it compiles AND/OR runs unit tests. Also make the job names more concise so its easier to see what's running in the action summary window on GitHub.

* fixed directory to copy truth data into -- copy command was copying the content of the directory, not including the directory itself

* Per #1907, added warning about switch from Ensemble-Stat to Gen-Ens-Prod (#2032)

Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>

* 2028 Check null for header data

* Removed un-reachable code

* #2028 Check if the pointer (d) is null

* #2015 Changed warning to debug message

* #2028 Passing two dimensionl cur and dim array

* #2028 Set obs_data

* Feature 2003 briercl (#2034)

Co-authored-by: jprestop <jpresto@ucar.edu>
Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>
Co-authored-by: Seth Linden <linden@ucar.edu>
Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu>
Co-authored-by: j-opatz <59586397+j-opatz@users.noreply.github.com>
Co-authored-by: hsoh-u <hsoh@ucar.edu>
Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu>
Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Co-authored-by: John Halley Gotway <johnhg@seneca.rap.ucar.edu>
Co-authored-by: MET Tools Test Account <met_test@seneca.rap.ucar.edu>
Co-authored-by: mo-mglover <78152252+mo-mglover@users.noreply.github.com>
Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu>
Co-authored-by: Howard Soh <hsoh@seneca.rap.ucar.edu>
JohnHalleyGotway added a commit that referenced this pull request Feb 12, 2022
* Per #1906, modify code to pass entire path to make_temp_file_name instead of only the filename so that the function can tell whether or not the file exists. (#1952)

Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>

* Feature 1761 percent thresh (#1956)

* Per issue #1761 in set_perc() adding code to get FBIAS numeric value, like 1.0 or 0.9, etc. SL

* Per issue #1761: in set_perc(), modified actual percentile calculation at end to use the extracted FBIAS numeric value (float). SL

* Per issue #1761: modified the check on the perc_thresh_freq_bias, just has to be > 0 now. SL

* Per issue #1761: cleaned up code in set_perc(). SL

* Per #1761, updates to Simple_Node::set_perc() to handle variable frequency bias amounts.
Changes include:
- Reverting the formatting of this back to how it originally was in the develop branch. In general, just match the formatting of the existing file, so as the minimize the number of difference lines.
- Add logic to adjust the percentile to be found based on the requested FBIAS value. Multiplying or dividing the percentile by the FBIAS value depends on the inequality type and whether we're bias adjusting the forecast or observation data.
- Adjust the log messages slightly.

Please be aware that I'm not totally confident in these changes. They warrant much more testing. This logic is very, very confusing.

* Per #1761, call compute_percentile() when double-checking the percentile values.

* Per #1761, remove unused variable.

* Per #1761, add warning for percentiles > 100.

* Per #1761. In set_perc(), after testing cleaned up code. SL

* Per issue #1761: adding new config file for testing dynamic FBIAS values. SL

* Per issue #1761: added new unit test for dynamic FBIAS values when running grid_stat. SL

* Per issue #1761, modified FBIAS section to indicated that the user can use dynamic values that are not 1.0. SL

* Update met/docs/Users_Guide/config_options.rst

Co-authored-by: johnhg <johnhg@ucar.edu>

* Update met/docs/Users_Guide/config_options.rst

Co-authored-by: johnhg <johnhg@ucar.edu>

* Update met/docs/Users_Guide/config_options.rst

Co-authored-by: johnhg <johnhg@ucar.edu>

* Update test/config/GridStatConfig_fbias_perc_thresh

Co-authored-by: johnhg <johnhg@ucar.edu>

* Update test/config/GridStatConfig_fbias_perc_thresh

Co-authored-by: johnhg <johnhg@ucar.edu>

* Update test/config/GridStatConfig_fbias_perc_thresh

Co-authored-by: johnhg <johnhg@ucar.edu>

* Update test/config/GridStatConfig_fbias_perc_thresh

Co-authored-by: johnhg <johnhg@ucar.edu>

* Per issue #1761, set nc_pairs_flag = FALSE. SL

Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu>
Co-authored-by: John Halley Gotway <johnhg@ucar.edu>

* Feature 1905 ens_ctrl (#1955)

Co-authored-by: j-opatz <59586397+j-opatz@users.noreply.github.com>

* Hotfix after merging changing for #1761. Updating the list of expected output files.

* Per #1905, committing a hotfix directly to the develop branch. Reverting the logic for computing the ensemble range back to what it was previously. The new version produced very slight differences in the 6-th or 7-th decimal place when compared to previous results. There's not good reason for these changes which were caused by the order of operations in casting from doubles to floats. Reverting back to the old logic prevents diffs for anyone else downstream and is the prudent choice.

* Feature 1957 ascii2nc_python (#1958)

* Feature 1949 cf netcdf documentaton (#1951)

* #1949 Added CF compliant NetCDF into data IO

* #1949 Added commas

* #1948 Some corrections for typo and added the links for CF attributes

* #1948 Added Performance with NetCDF input data

* #1949 Corrected tyoe and applied Juloie's suggestions

Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu>

* Feature 1968 ens_ctrl (#1969)

* Feature 1809 gen prob (#1967)

* Feature 1970 v10.1.0-beta4 (#1973)

* Fix tiny typo in plot_data_plane usage statement.

* Hotfix for the develop branch to get met-10.1.0-beta4 compiling on WCOSS. The intel compiler does not allow adjacent >> characters when defining maps.

* Updating the beta4 release date from 11/16 to 11/17 since the beta4 release needs to be recreated.

* Update the MET PR template to list expected changes up front.

* Bugfix 1976 develop cdist (#1979)

* #1936 Excludes precip3hr, precip6hr, precip12hr, and precip10min from required variables for MESONET

* Per #1985, correcting typo found while creating V10.0.1 in the develop branch as well.

* Per #1985, VERY minor change to fix alignment of titles in Point-Stat... updating the develop branch.

* #1936 Added an unit test for newer MESONET file

* Feature 1989 sort (#1990)

* Feature 1991 VCNT (#1992)

* Feature 1993 grid_mask (#1994)

* #1844 Added vx_pointdata_python

* #1844 Added vx_pointdata_python to PYTHON_LIBS & make file for vx_pointdata_python

* #1844 Added vx_pointdata_python to SUBDIRS

* #1844 Initial release

* #1844 Added met_point_data.cc & met_point_data.h

* #1844 NcHeaderData is renamed to MetPointHeader and moved to met_point_dataq.h

* #1844 NcPointObsData is derived from MetPointObsData. Many methods are moved to the base class MetPointObsData

* #1844 Moved varianbles and methods to the base class MetPointData

* #1844 override the obs_data pointer to the derived class

* #1844 Added pyobject_as_bool & pyobject_as_string_array

* #1844 Cleanup include statements and addpointdata_python.h if python is enabled

* #18443 Support python embedding

* #1844 Initial release

* #1844 Make buf_size const

* Add GitHub Actions workflow to trigger METplus testing workflow (#2002)

* changed names of inputs to send to METplus to match changes to METplus repo

* #1965 Excludes the duplicated variable names from multiple input files

* #1965 Processed with the raw variable names and update them when the output is saved.

* #1965 Added unit test ioda2nc_same_input

* #1965 Processed with the raw variable names and update them when the output is saved.

* #1965 Added unit test ioda2nc_same_input

* #1965 initialize var_idx

* Update the development environment for seneca to add /usr/local/nco/bin and /usr/local/netcdf/bin to the path. Also define MET_TEST_RSCRIPT to point to a new enough version of RSCRIPT that has the ncdf4 package 1.17 or later.

* send email address of user who triggered event to METplus workflow as input

* Fixup the Rscript diffing logic to support running the nightly build on seneca. The problem here is that the ncdiff -x -v command line options that worked in version 4.7.0 NO LONGER work in 4.9.2. Added a check to skip over the time_bounds variable when processing the ncdiff output.

* No real changes here. Just formatting

* Feature 1974 message_type_group_map (#1999)

Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu>
Co-authored-by: John Halley Gotway <johnhg@ucar.edu>

* Feature 1996 uninitialized variables (#2004)

Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu>
Co-authored-by: John Halley Gotway <johnhg@ucar.edu>

* Feature 1695 ensemble single file (gen_ens_prod) (#2001)

Co-authored-by: johnhg <johnhg@ucar.edu>

* Feature 1965 NB faile with time summary by ioda2nc (#2008)

Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu>

* Feature 1810 shapes (#2005)

* #1844 Added log message for use_var_id

* #1844 Get use_var_id for python embedding

* #1844 Initial release

* #1844 Added met_point_obs.py and read_met_point_obs.py

* #1844 Added 4 unit test for python embedding of MET point data

* More changes to test_util.R to account for differences between 4.7.0 and 4.9.2 of ncdiff. The earlier version reported 0 diffs for the time_bounds, lat, lon, latitude, and longitude variables while the newer version reports their raw values. Simply ignore these variables for now. This isn't a great solution but when we reimplement this testing logic in python, we can address this issue then.

* #1844 Added python embedding for point observation data

* Feature 1926 gridstat openmp (#1977)

Co-authored-by: johnhg <johnhg@ucar.edu>
Co-authored-by: John Halley Gotway <johnhg@ucar.edu>
Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>

* feature 1695 ensemble single file (ensemble_stat) (#2007)

Co-authored-by: johnhg <johnhg@ucar.edu>

* Committing directly to the develop branch. Removing many, many instances of MET_BUILD_BASE and a couple instances of MET_BASE from the examples listed in Appendix A. The inconsistent use of these variables will only cause confusion. Removing them will help avoid that confusion. Big picture... MET_BASE defines the installed 'share/met' directory. It can be used to reference the location of map or polyline files. MET_BUILD_BASE is only used in the context of the test scripts. There, it's defined as the top-level source code directory in which the code was compiled. Its used to reference the location of sample data files or Rscript included in the tarball. I left a couple references to these variables in Appendix A where thier use is not confusing. But I removed all instances which are used to the define the location of the 'bin' directory. Instead, let's just assume the MET binaries are already in their path... or the user knows where to find them.

* feature 2011 v10.1.0-beta5 (#2014)

* feature 1695 fix issues with ensemble changes (#2012)

Co-authored-by: John Halley Gotway <johnhg@ucar.edu>
Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu>

* Hotfix for #1695 committed directly to the develop branch. The new Ensemble-Stat config files added for this issue don't define a random number generator seed. This results in different output for each run and prevents the regression test from producing repeatable results. Defining the seed here to fix that.

* Adding George to email list for the nightly build.

* Fix the links for the met-10.1.0-beta5 release notes.

* #1844 Make met_point_obs as abstract class

* #1844 correctedb for loop end condition on processing obs bdata

* Feature 1546 unit_tests (#2021)

* #2020 Added SonarQube related varibales

* #2020 Initial release

* #2015 Avoid the repeasted debug message if derived varibales are disabled

* #1996 Initialize right and left

* #1966 Call clear() instead of reset memory for Header variable

* #1966 Make sure the levels from variable  does not exceed the maxLevel

* #1966 Removed unreachable codes

* #1966 Do not write into NetcDF if empty data

* #2015 Corrected "retained or derived" count

* Feature 1546 CI testing (#2029)

Co-authored-by: John Halley Gotway <johnhg@ucar.edu>

* fixed broken workflow by setting environment variable expected for docker build script

* add missing docker tag from push command

* added correct docker tag value

* fixed incorrect truth data version for updating -ref reference data

* Updating develop with changes to the unit tests names. Renaming unit_test.yml to a more generic testing.yml name since it compiles AND/OR runs unit tests. Also make the job names more concise so its easier to see what's running in the action summary window on GitHub.

* fixed directory to copy truth data into -- copy command was copying the content of the directory, not including the directory itself

* Per #1907, added warning about switch from Ensemble-Stat to Gen-Ens-Prod (#2032)

Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>

* 2028 Check null for header data

* Removed un-reachable code

* #2028 Check if the pointer (d) is null

* #2015 Changed warning to debug message

* #2028 Passing two dimensionl cur and dim array

* #2028 Set obs_data

* Feature 2003 briercl (#2034)

* do not run testing workflow if changes are isolated to the met/docs directory

* Per #2013, changed source and README.  ci-run-unit (#2039)

* Feature 1055 read rot latlon (#2041)

* CI: output summary of differences in GHA log to easily see results without having to download the log artifact

* #2027 Added a debug message

* #2027 ci-run-unit Changed wind thres

* #2027 ci-run-unit Increased the precision to debug message

* print end of script after error summary, ci-run-unit

* #2027 Increased the buffer and cheking the status of sprintf

* Feature 1998 standard sections (#2038)

* fixing section headers to be consistent with METplus #1998

* fixing section headers to be consistent with METplus #1998

* fixing section headers to be consistent with METplus #1998 missed one

* fixing section headers to be consistent with METplus #1998 try again

* fixing section headers to be consistent with METplus #1998 I had it right the first time

* fixing section headers to be consistent with METplus #1998

* fixing section headers to be consistent with METplus #1998 fixing mistake

* fixing section headers to be consistent with METplus #1998

* fixing section headers to be consistent with METplus #1998

* fixing section headers to be consistent with METplus #1998

* fixing section headers to be consistent with METplus #1998

* fixing section header underscore to dash #1998

* updating TOC vs ref 1998

* updating TOC vs ref 1998 completed

* trying to fix link #1998

* trying to fix link adding reference back in #1998

* updating TOC again underscore vs dash #1998

* updating TOC again underscore vs dash #1998

* updating TOC vs ref 1998 try

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998 take 2

* standardizing TOC sections #1998 take 3

* re-standardizing TOC sections #1998

* re-standardizing TOC sections #1998

* re-standardizing TOC sections #1998

* re-standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998

* updating questions into the TOC.  test #1998

* updating questions into the TOC. #1998

* standardizing TOC sections #1998

* standardizing TOC sections #1998 fixing typo

* standardizing TOC sections #1998 fixing typo

* standardizing TOC sections #1998 fixing typo

* standardizing TOC sections #1998 fixing typo

* standardizing TOC sections #1998 fixing typo

* standardizing TOC sections #1998 fixing typo

* cleaning up questions. removing section title from questions.

* adding a period #1989.

* adding the line breaks back in to match other formatting within MET #1989.

* Changed some "^^^" to "----"

* Changed "###" to "***"

Co-authored-by: jprestop <jpresto@ucar.edu>

* Update met_stats.cc

#2047 Removed the debug message

* Update met_stats.cc

Removing variable that was set but never used because SonarQube might complain about that, like Fortify does.

* Feature 2040 parse timing (#2048)

Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>

* CI: Add logic to auto update input data (#2046)

* Bugfix 2045 develop hira (#2049)

Co-authored-by: jprestop <jpresto@ucar.edu>
Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>
Co-authored-by: Seth Linden <linden@ucar.edu>
Co-authored-by: Seth Linden <linden@kiowa.rap.ucar.edu>
Co-authored-by: j-opatz <59586397+j-opatz@users.noreply.github.com>
Co-authored-by: hsoh-u <hsoh@ucar.edu>
Co-authored-by: Howard Soh <hsoh@kiowa.rap.ucar.edu>
Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Co-authored-by: John Halley Gotway <johnhg@seneca.rap.ucar.edu>
Co-authored-by: MET Tools Test Account <met_test@seneca.rap.ucar.edu>
Co-authored-by: mo-mglover <78152252+mo-mglover@users.noreply.github.com>
Co-authored-by: John Halley Gotway <johnhg@kiowa.rap.ucar.edu>
Co-authored-by: Howard Soh <hsoh@seneca.rap.ucar.edu>
Co-authored-by: davidalbo <dave@ucar.edu>
Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com>
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Enhance TC-Gen to verify genesis probabilities from ATCF e-deck files.
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