ci: migrate to GH Actions (#116)

Co-authored-by: Alex Kanitz <alexander.kanitz@alumni.ethz.ch>

.github/workflows/checks.yml

@@ -0,0 +1,91 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ dev ]
+  pull_request:
+    branches: [ dev ]
+
+jobs:
+  Test:
+    name: Run linting and unit tests
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install requirements
+        run: |
+          pip install -e .
+          pip install -r requirements_dev.txt
+      - name: Lint with flake8
+        run: flake8
+      - name: Calculate unit test coverage
+        run: |
+          coverage run --source foca -m pytest
+          coverage xml
+      - name: Submit Report to Codecov
+        uses: codecov/codecov-action@v2
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          fail_ci_if_error: true
+          verbose: true
+      - name: Run tests on petstore app
+        run: |
+          cd ./examples/petstore
+          docker-compose up --build -d
+          cd ../..
+          sleep 10
+          pytest ./tests/integration_tests.py
+
+  Docker:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version-tag: [["3.7", "3.7"], ["3.8", "3.8"], ["3.9", "3.9"], ["3.9", "latest"]]
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+      - name: Build & Publish image to DockerHub
+        env:
+          docker_username: ${{ secrets.DOCKER_USERNAME }}
+          docker_password: ${{ secrets.DOCKER_PASSWORD }}
+          docker_org: ${{ secrets.DOCKER_ORG }}
+          repo_name: ${{ github.event.repository.name }}
+        run: |
+          export branch_name=${GITHUB_HEAD_REF##*/}
+          if [[ "$branch_name" == "dev" ]]; then
+              export tag="$(date '+%Y%m%d')"
+          else
+              export tag=${branch_name}
+          fi
+          if [[ ${{ matrix.python-version-tag[1] }} == "latest" ]]; then
+              export tag=${{ matrix.python-version-tag[1] }}
+          else
+              export tag=${tag}-py${{ matrix.python-version-tag[1] }}
+          fi
+          docker build . -t ${docker_org}/${repo_name}:latest \
+            -f docker/Dockerfile_py${{ matrix.python-version-tag[0] }}
+          docker tag ${docker_org}/${repo_name} ${docker_org}/${repo_name}:${tag}
+          echo $docker_password | docker login -u $docker_username --password-stdin
+          if [[ "$tag" == "latest" ]]; then
+              if [[ "$branch_name" == "dev" ]]; then
+                  docker push ${docker_org}/${repo_name}:${tag}
+              fi
+          else
+             docker push ${docker_org}/${repo_name}:${tag}
+          fi
+          rm ${HOME}/.docker/config.json

README.md

@@ -489,13 +489,13 @@ question etc.
 ![Logo_banner][img-logo-banner]
 
 [badge-build-status]: <https://travis-ci.com/elixir-cloud-aai/foca.svg?branch=dev>
-[badge-coverage]: <https://img.shields.io/coveralls/github/elixir-cloud-aai/foca>
+[badge-coverage]: <https://codecov.io/gh/elixir-cloud-aai/foca/branch/dev/graph/badge.svg?branch=dev>
 [badge-docs]: <https://readthedocs.org/projects/foca/badge/>
 [badge-github-tag]: <https://img.shields.io/github/v/tag/elixir-cloud-aai/foca?color=C39BD3>
 [badge-license]: <https://img.shields.io/badge/license-Apache%202.0-blue.svg>
 [badge-pypi]: <https://img.shields.io/pypi/v/foca.svg?style=flat&color=C39BD3>
 [badge-url-build-status]: <https://travis-ci.com/elixir-cloud-aai/foca>
-[badge-url-coverage]: <https://coveralls.io/github/elixir-cloud-aai/foca>
+[badge-url-coverage]: <https://codecov.io/gh/elixir-cloud-aai/foca?branch=dev>
 [badge-url-docs]: <https://foca.readthedocs.io/en/latest/>
 [badge-url-github-tag]: <https://github.com/elixir-cloud-aai/foca/releases>
 [badge-url-license]: <http://www.apache.org/licenses/LICENSE-2.0>

foca/__init__.py

@@ -1,3 +1,3 @@
 """FOCA root package."""
 
-__version__ = '0.7.0'
+__version__ = '0.8.0'

foca/foca.py

@@ -30,26 +30,26 @@ def foca(config: Optional[str] = None) -> App:
 
     # Parse config parameters and format logging
     conf = ConfigParser(config, format_logs=True).config
-    logger.info(f"Log formatting configured.")
+    logger.info("Log formatting configured.")
     if config:
         logger.info(f"Configuration file '{config}' parsed.")
     else:
-        logger.info(f"Default app configuration used.")
+        logger.info("Default app configuration used.")
 
     # Create Connexion app
     cnx_app = create_connexion_app(conf)
-    logger.info(f"Connexion app created.")
+    logger.info("Connexion app created.")
 
     # Register error handlers
     cnx_app = register_exception_handler(cnx_app)
-    logger.info(f"Error handler registered.")
+    logger.info("Error handler registered.")
 
     # Enable cross-origin resource sharing
     if(conf.security.cors.enabled is True):
         enable_cors(cnx_app.app)
-        logger.info(f"CORS enabled.")
+        logger.info("CORS enabled.")
     else:
-        logger.info(f"CORS not enabled.")
+        logger.info("CORS not enabled.")
 
     # Register OpenAPI specs
     if conf.api.specs:
@@ -58,23 +58,23 @@ def foca(config: Optional[str] = None) -> App:
             specs=conf.api.specs,
         )
     else:
-        logger.info(f"No OpenAPI specifications provided.")
+        logger.info("No OpenAPI specifications provided.")
 
     # Register MongoDB
     if conf.db:
         cnx_app.app.config['FOCA'].db = register_mongodb(
             app=cnx_app.app,
             conf=conf.db,
         )
-        logger.info(f"Database registered.")
+        logger.info("Database registered.")
     else:
-        logger.info(f"No database support configured.")
+        logger.info("No database support configured.")
 
     # Create Celery app
     if conf.jobs:
         create_celery_app(cnx_app.app)
-        logger.info(f"Support for background tasks set up.")
+        logger.info("Support for background tasks set up.")
     else:
-        logger.info(f"No support for background tasks configured.")
+        logger.info("No support for background tasks configured.")
 
     return cnx_app

requirements.txt

@@ -1,16 +1,16 @@
 addict==2.2.1
 celery==5.2.2
-connexion==2.7.0
-Flask==1.1.2
+connexion==2.11.2
+cryptography==36.0.2
+Flask==2.0.3
 Flask-Cors==3.0.9
 Flask-PyMongo==2.3.0
-mongomock==3.19.0
 pydantic==1.8.2
 PyJWT==1.7.1
 pymongo==3.10.1
 PyYAML==5.4
-requests==2.23.0
+requests==2.27.1
 swagger-ui-bundle==0.0.6
 toml==0.10.0
 typing==3.7.4.1
-Werkzeug==1.0.1
+Werkzeug==2.0.3

requirements_dev.txt

@@ -1,7 +1,6 @@
-coverage==5.1
-coveralls==2.0.0
-flake8==3.7.9
-mongomock==3.19.0
-pylint==2.5.3
-pytest==5.4.3
-python-semantic-release==7.15.0
+coverage==6.3.2
+flake8==4.0.1
+mongomock==4.0.0
+pylint==2.13.2
+pytest==7.1.1
+python-semantic-release==7.27.0

setup.cfg

@@ -1,5 +1,5 @@
 [flake8]
-exclude = .git,venv,env
+exclude = .git,.eggs,build,venv,env
 max-line-length = 79
 
 [semantic_release]

setup.py

@@ -62,6 +62,6 @@
     include_package_data=True,
     setup_requires=[
         "setuptools_git==1.2",
-        "twine==3.1.1"
+        "twine==3.8.0"
     ],
 )