update: new CI/CD workflows for deployment

.github/workflows/prod-deploy.yml

@@ -0,0 +1,63 @@
+name: Deploy to Production
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python version
+        uses: actions/setup-python@v1
+        with:
+          python-version: "3.10"
+
+      - name: Create and start virtual environment
+        run: |
+          python -m venv venv
+          source venv/bin/activate
+
+      - name: Install dependencies
+        run: pip install -r requirements.txt
+
+      - name: Test with pytest
+        run: |
+          pip install pytest
+          pip install pytest-cov
+          pytest tests/
+
+      - name: Upload artifact for deployment jobs
+        uses: actions/upload-artifact@v2
+        with:
+          name: python-app
+          path: |
+            . 
+            !venv/
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: build
+    concurrency: production
+    environment:
+      name: "production"
+      url: ${{ vars.AZURE_WEBAPP_URL }}
+
+    steps:
+      - name: Download artifact from build job
+        uses: actions/download-artifact@v2
+        with:
+          name: python-app
+          path: .
+
+      - name: "Deploy to Azure Web App"
+        uses: azure/webapps-deploy@v2
+        id: deploy-to-webapp
+        with:
+          app-name: ${{ vars.AZURE_WEBAPP_NAME }}
+          publish-profile: ${{ secrets.PROD_AZURE_PUBLISH_PROFILE }}

.github/workflows/staging-deploy.yml

@@ -0,0 +1,62 @@
+name: Deploy to Staging
+
+on:
+  push:
+    branches:
+      - develop
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python version
+        uses: actions/setup-python@v1
+        with:
+          python-version: "3.10"
+
+      - name: Create and start virtual environment
+        run: |
+          python -m venv venv
+          source venv/bin/activate
+
+      - name: Install dependencies
+        run: pip install -r requirements.txt
+
+      - name: Test with pytest
+        run: |
+          pip install pytest
+          pip install pytest-cov
+          pytest tests/
+
+      - name: Upload artifact for deployment jobs
+        uses: actions/upload-artifact@v2
+        with:
+          name: python-app
+          path: |
+            . 
+            !venv/
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: build
+    concurrency: staging
+    environment:
+      name: "staging"
+      url: ${{ vars.AZURE_WEBAPP_URL }}
+
+    steps:
+      - name: Download artifact from build job
+        uses: actions/download-artifact@v2
+        with:
+          name: python-app
+          path: .
+
+      - name: "Deploy to Azure Web App"
+        uses: azure/webapps-deploy@v2
+        id: deploy-to-webapp
+        with:
+          app-name: ${{ vars.AZURE_WEBAPP_NAME }}
+          publish-profile: ${{ secrets.STAGING_AZURE_PUBLISH_PROFILE }}

.github/workflows/test-pull-request.yml

@@ -0,0 +1,35 @@
+name: Testing Workflow
+
+on:
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python 3.10.6
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.10.6
+          cache: "pip"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Lint with flake8
+        run: |
+          export PYTHONPATH=$PYTHONPATH:/home/runner/work/drug-screening/drug-screening/src
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics # temporary comment for tests
+          # 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
+          pip install pytest-cov
+          pytest tests/

README.md

@@ -1,28 +1,42 @@
-![testing workflow](https://github.com/zuzg/drug-screening/actions/workflows/main.yml/badge.svg)
+![Latest PR Test](https://github.com/zuzg/drug-screening/actions/workflows/test-pull-request.yml/badge.svg)
+![Prod Deployment](https://github.com/zuzg/drug-screening/actions/workflows/prod-deploy.yml/badge.svg)
+![Staging Deployment](https://github.com/zuzg/drug-screening/actions/workflows/staging-deploy.yml/badge.svg)
 
 [![badges-are-fun](https://img.shields.io/badge/badges_are-fun-deeppink.svg)](https://tenor.com/view/excited-ron-swanson-giggle-so-much-fun-gif-14647008)
 ![fail](https://img.shields.io/badge/unless_they-fail-red.svg)
+
 # drug-screening
+
 ## About
+
 A project examining data from High Throughput Screening center in Poznan. HTS goal is to identify active compounds from hundreds of thousands.
+
 ## Setup
+
 ### Prepare repository
+
 ```
 git clone https://github.com/zuzg/drug-screening.git
-``` 
+```
+
 ```
 cd drug-screening
 ```
+
 ### Prepare environment
+
 ```
 conda env create -f environment.yml
 ```
+
 ```
 conda activate drug-screening
 ```
+
 ### Starting the dashboard
 
 To start the dashboard enter the following command in the terminal (active in the root project directory) while the conda environment is active:
+
 ```
 python -m dashboard
-```
+```