Update develop-ref after dtcenter/MET#2892 #2598

… tests (#2237) Co-authored-by: j-opatz <jopatz@ucar.edu>

Co-authored-by: Daniel Adriaansen <dadriaan@ucar.edu> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

This updates the use-case documentation to go along with the multivariate MODE enhancements.

…2243)

…t is deleted to close log handlers. This prevents OSError: [Errno 24] Too many open files from running all pytests

Co-authored-by: Jonathan Vigh <jvigh@ucar.edu>

… look the same visually

…iceable diffs in png images

Co-authored-by: root <root@localhost>

…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

… to push this change and the NOAA OAR reporting label to all the METplus repos.

…lso fixing the get_lablels.sh to search for up to 200 existing labels. Also work on the log messages.

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

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

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

…Plotter (#2347) Co-authored-by: John Halley Gotway <johnhg@ucar.edu>

…geovista python package

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

Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com>

…re python packages required to build RTD have disappeared from the automatically generated commands from RTD

…of sphinx-gallery: see https://blog.readthedocs.com/defaulting-latest-build-tools/ for more info on why this was necessary

… disk space when running use cases, ci-run-all-diff

…eplaced with METplotpy logic

* changing _ to - for header consistency * changing _ to - for header consistency * updating all headers for consistency * updating all headers for consistency and adding spacing The spacing doesn't seem to be required but it is the convention that we follow for headers. * updating all headers for consistency * updating headers for consistency and adding capital letters to headers * Using the overline ### to keep index consistent with other indexes * updating all headers for consistency * update requirements for building docs to get around build failure where python packages required to build RTD have disappeared from the automatically generated commands from RTD * updating all headers and some spacing for consistency * updating headers for consistency * changing to ### for consistency * Per #898, fixed the headers for the Release Guide part, chapters, and sections. * Duplicating changes in develop branch for requirements.txt file * updating headers * Per #2669, updated header formatting to resolve errors * Per #2669, udpating header * Per #2669, udpating headers * Per #2669, udpating header * Per #2669, updated header formatting * Per #2669, update header formatting * updating headers * Per #898, removed space in front of title * Capitalizing Please * changing to just italics to match standard formatting * indenting for consistent formatting * fixing italics again * changing from note to warning for consistency * updating headers, adding some capitalizing to the headers * fixing typo Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * This file was committed but never updated or used Per Minna, ok to delete. * Restructuring table of contents to make it more clear which guides are for users and which are for contributors * fixing formatting for clairity Co-authored-by: Julie Prestopnik <jpresto@ucar.edu> --------- Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: Julie Prestopnik <jpresto@ucar.edu>

…2386)

Co-authored-by: Tracy <tracy.hertneky@noaa.gov>

…LE, to easily see which variable should be removed

…puting the index for the season requested instead of all seasons all the time, which also fixes a bug selecting which season the user requested. Results are identical for all seasons for the test data for the use case.

* New additions based on the old branch feature_1667_updating_overview * Moving the release-notes reference label * Added label for METplus_glossary for use in Documentation conentions section. * Adding images for the Documentation Conventions section * Modifying wording and testing formatting in Internal Links section * Second take on formatting * Third attempt at formatting * Fourth attempt at formatting * Modified wording, sections, and formatting * Minor modifications * Added period * Changed Pretty Table to PrettyTable * Modify informationg about converting an existing table and adding images * Resolving errors * Reformatting * Moving placement of reference label * Attempting to fix table title * Fixed incorrect alignment * Made changes based on Lisa's suggestions * Made changes based on Lisa's suggestions * Made corrections * Made corrections * Per #1667, fixing typos * Per #1667, corrected text --------- Co-authored-by: Julie Prestopnik <jpresto@ucar.edu>

…rder that they appear in the wrapped MET config file

…e used to 1.6.2

…ts often

…id specification string with spaces will be an accepted value

…/xESMF#246

…, CSU/CIRA, and Australian BOM ci-skip-all

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

…files within a time window, ci-run-all-diff

Co-authored-by: j-opatz <59586397+j-opatz@users.noreply.github.com>

…case because changes to the wrapper are needed to fix it after changes to the MET tool were merged

…ions (#2444)

…quests via apk instead of pip because the pip commands began failing -- see PEP668 https://peps.python.org/pep-0668/ -- also changed scripts to create conda environments for use case tests to install all packages in a single call to mamba instead of individual calls

…talled from conda

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

…req (#2439)

* added pics, updated desc * add last two imgs

* adding documentation in different sections * adding grid table section * fixing links * grammar updates * Per #2454, updated sections and wording. * Per #2454, added a period to the end of a sentence. * Per #2454, fixing formatting * Per #2454, updating wording * adding a section for line breaks in a table * adding :code: information * trying to fix warning * take 2 * take 3 or 4 * maybe fixed * updating link * fixing web link again * web link saga continues * Changed "ReadTheDocs" to "Read the Docs" * Updated "main_v" references to be "main_v12.0" * Removed references to main_v*, replacing with raw RST It is not maintainable to have links to branches which will become old. Since we can avoid it by adding the raw RST in the documentation, I have removed all references to main_v* in favor of placing the raw RST in the documentation. * Modified the "Code in a Paragraph" section * Reworded for consistency within the document * Added back the link for Sphinx code blocks --------- Co-authored-by: Julie Prestopnik <jpresto@ucar.edu>

…ed for tests can be easily overridden to test changes in a MET PR before merging

* per dtcenter/MET#2796, update versions of actions to prevent deprecated node warnings in GHA runs * change arguments to workflow dispatch so they are no longer required -- these are not needed to be set when triggering by hand through the web interface

…2475)

…pendabot in PR #2477

… and conda env image

…ge is built on the fly (when PR is coming from fork) then the tag exists, but if not, the image tag is set to <none>

… docker image pruning step

* new docs, files for use case * new files * updating to run use case * updated python libraries, changed test env * trying new point logic * added to script for nan removal * redid Python script to take adv of new MET ability for nans * Update run status * removed unused settings

…if that resolves the disk space issues

…hub.com/apache/flink/blob/master/tools/azure-pipelines/free_disk_space.sh, ci-run-all-cases

* issue #2406 RRFS use case files * issue #2406 added usecase to tests * Issue #2406 added metplotpy and metcalcpy as dependencies

* changed template to use datetime format that works on MacOS * update logic to only write a file list file if there are more than 1 files, updated unit tests to match new behavior, added exception handling to series analysis to prevent crash if file does not exist * use getraw instead of getstr to prevent crash if providing a filename template tag to override a config variable on the command line * Add optional argument to subset file function to always write a file list text file even if there is only 1 file found. Use this argument in UserScript wrapper so that the environment variables that contain paths to file list files are consistent in format for use in user scripts * enhanced function to support different output variable types * removed the need for overriding clear function in specific wrappers and added optional argument to skip clearing input file list * clean up formatting * per #2460, start to implement logic to prevent errors when some input files are not found * isolate logic to find input files into find_input_files functions. clean up those functions to return boolean instead of sometimes returning None or a list of files to be consistent * remove python embedding checks because MET is now smart enough to determine if a python script is used with always setting file_type * turn on use cases to test error handling * merge artifacts * run only failed cases * always run merge step * run on a case that will succeed to test error log merge step * only run error log merge step if there were 'Save error logs' jobs that succeeded * run cases that will fail * fix condition to merge error logs * run group that will succeed but have diffs - check error logs doesn't fail * testing - add use case group that will succeed but will cause diffs becaus there is no truth data - to confirm that the error log merge step behaves properly in this case * run 3 jobs, 2 should error, to confirm that error_logs is created properly * repeat diff no error test but with * per dtcenter/MET#2796, fix error log artifact creation by merging error logs if any of the 'Save error logs' steps ran successfully * run test to confirm diff does not cause merge error logs to fail * Revert "run test to confirm diff does not cause merge error logs to fail" This reverts commit ff2d1ca. * run test to confirm error logs are merged properly when 2 use case groups have errors * try checking output variable as string instead of boolean * Revert "run test to confirm error logs are merged properly when 2 use case groups have errors" This reverts commit 8106666. * run test again * test again * move check for error logs for shell script and use github env vars * Revert "run test again" This reverts commit 7a0a99c. * break 2 use cases to test that error logs are still created properly * checkout repo to get script used to merge error logs * Revert "break 2 use cases to test that error logs are still created properly" This reverts commit cb6d0b4. * test merge error log again on no error diff run * fix script * move merge error logic back to workflow * break 2 use cases to test that error logs are still created properly * Revert "break 2 use cases to test that error logs are still created properly" This reverts commit 82aa0e1. * remove testing use case group * Revert "remove python embedding checks because MET is now smart enough to determine if a python script is used with always setting file_type" This reverts commit de3b4b0. * clean up lines * update logic to check that python embedding is set up properly to only try to set file_type automatically if it is not already set and if the wrapper is a tool that supports multiple input files via python embedding (which require file_type to be set). also changed error if not set properly to warning and use PYTHON_NUMPY as a default * remove run_count increment before run_at_time_once - set closer to find_input_files so run count and missing input count are consistent * return boolean from find_input_files function to be consistent with other functions * per #2460, warn instead of error if missing inputs are allowed, track counters for number of runs and missing inputs * per #2460, added check to report error if allowed missing input threshold is met * run clear before running plot_data_plane * removed test group * report warning instead of error if ALLOW_MISSING_INPUTS is True * cleanup * change function to pytest fixture so it can be used by other test scripts * update ascii2nc test to process more than 1 time to ensure commands are built properly for each run * add unit tests to ensure missing input file logic works properly for ascii2nc and grid_stat * set variable to skip RuntimeFreq logic to find input files to prevent duplicate increment of run_count -- these will be removed when the wrapper has been updated to find files using RuntimeFreq logic * remove unneccesary error checking * cleanup * call function to handle input templates that need to be handled separately for each item in the comma-separated list (for UserScript and GridDiag only) * add time_info to ALL_FILES dictionaries to be consistent with other wrappers * clean up logging for reporting error when missing inputs exceeds threshold * added function to get files for a single run time to be consistent with other functions * skip increment of run_count when FIND_FILES=True and RuntimeFreq input file logic is skipped to prevent duplicate increments * added empty test files * remove redundant variables * view warnings on a failed test run * add more empty test files * added unit tests for missing input logic * remove MANDATORY setting for EnsembleStat and GenEnsProd and instead pass mandatory argument to call to find model files so warnings/errors are properly displayed for other inputs * cleanup * remove allow missing input logic from ExtractTiles wrapper * added functions to parse template/dir variables from config, removed explicit calls to read those variables from GridStat * remove error if more labels than inputs are provided (for UserScript and GridDiag only) -- extra labels will just be ignored * added required boolean for input templates * per #2460, change warning messages to debug when checking a list of DA offsets since it is common that a given offset will not always be found in the files * added tests for missing input logic for many wrappers * cleanup * fix increment of number of runs * skip missing input logic * change how required is handled for input templates * warn instead of error if missing input is allowed * remove increment of missing input counters because it is handled in RuntimeFreq * check status of input files and increment counters in overridden run_once_per_lead. remove increment of missing input counters because it is handled in run_once_per_lead * added unit tests for missing input logic * skip missing input logic * cleanup * cleanup, use fixture for tests, add unit tests for missing input, bypass missing input logic on wrappers that don't need it * removed file that is not needed * added unit tests for pb2nc to test -valid_beg/end arguments and changes to properly support any runtime frequencies * warn instead of error if allowing missing inputs * cleanup * implement changes to properly support all runtime frequencies for pb2nc. previously all files that match a wildcard will be used instead of selecting only files that fall within the specified time range. some functions moved into pb2nc wrapper will eventually be moved up so that they are used by all wrappers to be consistent * added unit tests that will fail until wrapper is updated * replace functions in RuntimeFreq wrapper used to find input files so they can be used by all wrappers, updated ioda2nc wrapper to find input files properly to fix tests * cleanup * removed mtd version of get_input_templates and added logic to RuntimeFreq's version to get the same behavior * added unit tests for MTD missing input checks * per #2491, add release notes for beta3

* update version for beta3 release * fixed typos in release notes

… updating truth data to avoid branch protection rules. I added a step to delete the intermediate branch locally if it exists to prevent conflicts with the update

This reverts commit e7dffb6.

This reverts commit c1cb3c4.

…anch for updating truth data to avoid branch protection rules. I added a step to delete the intermediate branch locally if it exists to prevent conflicts with the update" This reverts commit 525809d.

Feature 1344 stratosphere bias

…w use case category directory if it does not already exist, move step to remove old data to be completed just after new data is copied to vX.Y

…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.

…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

…plate

…ESM_obsFLUXNET2015_TCI.py Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

Feature 2388 update tci

* update version for beta4 release * added release notes for beta4 release

dtcenter/METviewer#525

* update version for release * added new use case that was missing * Bugfix #2279 main_v5.1 - buoy station file from 2022 (#2281) * Fix typo in pull_request_template.md * added notes to make it clear that upgrade instructions are not needed if upgrading from 5.0 to 5.1 * New issue template: Update Truth (#2332) Co-authored-by: John Halley Gotway <johnhg@ucar.edu> (cherry picked from commit 44335f3) * add GitHub Actions workflow that is used to create Docker images that hold the conda environment used for the automated tests -- adding this to the default main_v5.1 branch so that it will become available to run for other branches as a workflow_dispatch workflow * Per #2433, added support for setting the ugrid MET config variables for GridStat and PointStat wrappers. Also moved the seeps variable up so that it matches the order of the default config files in the MET repo * add argument to workflow dispatch event so that MET DockerHub repo used for tests can be easily overridden to test changes in a MET PR before merging * Feature dtcenter/MET#2796 main_v5.1 GHA Node20 deprecation warnings (#2474) * per dtcenter/MET#2796, update versions of actions to prevent deprecated node warnings in GHA runs - main_v5.1 * fix ReadTheDocs requirements to include pillow which is a dependency of sphinx-gallery: see https://blog.readthedocs.com/defaulting-latest-build-tools/ for more info on why this was necessary * install python packages via apk instead of pip to prevent GHA failures that were fixed in develop but not in main_v5.1 * per dtcenter/MET#2796, fix error log merging for main_v5.1 same as develop * Bump pillow from 10.0.1 to 10.2.0 in /docs (#2477) Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.0.1 to 10.2.0. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](python-pillow/Pillow@10.0.1...10.2.0) --- updated-dependencies: - dependency-name: pillow dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Create 5.1.0_casper * per #2433, add support for setting the optional -config argument for a ugrid config file for PointStat and GridStat. Also moved the optional arguments to be added to the command after all of the required arguments so the command is easier to read * per #2433 and discussion on meeting 3/21/2024, change command line argument from -config to -ugrid_config * update unit tests to check for new command line argument name -ugrid_config * Updates information about GDAS surface winds having a QC value that is above the default settings in the PB2NC config file. --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Julie Prestopnik <jpresto@ucar.edu> Co-authored-by: Daniel Adriaansen <dadriaan@ucar.edu>

* run code coverage before SonarQube scan * generate xml report and configure SQ to read coverage.xml * exclude more files from code coverage report * exclude more files that should not be included in the code coverage report * more changes to code coverage exclude list * removed bad characters accidentally added * exclude cyclone plotter wrapper because it is excluded from code coverage report

* Updating MTD conv radius/thresh description * Update glossary.rst * Update docs/Users_Guide/glossary.rst Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Update docs/Users_Guide/glossary.rst Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> --------- Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

* Adding 6.0.0 file for derecho and removing 5.1.0 file for cheyenne * Updating modulefiles * Updating orion file * Adding file for hercules * Adding file for casper * Update internal/scripts/installation/modulefiles/6.0.0_casper Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> --------- Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com>

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

@georgemccabe

* 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

@georgemccabe

* 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

Commits on Aug 9, 2023

Feature #2294 LSR use case (#2295 )

georgemccabe authored Aug 9, 2023

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Feature 2253 tc csv writer (#2373 )

John-Sharples authored Oct 2, 2023

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Update and rename 5.1.0_jet to 6.0.0_jet

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Commits on Oct 11, 2023

Added libssh

jprestop authored Oct 11, 2023

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Commits on Jan 9, 2024

added use cases with pygrib

j-opatz committed Jan 9, 2024

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Fixing spelling and capitalization

jprestop authored Jan 18, 2024

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Setting tests to false for merge

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Testing for old use cases

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Update the beta4 release date wording

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Update develop-ref after dtcenter/MET#2892 #2598

Update develop-ref after dtcenter/MET#2892 #2598

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