Merge remote-tracking branch 'upstream/develop' into develop

Author: mangala915

docs/CONTRIBUTING.md

@@ -26,11 +26,12 @@ As of March 21, help is especially wanted from contributors with experience in K
 
 - [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [CodeforPhilly/chime](https://github.com/CodeForPhilly/chime) repo.
 - Base your work on the `develop` branch.
+- Take a few minutes to review this [resource](https://developer.mozilla.org/en-US/docs/Mozilla/Developer_guide/Reviewer_Checklist) for contributors and reviewers, to accelerate the adoption of your contribution (thanks to the good folks at Mozilla for this).
 - Submit pull requests from your fork, also against the `develop` branch of the `CodeforPhilly/chime` repo.
 - Request review from the relevant maintainer(s).
 - Check your pull request periodically to see if any changes have been requested or any merge conflicts have arisen.
 - If a merge conflict arises, rebase against the latest `develop` branch and force-push the new branch as early as you can. You may need to do this more than once before your changes get merged. Do your best to keep your branch in a mergeable state until it is finished being reviewed and accepted.
-- If your change affects the results calculated or presented, update `change_date` in `src/penn_chime/parameters.py` when the pull request is ready for merge, so users can see when results have last changed
+- If your change affects the results calculated or presented, update `change_date` in `src/penn_chime/constants.py` when the pull request is ready for merge, so users can see when results have last changed
 - Note: Frequent contributors with write access can submit pull requests from a new branch in the `CodeforPhilly/chime` repository.
 
 ## Review & Release

setup.py

@@ -3,8 +3,7 @@
 __version__ = "1.1.3"  # update VERSION in constants.py
 __author__ = "Predictive Healthcare @ Penn Medicine"
 
-from os import path
-from setuptools import setup, find_packages, find_namespace_packages
+from setuptools import setup, find_namespace_packages
 
 
 setup(
@@ -24,6 +23,7 @@
     install_requires=[
         "altair",
         "black",
+        "gspread",
         "gunicorn",
         "dash",
         "dash_bootstrap_components",
@@ -42,10 +42,9 @@
         "Operating System :: OS Independent",
     ],
     python_requires='>=3.7',
-    entry_points = {
+    entry_points={
         'console_scripts': ['penn_chime=penn_chime.cli:main'],
     },
     keywords=[],
     include_package_data=True,
 )
-

src/penn_chime/models.py

@@ -64,21 +64,40 @@ def __init__(self, p: Parameters):
             logger.info('Using doubling_time: %s', p.doubling_time)
 
             intrinsic_growth_rate = get_growth_rate(p.doubling_time)
-
             self.beta = get_beta(intrinsic_growth_rate,  gamma, self.susceptible, 0.0)
             self.beta_t = get_beta(intrinsic_growth_rate, self.gamma, self.susceptible, p.relative_contact_rate)
 
-            self.i_day = 0 # seed to the full length
-            raw = self.run_projection(p, [(self.beta, p.n_days)])
-            self.i_day = i_day = int(get_argmin_ds(raw["census_hospitalized"], p.current_hospitalized))
+            if p.mitigation_date is None:
+                self.i_day = 0 # seed to the full length
+                raw = self.run_projection(p, [(self.beta, p.n_days)])
+                self.i_day = i_day = int(get_argmin_ds(raw["census_hospitalized"], p.current_hospitalized))
 
-            self.raw = self.run_projection(p, self.gen_policy(p))
+                self.raw = self.run_projection(p, self.gen_policy(p))
+
+                logger.info('Set i_day = %s', i_day)
+            else:
+                projections = {}
+                best_i_day = -1
+                best_i_day_loss = float('inf')
+                for i_day in range(p.n_days):
+                    self.i_day = i_day
+                    raw = self.run_projection(p, self.gen_policy(p))
+
+                    # Don't fit against results that put the peak before the present day
+                    if raw["census_hospitalized"].argmax() < i_day:
+                        continue
+
+                    loss = get_loss(raw["census_hospitalized"][i_day], p.current_hospitalized)
+                    if loss < best_i_day_loss:
+                        best_i_day_loss = loss
+                        best_i_day = i_day
+                        self.raw = raw
+
+                self.i_day = best_i_day
 
-            logger.info('Set i_day = %s', i_day)
-            p.date_first_hospitalized = p.current_date - timedelta(days=i_day)
             logger.info(
                 'Estimated date_first_hospitalized: %s; current_date: %s; i_day: %s',
-                p.date_first_hospitalized,
+                p.current_date - timedelta(days=self.i_day),
                 p.current_date,
                 self.i_day)
 

src/penn_chime/parameters.py

@@ -19,6 +19,7 @@
 )
 from .validators import (
     Date,
+    GteOne,
     OptionalDate,
     OptionalValue,
     OptionalStrictlyPositive,
@@ -64,7 +65,7 @@ class Disposition(_Disposition):
     @classmethod
     def create(cls, *, days: int, rate: float):
         """Mandate key word arguments."""
-        Positive(key="days", value=days)
+        GteOne(key="days", value=days)
         Rate(key="rate", value=rate)
         return cls(days, rate)
 
@@ -201,7 +202,7 @@ def validate(string):
     (
         "hospitalized_days",
         int,
-        0,
+        1,
         None,
         True,
     ),
@@ -215,7 +216,7 @@ def validate(string):
     (
         "icu_days",
         int,
-        0,
+        1,
         None,
         True,
     ),
@@ -285,7 +286,7 @@ def validate(string):
     (
         "ventilated_days",
         int,
-        0,
+        1,
         None,
         True,
     ),

src/penn_chime/presentation.py

@@ -220,7 +220,11 @@ def display_sidebar(st, d: Parameters) -> Parameters:
         step=1.0,
     )
     hospitalized_pct_input = PercentInput(
-        st_obj, "Hospitalization %(total infections)", value=d.hospitalized.rate,
+        st_obj,
+        "Hospitalization %(total infections)",
+        value=d.hospitalized.rate,
+        min_value=FLOAT_INPUT_MIN,
+        max_value=100.0
     )
     icu_pct_input = PercentInput(st_obj,
         "ICU %(total infections)",
@@ -234,23 +238,23 @@ def display_sidebar(st, d: Parameters) -> Parameters:
     hospitalized_days_input = NumberInput(
         st_obj,
         "Average hospital length of stay (in days)",
-        min_value=0,
+        min_value=1,
         value=d.hospitalized.days,
         step=1,
         format="%i",
     )
     icu_days_input = NumberInput(
         st_obj,
         "Average days in ICU",
-        min_value=0,
+        min_value=1,
         value=d.icu.days,
         step=1,
         format="%i",
     )
     ventilated_days_input = NumberInput(
         st_obj,
         "Average days on ventilator",
-        min_value=0,
+        min_value=1,
         value=d.ventilated.days,
         step=1,
         format="%i",
@@ -272,7 +276,7 @@ def display_sidebar(st, d: Parameters) -> Parameters:
     infectious_days_input = NumberInput(
         st_obj,
         "Infectious days",
-        min_value=0,
+        min_value=1,
         value=d.infectious_days,
         step=1,
         format="%i",

src/penn_chime/validators/__init__.py

@@ -15,6 +15,7 @@
 OptionalStrictlyPositive = ValOptionalBounded(lower_bound=EPSILON)
 StrictlyPositive = ValBounded(lower_bound=EPSILON)
 Positive = ValBounded(lower_bound=-EPSILON)
+GteOne = ValBounded(lower_bound=1)
 Rate = ValRate()
 Date = ValDate()
 OptionalDate = ValOptionalDate()