Merge branch 'develop' into unit_test_dash_utils

grahamalama · web-flow · commit c5718f01bf1f · 2020-04-11T14:11:49.000-04:00
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -0,0 +1,15 @@
+<!-- Please read the contributing guidelines before submitting: https://codeforphilly.github.io/chime/CONTRIBUTING.html -->
+
+<!--
+- If this PR affects devops or model, start your PR title with `[DevOps]` or `[Model]`
+- Update the user or developer documentation, if affected.
+-->
+
+### Link to issue
+- Fixes #(issue number)
+
+### Changelog entry
+- Short description of problem & solution (1-3 sentences, depending on scope of change)
+
+### Additional info
+- Anything else reviewers and future readers should know
diff --git a/Procfile b/Procfile
@@ -1 +1 @@
-web: STREAMLIT_SERVER_PORT=$PORT streamlit run src/app.py
+web: PARAMETERS=defaults/webapp.cfg STREAMLIT_SERVER_PORT=$PORT streamlit run src/app.py
diff --git a/defaults/cli.cfg b/defaults/cli.cfg
@@ -1,14 +1,14 @@
 --current-hospitalized 69
---doubling-time 4.0
+--doubling-time 5.0
 --hospitalized-days 7
 --hospitalized-rate 0.025
 --icu-days 9
 --icu-rate 0.0075
---infectious-days 14
+--infectious-days 10
 --market-share 0.15
 --n-days 100
 --population 3600000
 --recovered 0
---relative-contact-rate 0.3
+--relative-contact-rate 0.45
 --ventilated-days 10
 --ventilated-rate 0.005
diff --git a/defaults/webapp.cfg b/defaults/webapp.cfg
@@ -1,15 +1,15 @@
 --current-hospitalized 69
 --date-first-hospitalized 2020-03-07
---doubling-time 4.0
+--doubling-time 5.0
 --hospitalized-days 7
 --hospitalized-rate 0.025
 --icu-days 9
 --icu-rate 0.0075
---infectious-days 14
+--infectious-days 10
 --market-share 0.15
 --n-days 100
 --population 3600000
 --recovered 0
---relative-contact-rate 0.3
+--relative-contact-rate 0.45
 --ventilated-days 10
 --ventilated-rate 0.005
diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md
@@ -28,6 +28,10 @@ As of March 21, help is especially wanted from contributors with experience in K
 - 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.
+- As part of your pull request, please ensure you provide the following information
+  - References to the issue/PR resolved with your contribution(s) (use key word e.g. Fixes #123, #321 See #213)
+  - Explicitly identify the scope/area the change impacts (ex: Operations/Deployment/Model/Documentation)
+  - Describe any necessary follow on work, ideally with links to any already open issues
 - 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.
diff --git a/docs/contributing/app-dev.md b/docs/contributing/app-dev.md
@@ -24,7 +24,7 @@ See [Streamlit's Getting Started guide](https://docs.streamlit.io/getting_starte
 ```bash
 pipenv shell
 pipenv sync --dev
-streamlit run src/app.py
+PARAMETERS=defaults/webapp.cfg streamlit run src/app.py
 ```
 
 ### With `conda`
@@ -33,16 +33,15 @@ streamlit run src/app.py
 conda env create -f environment.yml
 source activate chime
 pip install streamlit
-streamlit run src/app.py
+PARAMETERS=defaults/webapp.cfg streamlit run src/app.py
 ```
 
 ### Choosing a Different Port
 
 If you need to run the application on a different port than the default (8000), you can export a variable in your shell session to override it with any port number of your choice before running:
 
 ```bash
-export STREAMLIT_SERVER_PORT=1234
-streamlit run src/app.py
+STREAMLIT_SERVER_PORT=1234 PARAMETERS=defaults/webapp.cfg streamlit run src/app.py
 ```
 
 ## Project Layout
diff --git a/docs/operations/README.md b/docs/operations/README.md
@@ -1,6 +1,6 @@
 # Operations guide to resources
 
-This guide will show you where nodes, and k8s clusters are stored and their heirarchy.
+This guide will show you where nodes, and k8s clusters are stored and their hierarchy.
 
 ## Production
 
@@ -13,4 +13,4 @@ Production k8s cluster is available on linode datacenter.
 
 Pre Production k8s cluster is available on linode datacenter.
 
-`chime-bus`
+`chime-bus`
diff --git a/docs/operations/prepare-new-chime-release.md b/docs/operations/prepare-new-chime-release.md
@@ -37,4 +37,4 @@ At the end of following this process you will have deployed a new CHIME version
  the review of another DevOps admin whenever possible. Ensure to link
  to the PR in the deployment issue previously opened on GitHub.
 
-6. One approved you will need to [create a release to auto deploy](release-process.md)
+6. Once approved, you will need to [create a release to auto deploy](release-process.md)
diff --git a/e2e/cypress/integration/tests/steppers.spec.js b/e2e/cypress/integration/tests/steppers.spec.js
@@ -6,7 +6,7 @@ context('Increment steppers', () => {
   });
 
   it('Increment regional population', () => {
-    cy.contains('Hospitalized Admissions peaks at 300');
+    cy.contains('Regional population (3600000)');
 
     cy.get('input[type=number]').eq(0)
       .should('has.value', '3600000');
@@ -16,11 +16,11 @@ context('Increment steppers', () => {
     cy.get('input[type=number]').eq(0)
       .should('has.value', '3600001');
 
-    cy.contains('Hospitalized Admissions peaks at 300');
+    cy.contains('Regional population (3600001)');
   });
 
   it('Increment hospital market share', () => {
-    cy.contains('Hospitalized Admissions peaks at 300');
+    cy.contains('The estimated number of currently infected individuals is 20128.');
 
     cy.get('input[type=number]').eq(1)
       .should('has.value', '15');
@@ -30,11 +30,11 @@ context('Increment steppers', () => {
     cy.get('input[type=number]').eq(1)
       .should('has.value', '15.1');
 
-    cy.contains('Hospitalized Admissions peaks at 302');
+    cy.contains('The estimated number of currently infected individuals is 19996.');
   });
 
   it('Increment doubling time', () => {
-    cy.contains('Hospitalized Admissions peaks at 300');
+    cy.contains('An initial doubling time of 4.0 days');
 
     cy.get('input[type=number]').eq(3)
       .should('has.value', '4');
@@ -44,6 +44,6 @@ context('Increment steppers', () => {
     cy.get('input[type=number]').eq(3)
       .should('has.value', '4.25');
 
-    cy.contains('Hospitalized Admissions peaks at 272');
+    cy.contains('An initial doubling time of 4.25 days');
   });
 });
diff --git a/k8s/app.yaml b/k8s/app.yaml
@@ -25,53 +25,21 @@ spec:
         app: chime
     spec:
       containers:
-      - image: docker.pkg.github.com/codeforphilly/chime/penn-chime:1.1.2
+      - image: docker.pkg.github.com/codeforphilly/chime/penn-chime:1.1.3
         name: chime
-        env:
-          - name: GAPI_CRED_TYPE
-            valueFrom:
-              secretKeyRef:
-                name: google-api-creds
-                key: type
-          - name: GAPI_CRED_PROJECT_ID
-            valueFrom:
-              secretKeyRef:
-                name: google-api-creds
-                key: project_id
-          - name: GAPI_CRED_PRIVATE_KEY_ID
-            valueFrom:
-              secretKeyRef:
-                name: google-api-creds
-                key: private_key_id
-          - name: GAPI_CRED_PRIVATE_KEY
-            valueFrom:
-              secretKeyRef:
-                name: google-api-creds
-                key: private_key
-          - name: GAPI_CRED_CLIENT_EMAIL
-            valueFrom:
-              secretKeyRef:
-                name: google-api-creds
-                key: client_email
-          - name: GAPI_CRED_CLIENT_ID
-            valueFrom:
-              secretKeyRef:
-                name: google-api-creds
-                key: client_id
-          - name: GAPI_CRED_AUTH_PROVIDER_X509_CERT_URL
-            valueFrom:
-              secretKeyRef:
-                name: google-api-creds
-                key: auth_provider_x509_cert_url
-          - name: GAPI_CRED_CLIENT_X509_CERT_URL
-            valueFrom:
-              secretKeyRef:
-                name: google-api-creds
-                key: client_x509_cert_url
         ports:
         - containerPort: 8000
           name: http
           protocol: TCP
+        volumeMounts:
+          - name: google-api-creds
+            mountPath: "/mnt/google-api-creds"
+            readOnly: true
+      volumes:
+        - name: google-api-creds
+          secret:
+            secretName: google-api-creds-json
+        
           
       imagePullSecrets:
       - name: regcred
diff --git a/src/app.py b/src/app.py
@@ -17,9 +17,7 @@
 from penn_chime.charts import (
     build_admits_chart,
     build_census_chart,
-    build_descriptions,
     build_sim_sir_w_date_chart,
-    build_table,
 )
 
 # This is somewhat dangerous:
@@ -35,49 +33,25 @@
 display_header(st, m, p)
 
 st.subheader("New Admissions")
-st.markdown("Projected number of **daily** COVID-19 admissions. \n\n _NOTE: Now including estimates of prior admissions for comparison._")
+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)
-st.markdown(build_descriptions(chart=admits_chart, labels=p.labels, prefix="admits_", suffix=" Admissions"))
 display_download_link(
     st,
     filename=f"{p.current_date}_projected_admits.csv",
     df=m.admits_df,
 )
 
-if st.checkbox("Show Projected Admissions in tabular form"):
-    admits_modulo = 1
-    if not st.checkbox("Show Daily Counts"):
-        admits_modulo = 7
-    table_df = build_table(
-        df=m.admits_floor_df,
-        labels=p.labels,
-        modulo=admits_modulo)
-    st.table(table_df)
-
-
 st.subheader("Admitted Patients (Census)")
-st.markdown("Projected **census** of COVID-19 patients, accounting for arrivals and discharges \n\n _NOTE: Now including estimates of prior census for comparison._")
+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)
-st.markdown(build_descriptions(chart=census_chart, labels=p.labels, prefix="census_", suffix=" Census"))
 display_download_link(
     st,
     filename=f"{p.current_date}_projected_census.csv",
     df=m.census_df,
 )
 
-if st.checkbox("Show Projected Census in tabular form"):
-    census_modulo = 1
-    if not st.checkbox("Show Daily Census Counts"):
-        census_modulo = 7
-    table_df = build_table(
-        df=m.census_floor_df,
-        labels=p.labels,
-        modulo=census_modulo)
-    st.table(table_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)
@@ -88,10 +62,4 @@
     df=m.sim_sir_w_date_df,
 )
 
-if st.checkbox("Show SIR Simulation in tabular form"):
-    table_df = build_table(
-        df=m.sim_sir_w_date_floor_df,
-        labels=p.labels)
-    st.table(table_df)
-
 display_footer(st)
diff --git a/src/chime_dash/README.md b/src/chime_dash/README.md
@@ -119,7 +119,7 @@ Install the chime base module
 ```
 and run
 ```bash
-> python src/dash_app.py
+> PARAMETERS=defaults/webapp.cfg python src/dash_app.py
 ```
 in the project root and visit the local url.
 
diff --git a/src/chime_dash/app/components/intro.py b/src/chime_dash/app/components/intro.py
@@ -15,7 +15,7 @@
 class Intro(Component):
     """
     """
-    localization_file = "intro.md"
+    localization_file = "intro.yml"
 
     def get_html(self) -> List[ComponentMeta]:  # pylint: disable=W0613
         """Initializes the header dash html
@@ -28,33 +28,31 @@ def build(self, model, pars):
         if model and pars:
             intro = self.content
             infected_population_warning_str = (
-                "(Warning:"
-                " The number of estimated infections is greater than"
-                " the total regional population."
-                " Please verify the values entered in the sidebar.)"
-                ""
+                intro["infected-population-warning"]
                 if model.infected > pars.population
                 else ""
             )
-            result = intro.format(
+            mitigation_rt_str = (
+                intro["mitigation-rt-less-than-1"]
+                if model.r_t < 1
+                else intro["mitigation-rt-more-than-equal-1"]
+            )
+
+            result = intro["description-total-infection"].format(
                 total_infections=model.infected,
                 current_hosp=pars.current_hospitalized,
                 hosp_rate=pars.hospitalized.rate,
                 S=pars.population,
-                market_share=pars.market_share,
+                market_share=pars.market_share
+            ) + "\n\n" + infected_population_warning_str + "\n\n" + intro["description-doubling-time"].format(
+                doubling_time=pars.doubling_time,
                 recovery_days=pars.infectious_days,
                 r_naught=model.r_naught,
-                doubling_time=pars.doubling_time,
+                daily_growth=model.daily_growth_rate * 100.0
+            ) + "\n\n" + mitigation_rt_str.format(
                 relative_contact_rate=pars.relative_contact_rate,
-                r_t=model.r_t,
                 doubling_time_t=model.doubling_time_t,
-                impact_statement=(
-                    "halves the infections every"
-                    if model.r_t < 1
-                    else "reduces the doubling time to"
-                ),
-                daily_growth=model.daily_growth_rate * 100.0,
-                daily_growth_t=model.daily_growth_rate_t * 100.0,
-                infected_population_warning_str=infected_population_warning_str,
+                r_t=model.r_t,
+                daily_growth_t=model.daily_growth_rate_t * 100.0
             )
         return [result]
diff --git a/src/chime_dash/app/templates/en/intro.md b/src/chime_dash/app/templates/en/intro.md
diff --git a/src/chime_dash/app/templates/en/intro.yml b/src/chime_dash/app/templates/en/intro.yml
@@ -0,0 +1,18 @@
+description-total-infection: "
+The estimated number of currently infected individuals is **{total_infections:.0f}**. This is based on current inputs for
+Hospitalizations (**{current_hosp}**), Hospitalization rate (**{hosp_rate:.0%}**), Regional population (**{S}**),
+and Hospital market share (**{market_share:.0%}**)."
+infected-population-warning: "
+(Warning: The number of estimated infections is greater than the total regional population. Please verify the values entered in the sidebar.)"
+description-doubling-time: "
+An initial doubling time of **{doubling_time}** days and a recovery time of **{recovery_days}** days imply an **`R0`** of
+**{r_naught:.2f}** and daily growth rate of **{daily_growth:.2f}%**."
+mitigation-rt-less-than-1: "
+**Mitigation**: A **{relative_contact_rate:.0%}** reduction in social contact after the onset of the
+outbreak **halves the infections every {doubling_time_t:.1f}** days, implying an effective **`R(t)`** of **{r_t:.2f}**
+and daily growth rate of **{daily_growth_t:.2f}%**."
+mitigation-rt-more-than-equal-1: "
+**Mitigation**: A **{relative_contact_rate:.0%}** reduction in social contact after the onset of the
+outbreak **reduces the doubling time to {doubling_time_t:.1f}** days, implying an effective **`R(t)`** of **{r_t:.2f}**
+and daily growth rate of **{daily_growth_t:.2f}%**."
+
diff --git a/src/penn_chime/charts.py b/src/penn_chime/charts.py
diff --git a/src/penn_chime/models.py b/src/penn_chime/models.py
diff --git a/tests/penn_chime/test_charts.py b/tests/penn_chime/test_charts.py

Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-web: STREAMLIT_SERVER_PORT=$PORT streamlit run src/app.py`
	`1`	`+web: PARAMETERS=defaults/webapp.cfg STREAMLIT_SERVER_PORT=$PORT streamlit run src/app.py`