Patch all

Author: jlubken

src/penn_chime/cli.py

@@ -8,8 +8,9 @@
 
 from pandas import DataFrame
 
-from penn_chime.parameters import Parameters, RateLos
-from penn_chime.models import SimSirModel as Model, change_date
+from .constants import CHANGE_DATE
+from .parameters import Parameters, RateLos
+from .models import SimSirModel as Model
 
 
 class FromFile(Action):
@@ -45,7 +46,7 @@ def validate(string):
 
 def parse_args():
     """Parse args."""
-    parser = ArgumentParser(description=f"penn_chime: {change_date()}")
+    parser = ArgumentParser(description=f"penn_chime: {CHANGE_DATE}")
     parser.add_argument("--file", type=open, action=FromFile)
 
     for arg, cast, min_value, max_value, help, required in (
@@ -84,14 +85,6 @@ def parse_args():
         ),
         ("--icu-los", int, 0, None, "ICU Length of Stay (days)", True),
         ("--icu-rate", float, 0.0, 1.0, "ICU Rate: 0.0 - 1.0", True),
-        (
-            "--known-infected",
-            int,
-            0,
-            None,
-            "Currently Known Regional Infections (>=0) (only used to compute detection rate - does not change projections)",
-            True,
-        ),
         (
             "--market_share",
             float,
@@ -127,7 +120,6 @@ def main():
         date_first_hospitalized=a.date_first_hospitalized,
         doubling_time=a.doubling_time,
         infectious_days=a.infectious_days,
-        known_infected=a.known_infected,
         market_share=a.market_share,
         n_days=a.n_days,
         relative_contact_rate=a.relative_contact_rate,

tests/by_date_first_hospitalized/settings.cfg

@@ -5,7 +5,6 @@
 --icu-los 9
 --icu-rate 0.0075
 --infectious-days 14
---known-infected 510
 --market_share 0.15
 --n-days 60
 --population 4119405

tests/by_doubling_time/settings.cfg

@@ -5,7 +5,6 @@
 --icu-los 9
 --icu-rate 0.0075
 --infectious-days 14
---known-infected 510
 --market_share 0.15
 --n-days 60
 --population 4119405

tests/test_app.py

@@ -42,7 +42,6 @@
     current_hospitalized=14,
     date_first_hospitalized=datetime(year=2020, month=3, day=7),
     doubling_time=4.0,
-    known_infected=510,
     n_days=60,
     market_share=0.15,
     relative_contact_rate=0.3,
@@ -54,7 +53,6 @@
 PARAM = Parameters(
     current_hospitalized=100,
     doubling_time=6.0,
-    known_infected=5000,
     market_share=0.05,
     relative_contact_rate=0.15,
     population=500000,
@@ -67,7 +65,6 @@
 HALVING_PARAM = Parameters(
     current_hospitalized=100,
     doubling_time=6.0,
-    known_infected=5000,
     market_share=0.05,
     relative_contact_rate=0.7,
     population=500000,