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Feature 1908 remove ens #2265

Merged
merged 26 commits into from
Sep 21, 2022
Merged

Feature 1908 remove ens #2265

merged 26 commits into from
Sep 21, 2022

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JohnHalleyGotway
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@JohnHalleyGotway JohnHalleyGotway commented Sep 19, 2022

As promised, these changes REMOVE ensemble post-processing logic from the Ensemble-Stat tool for MET version 11.0.0. That functionality has moved entirely to Gen-Ens-Prod.

Expected Differences

  • Do these changes introduce new tools, command line arguments, or configuration file options? [Yes]

    If yes, please describe:

Listed below are some significant differences to note:

  • The ens, nbrhd_prob, nmep_smooth dictionaries have been removed from the Ensemble-Stat config file.

  • The ens_thresh and vld_thresh options have been moved from the ens dictionary to the fcst dictionary.

  • The ensemble_flag dictionary has been renamed as nc_orank_flag since it controls the output of the "_orank.nc" file. Its contents has also been updated.

  • Do these changes modify the structure of existing or add new output data types (e.g. statistic line types or NetCDF variables)? [Yes]

    If yes, please describe:

The Ensemble-Stat tool no longer generates "_ens.nc" NetCDF output files. Any processing that previously relied on that output should be modified to call Gen-Ens-Prod to create it instead.

Pull Request Testing

  • Describe testing already performed for these changes:

    Confirmed that the code compiles.
    Confirmed that the unit tests run without runtime errors.
    Diffed the unit tests output against develop-ref and looked through the diffs. Please see this GHA run.

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

Please review the config file changes, documentation updates, and changes introduced in the regression test output.

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

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

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

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

  • 20 "_ens.nc" output file previously generated by Ensemble-Stat are no longer created, as expected.

  • A couple "_orank.nc" output files are added based on the config settings.
    NOTE: @JohnHalleyGotway should check the GHA run and update the unit test xml files accordingly.

  • Differences are introduced in 41 files:

    • 18 .stat files
    • 6 _ecnt.txt files, 6 _ssvar.txt files, 11 _orank.nc files

Most of the numeric differences are very small (e.g. 0.0001) are are likely caused by the previously writing the ensemble mean to a NetCDF file and then reading it back in. Now, its all handled in memory, which should like provide better precision.

The following differences should be checked more carefully:

Make sure the _orank.nc output variables are reasonable.

file1: /data/output/met_test_truth/ensemble_stat/ensemble_stat_SINGLE_FILE_GRIB_WITH_CTRL_20160608_060000V.stat
ERROR: found     1 differences in row type ECNT         column CRPS          - max abs: 0.042 
ERROR: found     1 differences in row type ECNT         column IGN           - max abs: 0.00744 
ERROR: found     1 differences in row type ECNT         column ME            - max abs: 0.00001 
ERROR: found     1 differences in row type ECNT         column SPREAD        - max abs: 0.9927 
ERROR: failed tests for ECNT: num

and

file1: /data/output/met_test_truth/ensemble_stat/ensemble_stat_SINGLE_FILE_GRIB_WITH_CTRL_20160608_060000V.stat
ERROR: found     1 differences in row type ECNT         column CRPS          - max abs: 0.042 
ERROR: found     1 differences in row type ECNT         column IGN           - max abs: 0.00744 
ERROR: found     1 differences in row type ECNT         column ME            - max abs: 0.00001 
ERROR: found     1 differences in row type ECNT         column SPREAD        - max abs: 0.9927 
ERROR: failed tests for ECNT: num

and

file1: /data/output/met_test_truth/stat_analysis_es/AGG_SSVAR_out.stat
ERROR: found     2 differences in row type SSVAR        column FBAR_NCL      - max abs: 89837.42 
ERROR: found     2 differences in row type SSVAR        column FBAR_NCU      - max abs: 89837.42 
ERROR: found     2 differences in row type SSVAR        column FSTDEV        - max abs: 9999.003 
ERROR: found     2 differences in row type SSVAR        column FSTDEV_NCL    - max abs: 5206.059 
ERROR: found     3 differences in row type SSVAR        column FSTDEV_NCU    - max abs: 319069.9 
ERROR: found     1 differences in row type SSVAR        column PR_CORR       - max abs: 0.00001 
ERROR: found     1 differences in row type SSVAR        column PR_CORR_NCL   - max abs: 0.00001 
ERROR: found     1 differences in row type SSVAR        column ME_NCL        - max abs: 0.00522 
ERROR: found     1 differences in row type SSVAR        column ME_NCU        - max abs: 0.00522 
ERROR: found     2 differences in row type SSVAR        column ESTDEV        - max abs: 0.0020998 
ERROR: found     1 differences in row type SSVAR        column ESTDEV_NCL    - max abs: 0.0010932 
ERROR: found     1 differences in row type SSVAR        column ESTDEV_NCU    - max abs: 0.013197 
ERROR: found     1 differences in row type SSVAR        column MSE           - max abs: 0.00001 
ERROR: found     2 differences in row type SSVAR        column BCMSE         - max abs: 0.00001 
ERROR: found     1 differences in row type SSVAR        column RMSE          - max abs: 0.00002 
  • Please complete this pull request review by [Tuesday 9/20/22].

Pull Request Checklist

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  • 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)
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    Select: Milestone as the version that will include these changes
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…t use ens_file_list and ens_file_vld instead.
… compiles and runs, but I still need to do more testing and refinement.
…Move vld_thresh and ens_thresh into the fcst dictionary.
…ing the config options related to ensemble post-processing.
…when we tack the control file to the end of the list of ensemble files, we also increment the n_ens_files counter.
…nsemble_stat_SINGLE_FILE_NC_WITH_CTRL run. When all members are read from the same input file, DO NOT append the control file to the of the ensemble file list.
@JohnHalleyGotway
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Met with @georgemccabe and @j-opatz on 9/19/22 about this.

Determine whether or not this PR should go into beta3 by doing the following:

  1. Define tag for the feature_1908_remove_ens branch.
  2. Create a METplus branch for testing and modify this file to define MET_FORCE_TAG = {feature branch tag name}
  3. Git push using ci-run-all-cases in the commit message to trigger all the use cases to run.

If no runtime errors occur, this is a success and we should include it in beta3.
If runtime errors do occur, talk to @georgemccabe about those diffs to decided whether we should push to beta4 instead.

…_flag to nc_orank_flag and update its contents. Also make it configurable separetly for each vx task. Also update the User's Guide with this info.
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These changes involve removing ensemble verification from ensemble_stat because it is now only handled in gen_ens_prod. I see that some config options have been removed from the EnsembleStatConfig files because they are no longer relevant to that app.

The documentation changes are clear and descriptive of the new state of the app.

We reviewed the differences in the regression test output and confirmed they are expected. Files ending with _ens.nc are no longer generated by ensemble_stat. In some cases an _orank.nc is now generated when it was not previously. The differences in the stat output are rounding differences due to the new approach to obtaining these data -- previously the data was written to a NetCDF file and reread to generate the stat output, but now the data is stored in memory. Precision was likely lost with the old method, so these changes are improvements. We noticed that the FFBAR differences were a bit high (~0.1), but @JohnHalleyGotway mentioned that this is likely because the values are the squared result of another value.

I approve.

…stat runs. Needed to add 3 that are now being created.
…compute normal ci's when the forecast, observation, and error standard deviations are bad data.
@JohnHalleyGotway
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Did some additional work rectifying the diffs:

  • Update the unit test xml's to list 4 additional orank.nc files that are now being created: DONE
ERROR: folder /data/output/met_test_truth missing 4 files
    grid_weight/ensemble_stat_AREA_WEIGHT_20120410_120000V_orank.nc 
    grid_weight/ensemble_stat_COS_LAT_WEIGHT_20120410_120000V_orank.nc 
    grid_weight/ensemble_stat_NO_WEIGHT_20120410_120000V_orank.nc 
    python/ensemble_stat_PYTHON_20050807_120000V_orank.nc 
  • Inspect large diffs in ensemble_stat/ensemble_stat_SINGLE_FILE_GRIB_WITH_CTRL_20160608_060000V.stat: DONE
ERROR: found     1 differences in row type ECNT         column CRPS          - max abs: 0.042 
ERROR: found     1 differences in row type ECNT         column IGN           - max abs: 0.00744 
ERROR: found     1 differences in row type ECNT         column ME            - max abs: 0.00001 
ERROR: found     1 differences in row type ECNT         column SPREAD        - max abs: 0.9927 

There was actually a bug in the develop branch where doing gridded verification for all members in the same input file. The control member's value was included in the variance computation in place of the first ensemble member! And thus the SPREAD value is different. This bug is corrected in this feature branch. The other diffs are due to the relatively large values of pressure (101300+). Storing sums and sums of squares are large values decreases precision.

  • Inspect large diffs in ensemble_stat/ensemble_stat_SINGLE_FILE_NC_WITH_CTRL_19820701_000000V.stat: DONE
ERROR: found     1 differences in row type ECNT         column CRPS          - max abs: 0.0007 
ERROR: found     1 differences in row type ECNT         column IGN           - max abs: 0.00772 
ERROR: found     1 differences in row type ECNT         column SPREAD        - max abs: 0.01075 

See above for bugfix in the handling of ensemble control values when all members are in the same input file.

  • Inspect large diffs in stat_analysis_es/AGG_SSVAR_out.stat: DONE
ERROR: found     2 differences in row type SSVAR        column FBAR_NCL      - max abs: 89837.42 
ERROR: found     2 differences in row type SSVAR        column FBAR_NCU      - max abs: 89837.42 
ERROR: found     2 differences in row type SSVAR        column FSTDEV        - max abs: 9999.003 
ERROR: found     2 differences in row type SSVAR        column FSTDEV_NCL    - max abs: 5206.059 
ERROR: found     3 differences in row type SSVAR        column FSTDEV_NCU    - max abs: 319069.9 

Added more checks for bad data to CNTInfo::compute_ci(). Compute compute normal ci's when the forecast, observation, and error standard deviations are bad data.

  • Confirm that the ensemble_flag and nc_orank_flag are consistent across versions: DONE
    By default, all nc_orank_flag settings are TRUE except for weight and that is consistent with the previous default settings for ensemble_flag.

…ta as bad_data_double (-9999) instead of -999.
@JohnHalleyGotway
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Reviewed the final GHA run for this PR to confirm that the changes from earlier today actually had the desired effect.

Note the following:

  1. I see the same set of 4 new "_orank.nc" files as in the previous run.
  2. I see the same set of 20 old Ensemble-Stat "_ens.nc" files that are removed as in the previous run.
  3. I see the same set of 41 files containing differences as in the previous run (18 .stat, 6 _ecnt.txt, 6 _ssvar.txt, and 11 _orank.nc).
  4. Reviewing the 41 diff files, the following are of note:
    • Large diffs in the SPREAD values in ensemble_stat_SINGLE_FILE_GRIB_WITH_CTRL_20160608_060000V.stat and ensemble_stat_SINGLE_FILE_NC_WITH_CTRL_19820701_000000V.stat, as explained above because this feature branch fixes a bug in the handling of the control member when all members are read from the same input file.
    • Very large diffs are noted in AGG_SSVAR_out.stat. However I manually inspected those diffs and see that the new output is preferred. Previously, we were using -9999 values of standard deviation in the computation of normal ci limits. Those unreasonably large values have changed to NA, as expected.
  5. Manually ran unit_ascii2nc.xml and inspected the AIRNOW output files. The previous records containing -999 now contain -9999 instead, which is reported in the output of the pntnc2ascii.R Rscript as NA.

@JohnHalleyGotway JohnHalleyGotway merged commit 80e9095 into develop Sep 21, 2022
@JohnHalleyGotway JohnHalleyGotway deleted the feature_1908_remove_ens branch September 21, 2022 05:18
JohnHalleyGotway added a commit that referenced this pull request Sep 21, 2022
Co-authored-by: Howard Soh <[email protected]>
Co-authored-by: jprestop <[email protected]>
Co-authored-by: Julie Prestopnik <[email protected]>
Co-authored-by: j-opatz <[email protected]>
Co-authored-by: Randy Bullock <[email protected]>
Co-authored-by: davidfillmore <[email protected]>
Co-authored-by: rgbullock <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: johnhg <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: Seth Linden <[email protected]>
Co-authored-by: George McCabe <[email protected]>
Co-authored-by: Seth Linden <[email protected]>
Co-authored-by: Howard Soh <[email protected]>
Co-authored-by: Seth Linden <[email protected]>
Co-authored-by: hsoh-u <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: MET Tools Test Account <[email protected]>
Co-authored-by: mo-mglover <[email protected]>
Co-authored-by: davidalbo <[email protected]>
Co-authored-by: lisagoodrich <[email protected]>
Co-authored-by: Dan Adriaansen <[email protected]>
Co-authored-by: Dave Albo <[email protected]>
Co-authored-by: Lisa Goodrich <[email protected]>
Co-authored-by: Molly Smith <[email protected]>
Co-authored-by: Jonathan Vigh <[email protected]>
Co-authored-by: bikegeek <[email protected]>
georgemccabe added a commit to dtcenter/METplus that referenced this pull request Sep 21, 2022
Co-authored-by: Hank Fisher <[email protected]>
Co-authored-by: George McCabe <[email protected]>
Co-authored-by: Mrinal Biswas <[email protected]>
Co-authored-by: jprestop <[email protected]>
Co-authored-by: johnhg <[email protected]>
Co-authored-by: Mrinal Biswas <[email protected]>
Co-authored-by: Julie Prestopnik <[email protected]>
Co-authored-by: j-opatz <[email protected]>
Co-authored-by: Kathryn Newman <[email protected]>
Co-authored-by: j-opatz <[email protected]>
Co-authored-by: Lisa Goodrich <[email protected]>
Co-authored-by: Julie Prestopnik <[email protected]>
Co-authored-by: Christina Kalb <[email protected]>
Co-authored-by: cristianastan2 <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: Hank Fisher <[email protected]>
Co-authored-by: mrinalbiswas <[email protected]>
Co-authored-by: bikegeek <[email protected]>
Co-authored-by: lisagoodrich <[email protected]>
Co-authored-by: Christina Kalb <[email protected]>
Co-authored-by: Howard Soh <[email protected]>
Co-authored-by: Molly Smith <[email protected]>
Co-authored-by: hsoh-u <[email protected]>
Co-authored-by: bikegeek <[email protected]>
JohnHalleyGotway added a commit that referenced this pull request Nov 3, 2022
* Initialze obs_data at constructor to avoid warninjg on building

* Initialze obs_data at constructor to avoid a warning by compiler

* #1824 ci-run-test Removed the duplicated code

* Feature 1810 expand asciitable (#2086)

* Feature 1583 skip_mean (#2090)

* Feature 1275 MODE Object Count (#2091)

* for #1275, fix issue with more than 1000 object for mode, ci-run-unit

* Per #1275, just deleting stale, commented-out code.

Co-authored-by: Randy Bullock <[email protected]>

* Feature 1184 dryline (#2088)

Co-authored-by: davidfillmore <[email protected]>
Co-authored-by: rgbullock <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>

* Feature 1184 replace_env (#2093)

* Feature 2092 v10.1.0-rc1 (#2094)

* Hotfix to the develop branch to fix the MODE Makefile for the MET-10.1.0-rc1 release.

* Second hotfix for the MODE Makefile in the develop branch.

* Feature 1844 docs (#2096)

* Feature 2097 v10.1.0 (#2099)

* Feature 2098 gen ens prod doc (#2100)

* update job control rules for GHA testing workflow to use version specific input data if running tests on main_v branch

* Migrating a small tweak added to the v10.1.0 release into the develop branch.

* Adding SonarQube location to development.seneca file.

* Bugfix #2102 develop initialize modified_hdr_typ (#2104)

Co-authored-by: Howard Soh <[email protected]>
Co-authored-by: johnhg <[email protected]>

* added logic to manually trigger a workflow via the GitHub… (develop) (#2109)

Co-authored-by: John Halley Gotway <[email protected]>

* Feature update installation info (#2114)

* Updating configuration and modulefiles

* Removed jet files

* create DockerHub tag that ends with -lite to use when triggering the METplus testing workflow

* Bugfix #2115 develop Rotated LatLon (#2117)

* Feature 1950 sort station list (#2121)

* Update the top-level README file to list ioda2nc, but also to trigger GHA to run for this new main_v10.1-ref branch.

* Added bool Sorted variable, set to true or false in relevant functions. Updated sort() function. SL

* In parse_sid_mask(), added the line: mask_sid.sort(). SL

* Per issue #1950, put in some cout statements for testing. SL

* Per issue #1950, working in has() function, checking for Sort and put in initial cout's for testing. SL

* Per issue #1950: Cleaned up some cout (print) statements. Left one in there that is commented out for future testing. SL

* Per issue #1950: modified has() function. Added lower_bound search for sorted arrays. Left some print (cout) statements in there for further testing. SL

* Per issue #1950: In has(), I commented out the print (cout) statements for time testing. SL

* added logic to manually trigger a workflow via the GitHub… (#2107)

* Per issue #1950, put back in some print (cout) statements for testing. SL

* Per issue #1950: in has() function, experimenting using the upper_bound() search instead of lower_bound() for sorted vectors. In progress. SL

* Per issue #1950: added a new has function that uses binary_search. Re-working the other has() functions related to this. SL

* Per issue #1950: re-worked original has(), basically reverted back to what it was...but it's now only used for unsorted vectors or for a case insensitive search. Cleaned up. SL

* Per issue #1950: in section that checks Obs Station Id in SID masking list, changed cout to a mlog (debug) statement. SL

* Per issue #1950: created new mask station id list (CONUS METARs) and modified the PointStatConfig_MASK_SID config file to use this list along with the existing lists. SL

* Per issue #1950: reverted back to orginal sid mask site-lists. SL

* Per issue #1950: checking in this site-list that was used for testing point_stat. SL

* Per issue #1950, modified and added better debugging to figure out current issue with ascii2nc. SL

* Per #1950, small tweak in ascii2nc to make it slightly more efficient. After adding the new obs varable name to the end of the list, we can compute var_index direclty without needing to call StringArray::has() a second time.

* Per #1950: removed mlog and cout print statements from has() functions. Cleaned up. SL

* Update met/src/basic/vx_log/string_array.cc

Co-authored-by: johnhg <[email protected]>

* Update met/src/basic/vx_log/string_array.cc

Co-authored-by: johnhg <[email protected]>

* Update met/src/basic/vx_log/string_array.cc

Co-authored-by: johnhg <[email protected]>

* Update met/src/basic/vx_log/string_array.cc

Co-authored-by: johnhg <[email protected]>

* Update met/src/basic/vx_log/string_array.cc

Co-authored-by: johnhg <[email protected]>

* Update met/src/basic/vx_log/string_array.h

Co-authored-by: johnhg <[email protected]>

* Delete SID_CONUS.txt

* Delete SID_CONUS_times11.txt

Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: Seth Linden <[email protected]>
Co-authored-by: George McCabe <[email protected]>

* Bugfix #2118 develop grib1_rotll (#2130)

Co-authored-by: George McCabe <[email protected]>

* Bugfix 2123 nccf valid time (#2127)

Co-authored-by: Howard Soh <[email protected]>
Co-authored-by: johnhg <[email protected]>

* Feature #2132 version 11.0.0 (#2133)

* Bugfix #2106 develop gcc (#2135)

Co-authored-by: Julie Prestopnik <[email protected]>
Co-authored-by: johnhg <[email protected]>
Co-authored-by: Seth Linden <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: j-opatz <[email protected]>
Co-authored-by: Howard Soh <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: jprestop <[email protected]>
Co-authored-by: Howard Soh <[email protected]>
Co-authored-by: Randy Bullock <[email protected]>
Co-authored-by: davidfillmore <[email protected]>
Co-authored-by: rgbullock <[email protected]>
Co-authored-by: Seth Linden <[email protected]>
Co-authored-by: hsoh-u <[email protected]>
Co-authored-by: George McCabe <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: MET Tools Test Account <[email protected]>
Co-authored-by: mo-mglover <[email protected]>
Co-authored-by: davidalbo <[email protected]>
Co-authored-by: lisagoodrich <[email protected]>
Co-authored-by: Dan Adriaansen <[email protected]>

* Doc-only update to expliciltly list the maximum character lengths for variable-length strings passed to ascii2nc.

* Added pcp_combine -subtract example (#2153)

* Add testing and docs status badges.

* Feature #2152 poly_xy (#2154)

* #14 Using literal instead of numbers and make sure no overflow

* #14 Using literal instead of numbers

* #14 Added tmp_buf_size

* #14 Define n_kw_infos first

* #14 Using literal instead of numbers

* Bugfix #2148 develop misses (#2150)

* dtcenter/METplus-Internal#14 formatting code

* METplus-Internal #16 Added python scanning

* METplus-Internal #16 changed name

* METplus-Internal #16 initial release for python scanning

* METplus-Internalv#19 added maic.cc & main.h

* METplus-Internalv#19 renamed main to met_main and added get_tool_name

* METplus-Internalv#19 Initial release

* changing 'Linked issue' to 'Development issue'

* change Linked issue/Development issue ci-skip-all

* change Linked issue/Development issue ci-skip-all

* change Linked issue/Development issue ci-skip-all

* Feature 1920 repo (#2161)

* List line types that can be aggregated per dtcenter/METplus#1625

* Hotfix for the develop branch to correct a bad MET_TEST_BASE path that causes the nightly build to fail.

* Feature 2072 tc rmw winds (#2165)

* bug fix for NAN and for using missing data as if its not missing

* added parameters to control converting winds to tangential/radial components

* bug fixes

* Refactored to put wind conversion into it's own class TCRMW_WindConverter

* changed default for converting winds to TRUE, and put parameters for wind conversion into the unit test config files

* Per #2072, updating tc_rmw Makefile.in to compile new files.

* Per #2072, update to the output from the lex/yacc version on seneca.

* Changed Error to Warning in mlog messages, for consistency with MET conventions

* Removing commented out code.

* Per #2072, combine warnings spread across multiple lines into a single call to the logger. Replace references to ugrid/vgrid with u/v wind. Fix a typo and clean up some whitespace.

Co-authored-by: Dave Albo <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>

* change Linked issue/Development issue ci-skip-all

* Bugfix #2173 develop shift_data_plane (#2175)

* Bugfix #2170 develop agg_ecnt (#2177)

* Feature 2022 anom corr to vcnt (#2171)

* Per #2022: Added ANOM_CORR, ANOM_CORR_BCL, ANOM_CORR_BCU to vcnt_columns. SL

* Per #2022: Added ANOM_CORR, ANOM_CORR_BCL, ANOM_CORR_BCU to write_vcnt_cols. SL

* Per #2022: Added ANOM_CORR to VL1L2Info. SL

* Per #2022: updated the VL1L2Info functions to initialize and compute ANOM_CORR. SL

* Per #2022: in calc_ncep_stats modified calculation for ANOM_CORR to check for bad data in the denominator first. SL

* Per #2022: for the VL1L2Info, changed all derived VCNT variables to be CIInfo objects (instead of doubles). SL

* Per #2022: making changes to VL1L2Info related to making all VCTN variables CIInfo objects. In progress. SL

* Per #2022: Added ANOM_CORR_UNCNTR. SL

* Per issue 2022: Modified functions in the VL1L2Info class to set the NCEP stat variables correctly since they are now CIInfo class memembers. SL

* Per issue 2022: Added ANOM_CORR_UNCNTR (_BCL, _BCU). SL

* Per issue 2022: modified write_vcnt_cols(), added ANOM_CORR_UNCNTR (_BCL, _BCU). SL

* Per issue #2022: updated write_vcnt_cols. VCNT variables are now CIInfo objects to have to .v for the value. SL

* Per issue #2022: In calc_ncep_stats, put in place-holder for ANOM_CORR.v value SL

* Per issue #2022: in calc_ncep_stats(), changed placeholder for ANOM_CORR. SL

* Per issue #2022: moved alpha initialization to the init_from_scratch() function. SL

* Per issue #2022: in calc_ncep_stats(), set ANOM_CORR to bad_data_double as a placeholder for now. SL

* Per issue #2022: in vcnt_cols(), added ANOM_CORR_NCL/NCU. SL

* Per issue #2022: in write_vcnt_cols(), added ANOM_CORR_NCL/NCU variables. SL

* Per #2022, adding new VCNT columns to the header table files, User's Guide documentation, and lining some code up more consistently.

* Per #2022, added FA_SPEED_BAR and OA_SPEEED_BAR to the VAL1L2 line type. Added code to compute the ANOM_CORR confidence interval. However, I still need to update the writing of the VCNT line type to set the alpha value and actually write the computed CI's.

* Per #2022, update the writing of the VCNT output line to write the alpha value and anomaly correlation CI's.

* Per #2022, update point_stat and grid_stat to allocate alpha values for VL1L2Info objects to store CI's.

* Per #2022, call VL1L2Info::zero_out() instead of clear() so that we don't throw away allocated alpha values.

* Per #2022, update the Point-Stat and Grid-Stat logic to include the number of alpha values when deciding how many VCNT lines to write.

* Per #2022, update the VL1L2Info::operator+= logic to copy over the allocated alpha values.

* Per #2022, enhance stat_analysis to support an aggregate_stat job type for VAL1L2->VCNT. This writes ANOM_CORR and ANOM_CORR_UNCNTR output columns. However, there are still things to address. The other stats should be written as NA instead of 0. Recommend changing the VL1L2Info::zero_out() function to intialize stat values to NA instead of 0. Need to update the docs to reflect this support. Also need to actually compute the parametric CI's for ANOM_CORR. Big picture, we should store the VCNT stats in a new VCNTInfo class... just like the SL1L2Info/CNTInfo setup. Storing the sums AND stats in the same VL1L2Info class is unnecessarily confusing.

* Per #2022, update Stat-Analysis docs to list VAL1L2 -> VCNT as a supported conversion type.

* Per #2022, when computing VL1L2Info CI's, n should be set to vacount rather than the number of input pairs.

* Per #2022, add a new call to Stat-Analysis to exercise the VAL1L2 to VCNT conversion.

* Per #2022, ci-run-unit fix an aggregation bug in VL1L2Info::operator+=().

* Per issue #2022, added _vcnt.txt output files to check to relevant tests based on if vcnt output file is being generated via the config file. SL

Co-authored-by: Seth Linden <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>

* #1815 Renamed time_as_offset to Is_offset

* #1815 Added vx_data2d_dim_by_value

* #1815 Added convert_value_to_offset and renamed _time_dim_offset to _cur_time_index

* #1815 Added convert_value_to_offset and renamed _time_dim_offset to _cur_time_index. Support value instead of offset for time and z level

* #1815 Support @ for the value insteaed of offset for slicing

* #1815 Support value insteaed of offset for slicing

* #1815 Deleted unused local variable

* #1815 Deleted unused local variable

* #1815 Added level by value with @

* #1815 Added plot_data_plane_NCCF_latlon_by_value

* #1815 Added level by value with @

* Feature #2180 develop kft (#2181)

* dtcenter/METplus-Internal#16 Moved from scripts/sonarqube to internal/scripts/sonarqube

* #1815 Updated level

* Feature 2022 stat_analysis (#2185)

Proceeding with the merge without an external review based on the details listed above.

* Feature #2147 HSS (#2169)

* #1815 call is_eq to comapre two double values

* Per #2147, this is a HOTFIX to the develop branch after PR #2169 added new CTC and CTS columns. Prevoiusly the CTC columns = NBRCTC columns and CTS = NBRCTS. But that is no longer the case. This updates write_nbrctc_cols() and write_nbrcts_cols() to actually write them rather than just calling the functions to write CTC and CTS cols, respectively.

* #2187 Added add_offset_att_name & scale_factor_att_name

* #2187 Apply add_offse or scale_factor if defined

* ##2187 Removed handling add_offset and scale factor. They are applied at the base API

* #2187 Changed a log message

* Per #2193, add release notes for met-11.0.0-beta1. (#2195)

Co-authored-by: MET Tools Test Account <[email protected]>

* Hotfix to develop since I forgot to update the version number in conf.py.

* #1815 Added more attribute names

* #1815 Added get_index_for_dim

* #1815 Formatting

* #1815 Support a differnt dimension name from thw first data variable

* #1815 Use constants for attr names

* Hotfix to the develop branch to fix paths in Dockefiles after restructuing the MET repo.

* Another hotfix to develop to get the Docker build step working again.

The failure from the configure script is caused by the version of the "alocal" executable.
The contents of develop are based on seneca, which has:
  aclocal (GNU automake) 1.16.1
By comparison, my laptop does NOT require that bootstrap be run for:
  aclocal (GNU automake) 1.16.5
But the Docker image has an older version which triggers the error:
  aclocal (GNU automake) 1.13.4

Any machine with aclocal 1.16.x works fine. Likely any machine with a version that differs from 1.16.x does not. Running bootstrap fixes that... but also changes the contents of all the Makefile.in files making them appear as a large set of diffs in the repo. This is not an issue inside the docker image since we generally remove the source code after compiling anyway.

* Updating the png version of the older flowcharts.

* #1815 cleanup

* #1815 cleanup

* #1851 cleanup

* #1851 cleanup

* #1815 Added get_att_unixtime

* #1851 cleanup

* #1815 cleanup

* #1815 cleanup

* #1815 Support @ for pinterp

* #1815 Do not call to_string

* #1815 cleanup

* Per issue #2081, updated thecontents to match MRMS Version 12.2. Updated existing entries, removed old entries, added new entries. SL (#2199)

Co-authored-by: Seth Linden <[email protected]>

* #1815 Changed @time to time at plot_data_plane_NCCF_time

* Revert "Feature 1815 level value" (#2201)

* #1815 Use NcVarInfo members instead API calls

* #1815 Added find_var_by_dim_name

* #1815 Restored changes for this branch. The changes were reset after revert and merging with latest develop branch

* #METplus-Internal_19 cleanup

* #METplus-Internal_19 Added more functiofnds and corrected typo

* #METplus-Internal_19 Added main.h and main.cc

* #METplus-Internal_19 adjusted link order to set oom

* #METplus-Internal_19 Renamed main to met_main. Moved oom handler to base API

* #METplus-Internal commented out segv_handler which failed to compile at Docker

* Fix typo - maintianing

* Feature #2204 sum (#2205)

* #2202 Added APIs to check the point data (missing data and data types)

* #2202 Renamed pointdata_from_xarray to pointdata_from_python_list

* #2202 Support python list

* #2202 Avoid seg fault by checking point data from python embedding and provides the better log messages

* #2202 Support python list

* #2202 Added APIs to check the point data (missing data and data types)

* #2202 Added APIs to check the point data (missing data and data types)

* #2202 Added APIs to check the point data (missing data and data types)

* #2202 Added MaskedArray to allowed array data type

* Per #2211, enhance warning/error messages when parsing threshold types in dictionary.cc.

* #2208 Check existence of ensemble member data before checking bad_data

* 2215 Added station_ob to message_type & station_id to station_id for metadata_map

* 2215 Add log message for missing message_type and station_id metadata variables. Set NA if a message type is empty string

* 2215 Filter out XXX@RecMetaData variables from @metadata variables

* Per #2215, update the user's guide to make it consistent with the default ioda2nc config file.

* #METplus-Internal_19 Renamed main to met_main and added get_tool_name

* Feature sonarqube v11 beta2 (#2222)

Co-authored-by: Howard Soh <[email protected]>

* Per #2220, update the version number and release notes.

* Per #2220, fix typo.

* Per #2220, format the METplus-Internal release notes for MET in the same way they were handled for the METplus beta1 release.

* Added *hpp

* Separated template functions

* Separated template functions

* Changed argument for get_var_fill_value

* Feature 1971 mtd error to warning (#2221)

Co-authored-by: Dave Albo <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>

* #2225 @Level string is not applied as an index and index string without @ is not applied as value

* Feature #2220 v11.0.0-beta2_try2 (#2228)

* Updating Hera and Jet files for 11.0.0 release

* Adding 11.0.0 modulefiles for Hera and Jet

* Updating cheyenne installation files

* Reformatted slashes in paths for hera config files

* Updating installation files for Orion

* Removed beta2 references

* Adding configuration and modulefiles for gaea installation

* Changing METdatadb references to METdataio

* Documentation-only commit directly to develop to correct a typo. The default dotsize if 1.0 rather than 10.

* Feature 2055 nbm grib2 update (#2234)

* Per issue #2055, in read_grib2_record_list() added new PDS numbers 6, 10, 15 (for NBM data). SL

* Per issue #2055: in read_grib2_record_list(), in section that validates PDS number changed, for undefined PDS numbers, changed Error to Warning and continue (instead of exit). SL

* Per issue #2055, created new entries for NBM grib2 data fields. SL

* Per issue #2055. Added more NBM fields based on a 12z, f003 file. SL

* Per issue #2055, after interogating several NBM lead-time files, added TMAX field. SL

* Per issue #2055, added grib2_nbm.txt to the list. SL

* Per #2055, update the grib2_nbm.txt file entries in the table_files Makefiles.

* Per issue #2055, fixed syntax entry for TSTM field. SL

* Per issue #2055, fixed a few more syntax errors for some of the fields. SL

* Per issue #2055, in read_grib2_record_list(), added section to set level values for template number 6 (NBM data). Also added some temporary print statements. SL

* Per issue  #2055, in read_grib2_record_list(), added code to set levels for table number 10 (like 6). SL

* Per #2055, adding support for new GRIB2_perc_val configuration option to filter records based on the forecast percentile value used by GRIB2 product definition templates 6 and 10. Seth, note that I also included the probability filtering logic tweak we discussed, since it was already present in that same file.

* Per issue #2055: in find_record_matches(), in section that resolves Prob fields, changed 'break' to 'continue' for non Probs. SL

* Per issue #2055, in read_grib2_record_list() cleaned up some commented out code. SL

* Per issue #2055, in read_grib2_record_list() cleaned up all print statements. SL

* Per issue #2055, added 5 new unit tests for NBM data. SL

* Update data2d_grib2.cc

* Update data2d_grib2.cc

Co-authored-by: Seth Linden <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>

* Feature 2207 map (#2241)

* Feature #2237 tmp_dir (#2242)

* Per #2196, updating files for changes to met base image (#2246)

* Hotfix to the develop branch to fix typos in the names of 3 tools (grid_stat, gribtab_dat_to_flat, and gsidens2orank). Also removed commented out code from main.cc.

* Feature 2250 accum (#2251)

* Feature 2198 zenodo (#2252)

* Per #2198, adding Seth Linden and Dave Albo to the Author List

* Per #2198, updated Dave Albo to David Albo

* Per #2198, added three new authors based on submitted AMS abstract

* Per #2198, adding .zenodo.json file

* Per #2198, adding orcids for all based on Tatiana's suggestion

* Update .zenodo.json

Co-authored-by: johnhg <[email protected]>

* Update .zenodo.json

Co-authored-by: johnhg <[email protected]>

* Update .zenodo.json

Co-authored-by: johnhg <[email protected]>

Co-authored-by: johnhg <[email protected]>

* Per #1744, adding names for rst files in index.rst

* Reword to Grid-Stat opening paragraph

* Feature 2196 update dockerfile (#2249)

* Per #2196, update for upgrade to Python 3.8.6

* Updated based on new structure of METbaseimage

* Changed MET_BASE_IMAGE references to MET_BASE_TAG; Added information to the README.md file

* Changed MET_BASE_IMAGE references to MET_BASE_TAG; Updated the version from v1.0 to v1.1

* Update internal/scripts/docker/README.md

Based on suggestion from John HG.

Co-authored-by: johnhg <[email protected]>

* Update internal/scripts/docker/README.md

Based on suggestion from John HG.

Co-authored-by: johnhg <[email protected]>

* Update internal/scripts/docker/README.md

Based on suggestion from John HG.

Co-authored-by: johnhg <[email protected]>

* Update internal/scripts/docker/README.md

Based on suggestion from John HG.

Co-authored-by: johnhg <[email protected]>

* Per #2196, updating README.md based on suggestions from John HG

Co-authored-by: johnhg <[email protected]>

* Feature 1774 contrib outline (#2253)

* creating chapter files

* putting a space in to work through the git add and commit process.

* Changed formatting of one header

Co-authored-by: Lisa Goodrich <[email protected]>
Co-authored-by: jprestop <[email protected]>

* Fine tune to grid-stat opening paragraph

* Feature 2206 fair crps to ecnt (#2247)

* Per issue #2206, for the ECNT line type, added CRPS_EMP_FAIR. SL

* Per issue #2206, for ECNT line type, added CRPS_EMP_FAIR. SL

* Per issue #2206, for ecnt_columns, added CRPS_EMP_FAIR. SL

* Per issue #2206, in write_ecnt_cols(), added crps_emp_fair. SL

* Per issue #2206, in ECNTInfo, added crps_emp_fair. SL

* Per issue #2206, started stubbing code pieced to calculate crps_emp_fair. SL

* Per issue #2206, added new function mean_abs_diff(). SL

* Per issue #2206, in compute_pair_vals() updated the code to calculate crps_emp and crps_emp_fair. SL

* Per issue #2206, added crps_emp_fair (CRPS_EMP_FAIR) to relevant code pieces. SL

* Per issue #2206, added wording for CRPS_EMP_FAIR, also added it to last column of ECNT line type. SL

* Per issue #2206, added info for CRPS_EMP_FAIR and also added the math equation for this. SL

* Per issue #2206, update the math equation for CRPS_EMP_FAIR. SL

* Per issue #2206, added new function weighted_mean_absolute_diff(). SL

* Per issue #2206, updated the crps_emp_fair calculation to subtract the weighted_mean_abs_diff. SL

* Per issue #2206, in aggr_orank_lines(), updated calculation for crps_emp_fair to use weighted_mean_abs_diff. SL

* Per issue #2206, renamed weighted_mean_abs_diff() to wmean_abs_diff(). SL

* Per issue #2206, for the crps_emp_fair calculation, changed weighted_mean_abs_diff() to wmean_abs_diff(). SL

* Per issue #2206, in aggr_orank_lines(), for the crps_emp_fair calculation, changed weighted_mean_abs_diff() to wmean_abs_diff(). SL

* Per issue #2206, updated the math equation for the CRPS_EMP_FAIR calculation. SL

* Per issue #2206, fixed a bug in the wmean_abs_diff() function. SL

* Per issue #2206, added code for crps_emp_fair. SL

* Per issue #2206, in set() function, added checks for crps_emp and crps_emp_fair, for values of 0.0. SL

Co-authored-by: Seth Linden <[email protected]>

* automated tests: added ability to trigger build of develop-lite docker image that it used in the METplus automated tests

* to fix issues with python embedding when the path changes, update development.docker file (apparently unused or rarely previously) to include changes for Python 3.8 including setting the LDFLAG to include -rpath to prevent needing LD_LIBRARY_PATH set to run the tools. Source the env file in the build MET docker script instead of setting the env vars in the configure command

* Hotfix to the develop branch to revert the python version from 3.8 back to 3.6. This is done by rolling back the base image in the MET Dockerfiles to dtcenter/met-base:v1.0. Using 3.8 caused the downstream METplus python embedding examples to fail via GHA in the METplus repo. Will write up an issue to investigate more during the MET-11.0.0-beta4 development cycle.

* Tweak the build_docker_image.sh script by removing references to MET_BASE_IMAGE and MET_BASE_TAG since those variables are hard-coded in the Dockerfiles themselves and this script includes no logic to handle them.

* Revert "Tweak the build_docker_image.sh script by removing references to MET_BASE_IMAGE and MET_BASE_TAG since those variables are hard-coded in the Dockerfiles themselves and this script includes no logic to handle them."

This reverts commit 5efc65e.

* Hotfix, found 2 more spots where I needed to change v1.1 to v1.0. We should really revisit having this setting spread across so many locations.

* Bugfix 2238 link error (#2255)

Co-authored-by: Howard Soh <[email protected]>

* Feature dtcenter/METplus-Internal#15 add checksum to release (#2254)

Co-authored-by: jprestop <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>

* feature 2216 ioda2nc station_id (#2259)

Co-authored-by: Howard Soh <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>

* Feature 1942 seeps (#2257)

Co-authored-by: Howard Soh <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: MET Tools Test Account <[email protected]>

* Feature 2142 ascii2nc airnow (#2256)

Co-authored-by: Dave Albo <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>

* Feature 1954 semilatlon (#2262)

Co-authored-by: j-opatz <[email protected]>

* Removed future imports since they were used to transition from python 2 to 3. Rearranged logic to be more readible by checking error conditions and exiting if they are not met instead of putting all of the logic to run inside the if statement

* Feature 1908 remove ens (#2265)

* Feature 2266 v11.0.0-beta3 (#2268)

* Minor hotfix for the develop branch. Running bootstrap for develop on seneca changes the order of vx_grid semilatlon slightly. We probably manually editted that file instead of running bootstrap to regenerate it.

* Bugfix #2271 develop nbrctc (#2272)

Co-authored-by: George McCabe <[email protected]>

* Feature 2282 docs (#2283)

* #2270 Removed version number for SonrQube scanner pathdiff

* Feature #2286 grib_lookup (#2288)

* Feature 2227 namespace (#2290)

* Per #2227 changes in this commit resolve all errors from removing 'using namespace std' from all header files in the src/basic directory

* Attempt to resolve errors in GitHub actions from removing 'using namepsace std' from all src/basic/ libraries, plus removal from src/libcode/vx_gnomon/gnomon.h and src/libcode/vx_nc_util/nc_utils.h

* Attempt to fix GHA errors with compilation after removal of 'using namespace std'; locally compiles fine

* Per #2227, attempting to fix GHA compilation; Compiltion on seneca works fine

* Per #2227, attempt to resolve GHA compilation issues; seneca compilation works fine

* Per #2227, attempt to resolve GHA compilation issues; seneca compilation works fine

* Per #2227, removing namespace from vx_series_data library

* Per #2227, removing namespace std from vx_shapedata library

* Per #2227, removing namespace std from vx_data2d_grib2 and vx_data2d_grib libraries

* Per #2227, removing namespace std from vx_statistics library

* Per #2227, removing namespace std from src/tools/tc_utils

* Per #2227, removed namespace std from /src/tools/core header files

* Per #2227, clean up and continued work

* Per #2227, changes to remove namespace std and netCDF from header files

* Per #2227, resolve errors in GitHub Actions build

* Per #2227, resolve new errors in GitHub Actions build

* Per #2227, resolve new errors in GitHub Actions build

* Per #2227, resolve new errors in GitHub Actions build

* Per #2227, realign variables

* Per #2227, updating comment

* Per #2227, updating comment

* Per #2227, realign variables

* Per #2227, realign variables

* Per #2227, realign variables

* Per #2227, updating comment

* Update src/basic/vx_config/config.tab.cc

Co-authored-by: johnhg <[email protected]>

Co-authored-by: Julie Prestopnik <[email protected]>
Co-authored-by: johnhg <[email protected]>

* Feature #2237 test_empty_config (#2291)

* Feature #2297 gha (#2299)

* GHA hotfix to develop

Changes for #2297 included a small typo that I'm fixing directly in the develop branch.

* Feature #2297 hotfix to develop

A final hotfix to the develop branch to get the build_docker_trigger_metplus.yml workflow working again. I tested on feature_2297_gha branch to confirm that no double-quotes are actually needed.

* Update GHA versions

* Feature 2281 linker (#2296)

Co-authored-by: Julie Prestopnik <[email protected]>

* Feature 2036 enhance tc pairs (#2301)

Co-authored-by: Seth Linden <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>

* Feature 2276 enhance ascii2nc to read ndbc buoy data (#2294)

Co-authored-by: Dave Albo <[email protected]>
Co-authored-by: MET Tools Test Account <[email protected]>

* Feature 2155 time units months and years (#2300)

Co-authored-by: Howard Soh <[email protected]>

* removing release-notes out of overview and creating a seperate chapter for this information. (#2304)

* Bugfix #2309 develop tcmpr (#2310)

* Bugfix #2306 ascii2nc airnow hourly (#2314)

Co-authored-by: Dave Albo <[email protected]>

* Feature #2058 bias_ratio (#2317)

* Feature 2232 refine grid diag (#2316)

Co-authored-by: Seth Linden <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: MET Tools Test Account <[email protected]>

* Feature #392 tcdiag_line_type (#2315)

* Feature #2068 ioda2nc v2.0 (#2307)

Co-authored-by: Howard Soh <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: MET Tools Test Account <[email protected]>

* Feature #2322 v11.0.0-beta4 (#2323)

* Feature #2325 ECNT_MAE (#2326)

* Hotfix to the develop branch to correct the column numbers in the CNT line type table for the RMSOA, ANOM_CORR_UNCNTR, and SI statistics.

* Feature #2332 spread_md (#2333)

* Per #2232, add SPREAD_MD to the ECNT line type from Ensemble-Stat and computed for HiRA.

* Per #2332, fix compilation error.

* Per #2332, update date and release notes for met-11.0.0-beta4.

* Per #2332, fix compilation error.

Co-authored-by: Howard Soh <[email protected]>
Co-authored-by: hsoh-u <[email protected]>
Co-authored-by: Randy Bullock <[email protected]>
Co-authored-by: davidfillmore <[email protected]>
Co-authored-by: rgbullock <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: Dan Adriaansen <[email protected]>
Co-authored-by: George McCabe <[email protected]>
Co-authored-by: MET Tools Test Account <[email protected]>
Co-authored-by: jprestop <[email protected]>
Co-authored-by: Seth Linden <[email protected]>
Co-authored-by: Seth Linden <[email protected]>
Co-authored-by: Julie Prestopnik <[email protected]>
Co-authored-by: Seth Linden <[email protected]>
Co-authored-by: j-opatz <[email protected]>
Co-authored-by: Howard Soh <[email protected]>
Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: mo-mglover <[email protected]>
Co-authored-by: davidalbo <[email protected]>
Co-authored-by: lisagoodrich <[email protected]>
Co-authored-by: Molly Smith <[email protected]>
Co-authored-by: Dave Albo <[email protected]>
Co-authored-by: Jonathan Vigh <[email protected]>
Co-authored-by: bikegeek <[email protected]>
Co-authored-by: Lisa Goodrich <[email protected]>
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Remove ensemble post-processing from the Ensemble-Stat tool.
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