…for pandas the only dimension is time (but it is un-named). Therefore the numerator for the covariance term had to be split out between the fcst and obs case.

* creating test dropdown menus

* fixing warnings

* fixing warnings

* fixing warnings 3

* fixing warnings 4

* Attempt to fix documentation errors

* adding 2 more test dropdowns

please note.  There is still a message about 
WARNING: Duplicate explicit target name: "gridstat: cloud fractions with neighborhood and probabilities (pygrib)".
John O will fix this.  I should not touch it.

* fixing spacing

* trying to fix link

* take 2

* Removing double underscores added earlier

* moving dropdown menus

* Adding version to dropdown menu title

* fixing spacing

* dropdowns date util, eofs, h5py

* fixing formatting

* fixing formatting

* Per #2463, adding template for future entries

* adding imageio, lxml & matplotlib

* dropdown up to nc-time-axis

* fixing spacing problems

* Fixing broken s2s links and other incorrect links

* Fixing spelling and capitalization

* Removing the dash in front of 1.4 for nc-time-axis

* Modifying formatting

* adding dropdowns thru pylab

* fixing problems

* dropdowns thru scikit-learn

* fixing spacing

* final dropdowns thru yaml

* fixing spacing

* fixing loose ends

* Per #2463, moving information to an Appendix and adding text and links in an overview

* Per #2463, adding to index.rst

* Per #2463, reworded language and updated Python 3.8 reference

* Per #2463, fixing errors

* Per #2463, made updates based on feedback at the METplus Engineering meeting.

* removing tables, changing most METplus wrappers, version numbers.

* trying to fix met_version

* Per #2463, adding necessary code for substitutions

* Per #2463, fixing syntax error

* adding period

* removing section 1.5

* Per #2463, replace old label reference with new label reference and updated text to reflect the move to drop down menus

* read python version from file to replace in docs

* fixed typo in variable name

* adding python_version to the overview.

---------

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

…f METplus version

…ization (#2522)

* per PyCharm documentation, only ignore workspace.xml idea file and commit the rest of the .idea files to version control

* per #2520, create function to get METplus wrapper class without initializing it and use that function to read list of deprecated env vars to prevent redundant initialization of wrappers that can cause unintended side effects

* handle file_window variables consistently by using CommandBuilder function

* comment out optional config variables that previously caused a failure when unset

Fix typo in the update_truth issue template in the develop branch.

Update wording in the update_truth issue template.

* Per #2530, add a development timeline to the METplus Release Information section of the User's Guide. Also update the Release Guide instructions.

* Per #2530, tweak the wording.

* Update docs/Release_Guide/release_steps/update_release_notes_development.rst

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

---------

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

…XNET observations.

… 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.

…her python version unit test if one fails

* add release notes

* update version for beta2 release

* update beta2 release date

* update info about DockerHub images for beta2

* update date of release

* Update docs/Users_Guide/release-notes.rst

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

* per suggestion from @jprestop, add info about python version upgrade to the upgrade instructions

* disable doxygen by default

* fix formatting of note

---------

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

…chelleharrold.

* Per #2953, update Orion file for Python 3.12

* Per #2953, updating Existing Builds page for installation on Orion

* Per #2953, updating Casper file for Python 3.12

* Per #2953, adding script for METplus-6.1 using Python 3.12

* Per #2953, updated installation information for Casper

* Per #2953, updated compiler for Orion

* Per #2953 updating compiler in Existing Builds for Orion

* Per #2953, added qhull needed for atlas on hera

* Per #2953, remove qhull as it was actually causing problems on hera

* Per #2953, updating hera file for Python 3.12

* Per #2953, updating with hera information

* Per #2953, updating jet file for Python 3.12

* Per

* Per #2953, adding internal/scripts/installation to paths-ignore

* add quotation marks around file path if it includes spaces

* update use case to read WRF fire field on subgrid directly instead of using Python Embedding

* update instructions for updating web server data to use MET scripts

* add a test for python embedding input

* fix issue introduced where double quotes are added

* prevent incorrect error when running PyEmbedIngest

* fix URL link

* update use case doc to note that Python Embedding is no longer used

* remove keyword to set up Python Embedding in automated tests because it is no longer used

* per PR review suggestion from Copilot, add comment to describe why variable is set

* override output units/level

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

* fix formatting of set_attr options

---------

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

… conflict with reserved env var used by METplus to set parm base

…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)

…_51b4335a