Merge branch 'develop' into PhilMiller/model-performance

Author: jlubken

.github/workflows/pythonapp.yml

@@ -15,7 +15,6 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python 3.8
@@ -33,6 +32,11 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Check formatting with black
+      run: |
+        # exit if any files still need formatting
+        bash script/format --check
+      continue-on-error: true
     - name: Test with pytest
       run: |
         pip install pytest

.gitignore

@@ -1,5 +1,6 @@
 # Editors
 .idea/
+.vscode/settings.json
 
 # Environments
 .env

Pipfile

@@ -4,12 +4,13 @@ url = "https://pypi.org/simple"
 verify_ssl = true
 
 [dev-packages]
+black = "==19.10b0"
+pytest = "*"
 
 [packages]
 streamlit = "*"
 pandas = "*"
 numpy = "*"
-pytest = "*"
 altair = "*"
 dash = "*"
 dash-bootstrap-components = "*"
@@ -18,3 +19,6 @@ PyYAML = "*"
 
 [requires]
 python_version = "3.7"
+
+[pipenv]
+allow_prereleases = true

Pipfile.lock

@@ -23,7 +23,7 @@ See [Streamlit's Getting Started guide](https://docs.streamlit.io/getting_starte
 
 ```bash
 pipenv shell
-pipenv install
+pipenv sync --dev
 streamlit run src/app.py
 ```
 

docs/contributing/app-dev.md

@@ -13,22 +13,13 @@ metadata:
     # 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;
-      }
+      # Inject Google Tag Manager:
+
+      proxy_set_header Accept-Encoding ""; # upstream compression must be disabled
+
+      sub_filter '</head>' '<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></head>';
+
+      sub_filter '</body>' '<noscript><iframe src="https://www.googletagmanager.com/ns.html?id=GTM-KBZ6ZKX" height="0" width="0" style="display:none;visibility:hidden"></iframe></noscript></body>';
 spec:
   tls:
   - hosts:
@@ -62,7 +53,6 @@ metadata:
       proxy_cache_bypass $http_x_purge;
       proxy_cache_key $proxy_upstream_name$request_uri;
       proxy_cache_lock on;
-      proxy_cache_use_stale updating;
       add_header X-Cache-Status $upstream_cache_status;
 spec:
   rules:

k8s.preprod/app-ingress.yaml

@@ -12,6 +12,14 @@ 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: |
+      # Inject Google Tag Manager:
+
+      proxy_set_header Accept-Encoding ""; # upstream compression must be disabled
+
+      sub_filter '</head>' '<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></head>';
+
+      sub_filter '</body>' '<noscript><iframe src="https://www.googletagmanager.com/ns.html?id=GTM-KBZ6ZKX" height="0" width="0" style="display:none;visibility:hidden"></iframe></noscript></body>';
 spec:
   tls:
   - hosts:
@@ -71,7 +79,6 @@ metadata:
       proxy_cache_bypass $http_x_purge;
       proxy_cache_key $proxy_upstream_name$request_uri;
       proxy_cache_lock on;
-      proxy_cache_use_stale updating;
       add_header X-Cache-Status $upstream_cache_status;
 spec:
   rules:

k8s.prod/app-ingress.yaml

@@ -0,0 +1,14 @@
+#!/bin/sh
+
+# script/format: Format python code
+
+set -e
+cd "$(dirname "$0")/.."
+
+FILES_TO_FORMAT="src/ tests/ setup.py"
+
+if [ "$1" = "--check" ]; then
+  python -m black --check ${FILES_TO_FORMAT}
+else
+  python -m black ${FILES_TO_FORMAT}
+fi

script/format

@@ -22,16 +22,17 @@
     package_dir={'': 'src'},
     packages=find_namespace_packages(where='src', exclude=('tests')),
     install_requires=[
-        "streamlit",
-        "pandas",
-        "numpy",
         "altair",
-        "pytest",
+        "black",
+        "gunicorn",
         "dash",
         "dash_bootstrap_components",
+        "numpy",
+        "pandas",
+        "pytest",
         "pyyaml",
-        "gunicorn",
-        "selenium"
+        "selenium",
+        "streamlit",
     ],
     classifiers=[
         "Programming Language :: Python :: 3",

setup.py

@@ -57,7 +57,7 @@ def __init__(
         relative_contact_rate: float,
         mitigation_date: Optional[date] = None,
         ventilated: Disposition,
-        current_date: date = date.today(),
+        current_date: Optional[date] = None,
         date_first_hospitalized: Optional[date] = None,
         doubling_time: Optional[float] = None,
         infectious_days: int = 14,
@@ -69,7 +69,6 @@ def __init__(
         region: Optional[Regions] = None,
     ):
         self.current_hospitalized = Positive(value=current_hospitalized)
-
         Rate(value=hospitalized.rate), Rate(value=icu.rate), Rate(value=ventilated.rate)
         StrictlyPositive(value=hospitalized.days), StrictlyPositive(value=icu.days),
         StrictlyPositive(value=ventilated.days)
@@ -87,8 +86,10 @@ def __init__(
         else:
             raise AssertionError('population or regions must be provided.')
 
+        if current_date is None:
+            current_date = date.today()
         self.current_date = Date(value=current_date)
-       
+
         self.date_first_hospitalized = OptionalDate(value=date_first_hospitalized)
         self.doubling_time = OptionalStrictlyPositive(value=doubling_time)