Add hhs geo level aggregation for NSSP #2036
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dsweber2
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Aug 27, 2024
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Glad to see this included quickly! This will definitely work, though it would be better if this were implemented as a method in the geomapper itself, for 2 reasons: reuse, and speed. aggregate_by_weighted_sum has to create the weights at every single time_value, which means it's definitely slower. Otoh, I doubt its enough of a speed penalty to be worth putting off having this geo level available. lgtm!
I think this is all we need for doc updates?
This was referenced Sep 11, 2024
minhkhul
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Sep 12, 2024
* doc: add logger examples to README and format * deployment + staging details * wrap lines * Update _template_python/INDICATOR_DEV_GUIDE.md Co-authored-by: David Weber <[email protected]> * Update _template_python/INDICATOR_DEV_GUIDE.md Co-authored-by: David Weber <[email protected]> * Update _template_python/INDICATOR_DEV_GUIDE.md Co-authored-by: David Weber <[email protected]> * Update INDICATOR_DEV_GUIDE.md with mysql syntax * Update INDICATOR_DEV_GUIDE.md reorder instruction on cron jobs * switch from input_file to input_dir (#1995) * adjust nssp max_age * add pyproject.toml * made changes based on suggestion * update ci config * separate new line Co-authored-by: Dmitry Shemetov <[email protected]> * fix: add explicit boto and moto dependencies to indicators * trying to get package data to show * installing dev package before testing in ci * adding dependency * move comment to right package * Update _delphi_utils_python/pyproject.toml Co-authored-by: Dmitry Shemetov <[email protected]> * Revert "Clean up delphi_utils " * refactoring date parsing to seperate file * first implimentation * small cleanup and adding missing data * changed wording and some logic * made test more explicit * add missing file * cleaning up tests * consolidating tests into one * fixed wording * consolidating test/fixture * clean up test * Update google_symptoms/delphi_google_symptoms/patch.py remove old code; not used anymore Co-authored-by: nmdefries <[email protected]> * clean up lint * remove teardown * cleaning and renaming * more explicit branching for regular run vs patching, renaming, cleaning * cleanup and rewrite logic * avoid linking keywords in PR template * Update _delphi_utils_python/README.md Co-authored-by: george <[email protected]> * Refactor Jenkins pipeline - Remove usage of parallel in the build and package stages - Retain usage of parallel in the deploy stages - Separate build and package into separate scripts to support build-only stages - Add a build-only stage for dev/feature branches * Add separate build and package scripts * Update script comments * Remove unused script * changes based on suggestion * standardizing output dir in test * changing back to session scope * more logging and update params * adding back conditional for num_export_days * test_run does not like fixtures * make deep copies of params fixtures * linting * test patch check if num_export_days is set or not * patch fn takes params as an arg, like run_module * list values added using actual day as an example * move pull date creation into pull_gs_data * don't modify num_export_days; define start/end date in terms of it and lag * refer to params by name; patch_flag -> custom_run flag * use test data based on recent actual indicator run * say where gold test data came from * not all date_utils tests need metadata * formatting * fn docs * lint and cleanup * adding more tests * removed extra lag and made test more robust * export_start_date is optional since the first available date is baked in * need to account for historical / current run for adding lag * adding validation script * fix typo * fixing typo in test * lint * sample run for validation * remove unused input Co-authored-by: nmdefries <[email protected]> * remove unused import * added progress chunk to limit logging (#2024) * added progress chunk to limit logging * lint * comment based on suggestion * add hhs geo level (#2036) * Add discussion of patching functionality to indicator manual (#2031) * basic patching info * custom_run * add hhs to geo section * de-emphasize R in contributing doc, and add links * ref/issue date intro * naming and force push standards * secret and params links * Clean up delphi_utils (take 2) (#2014) * add pyproject.toml * made changes based on suggestion * update ci config * separate new line Co-authored-by: Dmitry Shemetov <[email protected]> * fix: add explicit boto and moto dependencies to indicators * trying to get package data to show * installing dev package before testing in ci * adding dependency * move comment to right package * Update _delphi_utils_python/pyproject.toml Co-authored-by: Dmitry Shemetov <[email protected]> * more suggestion * adding pyproject.toml to template * Update changehc/Makefile * Update claims_hosp/Makefile * Update doctor_visits/Makefile * Update google_symptoms/Makefile * Update hhs_hosp/Makefile * Update nchs_mortality/Makefile * Update nssp/Makefile * Update nwss_wastewater/Makefile * Update quidel_covidtest/Makefile * Update sir_complainsalot/Makefile * fix: dependence bugs and cleanup * pandas[excel]<2 doesn't work, go back to xlrd and comment * add mock to changehc * add requests * remove setup.py from template * build: fix Jenkins build script --------- Co-authored-by: Amaris Sim <[email protected]> Co-authored-by: aysim319 <[email protected]> Co-authored-by: Dmitry Shemetov <[email protected]> * fix: build-indicators.sh looks for setup.py and pyproject.toml (#2048) * fix: build-indicators.sh looks for setup.py again Reverting a premature change. * fix: readability and future-proof * fix: more readability * chore: bump delphi_utils to 0.3.25 * chore: bump covidcast-indicators to 0.3.56 * [create-pull-request] automated change --------- Co-authored-by: Dmitry Shemetov <[email protected]> Co-authored-by: minhkhul <[email protected]> Co-authored-by: Nat DeFries <[email protected]> Co-authored-by: minhkhul <[email protected]> Co-authored-by: David Weber <[email protected]> Co-authored-by: george <[email protected]> Co-authored-by: Amaris Sim <[email protected]> Co-authored-by: aysim319 <[email protected]> Co-authored-by: Brian Clark <[email protected]> Co-authored-by: Delphi Deploy Bot <[email protected]> Co-authored-by: minhkhul <[email protected]>
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Description
This PR adds hhs geo level aggregation for NSSP indicator. It allows us to generate hhs data from state data.
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