Short answer: there isn’t a built-in “exclude directories” setting for discovery in Prefect 3.x. If

prefect deploy

is walking your project and hitting your virtualenv, the best fix is to avoid discovery by explicitly targeting your flows. Options that work well: - Pass an explicit entrypoint when deploying

prefect deploy path/to/flow_file.py:flow_function

This skips scanning the rest of the tree. - Define deployments with explicit entrypoints in prefect.yaml and deploy by name

# prefect.yaml
  name: my-project
  deployments:
    - name: etl-dev
      entrypoint: flows/etl.py:etl
      work_pool: default

Then run:

prefect deploy --name etl-dev

- Make your project root not include the virtualenv - Move

.venv/

outside the project directory that contains

prefect.yaml

- Or keep

prefect.yaml

in a subfolder that contains only your code, then either run

prefect deploy

from that subfolder or reference it with:

prefect deploy --prefect-file subdir/prefect.yaml

Note:

.prefectignore

can keep

.venv/

out of packaged code, but it doesn’t change flow discovery behavior. It’s still a good idea to include:

# .prefectignore
.venv/
venv/

Docs for reference: - Prefect YAML and deployments: prefect.yaml - Deployment how-to: Deployments guide If you share how you’re invoking

prefect deploy

(e.g., with or without an entrypoint, relying on discovery vs. named deployments), I can suggest the most streamlined change for your setup.