Merge pull request #26 from fengsh27/main

create ci for pull request

.github/workflows/ci.yml

@@ -0,0 +1,59 @@
+name: biochatter Continuous Integration
+
+on: [pull_request, push]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+
+      - name: Install Docker
+        run: |
+          sudo apt remove containerd.io
+          sudo apt install -y docker.io
+
+      - name: Install Docker Compose
+        run: |
+          sudo curl -L "https://github.com/docker/compose/releases/latest/download/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
+          sudo chmod +x /usr/local/bin/docker-compose
+
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+      - name: Install dependencies
+        run: |
+          poetry install
+          poetry install -E podcast
+
+      - name: Start Milvus server
+        run: |
+          docker-compose -f milvus-docker-compose.yml up -d
+
+      - name: Set API key
+        run: |
+          echo ${{ secrets.OPENAI_API_KEY }} > api_key.txt
+          echo ${{ secrets.AZURE_TEST_OPENAI_MODEL_NAME }} > azure_test_model.txt
+          echo ${{ secrets.AZURE_TEST_OPENAI_DEPLOYMENT_NAME }} > azure_test_deployment.txt
+          echo ${{ secrets.AZURE_TEST_OPENAI_API_VERSION }} > azure_test_api_version.txt
+          echo ${{ secrets.AZURE_TEST_OPENAI_API_BASE }} > azure_test_api_base.txt
+          echo ${{ secrets.AZURE_TEST_OPENAI_API_KEY }} > azure_test_api_key.txt
+
+      - name: Set environment variable
+        run: |
+          echo "OPENAI_API_KEY=$(cat api_key.txt)" >> $GITHUB_ENV
+          echo "AZURE_TEST_OPENAI_MODEL_NAME=$(cat azure_test_model.txt)" >> $GITHUB_ENV
+          echo "AZURE_TEST_OPENAI_DEPLOYMENT_NAME=$(cat azure_test_deployment.txt)" >> $GITHUB_ENV
+          echo "AZURE_TEST_OPENAI_API_VERSION=$(cat azure_test_api_version.txt)" >> $GITHUB_ENV
+          echo "AZURE_TEST_OPENAI_API_BASE=$(cat azure_test_api_base.txt)" >> $GITHUB_ENV
+          echo "AZURE_TEST_OPENAI_API_KEY=$(cat azure_test_api_key.txt)" >> $GITHUB_ENV
+
+      - name: Run tests
+        run: |
+          poetry run pytest --ignore=./volumes

milvus-docker-compose.yml

@@ -0,0 +1,47 @@
+
+version: '3.5'
+
+services:
+  etcd:
+    container_name: milvus-etcd
+    image: quay.io/coreos/etcd:v3.5.5
+    environment:
+      - ETCD_AUTO_COMPACTION_MODE=revision
+      - ETCD_AUTO_COMPACTION_RETENTION=1000
+      - ETCD_QUOTA_BACKEND_BYTES=4294967296
+      - ETCD_SNAPSHOT_COUNT=50000
+    volumes:
+      - ${DOCKER_VOLUME_DIRECTORY:-.}/volumes/etcd:/etcd
+    command: etcd -advertise-client-urls=http://127.0.0.1:2379 -listen-client-urls http://0.0.0.0:2379 --data-dir /etcd
+
+  minio:
+    container_name: milvus-minio
+    image: minio/minio:RELEASE.2022-03-17T06-34-49Z
+    environment:
+      MINIO_ACCESS_KEY: minioadmin
+      MINIO_SECRET_KEY: minioadmin
+    volumes:
+      - ${DOCKER_VOLUME_DIRECTORY:-.}/volumes/minio:/minio_data
+    command: minio server /minio_data
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:9000/minio/health/live"]
+      interval: 30s
+      timeout: 20s
+      retries: 3
+
+  standalone:
+    container_name: milvus-standalone
+    image: milvusdb/milvus:v2.2.8
+    command: ["milvus", "run", "standalone"]
+    environment:
+      ETCD_ENDPOINTS: etcd:2379
+      MINIO_ADDRESS: minio:9000
+    volumes:
+      - ${DOCKER_VOLUME_DIRECTORY:-.}/volumes/milvus:/var/lib/milvus
+    ports:
+      - "19530:19530"
+      - "9091:9091"
+    depends_on:
+      - "etcd"
+      - "minio"
+

pyproject.toml

@@ -38,4 +38,4 @@ requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.black]
-line-length = 80
+line-length = 80

test/test_llm_connect.py

@@ -105,7 +105,6 @@ def test_azure_raises_request_error():
     with pytest.raises(NotFoundError):
         convo.set_api_key("fake_key")
 
-
 def test_azure():
     """
     Test OpenAI Azure endpoint functionality. Azure connectivity is enabled by
@@ -122,3 +121,4 @@ def test_azure():
     )
 
     assert convo.set_api_key(os.getenv("AZURE_TEST_OPENAI_API_KEY"))
+

test/test_vectorstore_host.py

@@ -10,9 +10,7 @@
 from biochatter.vectorstore_host import VectorDatabaseHostMilvus
 
 """
-This test needs OPENAI_API_KEY in the environment and a local milvus server. The
-entire module needs to be run in one go, as the collections are created and
-called in different tests.
+This test needs OPENAI_API_KEY in the environment and a local milvus server. 
 """
 
 # setup milvus connection