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Variables in the templates are then substituted at runtime to generate the COM paths via the use of `envsubst`. To facilitate this, there is a new function, `generate_com` (see below), provided to automatically generate the COM paths.\r\n\r\nWhere possible, COM paths are defined at the j-job level and made read-only. However, many of the EnKF scripts loop over the ensemble members, forcing the definitions to be made at the exscript level instead (and be mutable).\r\n\r\nThe arguments to `generate_com()` are the list of COM variables to generate, optionally accompanied by a template to use using a colon to separate them. When no template is specified, the variable will be generated using the ${varname}_TMPL template. Two options are accepted, `-r` and `-x`, which will mark the variable as read-only and for export, respectively (the same as with the `declare` builtin). It is best practice to define any additional variables needed by the template on the same line to avoid adding them to the calling script’s scope. Here are some examples used in the code:\r\n\r\nGenerate the path to the atmos analysis directory for the current cycle and `$RUN` (implicitly from the `$COM_ATMOS_ANALYSIS_TMPL` template) and mark as read-only and export:\r\n```\r\nYMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_ANALYSIS\r\n```\r\n\r\nGenerate the path to the atmos history directory for the previous cycle's gdas from the `$COM_ATMOS_HISTORY_TMPL` template and mark as read-only and export:\r\n```\r\nRUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx \\\r\n COM_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL\r\n```\r\n\r\nGenerate the path to the first ensemble member's history directory of the current cycle and `$RUN` and mark for export:\r\n```\r\nMEMDIR=’mem001’ YMD=${PDY} HH=${cyc} generate_com -x COM_ATMOS_HISTORY\r\n```\r\n\r\n## Additional information\r\nThe staging of initial conditions in `setup_expy.py` has been updated to stage in the new locations. The source of the initial conditions can **either** be in the new hierarchical structure or in the old flat structure and the script will stage the files in the new structure. The destination paths are hard-coded here, so if any changes are made to the analysis, input, or restart templates, they will need to be mirrored in `setup_expy.py`.\r\n\r\n### Stipulations\r\nAll changes in this PR are subject to approval by several stakeholders, including NCO. Sample COM trees above are subject to revision based on feedback (for instance, file X isn't really an obs file).\r\n\r\nFile name updates are not included in this PR. File names (primarily for coupled components) will be updated to comply with NCO standards in a future PR.\r\n\r\nAWIPS jobs are now almost working (they do not in current develop), but one last program is still ending with an error.\r\n\r\nWork on fit2obs is deferred, so that portion of the verify job does not work.\r\n\r\nWAFS scripts are all external and have not yet been updated. WAFS is expected to be packaged separately going forward, so will need to be updated like any other downstream package.\r\n\r\nSome scripts that are not part of our normal development workflow have not yet been updated. I may be able to knock a few more off this list, but some just aren’t available in development mode currently:\r\n- All UFSDA app jobs (to be handled separately)\r\n- With associated dev jobs (may still modify and test)\r\n - JGDAS_ATMOS_GLDAS\r\n - ~~JGLOBAL_WAVE_GEMPAK~~\r\n - ~~JGLOBAL_WAVE_POST_BNDPNT~~\r\n - ~~JGLOBAL_WAVE_POST_BNDPNTBLL~~\r\n - ~~JGLOBAL_WAVE_PRDGEN_BULLS~~\r\n - ~~JGLOBAL_WAVE_PRDGEN_GRIDDED~~\r\n - ~~JGLOBAL_WAVE_PREP~~\r\n- With no associated dev job\r\n - JGDAS_ATMOS_GEMPAK_META_NCDCJGFS_ATMOS_FBWIND\r\n - JGFS_ATMOS_FSU_GENESIS\r\n - JGFS_ATMOS_GEMPAK_META\r\n - JGFS_ATMOS_GEMPAK_NCDC_UPAPGIF\r\n - JGLOBAL_ATMOS_EMCSFC_SFC_PREP\r\n - JGLOBAL_ATMOS_POST_MANAGER\r\n - JGLOBAL_ATMOS_TROPCY_QC_RELOC\r\n+ All downstream scripts for the above\r\n\r\nThere are also a few scripts that are not available to the development workflow that I have already made a good-faith effort at updating:\r\n- JGDAS_ATMOS_GEMPAK\r\n- JGFS_ATMOS_PGRB2_SPEC_NPOESS\r\n\r\n## Related Issues\r\nCloses #761\r\nFixes #978\r\nFixes #999\r\nFixes #1207\r\nPartially addresses #198\r\nPartially addresses #289\r\nPartially addresses #293\r\nPartially addresses #1299\r\nPartially addresses #1326","shortMessageHtmlLink":"Reorganize COM and refactor to use templates (NOAA-EMC#1421)"}},{"before":"3cfdbe04e864847a3f89b6f8b89799b18b7e1f5e","after":"0d1e993b2b5db6160c4a6b88b67899dc8e9754f8","ref":"refs/heads/develop","pushedAt":"2023-03-31T15:00:38.741Z","pushType":"push","commitsCount":2,"pusher":{"login":"XianwuXue-NOAA","name":"Xianwu Xue - NOAA","path":"/XianwuXue-NOAA","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/48287866?s=80&v=4"},"commit":{"message":"Remove para module paths for ncdiag on WCOSS2 (#1437)\n\nThe ncdiag/1.0.0 module moved from para to prod on WCOSS2 on March 27th (RFC 10769).\r\n\r\n* Remove para module paths for ncdiag on WCOSS2 in global-workflow module_base.wcoss2.lua\r\n* Update GSI-EnKF hash to update ncio and ncdiag\r\n* Update GSI-Monitor hash to update ncdiag\r\n\r\nRefs #1426","shortMessageHtmlLink":"Remove para module paths for ncdiag on WCOSS2 (NOAA-EMC#1437)"}},{"before":"c549acb914c7ae479740c8f1007f5f3f36b91db5","after":"3cfdbe04e864847a3f89b6f8b89799b18b7e1f5e","ref":"refs/heads/develop","pushedAt":"2023-03-30T13:14:29.939Z","pushType":"push","commitsCount":3,"pusher":{"login":"XianwuXue-NOAA","name":"Xianwu Xue - NOAA","path":"/XianwuXue-NOAA","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/48287866?s=80&v=4"},"commit":{"message":"Enforce rstprod on relevant tarballs (#1436)\n\nEnsures that tarballs that contain restricted data are properly restricted to the rstprod group.\r\n\r\nFixes #1433","shortMessageHtmlLink":"Enforce rstprod on relevant tarballs (NOAA-EMC#1436)"}},{"before":"478f48ede4ee28e8193ff02befb0a954bd7eca61","after":"c549acb914c7ae479740c8f1007f5f3f36b91db5","ref":"refs/heads/develop","pushedAt":"2023-03-27T14:50:50.726Z","pushType":"push","commitsCount":6,"pusher":{"login":"XianwuXue-NOAA","name":"Xianwu Xue - NOAA","path":"/XianwuXue-NOAA","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/48287866?s=80&v=4"},"commit":{"message":"Updates in the aerosol tasks (#1420)\n\n-removes the definition of environment variables in the shell script j-jobs\r\n-eliminates the use of !ENV in the yaml files for aerosol jobs.\r\n-eliminates use of CDATE in the python tasks. 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