Merge branch 'develop' into dependabot/pip/bleach-3.1.4

Author: themightychris

e2e/cypress/integration/tests/actions.spec.js

@@ -0,0 +1,49 @@
+/// <reference types="cypress" />
+
+context('Increment steppers', () => {
+  beforeEach(() => {
+    cy.visit('/')
+  });
+
+  it('Increment regional population', () => {
+    cy.contains('Hospitalized Admissions peaks at 301');
+
+    cy.get('input.st-al').eq(0)
+      .should('has.value', '3600000');
+
+    cy.get('.step-up').eq(0).click();
+
+    cy.get('input.st-al').eq(0)
+      .should('has.value', '3600001');
+
+    cy.contains('Hospitalized Admissions peaks at 301');
+  });
+
+  it('Increment hospital market share', () => {
+    cy.contains('Hospitalized Admissions peaks at 301');
+
+    cy.get('input.st-al').eq(1)
+      .should('has.value', '15');
+
+    cy.get('.step-up').eq(1).click();
+
+    cy.get('input.st-al').eq(1)
+      .should('has.value', '15.1');
+
+    cy.contains('Hospitalized Admissions peaks at 303');
+  });
+
+  it('Increment doubling time', () => {
+    cy.contains('Hospitalized Admissions peaks at 301');
+
+    cy.get('input.st-al').eq(3)
+      .should('has.value', '4');
+
+    cy.get('.step-up').eq(3).click();
+
+    cy.get('input.st-al').eq(3)
+      .should('has.value', '4.25');
+
+    cy.contains('Hospitalized Admissions peaks at 273');
+  });
+});

e2e/cypress/integration/tests/steppers.spec.js

@@ -12,6 +12,23 @@ metadata:
     certmanager.k8s.io/cluster-issuer: letsencrypt-prod
     # allow requests larger than 1MiB
     nginx.ingress.kubernetes.io/proxy-body-size: "0"
+    nginx.ingress.kubernetes.io/configuration-snippet: |
+      location / {
+      sub_filter </head>
+        '<!-- Google Tag Manager -->
+        <script>(function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':
+        new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],
+        j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src=
+        'https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);
+        })(window,document,'script','dataLayer','GTM-KBZ6ZKX');</script>
+        <!-- End Google Tag Manager -->';
+      sub_filter </body>
+        '<!-- Google Tag Manager (noscript) -->
+        <noscript><iframe src="https://www.googletagmanager.com/ns.html?id=GTM-KBZ6ZKX"
+        height="0" width="0" style="display:none;visibility:hidden"></iframe></noscript>
+        <!-- End Google Tag Manager (noscript) -->'
+        sub_filter_once on;
+      }
 spec:
   tls:
   - hosts:
@@ -28,32 +45,6 @@ spec:
 
 ---
 
-apiVersion: extensions/v1beta1
-kind: Ingress
-metadata:
-  name: chime-alt
-  namespace: chime
-  annotations:
-    kubernetes.io/ingress.class: nginx
-    certmanager.k8s.io/cluster-issuer: letsencrypt-prod
-    # allow requests larger than 1MiB
-    nginx.ingress.kubernetes.io/proxy-body-size: "0"
-spec:
-  tls:
-  - hosts:
-    - penn-chime-alt.bus.phl.io
-    secretName: tls-chime-alt
-  rules:
-  - host: penn-chime-alt.bus.phl.io
-    http:
-      paths:
-      - path: /
-        backend:
-          serviceName: chime
-          servicePort: 80
-
----
-
 apiVersion: extensions/v1beta1
 kind: Ingress
 metadata:
@@ -64,22 +55,6 @@ metadata:
   annotations:
     nginx.ingress.kubernetes.io/proxy-buffering: "on"  # Important!
     nginx.ingress.kubernetes.io/configuration-snippet: |
-      location / {
-      sub_filter </head>
-        '<!-- Google Tag Manager -->
-        <script>(function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':
-        new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],
-        j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src=
-        'https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);
-        })(window,document,'script','dataLayer','GTM-KBZ6ZKX');</script>
-        <!-- End Google Tag Manager -->';
-      sub_filter </body>
-        '<!-- Google Tag Manager (noscript) -->
-        <noscript><iframe src="https://www.googletagmanager.com/ns.html?id=GTM-KBZ6ZKX"
-        height="0" width="0" style="display:none;visibility:hidden"></iframe></noscript>
-        <!-- End Google Tag Manager (noscript) -->'
-        sub_filter_once on;
-      }
       proxy_cache static-cache;
       proxy_cache_valid 404 1m;
       proxy_cache_valid 200 10m;
@@ -98,10 +73,3 @@ spec:
         backend:
           serviceName: chime
           servicePort: 80
-  - host: penn-chime-alt.bus.phl.io
-    http:
-      paths:
-      - path: /static/
-        backend:
-          serviceName: chime
-          servicePort: 80

k8s.preprod/app-ingress.yaml

@@ -1,4 +1,5 @@
 ---
+
 apiVersion: extensions/v1beta1
 kind: Ingress
 metadata:
@@ -52,6 +53,7 @@ spec:
           servicePort: 80
 
 ---
+
 apiVersion: extensions/v1beta1
 kind: Ingress
 metadata:

k8s.prod/app-ingress.yaml

@@ -25,14 +25,15 @@ spec:
         app: chime
     spec:
       containers:
-      - image: docker.pkg.github.com/codeforphilly/chime/penn-chime:1.0.0
+      - image: docker.pkg.github.com/codeforphilly/chime/penn-chime:1.1.0-rc.5
         name: chime
         ports:
         - containerPort: 8000
           name: http
           protocol: TCP
       imagePullSecrets:
       - name: regcred
+
 ---
 
 apiVersion: v1

k8s/app.yaml

@@ -45,7 +45,7 @@ def build_admits_chart(
         .transform_filter(alt.datum.day == 0)
         .mark_rule(color="black", opacity=0.35, size=2)
     )
-    return alt.layer(points, bar, data=admits_df)
+    return alt.layer(points, bar, data=ceil_df)
 
 
 

src/penn_chime/charts.py

@@ -312,7 +312,7 @@ def build_census_df(
         'date': admits_df.date,
         **{
             key: (
-                admits_df[key].cumsum().iloc[:-los]
+                admits_df[key].cumsum()
                 - admits_df[key].cumsum().shift(los).fillna(0)
             ).apply(np.ceil)
             for key, los in lengths_of_stay.items()

src/penn_chime/models.py

@@ -245,7 +245,7 @@ def test_admits_chart():
     admits_df = pd.read_csv("tests/by_doubling_time/2020-03-28_projected_admits.csv")
     chart = build_admits_chart(alt=alt, admits_df=admits_df)
     assert isinstance(chart, (alt.Chart, alt.LayerChart))
-    assert round(chart.data.iloc[40].icu, 0) == 38
+    assert round(chart.data.iloc[40].icu, 0) == 39
 
     # test fx call with no params
     with pytest.raises(TypeError):