Update menu and fix charts

Update menu and fix charts

Author: jlubken

src/chime_dash/app/components/menu.py

@@ -23,25 +23,13 @@ def get_html(self) -> List[ComponentMeta]:
                     "Predictive Healthcare",
                     href="http://predictivehealthcare.pennmedicine.org/",
                     external_link=True,
+                    target="_blank",
                 ),
                 dbc.DropdownMenuItem(
-                    "Contact Us",
-                    href="http://predictivehealthcare.pennmedicine.org/contact/",
-                    external_link=True,
-                ),
-                dbc.DropdownMenuItem(
-                    "User Docs",
+                    "How to Use CHIME",
                     href="https://code-for-philly.gitbook.io/chime/",
                     external_link=True,
-                ),
-                dbc.DropdownMenuItem(
-                    "GitHub",
-                    href="https://github.com/CodeForPhilly/chime",
-                    external_link=True,
-                ),
-                dbc.DropdownMenuItem(
-                    "Slack",
-                    href="https://codeforphilly.org/chat?channel=covid19-chime-penn",
+                    target="_blank",
                 ),
             ],
             in_navbar=True,

src/chime_dash/app/templates/en/header.yml

@@ -1,2 +1,5 @@
 title: "CHIME: COVID-19 Hospital Impact Model for Epidemics"
-description: "*This tool was developed by the [Predictive Healthcare team](http://predictivehealthcare.pennmedicine.org/) at Penn Medicine to assist hospitals and public health officials with hospital capacity planning, but can be used anywhere in the world. Customize it for your region by modifying inputs in the left pane, or read the [User Documentation](https://code-for-philly.gitbook.io/chime/) to learn more.*"
+description: "
+**Notice**: *There is a high degree of uncertainty about the details of COVID-19 infection, transmission, and the effectiveness of social distancing measures. Long-term projections made using this simplified model of outbreak progression should be treated with extreme caution.*\n
+
+This tool was developed by [Predictive Healthcare](http://predictivehealthcare.pennmedicine.org/) at Penn Medicine to assist hospitals and public health officials with hospital capacity planning. Please read [How to Use CHIME](https://code-for-philly.gitbook.io/chime/) to customize inputs for your region."

src/penn_chime/charts.py

@@ -30,25 +30,23 @@ def build_admits_chart(
         .encode(x=alt.X(**x), y=alt.Y(**y), color=color, tooltip=tooltip)
         .mark_line(point=True)
         .encode(
-            x=alt.X(**x_kwargs),
-            y=alt.Y("value:Q", title="Daily admissions", scale=y_scale),
-            color="key:N",
-            tooltip=[
-                tooltip_dict[as_date],
-                alt.Tooltip("value:Q", format=".0f", title="Admissions"),
-                "key:N",
-            ],
+            x=alt.X(**x),
+            y=alt.Y(**y),
+            color=color,
+            tooltip=tooltip,
         )
-        .configure_legend(orient="bottom")
-        .interactive()
     )
     bar = (
         alt.Chart()
         .encode(x=alt.X(**x))
         .transform_filter(alt.datum.day == 0)
         .mark_rule(color="black", opacity=0.35, size=2)
     )
-    return alt.layer(points, bar, data=admits_floor_df)
+    return (
+        alt.layer(points, bar, data=admits_floor_df)
+        .configure_legend(orient="bottom")
+        .interactive()
+    )
 
 
 def build_census_chart(
@@ -71,25 +69,23 @@ def build_census_chart(
         .encode(x=alt.X(**x), y=alt.Y(**y), color=color, tooltip=tooltip)
         .mark_line(point=True)
         .encode(
-            x=alt.X(**x_kwargs),
-            y=alt.Y("value:Q", title="Census", scale=y_scale),
-            color="key:N",
-            tooltip=[
-                idx,
-                alt.Tooltip("value:Q", format=".0f", title="Census"),
-                "key:N",
-            ],
+            x=alt.X(**x),
+            y=alt.Y(**y),
+            color=color,
+            tooltip=tooltip,
         )
-        .configure_legend(orient="bottom")
-        .interactive()
     )
     bar = (
         alt.Chart()
         .encode(x=alt.X(**x))
         .transform_filter(alt.datum.day == 0)
         .mark_rule(color="black", opacity=0.35, size=2)
     )
-    return alt.layer(points, bar, data=census_floor_df)
+    return (
+        alt.layer(points, bar, data=census_floor_df)
+        .configure_legend(orient="bottom")
+        .interactive()
+    )
 
 
 def build_sim_sir_w_date_chart(
@@ -112,21 +108,23 @@ def build_sim_sir_w_date_chart(
         .encode(x=alt.X(**x), y=alt.Y(**y), color=color, tooltip=tooltip)
         .mark_line()
         .encode(
-            x=alt.X(**x_kwargs),
-            y=alt.Y("value:Q", title="Case Volume", scale=y_scale),
-            tooltip=["key:N", "value:Q"],
-            color="key:N",
+            x=alt.X(**x),
+            y=alt.Y(**y),
+            color=color,
+            tooltip=tooltip,
         )
-        .configure_legend(orient="bottom")
-        .interactive()
     )
     bar = (
         alt.Chart()
         .encode(x=alt.X(**x))
         .transform_filter(alt.datum.day == 0)
         .mark_rule(color="black", opacity=0.35, size=2)
     )
-    return alt.layer(points, bar, data=sim_sir_w_date_floor_df)
+    return (
+        alt.layer(points, bar, data=sim_sir_w_date_floor_df)
+        .configure_legend(orient="bottom")
+        .interactive()
+    )
 
 
 def build_descriptions(

src/penn_chime/presentation.py

@@ -51,22 +51,17 @@ def display_header(st, m, p):
     """,
         unsafe_allow_html=True,
     )
-    st.markdown(
-        """[Documentation]({docs_url}) | [Github](https://github.com/CodeForPhilly/chime/) |
-[Slack](https://codeforphilly.org/chat?channel=covid19-chime-penn)""".format(
-            docs_url=DOCS_URL
-        )
-    )
-    st.markdown(
-        """*This tool was developed by the [Predictive Healthcare team](http://predictivehealthcare.pennmedicine.org/) at
-    Penn Medicine to assist hospitals and public health officials with hospital capacity planning.*"""
-    )
     st.markdown(
         """**Notice**: *There is a high
-    degree of uncertainty about the details of COVID-19 infection, transmission, and the effectiveness of social distancing
-    measures. Long-term projections made using this simplified model of outbreak progression should be treated with extreme caution.*
+degree of uncertainty about the details of COVID-19 infection, transmission, and the effectiveness of social distancing
+measures. Long-term projections made using this simplified model of outbreak progression should be treated with extreme caution.*
     """
     )
+    st.markdown(
+        """
+This tool was developed by [Predictive Healthcare](http://predictivehealthcare.pennmedicine.org/) at
+Penn Medicine to assist hospitals and public health officials with hospital capacity planning.
+Please read [How to Use CHIME]({docs_url}) to customize inputs for your region.""".format(docs_url=DOCS_URL))
 
     st.markdown(
         """The estimated number of currently infected individuals is **{total_infections:.0f}**. This is based on current inputs for