Feature #1610 first round of SonarQube fixes #2200

georgemccabe · 2023-06-06T17:18:57Z

Pull Request Testing

Describe testing already performed for these changes:

Ensured all tests pass

Recommend testing for the reviewer(s) to perform, including the location of input datasets, and any additional instructions:

Review code changes, ensure all automated tests pass

Do these changes include sufficient documentation updates, ensuring that no errors or warnings exist in the build of the documentation? [Yes]
Do these changes include sufficient testing updates? [Yes]
Will this PR result in changes to the test suite? [No]

If yes, describe the new output and/or changes to the existing output:
Please complete this pull request review by 6/6/2023.

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… SQ code smell (cognitive complexity)

…on:S3776

… python:S3776

…y for SonarQube

…hen diff cannot be performed, ci-run-all-diff

…-diff

… all tests

…occurred in the diff logic for existing use cases, ci-run-diff

… is NaN values are found in either field, reduce cognitive complexity to satisfy SonarQube

…satisfy SonarQube, ci-run-all-diff

…riables in METplus wrappers to satisfy SonarQube

hankenstein2 · 2023-06-06T19:17:52Z

metplus/util/diff_util.py

Is this file expected to be empty?

I found that message misleading too. The file is not actually empty, but it contains no code changes. I reverted the content of that file back to the original because I wanted to add more tests to ensure it works properly since it is used to find differences in use case output. I had changed the file permissions so it could be run directly so that is why it still shows up in this diff. Sorry, I should have put a note about that!

hankenstein2

This all looks good pending the validation the util/diff_util.py is supposed to be empty vs deleted or actually containing something.

hankenstein2 · 2023-06-06T19:31:31Z

That is very confusing by github. Good that it is expected.

…

On Tue, Jun 6, 2023 at 1:22 PM George McCabe ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ On metplus/util/diff_util.py <#2200 (comment)>: I found that message misleading too. The file is not actually empty, but it contains no code changes. I reverted the content of that file back to the original because I wanted to add more tests to ensure it works properly since it is used to find differences in use case output. I had changed the file permissions so it could be run directly so that is why it still shows up in this diff. Sorry, I should have put a note about that! — Reply to this email directly, view it on GitHub <#2200 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHAUIKG6RNJN6DWQV47JJA3XJ57P5ANCNFSM6AAAAAAY4XCJOM> . You are receiving this because your review was requested.Message ID: ***@***.***>

-- -------------------------------------------------------------- Hank Fisher Research Applications Laboratory 303-497-2817 National Center for Atmospheric Research ***@***.*** P.O. Box 3000, Boulder CO 80307-3000 --------------------------------------------------------------

@georgemccabe

* fixed TCPairs unit tests to handle default value for match_points * bugfix #1691 remove whitespace from output file paths (#1721) * added variables that are needed for use case and were accidentally removed * log error and increment error count if required lat/lon bound variables are not set instad of calling sys.exit * skip metplus_final.conf in check for new output to prevent false alarm diffs * Update index.rst replace METdatadb with METdataio * Update metdatadb.rst Replace metdatadb with metdataio * renamed from metdatadb * replacing all other instances of metdatdb/METdatadb with metdataio/METdataio * after renaming directory from metdatadb to metdataio * replace METdatadb with METdataio * copied and replaced with metdataio filenames * replaced with metdataio version * Update the Release Guide while creating the MET-11.0.0-beta2 development release. Automatic Zenodo updates for each MET release have been DISABLED since they were being created for each development release. Revise the MET instructions to manually update the MET version on Zenodo only for official releases, not development or bugfix releases. * Changed version number * Added release notes * Update the labels scripts by adding 1 new one and renaming metdatadb to metdataio. * updated pandas version used for METdataio use cases to use 1.2.3 instead of 1.4.3 * update version to show development towards beta3 release * Changed METdatadb references to METdataio * Adding modulefiles for installation on various machines. (#1750) * Feature 1746 recreate release (#1751) * Adding instructions for recreating and existing release * Reorder the step's based on suggestions from @georgemccabe * Feature #1489 plot point obs wrapper (#1753) * Fixing typo * Feature #1657 clean up directory creation (#1756) * Feature update labels (#1765) * Modifications for METbaseimage * Update README.md Co-authored-by: johnhg <[email protected]> * feature dtcenter/METplus-Internal#20 add user ID to log output (#1771) * Per dtcenter/METplus-Internal#20, change log output to always include username and include user ID if it is available * Per dtcenter/METplus-Internal#20, fixed bug introduced from commit 458714c to develop where error is thrown if username cannot be obtained, which occurs in environment running GHA tests * Revert "Per dtcenter/METplus-Internal#20, fixed bug introduced from commit 458714c to develop where error is thrown if username cannot be obtained, which occurs in environment running GHA tests" This reverts commit fb2d093. * Revert "Per dtcenter/METplus-Internal#20, change log output to always include username and include user ID if it is available" This reverts commit 458714c. * per dtcenter/METplus-Internal#20, implemented working solution to user info logging * change file path based on change to MODE output from dtcenter/MET#2251 * fix Contributor's Guide GitHub Workflow page (#1774) * Feature dtcenter/METplus-Internal#32 add timestamp to final conf and file_lists (#1763) * Feature dtcenter/METplus-Internal#15 checksum for release (#1769) Co-authored-by: Julie Prestopnik <[email protected]> * Feature dtcenter/METplus-Internal#32 change SCRUB_STAGING_DIR default and add documentation (#1784) * fix to allow wildcard characters in UserScript input templates, ci-run-all-diff * per #1787, allow NA instead of only integers for climo_mean/stdev hour_interval * per #1787, added test for setting NA for climo_mean hour_interval * Updating note format * update Python version to 3.8.6 * Revert "update Python version to 3.8.6" This reverts commit c1e6cbc. * added return value checking to error and exit a non-zero value if docker build or docker push fail * update instructions to find issues for a bugfix release (#1790) * Feature dtcenter/METplus-Internal#34 set the log time to UTC/GMT (#1793) * Feature #1330 MJO ENSO use case (#1794) Co-authored-by: cristianastan2 <[email protected]> * Feature #1816 ensemble vx removal from EnsembleStat (#1820) Co-authored-by: John Halley Gotway <[email protected]> * Feature #1816 rename cases and files (#1823) Co-authored-by: John Halley Gotway <[email protected]> * Move files under internal_tests into internal/tests (#1818) * info for new use case * renamed picture of unrelated use case to properly display * Minor tweak to the release guide instructions for MET development releases. * Feature #1817 5.0.0-beta3 release (#1825) Co-authored-by: bikegeek <[email protected]> * Update VERSION * updated file name * updated MET file locations * explicitly set units for obs read via python embedding since PR dtcenter/MET#2288 no longer guesses units based on grib table units (which can be inaccurate of the actual data) * turn off precip use case group * Feature #1829 set unique ID in config (#1830) * fixed typo in use case setting that causes differences in the test output * Feature #1687 RuntimeFreq read only files needed for given run (#1841) * Feature 1847 release (#1850) * Per #1847, moved release notes to be its own chapter, reformatted component release notes, and added new section for upgrade instructions * Per #1847, added release-notes internal tag * Per #1847, fix error and reformat link * Per #1847, modified release instructions to add a section about upgrade instructions * Per #1847, modified release instructions to add a section about upgrade instructions * Per #1847, resolve doc warnings * Per #1847, updated instructions for clarity. * Per #1847, modified text and link. * Per #1847, modified wording and resolve error with note * Feature #1863 fix GitHub Actions warnings (#1864) * Feature #1874 prevent false diffs (#1875) * Feature 1842 StatAnalysis - multiple issues (#1869) * Bugfix #1884 develop PCPCombine {custom} in subtract method (#1887) * Feature 1852 use case physics tendency (#1881) * Issue #1852 initial work for the Planview plot * Issue #1852 planview plot for physics tendency * issue #1852 cleared away unused/unneccessary code * Issue #1852 update script command * Issue #1852 first draft, doesn't have correct content * Issue #1852 updated name of output plot to include short_range in name * Issue #1852 renamed to include fcstOnly label * Issue #1852 initial commit * Issue #1852 * Issue #1852 * Issue #1852 initial commit * issue #1852 vertical cross section * Issue 1852 clean up unused lines * Issue #1852 initial commit * Issue #1852 * Issue #1852 updates * Issue #1852 fixed documentation warnings, but some problems remain * fixing line length for chapter and section headers and one letter capitalization * cleaning up line spacing and trying to fix a critical error. * trying to fix critical error again * Issue #1852 more description for data and dependency on METplotpy with additional instructions * Issue #1852 update location of input data to single directory * Removing duplicate files with a misformatted name that are not needed * Per #1852, making changes to formatting to eliminate errors * Issue #1852 remove redundant yaml config file * Issue #1852 update PYTHONPATH information * Issue #1852 fixed conflicts * Issue #1852 update path to shapefile * Issue #1852 fixed copy and paste error * Issue #1852 add three use case entries: Planview, VerticalProfile, and VerticalCrossSection for the short range Physics tendency use case * Issue #1852 add latest short range tests to top, move down list when everything passes * Update use_case_groups.json move short_range use cases #10-12 to below the short range test for #9 * Issue #1852 clean up conf files by providing variables for the input netCDF files and for the planview plot, allow user to indicate pressure levels * Issue #1852 Indicate external Python packages * Issue #1852 added external dependency section * removed env vars that don't need to be set -- METPLOTPY_BASE is set by the automated test conf (.github/parm/test_settings.conf) and PYTHONPATH doesn't need to be set because METplotpy is installed in Python environment for use case tests * Update UserScript_fcstFV3_fcstOnly_PhysicsTendency_Planview.py Fixed one typo * Update UserScript_fcstFV3_fcstOnly_PhysicsTendency_VerticalCrossSection.py Fixed a typo * Update UserScript_fcstFV3_fcstOnly_PhysicsTendency_VerticalProfile.py Same typo, same fix * Issue #1852 remove extraneous entry for USER_SCRIPT_COMMAND, a hold-over from the original implementation which doesn't allow the user to easily specify the FV3 history file and grid spec netCDF file * Update UserScript_fcstFV3_fcstOnly_PhysicsTendency_VerticalProfile.conf Removed the incorrect USER_SCRIPT_COMMAND in previous commit. Reinstated the correct version and removed the incorrect command. * update html file from Planview to VerticalProfile Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: Hank Fisher <[email protected]> * Feature #1893 StatAnalysis custom looping (#1894) * Feature dtcenter/METplus-Internal#24 test failure (#1895) * updated version for creating release (#1897) * update release number for development towards beta5 * Adding one sentence to about daily follow up on discussions. * initial changes for new use case * updated paths, documentation * updated automated testing files * Feature #344 rearrange utils (#1900) * first additions for new use case, corrected documentation for old use case * Move Docker scripts to be consistent with other METplus components (#1907) * added picture * Correct spelling mistake * handle if input to format_thresh is already a list * Revert "handle if input to format_thresh is already a list" This reverts commit d329275. * handle if input to format_thresh is already a list * per #1910, added time util function to add field info to time info dictionary and updated wrapper logic to use this function to add this info instead of passing field info (var_info) to CommandBuilder.find_data to get level info, ci-run-all-diff * change logic to preserve full level string for [fcst/obs]_level so SeriesAnalysis cases build the same file names, but parse out time info for setting generic level for string sub to preserve previous behavior * try setting all input values in output dictionary, ci-run-all-diff * removed commented code * add quotes around input files to plot_point_obs command to allow support for Python Embedding as input * put all arguments on single line * remove commented code * per #1910, added unit tests to ensure that level is set properly in the forecast input template * added script to create geovista conda environment via Docker to use in the automated use case tests * Feature 1561 use case ugrid python embedding (#1927) Co-authored-by: George McCabe <[email protected]> * Feature 1453 use case iodav2 python embedding (#1930) Co-authored-by: George McCabe <[email protected]> * fix permissions for script that were somehow changed to be not executable * Bugfix #1939 develop - failure reading obs when zipped file also exists (#1941) * Feature #1819 alert users if updates to EnsembleStat use cases are needed (#1945) Co-authored-by: Dan Adriaansen <[email protected]> * fixed underline that did not match title * Feature #1898 tc new options (#1932) close undefined * fixed broken doc util logic from bad PR merge * Feature #1569 EnsembleStat -ens_mean argument (#1952) * Feature #1953 seeps config in GridStat and PointStat (#1954) Co-authored-by: johnhg <[email protected]> * Feature #1566 update Python version to 3.8.6 (#1958) * Feature #1956 5.0.0-beta4 release (#1963) * Update VERSION * added warning in release notes that location of METplus Dockerfile has changed * combined release notes for all betas for the v5.0.0 release * updated tags for each METplus component to match the upcoming release * Feature #1885 gh_projects (#1973) Co-authored-by: George McCabe <[email protected]> * Switch from double to single quotes. * Update formatting of the GitHub project filters so that they can be copy/pasted directly from RTD into the GitHub project filter. * Feature #1953 PointStat output_flag.seeps and output_flag.seeps_mpr (#1976) * Feature #1711, #1783, #1814, and #1835 Documentation - Multiple files, PCPCombine constant init, Docker instructions, and MET links (#1967) Co-authored-by: Dan Adriaansen <[email protected]> * run diff logic on push for develop and main_v* branches, fix logic to properly run all use cases * fixed name of external * added Bugfix: to default title of new bugfix issue * added space after New Use Case: * changed references to METdatadb to METdataio that were missed * Update overview.rst Removed statsmodels from the table, this package is no longer a requirement. The necessary functionality was pulled out of the statsmodels repository and incorporated into the METcalcpy repository * Update overview.rst METdataio *must* only use pandas 1.2.3. METdataio also requires pyyaml. * Update overview.rst METdatio uses pytest to test aspects of the METreformat module * Update rotate_authorship.rst Explicitly add the step to commit and push changes to the file containing the author list. * Update overview.rst Added METdataio for lxml, numpy, pandas, and pymysql * Update finalize_release_on_github_official.rst added branch protection rules step and the interface to Github was modified, you need to click on the stacked '->' icon to switch default branches * CI: replace / with _ to prevent errors creating docker tags for tests * Update overview.rst included METdataio for python 3.8.6+ requirement * Update overview.rst psutil no longer needed in METplotpy and METcalcpy * Update overview.rst METcalcpy no longer requires imutils and allow versions 0.5.3 and above * Update overview.rst cleaned up formatting for imutils * change asterisk to double asterisk to match branches that include forward slash / * update version of certifi based on dependabot auto-generated PR #1982 * Feature 1819 format doc (#1981) Co-authored-by: George McCabe <[email protected]> * Update use case keywords (#1984) * Feature #1980 Use the main_vX.Y of METplus components for main METplus tests (#1985) * Feature #1986 v5.0.0 release (#1987) Closes #1986 * updated version for development towards beta1 of 5.1.0 * allow rest of workflow to run even if job to update data volumes fails in case server is down * updated version for action to update input data volumes and added max number of DockerHub tag pages to search to 15 * updated release notes for official METplus release to untar the sample data for next version directory * Update release guide to create the input test data directory for official MET releases. * Follow the METplus naming conventions for updating the the DTC web server data. * install library needed for geovista package, remove editable flag so geovista code will be added directly to python instead of reading it from the source code location, ci-skip-all * Feature 685 log updates (#1992) * add script to create conda environment with MetPy 1.4 for SWPC use case * Bugfix develop Fix broken documentation links (#2004) * fixed bug to set environment variables in the RegridDataPlane environment instead of the PyEmbedIngest environment * Feature #2015 modulefiles (#2024) * Adding modulefile for WCOSS2 * Updated references of 4.1.1 to 5.0.0 * Feature #2005 updates to create v5.1 conda environments that use debian10 and Python 3.10.4 (#2043) * update versions to fix bugs for METplotpy/calcpy use cases * Bugfix #2026 develop StatAnalysis looping (#2028) * Feature #2022 update python version to 3.10.4 for repo files (#2047) * Feature #2022 Use Debian 10 / Python 3.10.4 in automated tests (#2050) * add use case group name to output path so that output and error logs will contain use case category to more easily see which case was run * remove -group0 from group names for output path * add manual workflow to update truth data * ci: set gh token on checkout to enable push, ci-skip-all * Set user name/email via git config to allow push * add token to checkout * Feature #2049 Multiple interp.type.method/width (#2051) * added missing argument to script if building envs locally * get main_vX.Y truth data if running on main_vX.Y branch * Updating README.md for label creation and adding bold to common_labels.txt * Updated color for bold label * Feature #2054 consensus.write_members in TCPairs (#2057) * Create LICENSE.md (#2061) * per #2006, fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) * Feature 2065 v5.1.0 beta1 (#2066) * updated version number * added release notes * Update docs/Users_Guide/release-notes.rst Co-authored-by: John Halley Gotway <[email protected]> --------- Co-authored-by: John Halley Gotway <[email protected]> * updated version with -dev * adding sphinx design to 3 files so dropdown menus will work in the release notes. * fix version numbers for python requirements for building documentation * fixed tab vs spaces * Bugfix #2070 var list numeric order (#2072) * Adding files for jet and hera * added commented process list that was accidentally removed -- this is used if the pre-processing steps are needed * Bugfix #2087 develop docs_pdf (#2091) * Feature 2076 release dropdown menu (#2083) * test dropdowns * Update release-notes.rst Attempting to resolve WARNING * testing dropdowns * adding dropdown menus * testing dropdown remove from warning section * dropdown testing * dropdown menu tests * dropdown menus after the warnings section, the dropdown menu only has one space instead of the normal 2 spaces. If it has 2 spaces, it gets sucked into the warning section. * spaces with warning * no spaces for warning * Update release-notes.rst warning note has to be indented 1 space. Originally it was no spaces but then all of the dropdown menus end up in the warning message. If it's 2 spaces, as is normal, then the warning is indented, which is unnecessary. 1 space is slightly indented and keeps the dropdown menus separate. --------- Co-authored-by: jprestop <[email protected]> * Bugfix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) * Feature 1516 use case mvmode (#2094) Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: George McCabe <[email protected]> * Fix for Dockerfile smell DL4000 (#2112) Co-authored-by: Giovanni Rosa <[email protected]> * Changed "PROJECT" to "CYCLE" ASSIGNMENT * Feature 2115 update use cases (#2133) * Bugfix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) * Bugfix #2137 develop PointStat -obs_valid_beg/end (#2141) * Feature #2143 5.1.0-beta2 release (#2144) * update release guide steps with new info based on changes to GitHub web interface * update version for development towards rc1 release * Feature #1977 ARGO use case (#2148) Co-authored-by: j-opatz <[email protected]> * Feature develop cycle change (#2150) * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * Added paths to ignore --------- Co-authored-by: jprestop <[email protected]> * Documentation: Update Truth Data instructions (#2154) * upgrade python to 3.10 for documentation builds to fix failured introduced by urllib3 (see urllib3/urllib3#2168) * update workflow to update input test data to use branch from pull down or enter branch by hand if branch does not exist in dtcenter/METplus repo, e.g. if updating data for a PR coming from a fork * Bugfix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) * changed order of workflow event triggering info to more easily see the repository and commit sha that triggered the workflow * fix docker compose install and call -- needed due to new Alpine Linux release 3.18.0 that does not include docker-compose in the apk repository * Bugfix #2168 develop - StatAnalysis time shift (#2169) * Feature 1978 update pyreq doc (#2177) * Updating for 5.1.0 * Adding greater than or equal to signs * Feature 2106 release support (#2182) * Added a paragraph for Release Support Policy * Added a sentence about contacting the team through the METplus GitHub Discussions Forum. * Added Release Support Policy info * Per #2159, modify instructions to reflect that we only want a coordinated release for the official releases and updates to the coordinated release section for the bugfix releases. (#2183) * Feature 2147 workflow doc (#2185) * Add new images for github workflow * Added PR section * Modified the Find the GitHub Issue to be Find or Create a GitHub issue * Trying out image keyword compared with figure keyword * Trying out various widths * Added new figures * Reverting to figures from images after modifying figures * Adding the old images which are better quality * Trying out new indention * Working on formatting again * Reducing image widths * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update github_workflow.rst --------- Co-authored-by: George McCabe <[email protected]> * added scripts to create new conda environment for PANDA-C use cases * Bugfix #2189 develop - spaces in complex thresholds (#2191) * added release notes for completed issues for rc1 * Feature 2011 tci from cesm fluxnet2015 netcdf (#2192) Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2179 develop TCPairs fix -diag argument (#2187) * sort list of files to make command more readable and make logic more easily testable * fix unit test to expect alphabetical order of files * Feature #2197 MODE new multi-variate options (#2203) * added to release notes * added release notes for other items completed for rc1 release * Feature #1626 TCDiag Wrapper (#2201) * Feature #1610 first round of SonarQube fixes (#2200) * Feature #2195 create v5.1.0-rc1 release (#2204) * Update version for development towards official release * updated script to use metplotpy as base and install pygrib because conda was failing trying to install matplotlib in Docker for some strange reason * Feature 2188 use case panda c (#2202) * added first use case, need to finish docs and add to list * added documentation files, 3 new cases * added 5th use case, docs * final use case, corrected paths for output * Update GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.py * removed chars, added space to last section --------- Co-authored-by: George McCabe <[email protected]> Co-authored-by: bikegeek <[email protected]> Co-authored-by: bikegeek <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: cristianastan2 <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Will Mayfield <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]>

Co-authored-by: johnhg <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: cristianastan2 <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: bikegeek <[email protected]> Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: jprestop <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: bikegeek <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Will Mayfield <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> fix Contributor's Guide GitHub Workflow page (#1774) fix release (#1790) fix GitHub Actions warnings (#1864) fix #1884 develop PCPCombine {custom} in subtract method (#1887) fix #1939 develop - failure reading obs when zipped file also exists (#1941) Closes #1986 fix develop Fix broken documentation links (#2004) fix #2026 develop StatAnalysis looping (#2028) fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) fix #2070 var list numeric order (#2072) fix #2087 develop docs_pdf (#2091) fix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) Fix for Dockerfile smell DL4000 (#2112) fix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) fix #2137 develop PointStat -obs_valid_beg/end (#2141) fix failured introduced by urllib3 (see urllib3/urllib3#2168) fix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) fix #2168 develop - StatAnalysis time shift (#2169) fix releases. (#2183) fix #2189 develop - spaces in complex thresholds (#2191) fix #2179 develop TCPairs fix -diag argument (#2187) fixes (#2200)

Co-authored-by: johnhg <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: cristianastan2 <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: bikegeek <[email protected]> Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: jprestop <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: bikegeek <[email protected]> Co-authored-by: Will Mayfield <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: jason-english <[email protected]> fix Contributor's Guide GitHub Workflow page (#1774) fix release (#1790) fix GitHub Actions warnings (#1864) fix #1884 develop PCPCombine {custom} in subtract method (#1887) fix #1939 develop - failure reading obs when zipped file also exists (#1941) Closes #1986 fix develop Fix broken documentation links (#2004) fix #2026 develop StatAnalysis looping (#2028) fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) fix #2070 var list numeric order (#2072) fix #2087 develop docs_pdf (#2091) fix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) Fix for Dockerfile smell DL4000 (#2112) fix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) fix #2137 develop PointStat -obs_valid_beg/end (#2141) fix failured introduced by urllib3 (see urllib3/urllib3#2168) fix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) fix #2168 develop - StatAnalysis time shift (#2169) fix releases. (#2183) fix #2189 develop - spaces in complex thresholds (#2191) fix #2179 develop TCPairs fix -diag argument (#2187) fixes (#2200) fix diff tests (#2217) fix automated tests (#2237) fix #2235 rename multivar_itensity to multivar_intensity_flag (#2236)

Co-authored-by: johnhg <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: cristianastan2 <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: bikegeek <[email protected]> Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: jprestop <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: bikegeek <[email protected]> Co-authored-by: Will Mayfield <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: jason-english <[email protected]> fix Contributor's Guide GitHub Workflow page (#1774) fix release (#1790) fix GitHub Actions warnings (#1864) fix #1884 develop PCPCombine {custom} in subtract method (#1887) fix #1939 develop - failure reading obs when zipped file also exists (#1941) Closes #1986 fix develop Fix broken documentation links (#2004) fix #2026 develop StatAnalysis looping (#2028) fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) fix #2070 var list numeric order (#2072) fix #2087 develop docs_pdf (#2091) fix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) Fix for Dockerfile smell DL4000 (#2112) fix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) fix #2137 develop PointStat -obs_valid_beg/end (#2141) fix failured introduced by urllib3 (see urllib3/urllib3#2168) fix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) fix #2168 develop - StatAnalysis time shift (#2169) fix releases. (#2183) fix #2189 develop - spaces in complex thresholds (#2191) fix #2179 develop TCPairs fix -diag argument (#2187) fixes (#2200) fix diff tests (#2217) fix automated tests (#2237) fix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) fix #2241 Create directory containing -out_stat file (#2242) fix #2245 use unique run ID to name logger instance (#2247) fix #2244 develop fix diff tests (#2254)

Co-authored-by: cristianastan2 <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: bikegeek <[email protected]> Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: johnhg <[email protected]> Co-authored-by: jprestop <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: root <root@localhost> Co-authored-by: bikegeek <[email protected]> Co-authored-by: Will Mayfield <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: John Sharples <[email protected]> fix release (#1790) fix GitHub Actions warnings (#1864) fix #1884 develop PCPCombine {custom} in subtract method (#1887) fix #1939 develop - failure reading obs when zipped file also exists (#1941) Closes #1986 fix develop Fix broken documentation links (#2004) fix #2026 develop StatAnalysis looping (#2028) fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) fix #2070 var list numeric order (#2072) fix #2087 develop docs_pdf (#2091) fix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) Fix for Dockerfile smell DL4000 (#2112) fix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) fix #2137 develop PointStat -obs_valid_beg/end (#2141) fix failured introduced by urllib3 (see urllib3/urllib3#2168) fix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) fix #2168 develop - StatAnalysis time shift (#2169) fix releases. (#2183) fix #2189 develop - spaces in complex thresholds (#2191) fix #2179 develop TCPairs fix -diag argument (#2187) fixes (#2200) fix diff tests (#2217) fix automated tests (#2237) fix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) fix #2241 Create directory containing -out_stat file (#2242) fix #2245 use unique run ID to name logger instance (#2247) fix #2244 develop fix diff tests (#2254) fixture to set pytest tmpdir (#2261) fix #1853 develop - PointStat don't require mask variables to be set (#2262) fix #2279 develop - buoy station file from 2022 (#2280)

Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: johnhg <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: jprestop <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: root <root@localhost> Co-authored-by: bikegeek <[email protected]> Co-authored-by: Will Mayfield <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: John Sharples <[email protected]> fix GitHub Actions warnings (#1864) fix #1884 develop PCPCombine {custom} in subtract method (#1887) fix #1939 develop - failure reading obs when zipped file also exists (#1941) Closes #1986 fix develop Fix broken documentation links (#2004) fix #2026 develop StatAnalysis looping (#2028) fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) fix #2070 var list numeric order (#2072) fix #2087 develop docs_pdf (#2091) fix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) Fix for Dockerfile smell DL4000 (#2112) fix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) fix #2137 develop PointStat -obs_valid_beg/end (#2141) fix failured introduced by urllib3 (see urllib3/urllib3#2168) fix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) fix #2168 develop - StatAnalysis time shift (#2169) fix releases. (#2183) fix #2189 develop - spaces in complex thresholds (#2191) fix #2179 develop TCPairs fix -diag argument (#2187) fixes (#2200) fix diff tests (#2217) fix automated tests (#2237) fix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) fix #2241 Create directory containing -out_stat file (#2242) fix #2245 use unique run ID to name logger instance (#2247) fix #2244 develop fix diff tests (#2254) fixture to set pytest tmpdir (#2261) fix #1853 develop - PointStat don't require mask variables to be set (#2262) fix #2279 develop - buoy station file from 2022 (#2280)

Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: johnhg <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: jprestop <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: root <root@localhost> Co-authored-by: bikegeek <[email protected]> Co-authored-by: Will Mayfield <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: John Sharples <[email protected]> fix GitHub Actions warnings (#1864) fix #1884 develop PCPCombine {custom} in subtract method (#1887) fix #1939 develop - failure reading obs when zipped file also exists (#1941) Closes #1986 fix develop Fix broken documentation links (#2004) fix #2026 develop StatAnalysis looping (#2028) fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) fix #2070 var list numeric order (#2072) fix #2087 develop docs_pdf (#2091) fix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) Fix for Dockerfile smell DL4000 (#2112) fix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) fix #2137 develop PointStat -obs_valid_beg/end (#2141) fix failured introduced by urllib3 (see urllib3/urllib3#2168) fix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) fix #2168 develop - StatAnalysis time shift (#2169) fix releases. (#2183) fix #2189 develop - spaces in complex thresholds (#2191) fix #2179 develop TCPairs fix -diag argument (#2187) fixes (#2200) fix diff tests (#2217) fix automated tests (#2237) fix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) fix #2241 Create directory containing -out_stat file (#2242) fix #2245 use unique run ID to name logger instance (#2247) fix #2244 develop fix diff tests (#2254) fixture to set pytest tmpdir (#2261) fix #1853 develop - PointStat don't require mask variables to be set (#2262) fix #2279 develop - buoy station file from 2022 (#2280) fix (#2313)

Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: johnhg <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: jprestop <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: root <root@localhost> Co-authored-by: bikegeek <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: Will Mayfield <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: John Sharples <[email protected]> fix #1884 develop PCPCombine {custom} in subtract method (#1887) fix #1939 develop - failure reading obs when zipped file also exists (#1941) Closes #1986 fix develop Fix broken documentation links (#2004) fix #2026 develop StatAnalysis looping (#2028) fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) fix #2070 var list numeric order (#2072) fix #2087 develop docs_pdf (#2091) fix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) Fix for Dockerfile smell DL4000 (#2112) fix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) fix #2137 develop PointStat -obs_valid_beg/end (#2141) fix failured introduced by urllib3 (see urllib3/urllib3#2168) fix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) fix #2168 develop - StatAnalysis time shift (#2169) fix releases. (#2183) fix #2189 develop - spaces in complex thresholds (#2191) fix #2179 develop TCPairs fix -diag argument (#2187) fixes (#2200) fix diff tests (#2217) fix automated tests (#2237) fix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) fix #2241 Create directory containing -out_stat file (#2242) fix #2245 use unique run ID to name logger instance (#2247) fix #2244 develop fix diff tests (#2254) fixture to set pytest tmpdir (#2261) fix #1853 develop - PointStat don't require mask variables to be set (#2262) fix #2279 develop - buoy station file from 2022 (#2280) fix (#2313)

* Feature dtcenter/METplus-Internal#24 test failure (#1895) * updated version for creating release (#1897) * update release number for development towards beta5 * Adding one sentence to about daily follow up on discussions. * initial changes for new use case * updated paths, documentation * updated automated testing files * Feature #344 rearrange utils (#1900) * first additions for new use case, corrected documentation for old use case * Move Docker scripts to be consistent with other METplus components (#1907) * added picture * Correct spelling mistake * handle if input to format_thresh is already a list * Revert "handle if input to format_thresh is already a list" This reverts commit d329275. * handle if input to format_thresh is already a list * per #1910, added time util function to add field info to time info dictionary and updated wrapper logic to use this function to add this info instead of passing field info (var_info) to CommandBuilder.find_data to get level info, ci-run-all-diff * change logic to preserve full level string for [fcst/obs]_level so SeriesAnalysis cases build the same file names, but parse out time info for setting generic level for string sub to preserve previous behavior * try setting all input values in output dictionary, ci-run-all-diff * removed commented code * add quotes around input files to plot_point_obs command to allow support for Python Embedding as input * put all arguments on single line * remove commented code * per #1910, added unit tests to ensure that level is set properly in the forecast input template * added script to create geovista conda environment via Docker to use in the automated use case tests * Feature 1561 use case ugrid python embedding (#1927) Co-authored-by: George McCabe <[email protected]> * Feature 1453 use case iodav2 python embedding (#1930) Co-authored-by: George McCabe <[email protected]> * fix permissions for script that were somehow changed to be not executable * Bugfix #1939 develop - failure reading obs when zipped file also exists (#1941) * Feature #1819 alert users if updates to EnsembleStat use cases are needed (#1945) Co-authored-by: Dan Adriaansen <[email protected]> * fixed underline that did not match title * Feature #1898 tc new options (#1932) close undefined * fixed broken doc util logic from bad PR merge * Feature #1569 EnsembleStat -ens_mean argument (#1952) * Feature #1953 seeps config in GridStat and PointStat (#1954) Co-authored-by: johnhg <[email protected]> * Feature #1566 update Python version to 3.8.6 (#1958) * Feature #1956 5.0.0-beta4 release (#1963) * Update VERSION * added warning in release notes that location of METplus Dockerfile has changed * combined release notes for all betas for the v5.0.0 release * updated tags for each METplus component to match the upcoming release * Feature #1885 gh_projects (#1973) Co-authored-by: George McCabe <[email protected]> * Switch from double to single quotes. * Update formatting of the GitHub project filters so that they can be copy/pasted directly from RTD into the GitHub project filter. * Feature #1953 PointStat output_flag.seeps and output_flag.seeps_mpr (#1976) * Feature #1711, #1783, #1814, and #1835 Documentation - Multiple files, PCPCombine constant init, Docker instructions, and MET links (#1967) Co-authored-by: Dan Adriaansen <[email protected]> * run diff logic on push for develop and main_v* branches, fix logic to properly run all use cases * fixed name of external * added Bugfix: to default title of new bugfix issue * added space after New Use Case: * changed references to METdatadb to METdataio that were missed * Update overview.rst Removed statsmodels from the table, this package is no longer a requirement. The necessary functionality was pulled out of the statsmodels repository and incorporated into the METcalcpy repository * Update overview.rst METdataio *must* only use pandas 1.2.3. METdataio also requires pyyaml. * Update overview.rst METdatio uses pytest to test aspects of the METreformat module * Update rotate_authorship.rst Explicitly add the step to commit and push changes to the file containing the author list. * Update overview.rst Added METdataio for lxml, numpy, pandas, and pymysql * Update finalize_release_on_github_official.rst added branch protection rules step and the interface to Github was modified, you need to click on the stacked '->' icon to switch default branches * CI: replace / with _ to prevent errors creating docker tags for tests * Update overview.rst included METdataio for python 3.8.6+ requirement * Update overview.rst psutil no longer needed in METplotpy and METcalcpy * Update overview.rst METcalcpy no longer requires imutils and allow versions 0.5.3 and above * Update overview.rst cleaned up formatting for imutils * change asterisk to double asterisk to match branches that include forward slash / * update version of certifi based on dependabot auto-generated PR #1982 * Feature 1819 format doc (#1981) Co-authored-by: George McCabe <[email protected]> * Update use case keywords (#1984) * Feature #1980 Use the main_vX.Y of METplus components for main METplus tests (#1985) * Feature #1986 v5.0.0 release (#1987) Closes #1986 * updated version for development towards beta1 of 5.1.0 * allow rest of workflow to run even if job to update data volumes fails in case server is down * updated version for action to update input data volumes and added max number of DockerHub tag pages to search to 15 * updated release notes for official METplus release to untar the sample data for next version directory * Update release guide to create the input test data directory for official MET releases. * Follow the METplus naming conventions for updating the the DTC web server data. * install library needed for geovista package, remove editable flag so geovista code will be added directly to python instead of reading it from the source code location, ci-skip-all * Feature 685 log updates (#1992) * add script to create conda environment with MetPy 1.4 for SWPC use case * Bugfix develop Fix broken documentation links (#2004) * fixed bug to set environment variables in the RegridDataPlane environment instead of the PyEmbedIngest environment * Feature #2015 modulefiles (#2024) * Adding modulefile for WCOSS2 * Updated references of 4.1.1 to 5.0.0 * Feature #2005 updates to create v5.1 conda environments that use debian10 and Python 3.10.4 (#2043) * update versions to fix bugs for METplotpy/calcpy use cases * Bugfix #2026 develop StatAnalysis looping (#2028) * Feature #2022 update python version to 3.10.4 for repo files (#2047) * Feature #2022 Use Debian 10 / Python 3.10.4 in automated tests (#2050) * add use case group name to output path so that output and error logs will contain use case category to more easily see which case was run * remove -group0 from group names for output path * add manual workflow to update truth data * ci: set gh token on checkout to enable push, ci-skip-all * Set user name/email via git config to allow push * add token to checkout * Feature #2049 Multiple interp.type.method/width (#2051) * added missing argument to script if building envs locally * get main_vX.Y truth data if running on main_vX.Y branch * Updating README.md for label creation and adding bold to common_labels.txt * Updated color for bold label * Feature #2054 consensus.write_members in TCPairs (#2057) * Create LICENSE.md (#2061) * per #2006, fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) * Feature 2065 v5.1.0 beta1 (#2066) * updated version number * added release notes * Update docs/Users_Guide/release-notes.rst Co-authored-by: John Halley Gotway <[email protected]> --------- Co-authored-by: John Halley Gotway <[email protected]> * updated version with -dev * adding sphinx design to 3 files so dropdown menus will work in the release notes. * fix version numbers for python requirements for building documentation * fixed tab vs spaces * Bugfix #2070 var list numeric order (#2072) * Adding files for jet and hera * added commented process list that was accidentally removed -- this is used if the pre-processing steps are needed * Bugfix #2087 develop docs_pdf (#2091) * Feature 2076 release dropdown menu (#2083) * test dropdowns * Update release-notes.rst Attempting to resolve WARNING * testing dropdowns * adding dropdown menus * testing dropdown remove from warning section * dropdown testing * dropdown menu tests * dropdown menus after the warnings section, the dropdown menu only has one space instead of the normal 2 spaces. If it has 2 spaces, it gets sucked into the warning section. * spaces with warning * no spaces for warning * Update release-notes.rst warning note has to be indented 1 space. Originally it was no spaces but then all of the dropdown menus end up in the warning message. If it's 2 spaces, as is normal, then the warning is indented, which is unnecessary. 1 space is slightly indented and keeps the dropdown menus separate. --------- Co-authored-by: jprestop <[email protected]> * Bugfix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) * Feature 1516 use case mvmode (#2094) Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: George McCabe <[email protected]> * Fix for Dockerfile smell DL4000 (#2112) Co-authored-by: Giovanni Rosa <[email protected]> * Changed "PROJECT" to "CYCLE" ASSIGNMENT * Feature 2115 update use cases (#2133) * Bugfix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) * Bugfix #2137 develop PointStat -obs_valid_beg/end (#2141) * Feature #2143 5.1.0-beta2 release (#2144) * update release guide steps with new info based on changes to GitHub web interface * update version for development towards rc1 release * Feature #1977 ARGO use case (#2148) Co-authored-by: j-opatz <[email protected]> * Feature develop cycle change (#2150) * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * Added paths to ignore --------- Co-authored-by: jprestop <[email protected]> * Documentation: Update Truth Data instructions (#2154) * upgrade python to 3.10 for documentation builds to fix failured introduced by urllib3 (see urllib3/urllib3#2168) * update workflow to update input test data to use branch from pull down or enter branch by hand if branch does not exist in dtcenter/METplus repo, e.g. if updating data for a PR coming from a fork * Bugfix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) * changed order of workflow event triggering info to more easily see the repository and commit sha that triggered the workflow * fix docker compose install and call -- needed due to new Alpine Linux release 3.18.0 that does not include docker-compose in the apk repository * Bugfix #2168 develop - StatAnalysis time shift (#2169) * Feature 1978 update pyreq doc (#2177) * Updating for 5.1.0 * Adding greater than or equal to signs * Feature 2106 release support (#2182) * Added a paragraph for Release Support Policy * Added a sentence about contacting the team through the METplus GitHub Discussions Forum. * Added Release Support Policy info * Per #2159, modify instructions to reflect that we only want a coordinated release for the official releases and updates to the coordinated release section for the bugfix releases. (#2183) * Feature 2147 workflow doc (#2185) * Add new images for github workflow * Added PR section * Modified the Find the GitHub Issue to be Find or Create a GitHub issue * Trying out image keyword compared with figure keyword * Trying out various widths * Added new figures * Reverting to figures from images after modifying figures * Adding the old images which are better quality * Trying out new indention * Working on formatting again * Reducing image widths * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update github_workflow.rst --------- Co-authored-by: George McCabe <[email protected]> * added scripts to create new conda environment for PANDA-C use cases * Bugfix #2189 develop - spaces in complex thresholds (#2191) * added release notes for completed issues for rc1 * Feature 2011 tci from cesm fluxnet2015 netcdf (#2192) Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2179 develop TCPairs fix -diag argument (#2187) * sort list of files to make command more readable and make logic more easily testable * fix unit test to expect alphabetical order of files * Feature #2197 MODE new multi-variate options (#2203) * added to release notes * added release notes for other items completed for rc1 release * Feature #1626 TCDiag Wrapper (#2201) * Feature #1610 first round of SonarQube fixes (#2200) * Feature #2195 create v5.1.0-rc1 release (#2204) * Update version for development towards official release * updated script to use metplotpy as base and install pygrib because conda was failing trying to install matplotlib in Docker for some strange reason * Feature 2188 use case panda c (#2202) * added first use case, need to finish docs and add to list * added documentation files, 3 new cases * added 5th use case, docs * final use case, corrected paths for output * Update GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.py * removed chars, added space to last section * turn off 5/6 new air quality and comp use cases because they are causing the disk to fill up in the automated tests and only 1 is needed to test the new behavior. Reordered use case groups to be alphabetical * disabled other new air quality use case because the disk is still filling up from this case * Feature 2136 cross spectra (#2208) * per #2212, continue instead of return so other forecast leads will not be skipped * Feature #2210 MODE multi-variate variable rename (#2211) * Bugfix diff tests (#2217) * added change from NCEP produtil that was somehow not included in the changes pulled from their repo before starting SonarQube work * Feature #2228 v5.1.0-rc2 release (#2229) * update version after rc2 release to note development towards official 5.1.0 release * Feature #2188 move PANDA-C cases to clouds category and fix automated tests (#2237) Co-authored-by: j-opatz <[email protected]> * Feature 2198 use case amdar pbl (#2206) Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) * Feature #2230 MvMODE usecase doc updates (#2239) This updates the use-case documentation to go along with the multivariate MODE enhancements. * combine release notes from development releases for 5.1.0 release * fix indentation to prevent incorrect nesting of drop down menus * Bugfix #2241 Create directory containing -out_stat file (#2242) * Enhance diff logic to control decimal precision to prevent failures (#2243) * Bugfix #2245 use unique run ID to name logger instance (#2247) * per #2245, add METplusConfig class function that is called when object is deleted to close log handlers. This prevents OSError: [Errno 24] Too many open files from running all pytests * Feature #1626 TCDiag updates to wrapper and basic use case (#2248) Co-authored-by: Jonathan Vigh <[email protected]> * move new use case into another group * Bugfix #2244 develop fix diff tests (#2254) * skip diff for specific png images that produce diffs occasionally but look the same visually * add 2 more keywords for use cases that occasionally flag small, unnoticeable diffs in png images * Feature #2253 update tests for diff_util (#2256) Co-authored-by: root <root@localhost> * Feature #1974 Documentation: update coding standards section (#2260) * Feature #2253 conftest fixture to set pytest tmpdir (#2261) * Feature #2151 Documentation: Add quick search keywords METplotpy/calcpy use cases (#2259) * Feature #2138 CI enhance MET Docker tag override (#2258) * Updating development instructions. * fixed typo * fixed another typo * Feature #2207 Documentation - Updates to Contributor's Guide (#2263) Co-authored-by: Dan Adriaansen <[email protected]> * Feature develop update install files (#2266) * 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 * Bugfix #1853 develop - PointStat don't require mask variables to be set (#2262) * update version of certifi to match auto-generated dependabot PR #2267 * feature #2253 more tests for diff_util.py (#2264) * update versions of METplus components for the next official release * updated release notes for 5.1.0 release * removed duplicate entries in release notes * Added EC2 instance recipee with S3 mounting ability (#2269) * Updating the Subsetting Tests by Marker section (#2272) * update release date for 5.1.0 release (#2276) * update version for development towards 6.0.0-beta1 release * added new use case that was missing * Bugfix #2279 develop - buoy station file from 2022 (#2280) * Feature 2253 series analysis tests (#2277) * Fix typo in pull_request_template.md * Make code coverage report available (#2287) * Use updated dtcenter/metplus-action-data-update tag that fixes bug that 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 * removed climatology keyword from use cases that aren't relevant that were accidentally added with PR #1984 * update readme with current information * Feature #2282 coord_release_docs (#2288) Co-authored-by: George McCabe <[email protected]> * continue workflow if coveralls step fails -- this typically happens on a pull request from a fork because the authentication fails * Feature 2253 system util tests (#2297) * Feature #2294 LSR use case (#2295) * Feature 2253 run util tests (#2307) * Release Guide - remove beta/rc tags/releases (#2309) * Add 'component: repository maintenance' label. Already ran the script to push this change and the NOAA OAR reporting label to all the METplus repos. * Hotfix for labels, adding a new one for 'component: input data' and also fixing the get_lablels.sh to search for up to 200 existing labels. Also work on the log messages. * Fix typo in comment * Feature #2283 time looping consolidation (#2311) Co-authored-by: John Halley Gotway <[email protected]> * New issue template: Update Truth (#2332) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for run_util, 'Usage' bugfix (#2313) * Feature #2338 Debian 12 Conda environments (#2341) Co-authored-by: John Halley Gotway <[email protected]> * Feature 1488 usecase satwinds (#2324) Co-authored-by: George McCabe <[email protected]> * Feature #2283 include times (#2345) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for config_validate, mock logger in conftest (#2320) * Feature #2299 / #2310 Remove deprecated MET config env vars and TCMPRPlotter (#2347) Co-authored-by: John Halley Gotway <[email protected]> * remove MODEL and OBTYPE to use defaults from MET config * Feature #2348 v6.0.0-beta1 release (#2351) * update version for development towards 6.0.0-beta2 release * copy libGL and libEGL files into docker image to prevent errors with geovista python package * run use that uses geovista to test --------- Co-authored-by: George McCabe <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: Will Mayfield <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: johnhg <[email protected]> Co-authored-by: bikegeek <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: John Sharples <[email protected]> Co-authored-by: root <root@localhost>

Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: johnhg <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: jprestop <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: root <root@localhost> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: Tracy <[email protected]> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: bikegeek <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: John Sharples <[email protected]> Co-authored-by: reza-armuei <[email protected]> fix #1939 develop - failure reading obs when zipped file also exists (#1941) Closes #1986 fix develop Fix broken documentation links (#2004) fix #2026 develop StatAnalysis looping (#2028) fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) fix #2070 var list numeric order (#2072) fix #2087 develop docs_pdf (#2091) fix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) Fix for Dockerfile smell DL4000 (#2112) fix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) fix #2137 develop PointStat -obs_valid_beg/end (#2141) fix failured introduced by urllib3 (see urllib3/urllib3#2168) fix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) fix #2168 develop - StatAnalysis time shift (#2169) fix releases. (#2183) fix #2189 develop - spaces in complex thresholds (#2191) fix #2179 develop TCPairs fix -diag argument (#2187) fixes (#2200) fix diff tests (#2217) fix automated tests (#2237) fix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) fix #2241 Create directory containing -out_stat file (#2242) fix #2245 use unique run ID to name logger instance (#2247) fix #2244 develop fix diff tests (#2254) fixture to set pytest tmpdir (#2261) fix #1853 develop - PointStat don't require mask variables to be set (#2262) fix #2279 develop - buoy station file from 2022 (#2280) fix (#2313) 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

Co-authored-by: johnhg <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: jprestop <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: root <root@localhost> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: Tracy <[email protected]> Co-authored-by: bikegeek <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: John Sharples <[email protected]> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: reza-armuei <[email protected]> Closes #1986 fix develop Fix broken documentation links (#2004) fix #2026 develop StatAnalysis looping (#2028) fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) fix #2070 var list numeric order (#2072) fix #2087 develop docs_pdf (#2091) fix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) Fix for Dockerfile smell DL4000 (#2112) fix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) fix #2137 develop PointStat -obs_valid_beg/end (#2141) fix failured introduced by urllib3 (see urllib3/urllib3#2168) fix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) fix #2168 develop - StatAnalysis time shift (#2169) fix releases. (#2183) fix #2189 develop - spaces in complex thresholds (#2191) fix #2179 develop TCPairs fix -diag argument (#2187) fixes (#2200) fix diff tests (#2217) fix automated tests (#2237) fix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) fix #2241 Create directory containing -out_stat file (#2242) fix #2245 use unique run ID to name logger instance (#2247) fix #2244 develop fix diff tests (#2254) fixture to set pytest tmpdir (#2261) fix #1853 develop - PointStat don't require mask variables to be set (#2262) fix #2279 develop - buoy station file from 2022 (#2280) fix (#2313) 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 fix bug described in pangeo-data/xESMF#246

Co-authored-by: George McCabe <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: jprestop <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: root <root@localhost> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: Tracy <[email protected]> Co-authored-by: johnhg <[email protected]> Co-authored-by: bikegeek <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: John Sharples <[email protected]> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: reza-armuei <[email protected]> Closes #1986 fix develop Fix broken documentation links (#2004) fix #2026 develop StatAnalysis looping (#2028) fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) fix #2070 var list numeric order (#2072) fix #2087 develop docs_pdf (#2091) fix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) Fix for Dockerfile smell DL4000 (#2112) fix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) fix #2137 develop PointStat -obs_valid_beg/end (#2141) fix failured introduced by urllib3 (see urllib3/urllib3#2168) fix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) fix #2168 develop - StatAnalysis time shift (#2169) fix releases. (#2183) fix #2189 develop - spaces in complex thresholds (#2191) fix #2179 develop TCPairs fix -diag argument (#2187) fixes (#2200) fix diff tests (#2217) fix automated tests (#2237) fix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) fix #2241 Create directory containing -out_stat file (#2242) fix #2245 use unique run ID to name logger instance (#2247) fix #2244 develop fix diff tests (#2254) fixture to set pytest tmpdir (#2261) fix #1853 develop - PointStat don't require mask variables to be set (#2262) fix #2279 develop - buoy station file from 2022 (#2280) fix (#2313) 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 fix bug described in pangeo-data/xESMF#246

Co-authored-by: George McCabe <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: jprestop <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: root <root@localhost> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: Tracy <[email protected]> Co-authored-by: bikegeek <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: John Sharples <[email protected]> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: reza-armuei <[email protected]> Co-authored-by: Mallory Row <[email protected]> Closes #1986 fix develop Fix broken documentation links (#2004) fix #2026 develop StatAnalysis looping (#2028) fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) fix #2070 var list numeric order (#2072) fix #2087 develop docs_pdf (#2091) fix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) Fix for Dockerfile smell DL4000 (#2112) fix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) fix #2137 develop PointStat -obs_valid_beg/end (#2141) fix failured introduced by urllib3 (see urllib3/urllib3#2168) fix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) fix #2168 develop - StatAnalysis time shift (#2169) fix releases. (#2183) fix #2189 develop - spaces in complex thresholds (#2191) fix #2179 develop TCPairs fix -diag argument (#2187) fixes (#2200) fix diff tests (#2217) fix automated tests (#2237) fix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) fix #2241 Create directory containing -out_stat file (#2242) fix #2245 use unique run ID to name logger instance (#2247) fix #2244 develop fix diff tests (#2254) fixture to set pytest tmpdir (#2261) fix #1853 develop - PointStat don't require mask variables to be set (#2262) fix #2279 develop - buoy station file from 2022 (#2280) fix (#2313) 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 fix bug described in pangeo-data/xESMF#246 fix failing use case tests -- install python packages dateutil and requests 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

* Update release guide to create the input test data directory for official MET releases. * Follow the METplus naming conventions for updating the the DTC web server data. * install library needed for geovista package, remove editable flag so geovista code will be added directly to python instead of reading it from the source code location, ci-skip-all * Feature 685 log updates (#1992) * add script to create conda environment with MetPy 1.4 for SWPC use case * Bugfix develop Fix broken documentation links (#2004) * fixed bug to set environment variables in the RegridDataPlane environment instead of the PyEmbedIngest environment * Feature #2015 modulefiles (#2024) * Adding modulefile for WCOSS2 * Updated references of 4.1.1 to 5.0.0 * Feature #2005 updates to create v5.1 conda environments that use debian10 and Python 3.10.4 (#2043) * update versions to fix bugs for METplotpy/calcpy use cases * Bugfix #2026 develop StatAnalysis looping (#2028) * Feature #2022 update python version to 3.10.4 for repo files (#2047) * Feature #2022 Use Debian 10 / Python 3.10.4 in automated tests (#2050) * add use case group name to output path so that output and error logs will contain use case category to more easily see which case was run * remove -group0 from group names for output path * add manual workflow to update truth data * ci: set gh token on checkout to enable push, ci-skip-all * Set user name/email via git config to allow push * add token to checkout * Feature #2049 Multiple interp.type.method/width (#2051) * added missing argument to script if building envs locally * get main_vX.Y truth data if running on main_vX.Y branch * Updating README.md for label creation and adding bold to common_labels.txt * Updated color for bold label * Feature #2054 consensus.write_members in TCPairs (#2057) * Create LICENSE.md (#2061) * per #2006, fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) * Feature 2065 v5.1.0 beta1 (#2066) * updated version number * added release notes * Update docs/Users_Guide/release-notes.rst Co-authored-by: John Halley Gotway <[email protected]> --------- Co-authored-by: John Halley Gotway <[email protected]> * updated version with -dev * adding sphinx design to 3 files so dropdown menus will work in the release notes. * fix version numbers for python requirements for building documentation * fixed tab vs spaces * Bugfix #2070 var list numeric order (#2072) * Adding files for jet and hera * added commented process list that was accidentally removed -- this is used if the pre-processing steps are needed * Bugfix #2087 develop docs_pdf (#2091) * Feature 2076 release dropdown menu (#2083) * test dropdowns * Update release-notes.rst Attempting to resolve WARNING * testing dropdowns * adding dropdown menus * testing dropdown remove from warning section * dropdown testing * dropdown menu tests * dropdown menus after the warnings section, the dropdown menu only has one space instead of the normal 2 spaces. If it has 2 spaces, it gets sucked into the warning section. * spaces with warning * no spaces for warning * Update release-notes.rst warning note has to be indented 1 space. Originally it was no spaces but then all of the dropdown menus end up in the warning message. If it's 2 spaces, as is normal, then the warning is indented, which is unnecessary. 1 space is slightly indented and keeps the dropdown menus separate. --------- Co-authored-by: jprestop <[email protected]> * Bugfix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) * Feature 1516 use case mvmode (#2094) Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: George McCabe <[email protected]> * Fix for Dockerfile smell DL4000 (#2112) Co-authored-by: Giovanni Rosa <[email protected]> * Changed "PROJECT" to "CYCLE" ASSIGNMENT * Feature 2115 update use cases (#2133) * Bugfix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) * Bugfix #2137 develop PointStat -obs_valid_beg/end (#2141) * Feature #2143 5.1.0-beta2 release (#2144) * update release guide steps with new info based on changes to GitHub web interface * update version for development towards rc1 release * Feature #1977 ARGO use case (#2148) Co-authored-by: j-opatz <[email protected]> * Feature develop cycle change (#2150) * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * Added paths to ignore --------- Co-authored-by: jprestop <[email protected]> * Documentation: Update Truth Data instructions (#2154) * upgrade python to 3.10 for documentation builds to fix failured introduced by urllib3 (see urllib3/urllib3#2168) * update workflow to update input test data to use branch from pull down or enter branch by hand if branch does not exist in dtcenter/METplus repo, e.g. if updating data for a PR coming from a fork * Bugfix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) * changed order of workflow event triggering info to more easily see the repository and commit sha that triggered the workflow * fix docker compose install and call -- needed due to new Alpine Linux release 3.18.0 that does not include docker-compose in the apk repository * Bugfix #2168 develop - StatAnalysis time shift (#2169) * Feature 1978 update pyreq doc (#2177) * Updating for 5.1.0 * Adding greater than or equal to signs * Feature 2106 release support (#2182) * Added a paragraph for Release Support Policy * Added a sentence about contacting the team through the METplus GitHub Discussions Forum. * Added Release Support Policy info * Per #2159, modify instructions to reflect that we only want a coordinated release for the official releases and updates to the coordinated release section for the bugfix releases. (#2183) * Feature 2147 workflow doc (#2185) * Add new images for github workflow * Added PR section * Modified the Find the GitHub Issue to be Find or Create a GitHub issue * Trying out image keyword compared with figure keyword * Trying out various widths * Added new figures * Reverting to figures from images after modifying figures * Adding the old images which are better quality * Trying out new indention * Working on formatting again * Reducing image widths * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update github_workflow.rst --------- Co-authored-by: George McCabe <[email protected]> * added scripts to create new conda environment for PANDA-C use cases * Bugfix #2189 develop - spaces in complex thresholds (#2191) * added release notes for completed issues for rc1 * Feature 2011 tci from cesm fluxnet2015 netcdf (#2192) Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2179 develop TCPairs fix -diag argument (#2187) * sort list of files to make command more readable and make logic more easily testable * fix unit test to expect alphabetical order of files * Feature #2197 MODE new multi-variate options (#2203) * added to release notes * added release notes for other items completed for rc1 release * Feature #1626 TCDiag Wrapper (#2201) * Feature #1610 first round of SonarQube fixes (#2200) * Feature #2195 create v5.1.0-rc1 release (#2204) * Update version for development towards official release * updated script to use metplotpy as base and install pygrib because conda was failing trying to install matplotlib in Docker for some strange reason * Feature 2188 use case panda c (#2202) * added first use case, need to finish docs and add to list * added documentation files, 3 new cases * added 5th use case, docs * final use case, corrected paths for output * Update GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.py * removed chars, added space to last section * turn off 5/6 new air quality and comp use cases because they are causing the disk to fill up in the automated tests and only 1 is needed to test the new behavior. Reordered use case groups to be alphabetical * disabled other new air quality use case because the disk is still filling up from this case * Feature 2136 cross spectra (#2208) * per #2212, continue instead of return so other forecast leads will not be skipped * Feature #2210 MODE multi-variate variable rename (#2211) * Bugfix diff tests (#2217) * added change from NCEP produtil that was somehow not included in the changes pulled from their repo before starting SonarQube work * Feature #2228 v5.1.0-rc2 release (#2229) * update version after rc2 release to note development towards official 5.1.0 release * Feature #2188 move PANDA-C cases to clouds category and fix automated tests (#2237) Co-authored-by: j-opatz <[email protected]> * Feature 2198 use case amdar pbl (#2206) Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) * Feature #2230 MvMODE usecase doc updates (#2239) This updates the use-case documentation to go along with the multivariate MODE enhancements. * combine release notes from development releases for 5.1.0 release * fix indentation to prevent incorrect nesting of drop down menus * Bugfix #2241 Create directory containing -out_stat file (#2242) * Enhance diff logic to control decimal precision to prevent failures (#2243) * Bugfix #2245 use unique run ID to name logger instance (#2247) * per #2245, add METplusConfig class function that is called when object is deleted to close log handlers. This prevents OSError: [Errno 24] Too many open files from running all pytests * Feature #1626 TCDiag updates to wrapper and basic use case (#2248) Co-authored-by: Jonathan Vigh <[email protected]> * move new use case into another group * Bugfix #2244 develop fix diff tests (#2254) * skip diff for specific png images that produce diffs occasionally but look the same visually * add 2 more keywords for use cases that occasionally flag small, unnoticeable diffs in png images * Feature #2253 update tests for diff_util (#2256) Co-authored-by: root <root@localhost> * Feature #1974 Documentation: update coding standards section (#2260) * Feature #2253 conftest fixture to set pytest tmpdir (#2261) * Feature #2151 Documentation: Add quick search keywords METplotpy/calcpy use cases (#2259) * Feature #2138 CI enhance MET Docker tag override (#2258) * Updating development instructions. * fixed typo * fixed another typo * Feature #2207 Documentation - Updates to Contributor's Guide (#2263) Co-authored-by: Dan Adriaansen <[email protected]> * Feature develop update install files (#2266) * 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 * Bugfix #1853 develop - PointStat don't require mask variables to be set (#2262) * update version of certifi to match auto-generated dependabot PR #2267 * feature #2253 more tests for diff_util.py (#2264) * update versions of METplus components for the next official release * updated release notes for 5.1.0 release * removed duplicate entries in release notes * Added EC2 instance recipee with S3 mounting ability (#2269) * Updating the Subsetting Tests by Marker section (#2272) * update release date for 5.1.0 release (#2276) * update version for development towards 6.0.0-beta1 release * added new use case that was missing * Bugfix #2279 develop - buoy station file from 2022 (#2280) * Feature 2253 series analysis tests (#2277) * Fix typo in pull_request_template.md * Make code coverage report available (#2287) * Use updated dtcenter/metplus-action-data-update tag that fixes bug that 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 * removed climatology keyword from use cases that aren't relevant that were accidentally added with PR #1984 * update readme with current information * Feature #2282 coord_release_docs (#2288) Co-authored-by: George McCabe <[email protected]> * continue workflow if coveralls step fails -- this typically happens on a pull request from a fork because the authentication fails * Feature 2253 system util tests (#2297) * Feature #2294 LSR use case (#2295) * Feature 2253 run util tests (#2307) * Release Guide - remove beta/rc tags/releases (#2309) * Add 'component: repository maintenance' label. Already ran the script to push this change and the NOAA OAR reporting label to all the METplus repos. * Hotfix for labels, adding a new one for 'component: input data' and also fixing the get_lablels.sh to search for up to 200 existing labels. Also work on the log messages. * Fix typo in comment * Feature #2283 time looping consolidation (#2311) Co-authored-by: John Halley Gotway <[email protected]> * New issue template: Update Truth (#2332) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for run_util, 'Usage' bugfix (#2313) * Feature #2338 Debian 12 Conda environments (#2341) Co-authored-by: John Halley Gotway <[email protected]> * Feature 1488 usecase satwinds (#2324) Co-authored-by: George McCabe <[email protected]> * Feature #2283 include times (#2345) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for config_validate, mock logger in conftest (#2320) * Feature #2299 / #2310 Remove deprecated MET config env vars and TCMPRPlotter (#2347) Co-authored-by: John Halley Gotway <[email protected]> * remove MODEL and OBTYPE to use defaults from MET config * Feature #2348 v6.0.0-beta1 release (#2351) * update version for development towards 6.0.0-beta2 release * copy libGL and libEGL files into docker image to prevent errors with geovista python package * run use that uses geovista to test * Feature #2156 release_acceptance_testing (#2352) * feature #2253 print error logs from conftest (#2358) * feature #2253 met_db_load tests (#2355) * Rename 5.1.0.lua_wcoss2 to 6.0.0.lua_wcoss2 * Update and rename 5.1.0_acorn to 6.0.0_acorn * Update 6.0.0_acorn * feature #2253 add tests for gfdl_tracker (#2354) Co-authored-by: George McCabe <[email protected]> * Create 6.0.0_gaea * Update and rename 5.1.0_hera to 6.0.0_hera * Feature #2156 release_acceptance_testing take2 (#2361) Co-authored-by: lisagoodrich <[email protected]> * Feature #2329 Docker info in Installation Chapter (#2366) * feature_2253_extract_tiles_tests (#2368) * Feature 2253 tc pairs tests (#2369) * Feature 2253 tc csv writer (#2373) * 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 * 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 * Feature #2340 TCDiag one_time_per_file_flag (#2374) * Update and rename 5.1.0_jet to 6.0.0_jet * Added libssh * prune docker files before running use cases to prevent running out of disk space when running use cases, ci-run-all-diff * Feature 2253 command builder tests (#2378) * Feature 2253 series analysis test (#2380) * Feature 2253 py embed test (#2379) * ignore cyclone plotter from code coverage report because it will be replaced with METplotpy logic * Feature 898 headers (#2389) * 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 <[email protected]> * 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 <[email protected]> --------- Co-authored-by: George McCabe <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> * Feature #2349 upgrade instructions for deprecated MET config files (#2386) * Feature 2123 di doc update (#2392) Co-authored-by: Tracy <[email protected]> * change log to list name of config variable , e.g. GRID_STAT_CONFIG_FILE, to easily see which variable should be removed * Feature 1667 doc conventions (#2397) * 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 <[email protected]> * Feature #2377 Log to terminal only (#2398) * Update conda envs to use conda-forge only (#2402) * rearrange MET config env var tables for GridStat so they are in the order that they appear in the wrapped MET config file * use mamba instead of conda and update version of netcdf python package used to 1.6.2 * skip s2s_mid_lat WeatherRegime use case that produces different results often * updated version of xesmf because <0.7.1 does not work with mamba * per #2412, fix bug in GenVxMask to put quotes around argument so a grid specification string with spaces will be an accepted value * downgrade version of esmf package to fix bug described in pangeo-data/xESMF#246 * Feature #2219 SeriesAnalysis multiple input files (#2408) * Adding 3 new requestors to the list of common_labels.txt for NOAA/NHC, CSU/CIRA, and Australian BOM ci-skip-all * Feature 2405 match tables2wrapper (#2416) Co-authored-by: George McCabe <[email protected]> * per #2423, follow symbolic links when traversing directories to find files within a time window, ci-run-all-diff * Feature #2252 WaveletStat wrapper (#2427) Co-authored-by: j-opatz <[email protected]> * add WaveletStat use case to group and temporarily disable TCDiag use case because changes to the wrapper are needed to fix it after changes to the MET tool were merged * update version number for beta2 release (#2431) * update version for dev towards beta3 * Feature #2371 Embed use case upgrade demo video into upgrade instructions (#2444) * fix failing use case tests -- install python packages dateutil and requests 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 * remove commands to install geovista from source because it is now installed from conda * Feature #1989: Add OMI use case (#2457) Co-authored-by: George McCabe <[email protected]> * Feature #2432 TCDiag new config changes (#2453) * move medium range 10 use case into group with 3-5 to speed up runs * Feature #2334 land_mask (and topo_mask) in PointStat (#2456) * added use cases with pygrib * Feature #2430 TCPairs consensus.diag_required and consensus.diag_min_req (#2439) * Quickfix cloud use case desc imgs (#2464) * added pics, updated desc * add last two imgs * Fixing spelling and capitalization * Feature 2454 doc overview conv (#2471) * 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 <[email protected]> * 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 GHA Node20 deprecation warnings (#2473) * 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 * Feature dtcenter/MET#2796 develop - Fix error log artifact creation (#2475) * updated version of pillow to fix security vulnerability alerted by dependabot in PR #2477 * remove docker image after runtime image is created from metplus image and conda env image * turn on use case to test image removal * prune images if image tag doesn't exist -- it appears that if the image 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> * support commands that must run in the shell to see if || will work in docker image pruning step * try to fix image removal * Feature 2383 use case sat alt (#2480) * 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 * run image prune commands separately * changed shell back to false * split up use case groups so the same envs are used by a group to see if that resolves the disk space issues * turn off use cases * feature 2253 fix empty pytest logs (#2485) * added more commands to free up disk space as suggested in https://github.com/apache/flink/blob/master/tools/azure-pipelines/free_disk_space.sh, ci-run-all-cases * Feature 2406 redo usecase rrfs (#2488) * issue #2406 RRFS use case files * issue #2406 added usecase to tests * Issue #2406 added metplotpy and metcalcpy as dependencies --------- Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: jprestop <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: John Sharples <[email protected]> Co-authored-by: root <root@localhost> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: reza-armuei <[email protected]> Co-authored-by: Tracy <[email protected]> Co-authored-by: Mallory Row <[email protected]> Co-authored-by: bikegeek <[email protected]>

@JohnHalleyGotway

* update versions to fix bugs for METplotpy/calcpy use cases * Bugfix #2026 develop StatAnalysis looping (#2028) * Feature #2022 update python version to 3.10.4 for repo files (#2047) * Feature #2022 Use Debian 10 / Python 3.10.4 in automated tests (#2050) * add use case group name to output path so that output and error logs will contain use case category to more easily see which case was run * remove -group0 from group names for output path * add manual workflow to update truth data * ci: set gh token on checkout to enable push, ci-skip-all * Set user name/email via git config to allow push * add token to checkout * Feature #2049 Multiple interp.type.method/width (#2051) * added missing argument to script if building envs locally * get main_vX.Y truth data if running on main_vX.Y branch * Updating README.md for label creation and adding bold to common_labels.txt * Updated color for bold label * Feature #2054 consensus.write_members in TCPairs (#2057) * Create LICENSE.md (#2061) * per #2006, fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) * Feature 2065 v5.1.0 beta1 (#2066) * updated version number * added release notes * Update docs/Users_Guide/release-notes.rst Co-authored-by: John Halley Gotway <[email protected]> --------- Co-authored-by: John Halley Gotway <[email protected]> * updated version with -dev * adding sphinx design to 3 files so dropdown menus will work in the release notes. * fix version numbers for python requirements for building documentation * fixed tab vs spaces * Bugfix #2070 var list numeric order (#2072) * Adding files for jet and hera * added commented process list that was accidentally removed -- this is used if the pre-processing steps are needed * Bugfix #2087 develop docs_pdf (#2091) * Feature 2076 release dropdown menu (#2083) * test dropdowns * Update release-notes.rst Attempting to resolve WARNING * testing dropdowns * adding dropdown menus * testing dropdown remove from warning section * dropdown testing * dropdown menu tests * dropdown menus after the warnings section, the dropdown menu only has one space instead of the normal 2 spaces. If it has 2 spaces, it gets sucked into the warning section. * spaces with warning * no spaces for warning * Update release-notes.rst warning note has to be indented 1 space. Originally it was no spaces but then all of the dropdown menus end up in the warning message. If it's 2 spaces, as is normal, then the warning is indented, which is unnecessary. 1 space is slightly indented and keeps the dropdown menus separate. --------- Co-authored-by: jprestop <[email protected]> * Bugfix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) * Feature 1516 use case mvmode (#2094) Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: George McCabe <[email protected]> * Fix for Dockerfile smell DL4000 (#2112) Co-authored-by: Giovanni Rosa <[email protected]> * Changed "PROJECT" to "CYCLE" ASSIGNMENT * Feature 2115 update use cases (#2133) * Bugfix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) * Bugfix #2137 develop PointStat -obs_valid_beg/end (#2141) * Feature #2143 5.1.0-beta2 release (#2144) * update release guide steps with new info based on changes to GitHub web interface * update version for development towards rc1 release * Feature #1977 ARGO use case (#2148) Co-authored-by: j-opatz <[email protected]> * Feature develop cycle change (#2150) * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * Added paths to ignore --------- Co-authored-by: jprestop <[email protected]> * Documentation: Update Truth Data instructions (#2154) * upgrade python to 3.10 for documentation builds to fix failured introduced by urllib3 (see urllib3/urllib3#2168) * update workflow to update input test data to use branch from pull down or enter branch by hand if branch does not exist in dtcenter/METplus repo, e.g. if updating data for a PR coming from a fork * Bugfix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) * changed order of workflow event triggering info to more easily see the repository and commit sha that triggered the workflow * fix docker compose install and call -- needed due to new Alpine Linux release 3.18.0 that does not include docker-compose in the apk repository * Bugfix #2168 develop - StatAnalysis time shift (#2169) * Feature 1978 update pyreq doc (#2177) * Updating for 5.1.0 * Adding greater than or equal to signs * Feature 2106 release support (#2182) * Added a paragraph for Release Support Policy * Added a sentence about contacting the team through the METplus GitHub Discussions Forum. * Added Release Support Policy info * Per #2159, modify instructions to reflect that we only want a coordinated release for the official releases and updates to the coordinated release section for the bugfix releases. (#2183) * Feature 2147 workflow doc (#2185) * Add new images for github workflow * Added PR section * Modified the Find the GitHub Issue to be Find or Create a GitHub issue * Trying out image keyword compared with figure keyword * Trying out various widths * Added new figures * Reverting to figures from images after modifying figures * Adding the old images which are better quality * Trying out new indention * Working on formatting again * Reducing image widths * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update github_workflow.rst --------- Co-authored-by: George McCabe <[email protected]> * added scripts to create new conda environment for PANDA-C use cases * Bugfix #2189 develop - spaces in complex thresholds (#2191) * added release notes for completed issues for rc1 * Feature 2011 tci from cesm fluxnet2015 netcdf (#2192) Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2179 develop TCPairs fix -diag argument (#2187) * sort list of files to make command more readable and make logic more easily testable * fix unit test to expect alphabetical order of files * Feature #2197 MODE new multi-variate options (#2203) * added to release notes * added release notes for other items completed for rc1 release * Feature #1626 TCDiag Wrapper (#2201) * Feature #1610 first round of SonarQube fixes (#2200) * Feature #2195 create v5.1.0-rc1 release (#2204) * Update version for development towards official release * updated script to use metplotpy as base and install pygrib because conda was failing trying to install matplotlib in Docker for some strange reason * Feature 2188 use case panda c (#2202) * added first use case, need to finish docs and add to list * added documentation files, 3 new cases * added 5th use case, docs * final use case, corrected paths for output * Update GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.py * removed chars, added space to last section * turn off 5/6 new air quality and comp use cases because they are causing the disk to fill up in the automated tests and only 1 is needed to test the new behavior. Reordered use case groups to be alphabetical * disabled other new air quality use case because the disk is still filling up from this case * Feature 2136 cross spectra (#2208) * per #2212, continue instead of return so other forecast leads will not be skipped * Feature #2210 MODE multi-variate variable rename (#2211) * Bugfix diff tests (#2217) * added change from NCEP produtil that was somehow not included in the changes pulled from their repo before starting SonarQube work * Feature #2228 v5.1.0-rc2 release (#2229) * update version after rc2 release to note development towards official 5.1.0 release * Feature #2188 move PANDA-C cases to clouds category and fix automated tests (#2237) Co-authored-by: j-opatz <[email protected]> * Feature 2198 use case amdar pbl (#2206) Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) * Feature #2230 MvMODE usecase doc updates (#2239) This updates the use-case documentation to go along with the multivariate MODE enhancements. * combine release notes from development releases for 5.1.0 release * fix indentation to prevent incorrect nesting of drop down menus * Bugfix #2241 Create directory containing -out_stat file (#2242) * Enhance diff logic to control decimal precision to prevent failures (#2243) * Bugfix #2245 use unique run ID to name logger instance (#2247) * per #2245, add METplusConfig class function that is called when object is deleted to close log handlers. This prevents OSError: [Errno 24] Too many open files from running all pytests * Feature #1626 TCDiag updates to wrapper and basic use case (#2248) Co-authored-by: Jonathan Vigh <[email protected]> * move new use case into another group * Bugfix #2244 develop fix diff tests (#2254) * skip diff for specific png images that produce diffs occasionally but look the same visually * add 2 more keywords for use cases that occasionally flag small, unnoticeable diffs in png images * Feature #2253 update tests for diff_util (#2256) Co-authored-by: root <root@localhost> * Feature #1974 Documentation: update coding standards section (#2260) * Feature #2253 conftest fixture to set pytest tmpdir (#2261) * Feature #2151 Documentation: Add quick search keywords METplotpy/calcpy use cases (#2259) * Feature #2138 CI enhance MET Docker tag override (#2258) * Updating development instructions. * fixed typo * fixed another typo * Feature #2207 Documentation - Updates to Contributor's Guide (#2263) Co-authored-by: Dan Adriaansen <[email protected]> * Feature develop update install files (#2266) * 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 * Bugfix #1853 develop - PointStat don't require mask variables to be set (#2262) * update version of certifi to match auto-generated dependabot PR #2267 * feature #2253 more tests for diff_util.py (#2264) * update versions of METplus components for the next official release * updated release notes for 5.1.0 release * removed duplicate entries in release notes * Added EC2 instance recipee with S3 mounting ability (#2269) * Updating the Subsetting Tests by Marker section (#2272) * update release date for 5.1.0 release (#2276) * update version for development towards 6.0.0-beta1 release * added new use case that was missing * Bugfix #2279 develop - buoy station file from 2022 (#2280) * Feature 2253 series analysis tests (#2277) * Fix typo in pull_request_template.md * Make code coverage report available (#2287) * Use updated dtcenter/metplus-action-data-update tag that fixes bug that 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 * removed climatology keyword from use cases that aren't relevant that were accidentally added with PR #1984 * update readme with current information * Feature #2282 coord_release_docs (#2288) Co-authored-by: George McCabe <[email protected]> * continue workflow if coveralls step fails -- this typically happens on a pull request from a fork because the authentication fails * Feature 2253 system util tests (#2297) * Feature #2294 LSR use case (#2295) * Feature 2253 run util tests (#2307) * Release Guide - remove beta/rc tags/releases (#2309) * Add 'component: repository maintenance' label. Already ran the script to push this change and the NOAA OAR reporting label to all the METplus repos. * Hotfix for labels, adding a new one for 'component: input data' and also fixing the get_lablels.sh to search for up to 200 existing labels. Also work on the log messages. * Fix typo in comment * Feature #2283 time looping consolidation (#2311) Co-authored-by: John Halley Gotway <[email protected]> * New issue template: Update Truth (#2332) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for run_util, 'Usage' bugfix (#2313) * Feature #2338 Debian 12 Conda environments (#2341) Co-authored-by: John Halley Gotway <[email protected]> * Feature 1488 usecase satwinds (#2324) Co-authored-by: George McCabe <[email protected]> * Feature #2283 include times (#2345) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for config_validate, mock logger in conftest (#2320) * Feature #2299 / #2310 Remove deprecated MET config env vars and TCMPRPlotter (#2347) Co-authored-by: John Halley Gotway <[email protected]> * remove MODEL and OBTYPE to use defaults from MET config * Feature #2348 v6.0.0-beta1 release (#2351) * update version for development towards 6.0.0-beta2 release * copy libGL and libEGL files into docker image to prevent errors with geovista python package * run use that uses geovista to test * Feature #2156 release_acceptance_testing (#2352) * feature #2253 print error logs from conftest (#2358) * feature #2253 met_db_load tests (#2355) * Rename 5.1.0.lua_wcoss2 to 6.0.0.lua_wcoss2 * Update and rename 5.1.0_acorn to 6.0.0_acorn * Update 6.0.0_acorn * feature #2253 add tests for gfdl_tracker (#2354) Co-authored-by: George McCabe <[email protected]> * Create 6.0.0_gaea * Update and rename 5.1.0_hera to 6.0.0_hera * Feature #2156 release_acceptance_testing take2 (#2361) Co-authored-by: lisagoodrich <[email protected]> * Feature #2329 Docker info in Installation Chapter (#2366) * feature_2253_extract_tiles_tests (#2368) * Feature 2253 tc pairs tests (#2369) * Feature 2253 tc csv writer (#2373) * 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 * 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 * Feature #2340 TCDiag one_time_per_file_flag (#2374) * Update and rename 5.1.0_jet to 6.0.0_jet * Added libssh * prune docker files before running use cases to prevent running out of disk space when running use cases, ci-run-all-diff * Feature 2253 command builder tests (#2378) * Feature 2253 series analysis test (#2380) * Feature 2253 py embed test (#2379) * ignore cyclone plotter from code coverage report because it will be replaced with METplotpy logic * Feature 898 headers (#2389) * 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 <[email protected]> * 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 <[email protected]> --------- Co-authored-by: George McCabe <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> * Feature #2349 upgrade instructions for deprecated MET config files (#2386) * Feature 2123 di doc update (#2392) Co-authored-by: Tracy <[email protected]> * change log to list name of config variable , e.g. GRID_STAT_CONFIG_FILE, to easily see which variable should be removed * Feature 1667 doc conventions (#2397) * 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 <[email protected]> * Feature #2377 Log to terminal only (#2398) * Update conda envs to use conda-forge only (#2402) * rearrange MET config env var tables for GridStat so they are in the order that they appear in the wrapped MET config file * use mamba instead of conda and update version of netcdf python package used to 1.6.2 * skip s2s_mid_lat WeatherRegime use case that produces different results often * updated version of xesmf because <0.7.1 does not work with mamba * per #2412, fix bug in GenVxMask to put quotes around argument so a grid specification string with spaces will be an accepted value * downgrade version of esmf package to fix bug described in pangeo-data/xESMF#246 * Feature #2219 SeriesAnalysis multiple input files (#2408) * Adding 3 new requestors to the list of common_labels.txt for NOAA/NHC, CSU/CIRA, and Australian BOM ci-skip-all * Feature 2405 match tables2wrapper (#2416) Co-authored-by: George McCabe <[email protected]> * per #2423, follow symbolic links when traversing directories to find files within a time window, ci-run-all-diff * Feature #2252 WaveletStat wrapper (#2427) Co-authored-by: j-opatz <[email protected]> * add WaveletStat use case to group and temporarily disable TCDiag use case because changes to the wrapper are needed to fix it after changes to the MET tool were merged * update version number for beta2 release (#2431) * update version for dev towards beta3 * Feature #2371 Embed use case upgrade demo video into upgrade instructions (#2444) * fix failing use case tests -- install python packages dateutil and requests 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 * remove commands to install geovista from source because it is now installed from conda * Feature #1989: Add OMI use case (#2457) Co-authored-by: George McCabe <[email protected]> * Feature #2432 TCDiag new config changes (#2453) * move medium range 10 use case into group with 3-5 to speed up runs * Feature #2334 land_mask (and topo_mask) in PointStat (#2456) * added use cases with pygrib * Feature #2430 TCPairs consensus.diag_required and consensus.diag_min_req (#2439) * Quickfix cloud use case desc imgs (#2464) * added pics, updated desc * add last two imgs * Fixing spelling and capitalization * Feature 2454 doc overview conv (#2471) * 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 <[email protected]> * 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 GHA Node20 deprecation warnings (#2473) * 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 * Feature dtcenter/MET#2796 develop - Fix error log artifact creation (#2475) * updated version of pillow to fix security vulnerability alerted by dependabot in PR #2477 * remove docker image after runtime image is created from metplus image and conda env image * turn on use case to test image removal * prune images if image tag doesn't exist -- it appears that if the image 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> * support commands that must run in the shell to see if || will work in docker image pruning step * try to fix image removal * Feature 2383 use case sat alt (#2480) * 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 * run image prune commands separately * changed shell back to false * split up use case groups so the same envs are used by a group to see if that resolves the disk space issues * turn off use cases * feature 2253 fix empty pytest logs (#2485) * added more commands to free up disk space as suggested in https://github.com/apache/flink/blob/master/tools/azure-pipelines/free_disk_space.sh, ci-run-all-cases * Feature 2406 redo usecase rrfs (#2488) * issue #2406 RRFS use case files * issue #2406 added usecase to tests * Issue #2406 added metplotpy and metcalcpy as dependencies * Feature #2460 allow missing input (#2493) * 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 * Feature #2491 v6.0.0 beta3 (#2495) * update version for beta3 release * fixed typos in release notes * update version to note development towards beta4 release * Per suggestion from @JohnHalleyGotway, create intermediate branch 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 * added quotes to prevent error in echo caused by parenthesis * fix incorrect command * Revert "fix incorrect command" This reverts commit e7dffb6. * Revert "added quotes to prevent error in echo caused by parenthesis" This reverts commit c1cb3c4. * Revert "Per suggestion from @JohnHalleyGotway, create intermediate branch 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. --------- Co-authored-by: George McCabe <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: John Sharples <[email protected]> Co-authored-by: root <root@localhost> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: reza-armuei <[email protected]> Co-authored-by: Tracy <[email protected]> Co-authored-by: Mallory Row <[email protected]> Co-authored-by: bikegeek <[email protected]>

@JohnHalleyGotway

* Feature 2065 v5.1.0 beta1 (#2066) * updated version number * added release notes * Update docs/Users_Guide/release-notes.rst Co-authored-by: John Halley Gotway <[email protected]> --------- Co-authored-by: John Halley Gotway <[email protected]> * updated version with -dev * adding sphinx design to 3 files so dropdown menus will work in the release notes. * fix version numbers for python requirements for building documentation * fixed tab vs spaces * Bugfix #2070 var list numeric order (#2072) * Adding files for jet and hera * added commented process list that was accidentally removed -- this is used if the pre-processing steps are needed * Bugfix #2087 develop docs_pdf (#2091) * Feature 2076 release dropdown menu (#2083) * test dropdowns * Update release-notes.rst Attempting to resolve WARNING * testing dropdowns * adding dropdown menus * testing dropdown remove from warning section * dropdown testing * dropdown menu tests * dropdown menus after the warnings section, the dropdown menu only has one space instead of the normal 2 spaces. If it has 2 spaces, it gets sucked into the warning section. * spaces with warning * no spaces for warning * Update release-notes.rst warning note has to be indented 1 space. Originally it was no spaces but then all of the dropdown menus end up in the warning message. If it's 2 spaces, as is normal, then the warning is indented, which is unnecessary. 1 space is slightly indented and keeps the dropdown menus separate. --------- Co-authored-by: jprestop <[email protected]> * Bugfix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) * Feature 1516 use case mvmode (#2094) Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: George McCabe <[email protected]> * Fix for Dockerfile smell DL4000 (#2112) Co-authored-by: Giovanni Rosa <[email protected]> * Changed "PROJECT" to "CYCLE" ASSIGNMENT * Feature 2115 update use cases (#2133) * Bugfix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) * Bugfix #2137 develop PointStat -obs_valid_beg/end (#2141) * Feature #2143 5.1.0-beta2 release (#2144) * update release guide steps with new info based on changes to GitHub web interface * update version for development towards rc1 release * Feature #1977 ARGO use case (#2148) Co-authored-by: j-opatz <[email protected]> * Feature develop cycle change (#2150) * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * Added paths to ignore --------- Co-authored-by: jprestop <[email protected]> * Documentation: Update Truth Data instructions (#2154) * upgrade python to 3.10 for documentation builds to fix failured introduced by urllib3 (see urllib3/urllib3#2168) * update workflow to update input test data to use branch from pull down or enter branch by hand if branch does not exist in dtcenter/METplus repo, e.g. if updating data for a PR coming from a fork * Bugfix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) * changed order of workflow event triggering info to more easily see the repository and commit sha that triggered the workflow * fix docker compose install and call -- needed due to new Alpine Linux release 3.18.0 that does not include docker-compose in the apk repository * Bugfix #2168 develop - StatAnalysis time shift (#2169) * Feature 1978 update pyreq doc (#2177) * Updating for 5.1.0 * Adding greater than or equal to signs * Feature 2106 release support (#2182) * Added a paragraph for Release Support Policy * Added a sentence about contacting the team through the METplus GitHub Discussions Forum. * Added Release Support Policy info * Per #2159, modify instructions to reflect that we only want a coordinated release for the official releases and updates to the coordinated release section for the bugfix releases. (#2183) * Feature 2147 workflow doc (#2185) * Add new images for github workflow * Added PR section * Modified the Find the GitHub Issue to be Find or Create a GitHub issue * Trying out image keyword compared with figure keyword * Trying out various widths * Added new figures * Reverting to figures from images after modifying figures * Adding the old images which are better quality * Trying out new indention * Working on formatting again * Reducing image widths * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update github_workflow.rst --------- Co-authored-by: George McCabe <[email protected]> * added scripts to create new conda environment for PANDA-C use cases * Bugfix #2189 develop - spaces in complex thresholds (#2191) * added release notes for completed issues for rc1 * Feature 2011 tci from cesm fluxnet2015 netcdf (#2192) Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2179 develop TCPairs fix -diag argument (#2187) * sort list of files to make command more readable and make logic more easily testable * fix unit test to expect alphabetical order of files * Feature #2197 MODE new multi-variate options (#2203) * added to release notes * added release notes for other items completed for rc1 release * Feature #1626 TCDiag Wrapper (#2201) * Feature #1610 first round of SonarQube fixes (#2200) * Feature #2195 create v5.1.0-rc1 release (#2204) * Update version for development towards official release * updated script to use metplotpy as base and install pygrib because conda was failing trying to install matplotlib in Docker for some strange reason * Feature 2188 use case panda c (#2202) * added first use case, need to finish docs and add to list * added documentation files, 3 new cases * added 5th use case, docs * final use case, corrected paths for output * Update GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.py * removed chars, added space to last section * turn off 5/6 new air quality and comp use cases because they are causing the disk to fill up in the automated tests and only 1 is needed to test the new behavior. Reordered use case groups to be alphabetical * disabled other new air quality use case because the disk is still filling up from this case * Feature 2136 cross spectra (#2208) * per #2212, continue instead of return so other forecast leads will not be skipped * Feature #2210 MODE multi-variate variable rename (#2211) * Bugfix diff tests (#2217) * added change from NCEP produtil that was somehow not included in the changes pulled from their repo before starting SonarQube work * Feature #2228 v5.1.0-rc2 release (#2229) * update version after rc2 release to note development towards official 5.1.0 release * Feature #2188 move PANDA-C cases to clouds category and fix automated tests (#2237) Co-authored-by: j-opatz <[email protected]> * Feature 2198 use case amdar pbl (#2206) Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) * Feature #2230 MvMODE usecase doc updates (#2239) This updates the use-case documentation to go along with the multivariate MODE enhancements. * combine release notes from development releases for 5.1.0 release * fix indentation to prevent incorrect nesting of drop down menus * Bugfix #2241 Create directory containing -out_stat file (#2242) * Enhance diff logic to control decimal precision to prevent failures (#2243) * Bugfix #2245 use unique run ID to name logger instance (#2247) * per #2245, add METplusConfig class function that is called when object is deleted to close log handlers. This prevents OSError: [Errno 24] Too many open files from running all pytests * Feature #1626 TCDiag updates to wrapper and basic use case (#2248) Co-authored-by: Jonathan Vigh <[email protected]> * move new use case into another group * Bugfix #2244 develop fix diff tests (#2254) * skip diff for specific png images that produce diffs occasionally but look the same visually * add 2 more keywords for use cases that occasionally flag small, unnoticeable diffs in png images * Feature #2253 update tests for diff_util (#2256) Co-authored-by: root <root@localhost> * Feature #1974 Documentation: update coding standards section (#2260) * Feature #2253 conftest fixture to set pytest tmpdir (#2261) * Feature #2151 Documentation: Add quick search keywords METplotpy/calcpy use cases (#2259) * Feature #2138 CI enhance MET Docker tag override (#2258) * Updating development instructions. * fixed typo * fixed another typo * Feature #2207 Documentation - Updates to Contributor's Guide (#2263) Co-authored-by: Dan Adriaansen <[email protected]> * Feature develop update install files (#2266) * 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 * Bugfix #1853 develop - PointStat don't require mask variables to be set (#2262) * update version of certifi to match auto-generated dependabot PR #2267 * feature #2253 more tests for diff_util.py (#2264) * update versions of METplus components for the next official release * updated release notes for 5.1.0 release * removed duplicate entries in release notes * Added EC2 instance recipee with S3 mounting ability (#2269) * Updating the Subsetting Tests by Marker section (#2272) * update release date for 5.1.0 release (#2276) * update version for development towards 6.0.0-beta1 release * added new use case that was missing * Bugfix #2279 develop - buoy station file from 2022 (#2280) * Feature 2253 series analysis tests (#2277) * Fix typo in pull_request_template.md * Make code coverage report available (#2287) * Use updated dtcenter/metplus-action-data-update tag that fixes bug that 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 * removed climatology keyword from use cases that aren't relevant that were accidentally added with PR #1984 * update readme with current information * Feature #2282 coord_release_docs (#2288) Co-authored-by: George McCabe <[email protected]> * continue workflow if coveralls step fails -- this typically happens on a pull request from a fork because the authentication fails * Feature 2253 system util tests (#2297) * Feature #2294 LSR use case (#2295) * Feature 2253 run util tests (#2307) * Release Guide - remove beta/rc tags/releases (#2309) * Add 'component: repository maintenance' label. Already ran the script to push this change and the NOAA OAR reporting label to all the METplus repos. * Hotfix for labels, adding a new one for 'component: input data' and also fixing the get_lablels.sh to search for up to 200 existing labels. Also work on the log messages. * Fix typo in comment * Feature #2283 time looping consolidation (#2311) Co-authored-by: John Halley Gotway <[email protected]> * New issue template: Update Truth (#2332) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for run_util, 'Usage' bugfix (#2313) * Feature #2338 Debian 12 Conda environments (#2341) Co-authored-by: John Halley Gotway <[email protected]> * Feature 1488 usecase satwinds (#2324) Co-authored-by: George McCabe <[email protected]> * Feature #2283 include times (#2345) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for config_validate, mock logger in conftest (#2320) * Feature #2299 / #2310 Remove deprecated MET config env vars and TCMPRPlotter (#2347) Co-authored-by: John Halley Gotway <[email protected]> * remove MODEL and OBTYPE to use defaults from MET config * Feature #2348 v6.0.0-beta1 release (#2351) * update version for development towards 6.0.0-beta2 release * copy libGL and libEGL files into docker image to prevent errors with geovista python package * run use that uses geovista to test * Feature #2156 release_acceptance_testing (#2352) * feature #2253 print error logs from conftest (#2358) * feature #2253 met_db_load tests (#2355) * Rename 5.1.0.lua_wcoss2 to 6.0.0.lua_wcoss2 * Update and rename 5.1.0_acorn to 6.0.0_acorn * Update 6.0.0_acorn * feature #2253 add tests for gfdl_tracker (#2354) Co-authored-by: George McCabe <[email protected]> * Create 6.0.0_gaea * Update and rename 5.1.0_hera to 6.0.0_hera * Feature #2156 release_acceptance_testing take2 (#2361) Co-authored-by: lisagoodrich <[email protected]> * Feature #2329 Docker info in Installation Chapter (#2366) * feature_2253_extract_tiles_tests (#2368) * Feature 2253 tc pairs tests (#2369) * Feature 2253 tc csv writer (#2373) * 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 * 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 * Feature #2340 TCDiag one_time_per_file_flag (#2374) * Update and rename 5.1.0_jet to 6.0.0_jet * Added libssh * prune docker files before running use cases to prevent running out of disk space when running use cases, ci-run-all-diff * Feature 2253 command builder tests (#2378) * Feature 2253 series analysis test (#2380) * Feature 2253 py embed test (#2379) * ignore cyclone plotter from code coverage report because it will be replaced with METplotpy logic * Feature 898 headers (#2389) * 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 <[email protected]> * 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 <[email protected]> --------- Co-authored-by: George McCabe <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> * Feature #2349 upgrade instructions for deprecated MET config files (#2386) * Feature 2123 di doc update (#2392) Co-authored-by: Tracy <[email protected]> * change log to list name of config variable , e.g. GRID_STAT_CONFIG_FILE, to easily see which variable should be removed * Feature 1667 doc conventions (#2397) * 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 <[email protected]> * Feature #2377 Log to terminal only (#2398) * Update conda envs to use conda-forge only (#2402) * rearrange MET config env var tables for GridStat so they are in the order that they appear in the wrapped MET config file * use mamba instead of conda and update version of netcdf python package used to 1.6.2 * skip s2s_mid_lat WeatherRegime use case that produces different results often * updated version of xesmf because <0.7.1 does not work with mamba * per #2412, fix bug in GenVxMask to put quotes around argument so a grid specification string with spaces will be an accepted value * downgrade version of esmf package to fix bug described in pangeo-data/xESMF#246 * Feature #2219 SeriesAnalysis multiple input files (#2408) * Adding 3 new requestors to the list of common_labels.txt for NOAA/NHC, CSU/CIRA, and Australian BOM ci-skip-all * Feature 2405 match tables2wrapper (#2416) Co-authored-by: George McCabe <[email protected]> * per #2423, follow symbolic links when traversing directories to find files within a time window, ci-run-all-diff * Feature #2252 WaveletStat wrapper (#2427) Co-authored-by: j-opatz <[email protected]> * add WaveletStat use case to group and temporarily disable TCDiag use case because changes to the wrapper are needed to fix it after changes to the MET tool were merged * update version number for beta2 release (#2431) * update version for dev towards beta3 * Feature #2371 Embed use case upgrade demo video into upgrade instructions (#2444) * fix failing use case tests -- install python packages dateutil and requests 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 * remove commands to install geovista from source because it is now installed from conda * Feature #1989: Add OMI use case (#2457) Co-authored-by: George McCabe <[email protected]> * Feature #2432 TCDiag new config changes (#2453) * move medium range 10 use case into group with 3-5 to speed up runs * Feature #2334 land_mask (and topo_mask) in PointStat (#2456) * added use cases with pygrib * Feature #2430 TCPairs consensus.diag_required and consensus.diag_min_req (#2439) * Quickfix cloud use case desc imgs (#2464) * added pics, updated desc * add last two imgs * Fixing spelling and capitalization * Feature 2454 doc overview conv (#2471) * 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 <[email protected]> * 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 GHA Node20 deprecation warnings (#2473) * 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 * Feature dtcenter/MET#2796 develop - Fix error log artifact creation (#2475) * updated version of pillow to fix security vulnerability alerted by dependabot in PR #2477 * remove docker image after runtime image is created from metplus image and conda env image * turn on use case to test image removal * prune images if image tag doesn't exist -- it appears that if the image 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> * support commands that must run in the shell to see if || will work in docker image pruning step * try to fix image removal * Feature 2383 use case sat alt (#2480) * 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 * run image prune commands separately * changed shell back to false * split up use case groups so the same envs are used by a group to see if that resolves the disk space issues * turn off use cases * feature 2253 fix empty pytest logs (#2485) * added more commands to free up disk space as suggested in https://github.com/apache/flink/blob/master/tools/azure-pipelines/free_disk_space.sh, ci-run-all-cases * Feature 2406 redo usecase rrfs (#2488) * issue #2406 RRFS use case files * issue #2406 added usecase to tests * Issue #2406 added metplotpy and metcalcpy as dependencies * Feature #2460 allow missing input (#2493) * 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 * Feature #2491 v6.0.0 beta3 (#2495) * update version for beta3 release * fixed typos in release notes * update version to note development towards beta4 release * Per suggestion from @JohnHalleyGotway, create intermediate branch 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 * added quotes to prevent error in echo caused by parenthesis * fix incorrect command * Revert "fix incorrect command" This reverts commit e7dffb6. * Revert "added quotes to prevent error in echo caused by parenthesis" This reverts commit c1cb3c4. * Revert "Per suggestion from @JohnHalleyGotway, create intermediate branch 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. * Hotfix: Allow symbolic link to run_metplus.py to run (#2500) * Adding use case tests * Changing test environment * Testing environment changes * Documentation update * Updating Documentation * Updating documentation for disk space failure * Added new use case category * Fixing use case test * Fixing bug in use case file * Testing s2s after data removal * add back use cases that were accidentally removed * fix incorrect use case added * Setting tests to false for merge * Testing for old use cases * Setting tests to false for merge * update tests to update develop data -- modified commands to create new 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 --------- Co-authored-by: j-opatz <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: John Sharples <[email protected]> Co-authored-by: root <root@localhost> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: reza-armuei <[email protected]> Co-authored-by: Tracy <[email protected]> Co-authored-by: Mallory Row <[email protected]> Co-authored-by: bikegeek <[email protected]>

@JohnHalleyGotway

* adding sphinx design to 3 files so dropdown menus will work in the release notes. * fix version numbers for python requirements for building documentation * fixed tab vs spaces * Bugfix #2070 var list numeric order (#2072) * Adding files for jet and hera * added commented process list that was accidentally removed -- this is used if the pre-processing steps are needed * Bugfix #2087 develop docs_pdf (#2091) * Feature 2076 release dropdown menu (#2083) * test dropdowns * Update release-notes.rst Attempting to resolve WARNING * testing dropdowns * adding dropdown menus * testing dropdown remove from warning section * dropdown testing * dropdown menu tests * dropdown menus after the warnings section, the dropdown menu only has one space instead of the normal 2 spaces. If it has 2 spaces, it gets sucked into the warning section. * spaces with warning * no spaces for warning * Update release-notes.rst warning note has to be indented 1 space. Originally it was no spaces but then all of the dropdown menus end up in the warning message. If it's 2 spaces, as is normal, then the warning is indented, which is unnecessary. 1 space is slightly indented and keeps the dropdown menus separate. --------- Co-authored-by: jprestop <[email protected]> * Bugfix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) * Feature 1516 use case mvmode (#2094) Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: George McCabe <[email protected]> * Fix for Dockerfile smell DL4000 (#2112) Co-authored-by: Giovanni Rosa <[email protected]> * Changed "PROJECT" to "CYCLE" ASSIGNMENT * Feature 2115 update use cases (#2133) * Bugfix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) * Bugfix #2137 develop PointStat -obs_valid_beg/end (#2141) * Feature #2143 5.1.0-beta2 release (#2144) * update release guide steps with new info based on changes to GitHub web interface * update version for development towards rc1 release * Feature #1977 ARGO use case (#2148) Co-authored-by: j-opatz <[email protected]> * Feature develop cycle change (#2150) * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * Added paths to ignore --------- Co-authored-by: jprestop <[email protected]> * Documentation: Update Truth Data instructions (#2154) * upgrade python to 3.10 for documentation builds to fix failured introduced by urllib3 (see urllib3/urllib3#2168) * update workflow to update input test data to use branch from pull down or enter branch by hand if branch does not exist in dtcenter/METplus repo, e.g. if updating data for a PR coming from a fork * Bugfix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) * changed order of workflow event triggering info to more easily see the repository and commit sha that triggered the workflow * fix docker compose install and call -- needed due to new Alpine Linux release 3.18.0 that does not include docker-compose in the apk repository * Bugfix #2168 develop - StatAnalysis time shift (#2169) * Feature 1978 update pyreq doc (#2177) * Updating for 5.1.0 * Adding greater than or equal to signs * Feature 2106 release support (#2182) * Added a paragraph for Release Support Policy * Added a sentence about contacting the team through the METplus GitHub Discussions Forum. * Added Release Support Policy info * Per #2159, modify instructions to reflect that we only want a coordinated release for the official releases and updates to the coordinated release section for the bugfix releases. (#2183) * Feature 2147 workflow doc (#2185) * Add new images for github workflow * Added PR section * Modified the Find the GitHub Issue to be Find or Create a GitHub issue * Trying out image keyword compared with figure keyword * Trying out various widths * Added new figures * Reverting to figures from images after modifying figures * Adding the old images which are better quality * Trying out new indention * Working on formatting again * Reducing image widths * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update github_workflow.rst --------- Co-authored-by: George McCabe <[email protected]> * added scripts to create new conda environment for PANDA-C use cases * Bugfix #2189 develop - spaces in complex thresholds (#2191) * added release notes for completed issues for rc1 * Feature 2011 tci from cesm fluxnet2015 netcdf (#2192) Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2179 develop TCPairs fix -diag argument (#2187) * sort list of files to make command more readable and make logic more easily testable * fix unit test to expect alphabetical order of files * Feature #2197 MODE new multi-variate options (#2203) * added to release notes * added release notes for other items completed for rc1 release * Feature #1626 TCDiag Wrapper (#2201) * Feature #1610 first round of SonarQube fixes (#2200) * Feature #2195 create v5.1.0-rc1 release (#2204) * Update version for development towards official release * updated script to use metplotpy as base and install pygrib because conda was failing trying to install matplotlib in Docker for some strange reason * Feature 2188 use case panda c (#2202) * added first use case, need to finish docs and add to list * added documentation files, 3 new cases * added 5th use case, docs * final use case, corrected paths for output * Update GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.py * removed chars, added space to last section * turn off 5/6 new air quality and comp use cases because they are causing the disk to fill up in the automated tests and only 1 is needed to test the new behavior. Reordered use case groups to be alphabetical * disabled other new air quality use case because the disk is still filling up from this case * Feature 2136 cross spectra (#2208) * per #2212, continue instead of return so other forecast leads will not be skipped * Feature #2210 MODE multi-variate variable rename (#2211) * Bugfix diff tests (#2217) * added change from NCEP produtil that was somehow not included in the changes pulled from their repo before starting SonarQube work * Feature #2228 v5.1.0-rc2 release (#2229) * update version after rc2 release to note development towards official 5.1.0 release * Feature #2188 move PANDA-C cases to clouds category and fix automated tests (#2237) Co-authored-by: j-opatz <[email protected]> * Feature 2198 use case amdar pbl (#2206) Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) * Feature #2230 MvMODE usecase doc updates (#2239) This updates the use-case documentation to go along with the multivariate MODE enhancements. * combine release notes from development releases for 5.1.0 release * fix indentation to prevent incorrect nesting of drop down menus * Bugfix #2241 Create directory containing -out_stat file (#2242) * Enhance diff logic to control decimal precision to prevent failures (#2243) * Bugfix #2245 use unique run ID to name logger instance (#2247) * per #2245, add METplusConfig class function that is called when object is deleted to close log handlers. This prevents OSError: [Errno 24] Too many open files from running all pytests * Feature #1626 TCDiag updates to wrapper and basic use case (#2248) Co-authored-by: Jonathan Vigh <[email protected]> * move new use case into another group * Bugfix #2244 develop fix diff tests (#2254) * skip diff for specific png images that produce diffs occasionally but look the same visually * add 2 more keywords for use cases that occasionally flag small, unnoticeable diffs in png images * Feature #2253 update tests for diff_util (#2256) Co-authored-by: root <root@localhost> * Feature #1974 Documentation: update coding standards section (#2260) * Feature #2253 conftest fixture to set pytest tmpdir (#2261) * Feature #2151 Documentation: Add quick search keywords METplotpy/calcpy use cases (#2259) * Feature #2138 CI enhance MET Docker tag override (#2258) * Updating development instructions. * fixed typo * fixed another typo * Feature #2207 Documentation - Updates to Contributor's Guide (#2263) Co-authored-by: Dan Adriaansen <[email protected]> * Feature develop update install files (#2266) * 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 * Bugfix #1853 develop - PointStat don't require mask variables to be set (#2262) * update version of certifi to match auto-generated dependabot PR #2267 * feature #2253 more tests for diff_util.py (#2264) * update versions of METplus components for the next official release * updated release notes for 5.1.0 release * removed duplicate entries in release notes * Added EC2 instance recipee with S3 mounting ability (#2269) * Updating the Subsetting Tests by Marker section (#2272) * update release date for 5.1.0 release (#2276) * update version for development towards 6.0.0-beta1 release * added new use case that was missing * Bugfix #2279 develop - buoy station file from 2022 (#2280) * Feature 2253 series analysis tests (#2277) * Fix typo in pull_request_template.md * Make code coverage report available (#2287) * Use updated dtcenter/metplus-action-data-update tag that fixes bug that 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 * removed climatology keyword from use cases that aren't relevant that were accidentally added with PR #1984 * update readme with current information * Feature #2282 coord_release_docs (#2288) Co-authored-by: George McCabe <[email protected]> * continue workflow if coveralls step fails -- this typically happens on a pull request from a fork because the authentication fails * Feature 2253 system util tests (#2297) * Feature #2294 LSR use case (#2295) * Feature 2253 run util tests (#2307) * Release Guide - remove beta/rc tags/releases (#2309) * Add 'component: repository maintenance' label. Already ran the script to push this change and the NOAA OAR reporting label to all the METplus repos. * Hotfix for labels, adding a new one for 'component: input data' and also fixing the get_lablels.sh to search for up to 200 existing labels. Also work on the log messages. * Fix typo in comment * Feature #2283 time looping consolidation (#2311) Co-authored-by: John Halley Gotway <[email protected]> * New issue template: Update Truth (#2332) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for run_util, 'Usage' bugfix (#2313) * Feature #2338 Debian 12 Conda environments (#2341) Co-authored-by: John Halley Gotway <[email protected]> * Feature 1488 usecase satwinds (#2324) Co-authored-by: George McCabe <[email protected]> * Feature #2283 include times (#2345) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for config_validate, mock logger in conftest (#2320) * Feature #2299 / #2310 Remove deprecated MET config env vars and TCMPRPlotter (#2347) Co-authored-by: John Halley Gotway <[email protected]> * remove MODEL and OBTYPE to use defaults from MET config * Feature #2348 v6.0.0-beta1 release (#2351) * update version for development towards 6.0.0-beta2 release * copy libGL and libEGL files into docker image to prevent errors with geovista python package * run use that uses geovista to test * Feature #2156 release_acceptance_testing (#2352) * feature #2253 print error logs from conftest (#2358) * feature #2253 met_db_load tests (#2355) * Rename 5.1.0.lua_wcoss2 to 6.0.0.lua_wcoss2 * Update and rename 5.1.0_acorn to 6.0.0_acorn * Update 6.0.0_acorn * feature #2253 add tests for gfdl_tracker (#2354) Co-authored-by: George McCabe <[email protected]> * Create 6.0.0_gaea * Update and rename 5.1.0_hera to 6.0.0_hera * Feature #2156 release_acceptance_testing take2 (#2361) Co-authored-by: lisagoodrich <[email protected]> * Feature #2329 Docker info in Installation Chapter (#2366) * feature_2253_extract_tiles_tests (#2368) * Feature 2253 tc pairs tests (#2369) * Feature 2253 tc csv writer (#2373) * 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 * 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 * Feature #2340 TCDiag one_time_per_file_flag (#2374) * Update and rename 5.1.0_jet to 6.0.0_jet * Added libssh * prune docker files before running use cases to prevent running out of disk space when running use cases, ci-run-all-diff * Feature 2253 command builder tests (#2378) * Feature 2253 series analysis test (#2380) * Feature 2253 py embed test (#2379) * ignore cyclone plotter from code coverage report because it will be replaced with METplotpy logic * Feature 898 headers (#2389) * 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 <[email protected]> * 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 <[email protected]> --------- Co-authored-by: George McCabe <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> * Feature #2349 upgrade instructions for deprecated MET config files (#2386) * Feature 2123 di doc update (#2392) Co-authored-by: Tracy <[email protected]> * change log to list name of config variable , e.g. GRID_STAT_CONFIG_FILE, to easily see which variable should be removed * Feature 1667 doc conventions (#2397) * 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 <[email protected]> * Feature #2377 Log to terminal only (#2398) * Update conda envs to use conda-forge only (#2402) * rearrange MET config env var tables for GridStat so they are in the order that they appear in the wrapped MET config file * use mamba instead of conda and update version of netcdf python package used to 1.6.2 * skip s2s_mid_lat WeatherRegime use case that produces different results often * updated version of xesmf because <0.7.1 does not work with mamba * per #2412, fix bug in GenVxMask to put quotes around argument so a grid specification string with spaces will be an accepted value * downgrade version of esmf package to fix bug described in pangeo-data/xESMF#246 * Feature #2219 SeriesAnalysis multiple input files (#2408) * Adding 3 new requestors to the list of common_labels.txt for NOAA/NHC, CSU/CIRA, and Australian BOM ci-skip-all * Feature 2405 match tables2wrapper (#2416) Co-authored-by: George McCabe <[email protected]> * per #2423, follow symbolic links when traversing directories to find files within a time window, ci-run-all-diff * Feature #2252 WaveletStat wrapper (#2427) Co-authored-by: j-opatz <[email protected]> * add WaveletStat use case to group and temporarily disable TCDiag use case because changes to the wrapper are needed to fix it after changes to the MET tool were merged * update version number for beta2 release (#2431) * update version for dev towards beta3 * Feature #2371 Embed use case upgrade demo video into upgrade instructions (#2444) * fix failing use case tests -- install python packages dateutil and requests 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 * remove commands to install geovista from source because it is now installed from conda * Feature #1989: Add OMI use case (#2457) Co-authored-by: George McCabe <[email protected]> * Feature #2432 TCDiag new config changes (#2453) * move medium range 10 use case into group with 3-5 to speed up runs * Feature #2334 land_mask (and topo_mask) in PointStat (#2456) * added use cases with pygrib * Feature #2430 TCPairs consensus.diag_required and consensus.diag_min_req (#2439) * Quickfix cloud use case desc imgs (#2464) * added pics, updated desc * add last two imgs * Fixing spelling and capitalization * Feature 2454 doc overview conv (#2471) * 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 <[email protected]> * 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 GHA Node20 deprecation warnings (#2473) * 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 * Feature dtcenter/MET#2796 develop - Fix error log artifact creation (#2475) * updated version of pillow to fix security vulnerability alerted by dependabot in PR #2477 * remove docker image after runtime image is created from metplus image and conda env image * turn on use case to test image removal * prune images if image tag doesn't exist -- it appears that if the image 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> * support commands that must run in the shell to see if || will work in docker image pruning step * try to fix image removal * Feature 2383 use case sat alt (#2480) * 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 * run image prune commands separately * changed shell back to false * split up use case groups so the same envs are used by a group to see if that resolves the disk space issues * turn off use cases * feature 2253 fix empty pytest logs (#2485) * added more commands to free up disk space as suggested in https://github.com/apache/flink/blob/master/tools/azure-pipelines/free_disk_space.sh, ci-run-all-cases * Feature 2406 redo usecase rrfs (#2488) * issue #2406 RRFS use case files * issue #2406 added usecase to tests * Issue #2406 added metplotpy and metcalcpy as dependencies * Feature #2460 allow missing input (#2493) * 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 * Feature #2491 v6.0.0 beta3 (#2495) * update version for beta3 release * fixed typos in release notes * update version to note development towards beta4 release * Per suggestion from @JohnHalleyGotway, create intermediate branch 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 * added quotes to prevent error in echo caused by parenthesis * fix incorrect command * Revert "fix incorrect command" This reverts commit e7dffb6. * Revert "added quotes to prevent error in echo caused by parenthesis" This reverts commit c1cb3c4. * Revert "Per suggestion from @JohnHalleyGotway, create intermediate branch 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. * Hotfix: Allow symbolic link to run_metplus.py to run (#2500) * Adding use case tests * Changing test environment * Testing environment changes * Documentation update * Updating Documentation * Updating documentation for disk space failure * Added new use case category * Fixing use case test * Fixing bug in use case file * Testing s2s after data removal * add back use cases that were accidentally removed * fix incorrect use case added * Setting tests to false for merge * Testing for old use cases * Setting tests to false for merge * update tests to update develop data -- modified commands to create new 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 * Feature 2463 modify table (#2508) * 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 <[email protected]> Co-authored-by: George McCabe <[email protected]> --------- Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Lisa Goodrich <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: John Sharples <[email protected]> Co-authored-by: root <root@localhost> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: reza-armuei <[email protected]> Co-authored-by: Tracy <[email protected]> Co-authored-by: Mallory Row <[email protected]> Co-authored-by: bikegeek <[email protected]>

@JohnHalleyGotway

* Adding files for jet and hera * added commented process list that was accidentally removed -- this is used if the pre-processing steps are needed * Bugfix #2087 develop docs_pdf (#2091) * Feature 2076 release dropdown menu (#2083) * test dropdowns * Update release-notes.rst Attempting to resolve WARNING * testing dropdowns * adding dropdown menus * testing dropdown remove from warning section * dropdown testing * dropdown menu tests * dropdown menus after the warnings section, the dropdown menu only has one space instead of the normal 2 spaces. If it has 2 spaces, it gets sucked into the warning section. * spaces with warning * no spaces for warning * Update release-notes.rst warning note has to be indented 1 space. Originally it was no spaces but then all of the dropdown menus end up in the warning message. If it's 2 spaces, as is normal, then the warning is indented, which is unnecessary. 1 space is slightly indented and keeps the dropdown menus separate. --------- Co-authored-by: jprestop <[email protected]> * Bugfix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) * Feature 1516 use case mvmode (#2094) Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: George McCabe <[email protected]> * Fix for Dockerfile smell DL4000 (#2112) Co-authored-by: Giovanni Rosa <[email protected]> * Changed "PROJECT" to "CYCLE" ASSIGNMENT * Feature 2115 update use cases (#2133) * Bugfix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) * Bugfix #2137 develop PointStat -obs_valid_beg/end (#2141) * Feature #2143 5.1.0-beta2 release (#2144) * update release guide steps with new info based on changes to GitHub web interface * update version for development towards rc1 release * Feature #1977 ARGO use case (#2148) Co-authored-by: j-opatz <[email protected]> * Feature develop cycle change (#2150) * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * Added paths to ignore --------- Co-authored-by: jprestop <[email protected]> * Documentation: Update Truth Data instructions (#2154) * upgrade python to 3.10 for documentation builds to fix failured introduced by urllib3 (see urllib3/urllib3#2168) * update workflow to update input test data to use branch from pull down or enter branch by hand if branch does not exist in dtcenter/METplus repo, e.g. if updating data for a PR coming from a fork * Bugfix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) * changed order of workflow event triggering info to more easily see the repository and commit sha that triggered the workflow * fix docker compose install and call -- needed due to new Alpine Linux release 3.18.0 that does not include docker-compose in the apk repository * Bugfix #2168 develop - StatAnalysis time shift (#2169) * Feature 1978 update pyreq doc (#2177) * Updating for 5.1.0 * Adding greater than or equal to signs * Feature 2106 release support (#2182) * Added a paragraph for Release Support Policy * Added a sentence about contacting the team through the METplus GitHub Discussions Forum. * Added Release Support Policy info * Per #2159, modify instructions to reflect that we only want a coordinated release for the official releases and updates to the coordinated release section for the bugfix releases. (#2183) * Feature 2147 workflow doc (#2185) * Add new images for github workflow * Added PR section * Modified the Find the GitHub Issue to be Find or Create a GitHub issue * Trying out image keyword compared with figure keyword * Trying out various widths * Added new figures * Reverting to figures from images after modifying figures * Adding the old images which are better quality * Trying out new indention * Working on formatting again * Reducing image widths * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update github_workflow.rst --------- Co-authored-by: George McCabe <[email protected]> * added scripts to create new conda environment for PANDA-C use cases * Bugfix #2189 develop - spaces in complex thresholds (#2191) * added release notes for completed issues for rc1 * Feature 2011 tci from cesm fluxnet2015 netcdf (#2192) Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2179 develop TCPairs fix -diag argument (#2187) * sort list of files to make command more readable and make logic more easily testable * fix unit test to expect alphabetical order of files * Feature #2197 MODE new multi-variate options (#2203) * added to release notes * added release notes for other items completed for rc1 release * Feature #1626 TCDiag Wrapper (#2201) * Feature #1610 first round of SonarQube fixes (#2200) * Feature #2195 create v5.1.0-rc1 release (#2204) * Update version for development towards official release * updated script to use metplotpy as base and install pygrib because conda was failing trying to install matplotlib in Docker for some strange reason * Feature 2188 use case panda c (#2202) * added first use case, need to finish docs and add to list * added documentation files, 3 new cases * added 5th use case, docs * final use case, corrected paths for output * Update GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.py * removed chars, added space to last section * turn off 5/6 new air quality and comp use cases because they are causing the disk to fill up in the automated tests and only 1 is needed to test the new behavior. Reordered use case groups to be alphabetical * disabled other new air quality use case because the disk is still filling up from this case * Feature 2136 cross spectra (#2208) * per #2212, continue instead of return so other forecast leads will not be skipped * Feature #2210 MODE multi-variate variable rename (#2211) * Bugfix diff tests (#2217) * added change from NCEP produtil that was somehow not included in the changes pulled from their repo before starting SonarQube work * Feature #2228 v5.1.0-rc2 release (#2229) * update version after rc2 release to note development towards official 5.1.0 release * Feature #2188 move PANDA-C cases to clouds category and fix automated tests (#2237) Co-authored-by: j-opatz <[email protected]> * Feature 2198 use case amdar pbl (#2206) Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) * Feature #2230 MvMODE usecase doc updates (#2239) This updates the use-case documentation to go along with the multivariate MODE enhancements. * combine release notes from development releases for 5.1.0 release * fix indentation to prevent incorrect nesting of drop down menus * Bugfix #2241 Create directory containing -out_stat file (#2242) * Enhance diff logic to control decimal precision to prevent failures (#2243) * Bugfix #2245 use unique run ID to name logger instance (#2247) * per #2245, add METplusConfig class function that is called when object is deleted to close log handlers. This prevents OSError: [Errno 24] Too many open files from running all pytests * Feature #1626 TCDiag updates to wrapper and basic use case (#2248) Co-authored-by: Jonathan Vigh <[email protected]> * move new use case into another group * Bugfix #2244 develop fix diff tests (#2254) * skip diff for specific png images that produce diffs occasionally but look the same visually * add 2 more keywords for use cases that occasionally flag small, unnoticeable diffs in png images * Feature #2253 update tests for diff_util (#2256) Co-authored-by: root <root@localhost> * Feature #1974 Documentation: update coding standards section (#2260) * Feature #2253 conftest fixture to set pytest tmpdir (#2261) * Feature #2151 Documentation: Add quick search keywords METplotpy/calcpy use cases (#2259) * Feature #2138 CI enhance MET Docker tag override (#2258) * Updating development instructions. * fixed typo * fixed another typo * Feature #2207 Documentation - Updates to Contributor's Guide (#2263) Co-authored-by: Dan Adriaansen <[email protected]> * Feature develop update install files (#2266) * 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 * Bugfix #1853 develop - PointStat don't require mask variables to be set (#2262) * update version of certifi to match auto-generated dependabot PR #2267 * feature #2253 more tests for diff_util.py (#2264) * update versions of METplus components for the next official release * updated release notes for 5.1.0 release * removed duplicate entries in release notes * Added EC2 instance recipee with S3 mounting ability (#2269) * Updating the Subsetting Tests by Marker section (#2272) * update release date for 5.1.0 release (#2276) * update version for development towards 6.0.0-beta1 release * added new use case that was missing * Bugfix #2279 develop - buoy station file from 2022 (#2280) * Feature 2253 series analysis tests (#2277) * Fix typo in pull_request_template.md * Make code coverage report available (#2287) * Use updated dtcenter/metplus-action-data-update tag that fixes bug that 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 * removed climatology keyword from use cases that aren't relevant that were accidentally added with PR #1984 * update readme with current information * Feature #2282 coord_release_docs (#2288) Co-authored-by: George McCabe <[email protected]> * continue workflow if coveralls step fails -- this typically happens on a pull request from a fork because the authentication fails * Feature 2253 system util tests (#2297) * Feature #2294 LSR use case (#2295) * Feature 2253 run util tests (#2307) * Release Guide - remove beta/rc tags/releases (#2309) * Add 'component: repository maintenance' label. Already ran the script to push this change and the NOAA OAR reporting label to all the METplus repos. * Hotfix for labels, adding a new one for 'component: input data' and also fixing the get_lablels.sh to search for up to 200 existing labels. Also work on the log messages. * Fix typo in comment * Feature #2283 time looping consolidation (#2311) Co-authored-by: John Halley Gotway <[email protected]> * New issue template: Update Truth (#2332) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for run_util, 'Usage' bugfix (#2313) * Feature #2338 Debian 12 Conda environments (#2341) Co-authored-by: John Halley Gotway <[email protected]> * Feature 1488 usecase satwinds (#2324) Co-authored-by: George McCabe <[email protected]> * Feature #2283 include times (#2345) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for config_validate, mock logger in conftest (#2320) * Feature #2299 / #2310 Remove deprecated MET config env vars and TCMPRPlotter (#2347) Co-authored-by: John Halley Gotway <[email protected]> * remove MODEL and OBTYPE to use defaults from MET config * Feature #2348 v6.0.0-beta1 release (#2351) * update version for development towards 6.0.0-beta2 release * copy libGL and libEGL files into docker image to prevent errors with geovista python package * run use that uses geovista to test * Feature #2156 release_acceptance_testing (#2352) * feature #2253 print error logs from conftest (#2358) * feature #2253 met_db_load tests (#2355) * Rename 5.1.0.lua_wcoss2 to 6.0.0.lua_wcoss2 * Update and rename 5.1.0_acorn to 6.0.0_acorn * Update 6.0.0_acorn * feature #2253 add tests for gfdl_tracker (#2354) Co-authored-by: George McCabe <[email protected]> * Create 6.0.0_gaea * Update and rename 5.1.0_hera to 6.0.0_hera * Feature #2156 release_acceptance_testing take2 (#2361) Co-authored-by: lisagoodrich <[email protected]> * Feature #2329 Docker info in Installation Chapter (#2366) * feature_2253_extract_tiles_tests (#2368) * Feature 2253 tc pairs tests (#2369) * Feature 2253 tc csv writer (#2373) * 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 * 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 * Feature #2340 TCDiag one_time_per_file_flag (#2374) * Update and rename 5.1.0_jet to 6.0.0_jet * Added libssh * prune docker files before running use cases to prevent running out of disk space when running use cases, ci-run-all-diff * Feature 2253 command builder tests (#2378) * Feature 2253 series analysis test (#2380) * Feature 2253 py embed test (#2379) * ignore cyclone plotter from code coverage report because it will be replaced with METplotpy logic * Feature 898 headers (#2389) * 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 <[email protected]> * 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 <[email protected]> --------- Co-authored-by: George McCabe <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> * Feature #2349 upgrade instructions for deprecated MET config files (#2386) * Feature 2123 di doc update (#2392) Co-authored-by: Tracy <[email protected]> * change log to list name of config variable , e.g. GRID_STAT_CONFIG_FILE, to easily see which variable should be removed * Feature 1667 doc conventions (#2397) * 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 <[email protected]> * Feature #2377 Log to terminal only (#2398) * Update conda envs to use conda-forge only (#2402) * rearrange MET config env var tables for GridStat so they are in the order that they appear in the wrapped MET config file * use mamba instead of conda and update version of netcdf python package used to 1.6.2 * skip s2s_mid_lat WeatherRegime use case that produces different results often * updated version of xesmf because <0.7.1 does not work with mamba * per #2412, fix bug in GenVxMask to put quotes around argument so a grid specification string with spaces will be an accepted value * downgrade version of esmf package to fix bug described in pangeo-data/xESMF#246 * Feature #2219 SeriesAnalysis multiple input files (#2408) * Adding 3 new requestors to the list of common_labels.txt for NOAA/NHC, CSU/CIRA, and Australian BOM ci-skip-all * Feature 2405 match tables2wrapper (#2416) Co-authored-by: George McCabe <[email protected]> * per #2423, follow symbolic links when traversing directories to find files within a time window, ci-run-all-diff * Feature #2252 WaveletStat wrapper (#2427) Co-authored-by: j-opatz <[email protected]> * add WaveletStat use case to group and temporarily disable TCDiag use case because changes to the wrapper are needed to fix it after changes to the MET tool were merged * update version number for beta2 release (#2431) * update version for dev towards beta3 * Feature #2371 Embed use case upgrade demo video into upgrade instructions (#2444) * fix failing use case tests -- install python packages dateutil and requests 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 * remove commands to install geovista from source because it is now installed from conda * Feature #1989: Add OMI use case (#2457) Co-authored-by: George McCabe <[email protected]> * Feature #2432 TCDiag new config changes (#2453) * move medium range 10 use case into group with 3-5 to speed up runs * Feature #2334 land_mask (and topo_mask) in PointStat (#2456) * added use cases with pygrib * Feature #2430 TCPairs consensus.diag_required and consensus.diag_min_req (#2439) * Quickfix cloud use case desc imgs (#2464) * added pics, updated desc * add last two imgs * Fixing spelling and capitalization * Feature 2454 doc overview conv (#2471) * 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 <[email protected]> * 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 GHA Node20 deprecation warnings (#2473) * 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 * Feature dtcenter/MET#2796 develop - Fix error log artifact creation (#2475) * updated version of pillow to fix security vulnerability alerted by dependabot in PR #2477 * remove docker image after runtime image is created from metplus image and conda env image * turn on use case to test image removal * prune images if image tag doesn't exist -- it appears that if the image 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> * support commands that must run in the shell to see if || will work in docker image pruning step * try to fix image removal * Feature 2383 use case sat alt (#2480) * 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 * run image prune commands separately * changed shell back to false * split up use case groups so the same envs are used by a group to see if that resolves the disk space issues * turn off use cases * feature 2253 fix empty pytest logs (#2485) * added more commands to free up disk space as suggested in https://github.com/apache/flink/blob/master/tools/azure-pipelines/free_disk_space.sh, ci-run-all-cases * Feature 2406 redo usecase rrfs (#2488) * issue #2406 RRFS use case files * issue #2406 added usecase to tests * Issue #2406 added metplotpy and metcalcpy as dependencies * Feature #2460 allow missing input (#2493) * 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 * Feature #2491 v6.0.0 beta3 (#2495) * update version for beta3 release * fixed typos in release notes * update version to note development towards beta4 release * Per suggestion from @JohnHalleyGotway, create intermediate branch 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 * added quotes to prevent error in echo caused by parenthesis * fix incorrect command * Revert "fix incorrect command" This reverts commit e7dffb6. * Revert "added quotes to prevent error in echo caused by parenthesis" This reverts commit c1cb3c4. * Revert "Per suggestion from @JohnHalleyGotway, create intermediate branch 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. * Hotfix: Allow symbolic link to run_metplus.py to run (#2500) * Adding use case tests * Changing test environment * Testing environment changes * Documentation update * Updating Documentation * Updating documentation for disk space failure * Added new use case category * Fixing use case test * Fixing bug in use case file * Testing s2s after data removal * add back use cases that were accidentally removed * fix incorrect use case added * Setting tests to false for merge * Testing for old use cases * Setting tests to false for merge * update tests to update develop data -- modified commands to create new 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 * Feature 2463 modify table (#2508) * 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 <[email protected]> Co-authored-by: George McCabe <[email protected]> * per #2509, automate MET version used in documentation to be X+6.Y.0 of METplus version * Bugfix #2520 ASCII2NC file window issue and redundant wrapper initialization (#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 * Update update_truth.md Fix typo in the update_truth issue template in the develop branch. * Update update_truth.md Update wording in the update_truth issue template. --------- Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: John Sharples <[email protected]> Co-authored-by: root <root@localhost> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: reza-armuei <[email protected]> Co-authored-by: Tracy <[email protected]> Co-authored-by: Mallory Row <[email protected]> Co-authored-by: bikegeek <[email protected]>

@JohnHalleyGotway

* Fix for Dockerfile smell DL4000 (#2112) Co-authored-by: Giovanni Rosa <[email protected]> * Changed "PROJECT" to "CYCLE" ASSIGNMENT * Feature 2115 update use cases (#2133) * Bugfix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) * Bugfix #2137 develop PointStat -obs_valid_beg/end (#2141) * Feature #2143 5.1.0-beta2 release (#2144) * update release guide steps with new info based on changes to GitHub web interface * update version for development towards rc1 release * Feature #1977 ARGO use case (#2148) Co-authored-by: j-opatz <[email protected]> * Feature develop cycle change (#2150) * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * change PROJECT ASSIGNMENT to CYCLE ASSIGNMENT * Added paths to ignore --------- Co-authored-by: jprestop <[email protected]> * Documentation: Update Truth Data instructions (#2154) * upgrade python to 3.10 for documentation builds to fix failured introduced by urllib3 (see urllib3/urllib3#2168) * update workflow to update input test data to use branch from pull down or enter branch by hand if branch does not exist in dtcenter/METplus repo, e.g. if updating data for a PR coming from a fork * Bugfix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) * changed order of workflow event triggering info to more easily see the repository and commit sha that triggered the workflow * fix docker compose install and call -- needed due to new Alpine Linux release 3.18.0 that does not include docker-compose in the apk repository * Bugfix #2168 develop - StatAnalysis time shift (#2169) * Feature 1978 update pyreq doc (#2177) * Updating for 5.1.0 * Adding greater than or equal to signs * Feature 2106 release support (#2182) * Added a paragraph for Release Support Policy * Added a sentence about contacting the team through the METplus GitHub Discussions Forum. * Added Release Support Policy info * Per #2159, modify instructions to reflect that we only want a coordinated release for the official releases and updates to the coordinated release section for the bugfix releases. (#2183) * Feature 2147 workflow doc (#2185) * Add new images for github workflow * Added PR section * Modified the Find the GitHub Issue to be Find or Create a GitHub issue * Trying out image keyword compared with figure keyword * Trying out various widths * Added new figures * Reverting to figures from images after modifying figures * Adding the old images which are better quality * Trying out new indention * Working on formatting again * Reducing image widths * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <[email protected]> * Update github_workflow.rst --------- Co-authored-by: George McCabe <[email protected]> * added scripts to create new conda environment for PANDA-C use cases * Bugfix #2189 develop - spaces in complex thresholds (#2191) * added release notes for completed issues for rc1 * Feature 2011 tci from cesm fluxnet2015 netcdf (#2192) Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2179 develop TCPairs fix -diag argument (#2187) * sort list of files to make command more readable and make logic more easily testable * fix unit test to expect alphabetical order of files * Feature #2197 MODE new multi-variate options (#2203) * added to release notes * added release notes for other items completed for rc1 release * Feature #1626 TCDiag Wrapper (#2201) * Feature #1610 first round of SonarQube fixes (#2200) * Feature #2195 create v5.1.0-rc1 release (#2204) * Update version for development towards official release * updated script to use metplotpy as base and install pygrib because conda was failing trying to install matplotlib in Docker for some strange reason * Feature 2188 use case panda c (#2202) * added first use case, need to finish docs and add to list * added documentation files, 3 new cases * added 5th use case, docs * final use case, corrected paths for output * Update GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.py * removed chars, added space to last section * turn off 5/6 new air quality and comp use cases because they are causing the disk to fill up in the automated tests and only 1 is needed to test the new behavior. Reordered use case groups to be alphabetical * disabled other new air quality use case because the disk is still filling up from this case * Feature 2136 cross spectra (#2208) * per #2212, continue instead of return so other forecast leads will not be skipped * Feature #2210 MODE multi-variate variable rename (#2211) * Bugfix diff tests (#2217) * added change from NCEP produtil that was somehow not included in the changes pulled from their repo before starting SonarQube work * Feature #2228 v5.1.0-rc2 release (#2229) * update version after rc2 release to note development towards official 5.1.0 release * Feature #2188 move PANDA-C cases to clouds category and fix automated tests (#2237) Co-authored-by: j-opatz <[email protected]> * Feature 2198 use case amdar pbl (#2206) Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) * Feature #2230 MvMODE usecase doc updates (#2239) This updates the use-case documentation to go along with the multivariate MODE enhancements. * combine release notes from development releases for 5.1.0 release * fix indentation to prevent incorrect nesting of drop down menus * Bugfix #2241 Create directory containing -out_stat file (#2242) * Enhance diff logic to control decimal precision to prevent failures (#2243) * Bugfix #2245 use unique run ID to name logger instance (#2247) * per #2245, add METplusConfig class function that is called when object is deleted to close log handlers. This prevents OSError: [Errno 24] Too many open files from running all pytests * Feature #1626 TCDiag updates to wrapper and basic use case (#2248) Co-authored-by: Jonathan Vigh <[email protected]> * move new use case into another group * Bugfix #2244 develop fix diff tests (#2254) * skip diff for specific png images that produce diffs occasionally but look the same visually * add 2 more keywords for use cases that occasionally flag small, unnoticeable diffs in png images * Feature #2253 update tests for diff_util (#2256) Co-authored-by: root <root@localhost> * Feature #1974 Documentation: update coding standards section (#2260) * Feature #2253 conftest fixture to set pytest tmpdir (#2261) * Feature #2151 Documentation: Add quick search keywords METplotpy/calcpy use cases (#2259) * Feature #2138 CI enhance MET Docker tag override (#2258) * Updating development instructions. * fixed typo * fixed another typo * Feature #2207 Documentation - Updates to Contributor's Guide (#2263) Co-authored-by: Dan Adriaansen <[email protected]> * Feature develop update install files (#2266) * 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 * Bugfix #1853 develop - PointStat don't require mask variables to be set (#2262) * update version of certifi to match auto-generated dependabot PR #2267 * feature #2253 more tests for diff_util.py (#2264) * update versions of METplus components for the next official release * updated release notes for 5.1.0 release * removed duplicate entries in release notes * Added EC2 instance recipee with S3 mounting ability (#2269) * Updating the Subsetting Tests by Marker section (#2272) * update release date for 5.1.0 release (#2276) * update version for development towards 6.0.0-beta1 release * added new use case that was missing * Bugfix #2279 develop - buoy station file from 2022 (#2280) * Feature 2253 series analysis tests (#2277) * Fix typo in pull_request_template.md * Make code coverage report available (#2287) * Use updated dtcenter/metplus-action-data-update tag that fixes bug that 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 * removed climatology keyword from use cases that aren't relevant that were accidentally added with PR #1984 * update readme with current information * Feature #2282 coord_release_docs (#2288) Co-authored-by: George McCabe <[email protected]> * continue workflow if coveralls step fails -- this typically happens on a pull request from a fork because the authentication fails * Feature 2253 system util tests (#2297) * Feature #2294 LSR use case (#2295) * Feature 2253 run util tests (#2307) * Release Guide - remove beta/rc tags/releases (#2309) * Add 'component: repository maintenance' label. Already ran the script to push this change and the NOAA OAR reporting label to all the METplus repos. * Hotfix for labels, adding a new one for 'component: input data' and also fixing the get_lablels.sh to search for up to 200 existing labels. Also work on the log messages. * Fix typo in comment * Feature #2283 time looping consolidation (#2311) Co-authored-by: John Halley Gotway <[email protected]> * New issue template: Update Truth (#2332) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for run_util, 'Usage' bugfix (#2313) * Feature #2338 Debian 12 Conda environments (#2341) Co-authored-by: John Halley Gotway <[email protected]> * Feature 1488 usecase satwinds (#2324) Co-authored-by: George McCabe <[email protected]> * Feature #2283 include times (#2345) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for config_validate, mock logger in conftest (#2320) * Feature #2299 / #2310 Remove deprecated MET config env vars and TCMPRPlotter (#2347) Co-authored-by: John Halley Gotway <[email protected]> * remove MODEL and OBTYPE to use defaults from MET config * Feature #2348 v6.0.0-beta1 release (#2351) * update version for development towards 6.0.0-beta2 release * copy libGL and libEGL files into docker image to prevent errors with geovista python package * run use that uses geovista to test * Feature #2156 release_acceptance_testing (#2352) * feature #2253 print error logs from conftest (#2358) * feature #2253 met_db_load tests (#2355) * Rename 5.1.0.lua_wcoss2 to 6.0.0.lua_wcoss2 * Update and rename 5.1.0_acorn to 6.0.0_acorn * Update 6.0.0_acorn * feature #2253 add tests for gfdl_tracker (#2354) Co-authored-by: George McCabe <[email protected]> * Create 6.0.0_gaea * Update and rename 5.1.0_hera to 6.0.0_hera * Feature #2156 release_acceptance_testing take2 (#2361) Co-authored-by: lisagoodrich <[email protected]> * Feature #2329 Docker info in Installation Chapter (#2366) * feature_2253_extract_tiles_tests (#2368) * Feature 2253 tc pairs tests (#2369) * Feature 2253 tc csv writer (#2373) * 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 * 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 * Feature #2340 TCDiag one_time_per_file_flag (#2374) * Update and rename 5.1.0_jet to 6.0.0_jet * Added libssh * prune docker files before running use cases to prevent running out of disk space when running use cases, ci-run-all-diff * Feature 2253 command builder tests (#2378) * Feature 2253 series analysis test (#2380) * Feature 2253 py embed test (#2379) * ignore cyclone plotter from code coverage report because it will be replaced with METplotpy logic * Feature 898 headers (#2389) * 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 <[email protected]> * 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 <[email protected]> --------- Co-authored-by: George McCabe <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> * Feature #2349 upgrade instructions for deprecated MET config files (#2386) * Feature 2123 di doc update (#2392) Co-authored-by: Tracy <[email protected]> * change log to list name of config variable , e.g. GRID_STAT_CONFIG_FILE, to easily see which variable should be removed * Feature 1667 doc conventions (#2397) * 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 <[email protected]> * Feature #2377 Log to terminal only (#2398) * Update conda envs to use conda-forge only (#2402) * rearrange MET config env var tables for GridStat so they are in the order that they appear in the wrapped MET config file * use mamba instead of conda and update version of netcdf python package used to 1.6.2 * skip s2s_mid_lat WeatherRegime use case that produces different results often * updated version of xesmf because <0.7.1 does not work with mamba * per #2412, fix bug in GenVxMask to put quotes around argument so a grid specification string with spaces will be an accepted value * downgrade version of esmf package to fix bug described in pangeo-data/xESMF#246 * Feature #2219 SeriesAnalysis multiple input files (#2408) * Adding 3 new requestors to the list of common_labels.txt for NOAA/NHC, CSU/CIRA, and Australian BOM ci-skip-all * Feature 2405 match tables2wrapper (#2416) Co-authored-by: George McCabe <[email protected]> * per #2423, follow symbolic links when traversing directories to find files within a time window, ci-run-all-diff * Feature #2252 WaveletStat wrapper (#2427) Co-authored-by: j-opatz <[email protected]> * add WaveletStat use case to group and temporarily disable TCDiag use case because changes to the wrapper are needed to fix it after changes to the MET tool were merged * update version number for beta2 release (#2431) * update version for dev towards beta3 * Feature #2371 Embed use case upgrade demo video into upgrade instructions (#2444) * fix failing use case tests -- install python packages dateutil and requests 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 * remove commands to install geovista from source because it is now installed from conda * Feature #1989: Add OMI use case (#2457) Co-authored-by: George McCabe <[email protected]> * Feature #2432 TCDiag new config changes (#2453) * move medium range 10 use case into group with 3-5 to speed up runs * Feature #2334 land_mask (and topo_mask) in PointStat (#2456) * added use cases with pygrib * Feature #2430 TCPairs consensus.diag_required and consensus.diag_min_req (#2439) * Quickfix cloud use case desc imgs (#2464) * added pics, updated desc * add last two imgs * Fixing spelling and capitalization * Feature 2454 doc overview conv (#2471) * 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 <[email protected]> * 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 GHA Node20 deprecation warnings (#2473) * 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 * Feature dtcenter/MET#2796 develop - Fix error log artifact creation (#2475) * updated version of pillow to fix security vulnerability alerted by dependabot in PR #2477 * remove docker image after runtime image is created from metplus image and conda env image * turn on use case to test image removal * prune images if image tag doesn't exist -- it appears that if the image 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> * support commands that must run in the shell to see if || will work in docker image pruning step * try to fix image removal * Feature 2383 use case sat alt (#2480) * 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 * run image prune commands separately * changed shell back to false * split up use case groups so the same envs are used by a group to see if that resolves the disk space issues * turn off use cases * feature 2253 fix empty pytest logs (#2485) * added more commands to free up disk space as suggested in https://github.com/apache/flink/blob/master/tools/azure-pipelines/free_disk_space.sh, ci-run-all-cases * Feature 2406 redo usecase rrfs (#2488) * issue #2406 RRFS use case files * issue #2406 added usecase to tests * Issue #2406 added metplotpy and metcalcpy as dependencies * Feature #2460 allow missing input (#2493) * 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 * Feature #2491 v6.0.0 beta3 (#2495) * update version for beta3 release * fixed typos in release notes * update version to note development towards beta4 release * Per suggestion from @JohnHalleyGotway, create intermediate branch 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 * added quotes to prevent error in echo caused by parenthesis * fix incorrect command * Revert "fix incorrect command" This reverts commit e7dffb6. * Revert "added quotes to prevent error in echo caused by parenthesis" This reverts commit c1cb3c4. * Revert "Per suggestion from @JohnHalleyGotway, create intermediate branch 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. * Hotfix: Allow symbolic link to run_metplus.py to run (#2500) * Adding use case tests * Changing test environment * Testing environment changes * Documentation update * Updating Documentation * Updating documentation for disk space failure * Added new use case category * Fixing use case test * Fixing bug in use case file * Testing s2s after data removal * add back use cases that were accidentally removed * fix incorrect use case added * Setting tests to false for merge * Testing for old use cases * Setting tests to false for merge * update tests to update develop data -- modified commands to create new 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 * Feature 2463 modify table (#2508) * 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 <[email protected]> Co-authored-by: George McCabe <[email protected]> * per #2509, automate MET version used in documentation to be X+6.Y.0 of METplus version * Bugfix #2520 ASCII2NC file window issue and redundant wrapper initialization (#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 * Update update_truth.md Fix typo in the update_truth issue template in the develop branch. * Update update_truth.md Update wording in the update_truth issue template. * Feature #2530 dev timeline (#2532) * 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 <[email protected]> --------- Co-authored-by: Julie Prestopnik <[email protected]> * Feature #2537 develop sonarqube_gha (#2541) * 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. * Update the 6.0.0 Coordinated Release development timeline in release-notes.rst * Added optional key/value to use_case_groups.json to prevent a use case group from running to easily disable it temporarily. Disable short_range:14 use case until it can be fixed with #2551 * update pillow version based on recommendation from dependabot: https://github.com/dtcenter/METplus/security/dependabot/5 --------- Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: Giovanni Rosa <[email protected]> Co-authored-by: jprestop <[email protected]> Co-authored-by: Dan Adriaansen <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: mrinalbiswas <[email protected]> Co-authored-by: Mrinal Biswas <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: John Sharples <[email protected]> Co-authored-by: root <root@localhost> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: reza-armuei <[email protected]> Co-authored-by: Tracy <[email protected]> Co-authored-by: Mallory Row <[email protected]> Co-authored-by: bikegeek <[email protected]>

@JohnHalleyGotway

* added release notes for other items completed for rc1 release * Feature #1626 TCDiag Wrapper (#2201) * Feature #1610 first round of SonarQube fixes (#2200) * Feature #2195 create v5.1.0-rc1 release (#2204) * Update version for development towards official release * updated script to use metplotpy as base and install pygrib because conda was failing trying to install matplotlib in Docker for some strange reason * Feature 2188 use case panda c (#2202) * added first use case, need to finish docs and add to list * added documentation files, 3 new cases * added 5th use case, docs * final use case, corrected paths for output * Update GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.py * removed chars, added space to last section * turn off 5/6 new air quality and comp use cases because they are causing the disk to fill up in the automated tests and only 1 is needed to test the new behavior. Reordered use case groups to be alphabetical * disabled other new air quality use case because the disk is still filling up from this case * Feature 2136 cross spectra (#2208) * per #2212, continue instead of return so other forecast leads will not be skipped * Feature #2210 MODE multi-variate variable rename (#2211) * Bugfix diff tests (#2217) * added change from NCEP produtil that was somehow not included in the changes pulled from their repo before starting SonarQube work * Feature #2228 v5.1.0-rc2 release (#2229) * update version after rc2 release to note development towards official 5.1.0 release * Feature #2188 move PANDA-C cases to clouds category and fix automated tests (#2237) Co-authored-by: j-opatz <[email protected]> * Feature 2198 use case amdar pbl (#2206) Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: George McCabe <[email protected]> * Bugfix #2235 rename multivar_itensity to multivar_intensity_flag (#2236) * Feature #2230 MvMODE usecase doc updates (#2239) This updates the use-case documentation to go along with the multivariate MODE enhancements. * combine release notes from development releases for 5.1.0 release * fix indentation to prevent incorrect nesting of drop down menus * Bugfix #2241 Create directory containing -out_stat file (#2242) * Enhance diff logic to control decimal precision to prevent failures (#2243) * Bugfix #2245 use unique run ID to name logger instance (#2247) * per #2245, add METplusConfig class function that is called when object is deleted to close log handlers. This prevents OSError: [Errno 24] Too many open files from running all pytests * Feature #1626 TCDiag updates to wrapper and basic use case (#2248) Co-authored-by: Jonathan Vigh <[email protected]> * move new use case into another group * Bugfix #2244 develop fix diff tests (#2254) * skip diff for specific png images that produce diffs occasionally but look the same visually * add 2 more keywords for use cases that occasionally flag small, unnoticeable diffs in png images * Feature #2253 update tests for diff_util (#2256) Co-authored-by: root <root@localhost> * Feature #1974 Documentation: update coding standards section (#2260) * Feature #2253 conftest fixture to set pytest tmpdir (#2261) * Feature #2151 Documentation: Add quick search keywords METplotpy/calcpy use cases (#2259) * Feature #2138 CI enhance MET Docker tag override (#2258) * Updating development instructions. * fixed typo * fixed another typo * Feature #2207 Documentation - Updates to Contributor's Guide (#2263) Co-authored-by: Dan Adriaansen <[email protected]> * Feature develop update install files (#2266) * 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 * Bugfix #1853 develop - PointStat don't require mask variables to be set (#2262) * update version of certifi to match auto-generated dependabot PR #2267 * feature #2253 more tests for diff_util.py (#2264) * update versions of METplus components for the next official release * updated release notes for 5.1.0 release * removed duplicate entries in release notes * Added EC2 instance recipee with S3 mounting ability (#2269) * Updating the Subsetting Tests by Marker section (#2272) * update release date for 5.1.0 release (#2276) * update version for development towards 6.0.0-beta1 release * added new use case that was missing * Bugfix #2279 develop - buoy station file from 2022 (#2280) * Feature 2253 series analysis tests (#2277) * Fix typo in pull_request_template.md * Make code coverage report available (#2287) * Use updated dtcenter/metplus-action-data-update tag that fixes bug that 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 * removed climatology keyword from use cases that aren't relevant that were accidentally added with PR #1984 * update readme with current information * Feature #2282 coord_release_docs (#2288) Co-authored-by: George McCabe <[email protected]> * continue workflow if coveralls step fails -- this typically happens on a pull request from a fork because the authentication fails * Feature 2253 system util tests (#2297) * Feature #2294 LSR use case (#2295) * Feature 2253 run util tests (#2307) * Release Guide - remove beta/rc tags/releases (#2309) * Add 'component: repository maintenance' label. Already ran the script to push this change and the NOAA OAR reporting label to all the METplus repos. * Hotfix for labels, adding a new one for 'component: input data' and also fixing the get_lablels.sh to search for up to 200 existing labels. Also work on the log messages. * Fix typo in comment * Feature #2283 time looping consolidation (#2311) Co-authored-by: John Halley Gotway <[email protected]> * New issue template: Update Truth (#2332) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for run_util, 'Usage' bugfix (#2313) * Feature #2338 Debian 12 Conda environments (#2341) Co-authored-by: John Halley Gotway <[email protected]> * Feature 1488 usecase satwinds (#2324) Co-authored-by: George McCabe <[email protected]> * Feature #2283 include times (#2345) Co-authored-by: John Halley Gotway <[email protected]> * feature #2253 tests for config_validate, mock logger in conftest (#2320) * Feature #2299 / #2310 Remove deprecated MET config env vars and TCMPRPlotter (#2347) Co-authored-by: John Halley Gotway <[email protected]> * remove MODEL and OBTYPE to use defaults from MET config * Feature #2348 v6.0.0-beta1 release (#2351) * update version for development towards 6.0.0-beta2 release * copy libGL and libEGL files into docker image to prevent errors with geovista python package * run use that uses geovista to test * Feature #2156 release_acceptance_testing (#2352) * feature #2253 print error logs from conftest (#2358) * feature #2253 met_db_load tests (#2355) * Rename 5.1.0.lua_wcoss2 to 6.0.0.lua_wcoss2 * Update and rename 5.1.0_acorn to 6.0.0_acorn * Update 6.0.0_acorn * feature #2253 add tests for gfdl_tracker (#2354) Co-authored-by: George McCabe <[email protected]> * Create 6.0.0_gaea * Update and rename 5.1.0_hera to 6.0.0_hera * Feature #2156 release_acceptance_testing take2 (#2361) Co-authored-by: lisagoodrich <[email protected]> * Feature #2329 Docker info in Installation Chapter (#2366) * feature_2253_extract_tiles_tests (#2368) * Feature 2253 tc pairs tests (#2369) * Feature 2253 tc csv writer (#2373) * 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 * 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 * Feature #2340 TCDiag one_time_per_file_flag (#2374) * Update and rename 5.1.0_jet to 6.0.0_jet * Added libssh * prune docker files before running use cases to prevent running out of disk space when running use cases, ci-run-all-diff * Feature 2253 command builder tests (#2378) * Feature 2253 series analysis test (#2380) * Feature 2253 py embed test (#2379) * ignore cyclone plotter from code coverage report because it will be replaced with METplotpy logic * Feature 898 headers (#2389) * 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 <[email protected]> * 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 <[email protected]> --------- Co-authored-by: George McCabe <[email protected]> Co-authored-by: Julie Prestopnik <[email protected]> * Feature #2349 upgrade instructions for deprecated MET config files (#2386) * Feature 2123 di doc update (#2392) Co-authored-by: Tracy <[email protected]> * change log to list name of config variable , e.g. GRID_STAT_CONFIG_FILE, to easily see which variable should be removed * Major refactor including elimination of unnecessary imports, only computing 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. * Feature 1667 doc conventions (#2397) * 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 <[email protected]> * Feature #2377 Log to terminal only (#2398) * Update conda envs to use conda-forge only (#2402) * rearrange MET config env var tables for GridStat so they are in the order that they appear in the wrapped MET config file * use mamba instead of conda and update version of netcdf python package used to 1.6.2 * skip s2s_mid_lat WeatherRegime use case that produces different results often * updated version of xesmf because <0.7.1 does not work with mamba * per #2412, fix bug in GenVxMask to put quotes around argument so a grid specification string with spaces will be an accepted value * downgrade version of esmf package to fix bug described in pangeo-data/xESMF#246 * Feature #2219 SeriesAnalysis multiple input files (#2408) * Adding 3 new requestors to the list of common_labels.txt for NOAA/NHC, CSU/CIRA, and Australian BOM ci-skip-all * Feature 2405 match tables2wrapper (#2416) Co-authored-by: George McCabe <[email protected]> * per #2423, follow symbolic links when traversing directories to find files within a time window, ci-run-all-diff * Feature #2252 WaveletStat wrapper (#2427) Co-authored-by: j-opatz <[email protected]> * add WaveletStat use case to group and temporarily disable TCDiag use case because changes to the wrapper are needed to fix it after changes to the MET tool were merged * update version number for beta2 release (#2431) * update version for dev towards beta3 * Feature #2371 Embed use case upgrade demo video into upgrade instructions (#2444) * fix failing use case tests -- install python packages dateutil and requests 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 * remove commands to install geovista from source because it is now installed from conda * Feature #1989: Add OMI use case (#2457) Co-authored-by: George McCabe <[email protected]> * Feature #2432 TCDiag new config changes (#2453) * move medium range 10 use case into group with 3-5 to speed up runs * Feature #2334 land_mask (and topo_mask) in PointStat (#2456) * added use cases with pygrib * Feature #2430 TCPairs consensus.diag_required and consensus.diag_min_req (#2439) * Quickfix cloud use case desc imgs (#2464) * added pics, updated desc * add last two imgs * Fixing spelling and capitalization * Feature 2454 doc overview conv (#2471) * 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 <[email protected]> * 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 GHA Node20 deprecation warnings (#2473) * 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 * Feature dtcenter/MET#2796 develop - Fix error log artifact creation (#2475) * updated version of pillow to fix security vulnerability alerted by dependabot in PR #2477 * remove docker image after runtime image is created from metplus image and conda env image * turn on use case to test image removal * prune images if image tag doesn't exist -- it appears that if the image 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> * support commands that must run in the shell to see if || will work in docker image pruning step * try to fix image removal * Feature 2383 use case sat alt (#2480) * 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 * run image prune commands separately * changed shell back to false * split up use case groups so the same envs are used by a group to see if that resolves the disk space issues * turn off use cases * feature 2253 fix empty pytest logs (#2485) * added more commands to free up disk space as suggested in https://github.com/apache/flink/blob/master/tools/azure-pipelines/free_disk_space.sh, ci-run-all-cases * Feature 2406 redo usecase rrfs (#2488) * issue #2406 RRFS use case files * issue #2406 added usecase to tests * Issue #2406 added metplotpy and metcalcpy as dependencies * Feature #2460 allow missing input (#2493) * 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 * Feature #2491 v6.0.0 beta3 (#2495) * update version for beta3 release * fixed typos in release notes * update version to note development towards beta4 release * Per suggestion from @JohnHalleyGotway, create intermediate branch 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 * added quotes to prevent error in echo caused by parenthesis * fix incorrect command * Revert "fix incorrect command" This reverts commit e7dffb6. * Revert "added quotes to prevent error in echo caused by parenthesis" This reverts commit c1cb3c4. * Revert "Per suggestion from @JohnHalleyGotway, create intermediate branch 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. * Hotfix: Allow symbolic link to run_metplus.py to run (#2500) * Adding use case tests * Changing test environment * Testing environment changes * Documentation update * Updating Documentation * Updating documentation for disk space failure * Added new use case category * Fixing use case test * Fixing bug in use case file * Testing s2s after data removal * add back use cases that were accidentally removed * fix incorrect use case added * Setting tests to false for merge * Removes extraneous imports. * Switches to function call for the coupling index. * Correct number of args in comment. * Testing for old use cases * Setting tests to false for merge * update tests to update develop data -- modified commands to create new 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 * Summation has to have a dimension supplied for the gridded data, but 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. * Feature 2463 modify table (#2508) * 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 <[email protected]> Co-authored-by: George McCabe <[email protected]> * per #2509, automate MET version used in documentation to be X+6.Y.0 of METplus version * Bugfix #2520 ASCII2NC file window issue and redundant wrapper initialization (#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 * Update update_truth.md Fix typo in the update_truth issue template in the develop branch. * Update update_truth.md Update wording in the update_truth issue template. * Feature #2530 dev timeline (#2532) * 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 <[email protected]> --------- Co-authored-by: Julie Prestopnik <[email protected]> * Adds static station lookup file for use with Python embedding for FLUXNET observations. * Major overhaul to forecast Python embedding script for the TCI use case. * Major overhaul to observation Python embedding script for the TCI use case, to compute TCI from raw observations rather than read pre-computed TCI. * Updates documentation file for TCI use case. * Adds METcalcpy version number. * Refactors wording and fixes typo. * Fixes RST formatting. * Finally fixed RST error. * Adds support to remove leap days if requested. * Updates command line args for Python embedding scripts. * Feature #2537 develop sonarqube_gha (#2541) * 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. * Updated conf file for use case. * Removes new TCI function because it is in METcalcpy now. * Removes old code, somsome reorganization and clarification and setting of params, and also switches the fluxnet metadata file to a command line argument instead of an environment variable. * Update the 6.0.0 Coordinated Release development timeline in release-notes.rst * Support for environment variables or default options for filtering and 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. * Makes DEBUG an env var for config via metplus wrappers. * Reorganization of config file, adds environment variables, and updates comments for use case changes. * Updates to documentation. * Fixes tables. * Adds table of contents to the top for users to click on. * Updates use case documentation file. * Updated config file with obs and fcst subirectories in the path. * Added optional key/value to use_case_groups.json to prevent a use case group from running to easily disable it temporarily. Disable short_range:14 use case until it can be fixed with #2551 * update pillow version based on recommendation from dependabot: https://github.com/dtcenter/METplus/security/dependabot/5 * Switches to using metplotpy_env to get metcalcpy dependency. * Adds filtering based on missing data values. * Finishing touches to debug statements for testing. * Fixing a few minor code smells from last week. * update link to METplus Components Python Requirements table in PR template * Update docs/use_cases/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI.py Co-authored-by: George McCabe <[email protected]> --------- Co-authored-by: George McCabe <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: metplus-bot <[email protected]> Co-authored-by: Christina Kalb <[email protected]> Co-authored-by: j-opatz <[email protected]> Co-authored-by: jason-english <[email protected]> Co-authored-by: Daniel Adriaansen <[email protected]> Co-authored-by: Tracy Hertneky <[email protected]> Co-authored-by: Jonathan Vigh <[email protected]> Co-authored-by: John Sharples <[email protected]> Co-authored-by: root <root@localhost> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: jprestop <[email protected]> Co-authored-by: Hank Fisher <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: reza-armuei <[email protected]> Co-authored-by: Tracy <[email protected]> Co-authored-by: Mallory Row <[email protected]> Co-authored-by: bikegeek <[email protected]>

georgemccabe added 30 commits March 22, 2023 11:08

add missing parameters to prevent SQ code smell

3daa6b9

renamed function argument to prevent SQ code smell

30a2fba

per #1610, break up large function into smaller components to prevent…

38fb680

… SQ code smell (cognitive complexity)

apply updates from NOAA-EMC/NCEPLIBS-pyprodutil metplus-python3 branch

c34e0ed

Merge branch 'develop' into feature_1610_sq

a7ccb9e

removed produtil testing scripts

f3a4a70

address SonarQube critical bugs

01961b8

refactor logic to prevent SonarQube complaint python:S3516

2ad493f

more sonarqube

6a8c30c

refactor to reduce cognitive complexity complaint from SonarQube pyth…

5a5ee55

…on:S3776

more refactor to reduce cognitive complexity complaint from SonarQube…

20562a8

… python:S3776

more refactor to remove SonarQube complaints

b8d64a2

Merge branch 'develop' into feature_1610_sq

8e0070f

fix SonarQube blocker bug - functions do not exist in file

de94923

reduce cognitive complexity for SonarQube

0ea32c7

catch specific exception for SonarQube

d109b30

added generator to get files to compare to reduce cognitive complexit…

8c00abd

…y for SonarQube

refactor to reduce cognitive complexity in diff logic, ci-run-all-diff

d89f888

remove redundant return

ae81cdf

more cognitive complexity cleanup for SonarQube

3a1d0db

test fix for no differences in NetCDF numeric data, ci-run-all-diff

49cb48e

log type of exceptions occur in NetCDF diff logic and capture cases w…

c546b41

…hen diff cannot be performed, ci-run-all-diff

capture type of exception in logs, only run cases that failed, ci-run…

b67c197

…-diff

add pytest argument to append coverage report to compile coverage for…

fa42ea3

… all tests

Merge branch 'develop' into feature_1610_sq

779d9ab

test if handling explicit exception catches all exceptions that have …

01aa34c

…occurred in the diff logic for existing use cases, ci-run-diff

added missing import for exception, ci-run-diff

9847d9a

refactor logic that compares NetCDF files to properly check for diffs…

21a6908

… is NaN values are found in either field, reduce cognitive complexity to satisfy SonarQube

reduced cognitive complexity in logic to diff text or .stat files to …

1786c3d

…satisfy SonarQube, ci-run-all-diff

refactored script to assist with adding new support for MET config va…

b0b0b9a

…riables in METplus wrappers to satisfy SonarQube

georgemccabe added this to the METplus-5.1.0 milestone Jun 6, 2023

georgemccabe linked an issue Jun 6, 2023 that may be closed by this pull request

Enhancement: Resolve findings from SonarQube for 6.0.0 #1610

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merged develop and resolved conflicts

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hankenstein2 reviewed Jun 6, 2023

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georgemccabe merged commit 042b394 into develop Jun 6, 2023

georgemccabe deleted the feature_1610_sq branch June 6, 2023 19:39

georgemccabe mentioned this pull request Jun 6, 2023

Enhancement: Resolve findings from SonarQube for 6.0.0 #1610

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Feature #1610 first round of SonarQube fixes #2200

Feature #1610 first round of SonarQube fixes #2200

georgemccabe commented Jun 6, 2023 •

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hankenstein2 commented Jun 6, 2023 via email

Feature #1610 first round of SonarQube fixes #2200

Feature #1610 first round of SonarQube fixes #2200

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georgemccabe commented Jun 6, 2023 • edited Loading

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georgemccabe commented Jun 6, 2023 •

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