sst/cdk deploy in CI: ModuleNotFoundError: No module named

Question

I am using sst to deploy a Python lambda function.

When I am trying to deploy it in Github actions, I get this error from the lambda.

ModuleNotFoundError: No module named 'asyncpg.protocol.protocol'

This lambda is executed as part of the deployment. Usually, I get this error on my local machine when I am not in the Python virtual environment.

During the SST deployment, I can see the Python dependencies installed. Some how the lambda does not have the dependencies linked.

Step 10/11 : RUN if [ -f 'requirements.txt' ]; then pip install -r requirements.txt -t .; else echo "requirements.txt not found"; fi
 ---> Running in 8a0ba257899d
Collecting aerich==0.7.1 (from -r requirements.txt (line 2))
  Downloading aerich-0.7.1-py3-none-any.whl (37 kB)
Collecting aiosqlite==0.17.0 (from -r requirements.txt (line 3))
  Downloading aiosqlite-0.17.0-py3-none-any.whl (15 kB)
Collecting anyio==3.7.0 (from -r requirements.txt (line 4))
  Downloading anyio-3.7.0-py3-none-any.whl (80 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.9/80.9 kB 22.0 MB/s eta 0:00:00
Collecting asyncpg==0.27.0 (from -r requirements.txt (line 5))
  Downloading asyncpg-0.27.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl (2.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.7/2.7 MB 91.3 MB/s eta 0:00:00
Collecting auth0-python==4.2.0 (from -r requirements.txt (line 6))

I can successfully deploy it on my local machine. Also, I can deploy in AWS Linux machine in EC2. For some reason I can't use Github Action to deploy it.

jobs:
  deploy:
    environment: 'development'
    runs-on: ubuntu-latest
    permissions:
      actions: write
      contents: read
      id-token: write
    steps:
      - uses: actions/setup-node@v3
        with:
          node-version: 18
      - name: Configure AWS credentials
        uses: aws-actions/configure-aws-credentials@v2
        with:
          role-to-assume: ${{ vars.AWS_DEPLOYMENT_ROLE }}
          aws-region:  ${{ vars.AWS_REGION }}
      - name: Checkout repo
        uses: actions/checkout@v3
        with:
          ref: ${{ github.event.pull_request.head.ref }}
          repository: ${{ github.event.pull_request.head.repo.full_name }}
      - name: Install root dependencies
        run: |
          git config --global --add safe.directory /__w/app
          yarn
      - uses: actions/setup-python@v4
        with:
          python-version: '3.9'
      - name: deploy
        run: |
          cd backend
          pip install -r requirements.txt
          cd ..
          npx sst deploy --stage test