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[develop] Make get_obs
tasks day-dependent in workflow; other improvements and bug fixes
#1137
[develop] Make get_obs
tasks day-dependent in workflow; other improvements and bug fixes
#1137
Commits on Jul 9, 2024
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Commits on Jul 11, 2024
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Bug fix from Michelle H. for prepbufr files: "On May 22, the name of …
…the tar file where the prepbufr files live changed"
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Bug fix for removing phantom 00-hour tasks from workflow. Bug found b…
…y Michelle Harrold, solution by Michael Kavulich.
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Commits on Jul 16, 2024
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Bug fix: Append cycle date to names of deterministic GridStat and Poi…
…ntStat tasks' METplus log files.
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Version of ex-script for pulling obs that works for multiple overlapp…
…ing cycles for CCPA and MRMS but not yet for NDAS or NOHRSC.
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Commits on Jul 17, 2024
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Changes to make get_obs_mrms tasks to work for mulitple cycles and wi…
…thout performing unnecessary repeated pulls.
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Commits on Jul 18, 2024
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Commits on Jul 19, 2024
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Commits on Jul 20, 2024
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Change names of raw directories for CCPA and MRMS to indicate whether…
… they're per-cycle or per-day.
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Version with NDAS changes that seems to work. Still need lots of clea…
…nup and comments.
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Commits on Jul 21, 2024
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Second set of NDAS changes so that there are no repeat pulls of NDAS …
…files from HPSS (and works with multiple cycles).
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Commits on Jul 22, 2024
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Commits on Jul 23, 2024
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Add debugging statement to clarify the current working directory wher…
…e cleanup is happening.
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Commits on Jul 25, 2024
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Add code to cause the script to wait until all the (processed) obs fi…
…les, that are expected to be created once the task is finished actually get created. This is needed because it is possible that for some forecast hours for which there is overlap between cycles, the files are being retrieved and processed by the get_obs_... task for another cycle.
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Fix the workflow task dependencies and ex-script for the GenEnsProd a…
…nd EnsembleStat tasks such that GenEnsProd does not depend on the completion of get_obs_... tasks (because it doesn't need observations) but only forecast output while EnsembleStat does.
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Bugfix to dependencies of ensemble vx tasks that come after GenEnsPro…
…d due to changes to dependencies of GenEnsProd tasks in previous commit(s).
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Commits on Jul 26, 2024
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Commits on Jul 28, 2024
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Increase default wallclock time for get_obs_ccpa tasks since they're …
…tending to time out for 48-hour forecasts.
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For each cycle except the last one, in the PcpCombine_obs tasks make …
…sure PcpCombine operates only on those hours unique to the cycle, i.e. for those times starting from the initial time of the cycle to just before the initial time of the next cycle. For the PcpCombine_obs task for the last cycle, allow it to operate on all hours of that cycle's forecast. This ensures that the PcpCombine tasks for the various cycles do not clobber each other's output. Accordingly, change the dependencies of downstream tasks that depend on PcpCombine obs output to make sure they include all PcpCombine_obs tasks that cover the forecast period of the that downstream task's cycle.
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Commits on Jul 29, 2024
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Fix still-existing problem of file clobbering with get_obs_mrms and p…
…ossibly also get_obs_ndas by putting in sleep commands.
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Commits on Jul 30, 2024
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Commits on Aug 15, 2024
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Commits on Aug 16, 2024
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Make the names of the deterministic and ensemble vx configuration fil…
…es user-specifiable.
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Commits on Aug 26, 2024
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Commits on Sep 3, 2024
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Change paths to archive files to make retrieve_data.py work with new …
…get_obs_...sh scripts.
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Move most of the code for getting obs files out of the ex-script exre…
…gional_get_verif_obs.sh since those are now in the ush/get_obs_[ccpa|mrms|ndas|nohrsc].sh scripts.
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Add ceil.sh to the set of scripts/functions that are sourced by sourc…
…e_util_funcs.sh.
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Changes to reflect the fact that the output of PcpCombine_obs tasks n…
…ow goes into a cycle-based subdirectory (under the experiment directory), as opposed to a obs day based subdirectory.
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Simplify names of some variables; add variable for where workflow tas…
…k flag files should be placed; fix template for output files from pcpcombine_obs tasks.
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Commits on Sep 4, 2024
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Modifications to exregional_run_met_pb2nc_obs.sh so that the correspo…
…nding task is day-based (i.e. it is run for each day for which obs are needed). The script now also creates a flag file indicating it completed successfully (needed for the workflow to work properly).
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Move sections of WE2E yaml files around to be consistent with the ord…
…er in config_defaults.yaml.
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Changes to workflow yaml files for vx portion of the workflow in orde…
…r to have cycledefs for obs-day-based tasks that include only the obs days for which obs are actually needed but not on any days (inbetween the first and last obs days over all cycles) for which obs are not needed.
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Commits on Sep 5, 2024
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Add code to be able to generate forecast output times and obs days, b…
…oth for instantaneous and cumulative fields, and pass this info to the ROCOTO xml generation system.
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Commits on Sep 8, 2024
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Add WE2E test configuration files for getting obs, doing vx pre-proce…
…ssing, and deterministic vx.
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Commits on Sep 9, 2024
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Commits on Sep 10, 2024
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Bug fix to remove crontab line once experiment is complete (regardles…
…s of whether it succeeded or failed).
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Get REMOVE_RAW_OBS... variables directly from var_defns.yaml file ins…
…tead of setting it as an enviroment variable in the rocoto xml. This makes it possible to change their settings by chaning the values in var_defns.yaml and rerunning the get_obs_... tasks.
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Commits on Sep 11, 2024
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Commits on Sep 12, 2024
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Commits on Sep 13, 2024
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Commits on Sep 16, 2024
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Commits on Sep 17, 2024
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Add check in setup.py to make sure that the accumulation periods of a…
…ccumlated vx fields are less than or equal to the forecast length. This check is also made in the workflow yaml files, but if all the accumulation periods happen to be greater than the forecast length, then the field must be completely removed from verification (i.e. its vx tasks must be removed from the workflow), and that can only be done via this check in setup.py; it can't be done in the workflow task yaml files.
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Commits on Sep 20, 2024
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Commits on Sep 25, 2024
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Changes to allow NOHRSC obs and ASNOW to be accumulated by PcpCombine…
… and verified in GridStat.
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Changes to get_obs/vx WE2E tests to get them working with staged fore…
…cast output at new location.
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Add WE2E test to get NOHRSC obs and do vx on 6-hour and 24-hour snowf…
…all accumulation.
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Add new variables specifying the time intervals at which different ty…
…pes of obs are available on NOAA HPSS. Use these new variables in file name templates.
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Rearrange the settings for the forecast file templates in config_defa…
…ult.sh so that they're more readable.
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Allow verification of 12 and 18-hourly accumulated snowfall since the…
…se are now obtained by adding 6-hourly in the obs (as opposed to before, where we just got the 6 or 24 hourly obs without the option to add the 6-hourly to get 12 and 18).
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In Pb2NC tasks, use the arrays in var_defns.py that specify the times…
… on a given day at which a given types of obs should be retrieved.
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In the get_obs tasks, use the arrays in var_defns.py that specify the…
… times on a given day at which a given types of obs should be retrieved. Remove the arrays that specify the combined forecast output times for all cycles.
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Add file (exregional_run_met_pb2nc_obs.sh) that should have been part…
… of commit hash cae50b5, and remove file (exregional_run_met_pcpcombine.sh) that should NOT have been.
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Commits on Sep 26, 2024
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Refactor the way the vx lead hours (i.e. the hours for which vx will …
…be run) are calculated (and corresponding files checked for), including renaming of the file set_vx_fhr_list.sh to set_leadhrs.sh.
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Commits on Sep 27, 2024
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Changes that allow checks on the verification parameters and generati…
…on of new vx config parameters to allow the workflow to have obs-day-based as well as cycle-based tasks.
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Commits on Sep 28, 2024
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Change name of cycledefs for obs days as was done in other files (pyt…
…hon scripts) in previous commits.
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Increase walltime for PcpCombine_fcst tasks since some WE2E tests are…
… running out of time.
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Modify metatask and task names for clarity; fix paths; add pcpcombine…
… task for NOHRSC; fix task dependencies.
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Commits on Sep 29, 2024
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Make adjustments to ASNOW settings to account for the fact that for A…
…SNOW obs, it's the netcdf files that come out of PcpCombine_obs tasks that are used for verification.
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Commits on Oct 1, 2024
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Commits on Oct 2, 2024
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Ensure that the observation file name templates specified in the SRW …
…App configuration file are used when running the Pb2nc task (as opposed to hard-coding file names).
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Add argument to mrms_pull_topofhour.py that specifies whether a subdi…
…rectory having the name of the valid day (of the form "YYYYMMDD") should be assumed to exist under the specified source directory, and whether such a subdirectory should be created under the specified output directory. Previously, such a subdirectory was always assumed to exist/created; now, it is an option.
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When retrieving files from different data stores (e.g. NOAA's HPSS), …
…make sure that the get_obs tasks place the files (and name them) according to the file name templates specified for each obs type in the SRW App configuration file. Also, remove the variable basedir_proc since it is redundant.
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Commits on Oct 3, 2024
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Commits on Oct 6, 2024
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Use new python script to get any of the allowed kinds of obs instead …
…of the four separate shell scripts.
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Commits on Oct 7, 2024
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Clean up and clarify comments; calculate list of processed obs file p…
…aths only once and save for later use; other minor code improvements.
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Move the two sets of variables [CCPA|NOHRSC|MRMS|NDAS]_OBS_DIR and RE…
…MOVE_RAW_OBS_[CCPA|NOHRSC|MRMS|NDAS] in the default app configuration file from the "platform" section to the "verification" section so that they are closer to the METplus file name template variables OBS_[...]_FN_TEMPLATE that they are closely coupled with.
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Fixes to WE2E test config files to reflect moving of variables from "…
…platform" section to "verification" section in config_defaults.yaml.
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Commits on Oct 8, 2024
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Commits on Oct 10, 2024
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Modify old test for set_cycle_dates to fit new version of this functi…
…on. This includes adding a new test for the case in which the output should be a list of datetime objects (the default is for the output to be a list of strings).
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Commits on Oct 11, 2024
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In config.community.yaml, move [CCPA|MRMS|NDAS]_OBS_DIR variables fro…
…m the "platform" to the "verification" section to be consistent with the changes in config_defaults.yaml.
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Commits on Oct 18, 2024
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Bug fix: the get_obs_nohrsc tasks need to be based on obs days for cu…
…mulative fields, not obs days for instantaneous fields (which is the default cycledef in verify_pre.yaml).
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Add new parameter VX_FCST_OUTPUT_INTVL_HRS into config_defaults.yaml …
…and use it as the forecast output interval when performing vx.
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Change arguments so the cycle start times don't need to be called mul…
…tiple times by different functions.
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Further changes to avoid calling the function that calculates the cyc…
…le start times multiple times.
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In order for the temporal consistency checks on various vx parameters…
… and corresponding adjustments to them to be effective (i.e. in order for any necessary adjustments to make it into the rocoto xml file), move the call to the function that performs these checks and adjustments to a place BEFORE the call to extend_yaml() that "freezes" (hard-codes) the accumulations for which the PcpCombine and other tasks are run (this freezing should happen AFTER any adjustments are made to the list of user-specified accumulations).
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Commits on Oct 20, 2024
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Drop the "_NDAS" and "_ndas" suffixes from pb2nc tasks since prepbufr…
… files can come from sources other than NDAS (e.g. GDAS).
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Commits on Oct 21, 2024
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Commits on Oct 22, 2024
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Commits on Oct 27, 2024
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Change name of App variable VX_FIELDS to VX_FIELD_GROUPS to more corr…
…ectly represent its contents since it contains a list of field groups (not just fields) to verify; fix comments and output messages related to this issue; rename some local variables related to this issue.
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Rename and reformat the App variables containing METplus templates fo…
…r obs files so that they are lists of strings (rather than just string scalars) that mimic python dictionaries, with pairs of elements specifying the field group(s) and corresponding file name template, respectively; fix comments accordingly; rename some local variables for clarity.
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Add a check to make sure obs base directories are distinct for the va…
…rious types of obs.
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(1) Reorganize verification section in config_defaults.yaml so that p…
…arameters are grouped together in a way that is more natural; (2) update and improve description of variables in the verification section of config_defaults.yaml; (3) update documentation in ConfigWorkflow.rst to reflect the updates in config_defaults.yaml.
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Commits on Oct 28, 2024
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Refactor some bash to python, import filename templating directly fro…
…m METplus (#3) * Replace call to custom templating script with direct invocation of metplus templating routines in get_obs.py * Replace set_leadhrs.sh with set_leadhrs.py * Fixes from pylint * Convert eval_METplus_timestr_tmpl.sh to python, redistribute some logic from set_leadhrs.py to this new script for efficiency; also fix some problems in set_leadhrs.py found by pylint * Refactor mrms_pull_topofhour.py to make it easily importable, call that function directly from get_obs.py * Remove the deprecated shell scripts * time_lag needs to be passed as an integer to set_leadhrs.py * Fixes to refactored mrms_pull_topofhour.py * Suggested test names
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Merge remote-tracking branch 'origin/feature/daily_obs_tasks' into fe…
…ature/daily_obs_tasks
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Merge remote-tracking branch 'origin/feature/daily_obs_tasks' into fe…
…ature/daily_obs_tasks
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Merge remote-tracking branch 'origin/feature/daily_obs_tasks' into fe…
…ature/daily_obs_tasks
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Commits on Oct 29, 2024
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First shot at modifications to enable variable forecast output interv…
…al in the verification.
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Introduce flag that specifies whether or not vx tasks are being run i…
…n the workflow; run checks on and/or adjustments to vx parameters only if this flag is true.
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Add WE2E tests for AI/ML models (FourCastNet, GraphCast, and PanguWea…
…ther) and GFS that all use a forecast output interval other than 1 hour (all use 6 hours) and use GDAS (instead of NDAS) as the obs in the verification.
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Commits on Oct 30, 2024
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Move vx configuration files, both the defaults and the custom ones us…
…ed for some WE2E tests, to parm/metplus/vx_configs.
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Commits on Nov 2, 2024
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Rename vx tasks, metatasks, and variables and update documentation. D…
…etails below. * Since the vx tasks under the deterministic and ensemble vx metatasks are grouped by verification field group, rename the metatasks (in verify_det.yaml and veriify_ens.yaml and elsewhere as necessary) so that they refer to the vx field groups they apply to instead of the obs types. For example: * Change "metatask_GridStat_NOHRSC_all_accums_all_mems" to "metatask_GridStat_ASNOW_all_accums_all_mems". * Change "metatask_GenEnsProd_EnsembleStat_CCPA" to "metatask_GenEnsProd_EnsembleStat_APCP_all_accums" (add the "_all_accums" at the end to be consistent with the way other metatask names for cumulative field groups are named). * Change "metatask_GridStat_MRMS_ensprob" to "metatask_GridStat_ensprob_REFC_RETOP". * Replace the "ADPSFC" and "ADPUPA" field groups with "SFC" and "UPA", respectively, since the "ADP" part is specific to NDAS obs, and we want the verification field groups to have general names that are not connected to the obs type. * Move "_obs" and "_fcst" substrings in the names of several pre-vx tasks/metatasks (in verify_pre.yaml) towards the end for clarity/consistency. * For clarity, change the environment variable "VAR" in the vx tasks (where it is set to the name of the field group to be verified) to "FIELD_GROUP". Make corresponding necessary changes elsewhere (e.g. in the ex-scripts for the vx tasks). * Expand jinja2 code in verify_pre.yaml from a one-liner to multiple lines to make it easier to understand. * Make corresponding modifications in documentation.
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Commits on Nov 3, 2024
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Move the 4 new WE2E vx tests that were recently added to coverage.jet…
… to the set of coverage tests for Hera since there is no data staged on Jet yet.
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Commits on Nov 4, 2024
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Bug fix in METplus conf templates to account for the field group name…
…s 'ADPSFC' and 'ADPUPA' being changed to 'SFC' and 'UPA'.
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Bug fix in vx configuration files to account for the field group name…
…s 'ADPSFC' and 'ADPUPA' being changed to 'SFC' and 'UPA'.
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Bug fix in ex-script and an auxiliary bash script to account for the …
…field group names 'ADPSFC' and 'ADPUPA' being changed to 'SFC' and 'UPA'.
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Bug fix: For ensemble vx tasks, add omitted cycle dates to the end of…
… the names of the METplus log files.
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Modify ensemble vx task and metatask names to match those for determi…
…nistic vx. Make corresponding changes in the docs.
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Merge remote-tracking branch 'refs/remotes/origin/feature/daily_obs_t…
…asks' into feature/daily_obs_tasks
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Commits on Nov 7, 2024
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Change locations of staged forecast and obs files in the new vx WE2E …
…test to use the "TEST_" variables from the machine files. This makes it easier to get the tests to run from EPIC directories.
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Set the locations of the staging directories for WE2E testing to pers…
…onal directories; add new testing directory for GDAS.
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Commits on Nov 12, 2024
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Change forecast and obs staging locations for WE2E tests to EPIC's di…
…rectories since the files for the new tests in PR ufs-community#1137 are staged now.
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Bug fixes to get the AI/ML and GFS tests to work with data staged at …
…EPIC locations on Hera.
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Commits on Nov 13, 2024
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Update doc/UsersGuide/BuildingRunningTesting/RunSRW.rst
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Change wallclock time for GenEnsProd task for SFC and UPA field group…
…s from 02:30:00 to 04:15:00 to account for unexpected increase in time needed to complete GenEnsProd for UPA fields in the WE2E test "MET_ensemble_verification_only_vx_time_lag".
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Merge remote-tracking branch 'refs/remotes/origin/feature/daily_obs_t…
…asks' into feature/daily_obs_tasks
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Update list of modules to be included in the tech docs (the rst file …
…for each new module was added in a previous commit).
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Fix indentation for argument and return value lists in the docstrings…
… of new python functions; add type for each argument and return value; use latex-style math formatting for equations; other minor formatting adjustments.
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Commits on Nov 15, 2024
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Include "metplus" in autodoc_mock_imports list in the configuration f…
…ile for sphinx (conf.py) (this will give sphinx access to METplus); remove definition of METPLUS_ROOT as an environment variable from the Makefile for the docs and instead define it in conf.py (as just a null string since it isn't actually used to load METplus).
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Commits on Nov 18, 2024
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Update doc/UsersGuide/BuildingRunningTesting/RunSRW.rst
Co-authored-by: Gillian Petro <96886803+gspetro-NOAA@users.noreply.github.com>
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