Refactor module

Author: jlubken

Dockerfile

@@ -9,5 +9,5 @@ COPY defaults defaults
 COPY src src
 RUN pip install -q .
 
-CMD ["streamlit", "run", "src/app.py"]
+CMD ["streamlit", "run", "st_app.py"]
 

src/app.py

@@ -3,22 +3,18 @@
 import os
 import sys
 
-from .parameters import Parameters
-from .models import SimSirModel as Model
+from .model.parameters import Parameters
+from .model.sir import Sir
 
 
 def main():
     """Main."""
     p = Parameters.create(os.environ, sys.argv[1:])
-    m = Model(p)
+    m = Sir(p)
 
     for df, name in (
         (m.sim_sir_w_date_df, "sim_sir_w_date"),
         (m.admits_df, "projected_admits"),
         (m.census_df, "projected_census"),
     ):
         df.to_csv(f"{p.current_date}_{name}.csv")
-
-
-if __name__ == "__main__":
-    main()

src/penn_chime/cli.py

@@ -13,7 +13,7 @@
 from sys import stdout
 from typing import Dict, List
 
-from .constants import (
+from ..constants import (
     CHANGE_DATE,
     VERSION,
 )

src/penn_chime/parameters.py src/penn_chime/model/parameters.py

@@ -6,15 +6,14 @@
 
 from __future__ import annotations
 
-from datetime import date, datetime, timedelta
+from datetime import datetime, timedelta
 from logging import INFO, basicConfig, getLogger
 from sys import stdout
-from typing import Dict, Generator, Tuple, Sequence, Optional
+from typing import Dict, Tuple, Sequence, Optional
 
 import numpy as np
 import pandas as pd
 
-from .constants import EPSILON, CHANGE_DATE
 from .parameters import Parameters
 
 
@@ -26,7 +25,7 @@
 logger = getLogger(__name__)
 
 
-class SimSirModel:
+class Sir:
 
     def __init__(self, p: Parameters):
 

src/penn_chime/models.py src/penn_chime/model/sir.py

@@ -1,6 +1,6 @@
 """the callable validator design pattern"""
 
-from ..constants import EPSILON
+from ...constants import EPSILON
 from .validators import (
     OptionalValue as ValOptionalValue,
     Bounded as ValBounded,

src/penn_chime/validators/__init__.py src/penn_chime/model/validators/__init__.py

@@ -1,13 +1,10 @@
-from datetime import datetime
-from math import ceil
 from typing import Dict, Optional
 
 from altair import Chart
 import pandas as pd
 import numpy as np
 
-from .constants import DATE_FORMAT
-from .parameters import Parameters
+from ..constants import DATE_FORMAT
 
 
 def build_admits_chart(

src/penn_chime/validators/base.py src/penn_chime/model/validators/base.py

@@ -0,0 +1,66 @@
+"""App."""
+
+import os
+
+import altair as alt  # type: ignore
+import streamlit as st  # type: ignore
+
+from ..model.parameters import Parameters
+from ..model.sir import Sir
+from .charts import (
+    build_admits_chart,
+    build_census_chart,
+    build_sim_sir_w_date_chart,
+)
+from .display import (
+    display_download_link,
+    display_footer,
+    display_header,
+    display_sidebar,
+    hide_menu_style,
+)
+
+
+def main():
+    # This is somewhat dangerous:
+    # Hide the main menu with "Rerun", "run on Save", "clear cache", and "record a screencast"
+    # This should not be hidden in prod, but removed
+    # In dev, this should be shown
+    st.markdown(hide_menu_style, unsafe_allow_html=True)
+
+    d = Parameters.create(os.environ, [])
+    p = display_sidebar(st, d)
+    m = Sir(p)
+
+    display_header(st, m, p)
+
+    st.subheader("New Admissions")
+    st.markdown("Projected number of **daily** COVID-19 admissions.")
+    admits_chart = build_admits_chart(alt=alt, admits_floor_df=m.admits_floor_df, max_y_axis=p.max_y_axis)
+    st.altair_chart(admits_chart, use_container_width=True)
+    display_download_link(
+        st,
+        filename=f"{p.current_date}_projected_admits.csv",
+        df=m.admits_df,
+    )
+
+    st.subheader("Admitted Patients (Census)")
+    st.markdown("Projected **census** of COVID-19 patients, accounting for arrivals and discharges.")
+    census_chart = build_census_chart(alt=alt, census_floor_df=m.census_floor_df, max_y_axis=p.max_y_axis)
+    st.altair_chart(census_chart, use_container_width=True)
+    display_download_link(
+        st,
+        filename=f"{p.current_date}_projected_census.csv",
+        df=m.census_df,
+    )
+
+    st.subheader("Susceptible, Infected, and Recovered")
+    st.markdown("The number of susceptible, infected, and recovered individuals in the hospital catchment region at any given moment")
+    sim_sir_w_date_chart = build_sim_sir_w_date_chart(alt=alt, sim_sir_w_date_floor_df=m.sim_sir_w_date_floor_df)
+    st.altair_chart(sim_sir_w_date_chart, use_container_width=True)
+    display_download_link(
+        st,
+        filename=f"{p.current_date}_sim_sir_w_date.csv",
+        df=m.sim_sir_w_date_df,
+    )
+    display_footer(st)

src/penn_chime/validators/validators.py src/penn_chime/model/validators/validators.py

@@ -1,26 +1,21 @@
-"""effectful functions for streamlit io"""
+"""Streamlit display."""
 
-from typing import Optional
-from datetime import date
-
-import altair as alt
-import numpy as np
 import os
 import json
+
 import pandas as pd
-import penn_chime.spreadsheet as sp
-from .constants import (
+
+from ..constants import (
     CHANGE_DATE,
     DOCS_URL,
     EPSILON,
     FLOAT_INPUT_MIN,
     FLOAT_INPUT_STEP,
     VERSION,
 )
-
-from .utils import dataframe_to_base64
-from .parameters import Parameters, Disposition
-from .models import SimSirModel as Model
+from ..model.parameters import Parameters, Disposition
+from ..utils import dataframe_to_base64
+from .spreadsheet import spreadsheet
 
 hide_menu_style = """
         <style>
@@ -130,7 +125,11 @@ def __init__(
         key=None,
     ):
         kwargs = dict(
-            min_value=min_value, max_value=max_value, step=step, format=format, key=key
+            min_value=min_value,
+            max_value=max_value,
+            step=step,
+            format=format,
+            key=key,
         )
         super().__init__(st_obj.number_input, label, value, kwargs)
 
@@ -154,7 +153,14 @@ def __init__(
         key=None,
     ):
         super().__init__(
-            st_obj, label, min_value, max_value, value * 100.0, step, format, key
+            st_obj,
+            label,
+            min_value,
+            max_value,
+            value * 100.0,
+            step,
+            format,
+            key,
         )
 
     def __call__(self):
@@ -226,7 +232,8 @@ def display_sidebar(st, d: Parameters) -> Parameters:
         min_value=FLOAT_INPUT_MIN,
         max_value=100.0
     )
-    icu_pct_input = PercentInput(st_obj,
+    icu_pct_input = PercentInput(
+        st_obj,
         "ICU %(total infections)",
         min_value=0.0,
         value=d.icu.rate,
@@ -442,7 +449,7 @@ def subscribe(st_obj):
 def send_subscription_to_google_sheet(st_obj, row):
     json_secret = readGoogleApiSecretsDict()
     #print(json_secret)
-    spr = sp.spreadsheet (st_obj, json_secret)
+    spr = spreadsheet(st_obj, json_secret)
     spr.writeToSheet("CHIME Form Submissions", row)
 
 def display_footer(st):

src/penn_chime/charts.py src/penn_chime/view/charts.py

@@ -0,0 +1,13 @@
+"""
+Run the streamlit app.
+
+`pip install .` is required.
+
+Module is in site-packages, and does not reflect any modifications made in the src directory.
+"""
+
+from penn_chime.view.st_app import main
+
+
+if __name__ == '__main__':
+    main()

src/penn_chime/spreadsheet.py src/penn_chime/view/spreadsheet.py

@@ -3,12 +3,15 @@
 import pytest
 import pandas as pd
 
-from src.penn_chime.parameters import (
+from penn_chime.model.parameters import (
     Parameters,
     Disposition,
     Regions,
 )
-from src.penn_chime.models import SimSirModel, build_floor_df
+from penn_chime.model.sir import (
+    Sir,
+    build_floor_df,
+)
 
 
 class MockStreamlit:
@@ -100,12 +103,12 @@ def halving_param():
 
 @pytest.fixture
 def model(param):
-    return SimSirModel(param)
+    return Sir(param)
 
 
 @pytest.fixture
 def halving_model(halving_param):
-    return SimSirModel(halving_param)
+    return Sir(halving_param)
 
 
 @pytest.fixture

src/penn_chime/view/st_app.py

@@ -1,6 +1,6 @@
 """Test Parameters."""
 
-from penn_chime.parameters import Parameters
+from penn_chime.model.parameters import Parameters
 
 
 def test_cypress_defaults():

src/penn_chime/presentation.py src/penn_chime/view/st_display.py

@@ -5,15 +5,14 @@
 import numpy as np
 from datetime import timedelta
 
-from penn_chime.models import (
+from penn_chime.constants import EPSILON
+from penn_chime.model.sir import (
     sir,
     sim_sir,
     get_growth_rate,
-    SimSirModel,
+    Sir,
 )
 
-from src.penn_chime.constants import EPSILON
-
 
 def test_sir():
     """
@@ -104,7 +103,7 @@ def test_model_first_hosp_fit(param):
     param.date_first_hospitalized = param.current_date - timedelta(days=43)
     param.doubling_time = None
 
-    my_model = SimSirModel(param)
+    my_model = Sir(param)
 
     assert abs(my_model.intrinsic_growth_rate - 0.123) / 0.123 < 0.01
     assert abs(my_model.beta - 4.21501347256401e-07) < EPSILON

st_app.py

@@ -1,7 +1,7 @@
 import altair as alt
 import pytest
 
-from penn_chime.charts import (
+from penn_chime.view.charts import (
     build_admits_chart,
     build_census_chart,
 )