Added workflows for building, testing, releasing (#16)

* added workflows

* settings fix

* skip integration tests in CI

.env.bak

@@ -0,0 +1,14 @@
+DATASOURCE_DB_USERNAME=postgres
+DATASOURCE_DB_PASSWORD=postgres
+DATASOURCE_DB_DATABASE=hutch-omop
+DATASOURCE_DB_SCHEMA=public
+DATASOURCE_DB_PORT=5432
+DATASOURCE_DB_HOST=localhost
+TASK_API_BASE_URL=https://brcdatarq.nottingham.ac.uk/link_connector_api
+TASK_API_USERNAME=link-test
+TASK_API_PASSWORD=zjC/FKL91V9QIwuRsfXtcGK9LfU=
+COLLECTION_ID=RQ-CC-98ac1cb4-b34f-4131-a393-3936e7a946cf
+TASK_API_TYPE=a
+LOW_NUMBER_SUPPRESSION_THRESHOLD=
+ROUNDING_TARGET=
+POLLING_INTERVAL=5

.github/workflows/check.container-build.yml

@@ -0,0 +1,25 @@
+name: Check Container Builds
+
+on:
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
+
+      - name: Build Docker image
+        uses: docker/[email protected]
+        with:
+          context: .
+          file: Dockerfile
+          push: false
+          platforms: linux/amd64,linux/arm64

.github/workflows/check.run-tests.yml

@@ -0,0 +1,30 @@
+name: Run Tests
+
+on:
+  pull_request:
+
+jobs:
+  run-tests:
+    name: Run Tests
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "0.5.16"
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+
+      - name: uv sync
+        run: uv sync --frozen --dev
+
+      - name: Run tests
+        run: uv run pytest tests

.github/workflows/release.dev.yml

@@ -0,0 +1,65 @@
+# This workflow is used for any merge to main and results in a built container image being pushed and tagged as a dev release
+# with commit hash and timestamp tags
+#
+# These are not stable or pre-release semver releases!
+name: Publish a Dev Release
+
+on:
+  push:
+    branches: [main]
+
+env:
+  image-name: hutch/bunny
+  repo-owner: ${{ github.repository_owner }}
+  registry: ghcr.io
+
+jobs:
+  publish-bunny:
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
+
+      - name: Docker Login
+        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0
+        with:
+          registry: ${{ env.registry }}
+          username: ${{github.actor}}
+          password: ${{secrets.GITHUB_TOKEN}}
+
+      - name: Set timestamp env var
+        run: echo "RUN_TIMESTAMP=$(TZ="Etc/UTC" date +'%Y%m%d%H%M%S')" >> $GITHUB_ENV
+
+      - name: Docker Metadata action
+        id: meta
+        uses: docker/[email protected]
+        with:
+          images: ${{ env.registry }}/${{ env.repo-owner}}/${{ env.image-name}}
+          tags: |
+            ${{ github.sha }}
+            ${{ env.RUN_TIMESTAMP }}
+            dev-latest
+          labels: |
+            org.opencontainers.image.title=Hutch Bunny
+            org.opencontainers.image.vendor=University of Nottingham
+            org.opencontainers.image.version=0.0.1
+          # TODO: version label should reflect current source version?
+          # Could add more custom labels in the future here
+
+      - name: Build and push Docker images
+        uses: docker/[email protected]
+        with:
+          context: .
+          file: Dockerfile
+          push: true
+          platforms: linux/amd64,linux/arm64
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

src/hutch_bunny/core/settings.py

@@ -36,7 +36,7 @@
 
 POLLING_INTERVAL_DEFAULT = 5
 ### currently no guards to ensure that POLLING_INTERVAL and POLLING_TIMEOUT are >=0
-POLLING_INTERVAL = int(environ.get("POLLING_INTERVAL")) or POLLING_INTERVAL_DEFAULT
+POLLING_INTERVAL = int(environ.get("POLLING_INTERVAL", POLLING_INTERVAL_DEFAULT))
 
 if POLLING_INTERVAL < 0:
     print("POLLING_INTERVAL must be a positive integer. Setting to default 5s...")

tests/test_demographics_distribution_query.py

@@ -9,6 +9,10 @@
 
 load_dotenv()
 
+pytestmark = pytest.mark.skipif(
+    os.environ.get("CI") is not None, reason="Skip integration tests in CI"
+)
+
 
 @pytest.fixture
 def db_manager():

tests/test_return.py

@@ -14,6 +14,10 @@
 
 load_dotenv()
 
+pytestmark = pytest.mark.skipif(
+    os.environ.get("CI") is not None, reason="Skip integration tests in CI"
+)
+
 
 @pytest.fixture
 def db_manager():