From 093ad76dadb30ed3bc8cfef6bf282d77a3850106 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 20 Mar 2024 14:40:56 -0600 Subject: [PATCH] Update develop-ref after dtcenter/MET#2838 (#2519) * 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 * 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 Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Fix for Dockerfile smell DL4000 (#2112) Co-authored-by: Giovanni Rosa * 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 <59586397+j-opatz@users.noreply.github.com> * 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 * Documentation: Update Truth Data instructions (#2154) * upgrade python to 3.10 for documentation builds to fix failured introduced by urllib3 (see https://github.com/urllib3/urllib3/issues/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 <23407799+georgemccabe@users.noreply.github.com> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Update docs/Contributors_Guide/github_workflow.rst Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Update github_workflow.rst --------- Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * 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 Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * 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 * Feature 2198 use case amdar pbl (#2206) Co-authored-by: Daniel Adriaansen Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * 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 * 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 * 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 * 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 <23407799+georgemccabe@users.noreply.github.com> * 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 * New issue template: Update Truth (#2332) Co-authored-by: John Halley Gotway * feature #2253 tests for run_util, 'Usage' bugfix (#2313) * Feature #2338 Debian 12 Conda environments (#2341) Co-authored-by: John Halley Gotway * Feature 1488 usecase satwinds (#2324) Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> * Feature #2283 include times (#2345) Co-authored-by: John Halley Gotway * 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 * 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 <23407799+georgemccabe@users.noreply.github.com> * 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 <33230218+lisagoodrich@users.noreply.github.com> * 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 <23407799+georgemccabe@users.noreply.github.com> * This file was committed but never updated or used Per Minna, ok to delete. * Restructuring table of contents to make it more clear which guides are for users and which are for contributors * fixing formatting for clairity Co-authored-by: Julie Prestopnik --------- Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: Julie Prestopnik * Feature #2349 upgrade instructions for deprecated MET config files (#2386) * Feature 2123 di doc update (#2392) Co-authored-by: Tracy * 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 * 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 https://github.com/pangeo-data/xESMF/issues/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 <23407799+georgemccabe@users.noreply.github.com> * 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 <59586397+j-opatz@users.noreply.github.com> * 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 <23407799+georgemccabe@users.noreply.github.com> * 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 * 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 * 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 ff2d1cac57c431a047ee250e9dae9b0a813a78ba. * 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 8106666a73685e654e0146d4fed56f2382f1bfc7. * 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 7a0a99c6e7031c5dafb1177d4b4ca3f32a999dac. * 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 cb6d0b46db353b4b4709183be2fe7e5ce64ff5ff. * 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 82aa0e11096aace3ccc2c79cd631533fc6426900. * 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 de3b4b03a45bb871c71e770ff9e602739d6b63d5. * 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 e7dffb6b0b351ab1b4bca5b563c1f5beef7737a9. * Revert "added quotes to prevent error in echo caused by parenthesis" This reverts commit c1cb3c4f0d7851bea720a50fac6011cd381017dc. * 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 525809dc3bd73ace969b046062967796035f4d86. * 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 Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> --------- Co-authored-by: metplus-bot <97135045+metplus-bot@users.noreply.github.com> Co-authored-by: Lisa Goodrich Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: Julie Prestopnik Co-authored-by: John Halley Gotway Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com> Co-authored-by: Tracy Hertneky <39317287+hertneky@users.noreply.github.com> Co-authored-by: Tracy Hertneky Co-authored-by: Giovanni Rosa Co-authored-by: Giovanni Rosa Co-authored-by: Dan Adriaansen Co-authored-by: j-opatz <59586397+j-opatz@users.noreply.github.com> Co-authored-by: mrinalbiswas Co-authored-by: Mrinal Biswas Co-authored-by: Christina Kalb Co-authored-by: j-opatz Co-authored-by: jason-english <73247785+jason-english@users.noreply.github.com> Co-authored-by: Jonathan Vigh Co-authored-by: John Sharples <41682323+John-Sharples@users.noreply.github.com> Co-authored-by: root Co-authored-by: Hank Fisher Co-authored-by: reza-armuei <144857501+reza-armuei@users.noreply.github.com> Co-authored-by: Tracy Co-authored-by: Mallory Row Co-authored-by: bikegeek <3753118+bikegeek@users.noreply.github.com> --- docs/Contributors_Guide/add_use_case.rst | 10 +- docs/Users_Guide/appendixA.rst | 565 ++++++++++++++++++++ docs/Users_Guide/index.rst | 2 +- docs/Users_Guide/installation.rst | 6 +- docs/Users_Guide/overview.rst | 632 +---------------------- docs/conf.py | 6 + metplus/__init__.py | 1 + 7 files changed, 592 insertions(+), 630 deletions(-) create mode 100644 docs/Users_Guide/appendixA.rst diff --git a/docs/Contributors_Guide/add_use_case.rst b/docs/Contributors_Guide/add_use_case.rst index eb6a4163e9..f66345ccbd 100644 --- a/docs/Contributors_Guide/add_use_case.rst +++ b/docs/Contributors_Guide/add_use_case.rst @@ -223,11 +223,11 @@ use case OR category directory for a model_applications use case * Update the description of the input data in the Datasets section. * Update the list of External Dependencies (if applicable) to include any - required Python packages. Update the :ref:`python_requirements_table` - table. If the package is already listed in the spreadsheet, add - a link to the documentation page for this new use case, following the - format in the table. If the package is not already listed, update - the table to include the name of the required package, the version, + required Python packages. Update the :ref:`components_python_packages` + section. If the package is already listed, add a link to the documentation + page for this new use case in the dropdown menu for that package, following the + format in the dropdown menu. If the package is not already listed, update + the dropdown menus to include the name of the required package, the version, the METplus component (e.g. METplus wrappers, METcalcpy, METplotpy), the source, a brief description of the package, and a link to this new use case that uses this new Python package. diff --git a/docs/Users_Guide/appendixA.rst b/docs/Users_Guide/appendixA.rst new file mode 100644 index 0000000000..0adda81b61 --- /dev/null +++ b/docs/Users_Guide/appendixA.rst @@ -0,0 +1,565 @@ +.. _components_python_packages: + +********************************************* +Appendix A METplus Components Python Packages +********************************************* + +Overview +======== + +.. note:: The information below is a union of the Python package requirements + across the following METplus components: METplus (including use + cases), MET Python Embedding, METcalcpy, METplotpy, and METdataio. + Many of the Python packages listed below are **OPTIONAL** and not + required. + +For information regarding the Python package requirements for each of the +METplus components, see the documentation links below for the desired +METplus component. Please note that the documentation for the METplus +Use Cases lists the required Python packages in the individual Use Cases +documentation. + + * :ref:`METplus Python Package Requirements ` + * `MET Python Embedding Requirements `_ + * `METcalcpy Python Package Requirements `_ + * `METdataio Python Package Requirements `_ + * `METplotpy Python Package Requirements `_ + * `METviewer Python Package Requirements `_ + * `METexpress Python Package Requirements `_ + +.. _metplus_components_python_packages: + +METplus Components Python Packages +================================== + +.. dropdown:: Python |python_version| + + + METplus Component: + | METplus wrappers, + | METcalcpy, + | METplotpy, + | METdataio + +.. dropdown:: cartopy >=0.21.1 + + METplus Component: + | Select METplus Use Cases, + | METcalcpy, + | METplotpy + + Source: + https://scitools.org.uk/cartopy/docs/latest/ + + Description: + Designed for geospatial data processing in order to produce maps and other geospatial data analyses + + Use Cases: + | `TCGen: Genesis Density Function (GDF) and Track Density Function (TDF) <../generated/model_applications/s2s/TCGen_fcstGFSO_obsBDECKS_GDF_TDF.html>`_ + | `CyclonePlotter: Extra-TC Tracker and Plotting Capabilities <../generated/model_applications/tc_and_extra_tc/CyclonePlotter_fcstGFS_obsGFS_UserScript_ExtraTC.html>`_ + +.. dropdown:: cfgrib + + METplus Component: + Select METplus Use Cases + + Source: + https://pypi.org/project/cfgrib/ + + Description: + Map GRIB files to the NetCDF Common Data Model following the CF Convention using ecCodes + + Use Cases: + `Multi_Tool: Feature Relative by Lead using Multiple User-Defined Fields + <../generated/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead_PyEmbed_Multiple_Diagnostics.html>`_ + +.. dropdown:: cmocean + + METplus Component: + | METcalcpy, + | METplotpy + + Source: + https://pypi.org/project/cmocean/ + + Description: + Contains colormaps for commonly-used oceanographic variables + +.. dropdown:: dateutil >=2.8.2 + + METplus Component: + METplus wrappers + + Source: + https://github.com/dateutil/dateutil/releases + + Description: + Provides powerful extensions to the standard datetime module + + Use Cases: + Most + +.. dropdown:: eofs + + METplus Component: + | Select METplus Use Cases, + | METcalcpy, + | METplotpy + + Source: + https://pypi.org/project/eofs/ + + Description: + Empirical orthogonal functions analysis of spatial-temporal data + + Use Cases: + | `WeatherRegime Calculation: RegridDataPlane, PcpCombine, and WeatherRegime python code <../generated/model_applications/s2s_mid_lat/UserScript_obsERA_obsOnly_WeatherRegime.html>`__ + | `WeatherRegime Calculation: GFS and ERA RegridDataPlane, PcpCombine, and WeatherRegime python code <../generated/model_applications/s2s_mid_lat/UserScript_fcstGFS_obsERA_WeatherRegime.html>`__ + +.. dropdown:: h5py + + METplus Component: + Select METplus Use Cases + + Source: + https://github.com/h5py/h5py + + Description: + Pythonic interface to the HDF5 binary data format + + Use Case: + `PCPCombine: Python Embedding Use Case <../generated/met_tool_wrapper/PCPCombine/PCPCombine_python_embedding.html>`_ + +.. dropdown:: imutils >=0.5.4 + + METplus Component: + METplotpy + + Source: + https://pypi.org/project/imutils/ + + Description: + A series of convenience functions to make basic image processing functions such as translation, rotation, resizing, skeletonization, displaying Matplotlib images, sorting contours, detecting edges, and much more easier + +.. dropdown:: imageio + + METplus Component: + | METcalcpy, + | METplotpy + + Source: + https://pypi.org/project/imageio/ + + Description: + Provides an easy interface to read and write a wide range of image data, including animated + images, volumetric data, and scientific formats + +.. dropdown:: lxml >=4.9.1 + + METplus Component: + | METcalcpy, + | METplotpy, + | METdataio + + Source: + https://pypi.org/project/lxml/ + + Description: + A Pythonic binding for the C libraries libxml2 and libxslt + +.. dropdown:: matplotlib >=3.6.3 + + METplus Component: + | Select METplus Use Cases, + | METcalcpy, + | METplotpy + + Source: + https://matplotlib.org/stable/users/installing/index.html + + Description: + A comprehensive library for creating static, animated, and interactive visualizations + + Use Case: + | `UserScript: Make OMI plot from calculated MJO indices with ERA obs only <../generated/model_applications/s2s_mjo/UserScript_obsERA_obsOnly_OMI.html>`__ + | `TCGen: Genesis Density Function and Track Density Function <../generated/model_applications/s2s/TCGen_fcstGFSO_obsBDECKS_GDF_TDF.html>`_ + | `UserScript: Make a Phase Diagram plot from input RMM or OMI <../generated/model_applications/s2s_mjo/UserScript_obsERA_obsOnly_PhaseDiagram.html>`_ + | `UserScript: Make OMI plot from calculated MJO indices with ERA obs and GFS fcst <../generated/model_applications/s2s_mjo/UserScript_fcstGFS_obsERA_OMI.html>`__ + | `UserScript: Make RMM plots from calculated MJO indices <../generated/model_applications/s2s_mjo/UserScript_obsERA_obsOnly_RMM.html>`__ + | `CyclonePlotter: Extra-TC Tracker and Plotting Capabilities <../generated/model_applications/tc_and_extra_tc/CyclonePlotter_fcstGFS_obsGFS_UserScript_ExtraTC.html>`_ + +.. dropdown:: metcalcpy + + METplus Component: + | Select METplus Use Cases, + | METcalcpy, + | METplotpy + + Source: + https://github.com/dtcenter/METcalcpy/releases + + Description: + A Python version of the statistics calculation functionality of METviewer, METexpress, + plotting packages in METplotpy and is a stand-alone package for any other application + + Use Case: + | `UserScript: Make a Hovmoeller plot <../generated/model_applications/s2s/UserScript_obsPrecip_obsOnly_Hovmoeller.html>`_ + | `UserScript: Compute Cross Spectra and Make a Plot <../generated/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.html>`__ + | `Grid-Stat: Verification of TC forecasts against merged TDR data <../generated/model_applications/tc_and_extra_tc/GridStat_fcstHAFS_obsTDR_NetCDF.html>`_ + | `UserScript: Calculate the Difficulty Index <../generated/model_applications/medium_range/UserScript_fcstGEFS_Difficulty_Index.html>`_ + | `UserScript: Make zonal and meridonial means <../generated/model_applications/s2s/UserScript_obsERA_obsOnly_Stratosphere.html>`_ + +.. dropdown:: metplotpy + + METplus Component: + Select METplus Use Cases + + Source: + https://github.com/dtcenter/METplotpy/releases + + Description: + Contains packages for plotting in METplus as stand-alone, or part of METplus use case, + Select METplus Use Cases, METexpress, or METviewer + + Use Case: + | `UserScript: Make a Hovmoeller plot <../generated/model_applications/s2s/UserScript_obsPrecip_obsOnly_Hovmoeller.html>`_ + | `UserScript: Compute Cross Spectra and Make a Plot <../generated/model_applications/s2s/UserScript_obsPrecip_obsOnly_CrossSpectraPlot.html>`__ + | `UserScript: Calculate the Difficulty Index <../generated/model_applications/medium_range/UserScript_fcstGEFS_Difficulty_Index.html>`_ + | `TCGen: Genesis Density Function (GDF) and Track Density Function (TDF) <../generated/model_applications/s2s/TCGen_fcstGFSO_obsBDECKS_GDF_TDF.html>`_ + +.. dropdown:: metpy >=1.4.0 + + METplus Component: + Select METplus Use Cases + + Source: + https://www.unidata.ucar.edu/software/metpy/ + + Description: + A collection of tools in Python for reading, visualizing, and performing calculations + with weather data + + Use Case: + `Multi_Tool: Feature Relative by Lead using Multiple User-Defined Fields <../generated/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead_PyEmbed_Multiple_Diagnostics.html>`_ + +.. dropdown:: nc-time-axis 1.4 + + METplus Component: + | METplotpy + | stratosphere_diagnostics + + Source: + | https://github.com/SciTools/nc-time-axis + + Description: + Extension to cftime - \**REQUIRES Python 3.7** + +.. dropdown:: netCDF4 >=1.6.2 + + METplus Component: + | Select METplus Use Cases, + | METcalcpy, + | METplotpy + + Source: + https://unidata.github.io/netcdf4-python/ + + Description: + + A Python interface to the netCDF C library + + Use Case: + For using MET Python embedding functionality in use cases + +.. dropdown:: numpy >=1.24.2 + + METplus Component: + | Select METplus Use Cases, + | METcalcpy, + | METplotpy, + | METdataio + + Source: + https://numpy.org/ + + Description: + NumPy offers comprehensive mathematical functions, random number generators, + linear algebra routines, Fourier transforms, and more. + + Use Case: + For using MET Python embedding functionality in use cases + +.. dropdown:: pandas >=1.5.2 + + METplus Component: + | Select METplus Use Cases, + | METcalcpy, + | METplotpy, + | METdataio + + Source: + https://pypi.org/project/pandas + + Description: + A fast, powerful, flexible and easy to use open source data analysis + and manipulation tool, built on top of the Python programming language + + Use Case: + For using MET Python embedding functionality in use cases + +.. dropdown:: pint >=0.20.1 + + METplus Component: + METcalcpy + + Source: + https://github.com/hgrecco/pint + + Description: + Python package to define, operate and manipulate physical quantities + +.. dropdown:: plotly >=5.13.0 + + METplus Component: + | METcalcpy, + | METplotpy + + Source: + https://github.com/plotly/plotly.py + + Description: + Makes interactive, publication-quality graphs + +.. dropdown:: pygrib + + METplus Component: + METplus wrappers + + Source: + https://github.com/jswhit/pygrib + + Description: + For reading/writing GRIB files + + Use Case: + | `Multi_Tool: Feature Relative by Lead using Multiple User-Defined Fields <../generated/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead_PyEmbed_Multiple_Diagnostics.html>`_ + | `GridStat: Cloud Fractions Using GFS and ERA5 Data <../generated/model_applications/clouds/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.html>`_ + | `GridStat: Cloud Height with Neighborhood and Probabilities <../generated/model_applications/clouds/GridStat_fcstMPAS_obsERA5_cloudBaseHgt.html>`_ + | `GridStat: Cloud Pressure and Temperature Heights <../generated/model_applications/clouds/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp.html>`_ + | `GridStat: Cloud Fractions Using GFS and MERRA2 Data <../generated/model_applications/clouds/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac.html>`_ + | `GridStat: Cloud Fractions Using MPAS and SatCORPS Data <../generated/model_applications/clouds/GridStat_fcstMPAS_obsSATCORPS_lowAndTotalCloudFrac.html>`_ + | `GridStat: Cloud Fractions Using MPAS and MERRA2 Data <../generated/model_applications/clouds/GridStat_fcstMPAS_obsMERRA2_lowAndTotalCloudFrac.html>`_ + + +.. dropdown:: pylab + + METplus Component: + Select METplus Use Cases + + Source: + https://pypi.org/project/matplotlib/ + + Description: + A convenience module that bulk imports matplotlib.pyplot (for plotting) and NumPy (for + Mathematics and working with arrays) in a single name space + + Use Case: + | `WeatherRegime Calculation: RegridDataPlane, PcpCombine, and WeatherRegime python code <../generated/model_applications/s2s_mid_lat/UserScript_obsERA_obsOnly_WeatherRegime.html>`__ + | `WeatherRegime Calculation: GFS and ERA RegridDataPlane, PcpCombine, and WeatherRegime python code <../generated/model_applications/s2s_mid_lat/UserScript_fcstGFS_obsERA_WeatherRegime.html>`__ + +.. dropdown:: pymysql >=1.0.2 + + METplus Component: + | METcalcpy, + | METplotpy, + | METdataio + + Source: + https://pypi.org/project/psutil/ + + Description: + A pure-Python MySQL client library, based on PEP 249 + +.. dropdown:: pyproj >=2.3.1 + + METplus Component: + Select METplus Use Cases + + Source: + https://github.com/pyproj4/pyproj/archive/v2.3.1rel.tar.gz + + Description: + Python interface to PROJ (cartographic projections and coordinate transformations library) + + Use Case: + | `GridStat: Python Embedding to read and process ice cover <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.html>`_ + +.. dropdown:: pyresample + + METplus Component: + Select METplus Use Cases + + METplus Component: + https://github.com/pytroll/pyresample + + Description: + For resampling geospatial image data + + Use Case: + | `GridStat: Python Embedding to read and process SST <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.html>`_ + | `GridStat: Python Embedding to read and process ice cover <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.html>`_ + | `GridStat: Python Embedding for sea surface salinity using level 3, 1 day composite obs <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMOS_climWOA_sss.html>`_ + | `GridStat: Python Embedding for sea surface salinity using level 3, 8 day mean obs <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss.html>`_ + +.. dropdown:: pytest >=7.2.1 + + METplus Component: + | METcalcpy, + | METplotpy, + | METdataio + + Source: + https://github.com/pytest-dev/pytest/archive/5.2.1.tar.gz + + Description: + A mature full-featured Python testing tool that helps to write better programs + +.. dropdown:: python-kaleido >=0.2.1 + + METplus Component: + | METcalcpy, + | METplotpy + + Source: + https://pypi.org/project/kaleido/ + + Description: + Provides a low-level Python API that is designed to be used by high-level plotting libraries like Plotly + +.. dropdown:: pyyaml >=6.0 + + METplus Component: + | METcalcpy, + | METplotpy, + | METdataio + + Source: + https://github.com/yaml/pyyaml + + Description: + A full-featured YAML framework for the Python programming language + +.. dropdown:: scikit-image >=0.19.3 + + METplus Component: + | METcalcpy, + | METplotpy + + Source: + https://scikit-image.org + + Description: + A collection of algorithms for image processing + +.. dropdown:: scikit-learn >=1.2.2 + + METplus Component: + | Select METplus Use Cases, + | METcalcpy, + | METplotpy + + Source: + https://github.com/scikit-learn/scikit-learn/releases + + Description: + Open Source library for Machine Learning in Python + + Use Case: + | `GridStat: Python Embedding to read and process SST <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.html>`_ + | `GridStat: Python Embedding to read and process ice cover <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.html>`_ + | `GridStat: Python Embedding for sea surface salinity using level 3, 1 day composite obs <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMOS_climWOA_sss.html>`_ + | `GridStat: Python Embedding for sea surface salinity using level 3, 8 day mean obs <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss.html>`_ + +.. dropdown:: scipy >=1.9.3 + + METplus Component: + | Select METplus Use Cases, + | METcalcpy, + | METplotpy + + Source: + https://www.scipy.org/ + + Description: + Wraps highly-optimized implementations written in low-level languages like Fortran, C, and C++ + + Use Case: + | `Blocking Calculation: ERA RegridDataPlane, PcpCombine, and Blocking python code <../generated/model_applications/s2s_mid_lat/UserScript_obsERA_obsOnly_Blocking.html>`_ + | `WeatherRegime Calculation: RegridDataPlane, PcpCombine, and WeatherRegime python code <../generated/model_applications/s2s_mid_lat/UserScript_obsERA_obsOnly_WeatherRegime.html>`__ + | `UserScript: Make OMI plot from calculated MJO indices with ERA obs only <../generated/model_applications/s2s_mid_lat/UserScript_obsERA_obsOnly_OMI.html>`__ + | `WeatherRegime Calculation: GFS and ERA RegridDataPlane, PcpCombine, and WeatherRegime python code <../generated/model_applications/s2s_mid_lat/UserScript_fcstGFS_obsERA_WeatherRegime.html>`__ + | `Blocking Calculation: GFS and ERA RegridDataPlane, PcpCombine, and Blocking python code <../generated/model_applications/s2s_mid_lat/UserScript_fcstGFS_obsERA_Blocking.html>`_ + | `UserScript: Make a Phase Diagram plot from input RMM or OMI <../generated/model_applications/s2s_mjo/UserScript_obsERA_obsOnly_PhaseDiagram.html>`__ + | `UserScript: Make OMI plot from calculated MJO indices with ERA obs and GFS fcst <../generated/model_applications/s2s_mjo/UserScript_fcstGFS_obsERA_OMI.html>`__ + | `UserScript: Make RMM plots from calculated MJO indices <../generated/model_applications/s2s_mjo/UserScript_obsERA_obsOnly_RMM.html>`__ + +.. dropdown:: sklearn + + METplus Component: + Select METplus Use Cases + + Source: + https://www.kite.com/python/docs/sklearn + + Description: + Simple and efficient tools for predictive data analysis + + Description: + | `WeatherRegime Calculation: RegridDataPlane, PcpCombine, and WeatherRegime python code <../generated/model_applications/s2s_mid_lat/UserScript_obsERA_obsOnly_WeatherRegime.html>`__ + | `WeatherRegime Calculation: GFS and ERA RegridDataPlane, PcpCombine, and WeatherRegime python code <../generated/model_applications/s2s_mid_lat/UserScript_fcstGFS_obsERA_WeatherRegime.html>`__ + + +.. dropdown:: xarray >=2023.1.0 + + METplus Component: + | Select METplus Use Cases, + | METcalcpy, + | METplotpy + + Source: + https://xarray.pydata.org/en/v0.17.0/ + + Description: + Makes working with labelled multi-dimensional arrays simple, efficient, and fun + + Use Case: + For using MET Python embedding functionality in use cases + +.. dropdown:: xesmf + + METplus Component: + Select METplus Use Cases + + Source: + NOTE: The xesmf package will not be installed on WCOSS2 and there is an open GitHub issue to + replace the package in the use case that uses it: + https://github.com/dtcenter/METplus/issues/1314 + + Description: + For regridding + + Use Case: + `PlotDataPlane: Python Embedding of tripolar coordinate file <../generated/model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar.html>`_ + + +.. dropdown:: yaml + + METplus Component: + | METcalcpy, + | METplotpy + + Source: + https://pypi.org/project/PyYAML/ + + Description: + To load, read, and write YAML files with PyYAML + diff --git a/docs/Users_Guide/index.rst b/docs/Users_Guide/index.rst index e5afd2f3df..345ec91e1e 100644 --- a/docs/Users_Guide/index.rst +++ b/docs/Users_Guide/index.rst @@ -88,7 +88,7 @@ is sponsored by NSF. glossary references statistics_list - + appendixA .. Indices and tables ================== diff --git a/docs/Users_Guide/installation.rst b/docs/Users_Guide/installation.rst index 3910bdca95..866060eabd 100644 --- a/docs/Users_Guide/installation.rst +++ b/docs/Users_Guide/installation.rst @@ -43,9 +43,9 @@ Software Requirements The following software is required to run METplus Wrappers: -- Python 3.8.6 or above +- Python |python_version| or above -- MET version 11.0.0 or above - +- MET version |met_version| or above - For information on installing MET please see the `Software Installation/Getting Started `_ section of the MET User's Guide. @@ -61,6 +61,8 @@ The following software is required to run METplus Wrappers: - convert (ImageMagick) utility - if generating images from the Postscript output +.. _python_package_requirements: + Python Package Requirements --------------------------- diff --git a/docs/Users_Guide/overview.rst b/docs/Users_Guide/overview.rst index 509394c58f..8ebbccc09e 100644 --- a/docs/Users_Guide/overview.rst +++ b/docs/Users_Guide/overview.rst @@ -41,11 +41,13 @@ researchers to test their own enhancements to models and providing a capability for the DTC to evaluate the strengths and weaknesses of advances in NWP prior to operational implementation. -METplus Wrappers will also be available to DTC visitors and the NOAA Unified Forecast System (UFS) and NCAR System for Integrated Modeling of the Atmosphere (SIMA) modeling communities for testing and evaluation of new model capabilities, -applications in new environments, and so on. The METplus Wrappers -release schedule is coincident with the MET release schedule and the -METplus Wrappers major release number is six less than the MET major -release number (e.g. MET 8.X is released with METplus Wrappers 2.X). +METplus Wrappers will also be available to DTC visitors and the NOAA +Unified Forecast System (UFS) and NCAR System for Integrated Modeling +of the Atmosphere (SIMA) modeling communities for testing and evaluation +of new model capabilities, applications in new environments, and so on. +The METplus Wrappers release schedule is coincident with the MET release +schedule and the METplus Wrappers major release number is six less than +the MET major release number (e.g. MET 8.X is released with METplus Wrappers 2.X). METplus Wrappers goals and design philosophy ============================================ @@ -67,7 +69,9 @@ their verification environments. Wrappers can be run individually, or as a group of wrappers that represent a sequence of MET processes. New wrappers can readily be added to the METplus Wrappers package due to this modular design. Currently, METplus Wrappers can easily be applied -by any user on their own computer platform that supports Python 3.8. We have deprecated support to Python 2.7. +by any user on their own computer platform that supports +Python |python_version|. + The METplus Wrappers code and documentation is maintained by the DTC in Boulder, Colorado. METplus Wrappers is freely available to the modeling, @@ -85,622 +89,6 @@ METplus Wrappers configuration files. Some Python wrappers do not correspond to a particular MET tool, but wrap utilities to extend METplus functionality. -.. _python_requirements_table: - -METplus Components Python Requirements -====================================== - -.. Number of characters per line: - Name - no more that 13 characters - Version - no more than 6 characters - METplus component - no more than 17 characters - Source - no more than 8 characters - Description - no more than 22 (was 20) characters - Use Cases - no more than 17 (was 10) characters - -.. role:: raw-html(raw) - :format: html - -.. list-table:: METplus Components Python Requirements - :widths: auto - :header-rows: 1 - - * - Name - - Version - - METplus Component - - Source - - Description - - Use Cases (only applicable for METplus wrappers component)(followed by - python package name) - * - Python 3.10.4+ - - - - METplus wrappers, :raw-html:`
` - METcalcpy, :raw-html:`
` - METplotpy, :raw-html:`
` - METdataio - - - - - - - * - cartopy - - >=0.21.1 - - METplus wrappers, :raw-html:`
` - METcalcpy, :raw-html:`
` - METplotpy - - https://scitools.org.uk/cartopy/docs/latest/ - - Designed for :raw-html:`
` - geospatial data :raw-html:`
` - processing in :raw-html:`
` - order to produce :raw-html:`
` - maps and other :raw-html:`
` - geospatial data :raw-html:`
` - analyses - - `TCGen: Genesis Density Function (GDF) - and Track Density Function (TDF) - (cartopy) - <../generated/model_applications/s2s/TCGen_fcstGFSO_obsBDECKS_GDF_TDF.html>`_ :raw-html:`
` - `CyclonePlotter: Extra-TC Tracker - and Plotting Capabilities - (cartopy) - <../generated/model_applications/tc_and_extra_tc/CyclonePlotter_fcstGFS_obsGFS_UserScript_ExtraTC.html>`_ - * - cfgrib - - - - METplus wrappers - - https://pypi.org/project/cfgrib/ - - map GRIB files :raw-html:`
` - to the NetCDF :raw-html:`
` - Common Data Model :raw-html:`
` - following the :raw-html:`
` - CF Convention :raw-html:`
` - using ecCodes - - `Multi_Tool: - Feature Relative by Lead using - Multiple User-Defined Fields - (cfgrib) - <../generated/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead_PyEmbed_Multiple_Diagnostics.html>`_ - * - cmocean - - - - METcalcpy, :raw-html:`
` - METplotpy - - https://pypi.org/project/cmocean/ - - contains colormaps :raw-html:`
` - for commonly-used :raw-html:`
` - oceanographic variables - - - * - dateutil - - >=2.8.2 - - METplus wrappers - - https://github.com/dateutil/dateutil/releases - - provides powerful :raw-html:`
` - extensions to the :raw-html:`
` - standard datetime :raw-html:`
` - module - - Most - * - eofs - - - - METplus wrappers, :raw-html:`
` - METcalcpy, :raw-html:`
` - METplotpy - - https://pypi.org/project/eofs/ - - empirical orthogonal :raw-html:`
` - functions analysis of :raw-html:`
` - spatial-temporal data - - `WeatherRegime Calculation: - RegridDataPlane, - PcpCombine, - and WeatherRegime python code - (eofs) - <../generated/model_applications/s2s/UserScript_obsERA_obsOnly_WeatherRegime.html>`_ :raw-html:`
` - `WeatherRegime Calculation: - GFS and ERA RegridDataPlane, - PcpCombine, and - WeatherRegime python code - (eofs) - <../generated/model_applications/s2s/UserScript_fcstGFS_obsERA_WeatherRegime.html>`_ - * - h5py - - - - METplus wrappers - - https://github.com/h5py/h5py - - Pythonic interface :raw-html:`
` - to the HDF5 :raw-html:`
` - binary data format - - `PCPCombine: - Python Embedding Use Case - (h5py) - <../generated/met_tool_wrapper/PCPCombine/PCPCombine_python_embedding.html>`_ - * - imutils - - >=0.5.4 - - METplotpy :raw-html:`
` - - https://pypi.org/project/imutils/ - - A series of convenience :raw-html:`
` - functions to make basic :raw-html:`
` - image processing :raw-html:`
` - functions such as :raw-html:`
` - translation, rotation, :raw-html:`
` - resizing, skeletonization, :raw-html:`
` - displaying Matplotlib :raw-html:`
` - images, sorting contours, :raw-html:`
` - detecting edges, :raw-html:`
` - and much more easier - - - * - imageio - - - - METcalcpy, :raw-html:`
` - METplotpy - - https://pypi.org/project/imageio/ - - provides an easy :raw-html:`
` - interface to read :raw-html:`
` - and write a wide :raw-html:`
` - range of image data, :raw-html:`
` - including animated :raw-html:`
` - images, volumetric data, :raw-html:`
` - and scientific formats - - - * - lxml - - >=4.9.1 - - METcalcpy, :raw-html:`
` - METplotpy, :raw-html:`
` - METdataio - - https://pypi.org/project/lxml/ - - a Pythonic binding for :raw-html:`
` - the C libraries :raw-html:`
` - libxml2 and libxslt - - - * - matplotlib - - >=3.6.3 - - METplus wrappers, :raw-html:`
` - METcalcpy, :raw-html:`
` - METplotpy - - https://matplotlib.org/stable/users/installing/index.html - - a comprehensive library :raw-html:`
` - for creating static, :raw-html:`
` - animated, and :raw-html:`
` - interactive visualizations - - `UserScript: - Make OMI plot from - calculated MJO indices (obs only) - (matplotlib) - <../generated/model_applications/s2s/UserScript_obsERA_obsOnly_OMI.html>`_ :raw-html:`
` - `TCGen: - Genesis Density Function (GDF) - and Track Density Function (TDF) - (matplotlib) - <../generated/model_applications/s2s/TCGen_fcstGFSO_obsBDECKS_GDF_TDF.html>`_ :raw-html:`
` - `UserScript: - Make a Phase Diagram plot - from input RMM or OMI - (matplotlib) - <../generated/model_applications/s2s/UserScript_obsERA_obsOnly_PhaseDiagram.html>`_ :raw-html:`
` - `UserScript: - Make OMI plot from - calculated MJO indices - (matplotlib) - <../generated/model_applications/s2s/UserScript_fcstGFS_obsERA_OMI.html>`_ :raw-html:`
` - `UserScript: - Make RMM plots from - calculated MJO indices - (matplotlib) - <../generated/model_applications/s2s/UserScript_obsERA_obsOnly_RMM.html>`_ :raw-html:`
` - `CyclonePlotter: - Extra-TC Tracker and - Plotting Capabilities - (matplotlib) - <../generated/model_applications/tc_and_extra_tc/CyclonePlotter_fcstGFS_obsGFS_UserScript_ExtraTC.html>`_ :raw-html:`
` - * - metcalcpy - - - - METplus wrappers, :raw-html:`
` - METcalcpy, :raw-html:`
` - METplotpy - - https://github.com/dtcenter/METcalcpy/releases - - a Python version of the :raw-html:`
` - statistics calculation :raw-html:`
` - functionality of :raw-html:`
` - METviewer, METexpress, :raw-html:`
` - plotting packages in :raw-html:`
` - METplotpy and is a :raw-html:`
` - stand-alone package for :raw-html:`
` - any other application - - `UserScript: - Make a Hovmoeller plot - (metcalcpy) - <../generated/model_applications/s2s/UserScript_obsPrecip_obsOnly_Hovmoeller.html>`_ :raw-html:`
` - `UserScript: - Make a Cross Spectra plot - (metcalcpy) - <../generated/model_applications/s2s/TCGen_fcstGFSO_obsBDECKS_GDF_TDF.html>`_ :raw-html:`
` - `Grid-Stat: - Verification of TC forecasts - against merged TDR data - (metcalcpy) - <../generated/model_applications/s2s/UserScript_obsPrecip_obsOnly_CrossSpectraPlot.html>`_ :raw-html:`
` - `UserScript: - Calculate the Difficulty Index - (metcalcpy) - <../generated/model_applications/medium_range/UserScript_fcstGEFS_Difficulty_Index.html>`_ :raw-html:`
` - `UserScript: - Make zonal and meridonial means - (metcalcpy) - <../generated/model_applications/s2s/UserScript_obsERA_obsOnly_Stratosphere.html>`_ :raw-html:`
` - * - metplotpy - - - - METplus wrappers - - https://github.com/dtcenter/METplotpy/releases - - contains packages for :raw-html:`
` - plotting in METplus as :raw-html:`
` - stand-alone, or part of :raw-html:`
` - METplus use case, :raw-html:`
` - METplus wrappers, :raw-html:`
` - METexpress, :raw-html:`
` - or METviewer - - `UserScript: - Make a Hovmoeller plot - (metplotpy) - <../generated/model_applications/s2s/UserScript_obsPrecip_obsOnly_Hovmoeller.html>`_ :raw-html:`
` - `UserScript: - Make a Cross Spectra plot - (metplotpy) - <../generated/model_applications/s2s/UserScript_obsPrecip_obsOnly_CrossSpectraPlot.html>`_ :raw-html:`
` - `UserScript: - Calculate the Difficulty Index - (metplotpy) - <../generated/model_applications/medium_range/UserScript_fcstGEFS_Difficulty_Index.html>`_ :raw-html:`
` - `TCGen: - Genesis Density Function (GDF) - and Track Density Function (TDF) - (metplotpy) - <../generated/model_applications/s2s/TCGen_fcstGFSO_obsBDECKS_GDF_TDF.html>`_ - * - metpy - - >=1.4.0 - - METplus wrappers - - https://www.unidata.ucar.edu/software/metpy/ - - a collection of tools :raw-html:`
` - in Python for reading, :raw-html:`
` - visualizing, and :raw-html:`
` - performing calculations :raw-html:`
` - with weather data - - `Multi_Tool: - Feature Relative by Lead using - Multiple User-Defined Fields - (metpy) - <../generated/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead_PyEmbed_Multiple_Diagnostics.html>`_ - * - nc-time-axis - - 1.4 - - METplotpy :raw-html:`
` - stratosphere_diagnostics - - https://github.com/SciTools/nc-time-axis - - extension to cftime :raw-html:`
` - \**REQUIRES Python 3.7 - - - * - netCDF4 - - >=1.6.2 - - METplus wrappers, :raw-html:`
` - METcalcpy, :raw-html:`
` - METplotpy - - https://unidata.github.io/netcdf4-python/ - - a Python interface to :raw-html:`
` - the netCDF C library - - For using MET Python embedding functionality in use cases - * - numpy - - >=1.24.2 - - METplus wrappers, :raw-html:`
` - METcalcpy, :raw-html:`
` - METplotpy, :raw-html:`
` - METdataio - - https://numpy.org/ - - NumPy offers :raw-html:`
` - comprehensive :raw-html:`
` - mathematical functions, :raw-html:`
` - random number generators, :raw-html:`
` - linear algebra routines, :raw-html:`
` - Fourier transforms, and more. - - For using MET Python embedding functionality in use cases - * - pandas - - >=1.5.2 - - METplus wrappers, :raw-html:`
` - METcalcpy, :raw-html:`
` - METplotpy, :raw-html:`
` - METdataio - - https://pypi.org/project/pandas - - a fast, powerful, :raw-html:`
` - flexible and easy to use :raw-html:`
` - open source data analysis :raw-html:`
` - and manipulation tool, :raw-html:`
` - built on top of the :raw-html:`
` - Python programming :raw-html:`
` - language - - For using MET Python embedding functionality in use cases - * - pint - - >=0.20.1 - - METcalcpy - - https://github.com/hgrecco/pint - - Python package to define, :raw-html:`
` - operate and manipulate :raw-html:`
` - physical quantities - - - * - plotly - - >=5.13.0 - - METcalcpy, :raw-html:`
` - METplotpy - - https://github.com/plotly/plotly.py - - makes interactive, :raw-html:`
` - publication-quality graphs - - - * - pygrib - - - - METplus wrappers - - https://github.com/jswhit/pygrib - - for reading/writing :raw-html:`
` - GRIB files - - `Multi_Tool: - Feature Relative by Lead - using Multiple User-Defined Fields - (pygrib) - <../generated/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead_PyEmbed_Multiple_Diagnostics.html>`_ :raw-html:`
` - `GridStat: - Cloud Fractions Using GFS - and ERA5 Data - (pygrib) - <../generated/model_applications/clouds/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.html>`_ :raw-html:`
` - `GridStat: - Cloud Height with Neighborhood - and Probabilities - (pygrib) - <../generated/model_applications/clouds/GridStat_fcstMPAS_obsERA5_cloudBaseHgt.html>`_ :raw-html:`
` - `GridStat: - Cloud Pressure and - Temperature Heights - (pygrib) - <../generated/model_applications/clouds/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp.html>`_ :raw-html:`
` - `GridStat: - Cloud Fractions Using GFS - and MERRA2 Data - (pygrib) - <../generated/model_applications/clouds/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac.html>`_ :raw-html:`
` - `GridStat: - Cloud Fractions Using MPAS - and SatCORPS Data - (pygrib) - <../generated/model_applications/clouds/GridStat_fcstMPAS_obsSATCORPS_lowAndTotalCloudFrac.html>`_ :raw-html:`
` - `GridStat: - Cloud Fractions Using MPAS - and MERRA2 Data - (pygrib) - <../generated/model_applications/clouds/GridStat_fcstMPAS_obsMERRA2_lowAndTotalCloudFrac.html>`_ - * - pylab - - - - METplus wrappers - - https://pypi.org/project/matplotlib/ - - a convenience module :raw-html:`
` - that bulk imports :raw-html:`
` - matplotlib.pyplot (for :raw-html:`
` - plotting) and NumPy (for :raw-html:`
` - Mathematics and working :raw-html:`
` - with arrays) in a :raw-html:`
` - single name space - - `WeatherRegime Calculation: - RegridDataPlane, PcpCombine, - and WeatherRegime python code - (pylab) - <../generated/model_applications/s2s/UserScript_obsERA_obsOnly_WeatherRegime.html>`_ :raw-html:`
` - `WeatherRegime Calculation: - GFS and ERA RegridDataPlane, - PcpCombine, and WeatherRegime - python code - (pylab) - <../generated/model_applications/s2s/UserScript_fcstGFS_obsERA_WeatherRegime.html>`_ - * - pymysql - - >=1.0.2 - - METcalcpy, :raw-html:`
` - METplotpy, :raw-html:`
` - METdataio - - https://pypi.org/project/psutil/ - - a pure-Python MySQL :raw-html:`
` - client library, :raw-html:`
` - based on PEP 249 - - - * - pyproj - - >=2.3.1 - - METplus wrappers - - https://github.com/pyproj4/pyproj/archive/v2.3.1rel.tar.gz - - Python interface to PROJ :raw-html:`
` - (cartographic projections and :raw-html:`
` - coordinate transformations library) - - `GridStat: - Python Embedding to read - and process ice cover - (pyproj) - <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.html>`_ - * - pyresample - - - - METplus wrappers - - https://github.com/pytroll/pyresample - - for resampling geospatial :raw-html:`
` - image data - - `GridStat: - Python Embedding to read and - process SST - (pyresample) - <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.html>`_ :raw-html:`
` - `GridStat: - Python Embedding to read and - process ice cover - (pyresample) - <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.html>`_ :raw-html:`
` - `GridStat: - Python Embedding for sea surface salinity - using level 3, 1 day composite obs - (pyresample) - <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMOS_climWOA_sss.html>`_ :raw-html:`
` - `GridStat: - Python Embedding for sea surface salinity - using level 3, 8 day mean obs - (pyresample) - <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss.html>`_ - * - pytest - - >=7.2.1 - - METcalcpy, :raw-html:`
` - METplotpy, :raw-html:`
` - METdataio - - https://github.com/pytest-dev/pytest/archive/5.2.1.tar.gz - - a mature full-featured :raw-html:`
` - Python testing tool that :raw-html:`
` - helps you write better :raw-html:`
` - programs - - - * - python-kaleido - - >=0.2.1 - - METcalcpy, :raw-html:`
` - METplotpy - - https://pypi.org/project/kaleido/ - - provides a low-level :raw-html:`
` - Python API that is :raw-html:`
` - designed to be used by :raw-html:`
` - high-level plotting :raw-html:`
` - libraries like Plotly - - - * - pyyaml - - >=6.0 - - METcalcpy, :raw-html:`
` - METplotpy, :raw-html:`
` - METdataio - - https://github.com/yaml/pyyaml - - a full-featured YAML :raw-html:`
` - framework for the Python :raw-html:`
` - programming language - - - * - scikit-image - - >=0.19.3 - - METcalcpy, :raw-html:`
` - METplotpy - - https://scikit-image.org - - a collection of :raw-html:`
` - algorithms for image :raw-html:`
` - processing - - - * - scikit-learn - - >=1.2.2 - - METplus wrappers, :raw-html:`
` - METcalcpy, :raw-html:`
` - METplotpy - - https://github.com/scikit-learn/scikit-learn/releases - - Open Source library for :raw-html:`
` - Machine Learning in Python - - `GridStat: - Python Embedding to read and process SST - (scikit-learn) - <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.html>`_ :raw-html:`
` - `GridStat: - Python Embedding to read and process ice cover - (scikit-learn) <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.html>`_ :raw-html:`
` - `GridStat: - Python Embedding for sea surface salinity using level 3, - 1 day composite obs - (scikit-learn) - <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMOS_climWOA_sss.html>`_ :raw-html:`
` - `GridStat: - Python Embedding for sea surface salinity using level 3, - 8 day mean obs - (scikit-learn) - <../generated/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss.html>`_ - * - scipy - - >=1.9.3 - - METplus wrappers, :raw-html:`
` - METcalcpy, :raw-html:`
` - METplotpy - - https://www.scipy.org/ - - wraps highly-optimized :raw-html:`
` - implementations written :raw-html:`
` - in low-level languages :raw-html:`
` - like Fortran, C, and C++ - - `Blocking Calculation: - ERA RegridDataPlane, - PcpCombine, and - Blocking python code - (scipy) - <../generated/model_applications/s2s/UserScript_obsERA_obsOnly_Blocking.html>`_ :raw-html:`
` - `WeatherRegime Calculation: - RegridDataPlane, PcpCombine, and WeatherRegime python code - (scipy) - <../generated/model_applications/s2s/UserScript_obsERA_obsOnly_WeatherRegime.html>`_ :raw-html:`
` - `UserScript: - Make OMI plot from calculated MJO indices - (obs only) (scipy) - <../generated/model_applications/s2s/UserScript_obsERA_obsOnly_OMI.html>`_ :raw-html:`
` - `WeatherRegime Calculation: - GFS and ERA RegridDataPlane, - PcpCombine, and - WeatherRegime python code - (scipy) - <../generated/model_applications/s2s/UserScript_fcstGFS_obsERA_WeatherRegime.html>`_ :raw-html:`
` - `Blocking Calculation: - GFS and ERA RegridDataPlane, - PcpCombine, and - Blocking python code - (scipy) - <../generated/model_applications/s2s/UserScript_fcstGFS_obsERA_Blocking.html>`_ :raw-html:`
` - `UserScript: - Make a Phase Diagram plot from input RMM or OMI - (scipy) - <../generated/model_applications/s2s/UserScript_obsERA_obsOnly_PhaseDiagram.html>`_ :raw-html:`
` - `UserScript: - Make OMI plot from calculated MJO indices - (scipy) - <../generated/model_applications/s2s/UserScript_fcstGFS_obsERA_OMI.html>`_ :raw-html:`
` - `UserScript: - Make RMM plots from calculated MJO indices - (scipy) - <../generated/model_applications/s2s/UserScript_obsERA_obsOnly_RMM.html>`_ - * - sklearn - - - - METplus wrappers - - https://www.kite.com/python/docs/sklearn - - Simple and efficient :raw-html:`
` - tools for predictive :raw-html:`
` - data analysis - - `WeatherRegime Calculation: - RegridDataPlane, PcpCombine, and WeatherRegime python code - (sklearn) - <../generated/model_applications/s2s/UserScript_obsERA_obsOnly_WeatherRegime.html>`_ :raw-html:`
` - `WeatherRegime Calculation: - GFS and ERA RegridDataPlane, PcpCombine, and WeatherRegime python code - (sklearn) - <../generated/model_applications/s2s/UserScript_fcstGFS_obsERA_WeatherRegime.html>`_ - * - xarray - - >=2023.1.0 - - METplus wrappers, :raw-html:`
` - METcalcpy, :raw-html:`
` - METplotpy - - https://xarray.pydata.org/en/v0.17.0/ - - makes working with :raw-html:`
` - labelled :raw-html:`
` - multi-dimensional arrays :raw-html:`
` - simple, efficient, :raw-html:`
` - and fun - - For using MET Python embedding functionality in use cases - * - xesmf - - - - METplus wrappers - - NOTE: The xesmf package :raw-html:`
` - will not be installed :raw-html:`
` - on WCOSS2 and there is :raw-html:`
` - an open GitHub issue to :raw-html:`
` - replace the package in :raw-html:`
` - the use case that uses it: :raw-html:`
` - https://github.com/dtcenter/METplus/issues/1314 - - for regridding - - `PlotDataPlane: - Python Embedding of - tripolar coordinate file - (xesmf) - <../generated/model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar.html>`_ - * - yaml - - - - METcalcpy, :raw-html:`
` - METplotpy - - https://pypi.org/project/PyYAML/ - - to load, read, and write :raw-html:`
` - YAML files with PyYAML - - - Future development plans ======================== diff --git a/docs/conf.py b/docs/conf.py index 35a1790c21..661d93e0bc 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -19,11 +19,14 @@ print(sys.path) from metplus import __version__, __release_date__ +from metplus import __python_version__ as python_version # -- Project information ----------------------------------------------------- project = 'METplus' +met_version = '12.0.0' + author = 'UCAR/NCAR, NOAA, CSU/CIRA, and CU/CIRES' # list of contributing authors currently involved with the project @@ -217,10 +220,13 @@ # -- Intersphinx control --------------------------------------------------------------- intersphinx_mapping = {'numpy':("https://docs.scipy.org/doc/numpy/", None)} +# -- Replace values in docs ------------------------------------------------------------ rst_epilog = f""" .. |copyright| replace:: {copyright} .. |author_list| replace:: {author_list} .. |release_date| replace:: {release_date} .. |release_year| replace:: {release_year} .. |release_info| replace:: {release_info} +.. |python_version| replace:: {python_version} +.. |met_version| replace:: {met_version} """ diff --git a/metplus/__init__.py b/metplus/__init__.py index 2696e90ad4..02a6079cfc 100644 --- a/metplus/__init__.py +++ b/metplus/__init__.py @@ -21,6 +21,7 @@ def get_metplus_info(info_rel_path): __version__ = get_metplus_version() __release_date__ = get_metplus_release_date() +__python_version__ = get_python_version() # import util and wrappers from .util import *