ci: replace Travis CI with GH Actions (#64)

* replaced travis ci with github actions

Signed-off-by: Prati28 <[email protected]>

* made some changes according to reviews

Signed-off-by: Prati28 <[email protected]>

* did some changes based on sourcery reviews

Signed-off-by: Prati28 <[email protected]>

* did some changes based on sourcery reviews

Signed-off-by: Prati28 <[email protected]>

* added py version

Signed-off-by: Prati28 <[email protected]>

* made some changes based on review

Signed-off-by: Prati28 <[email protected]>

* fix linting issue and py version

Signed-off-by: Prati28 <[email protected]>

* fix installation of package issue

Signed-off-by: Prati28 <[email protected]>

* fix command

Signed-off-by: Prati28 <[email protected]>

* added flask to requirements

Signed-off-by: Prati28 <[email protected]>

* added command for installation of packages

Signed-off-by: Prati28 <[email protected]>

* added github token

Signed-off-by: Prati28 <[email protected]>

* made changes

Signed-off-by: Prati28 <[email protected]>

---------

Signed-off-by: Prati28 <[email protected]>

.github/workflows/docker-build-publish-drs-filer.yml

@@ -0,0 +1,44 @@
+name: drs-filer
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+
+jobs:
+  publish_to_docker:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && github.ref == 'refs/heads/dev'
+
+    name: Build and publish to Docker
+    steps:
+      - name: Checkout repository
+        uses: actions/[email protected]
+
+      - name: Set up Docker Buildx
+        uses: docker/[email protected]
+
+      - name: Login to Docker Hub
+        uses: docker/[email protected]
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/[email protected]
+        with:
+          images: elixircloud/drs-filer
+
+      - name: Build and push Docker images
+        uses: docker/[email protected]
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/lint.yml

@@ -0,0 +1,45 @@
+name: Lint workflow
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+
+jobs:
+  linting_and_tests:
+    runs-on: ubuntu-latest
+
+    name: Run linting and unit tests
+    steps:
+      - name: Checkout repository
+        uses: actions/[email protected]
+
+      - name: Set up Python
+        uses: actions/[email protected]
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest coverage coveralls
+          pip install -r requirements-test.txt
+          pip install -r requirements.txt
+
+      - name: Lint with flake8
+        run: flake8
+
+      - name: Run unit tests with coverage
+        run: |
+          coverage run --source drs_filer -m pytest
+          coverage report -m
+      
+      - name: Send coverage data to Coveralls
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: coveralls

.github/workflows/test.yml

@@ -0,0 +1,45 @@
+name: Test Drs-filer API Endpoints
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/[email protected]
+
+    - name: Build and run Docker Compose
+      run: docker-compose up --build -d
+
+    - name: Wait for the services to be ready
+      run: |
+        echo "Waiting for the services to be ready..."
+        for i in {1..10}; do
+          if curl -sSf http://localhost:8080/ga4gh/drs/v1 > /dev/null; then
+            echo "Service is up!"
+            break
+          fi
+          echo "Waiting for the service to be ready..."
+          sleep 3
+        done
+      
+    - name: Set up Python
+      uses: actions/[email protected]
+      with:
+        python-version: 3.11
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest requests
+        
+    - name: Test with pytest
+      run: |
+        pytest tests/test.py -v -p no:warnings
+      env:
+        DRS_FILER_URL: http://localhost:8080/ga4gh/drs/v1
+
+    - name: Stop and remove Docker Compose services
+      run: docker-compose down

drs_filer/ga4gh/drs/server.py

@@ -22,6 +22,7 @@
 
 logger = logging.getLogger(__name__)
 
+
 @log_traffic
 def ListDrsObjects() -> List[Dict]:
     """Get all DRS objects.
@@ -33,10 +34,10 @@ def ListDrsObjects() -> List[Dict]:
         current_app.config.foca.db.dbs['drsStore'].
         collections['objects'].client
     )
-    cursor = db_collection.find({}, {'_id': 0})  
-    objects = []  
-    for obj in cursor:  
-        objects.append(obj)  
+    cursor = db_collection.find({}, {'_id': 0})
+    objects = []
+    for obj in cursor:
+        objects.append(obj)
     return objects
 
 

requirements-test.txt

@@ -1,3 +1,4 @@
+flask
 flake8
 mongomock
 pytest

setup.cfg

@@ -3,3 +3,6 @@ source =
     drs_filer
 omit =
     drs_filer/app.py
+
+[flake8]
+max-line-length = 88