diff --git a/.github/workflows/database.yml b/.github/workflows/database.yml
index 90c53f2..250dbab 100644
--- a/.github/workflows/database.yml
+++ b/.github/workflows/database.yml
@@ -27,7 +27,7 @@ jobs:
         run: uv python install 3.10
 
       - name: install python packages
-        run: uv pip install --system .
+        run: uv sync
 
       - name: track large files
         run: git lfs track "database/pipeline.pkl"
@@ -40,7 +40,7 @@ jobs:
           ZOTERO_API_KEY: ${{ secrets.ZOTERO_API_KEY }}
           ZOTERO_LIBRARY_ID: ${{ secrets.ZOTERO_LIBRARY_ID }}
           HUGGINGFACE_TOKEN: ${{ secrets.HUGGINGFACE_TOKEN }}
-        run: python run.py
+        run: uv run python run.py
 
       - name: commit files
         run: |
diff --git a/.github/workflows/flyio.yml b/.github/workflows/flyio.yml
index 3e6a216..b583460 100644
--- a/.github/workflows/flyio.yml
+++ b/.github/workflows/flyio.yml
@@ -15,7 +15,7 @@ jobs:
     name: Deploy app
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           lfs: true
       - uses: superfly/flyctl-actions/setup-flyctl@master
diff --git a/Dockerfile b/Dockerfile
index b4d8c25..d80e5f3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -3,20 +3,20 @@ FROM python:3.10-slim
 # Install uv
 COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
 
-# Clone the repository
 WORKDIR /code
 
 # Copy the necessary files
-COPY database/pipeline.pkl /code/database/pipeline.pkl
 COPY pyproject.toml /code/pyproject.toml
+COPY readme.md /code/readme.md
+COPY database/pipeline.pkl /code/database/pipeline.pkl
 COPY knowledge_database /code/knowledge_database
 COPY api /code/api
 
-# Install Python dependencies using uv
-RUN uv pip install --system .
+# Install Python dependencies using uv with a virtual environment
+RUN uv venv /code/.venv && uv pip install --python /code/.venv/bin/python .
 
 # Set up the secret environment variable for OpenAI API Key
 RUN --mount=type=secret,id=OPENAI_API_KEY sh -c 'echo "export OPENAI_API_KEY=$(cat /run/secrets/OPENAI_API_KEY)" >> /etc/profile.d/openai.sh'
 
 # Set the command to run the application
-CMD ["/bin/bash", "-c", "source /etc/profile && uvicorn api.api:app --host 0.0.0.0 --port 8080"]
+CMD ["/bin/bash", "-c", "source /etc/profile && /code/.venv/bin/uvicorn api.api:app --host 0.0.0.0 --port 8080"]