Add the SICdb dataset#310
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Prerequisite for the per-dataset registration PRs (#305 AUMCdb, #306 EHRShot, #307 HIRID, #308 INSPIRE, #309 NWICU, #310 SICdb, #311 eICU). Most of those datasets' upstream extractors don't ship a publicly installable demo, and the existing registry validation requires every dataset to declare a build_demo command. Switches the convention to: a dataset has a demo iff its commands declare build_demo. Absence is the signal — no separate metadata field. - `test_all_datasets_have_commands` now requires `build_full` (which every dataset still needs) and allows missing `build_demo`. - `tests/conftest.py` drops datasets without `build_demo` from the integration test matrix, so a per-dataset CI lane for one collects zero parametrized tests and passes cleanly rather than trying to build data the dataset can't produce. - `src/MEDS_DEV/datasets/__main__.py` raises a clear error when called with `demo=True` against a dataset that doesn't declare a build_demo command (instead of the previous KeyError). No dataset.yaml files change here — those changes ship with the sister per-dataset PRs that depend on this one. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Registers SICdb (Salzburg Intensive Care database) in
src/MEDS_DEV/datasets/SICdb/. Extraction is viaMEDS_extract-SICdbfrom the upstreamsicdb-medspackage (pinned to0.0.4).Files added:
dataset.yaml— metadata +build_fullshelling out toMEDS_extract-SICdb. Nobuild_demo(upstream doesn't ship a demo recipe; Makebuild_demooptional, skip demo-less datasets in tests #312 makes the key optional and ensures integration tests skip it).predicates.yaml— admission/discharge plus a couple of lab predicates. Regex syntax bugs (^X*form) and commented-out predicate stubs from the contributor's branch were cleaned up.requirements.txt—SICdb_MEDS==0.0.4(note: underscore in package name matches upstream).refs.bib,README.md.SICdb is not added to any task's
supported_datasets.Known issue (latent, not blocking)
The
icu_admission/icu_dischargepredicates use the same regex ashospital_admission/hospital_discharge(^ADMISSION//.*and^DISCHARGE//.*), so they don't distinguish ICU vs hospital events. Since SICdb isn't wired into themortality/in_icu/first_24htask here, this is latent — but worth fixing before listing SICdb in any ICU-specific task.Depends on #312
#312 makes
build_demooptional in the registry and skips datasets that don't declare it from the integration test matrix. Targeted atfeat/dataset-demo-availabilityfor now; once #312 merges, this PR retargets todev.Test plan
build_demooptional, skip demo-less datasets in tests #312.Supersedes / refs
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