Thanks for the details — a couple of gotchas here. First, in Prefect 3.x the step name is: -

prefect.deployments.steps.pull.git_clone

(not

prefect.deployments.steps.git_clone

) About Azure DevOps + PAT: - Do NOT base64 encode the PAT. Use the raw PAT. - You can authenticate either by: 1) Supplying

access_token:

and a clean HTTPS repo URL, or 2) Embedding a username and PAT in the URL (username can be anything non-empty) Here are two working patterns you can try in your prefect.yaml. Option A — use access_token (recommended; keep URL clean):

pull:
  - prefect.deployments.steps.pull.git_clone:
      repository: "<https://dev.azure.com/<org>/<project>/_git/<repo>>"
      branch: "my-branch"
      access_token: "${AZDO_PAT}"

- Set

AZDO_PAT

in your worker/work-pool environment. The PAT should have at least “Code: Read” scope. Option B — embed username + PAT in the URL (ensure URL-encoding if needed):

pull:
  - prefect.deployments.steps.pull.git_clone:
      repository: "<https://pat:${AZDO_PAT}@dev.azure.com/<org>/<project>/_git/<repo>>"
      branch: "my-branch"

- Any non-empty username is fine;

pat

is a common placeholder. - If your PAT contains special characters, URL-encode it before embedding. Common causes of exit code 128: - Auth failed: wrong/missing PAT, missing scope, or malformed URL - PAT accidentally base64-encoded - The branch name doesn’t exist (set

branch:

correctly) - The PAT is not available in the worker environment (e.g., env var not set) - Typos in the Azure DevOps path (verify with a manual

git ls-remote

on the worker) Quick verification tips: - On the same machine/environment your worker runs, try: - Using Option B’s URL directly with

git ls-remote <https://pat:<PAT>@dev.azure.com/<org>/<project>/_git/<repo>>

- Confirm the branch exists and the PAT has “Code (Read)” scope and org access - If it still fails, capture the full stderr from the step (not just exit code) — that often points to the exact auth or URL parsing issue. Docs: - Prefect step reference: prefect.deployments.steps.pull.git_clone - Prefect YAML guide: prefect.yaml how-to - Azure DevOps PAT usage: Use personal access tokens - Azure DevOps If you can share (sanitized) your current

prefect.yaml

step and the exact error output, I can pinpoint the issue quickly.

Nice catch on the branch! The “No pyproject.toml found” error almost always means the shell step didn’t run in the repo’s root. In prefect.yaml, you need to reference the output of the git clone step via its step id. If the clone step doesn’t have an id,

{{ git-clone.directory }}

won’t resolve and the command runs in the default working dir. Try this: - Give the clone step an id - Either set the working directory once, or pass it to run_shell_script Example 1 — set working directory once:

pull:
  - prefect.deployments.steps.pull.git_clone:
      id: git_clone
      repository: "<https://dev.azure.com/<org>/<project>/_git/<repo>>"
      branch: "my-branch"

  - prefect.deployments.steps.pull.set_working_directory:
      directory: "{{ git_clone.directory }}"

  - prefect.deployments.steps.utility.run_shell_script:
      script: uv sync

Example 2 — pass directory to the shell step:

pull:
  - prefect.deployments.steps.pull.git_clone:
      id: git_clone
      repository: "<https://dev.azure.com/<org>/<project>/_git/<repo>>"
      branch: "my-branch"

  - prefect.deployments.steps.utility.run_shell_script:
      script: uv sync
      directory: "{{ git_clone.directory }}"

Notes: - Use the canonical step path for the shell step:

prefect.deployments.steps.utility.run_shell_script

- If your project lives in a subdirectory of the repo, point to it: -

directory: "{{ git_clone.directory }}/path/to/project"

- To debug quickly, add a step:

- prefect.deployments.steps.utility.run_shell_script:
      script: "pwd && ls -la"
      directory: "{{ git_clone.directory }}"

Docs: - git_clone: prefect.deployments.steps.pull.git_clone - set_working_directory: prefect.deployments.steps.pull.set_working_directory - run_shell_script: prefect.deployments.steps.utility.run_shell_script If it still fails, share your full pull section and I’ll spot-check the templating and paths.

Thanks for the details — the error “[Errno 2] No such file or directory: ‘/prefect’” tells us Jinja rendered

{{ git_clone.directory }}

to an empty string, so your template became just

/prefect

. That means the git_clone step’s output isn’t being found by the template. Most common causes: - The step id isn’t attached correctly to the git_clone step (indentation/YAML structure) - The referenced id in the template doesn’t exactly match the step id - set_working_directory runs before git_clone - The step path is slightly off Use this minimal working example as a template:

pull:
  - prefect.deployments.steps.pull.git_clone:
      id: git_clone
      repository: "<https://dev.azure.com/<org>/<project>/_git/<repo>>"
      branch: "my-branch"

  # Optional: Debug what the template resolves to
  - prefect.deployments.steps.utility.run_shell_script:
      script: |
        echo "Repo dir: {{ git_clone.directory }}"
        ls -la "{{ git_clone.directory }}"
        ls -la "{{ git_clone.directory }}/prefect"

  - prefect.deployments.steps.pull.set_working_directory:
      directory: "{{ git_clone.directory }}/prefect"

  - prefect.deployments.steps.utility.run_shell_script:
      script: uv sync

Checklist: - Ensure the id is nested under the git_clone step (as shown). This is the correct syntax: - prefect.deployments.steps.pull.git_clone: id: git_clone ... - The template must match the id exactly:

{{ git_clone.directory }}

- set_working_directory must come after the git_clone step - The canonical path for the shell step is

prefect.deployments.steps.utility.run_shell_script

(not

prefect.deployments.steps.run_shell_script

) If the debug step prints an empty line for “Repo dir:”, the id reference isn’t resolving. In that case, please paste your full pull section and I’ll spot the mismatch. Docs for reference: - git_clone: prefect.deployments.steps.pull.git_clone - set_working_directory: prefect.deployments.steps.pull.set_working_directory - run_shell_script: prefect.deployments.steps.utility.run_shell_script

You’re right about the logging note — pull steps run on the worker and, with stream_output: true (the default), their stdout/stderr won’t be sent to the API/UI. To see those logs: - Check your Managed Worker logs in the UI (Work Pools -> your managed pool -> Worker logs) - Or temporarily set stream_output: false and write the output to a file in the repo if you need to retrieve it later; the result isn’t automatically shown in the UI either. That said, the “[Errno 2] No such file or directory: ‘/prefect’” means the Jinja template resolved to an empty string for the repo path, so the final path became “/prefect”. In other words, {{ git_clone.directory }} did not resolve. This almost always comes down to YAML structure or an id mismatch. Use this known-good structure:

pull:
  - prefect.deployments.steps.pull.git_clone:
      id: git_clone
      repository: "<https://dev.azure.com/<org>/<project>/_git/<repo>>"
      branch: "my-branch"

  # Quick debug: verify the resolved directory on the worker
  - prefect.deployments.steps.utility.run_shell_script:
      script: |
        echo "Repo dir: {{ git_clone.directory }}"
        ls -la "{{ git_clone.directory }}"
        ls -la "{{ git_clone.directory }}/prefect"
      stream_output: true

  # Option A: set CWD for subsequent steps
  - prefect.deployments.steps.pull.set_working_directory:
      directory: "{{ git_clone.directory }}/prefect"

  # Option B (simpler/less stateful): pass directory directly to each script
  - prefect.deployments.steps.utility.run_shell_script:
      script: uv sync
      directory: "{{ git_clone.directory }}/prefect"
      stream_output: true

Checklist: - The id must be nested under the git_clone step itself (indentation matters) - The reference must match exactly: {{ git_clone.directory }} - set_working_directory must come after git_clone - Use the canonical paths: - prefect.deployments.steps.pull.git_clone - prefect.deployments.steps.pull.set_working_directory - prefect.deployments.steps.utility.run_shell_script If the debug step prints “Repo dir:” as empty or errors on the ls command, the template isn’t resolving. In that case, please paste your full pull section and I’ll spot any indentation/id/path issues. Docs for reference: - git_clone: prefect.deployments.steps.pull.git_clone - set_working_directory: prefect.deployments.steps.pull.set_working_directory - run_shell_script: prefect.deployments.steps.utility.run_shell_script

Got it — that FileNotFoundError is happening because the path you’re giving set_working_directory is relative. The value from {{ git_clone.directory }} is typically the repo folder name (e.g. my_repo-my-branch), not an absolute path. On a managed worker, the initial CWD may not be the parent of that folder, so chdir to "my_repo-my-branch/prefect" fails. Two solid fixes: Option A — set a known base CWD before cloning - This ensures git_clone creates the repo under a directory you control (e.g. /tmp), so the relative path works.

pull:
  - prefect.deployments.steps.pull.set_working_directory:
      directory: "/tmp"

  - prefect.deployments.steps.pull.git_clone:
      id: git_clone
      repository: "<https://dev.azure.com/<org>/<project>/_git/<repo>>"
      branch: "my-branch"

  - prefect.deployments.steps.pull.set_working_directory:
      directory: "{{ git_clone.directory }}/prefect"

  - prefect.deployments.steps.utility.run_shell_script:
      script: uv sync

Option B — don’t change global CWD; point run_shell_script at the repo folder - Less stateful and easier to debug.

pull:
  - prefect.deployments.steps.pull.set_working_directory:
      directory: "/tmp"

  - prefect.deployments.steps.pull.git_clone:
      id: git_clone
      repository: "<https://dev.azure.com/<org>/<project>/_git/<repo>>"
      branch: "my-branch"

  - prefect.deployments.steps.utility.run_shell_script:
      script: uv sync
      directory: "{{ git_clone.directory }}/prefect"

Tip: Add a quick sanity check step to confirm the path on the worker (logs show up in Managed Worker logs, not the flow run UI):

- prefect.deployments.steps.utility.run_shell_script:
    script: |
      echo "PWD: $(pwd)"
      echo "Repo dir: {{ git_clone.directory }}"
      ls -la "{{ git_clone.directory }}"
      ls -la "{{ git_clone.directory }}/prefect"
    stream_output: true

Relevant refs: - set_working_directory: prefect.deployments.steps.pull.set_working_directory - git_clone: prefect.deployments.steps.pull.git_clone - run_shell_script: prefect.deployments.steps.utility.run_shell_script If you prefer a different base than /tmp, just set that in the first set_working_directory step and everything else will line up.