Merge branch 'develop' into docs-limited-kubeconfigs

Author: themightychris

.cache/v/cache/lastfailed

@@ -0,0 +1,3 @@
+{
+  "test_app.py": true
+}

.dockerignore

@@ -25,3 +25,4 @@ venv
 ENV
 env.bak
 venv.bak
+cypress

.github/ISSUE_TEMPLATE/general-bug-report.md

@@ -0,0 +1,27 @@
+---
+name: General bug report
+about: Create an report to help us improve.
+title: [bug]
+labels: 'bug'
+assignees: ''
+
+---
+
+<!--
+Before you begin, please help us manage volume by checking if this could be submitted another way:
+- Usage questions? Ask in Slack [#chime-help](https://codeforphilly.org/chat?channel=chime-help).
+- Feature ideas? Propose in Slack for discussion.
+- Is this something you can debug and fix? Pull requests are very welcome.
+-->
+
+### Description:
+
+### Steps to reproduce:
+1.
+2.
+3.
+
+### Expected behavior:
+
+### What I got instead:
+(screenshots if applicable)

.github/ISSUE_TEMPLATE/model.md

@@ -0,0 +1,26 @@
+---
+name: Bug report for model
+about: Feedback or bug report for the epidemiological model and analysis.
+title: [model]
+labels: 'models'
+assignees: ''
+
+---
+
+<!--
+Please note: Any changes to the model have a huge impact on rapidly evolving hospital system & public health decisions. The current model has been in use for a while now, and it has been validated against other similar models, so any changes to the model must meet a very high bar.
+
+However, these 2 types of issue reports are very welcome:
+- Bugs causing this model to produce invalid results. In this case, please include details and a suggested fix.
+- If this model is producing a significantly different result than another well-known epidemiological model. In this case, please include proof of this difference and a suggested fix to our approach.
+
+For questions or early discussion, please join us in [#chime-analysis](https://codeforphilly.org/chat?channel=chime-analysis) in Slack instead.
+-->
+
+### Summary
+
+
+### Additional details
+
+
+### Suggested fix

.github/workflows/dockerpublish.yml

@@ -0,0 +1,68 @@
+name: Docker
+
+on:
+  push:
+    # Publish `v1.2.3` tags as releases.
+    tags:
+      - v*
+
+  # Run tests for any PRs.
+  pull_request:
+
+env:
+  IMAGE_NAME: penn-chime
+
+jobs:
+  # Run tests.
+  # See also https://docs.docker.com/docker-hub/builds/automated-testing/
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Run tests
+        run: |
+          if [ -f docker-compose.test.yml ]; then
+            docker-compose --file docker-compose.test.yml build
+            docker-compose --file docker-compose.test.yml run sut
+          else
+            docker build . --file Dockerfile
+          fi
+
+  # Push image to GitHub Packages.
+  # See also https://docs.docker.com/docker-hub/builds/
+  push:
+    # Ensure test job passes before pushing image.
+    needs: test
+
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push'
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Build image
+        run: docker build . --file Dockerfile --tag image
+
+      - name: Log into registry
+        run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin
+
+      - name: Push image
+        run: |
+          IMAGE_ID="docker.pkg.github.com/${GITHUB_REPOSITORY,,}/${IMAGE_NAME}"
+
+          # Strip git ref prefix from version
+          VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
+
+          # Strip "v" prefix from tag name
+          [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
+
+          # Use Docker `latest` tag convention
+          [ "$VERSION" == "master" ] && VERSION=latest
+
+          echo IMAGE_ID=$IMAGE_ID
+          echo VERSION=$VERSION
+
+          docker tag image $IMAGE_ID:$VERSION
+          docker push $IMAGE_ID:$VERSION

.github/workflows/gh-pages.yml

@@ -3,7 +3,7 @@ name: Publish GitBook to GH Pages
 on:
   push:
     branches:
-      - 'master'
+      - 'develop'
 
 
 jobs:
@@ -25,6 +25,6 @@ jobs:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         HAB_LICENSE: accept
       with:
-        ref: master
+        ref: develop
         holobranch: gh-pages
         commit-to: gh-pages

.github/workflows/heroku.yml

@@ -0,0 +1,28 @@
+name: Deploy working development app to Heroku staging project
+
+on:
+  push:
+    branches:
+      - 'develop'
+
+env:
+  HEROKU_USER: 32dd7c8d-eb68-4420-bfe2-9ed047ef8fb0
+  HEROKU_SECRET: ${{ secrets.heroku_secret_key }}
+  HEROKU_APP: cfp-ci-chime
+  HEROKU_EMAIL: [email protected]
+
+jobs:
+  deploy-heroku-stg:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Deploy app
+        id: deploy_stg_job
+        uses: akhileshns/[email protected]
+        with:
+          heroku_api_key: ${HEROKU_SECRET}
+          heroku_app_name: ${HEROKU_APP}
+          heroku_email: ${HEROKU_EMAIL}
+      - name: Return app URL
+        run: |
+          echo "Deployed to: https://${HEROKU_APP}.herokuapp.com/"

.github/workflows/pythonapp.yml

@@ -0,0 +1,47 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Chime Lint and Test
+
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+    branches:
+      - develop
+      - 'releases/**'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+    - name: Lint with flake8
+      run: |
+        pip install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        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: Test with pytest
+      run: |
+        pip install pytest
+        python -m pytest
+    - name: Run App
+      run: |
+        streamlit run src/app.py &
+    - name: Cypress
+      uses: cypress-io/[email protected]
+      with:
+        working-directory: e2e
+

.gitignore

@@ -15,3 +15,4 @@ venv.bak/
 
 # mypy
 .mypy_cache/
+__pycache__/

Dockerfile

@@ -10,4 +10,4 @@ RUN pip install -q -r requirements.txt
 
 COPY . ./
 
-CMD ["streamlit", "run", "app.py"]
+CMD ["streamlit", "run", "src/app.py"]