…py use cases (#2259)

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

* Updating installation files

* Removing run_commands.sh

* Updated the file to add a MINICONDA_PATH

* Adding files for jet

* Adding orion file

* Removing beta references

* Corrected met version

* Adding files for WCOSS2 machines

* Removing rc1 from acorn file

* Removing beta1

…et (#2262)

…at causes GHA disk to exceed capacity when too many data volumes are created. Use specific commit of coveralls python action to ensure it will not change

…were accidentally added with PR #1984

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

…n a pull request from a fork because the authentication fails

Refs: #1989

* Per #2479, add support for setting time_offset_warning in all wrapped MET config files

* Per #2479, add documentation and examples to basic use case param files for time_offset_warning

* Per #2346, modifying issue templates

* Per #2346, modifying pull request template

* Per #2346, modifying entries based on suggestions by @georgemccabe

* per #2567, properly pass multiple point observation files to point_stat using the -point_obs argument

* per #2567, fix bug that caused file window logic to fail

* Revert "per #2567, fix bug that caused file window logic to fail"

This reverts commit 27fe822.

* per #2567, fix bug that caused file window logic to fail

* Per #1514, implement MADIS2NC wrapper and added example use case. Also updated the function to handle the time_summary dictionary in MET config files to support names that exactly match the name found in the dictionary, e.g. ASCII2NC_TIME_SUMMARY_OBS_VAR sets time_summary.obs_var (previously only ASCII2NC_TIME_SUMMARY_VAR_NAMES was supported and is still supported)

* remove execute permissions from image files

* Per #1514, add image for basic use case

* removed large image files that are no longer being used in documentation

* add support for time_offset_warning for MADIS2NC wrapper after the PR to add that support for other wrappers has been merged into develop

* report error if output template is not defined

* update contributor's guide with more up-to-date info on how to create a new wrapper and basic components of wrappers

* fix warnings in documentation

* fix formatting issues

* Per #1514, add new basic use case to automated test suite

* add step to comment out version number in wrapped MET config file

* turn off use case to prepare for PR

* added a pytest fixture to handle comparison of use case commands and environment variable values to remove a lot of redundant logic in each wrapper test. Added fake madis data

* removed commented code

* properly substitute template tags in all command line arguments

* properly handle unset rec_beg and rec_end to prevent missing value from being added to command lien arg

…ily disabled land_surface:0 until we can resolve the differences

* Per #2346, modifying issue templates

* Per #2346, modifying pull request template

* Per #2346, modifying entries based on suggestions by @georgemccabe

* Per 2346, making updates based on feedback at last MET Eng. Meeting

…to update *-ref branches and commit/append to a log file that tracks the reasons for updating the truth data. This is done to ensure that the *-ref branch testing workflow run that actually updates the truth data is always run even if there are no other changes to the METplus branch since the last update, e.g. when a change to another component like MET warrants the truth data update

…tead merge changes from -ref into the update branch

… Embedding in PointStat and EnsembleStat, which should fix the PBL use case -- #2246 -- so turned on diff test for PBL use case to ensure that results are consistent going forward

* prevent divide by zero if run_count is 0

* Per #2547, add support for setting -valid_beg and -valid_end command line arguments. Added changes to make ASCII2NC wrapper able to run for all runtime frequencies

* Refactored system_util preprocess_file function to reduce cognitive complexity and add quotation marks around 'filenames' that contain spaces (typically python embedding commands) so explicit handling of these cases don't need to be done downstream. Added unit tests to test more python embedding cases

* remove logic to add quotes around input file since it is handled already in preprocess_file

* changed find_input_files function to return None or a time_info dictionary to be consistent across wrappers

* added ReformatPointWrapper to use as parent class for ASCII2NC, MADIS2NC, PB2NC, and Point2Grid wrappers to consistently handle tools that reformat point observation data. Moved verbosity to the end of commands

* clean up pb2nc wrapper to be more consistent with other ReformatPoint wrappers

* per #2547, added glossary entries for new config variables to set -valid_beg/end and added commented example to basic use case config file

* added glossary entries for *_RUNTIME_FREQ variables

* Per #2513, remove TC_RMW_MAX_RANGE_KM

* Updated for new data

* Updated to match new data

* Updates due to new data/updates to data

* Updates due to new data/data variables

* Changes due to changes to data variables, date

* Updates due to changes to data

* Update the date to reflect the new data (with updates to variables)

* fixed error with formatting

* Remove redundant instructions.

* For testing

* Update use_case_groups.json

* Revert to original location of input data to use the same data for all three FV3 Physics Tendency use cases.

* Revert to original location of data from tarball

* Remove typo in file directory name

* Update use_case_groups.json

Returned 10-12 to follow 11

* Update use_case_groups.json

revert to false for testing the short range use cases for  FV3 physics tendency

* Update use_case_groups.json

fix alignment of opening curly brace

* Update use_case_groups.json

revert to original formatting

* removed config variable that should be set by the user because it is specific to the user's environment

---------

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

* refactoring to reduce duplicate/redundant code, reduce cognitive complexity to satisfy SonarQube, etc

* change wording of error log to satisfy test

* set -input_thresh argument if set for add, derive, and sum methods. refactor setting of method arguments, e.g. -add, -sum, etc., cleanup

* refactor how level is handled in find_data function so that if the level has already been set, it will use that value, otherwise try to get it from {data_type}_level, e.g. fcst_level, otherwise set it to 0 to prevent errors

* refactor duplicate code into function to satisfy SonarQube

* removed unused variable

* use find_data function to find input files to be consistent with other wrappers, only allow multiple input files to be found for a given call to find_data if using the -derive method

* fix typo in key

* suppress warnings when files aren't found because it is expected

* formatting to be consistent in doc string

* per #2578, add MISSING before file path that is not found if input_thresh is set and less than 1.0, added unit test to ensure correct behavior occurs

* add documentation blocks for new functions, ci-run-all-diff

* use pytest fixture instead of local function

* add support for setting -vld_thresh argument

* per #2578, added documentation and tests for setting -input_thresh and -vld_thresh

* moved verbosity argument to end of command to more easily change it when debugging

* refactor to reduce cognitive complexity to satisfy SonarQube

* update usage statement to include METplus version number

* add copy button for code blocks to easily copy/paste commands

* turn off copy button always visible but leave code block so it can be turned on easily if desired

Update METplus-6.0.0 development schedule.

…_bce1fbed