Merge branch 'develop' into unit_test_dash_utils

Author: grahamalama

.github/workflows/pythonapp.yml

@@ -43,7 +43,7 @@ jobs:
         python -m pytest
     - name: Run App
       run: |
-        streamlit run src/app.py &
+        PARAMETERS=./defaults/cypress.cfg streamlit run src/app.py &
     - name: Cypress
       uses: cypress-io/github-action@v1
       with:

Dockerfile

@@ -1,16 +1,13 @@
 FROM python:3.7.7-slim-buster
-RUN mkdir /app
+ENV PARAMETERS=./defaults/webapp.cfg
 WORKDIR /app
 COPY README.md .
 COPY setup.cfg .
 COPY setup.py .
-COPY requirements.txt .
-# Creating an empty src dir is a (hopefully) temporary hack to improve layer caching and speed up image builds
-# todo fix once the Pipfile, setup.py, requirements.txt, pyprojec.toml build/dist story is figured out
-RUN mkdir src && pip install -q .
 COPY .streamlit .streamlit
-COPY settings.cfg .
+COPY defaults defaults
 COPY src src
+RUN pip install -q .
 
 CMD ["streamlit", "run", "src/app.py"]
 

Dockerfile.dash

@@ -4,11 +4,14 @@ WORKDIR /code
 
 ARG PORT
 ENV PORT $PORT
+ENV PARAMETERS=./defaults/webapp.cfg
 
-COPY requirements.txt requirements.txt
-RUN pip install -r requirements.txt
-
+COPY README.md .
+COPY setup.py .
+COPY setup.cfg .
 COPY src src 
+COPY defaults ./src/defaults
+RUN pip install -q .
 
 # EXPOSE $PORT 
 

settings.cfg renamed to defaults/cli.cfg

@@ -1,13 +1,14 @@
---current-hospitalized 14
+--current-hospitalized 69
 --doubling-time 4.0
 --hospitalized-days 7
 --hospitalized-rate 0.025
 --icu-days 9
 --icu-rate 0.0075
 --infectious-days 14
---market_share 0.15
---n-days 60
---population 4119405
+--market-share 0.15
+--n-days 100
+--population 3600000
+--recovered 0
 --relative-contact-rate 0.3
 --ventilated-days 10
 --ventilated-rate 0.005

defaults/cypress.cfg

@@ -0,0 +1,15 @@
+--current-hospitalized 69
+--date-first-hospitalized 2020-03-07
+--doubling-time 4.0
+--hospitalized-days 7
+--hospitalized-rate 0.025
+--icu-days 9
+--icu-rate 0.0075
+--infectious-days 14
+--market-share 0.15
+--n-days 100
+--population 3600000
+--recovered 0
+--relative-contact-rate 0.3
+--ventilated-days 10
+--ventilated-rate 0.005

defaults/readme.txt

@@ -0,0 +1,3 @@
+Webapps need default values for both date_first_hosptalized and doubling_time. The ui overrides one of them.
+
+CLI needs either date_first_hospitalized xor doubling_time.

defaults/webapp.cfg

@@ -0,0 +1,15 @@
+--current-hospitalized 69
+--date-first-hospitalized 2020-03-07
+--doubling-time 4.0
+--hospitalized-days 7
+--hospitalized-rate 0.025
+--icu-days 9
+--icu-rate 0.0075
+--infectious-days 14
+--market-share 0.15
+--n-days 100
+--population 3600000
+--recovered 0
+--relative-contact-rate 0.3
+--ventilated-days 10
+--ventilated-rate 0.005

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

k8s/app.yaml

@@ -27,10 +27,52 @@ spec:
       containers:
       - image: docker.pkg.github.com/codeforphilly/chime/penn-chime:1.1.2
         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
+          
       imagePullSecrets:
       - name: regcred
 

setup.py

@@ -1,10 +1,9 @@
 """Setup file for chime
 """
-__version__ = "1.1.2"  # update VERSION in constants.py
+__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",
@@ -33,17 +33,18 @@
         "pyyaml",
         "selenium",
         "streamlit",
+        "gspread",
+        "oauth2client"
     ],
     classifiers=[
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: MIT License",
         "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,
 )
-