Merge pull request #11 from BBMRI-cz/CI_pipeline

Ci pipeline

.github/scripts/wait-for-url.sh

@@ -0,0 +1,14 @@
+#!/bin/bash -e
+
+URL=$1
+START_EPOCH="$(date +"%s")"
+
+eclipsed() {
+  EPOCH="$(date +"%s")"
+  echo $((EPOCH - START_EPOCH))
+}
+
+# wait at maximum 120 seconds
+while [[ ($(eclipsed) -lt 120) && ("$(curl -s -o /dev/null -w '%{response_code}' "$URL")" != "200") ]]; do
+  sleep 2
+done

.github/workflows/test.yml

@@ -0,0 +1,76 @@
+name: CI test
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+
+
+jobs:
+  py-lint:
+    name: Lint
+    continue-on-error: true
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+          cache: 'pip'
+
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: Run pylint
+        run: pylint --recursive=y .
+
+  unit-tests:
+    name: Unit tests
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+          cache: 'pip'
+
+      - name: Run unit tests
+        run: make test
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          flags: unit
+
+  integration-tests:
+    needs: unit-tests
+    name: Integration tests
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+          cache: 'pip'
+
+      - name: Run integration tests
+        run: make integration
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          flags: integration

Makefile

@@ -0,0 +1,16 @@
+PYTHON_INTERPRETER = python3
+PYTEST_COMMAND = $(PYTHON_INTERPRETER) -m pytest
+PYTEST_ARGS = -v -p no:cacheprovider --cov-report=xml --cov=./
+
+.PHONY: test setup clean validate
+setup: requirements.txt ## Install required packages
+	pip install -r requirements.txt
+test: setup ## Run unit test
+	$(PYTEST_COMMAND) $(PYTEST_ARGS) test/unit
+integration: setup ## Run integration test
+	docker run --name blaze --rm -d -e JAVA_TOOL_OPTIONS=-Xmx2g -p 8080:8080 samply/blaze:latest
+	.github/scripts/wait-for-url.sh  http://localhost:8080/health
+	$(PYTEST_COMMAND) $(PYTEST_ARGS) test/service
+	docker stop blaze
+clean:
+	rm -rf __pycache__