How to properly make prefect workers pull code from a private github repo?

[pro-jasonnagy]

I am currently trying to set up my prefect system to make the workers pull code from a private github repo but I keep getting errors from the prefect GUI saying "The system cannot find the file specified", though it doesnt state which file it is trying to find. Here is the CSV for the prefect log. Ive been following the guide to pulling from github but something has gone wrong with the process and I was hoping to get some help.

I am currently running a prefect server through docker and am trying to set up a deployment which uses code hosted in a private github repo. The deployment is made without an issue and appears in the web GUI. I can then launch a run manually. My deployment is defined at the bottom of my flow file, as shown below:

from prefect import flow, task
from prefect.runner.storage import GitRepository
from prefect_github import GitHubCredentials

# Happens in small python script before __main__
# Uses github fine-grain access token with read-only Contents and Metadata permissions
github_credentials_block = GitHubCredentials(token=TOKEN) 
github_credentials_block.save(name="access-token", overwrite=True)

if __name__ == "__main__":
    github_repo = GitRepository(
        url="https://github.com/org/repo.git",
        credentials=GitHubCredentials.load("access-token"),
        branch="dev",
        include_submodules=True
    )

    flow.from_source(
        source=github_repo,
        entrypoint="src/workflows/flows/flow.py:flow_main",
    ).deploy(
        name="flow_main",
        work_pool_name="local-pool",
    )

To use github, the webpage says I need to register the github block with prefect block register -m prefect_github but it doesnt say if this is needed on the server or client. Im also not sure how to modify the instructions for a prefect server hosted within docker. It seems that docker doesn't use the prefect.yaml or prefect profiles I created in the CLI and instead uses the settings passed to it through the environment settings of the docker compose so I am unsure how I need to modify my docker compose to provide access to the github credentials block I created on the bash CLI.

My prefect.yaml which lays in a folder above the folder I run my docker compoe from contains the following under the pull section. I am unsure if this needs to be modified since it doesnt seem like the prefect.yaml is getting touched.

pull:
- prefect.deployments.steps.git_clone:
  repository: https://github.com/org/repo.git
  credentials: "{{ prefect.blocks.github-credentials.access-token }}"

Any help would be greatly appreciated!

[desertaxle]

Hey @pro-jasonnagy! The key detail is that the failure is happening during Prefect’s deployment pull step, not when it tries to import your flow code.

In your log, Prefect gets to:

Running git_clone step...

and then fails with:

[WinError 2] The system cannot find the file specified

That traceback is coming from Prefect trying to execute git clone, so the missing “file” is almost certainly the git executable on the worker machine, not your flow file, prefect.yaml, or the GitHub block.

A few clarifications:

1. Because you created the deployment with flow.from_source(...).deploy(...), Prefect stores the pull instructions on the deployment itself. Your local prefect.yaml is not used at run time.
2. The worker pulls code at runtime. Your log is from a Windows ProcessWorker (C:\Users\...), so the clone is happening on the Windows worker host, not inside the Dockerized Prefect server.
3. prefect block register -m prefect_github does not need to be run specifically inside the server container. It just needs to happen in an environment that points to the same Prefect API. Also, saving a GitHubCredentials block in Python already registers its type/schema.

What I would check next on the machine where you run prefect worker start:

• Run where git
• Run git --version
• Run prefect config view and confirm the worker is pointing at the same PREFECT_API_URL as the environment where you saved the block
• Make sure prefect-github is installed in that worker environment if you’re using GitHubCredentials

If where git fails, install Git for Windows or add it to PATH, then restart the worker. If where git works in your terminal but Prefect still fails, the worker may be starting with a different PATH than your interactive shell.

So the immediate fix is to focus on the worker environment, not the Docker Compose for the Prefect server. The server container does not need your local prefect.yaml or local CLI profile for this particular issue.