… case, to compute TCI from raw observations rather than read pre-computed TCI.

* Per #2537, add SonarQube workflow for METplus

* Per #2537, update nightly build email list.

* Per #2537, fix cut/paste error configure_sonarqube.sh

* Per #2537, exclude test code from code coverage statistics.

…g of params, and also switches the fluxnet metadata file to a command line argument instead of an environment variable.

…notes.rst

…d filename patterns, DEBUG mode added and set to False by default, adjustment of print statements for logging, and refactoring filtering of stations to ensure we don't process a file that we shouldn't by better coupling of filenames and stations.

…s comments for use case changes.

…e group from running to easily disable it temporarily. Disable short_range:14 use case until it can be fixed with #2551

…//github.com/dtcenter/METplus/security/dependabot/5

…e available by other dependencies

* Adding Soil Moisture averaging case

* Adding a new use case to compare soil moisture of SFS-GSL vs ERA5. The use case uses a python embedding file to read the SFS-GSL files.

* Adding documentation to the soil moisture use case to compare SFS-GSL against ERA5

* Adding a thumbnail for the use case

* Adding updated soil moisture use case

* Updating title line

* Adding Use Case image

* Updating docs

* Trying to fix use case image

* Updating documentation

* Updating documentation

* Fixing documenation

* Updating documentation

* Updating directory

* Adding use case data

* Adding the s2s_soil_moisture directory

* Updating documentation location

* Adding Documentation README

* Adding config override for actions

* Fixing typo

* Testing Config overrides

* Testing new timeframe

* Changing CI overrides

* Renamed files and moved them to s2s_soil_moisture directory

* Updated file to change ERA to ERA5Land

* Moved file to the correct directory and updated

* Changed file name

* Fixed directory name

* Fixed directory name

* Fixed directory name

* Added test for the soil moisture use case

* Adding another use case

* Setting tests to false for pull requests

* Fixed image file name

* Testing sonar cube change

* Turning a test back on to check a change

* Update sfs_gsl_model_wrapper.py

* Testing a sonar cube update

* Updated documentation as per new template

* Updated documentation as per new template

* Gallery path update

* Update use_case_groups.json

* Turning tests off for PR

* Removed boilerplate language

* Changing log level

---------

Co-authored-by: Mrinal Biswas <biswas@ucar.edu>
Co-authored-by: j-opatz <59586397+j-opatz@users.noreply.github.com>

…pers use logic that requires that version and we are unable to run the unit tests for earlier versions in GitHub Actions

… numpy masked values (MaskedConstant)

* first pass over doc, basic files. Needs config update and finalize doc

* add rioxarray conda environment

* update out-of-date info

* added image, updated docs, attempt to resolve compile issue

* removing space for error

* updated remaining files, adjusted docs

* fix incorrect naming for another use case that had errors in use case doc rendering

* fix typos and formatting

* fix path to thumbnail image

* add py_embed keyword to tell automated test suite to set MET_PYTHON_EXE to the version of python in the rioxarray conda env

* fix SonarQube complaint "Fix this attribute access on a value that can be 'None'." despite the function cannot return None because it will exit the script if an invalid input is provided

---------

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

…g issue.

…conda-forge

* per #2962, begin implementation of RMWAnalysis wrapper

* start basic use case conf

* read BOTH_VAR<n> variables into data field

* change pycharm python interpreter

* ignore file generated by building docs locally

* update use case to read input data

* Per #2962, add documentation, unit tests, and basic use case for RMWAnalysis wrapper

* per #2962, added thumbnail for use case documentation

* fix incorrect formatting

* per feedback from @JohnHalleyGotway, change 5 config variables to support lists of values instead of a single string

* per #2890, refactor Example wrapper to support all EXAMPLE_RUNTIME_FREQ settings to expand its use and reproduce the bug to be addressed

* add docs for setting runtime freq for Example wrapper

* prevent crash checking an init or valid time that is a wildcard

* clean up function docs

* Per #2890, add more checks for skipping times so wrappers don't incorrectly report an error if an init/valid time is skipped. Create function to handle skip checks, logging run time, and adding instance/custom to templates to reduce duplicate code. Change skip logging from DEBUG to INFO so it is more clear what is being skipped. Rename run_at_time function to be more clear of its purpose

* update metplus_dev environment to include the documentation requirements

* Per #2890, added unit tests for example wrapper to increase code coverage on new code. Improved error reporting if incorrect time configs are set

* add release notes for rc1

* update DockerHub rc1 releases

* fix indentation

* Per #2984, updating title of issue 2863

---------

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

… removing data from original location as well

…roups that had differences in the last non-ref branch run. runs all use case groups if there is no previous non-ref run to handle first main_vX.Y-ref run before main_vX.Y has been created. also supports workflow dispatch to force update of all truth data as needed

…_6879f8b1

…empt 3