From a3e497de7d6c2651a000db3878bb237908f87412 Mon Sep 17 00:00:00 2001
From: bikegeek <3753118+bikegeek@users.noreply.github.com>
Date: Tue, 19 Oct 2021 16:48:37 -0600
Subject: [PATCH] Update develop-ref after #1000 (cycloneplotter) (#1211)

* feature 779 add support for output_flag, nc_pairs_flag, and climo_cdf dictionaries in GridStat (#858)

* Feature 779 compare pdf (#860)

* Feature 857 tc stat met config (2nd attempt) (#862)

* remove quotes around branch items

* only build docs in GHA

* added missing jobs item

* cd back to GITHUB_WORKSPACE

* cd back to github workspace

* removed html theme options needed for version selector that are no longer used

* moved documentation building into script, use sphinx_rtd_theme from pip instead of custom version, added info to contrib guide about CI

* rename jobs and steps

* Feature 767 ext dependencies doc update (#866)

Co-authored-by: George McCabe <mccabe@ucar.edu>

* feature CI documentation (#867)

* Feature 836 rtd release doc (#870)

* Added section for ReadTheDocs, added basic info about the Release Guide and Verification Datasets Guide, but more information on those needs to be added later

* Added information about the various versions available in the documentation

* Updated the ReadTheDocs section with information on hidden branches and how to access them; Modified dtcenter.github.io references

* Added section to add_use_case.rst about Accessing the Documentation and modified documentation.rst to indicate the docs can still be built manually

* Modified format of list

* Modified formatting

* Changed GitHub Pages links to Read the Docs links

* Modified formatting

* Fixed typo

* Updated Release Guide for Read The Docs

* Took out duplicate data and consolidated sections

* Update docs/Contributors_Guide/add_use_case.rst

Removed sentence

Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* Update docs/Contributors_Guide/add_use_case.rst

Fixed typo

Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* Update docs/Contributors_Guide/add_use_case.rst

Removed end of previously removed sentence.

Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* Adding NOAA/CPC to the list of requestors. Already ran the script to push this change to all the METplus repos.

* Adding common label for NOAA/OPC. The new label has already been pushed to all the METplus-related repos.

* sort list of files in directory to ensure the same result regardless of OS

* Feature 852 series by same name (#868)

* feature 871 TCGen new MET config variables (#872)

* Feature 728 update python embedding (#876)

Co-authored-by: George McCabe <mccabe@ucar.edu>

* Feature 629 metdbload (#882)

Co-authored-by: johnhg <johnhg@ucar.edu>
Co-authored-by: George McCabe <mccabe@dakota.rap.ucar.edu>

* feature_630_UIUC_GDF_TDF (#878)

Co-authored-by: George McCabe <mccabe@ucar.edu>

* moved new use case into another group

* Update MODE_fcstFV3_obsGOES_BrightnessTempObjs.py

* feature 880 improve field info handling (#881)

* Feature 686 hdr tdr (#885)

Co-authored-by: George McCabe <mccabe@ucar.edu>

* removed NEW from newly added use case

* feature 768 fix broken climo stdev (#886)

* Switched order of instructions to merge release branch and updating release notes.  Updating release notes should occur before merging the release branch.

* Feature 551 create pdf user guide (#890)

* Test latex_* settings in conf.py

* Test latex_* settings in conf.py

* Formatting in rst files for PDF

* Formatting in rst files for PDF

* Formatting in rst files for PDF

* Test rst file change for PDF formatting

* Change tocdepth to 3

* Change secnumdepth to 3

* Change secnumdepth/tocdepth to 4

* Change tocdepth to 3

* Change secnumdepth to 3

* Change secnumdepth/tocdepth to 4

* Test TOC settings

* Test TOC settings

* Test TOC settings

* Test reference section

* Test reference section

* Test quick search

* Test quick search

* Test quick search

* Test quick search

* Test quick search

* Test quick search

* Remove local pdf build lines

* Test quick search mods for PDF

* Test quick search mods for PDF

* Update quicksearch.rst

Format HTML and PDF separately

* Update quicksearch.rst

Fix typo in "only" directive

* Update quicksearch.rst

Fix typos in latex formatting

* Fix typo in quicksearch.rst

* Update systemconfiguration.rst

* Update conf.py

Address: WARNING: The config value `latex_show_pagerefs' has type `str', defaults to `bool'.

* Update conf.py

Fix typo, change master_doc variable to address warning

* Update conf.py

* Update conf.py

* Update conf.py

* Update conf.py

Test changing the root doc for PDF

* Update conf.py

Change latex_master_doc back to Users Guide

Co-authored-by: Keith Searight <searight@ucar.edu>

* Feature 779 add support for MODE and PointStat configs (#888)

* removed duplicate entry in glossary

* changed string to boolean to remove warning

* Added identifier to quicksearch.rst ci-docs-only

* Feature 779 pb2nc configs (#893)

* Feature 779 grid stat configs and climo_mean/stdev (#894)

* Changes to release guide steps for MET. Recommend making silimar changes for the other repos. For each release type, after the checkout_[develop|main]_branch.rst step, add a call to the new create_release_feature_branch.rst release step.

* Adding create_release_feature_branch.rst to all the release steps for METcalcpy, METplotpy, METdatadb, METviewer, and METexpress.

* Added argument to code-blocks

* Added release guide for METexpress development releases.

* Delete Regrid_PCP_obsERA_obsOnly_Blocking_orig.conf

Old configuration file

* Feature 626 hovmoeller diagram (#889)

Co-authored-by: Hank Fisher <fisherh@kiowa.rap.ucar.edu>
Co-authored-by: George McCabe <mccabe@ucar.edu>
Co-authored-by: MET Tools Test Account <met_test@kiowa.rap.ucar.edu>
Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* Feature 627 coherence spectra (#891)

Co-authored-by: Hank Fisher <fisherh@kiowa.rap.ucar.edu>
Co-authored-by: George McCabe <mccabe@ucar.edu>
Co-authored-by: MET Tools Test Account <met_test@kiowa.rap.ucar.edu>
Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* create 4.0.0-beta5 release (#897)

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

* Update pull_request_template.md

Added entry for completion date for pull request review.

* feature 900 single metplus_config.conf file (#901)

* update version for development towards rc1

* Feature authorship (#912)

* Add a direct link for the user's guide citation and then link to it from the top-level list of authors.

* Add a release_steps/rotate_authorship.rst step and update the official release instructions for MET, METcalcpy, METplotpy, and METplus. The other repos do not include a complete set of release instructions yet.

* Change top-level authorship list to alphabetical order.

* Define author_list in docs/conf.py and reference it in the citation.

* Adding author_list to the variables to be exported.

* Use CIRA and IMSG instead of CIR and IM, respectively.

* do not run documentation workflow on develop-ref branch, only run step to upload warnings artifact if there was a failure

* test sending slack message when a release is published

* tabs to spaces

* fixed multi line command

* removed old Travis-CI content

* clean docs, READMEs, and CI for release

* changed badge for testing workflow to display status of default branch instead of specific branch so users don't see accidental breaks in develop branch and we don't need to update it for each release

* fixed path to version file in docker hook helper script

* updated manage externals stable config and created symbolic link to Externals.cfg to avoid duplicate information

* updated METplus release instructions to isolate release specific changes to release branch to avoid having to change develop branch back to original content

* ci-run-diff

* run all use cases if push to develop or main_v* branches to ensure nothing breaks!

* run ALL use cases if push to develop on main_v*

* cast PosixPath to string to prevent crash when using Python 3.8.10

* feature 681 Modifed wording of regrid dictionary references (#916)

Co-authored-by: Julie.Prestopnik <jpresto@ucar.edu>
Co-authored-by: Lisa Goodrich <lisag@ucar.edu>

* bugfix 914 handle complex _VAR<n>_OPTIONS like MET dictionaries (#915)

* added test to recreate error, then fix it

* ci-run-diff

* Feature 673 metviewer release (#910)

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

* Updated directions per Tara's instructions.

* Added update_dtc_website.rst to metcalcpy and metplotpy subdirectories

* .. include:: release_steps/met/update_dtc_website.rst

* Corrected subdirectories from met to metcalcpy and metplotpy as needed

* Feature 903 update users guide (#919)

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

* Fixes to automation to handle main_vX.Y branches (#920)

* update version to show development towards 4.1.0-beta1

* changes made to main_v4.0 as bugfix to get docker data build to stop reporting a failure

* generate union of sample data with subset to force a successful build to remove failed check

* Added release guide for METexpress production releases.

* Added announcement section to release guide for METexpress production releases.

* Added rotate author section to release guide for METexpress production releases.

* Fixed length of title underlines for METexpress release guide.

* added useful logging messages to script that builds documentation so it is clear why it fails or if is succeeds

* Added new alert: REQUIRED FOR RELEASE label to all the METplus repos.

* modified steps for METplus to include updating release date and creating -ref branch to generate truth data for testing

* Added more content to METdatadb release guides, following model of METcalcpy (#927)

* added script to run on DTCenter web server to create a new input data directory for the next upcoming release and create symbolic links to the correct files from previous releases

* feature 928 PCPCombine option to skip lookback in derive mode (#930)

* Edits to METexpress release guide

* feature 924 support extra options in RegridDataPlane (#929)

* fixed minor bug in usage wrapper

* strip off whitespace from version numbers so they are read correctly when installing as a package

* Migrate issue and PR template changes from PR MET/#1803 into METplus develop branch.

* Update README.md

Adding GitHub Discussions info

* changed non-unicode apostrophe and fixed typo in URL

* feature 749 TCPairs refactor (#937)

* removed file that should have been deleted in merge

* Probability field threshold control in SeriesAnalysis (#942)

* Somehow the required labels weren't present. Adding 2 required: labels as well as one for requestor: NASA/other.

* feature 960 GenVxMask -type (#961)

* feature 926 TCMPRPlotter improvements (#959)

* changed variable name so that it does not overwrite author variable used in copyright

* add missing quick search items (#962)

* run pip freeze before use case commands to see python environment used to run in the logs

* Feature 933 cartopy hpc (#964)

* Modification to use NaturalEarth shapefiles that are already downloaded
and saved to file in location designated by the CARTOPY_DIR environment.

* Github Issue #933 Check for CARTOPY_DIR first, if unset, then proceed as
before.

* updated documentation for offline systems

* Updated docs based on feedback

Co-authored-by: Minna Win <minnawin@kiowa.rap.ucar.edu>

* Updated thumbnail path

* Feature 963 quick search (#965)

* Per #963, testing syntax

* Per #963, testing syntax again after error

* Per #963, testing string substitution

* Per #963, trying dot dot slash

* Per #963, found a relative path solution with dot dot slash, modified one line only

* updating quick search from develop to working branch with dot dot slash

* fixing typo

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

* Feature 839 conda envs in automation (#967)

* feature 641 MTD input to ExtractTiles (#968)

Co-authored-by: Daniel Adriaansen <dadriaan@ucar.edu>

* fixed documentation typos from bad merge

* Feature 834 use case ice cover (#970)

Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* doc updates (#972)

* fixed timing logs to show MM:SS instead of HH:MM

* fixed typo in doc

* feature 936 force MET version used for testing (#977)

* moved logic for creating conda environments for metplus base and py_embed base to a script so it can be called on a local machine to create these environments

* moved logic to update conda to docker file because update cannot be done on conda for a shared version

* updated instructions to include steps to create conda environments on a local machine

* Feature 963 quick search (#981)

* Per #963, testing syntax

* Per #963, testing syntax again after error

* Per #963, testing string substitution

* Per #963, trying dot dot slash

* Per #963, found a relative path solution with dot dot slash, modified one line only

* updating quick search from develop to working branch with dot dot slash

* fixing typo

* Per #963, removed replace directive since it is not being used

* Per #963, testing change to Note section for keywords

* Per #963, Testing return in note

* Per #963, removed note section under keywords and moved down the png name.

* Per #963, trying out various formatting options

* Per #963, trying out various formatting options

* Per #963, added additional keywords headers to get a better feel for what it would actually look like

* Added numbers to keywords for easier referencing

* Per #963, cleaned up examples and left with the formatting the team chose

* Per #963, try out adding a code block around a sphinx_gallery_thumbnail_path to see if it disappears because remove_config_comments was already set to True in the conf.py file, but this only removes configuration comments from code blocks, not from text blocks.

* Per #963, trying an additonal comment to eliminate sphinx_gallery_thumbnail_path

* Per #963, removing additonal comment to eliminate sphinx_gallery_thumbnail_path because it got rid of the thumbnail image

* Per #963, adding py to code-block to see if it eliminates sphinx_gallery_thumbnail_path

* Per #963, removing the code-block because it does not get rid of sphinx_gallery_thumbnail_path

* first attempt at note update without web links

* updating keywords area

* updating keywords area

* updating keywords area

* adding quick search link

* fixing quick search link

* updating keywords area

* fixing typo

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* fixing typo

* deleting empty spaces

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* fixing typo

* updating keywords area

* updating keywords area

* updating keywords area

* updating keywords area

* Changed ASCII2NC to ASCII2NCToolUseCase

* Modified list of keywords

* Fixed typo

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

* Feature 956 develop discussions (#988)

* Per 1833, changing met_help references to Discussions

* Per #1833, changed references to met_help@ucar.edu to Discussions and updated a couple of other links.

* Per #956, Fixed typo

* Per #956, fixed section referring to Known Issues as suggested by John HG.

* Per #956, removed met_help@ucar.edu reference. Checked to ensure author_email was not being used.

* feature 986 TCPairs valid time (#997)

* feature 986 TCPairs allow run all times when LOOP_ORDER = processes (#1013)

* Feature 1002 user script files (#1014)

* Update Blocking.py

Added some comments

* Update Blocking.py

* Added mpr output

* Added MPR output

* Updated documentation

* Fixed a path

* Updates to documentation

* call script to populate file list, output file list to output directory instead of under input base

* added env file so pytests can run easily on seneca

* improved logging readability

* moved functions up to parent class so they can be used by UserScript

* updated logic to match change to subset_input_files function return value

* in run_at_time function loop over custom list and get files for the current run time before running since this function is called only if LOOP_BY=times and does not call the function that handles this -- consider refactoring to move logic for CUSTOM_LOOP_LIST so that it is handled consistently across all wrappers instead of being handled inside each

* updated logic for UserScript to use the input dir/template variables to mimic logic in GridDiag to populate a list of files that are relevant for each run time of the use case

* always return True from get_all_files for UserScript because handling file lists is optional

* modified examples to call a script that checks environment variables and prints out the contents of file lists if they are set -- this better demonstrates how to use UserScript and how to get lists of files into a user's script, ci-run-diff

* don't loop to find files if time info is not set

* rerun use case that failed

* trigger other failing use cases to run

* changed name of config variable because name is now a reserved config variable

* skip use cases that are no longer failing

* Fixed a typo

* add skip times logic to function that finds all files to process

* added logic to put 'missing' for files that are not found for a given run time (for UserScript)

* added an extra lead time to example to demonstrate handling of missing files

* added logic to specify label for each input template file list, changed env var from METPLUS_<label> to METPLUS_FILELIST_<label>, changed user script example to find all keys that start with METPLUS_FILELIST_ to print

* added a label to demonstrate functionality

* added new config variables, ci-run-diff

* added documentation for new functionality for UserScript wrapper to find file paths

* Updated to use USER_SCRIPT text files

* Fixed typo

* Cleanup to .conf file

* Cleanup to UserScript_obsERA_obsOnly_Blocking.conf

* Updates to use the new file listing for UserScript

* Cleanup to old python programs

* Fixed a typo

* change branch for METplotpy to feature branch to test changes

* change METplotpy branch to develop since required change was merged into its develop branch

* changed use cases back to new = false so they don't run every workflow

Co-authored-by: Christina Kalb <kalb@ucar.edu>

* Feature 615 gfdl tc tracking (#1020)

Co-authored-by: George McCabe <mccabe@cheyenne1.cheyenne.ucar.edu>
Co-authored-by: George McCabe <mccabe@cheyenne5.cheyenne.ucar.edu>
Co-authored-by: George McCabe <mccabe@cheyenne4.cheyenne.ucar.edu>

* fixed incorrect length of overline

* error out if ouput data volumes fail to update

* don't fail if no volumes to build

* added error checking to script that updates docker data volumes that contain output truth data

* skip diff for binary index files created from GFDL tracker

* Feature 950 weather regime freq (#1024)

Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* Feature 952 blocking files (#1023)

* Added output MPR file for Blocking

* Cleanup and edits to creating mpr output

* Fixed a typo

* Added mpr output

* Fixed a typo

* Updated to use environment vars

* Updates to blocking documentation

* Delete conf file that was accidentally checked in

* removed unused scripts

Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* Feature 892 rmm omi drivers (#1028)

Co-authored-by: Christina Kalb <kalb@kiowa.rap.ucar.edu>
Co-authored-by: Minna Win <minnawin@kiowa.rap.ucar.edu>
Co-authored-by: bikegeek <3753118+bikegeek@users.noreply.github.com>
Co-authored-by: Christina Kalb <kalb@ucar.edu>
Co-authored-by: Hank Fisher <fisherh@kiowa.rap.ucar.edu>
Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* Changes for 4.1.0-beta1 release (#1027)

* changed version for beta1 release

* added release notes for 4.1.0-beta1

* removed unnecessary arguments to run_metplus.py

* removed release notes item that is pushed to next beta

* added line breaks between sections

* added OMI and RMM use cases

* update version to dev 4.1.0-beta2

* support skip times in example wrapper

* Feature 759 fr met py (#1025)

Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* updated list of use cases to run in tests to reflect use case that was removed

* remove log for copying files and modify log output for difference summary so it is easier to find

* bugfix 1021 develop climo mean/stdev field (#1039)

* fixed remove_quotes logic for handling config lists to only remove quotes around each value, not every quotation mark found -- changed logic for reading climo field to remove quotes around item to properly set dictionary items, ci-run-diff

* fixed unit tests to reflect actual values to set for climo field

* save script to update use case data directories on DTC web server

* move step to update version number in develop branch right after creating release to minimize time that development will be done with the incorrect version number

* removed step that is no longer needed after #963

* added step to set up next release data directory on DTC web server

* updated wording to be more clear

* Release Guide updates (#1041)

* added newline after each difference summary item for better readability

* use relative path for image

* added content from the GitHub wiki so I could remove the wiki pages

* feature 931 default wrapped MET config file (#1037)

* updated info for _CONFIG_FILE variables in glossary

* Feature 892 rmm omi tests (#1038)

Co-authored-by: Christina Kalb <kalb@kiowa.rap.ucar.edu>
Co-authored-by: Minna Win <minnawin@kiowa.rap.ucar.edu>
Co-authored-by: bikegeek <3753118+bikegeek@users.noreply.github.com>
Co-authored-by: Christina Kalb <kalb@ucar.edu>
Co-authored-by: Hank Fisher <fisherh@kiowa.rap.ucar.edu>

* feature 951 add support for setting hss_ec_value (#1048)

* Fix stale URL in GitHub issue and pull request templates.

* changed import to prevent error if location of variable changes when the util directory is refactored

* report error and exit if default metplus config files were somehow removed to prevent confusing errors that will result

* updated error message to list parm directory where default confs are searched to help debugging

* suggest that METPLUS_PARM_BASE may be the cause of the error

* Added note to update information in conf.py file for release

* updated link to instructions to upload data via FTP

* feature 1057 pass directory to tcmpr plot script (#1085)

* Feature 935 release guide (#1098)

* Per #935, made updates to Release Guide

* Per #935, made updates to Release Guide

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

* Changed component installation instructions to download MET as a tar file

* changed key in use case group list from 'new' to 'run' to be more clear

* Added lines to only build documentation for pull requests where only documentation changes have been made

* Added quotes to echo on line 21

* Feature 874 doc (#1115)

* Per #874, added information for the Release Guide and Verification Dataset Guide

* Per #874, change to fix Unexpected indentation warning.

* Added lines to only build documentation for pull requests where only documentation changes have been made

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

* Update task.md

Testing addition of new default labels

* Update task.md

Fixing syntax issue with addition of new default labels

* Update task.md

Reverting to original text before changes made for addition of labels.

* Added additional default labels

* Feature 1062 pcp combine level template (#1118)

* feature 1069 TCPairs write_valid, valid_inc, valid_exc (#1122)

* Feature 1103 PointStat orank output_flag (#1124)

* per comment in #1124, changed order of output flags to group related flags

* Feature 617 gfdl etc (#1121)

* added new use cases to existing use case group

* Feature 1001 blocking statanalysis (#1125)

Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* updated instructions for updating the truth dataset reference branch

* feature_1128_v4.1.0-beta2 (#1129)

* update version for development towards next beta release

* updated release guide instructions

* update instructions to remove references to NCAR/METplus

* Feature release guide (#1132)

* Moved create_release_extra.rst into the release_steps area as all components except for METplus use the same file; Added instructions to update_dtc_website.rst

* Removed text that was not supposed to be there.

* Update docs/Release_Guide/release_steps/common/update_dtc_website.rst

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

* Update docs/Release_Guide/release_steps/common/update_dtc_website.rst

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

* Update docs/Release_Guide/release_steps/common/update_dtc_website.rst

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

* Removed specific versions of update_dtc_website since they did not differ from the version in release_steps

* Added variable - otherWebsiteUpdates - and its value.

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

* changed to use PRMSL instead of MSLET for mean sea level pressure

* Committing directly to develop for a minor documentation change. Add a release note step about formatting major/important changes in bold.

* feature 1067 develop install instruct (#1156)

* Per #1067, modified installation instructions and system configuration to point to installation instructions for MET

* removed RTD python package requirements since they are already installed by RTD - fixes issue where bulleted lists bullets disappeared

Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>
Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* Removing version number from sphinx-gallery and adding one line to the update_release_notes files

* Part of Github issue #1000 METplus: added font size for legend label

* Github Issue #1000: major refactor to accommodate "sanitizing" of longitudes that could cross the International Date Line.

* Correctly returning the track dictionary in the get_points_by_track() method.

* removed extra import of pandas

* Update use_case_groups.json

* Cleaned up unneccessary comments and other things in retrieve_data() method.

* Previous checkin was missing text due to IDE settings.

* Add correction to retrieve_data() to create directory where ASCII csv file will be written

* Clean up logic that writes the csv output file.

* Reinstate saving the png file (final plot), initial checkin had hard-coded filename and location.

* Add support for when no CYCLONE_PLOTTER_MODEL value is set and reindex the subsetted dataframe to avoid array indexing issues.

* Add configuration setting for LOOP_BY

* Added CYCLONE_PLOTTER_ANNOTATION_FONT_SIZE and modified size of the marker sizes to smaller values.

* Updated config file with resolution setting, annotation size setting, and watermark on/off.

* Remove unneccessary debug logging message

* feature 1147 final conf sorting (#1152)

* removed config variable that is no longer used/needed

* cleaned up functions that handle setting CURRENT_[FCST/OBS]_[NAME/LEVEL]

* clean up

* expand path of config argument to run_metplus.py for easier debugging

* removed redundant logic and added comments

* cleanup

* added logic to move config variables that are runtime specific to a [runtime] section in the final conf that is written after the run completes

* changed how config arguments are read so that order that arguments are found is preserved instead of setting explicit overrides at the end

* minor change to trigger build, ci-run-all-cases

* rearranged logic to save list of config inputs with full paths for easier debugging

* move all config vars that start with LOG or end with BASE to runtime section

* remove vars that start with CURRENT from final conf

* removed confusing logic allowing override of parm base and cleaned up logging to be easier to read/understand

* added METPLUS_PARM_BASE env var logic back

* added old vs. new default value mismatch info for pb_report_type in PB2NC config file

* renamed config var name

* use PARM_BASE instead of METPLUS_BASE/parm since it will still be set

* use develop version of METviewer docker image (may need to make this configurable in testing.yml in the future)

* run cyclone plotter use case to test that new conda environment in docker image now contains missing cartopy map files

* added dockerfile to copy cartopy shape files into run image if cartopy is listed as dependencies

* download script used to download cartopy shape files and run it

* added copy of conda environment

* added logic to download cartopy shape files for metplotpy environment

* added cartopy dependency to use cases so the shapefiles are copied into run environment

* trigger 1 use case that uses metplotpy_env to test cartopy shapefiles are found properly

* added instructions to create weatherregime environment that was missing

* cleaned up list of packages used

* removed extra use case group used for testing

* removed netcdf package from env because it is already installed and version number was causing a conflict

* added cartopy shapefile copy to use case that needs it

* download cartopy shape files for weatherregime python environment because files were not found from base env (metplotpy)

* removed debug message that fills up log files with info that is not very useful

* updated input directories to use _WeatherRegime directory instead of _Blocking

* updated location of input data that was not found in UserScript_fcstGFS_obsERA_WeatherRegime

* updated readme with info on how to install metplotpy/metcalcpy in conda environments

* added 3rd group of cartopy shapefiles to download because they are used in weatherregime use cases

* try using cartopy download script from forked repo that has missing shapefile zip file added

* updated input paths to match new data locations

* use master branch of SciTools/cartopy since pull request was merged

* Feature 641 mtd feature relative (#1153)

Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* Feature 1004 usecase ghrsst marine (#1182)

* files for new use case

* added new use case and mod files

* upping verbosity for debug

* more debugging

* spelling fix

* testing for climo issues

* readded climo, changed python3 call in script

* skip docker pull because docker create command will pull if needed, print full name of data volume used for easier debugging, no longer pass docker create command output to /dev/null because logic is no longer called from shell script (previously value was passed to script via std out so any logging info would be added to content)

* moved new use case to its own section for testing

* fixed typo

* added PyEmbedIngest to process fcst/obs/climo data and read files into grid_stat to prevent out-of-memory errors

* refactored script to try to reduce the amount of unnecessary memory the script uses

* created config file to use PyEmbedIngest so use case can run as is on a machine with enough memory and run a modified version to work with the automated tests

* removed use case from test suite because it uses more memory than the docker environment has available

* removed old info

* rearranged variables for readability, removed commented out variables

Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* Upload file for new use case

* removed dependency on metplus function that is not needed

* Github Issue #1000 added legend label fontsize and central longitude to configuration

* Github Issue #1000 fix line plot (now use the Geodesic coordinate reference system), remove unneccessary code and comments, add support to read the central longitude from the config file.

* feature 1089 add distance_map to GridStat (#1190)

* Feature 1187 name update (#1193)

* updated file names for use case

* updated documentation for renaming, changing data

* Update docs/Contributors_Guide/add_use_case.rst

* split section into 2 sections for clarity

* added info about removing old data from sample input data, added info about conda environments used for running use cases and automated tests, added text to make instructions more clear if one of two commands should be run

* added missing parenthesis

Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* v4.1.0-beta3 release (#1195)

* updated version number for next development cycle

* Remove the setting for the central longitude, this should ALWAYS be 180 to center the map over the Pacific Ocean

* Change size of markers and remove setting for central longitude, this will always be set to 180 in the plotting script to center the map on the Pacific Ocean.

* Change class variable names to be more informative, add better commenting, cleaning up code, moving hard-coded values from the plotting method into initialization section.

* Added metplus-internal to list and changed /bin/sh to /bin/bash

* Added metplus-internal

* Removing alert: REQUIRED FOR RELEASE label in favor of already existing required labels for development and official release.

* Add DOI.

* Switch DOI to coordinated release.

* Github issue #1000, using the suggested gridlines command from https://github.com/SciTools/cartopy/issues/1401 and removing the original command of ax.gridlines(draw_labels=False, xlocs=[180, -180]) to prevent overlapping of 180E and 180W for central_longitude=180. Also fixed the sorting so the final ASCII (.csv) representation of the final data frame has been reindexed.

* Update use_case_groups.json

removed extra entry for met_tools to test the cycloneplotter wrapper earlier in the process.

* Update installation.rst

update cartopy version from 0.17 to 0.18 (the 0.18 version "fixes" the issue with overlapping 180/-180 longitude labels when the central longitude is set to 180).

Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Co-authored-by: George McCabe <mccabe@ucar.edu>
Co-authored-by: j-opatz <59586397+j-opatz@users.noreply.github.com>
Co-authored-by: jprestop <jpresto@ucar.edu>
Co-authored-by: John Halley Gotway <johnhg@ucar.edu>
Co-authored-by: George McCabe <mccabe@dakota.rap.ucar.edu>
Co-authored-by: Dan Adriaansen <dadriaan@ucar.edu>
Co-authored-by: Christina Kalb <kalb@ucar.edu>
Co-authored-by: mrinalbiswas <biswas@ucar.edu>
Co-authored-by: Keith Searight <keith.searight@noaa.gov>
Co-authored-by: Keith Searight <searight@ucar.edu>
Co-authored-by: Molly Smith <molly.b.smith@noaa.gov>
Co-authored-by: Hank Fisher <fisherh@ucar.edu>
Co-authored-by: Hank Fisher <fisherh@kiowa.rap.ucar.edu>
Co-authored-by: MET Tools Test Account <met_test@kiowa.rap.ucar.edu>
Co-authored-by: Lisa Goodrich <lisag@ucar.edu>
Co-authored-by: Tatiana Burek <tatiana@ucar.edu>
Co-authored-by: Venita Hagerty <38571614+venitahagerty@users.noreply.github.com>
Co-authored-by: Minna Win <minnawin@kiowa.rap.ucar.edu>
Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com>
Co-authored-by: George McCabe <mccabe@seneca.rap.ucar.edu>
Co-authored-by: George McCabe <mccabe@cheyenne1.cheyenne.ucar.edu>
Co-authored-by: George McCabe <mccabe@cheyenne5.cheyenne.ucar.edu>
Co-authored-by: George McCabe <mccabe@cheyenne4.cheyenne.ucar.edu>
Co-authored-by: Christina Kalb <kalb@kiowa.rap.ucar.edu>
Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu>
Co-authored-by: Minna Win <minnawin@seneca.rap.ucar.edu>
Co-authored-by: MET Tools Test Account <met_test@seneca.rap.ucar.edu>
Co-authored-by: j-opatz <jopatz@ucar.edu>
---
 .github/labels/README.md                      |    2 +-
 .github/labels/common_labels.txt              |    1 -
 .github/labels/post_patch_labels.sh           |    4 +-
 README.md                                     |    1 +
 docs/Users_Guide/installation.rst             |    4 +-
 docs/Users_Guide/release-notes.rst            |   32 +-
 metplus/VERSION                               |    2 +-
 metplus/wrappers/cyclone_plotter_wrapper.py   | 1162 ++++++++---------
 ...ter_fcstGFS_obsGFS_UserScript_ExtraTC.conf |    7 +-
 .../Plotter_fcstGFS_obsGFS_ExtraTC.conf       |   21 +-
 10 files changed, 618 insertions(+), 618 deletions(-)
 mode change 100755 => 100644 metplus/wrappers/cyclone_plotter_wrapper.py

diff --git a/.github/labels/README.md b/.github/labels/README.md
index a439050f0b..6add09e6b5 100644
--- a/.github/labels/README.md
+++ b/.github/labels/README.md
@@ -31,7 +31,7 @@ Sample commands for processing all METplus repos:
 ```
 # List of METplus repositories
 REPO_LIST="metplus met metplotpy metcalcpy metdatadb metviewer \
-                      metexpress metplus-training";
+                      metexpress metplus-training metplus-internal";
 
 # Build commands to add/update common labels
 for repo in ${REPO_LIST}; do
diff --git a/.github/labels/common_labels.txt b/.github/labels/common_labels.txt
index 06770eeb41..6f185cc919 100644
--- a/.github/labels/common_labels.txt
+++ b/.github/labels/common_labels.txt
@@ -1,7 +1,6 @@
 {"name": "alert: NEED ACCOUNT KEY","color": "ffff33","description": "Need to assign an account key to this issue"}
 {"name": "alert: NEED MORE DEFINITION","color": "ffff33","description": "Not yet actionable, additional definition required"}
 {"name": "alert: NEED PROJECT ASSIGNMENT","color": "ffff33","description": "Need to assign to a release development cycle"}
-{"name": "alert: REQUIRED FOR RELEASE","color": "e400f5","description": "Required to be done for the assigned release"}
 {"name": "component: CI/CD","color": "1d76db","description": "Continuous integration and deployment issues"}
 {"name": "component: build process","color": "1d76db","description": "Build process issue"}
 {"name": "component: code cleanup","color": "1d76db","description": "Code cleanup and maintenance issue"}
diff --git a/.github/labels/post_patch_labels.sh b/.github/labels/post_patch_labels.sh
index ba350ec83e..7a8134a41c 100755
--- a/.github/labels/post_patch_labels.sh
+++ b/.github/labels/post_patch_labels.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 
 # Must specify 4 arguments:
 #   - username
@@ -8,7 +8,7 @@
 
 if [[ $# -ne 4 ]]; then
   echo "ERROR: `basename $0` ... must specify the GitHub username, authorization key, repository name, and label file."
-  echo "ERROR:   repo names: metplus, met, metdatadb, metcalcpy, metplotpy, metviewer, metexpress, metplus-training"
+  echo "ERROR:   repo names: metplus, met, metdatadb, metcalcpy, metplotpy, metviewer, metexpress, metplus-training, metplus-internal"
   exit 1
 else
   user=$1
diff --git a/README.md b/README.md
index b9a335fc7c..65d62d2072 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,7 @@ Model Evaluation Tools Plus (METplus) Repository
 <!-- Start of Badges -->
 [![Tests](https://github.com/DTCenter/METplus/actions/workflows/testing.yml/badge.svg?event=push)](https://github.com/DTCenter/METplus/actions/workflows/testing.yml)
 [![Docs](https://img.shields.io/badge/Documentation-latest-brightgreen.svg)](https://metplus.readthedocs.io)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5567804.svg)](https://doi.org/10.5281/zenodo.5567804)
 
 Welcome to the METplus GitHub repository hosted to the community through
 the Developmental Testbed Center (DTC).
diff --git a/docs/Users_Guide/installation.rst b/docs/Users_Guide/installation.rst
index d9dbfdf4df..be724cc5a3 100644
--- a/docs/Users_Guide/installation.rst
+++ b/docs/Users_Guide/installation.rst
@@ -115,12 +115,12 @@ to run.
 
 -  MakePlots wrapper
 
-    - cartopy (0.17.0)
+    - cartopy (0.18.0)
     - pandas (1.0.5)
 
 -  CyclonePlotter wrapper
 
-    - cartopy (0.17.0)
+    - cartopy (0.18.0)
     - matplotlib (3.3.4)
 
 Cartopy, one of the dependencies of CyclonePlotter, attempts to download shapefiles from the internet to complete successfully. So if CyclonePlotter is run on a closed system (i.e. no internet), additional steps need to be taken. First, go to the Natural Earth Data webpage and download the small scale (1:110m) cultural and physical files that will have multiple extensions (e.g. .dbf, .shp, .shx). Untar these files in a noted location. Finally, create an environment variable in the user-specific system configuration file for CARTOPY_DIR, setting it to the location where the shapefiles are located. 
diff --git a/docs/Users_Guide/release-notes.rst b/docs/Users_Guide/release-notes.rst
index 3f0c0d8338..0f687db595 100644
--- a/docs/Users_Guide/release-notes.rst
+++ b/docs/Users_Guide/release-notes.rst
@@ -9,9 +9,9 @@ Release Notes - Latest Official Release
 
 * `MET <https://met.readthedocs.io/en/latest/Users_Guide/release-notes.html>`__
 * `METviewer <https://metviewer.readthedocs.io/en/latest/Users_Guide/release-notes.html>`__
-*  METplotpy - No Official Releases
-*  METcalcpy - No Official Releases
-*  METdatadb - No Official Releases
+* `METplotpy <https://metplotpy.readthedocs.io/en/latest/Users_Guide/release-notes.html>`__
+* `METcalcpy <https://metcalcpy.readthedocs.io/en/latest/Users_Guide/release-notes.html>`__
+* `METdatadb <https://metdatadb.readthedocs.io/en/latest/Users_Guide/release-notes.html>`__
 * `METexpress <https://github.com/dtcenter/METexpress/releases>`__
 * `METplus Wrappers <https://metplus.readthedocs.io/en/latest/Users_Guide/release-notes.html>`__
 
@@ -20,10 +20,10 @@ Release Notes - Development Release
 
 * `MET <https://met.readthedocs.io/en/develop/Users_Guide/release-notes.html>`__
 * `METviewer <https://metviewer.readthedocs.io/en/develop/Users_Guide/release-notes.html>`__
-* `METplotpy <https://github.com/dtcenter/METplotpy/releases>`__
-* `METcalcpy <https://github.com/dtcenter/METcalcpy/releases>`__
-*  METdatadb - No Development Releases
-*  METexpress - No Development Releases 
+* `METplotpy <https://metplotpy.readthedocs.io/en/develop/Users_Guide/release-notes.html>`__
+* `METcalcpy <https://metcalcpy.readthedocs.io/en/develop/Users_Guide/release-notes.html>`__
+* `METdatadb <https://metdatadb.readthedocs.io/en/develop/Users_Guide/release-notes.html>`__
+* `METexpress <https://github.com/dtcenter/METexpress/releases>`__
 * `METplus Wrappers <https://metplus.readthedocs.io/en/develop/Users_Guide/release-notes.html>`__
 
 METplus Wrappers Release Notes
@@ -33,6 +33,24 @@ When applicable, release notes are followed by the GitHub issue number which
 describes the bugfix, enhancement, or new feature:
 https://github.com/dtcenter/METplus/issues
 
+METplus Version 4.1.0-beta3 Release Notes (2021-10-06)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+* Enhancements:
+
+  * Add Grid-Stat configuration options for distance_map dictionary (`#1089 <https://github.com/dtcenter/METplus/issues/1089>`_)
+  * Fix installation instructions in User's Guide (`#1067 <https://github.com/dtcenter/METplus/issues/1067>`_)
+  * Add instructions to update old METplus configuration files that reference user-defined wrapped MET config files (`#1147 <https://github.com/dtcenter/METplus/issues/1147>`_)
+
+* New Use Cases:
+
+  * Satellite verification of sea surface temperature (GHRSST) against RTOFS output (`#1004 <https://github.com/dtcenter/METplus/issues/1004>`_)
+  * Feature Relative using MTD output for feature centroid lat/lon (`#641 <https://github.com/dtcenter/METplus/issues/641>`_)
+
+* Internal:
+
+  * Transition Community and Developer Support to Github Discussions (`#932 <https://github.com/dtcenter/METplus/issues/932>`_)
+  * Add documentation about the Release Guide and Verification Datasets Guide (`#874 <https://github.com/dtcenter/METplus/issues/874>`_)
 
 METplus Version 4.1.0-beta2 Release Notes (2021-08-31)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
diff --git a/metplus/VERSION b/metplus/VERSION
index bab2b017f2..594faefc69 100644
--- a/metplus/VERSION
+++ b/metplus/VERSION
@@ -1 +1 @@
-4.1.0-beta3-dev
\ No newline at end of file
+4.1.0-beta4-dev
\ No newline at end of file
diff --git a/metplus/wrappers/cyclone_plotter_wrapper.py b/metplus/wrappers/cyclone_plotter_wrapper.py
old mode 100755
new mode 100644
index d9062ada1f..82a16fa9fc
--- a/metplus/wrappers/cyclone_plotter_wrapper.py
+++ b/metplus/wrappers/cyclone_plotter_wrapper.py
@@ -1,600 +1,562 @@
-"""!@namespace ExtraTropicalCyclonePlotter
-A Python class that generates plots of extra tropical cyclone forecast data,
- replicating the NCEP tropical and extra tropical cyclone tracks and
- verification plots http://www.emc.ncep.noaa.gov/mmb/gplou/emchurr/glblgen/
-"""
-
-import os
-import time
-import datetime
-import re
-import sys
-import collections
-
-# handle if module can't be loaded to run wrapper
-WRAPPER_CANNOT_RUN = False
-EXCEPTION_ERR = ''
-try:
-    import matplotlib.pyplot as plt
-    import matplotlib.ticker as mticker
-    import cartopy.crs as ccrs
-    import cartopy.feature as cfeature
-    import cartopy
-    from cartopy.mpl.gridliner import LONGITUDE_FORMATTER, LATITUDE_FORMATTER
-    ##If the script is run on a limited-internet access machine, the CARTOPY_DIR environment setting
-    ##will need to be set in the user-specific system configuration file. Review the Installation section
-    ##of the User's Guide for more details.
-    if os.getenv('CARTOPY_DIR'):
-        cartopy.config['data_dir'] = os.getenv('CARTOPY_DIR', cartopy.config.get('data_dir'))
-
-except Exception as err_msg:
-    WRAPPER_CANNOT_RUN = True
-    EXCEPTION_ERR = err_msg
-
-import produtil.setup
-
-from ..util import met_util as util
-from ..util import do_string_sub
-from . import CommandBuilder
-
-
-
-class CyclonePlotterWrapper(CommandBuilder):
-    """! Generate plots of extra tropical storm forecast tracks.
-        Reads input from ATCF files generated from MET TC-Pairs
-    """
-
-    def __init__(self, config, instance=None, config_overrides={}):
-        self.app_name = 'cyclone_plotter'
-
-        super().__init__(config,
-                         instance=instance,
-                         config_overrides=config_overrides)
-
-        if WRAPPER_CANNOT_RUN:
-            self.log_error("There was a problem importing modules: "
-                           f"{EXCEPTION_ERR}\n")
-            return
-
-        self.input_data = self.config.getdir('CYCLONE_PLOTTER_INPUT_DIR')
-        self.output_dir = self.config.getdir('CYCLONE_PLOTTER_OUTPUT_DIR')
-        self.init_date = self.config.getraw('config',
-                                            'CYCLONE_PLOTTER_INIT_DATE')
-        self.init_hr = self.config.getraw('config', 'CYCLONE_PLOTTER_INIT_HR')
-
-        init_time_fmt = self.config.getstr('config', 'INIT_TIME_FMT', '')
-        if init_time_fmt:
-            clock_time = datetime.datetime.strptime(
-                self.config.getstr('config',
-                                   'CLOCK_TIME'),
-                '%Y%m%d%H%M%S'
-            )
-
-            init_beg = self.config.getraw('config', 'INIT_BEG')
-            if init_beg:
-                init_beg_dt = util.get_time_obj(init_beg,
-                                                init_time_fmt,
-                                                clock_time,
-                                                logger=self.logger)
-                self.init_date = do_string_sub(self.init_date, init=init_beg_dt)
-                self.init_hr = do_string_sub(self.init_hr, init=init_beg_dt)
-
-        self.model = self.config.getstr('config', 'CYCLONE_PLOTTER_MODEL')
-        self.title = self.config.getstr('config',
-                                        'CYCLONE_PLOTTER_PLOT_TITLE')
-        self.gen_ascii = (
-            self.config.getbool('config',
-                                'CYCLONE_PLOTTER_GENERATE_TRACK_ASCII')
-        )
-        # Create a set to keep track of unique storm_ids for each track file.
-        self.unique_storm_id = set()
-        # Data structure to separate data based on storm id.
-        self.storm_id_dict = {}
-        # Data/info which we want to retrieve from the track files.
-        self.columns_of_interest = ['AMODEL', 'STORM_ID', 'BASIN', 'INIT',
-                                    'LEAD', 'VALID', 'ALAT', 'ALON', 'BLAT',
-                                    'BLON', 'AMSLP', 'BMSLP']
-        self.circle_marker = (
-            self.config.getint('config',
-                               'CYCLONE_PLOTTER_CIRCLE_MARKER_SIZE')
-        )
-        self.annotation_font_size = (
-            self.config.getint('config',
-                               'CYCLONE_PLOTTER_ANNOTATION_FONT_SIZE')
-        )
-        self.cross_marker = (
-            self.config.getint('config',
-                               'CYCLONE_PLOTTER_CROSS_MARKER_SIZE')
-        )
-        self.resolution_dpi = (
-            self.config.getint('config',
-                               'CYCLONE_PLOTTER_RESOLUTION_DPI')
-        )
-
-        self.add_watermark = self.config.getbool('config',
-                                                 'CYCLONE_PLOTTER_ADD_WATERMARK',
-                                                 True)
-
-
-    def run_all_times(self):
-        """! Calls the defs needed to create the cyclone plots
-             run_all_times() is required by CommandBuilder.
-
-        """
-        self.retrieve_data()
-        self.create_plot()
-
-    def retrieve_data(self):
-        """! Retrieve data from track files and return the min and max lon.
-            Returns:
-               None
-        """
-        self.logger.debug("Begin retrieving data...")
-        all_tracks_list = []
-
-        # Store the data in the track list.
-        if os.path.isdir(self.input_data):
-            self.logger.debug("Generate plot for all files in the directory" +
-                              self.input_data)
-            # Get the list of all files (full file path) in this directory
-            all_init_files = util.get_files(self.input_data, ".*.tcst",
-                                            self.logger)
-
-            for init_file in all_init_files:
-                # Ignore empty files
-                if os.stat(init_file).st_size == 0:
-                    self.logger.info(f"Ignoring empty file {init_file}")
-                    continue
-
-                # logger.info("Consider all files under directory" +
-                #  init_file + " with " + " init time (ymd): " +
-                # self.init_date + " and lead time (hh):" + self.lead_hr)
-                with open(init_file, 'r') as infile:
-                    self.logger.debug("Parsing file {}".format(init_file))
-
-                    # Extract information from the header, which is
-                    # the first line.
-                    header = infile.readline()
-                    # print("header: {}".format(header))
-                    column_indices = self.get_columns_and_indices(header)
-
-                    # For the remaining lines of this file,
-                    # retrieve information from each row:
-                    # lon, lat, init time, lead hour, valid time,
-                    # model name, mslp, and basin.
-                    # NOTE: Some of these columns aren't used until we fully
-                    # emulate Guang Ping's plots (ie collect all columns).
-                    for line in infile:
-                        track_dict = {}
-                        col = line.split()
-                        lat = col[column_indices['ALAT']]
-                        lon = col[column_indices['ALON']]
-                        init_time = col[column_indices['INIT']]
-                        fcst_lead_hh = \
-                            str(col[column_indices['LEAD']]).zfill(3)
-                        model_name = col[column_indices['AMODEL']]
-                        valid_time = col[column_indices['VALID']]
-                        storm_id = col[column_indices['STORM_ID']]
-
-                        # Not needed until support for regional plots
-                        # is implemented.
-                        # mslp = col[column_indices['AMSLP']]
-                        # basin = col[column_indices['BASIN']]
-
-                        # Check for NA values in lon and lat, skip to
-                        # next line in file if 'NA' is encountered.
-                        if lon == 'NA' or lat == 'NA':
-                            continue
-                        else:
-                            # convert longitudes that are in the 0 to 360 scale
-                            # to the -180 to 180 scale
-                            track_dict['lon'] = self.rescale_lon(float(lon))
-                            track_dict['lat'] = float(lat)
-
-                        # If the lead hour is 'NA', skip to next line.
-                        # The track data was very likely generated with
-                        # TC-Stat set to match-pairs set to True.
-                        lead_hr = self.extract_lead_hr(fcst_lead_hh)
-                        if lead_hr == 'NA':
-                            continue
-
-                        # Check that the init date, init hour
-                        # and model name are what the user requested.
-                        init_ymd, init_hh = \
-                            self.extract_date_and_time_from_init(init_time)
-
-                        if init_ymd == self.init_date and \
-                                init_hh == self.init_hr:
-                            if model_name == self.model:
-                                # Check for the requested model,
-                                # if the model matches the requested
-                                # model name, then we have all the
-                                # necessary information to continue.
-                                # Store all data in dictionary
-                                track_dict['fcst_lead_hh'] = fcst_lead_hh
-                                track_dict['init_time'] = init_time
-                                track_dict['model_name'] = model_name
-                                track_dict['valid_time'] = valid_time
-                                track_dict['storm_id'] = storm_id
-
-                                # Identify the 'first' point of the
-                                # storm track.  If the storm id is novel, then
-                                # retrieve the date and hh from the valid time
-                                if storm_id in self.unique_storm_id:
-                                    track_dict['first_point'] = False
-                                    track_dict['valid_dd'] = ''
-                                    track_dict['valid_hh'] = ''
-                                else:
-                                    self.unique_storm_id.add(storm_id)
-                                    # Since this is the first storm_id with
-                                    # a valid value for lat and lon (ie not
-                                    # 'NA'), this is the first track point
-                                    # in the storm track and will be
-                                    # labelled with the corresponding
-                                    # date/hh z on the plot.
-                                    valid_match = \
-                                        re.match(r'[0-9]{6}([0-9]{2})_' +
-                                                 '([0-9]{2})[0-9]{4}',
-                                                 track_dict['valid_time'])
-                                    if valid_match:
-                                        valid_dd = valid_match.group(1)
-                                        valid_hh = valid_match.group(2)
-                                    else:
-                                        # Shouldn't get here if this is
-                                        # the first point of the track.
-                                        valid_dd = ''
-                                        valid_hh = ''
-                                    track_dict['first_point'] = True
-                                    track_dict['valid_dd'] = valid_dd
-                                    track_dict['valid_hh'] = valid_hh
-
-                                # Identify points based on valid time (hh).
-                                # Useful for plotting later on.
-                                valid_match = \
-                                    re.match(r'[0-9]{8}_([0-9]{2})[0-9]{4}',
-                                             track_dict['valid_time'])
-                                if valid_match:
-                                    # Since we are only interested in 00,
-                                    # 06, 12, and 18 hr times...
-                                    valid_hh = valid_match.group(1)
-
-                                if valid_hh == '00' or valid_hh == '12':
-                                    track_dict['lead_group'] = '0'
-                                elif valid_hh == '06' or valid_hh == '18':
-                                    track_dict['lead_group'] = '6'
-                                else:
-                                    # To gracefully handle any hours other
-                                    # than 0, 6, 12, or 18
-                                    track_dict['lead_group'] = ''
-
-                                all_tracks_list.append(track_dict)
-
-                                # For future work, support for MSLP when
-                                # generating regional plots-
-                                # implementation goes here...
-                                # Finishing up, do any cleaning up,
-                                # logging, etc.
-                                self.logger.info("All criteria met, " +
-                                                 "saving track data init " +
-                                                 track_dict['init_time'] +
-                                                 " lead " +
-                                                 track_dict['fcst_lead_hh'] +
-                                                 " lon " +
-                                                 str(track_dict['lon']) +
-                                                 " lat " +
-                                                 str(track_dict['lat']))
-
-                            else:
-                                # Not the requested model, move to next
-                                # row of data
-                                continue
-
-                        else:
-                            # Not the requested init ymd move to next
-                            # row of data
-                            continue
-
-                # Now separate the data based on storm id.
-                for cur_unique in self.unique_storm_id:
-                    cur_storm_list = []
-                    for cur_line in all_tracks_list:
-                        if cur_line['storm_id'] == cur_unique:
-                            cur_storm_list.append(cur_line)
-                        else:
-                            # Continue to next line in all_tracks_list
-                            continue
-
-                    # Create the storm_id_dict, which is the data
-                    # structure used to separate the storm data based on
-                    # storm id.
-                    self.storm_id_dict[cur_unique] = cur_storm_list
-
-        else:
-            self.log_error("{} should be a directory".format(self.input_data))
-            sys.exit(1)
-
-    def get_columns_and_indices(self, header):
-        """ Parse the header for the columns of interest and store the
-            information in a dictionary where the key is the column name
-            and value is the index/column number.
-            Returns:
-                column_dict:  A dictionary containing the column name
-                              and its index
-        """
-
-        all_columns = header.split()
-        column_dict = {}
-
-        # Retrieve the index number of the column of interest in the header.
-        for col in self.columns_of_interest:
-            index = all_columns.index(col)
-            column_dict[col] = index
-        return column_dict
-
-    @staticmethod
-    def extract_date_and_time_from_init(init_time_str):
-        """ Extract and return the YYYYMMDD portion and the
-            hh portion from the init time taken from the .tcst file.
-        """
-        match_ymd = re.match(r'([0-9]{8}).*', init_time_str)
-        match_hh = re.match(r'[0-9]{8}_([0-9]{2,3})[0-9]{4}', init_time_str)
-        # pylint:disable=no-else-return
-        # Explicitly return None if no match is found
-        if match_ymd and match_hh:
-            return match_ymd.group(1), match_hh.group(1)
-        else:
-            return None
-
-    @staticmethod
-    def extract_lead_hr(lead_str):
-        """ Extract and return the lead hours from the hhmmss lead string.
-        """
-        match = re.match(r'([0-9]{2,3})[0-9]{4}', str(lead_str))
-        if match:
-            return match.group(1)
-
-    def create_plot(self):
-        """! Create the plot, using Cartopy.
-
-        """
-
-
-        # Use PlateCarree projection for now
-        #use central meridian for central longitude
-        cm_lon = 180
-        ax = plt.axes(projection=ccrs.PlateCarree(central_longitude=cm_lon))
-        prj = ccrs.PlateCarree()
-
-        # Add land, coastlines, and ocean
-        ax.add_feature(cfeature.LAND)
-        ax.coastlines()
-        ax.add_feature(cfeature.OCEAN)
-        # keep map zoomed out to full world.  If this
-        # is absent, the default behavior is to zoom
-        # into the portion of the map that contains points.
-        ax.set_global()
-
-        # Add grid lines for longitude and latitude
-        ax.gridlines(draw_labels=False, xlocs=[180, -180])
-        gl = ax.gridlines(crs=prj,
-                          draw_labels=True, linewidth=1, color='gray',
-                          alpha=0.5, linestyle='--')
-        gl.xlabels_top = False
-        gl.ylabels_left = False
-        gl.xlines = True
-        gl.xformatter = LONGITUDE_FORMATTER
-        gl.yformatter = LATITUDE_FORMATTER
-        gl.xlabel_style = {'size': 9, 'color': 'blue'}
-        gl.xlabel_style = {'color': 'black', 'weight': 'normal'}
-
-        # Plot title
-        plt.title(self.title + "\nFor forecast with initial time = " +
-                  self.init_date)
-
-        # Create the NCAR watermark with a timestamp
-        # This will appear in the bottom right corner of the plot, below
-        # the x-axis.  NOTE: The timestamp is in the user's local time zone
-        # and not in UTC time.
-        if self.add_watermark:
-            ts = time.time()
-            st = datetime.datetime.fromtimestamp(ts).strftime(
-                '%Y-%m-%d %H:%M:%S')
-            watermark = 'DTC METplus\nplot created at: ' + st
-            plt.text(60, -130, watermark, fontsize=5, alpha=0.25)
-
-        # Make sure the output directory exists, and create it if it doesn't.
-        util.mkdir_p(self.output_dir)
-
-        # Iterate over each unique storm id in self.storm_id_dict and
-        # set the marker, marker size, and annotation
-        # before drawing the line and scatter plots.
-
-        # Use counters to set the labels for the legend. Since we don't
-        # want repetitions in the legend, do this for a select number
-        # of points.
-        circle_counter = 0
-        plus_counter = 0
-        dummy_counter = 0
-
-        lines_to_write = []
-        for cur_storm_id in sorted(self.unique_storm_id):
-            # Lists used in creating each storm track.
-            cyclone_points = []
-            lon = []
-            lat = []
-            marker_list = []
-            size_list = []
-            anno_list = []
-
-            # For this storm id, get a list of all data (corresponding
-            # to lines/rows in the tcst data file).
-            track_info_list = self.storm_id_dict[cur_storm_id]
-            if not track_info_list:
-                self.log_error("Empty track list, no data extracted " +
-                                  "from track files, exiting.")
-                return
-
-            for track in track_info_list:
-                # For now, all the marker symbols will be one color.
-                color_list = ['red' for _ in range(0, len(track_info_list))]
-
-                lon.append(float(track['lon']))
-                lat.append(float(track['lat']))
-
-                # Differentiate between the forecast lead "groups",
-                # i.e. 0/12 vs 6/18 hr and
-                # assign the marker symbol and size.
-                if track['lead_group'] == '0':
-                    marker = 'o'
-                    marker_list.append(marker)
-                    marker_size = self.circle_marker
-                    size_list.append(marker_size)
-                    label = "Indicates a position at 00 or 12 UTC"
-
-                elif track['lead_group'] == '6':
-                    marker = '+'
-                    marker_list.append(marker)
-                    marker_size = self.cross_marker
-                    size_list.append(marker_size)
-                    label = "\nIndicates a position at 06 or 18 UTC\n"
-
-                # Determine the first point, needed later to annotate.
-                # pylint:disable=invalid-name
-                dd = track['valid_dd']
-                hh = track['valid_hh']
-                if dd and hh:
-                    date_hr_str = dd + '/' + hh + 'z'
-                    anno_list.append(date_hr_str)
-                else:
-                    date_hr_str = ''
-                    anno_list.append(date_hr_str)
-
-                # Write to the ASCII track file, if requested
-                if self.gen_ascii:
-                    line_parts = ['model_name: ', track['model_name'], '   ',
-                                  'storm_id: ', track['storm_id'], '   ',
-                                  'init_time: ', track['init_time'], '   ',
-                                  'valid_time: ', track['valid_time'], '   ',
-                                  'lat: ', str(track['lat']), '   ',
-                                  'lon: ', str(track['lon']), '   ',
-                                  'lead_group: ', track['lead_group'], '   ',
-                                  'first_point:', str(track['first_point'])]
-                    line = ''.join(line_parts)
-                    lines_to_write.append(line)
-
-            # Create a scatter plot to add
-            # the appropriate marker symbol to the forecast
-            # hours corresponding to 6/18 hours.
-
-            # Annotate the first point of the storm track
-            for anno, adj_lon, adj_lat in zip(anno_list, lon, lat):
-                # Annotate the first point of the storm track by
-                # overlaying the annotation text over all points (all but
-                # one will have text). plt.annotate DOES NOT work with cartopy,
-                # instead, use the plt.text method.
-                plt.text(adj_lon+2, adj_lat+2, anno, transform=prj,
-                         fontsize=self.annotation_font_size, color='red')
-
-            # Generate the scatterplot, where the 6/18 Z forecast times
-            # are labelled with a '+'
-            for adj_lon, adj_lat, symbol, sz, colours in zip(lon, lat,
-                                                             marker_list,
-                                                             size_list,
-                                                             color_list):
-                # red line, red +, red o, marker sizes are recognized,
-                # no outline color of black for 'o'
-                # plt.scatter(x, y, s=sz, c=colours, edgecolors=colours,
-                # facecolors='none', marker=symbol, zorder=2)
-                # Solid circle, just like the EMC NCEP plots
-                # Separate the first two points so we can generate the legend
-                if circle_counter == 0 or plus_counter == 0:
-                    if symbol == 'o':
-                        plt.scatter(adj_lon, adj_lat, s=sz, c=colours,
-                                    edgecolors=colours, facecolors=colours,
-                                    marker='o', zorder=2,
-                                    label="Indicates a position " +
-                                    "at 00 or 12 UTC", transform=prj)
-                        circle_counter += 1
-                    elif symbol == '+':
-                        plt.scatter(adj_lon, adj_lat, s=sz, c=colours,
-                                    edgecolors=colours, facecolors=colours,
-                                    marker='+', zorder=2,
-                                    label="\nIndicates a position at 06 or " +
-                                    "18 UTC\n", transform=prj)
-                        plus_counter += 1
-
-                else:
-                    # Set the legend for additional text using a
-                    # dummy scatter point
-                    if dummy_counter == 0:
-                        plt.scatter(0, 0, zorder=2, marker=None, c='',
-                                    label="Date (dd/hhz) is the first " +
-                                    "time storm was able to be tracked " +
-                                    "in model")
-                        dummy_counter += 1
-                    plt.scatter(adj_lon, adj_lat, s=sz, c=colours,
-                                edgecolors=colours,
-                                facecolors=colours, marker=symbol, zorder=2,
-                                transform=prj)
-
-            # Finally, overlay the line plot to define the storm tracks
-            plt.plot(lon, lat, linestyle='-', color=colours, linewidth=.3,
-                     transform=prj)
-
-        # If requested, create an ASCII file with the tracks that are going to
-        # be plotted.  This is useful to debug or verify that what you
-        # see on the plot is what is expected.
-        if self.gen_ascii:
-            ascii_track_parts = [self.init_date, '.txt']
-            ascii_track_output_name = ''.join(ascii_track_parts)
-            track_filename = os.path.join(self.output_dir,
-                                         ascii_track_output_name)
-            self.logger.info(f"Writing ascii track info: {track_filename}")
-            with open(track_filename, 'w') as file_handle:
-                for line in lines_to_write:
-                    file_handle.write(f"{line}\n")
-
-        # Draw the legend on the plot
-        # If you wish to have the legend within the plot:
-        # plt.legend(loc='lower left', prop={'size':5}, scatterpoints=1)
-        # The legend is outside the plot, below the x-axis to
-        # avoid obscuring any storm tracks in the Southern
-        # Hemisphere.
-        # ax.legend(loc='lower left', bbox_to_anchor=(-0.03, -0.5),
-        #           fancybox=True, shadow=True, scatterpoints=1,
-        #           prop={'size': 6})
-        ax.legend(loc='lower left', bbox_to_anchor=(-0.01, -0.4),
-                  fancybox=True, shadow=True, scatterpoints=1,
-                  prop={'size': 6})
-
-        # Write the plot to the output directory
-        out_filename_parts = [self.init_date, '.png']
-        output_plot_name = ''.join(out_filename_parts)
-        plot_filename = os.path.join(self.output_dir, output_plot_name)
-        if self.resolution_dpi > 0:
-            plt.savefig(plot_filename, dpi=self.resolution_dpi)
-        else:
-            # use Matplotlib's default if no resolution is set in config file
-            plt.savefig(plot_filename)
-
-
-        # Plot data onto axes
-        # Uncomment the two lines below if you wish to have a pop up 
-        # window of the plot automatically appear, in addition to the creation
-        # of the .png version of the plot.
-        #self.logger.info("Plot is displayed in separate window.
-        # Close window to continue METplus execution")
-        # plt.show()
-
-
-    @staticmethod
-    def rescale_lon(lon):
-        """! Rescales longitude, using the same logic employed by MET
-        """
-
-        if float(lon) > 180.:
-            adj_lon = lon - 360.
-        else:
-            adj_lon = lon
-
-        return adj_lon
+"""!@namespace ExtraTropicalCyclonePlotter
+A Python class that generates plots of extra tropical cyclone forecast data,
+ replicating the NCEP tropical and extra tropical cyclone tracks and
+ verification plots http://www.emc.ncep.noaa.gov/mmb/gplou/emchurr/glblgen/
+"""
+
+import os
+import time
+import datetime
+import re
+import sys
+from collections import namedtuple
+
+
+# handle if module can't be loaded to run wrapper
+WRAPPER_CANNOT_RUN = False
+EXCEPTION_ERR = ''
+try:
+    import pandas as pd
+    import matplotlib.pyplot as plt
+    import matplotlib.ticker as mticker
+    import cartopy.crs as ccrs
+    import cartopy.feature as cfeature
+    import cartopy
+    from cartopy.mpl.gridliner import LONGITUDE_FORMATTER, LATITUDE_FORMATTER
+
+    ##If the script is run on a limited-internet access machine, the CARTOPY_DIR environment setting
+    ##will need to be set in the user-specific system configuration file. Review the Installation section
+    ##of the User's Guide for more details.
+    if os.getenv('CARTOPY_DIR'):
+        cartopy.config['data_dir'] = os.getenv('CARTOPY_DIR', cartopy.config.get('data_dir'))
+
+except Exception as err_msg:
+    WRAPPER_CANNOT_RUN = True
+    EXCEPTION_ERR = err_msg
+
+import produtil.setup
+
+from ..util import met_util as util
+from ..util import do_string_sub
+from . import CommandBuilder
+
+
+class CyclonePlotterWrapper(CommandBuilder):
+    """! Generate plots of extra tropical storm forecast tracks.
+        Reads input from ATCF files generated from MET TC-Pairs
+    """
+
+    def __init__(self, config, instance=None, config_overrides={}):
+        self.app_name = 'cyclone_plotter'
+
+        super().__init__(config,
+                         instance=instance,
+                         config_overrides=config_overrides)
+
+        if WRAPPER_CANNOT_RUN:
+            self.log_error("There was a problem importing modules: "
+                           f"{EXCEPTION_ERR}\n")
+            return
+
+        self.input_data = self.config.getdir('CYCLONE_PLOTTER_INPUT_DIR')
+        self.output_dir = self.config.getdir('CYCLONE_PLOTTER_OUTPUT_DIR')
+        self.init_date = self.config.getraw('config',
+                                            'CYCLONE_PLOTTER_INIT_DATE')
+        self.init_hr = self.config.getraw('config', 'CYCLONE_PLOTTER_INIT_HR')
+
+        init_time_fmt = self.config.getstr('config', 'INIT_TIME_FMT', '')
+
+        if init_time_fmt:
+            clock_time = datetime.datetime.strptime(
+                self.config.getstr('config',
+                                   'CLOCK_TIME'),
+                '%Y%m%d%H%M%S'
+            )
+
+            init_beg = self.config.getraw('config', 'INIT_BEG')
+            if init_beg:
+                init_beg_dt = util.get_time_obj(init_beg,
+                                                init_time_fmt,
+                                                clock_time,
+                                                logger=self.logger)
+                self.init_date = do_string_sub(self.init_date, init=init_beg_dt)
+                self.init_hr = do_string_sub(self.init_hr, init=init_beg_dt)
+
+        self.model = self.config.getstr('config', 'CYCLONE_PLOTTER_MODEL')
+        self.title = self.config.getstr('config',
+                                        'CYCLONE_PLOTTER_PLOT_TITLE')
+        self.gen_ascii = (
+            self.config.getbool('config',
+                                'CYCLONE_PLOTTER_GENERATE_TRACK_ASCII')
+        )
+        # Create a set to keep track of unique storm_ids for each track file.
+        self.unique_storm_id = set()
+        # Data structure to separate data based on storm id.
+        self.storm_id_dict = {}
+
+        # Data/info which we want to retrieve from the track files.
+        self.columns_of_interest = ['AMODEL', 'STORM_ID', 'INIT',
+                                    'LEAD', 'VALID', 'ALAT', 'ALON']
+        self.circle_marker_size = (
+            self.config.getint('config',
+                               'CYCLONE_PLOTTER_CIRCLE_MARKER_SIZE')
+        )
+        self.annotation_font_size = (
+            self.config.getint('config',
+                               'CYCLONE_PLOTTER_ANNOTATION_FONT_SIZE')
+        )
+
+        self.legend_font_size = (
+            self.config.getint('config',
+                               'CYCLONE_PLOTTER_LEGEND_FONT_SIZE')
+        )
+
+        # Map centered on Pacific Ocean
+        self.central_latitude = 180.0
+
+        self.cross_marker_size = (self.config.getint('config',
+                               'CYCLONE_PLOTTER_CROSS_MARKER_SIZE')
+        )
+        self.resolution_dpi = (
+            self.config.getint('config',
+                               'CYCLONE_PLOTTER_RESOLUTION_DPI')
+        )
+
+        self.add_watermark = self.config.getbool('config',
+                                                 'CYCLONE_PLOTTER_ADD_WATERMARK',
+                                                 True)
+        # Set the marker symbols, '+' for a small cross, '.' for a small circle.
+        # NOTE: originally, 'o' was used.  'o' is also a circle, but it creates a
+        # very large filled circle on the plots that appears too large.
+        self.cross_marker = '+'
+        self.circle_marker = '.'
+
+
+    def run_all_times(self):
+        """! Calls the defs needed to create the cyclone plots
+             run_all_times() is required by CommandBuilder.
+
+        """
+        self.sanitized_df = self.retrieve_data()
+        self.create_plot()
+
+
+    def retrieve_data(self):
+        """! Retrieve data from track files.
+            Returns:
+               sanitized_df:  a pandas dataframe containing the
+                              "sanitized" longitudes, as well as some markers and
+                              lead group information needed for generating
+                              scatter plots.
+
+        """
+        self.logger.debug("Begin retrieving data...")
+        all_tracks_list = []
+
+        # Store the data in the track list.
+        if os.path.isdir(self.input_data):
+            self.logger.debug("Get data from all files in the directory " +
+                              self.input_data)
+            # Get the list of all files (full file path) in this directory
+            all_input_files = util.get_files(self.input_data, ".*.tcst",
+                                            self.logger)
+
+            # read each file into pandas then concatenate them together
+            df_list = [pd.read_csv(file, delim_whitespace=True) for file in all_input_files]
+            combined = pd.concat(df_list, ignore_index=True)
+
+            # check for empty dataframe, set error message and exit
+            if combined.empty:
+                self.logger.error("No data found in specified files. Please check your config file settings.")
+                sys.exit("No data found.")
+
+            # if there are any NaN values in the ALAT, ALON, STORM_ID, LEAD, INIT, AMODEL, or VALID column,
+            # drop that row of data (axis=0).  We need all these columns to contain valid data in order
+            # to create a meaningful plot.
+            combined_df = combined.copy(deep=True)
+            combined_df = combined.dropna(axis=0, how='any',
+                                          subset=self.columns_of_interest)
+
+            # Retrieve and create the columns of interest
+            self.logger.debug(f"Number of rows of data: {combined_df.shape[0]}")
+            combined_subset = combined_df[self.columns_of_interest]
+            df = combined_subset.copy(deep=True)
+            df.allows_duplicate_labels = False
+            # INIT, LEAD, VALID correspond to the column headers from the MET
+            # TC tool output.  INIT_YMD, INIT_HOUR, VALID_DD, and VALID_HOUR are
+            # new columns (for a new dataframe) created from these MET columns.
+            df['INIT'] = df['INIT'].astype(str)
+            df['INIT_YMD'] = (df['INIT'].str[:8]).astype(int)
+            df['INIT_HOUR'] = (df['INIT'].str[9:11]).astype(int)
+            df['LEAD']  = df['LEAD']/10000
+            df['LEAD'] = df['LEAD'].astype(int)
+            df['VALID_DD'] = (df['VALID'].str[6:8]).astype(int)
+            df['VALID_HOUR'] = (df['VALID'].str[9:11]).astype(int)
+            df['VALID'] = df['VALID'].astype(int)
+
+            # Subset the dataframe to include only the data relevant to the user's criteria as
+            # specified in the configuration file.
+            init_date = int(self.init_date)
+            init_hh = int(self.init_hr)
+            model_name = self.model
+
+            if model_name:
+                self.logger.debug("Subsetting based on " + str(init_date) + " " + str(init_hh) +
+                                  ", and model:" + model_name )
+                mask = df[(df['AMODEL'] == model_name) & (df['INIT_YMD'] >= init_date) &
+                          (df['INIT_HOUR'] >= init_hh)]
+            else:
+                # no model specified, just subset on init date and init hour
+                mask = df[(df['INIT_YMD'] >= init_date) &
+                          (df['INIT_HOUR'] >= init_hh)]
+                self.logger.debug("Subsetting based on " + str(init_date) + ", and "+ str(init_hh))
+
+            user_criteria_df = mask
+            # reset the index so things are ordered properly in the new dataframe
+            user_criteria_df.reset_index(inplace=True)
+
+            # Aggregate the ALON values based on unique storm id to facilitate "sanitizing" the
+            # longitude values (to handle lons that cross the International Date Line).
+            unique_storm_ids_set = set(user_criteria_df['STORM_ID'])
+            self.unique_storm_ids = list(unique_storm_ids_set)
+            nunique = len(self.unique_storm_ids)
+            self.logger.debug(f" {nunique} unique storm ids identified")
+
+            # Use named tuples to store the relevant storm track information (their index value in the dataframe,
+            # track id, and ALON values and later on the SLON (sanitized ALON values).
+            TrackPt = namedtuple("TrackPt", "indices track alons alats")
+
+            # named tuple holding "sanitized" longitudes
+            SanTrackPt = namedtuple("SanTrackPt", "indices track alons slons")
+
+            # Keep track of the unique storm tracks by their storm_id
+            storm_track_dict = {}
+
+            for cur_unique in self.unique_storm_ids:
+                idx_list = user_criteria_df.index[user_criteria_df['STORM_ID'] == cur_unique].tolist()
+                alons = []
+                alats = []
+                indices = []
+
+                for idx in idx_list:
+                    alons.append(user_criteria_df.loc[idx, 'ALON'])
+                    alats.append(user_criteria_df.loc[idx, 'ALAT'])
+                    indices.append(idx)
+
+                # create the track_pt tuple and add it to the storm track dictionary
+                track_pt = TrackPt(indices, cur_unique, alons, alats)
+                storm_track_dict[cur_unique] = track_pt
+
+            # create a new dataframe to contain the sanitized lons (i.e. the original ALONs that have
+            # been cleaned up when crossing the International Date Line)
+            sanitized_df = user_criteria_df.copy(deep=True)
+
+            # Now we have a dictionary that helps in aggregating the data based on
+            # storm tracks (via storm id) and will contain the "sanitized" lons
+            sanitized_storm_tracks = {}
+            for key in storm_track_dict:
+                # "Sanitize" the longitudes to shift the lons that cross the International Date Line.
+                # Create a new SanTrackPt named tuple and add that to a new dictionary
+                # that keeps track of the sanitized data based on the storm id
+                # sanitized_lons = self.sanitize_lonlist(storm_track_dict[key].alons)
+                sanitized_lons = self.sanitize_lonlist(storm_track_dict[key].alons)
+                sanitized_track_pt = SanTrackPt(storm_track_dict[key].indices, storm_track_dict[key].track,
+                                                  storm_track_dict[key].alons, sanitized_lons)
+                sanitized_storm_tracks[key] = sanitized_track_pt
+
+                # fill in the sanitized dataframe, sanitized_df
+                for key in sanitized_storm_tracks:
+                    # now use the indices of the storm tracks to correctly assign the sanitized
+                    # lons to the appropriate row in the dataframe to maintain the row ordering of
+                    # the original dataframe
+                    idx_list = sanitized_storm_tracks[key].indices
+
+                    for i, idx in enumerate(idx_list):
+                        sanitized_df.loc[idx,'SLON'] = sanitized_storm_tracks[key].slons[i]
+
+                        # Set some useful values used for plotting.
+                        # Set the IS_FIRST value to True if this is the first
+                        # point in the storm track, False
+                        # otherwise
+                        if i == 0:
+                            sanitized_df.loc[idx, 'IS_FIRST'] = True
+                        else:
+                            sanitized_df.loc[idx, 'IS_FIRST'] = False
+
+                        # Set the lead group to the character '0' if the valid hour is 0 or 12,
+                        # or to the charcter '6' if the valid hour is 6 or 18. Set the marker
+                        # to correspond to the valid hour: 'o' (open circle) for 0 or 12 valid hour,
+                        # or '+' (small plus/cross) for 6 or 18.
+                        if sanitized_df.loc[idx, 'VALID_HOUR'] == 0 or sanitized_df.loc[idx, 'VALID_HOUR'] == 12:
+                            sanitized_df.loc[idx, 'LEAD_GROUP'] ='0'
+                            sanitized_df.loc[idx, 'MARKER'] = self.circle_marker
+                        elif sanitized_df.loc[idx, 'VALID_HOUR'] == 6 or sanitized_df.loc[idx, 'VALID_HOUR'] == 18:
+                            sanitized_df.loc[idx, 'LEAD_GROUP'] = '6'
+                            sanitized_df.loc[idx, 'MARKER'] = self.cross_marker
+
+            # Write output ASCII file (csv) summarizing the information extracted from the input
+            # which is used to generate the plot.
+            if self.gen_ascii:
+               self.logger.debug(f" output dir: {self.output_dir}")
+               util.mkdir_p(self.output_dir)
+               ascii_track_parts = [self.init_date, '.csv']
+               ascii_track_output_name = ''.join(ascii_track_parts)
+               final_df_filename = os.path.join(self.output_dir, ascii_track_output_name)
+
+               # Make sure that the dataframe is sorted by STORM_ID, INIT_YMD, INIT_HOUR, and LEAD
+               # to ensure that the line plot is connecting the points in the correct order.
+               # sanitized_df.sort_values(by=['STORM_ID', 'INIT_YMD', 'INIT_HOUR', 'LEAD'],
+               #                          inplace=True).reset_index(drop=True,inplace=True)
+               # sanitized_df.reset_index(inplace=True,drop=True)
+               final_df = sanitized_df.sort_values(by=['STORM_ID', 'INIT_YMD', 'INIT_HOUR', 'LEAD'], ignore_index=True)
+               final_df.to_csv(final_df_filename)
+        else:
+            # The user's specified directory isn't valid, log the error and exit.
+            self.logger.error("CYCLONE_PLOTTER_INPUT_DIR isn't a valid directory, check config file.")
+            sys.exit("CYCLONE_PLOTTER_INPUT_DIR isn't a valid directory.")
+        return final_df
+
+
+    def create_plot(self):
+        """
+         Create the plot, using Cartopy
+
+        """
+
+        # Use PlateCarree projection for scatter plots
+        # and Geodetic projection for line plots.
+        cm_lon = self.central_latitude
+        ax = plt.axes(projection=ccrs.PlateCarree(central_longitude=cm_lon))
+        prj = ccrs.PlateCarree()
+        # for transforming the annotations (matplotlib to cartopy workaround from Stack Overflow)
+        transform = ccrs.PlateCarree()._as_mpl_transform(ax)
+
+        # Add land, coastlines, and ocean
+        ax.add_feature(cfeature.LAND)
+        ax.coastlines()
+        ax.add_feature(cfeature.OCEAN)
+
+        # keep map zoomed out to full world.  If this
+        # is absent, the default behavior is to zoom
+        # into the portion of the map that contains points.
+        ax.set_global()
+
+        # Add grid lines for longitude and latitude
+        gl = ax.gridlines(crs=prj,
+                          draw_labels=True, linewidth=1, color='gray',
+                          alpha=0.5, linestyle='--')
+        gl.xlabels_top = False
+        gl.ylabels_left = False
+        gl.xlines = True
+        gl.xformatter = LONGITUDE_FORMATTER
+        gl.yformatter = LATITUDE_FORMATTER
+        gl.xlabel_style = {'size': 9, 'color': 'blue'}
+        gl.xlabel_style = {'color': 'black', 'weight': 'normal'}
+
+        # Plot title
+        plt.title(self.title + "\nFor forecast with initial time = " +
+                  self.init_date)
+
+        # Optional: Create the NCAR watermark with a timestamp
+        # This will appear in the bottom right corner of the plot, below
+        # the x-axis.  NOTE: The timestamp is in the user's local time zone
+        # and not in UTC time.
+        if self.add_watermark:
+            ts = time.time()
+            st = datetime.datetime.fromtimestamp(ts).strftime(
+                '%Y-%m-%d %H:%M:%S')
+            watermark = 'DTC METplus\nplot created at: ' + st
+            plt.text(60, -130, watermark, fontsize=5, alpha=0.25)
+
+        # Make sure the output directory exists, and create it if it doesn't.
+        util.mkdir_p(self.output_dir)
+
+        # get the points for the scatter plots (and the relevant information for annotations, etc.)
+        points_list = self.get_plot_points()
+
+        # Legend labels
+        lead_group_0_legend = "Indicates a position at 00 or 12 UTC"
+        lead_group_6_legend = "Indicates a position at 06 or 18 UTC"
+
+        # to be consistent with the NOAA website, use red for annotations, markers, and lines.
+        pt_color = 'red'
+        cross_marker_size = self.cross_marker_size
+        circle_marker_size = self.circle_marker_size
+
+        # Get all the lat and lon (i.e. x and y) points for the '+' and 'o' marker types
+        # to be used in generating the scatter plots (one for the 0/12 hr and one for the 6/18 hr lead
+        # groups).  Also collect ALL the lons and lats, which will be used to generate the
+        # line plot (the last plot that goes on top of all the scatter plots).
+        cross_lons = []
+        cross_lats = []
+        cross_annotations = []
+        circle_lons = []
+        circle_lats = []
+        circle_annotations = []
+
+        for idx,pt in enumerate(points_list):
+            if pt.marker == self.cross_marker:
+                cross_lons.append(pt.lon)
+                cross_lats.append(pt.lat)
+                cross_annotations.append(pt.annotation)
+                # cross_marker = pt.marker
+            elif pt.marker == self.circle_marker:
+                circle_lons.append(pt.lon)
+                circle_lats.append(pt.lat)
+                circle_annotations.append(pt.annotation)
+                # circle_marker = pt.marker
+
+        # Now generate the scatter plots for the lead group 0/12 hr ('+' marker) and the
+        # lead group 6/18 hr ('.' marker).
+        plt.scatter(circle_lons, circle_lats, s=self.circle_marker_size, c=pt_color,
+                    marker=self.circle_marker, zorder=2, label=lead_group_0_legend, transform=prj )
+        plt.scatter(cross_lons, cross_lats, s=self.cross_marker_size, c=pt_color,
+                    marker=self.cross_marker, zorder=2, label=lead_group_6_legend, transform=prj)
+
+        # annotations for the scatter plots
+        counter = 0
+        for x,y in zip(circle_lons, circle_lats):
+            plt.annotate(circle_annotations[counter], (x,y+1), xycoords=transform, color=pt_color,
+                         fontsize=self.annotation_font_size)
+            counter += 1
+
+        counter = 0
+        for x, y in zip(cross_lons, cross_lats):
+            plt.annotate(cross_annotations[counter], (x, y + 1), xycoords=transform, color=pt_color,
+                         fontsize=self.annotation_font_size)
+            counter += 1
+
+        # Dummy point to add the additional label explaining the labelling of the first
+        # point in the storm track
+        plt.scatter(0, 0, zorder=2, marker=None, c='',
+                    label="Date (dd/hhz) is the first " +
+                            "time storm was able to be tracked in model")
+
+        # Settings for the legend box location.
+        ax.legend(loc='lower left', bbox_to_anchor=(0, -0.4),
+                  fancybox=True, shadow=True, scatterpoints=1,
+                  prop={'size':self.legend_font_size})
+
+        # Generate the line plot
+        # First collect all the lats and lons for each storm track. Then for each storm track,
+        # generate a line plot.
+        pts_by_track_dict = self.get_points_by_track()
+
+        for key in pts_by_track_dict:
+            lons = []
+            lats = []
+            for idx, pt in enumerate(pts_by_track_dict[key]):
+                lons.append(pt.lon)
+                lats.append(pt.lat)
+
+            # Create the line plot for the current storm track, use the Geodetic coordinate reference system
+            # to correctly connect adjacent points that have been sanitized and cross the
+            # International Date line or the Prime Meridian.
+            plt.plot(lons, lats, linestyle='-', color=pt_color, linewidth=.4, transform=ccrs.Geodetic(), zorder=3)
+
+        # Write the plot to the output directory
+        out_filename_parts = [self.init_date, '.png']
+        output_plot_name = ''.join(out_filename_parts)
+        plot_filename = os.path.join(self.output_dir, output_plot_name)
+        if self.resolution_dpi > 0:
+            plt.savefig(plot_filename, dpi=self.resolution_dpi)
+        else:
+            # use Matplotlib's default if no resolution is set in config file
+            plt.savefig(plot_filename)
+
+
+    def get_plot_points(self):
+        """
+           Get the lon and lat points to be plotted, along with any other plotting-relevant
+           information like the marker, whether this is a first point (to be used in
+           annotating the first point using the valid day date and valid hour), etc.
+
+        :return:  A list of named tuples that represent the points to plot with corresponding
+                  plotting information
+        """
+
+        # Create a named tuple to store the point information
+        PlotPt = namedtuple("PlotPt", "storm_id lon lat is_first marker valid_dd valid_hour annotation")
+
+        points_list = []
+        storm_id = self.sanitized_df['STORM_ID']
+        lons = self.sanitized_df['SLON']
+        lats = self.sanitized_df['ALAT']
+        is_first_list = self.sanitized_df['IS_FIRST']
+        marker_list = self.sanitized_df['MARKER']
+        valid_dd_list = self.sanitized_df['VALID_DD']
+        valid_hour_list = self.sanitized_df['VALID_HOUR']
+        annotation_list = []
+
+        for idx, cur_lon in enumerate(lons):
+            if is_first_list[idx] is True:
+                annotation = str(valid_dd_list[idx]).zfill(2) + '/' + \
+                             str(valid_hour_list[idx]).zfill(2) + 'z'
+            else:
+                annotation = None
+
+            annotation_list.append(annotation)
+            cur_pt = PlotPt(storm_id, lons[idx], lats[idx], is_first_list[idx], marker_list[idx],
+                            valid_dd_list[idx], valid_hour_list[idx], annotation)
+            points_list.append(cur_pt)
+
+        return points_list
+
+
+    def get_points_by_track(self):
+        """
+            Get all the lats and lons for each storm track. Used to generate the line
+            plot of the storm tracks.
+
+            Args:
+
+            :return:
+                points_by_track:  Points aggregated by storm track.
+                                Returns a dictionary where the key is the storm_id
+                                and values are the points (lon,lat) stored in a named tuple
+        """
+        track_dict = {}
+        LonLat = namedtuple("LonLat", "lon lat")
+        for cur_unique in self.unique_storm_ids:
+            # retrieve the ALAT and ALON values that correspond to the rows for a unique storm id.
+            # i.e. Get the index value(s) corresponding to this unique storm id
+            idx_list = self.sanitized_df.index[self.sanitized_df['STORM_ID'] == cur_unique].tolist()
+            sanitized_lons_and_lats = []
+            indices = []
+            for idx in idx_list:
+                cur_lonlat = LonLat(self.sanitized_df.loc[idx, 'SLON'], self.sanitized_df.loc[idx, 'ALAT'])
+                sanitized_lons_and_lats.append(cur_lonlat)
+                indices.append(idx)
+
+            # update the track dictionary
+            track_dict[cur_unique] = sanitized_lons_and_lats
+
+        return track_dict
+
+
+    @staticmethod
+    def sanitize_lonlist(lon):
+        """
+        Solution from Stack Overflow for "sanitizing" longitudes that cross the International Date Line
+        https://stackoverflow.com/questions/67730660/plotting-line-across-international-dateline-with-cartopy
+
+        Args:
+           @param lon:  A list of longitudes (float) that correspond to a storm track
+
+        Returns:
+            new_list: a list of "sanitized" lons that are "corrected" for crossing the
+            International Date Line
+        """
+
+        new_list = []
+        oldval = 0
+        # used to compare adjacent longitudes in a storm track
+        treshold = 10
+        for ix, ea in enumerate(lon):
+            diff = oldval - ea
+            if (ix > 0):
+                if (diff > treshold):
+                    ea = ea + 360
+            oldval = ea
+            new_list.append(ea)
+        return new_list
\ No newline at end of file
diff --git a/parm/use_cases/model_applications/tc_and_extra_tc/CyclonePlotter_fcstGFS_obsGFS_UserScript_ExtraTC.conf b/parm/use_cases/model_applications/tc_and_extra_tc/CyclonePlotter_fcstGFS_obsGFS_UserScript_ExtraTC.conf
index 69d33171dd..94a0773846 100644
--- a/parm/use_cases/model_applications/tc_and_extra_tc/CyclonePlotter_fcstGFS_obsGFS_UserScript_ExtraTC.conf
+++ b/parm/use_cases/model_applications/tc_and_extra_tc/CyclonePlotter_fcstGFS_obsGFS_UserScript_ExtraTC.conf
@@ -15,6 +15,7 @@ PROCESS_LIST = UserScript, TCPairs, CyclonePlotter
 
 LOOP_BY = INIT
 
+
 # The init time begin and end times, increment, and last init hour.
 INIT_TIME_FMT = %Y%m%d%H
 INIT_BEG = 2020100700
@@ -102,6 +103,7 @@ CYCLONE_PLOTTER_INIT_HR ={init?fmt=%H}
 CYCLONE_PLOTTER_MODEL = GFSO
 CYCLONE_PLOTTER_PLOT_TITLE = Model Forecast Storm Tracks
 
+
 ##
 #  Indicate the size of symbol (point size)
 CYCLONE_PLOTTER_CIRCLE_MARKER_SIZE = 2
@@ -109,7 +111,10 @@ CYCLONE_PLOTTER_CROSS_MARKER_SIZE = 3
 
 ##
 # Indicate text size of annotation label
-CYCLONE_PLOTTER_ANNOTATION_FONT_SIZE=3
+CYCLONE_PLOTTER_ANNOTATION_FONT_SIZE = 3
+
+# Indicate the text size for the legend labels
+CYCLONE_PLOTTER_LEGEND_FONT_SIZE = 3
 
 ##
 # Resolution of saved plot in dpi (dots per inch)
diff --git a/parm/use_cases/model_applications/tc_and_extra_tc/Plotter_fcstGFS_obsGFS_ExtraTC.conf b/parm/use_cases/model_applications/tc_and_extra_tc/Plotter_fcstGFS_obsGFS_ExtraTC.conf
index 99cc165b09..7734c929d9 100644
--- a/parm/use_cases/model_applications/tc_and_extra_tc/Plotter_fcstGFS_obsGFS_ExtraTC.conf
+++ b/parm/use_cases/model_applications/tc_and_extra_tc/Plotter_fcstGFS_obsGFS_ExtraTC.conf
@@ -28,6 +28,7 @@ TC_PAIRS_OUTPUT_TEMPLATE = {date?fmt=%Y%m}/{basin?fmt=%s}q{date?fmt=%Y%m%d%H}.gf
 PROCESS_LIST = TCPairs, CyclonePlotter
 
 LOOP_ORDER = processes
+LOOP_BY = init
 
 ## Config options below used by tc_pairs_wrapper module.
 # -------------------------------------------------------
@@ -62,7 +63,6 @@ INIT_EXCLUDE =
 # Specify model valid time window in format YYYYMM[DD[_hh]].  
 # Only tracks that fall within the valid time window will
 # be used.
-#
 VALID_BEG =
 VALID_END =
 
@@ -135,8 +135,15 @@ CYCLONE_PLOTTER_PLOT_TITLE = Model Forecast Storm Tracks
 
 ##
 #  Indicate the size of symbol (point size)
-CYCLONE_PLOTTER_CIRCLE_MARKER_SIZE = 41
-CYCLONE_PLOTTER_CROSS_MARKER_SIZE = 51
+CYCLONE_PLOTTER_CIRCLE_MARKER_SIZE = 2
+CYCLONE_PLOTTER_CROSS_MARKER_SIZE = 3
+
+##
+# Indicate text size of annotation label
+CYCLONE_PLOTTER_ANNOTATION_FONT_SIZE = 3
+
+# Indicate the text size for the legend labels
+CYCLONE_PLOTTER_LEGEND_FONT_SIZE = 3
 
 ##
 #  Turn on/off the generation of an ASCII output file listing all the
@@ -144,3 +151,11 @@ CYCLONE_PLOTTER_CROSS_MARKER_SIZE = 51
 #  that what is plotted is consistent with the data.
 #
 CYCLONE_PLOTTER_GENERATE_TRACK_ASCII = yes
+
+CYCLONE_PLOTTER_ADD_WATERMARK = False
+
+##
+# Resolution of saved plot in dpi (dots per inch)
+# Set to 0 to allow Matplotlib to determine, based on your computer
+CYCLONE_PLOTTER_RESOLUTION_DPI = 400
+