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Merged
albrja merged 3 commits into from
Feb 3, 2026
Merged

Albrja/mic-6791/Treatment observer bugfix #67

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1ecfab4
Change on_time_step metho in treatment to on_time_step_cleanup
albrja Jan 30, 2026
200a272
Update ramp start and artifact paths
albrja Jan 30, 2026
dc967ad
Revert config changes
albrja Jan 30, 2026
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24 changes: 16 additions & 8 deletions src/vivarium_csu_alzheimers/components/treatment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -200,9 +200,10 @@ def on_initialize_simulants(self, pop_data: SimulantData) -> None:
COLUMNS.WAITING_FOR_TREATMENT_EVENT_COUNT,
],
] = [TREATMENT_DISEASE_MODEL.WAITING_FOR_TREATMENT_STATE, event_time, 1]
update.loc[
start_treatment_idx, COLUMNS.TREATMENT_DURATION
] = self.get_treatment_duration(start_treatment_idx)
if not start_treatment_idx.empty:
update.loc[
start_treatment_idx, COLUMNS.TREATMENT_DURATION
] = self.get_treatment_duration(start_treatment_idx)

update.loc[
decline_treatment_idx,
Expand All @@ -215,16 +216,23 @@ def on_initialize_simulants(self, pop_data: SimulantData) -> None:

self.population_view.update(update)

def on_time_step(self, event: Event) -> None:
def on_time_step_cleanup(self, event: Event) -> None:
"""Set treatment duration for simulants in waiting_for_treatment state.
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@stevebachmeier stevebachmeier Feb 3, 2026

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ugh, sneaky


This runs after the state machine transitions (priority 8) to ensure
all simulants who entered waiting_for_treatment during this time step
have their treatment duration set.
"""
pop = self.population_view.get(event.index)
waiting_for_treatment_idx = pop.index[
pop[COLUMNS.TREATMENT_STATE]
== TREATMENT_DISEASE_MODEL.WAITING_FOR_TREATMENT_STATE
]
pop.loc[
waiting_for_treatment_idx, COLUMNS.TREATMENT_DURATION
] = self.get_treatment_duration(waiting_for_treatment_idx)
self.population_view.update(pop)
if not waiting_for_treatment_idx.empty:
pop.loc[
waiting_for_treatment_idx, COLUMNS.TREATMENT_DURATION
] = self.get_treatment_duration(waiting_for_treatment_idx)
self.population_view.update(pop)

def _create_treatment_mode(self) -> TreatmentModel:

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3 changes: 2 additions & 1 deletion src/vivarium_csu_alzheimers/constants/data_values.py
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Original file line number Diff line number Diff line change
Expand Up @@ -176,8 +176,9 @@ class __BBBMTestResults(NamedTuple):
]
BBBM_TESTING_START_DATE = BBBM_TESTING_RATES[0][0]

# TODO: update time start of ramp with test model updates
TREATMENT_PROBS_RAMP = [
(pd.Timestamp("2027-01-01"), 0.0),
(pd.Timestamp("2030-01-01"), 0.0),
(pd.Timestamp("2035-01-01") + pd.Timedelta(days=182), 0.3),
(pd.Timestamp("2100-01-01"), 0.8),
]
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20 changes: 10 additions & 10 deletions src/vivarium_csu_alzheimers/model_specifications/branches/scenarios.yaml
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Expand Up @@ -9,13 +9,13 @@ branches:
- bbbm_testing_and_treatment
input_data:
artifact_path:
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/united_states_of_america.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/china.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/brazil.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/germany.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/israel.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/japan.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/spain.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/sweden.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/taiwan_(province_of_china).hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/united_kingdom.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model10.0/united_states_of_america.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model10.0/china.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model10.0/brazil.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model10.0/germany.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model10.0/israel.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model10.0/japan.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model10.0/spain.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model10.0/sweden.hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model10.0/taiwan_(province_of_china).hdf'
- '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model10.0/united_kingdom.hdf'
2 changes: 1 addition & 1 deletion src/vivarium_csu_alzheimers/model_specifications/model_spec.yaml
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Expand Up @@ -24,7 +24,7 @@ components:
configuration:
input_data:
input_draw_number: 0
artifact_path: '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/united_states_of_america.hdf'
artifact_path: '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model10.0/united_states_of_america.hdf'
interpolation:
order: 0
extrapolate: True
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