Align june_events sentinel handling with engine's consistent-sentinel rollout#19
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mtcorread merged 8 commits intoJul 23, 2026
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May 28, 2026 15:00
Reproducible conda environment for building and running JUNE2. Includes cxx-compiler (GCC on Linux), cmake, hdf5, yaml-cpp, openmpi, Python test deps (h5py, numpy), and optional deps metis and gperftools.
…ollout IDAS-Durham#16 narrowed infector_symptom_id uint16_t->uint8_t & made the engine write kNoSymptomId (255) directly for no-infector rows (seed/fomite/compartmental), replacing the old ambiguous 0 ("recovered"). june_events predated that fix: decode/sentinels.py only had one generic UNSET_REGISTRY_INDEX=255, and load_enriched.py worked around the ambiguity with a manual NaN-masking pass keyed on infector_id==-1 before registry decode. - decode/sentinels.py, decode/__init__.py: split UNSET_REGISTRY_INDEX into DEFAULT_ENCOUNTER_TYPE_ID and NO_SYMPTOM_ID, mirroring kDefaultEncounterTypeId and kNoSymptomId in include/core/types.h even though both are 255 - the engine no longer treats them as one concept, so neither should this module. - load_enriched.py: drop _mask_infector_symptom_for_no_infector; register infector_symptom_id's sentinel/label in REGISTRY_SENTINELS/ UNSET_LABEL_OVERRIDES instead, same path already used for encounter_type_id. - tests/test_load_enriched.py: update no-infector fixture row to uint8/255 (was uint16/0) to match the engine's actual wire format post-IDAS-Durham#16. - CONTEXT.md, PDR.md: document the two distinct 255 sentinels and flag that tests/fixtures/simulation_events_fixture.h5 still predates IDAS-Durham#16 (uint16 infector_symptom_id, 0 for no-infector) until rebuilt via build_fixture.py against a current simulation_events.h5.
mtcorread
approved these changes
Jul 23, 2026
mtcorread
approved these changes
Jul 23, 2026
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Summary
infector_symptom_iduint16_t -> uint8_t and made the engine writekNoSymptomId(255) directly for no-infector rows (seed/fomite/compartmental infections), replacing the old ambiguous0("recovered").june_eventspredated that fix.decode/sentinels.py's single genericUNSET_REGISTRY_INDEXintoDEFAULT_ENCOUNTER_TYPE_IDandNO_SYMPTOM_ID, mirroringkDefaultEncounterTypeId/kNoSymptomIdininclude/core/types.h, even though both are 255.load_enriched.py's manual NaN-masking workaround forinfector_symptom_id; it's now handled byREGISTRY_SENTINELS/UNSET_LABEL_OVERRIDES, the same path already used forencounter_type_id.CONTEXT.md/PDR.mdto document the two distinct 255 sentinels, and flagged thattests/fixtures/simulation_events_fixture.h5still predates Consistent sentinels for event-logging IDs, encounter types, symptoms #16 (uint16infector_symptom_id, 0 for no-infector) until rebuilt viabuild_fixture.pyagainst a currentsimulation_events.h5.Test plan
pytest analysis_tools/june_events/tests/— 41 passed