My general solution to project management problems with PEP 723 scripts is to develop the script as a regular Python application that has `pyproject.toml`. It lets you use all of your normal tooling. While I don't use an LSP-based editor, it makes things easy with Ruff and Pyright. I run my standard Poe the Poet (https://poethepoet.natn.io/) tasks for formatting, linting, and type checking as in any other project.

One drawback of this workflow is that by default, you duplicate the dependencies: you have them both in the PEP 723 script itself and `pyproject.toml`. I just switched a small server application from shiv (https://github.com/linkedin/shiv) to inline script metadata after a binary dependency broke the zipapp. I experimented with having `pyproject.toml` as the single source of truth for metadata in this project. I wrote the following code to embed the metadata in the script before it was deployed on the server. In a project that didn't already have a build and deploy step, you'd probably want to modify the PEP 723 script in place.

  #! /usr/bin/env python3
  # License: https://dbohdan.mit-license.org/@2025/license.txt
  
  import re
  import tomllib
  from pathlib import Path
  from string import Template
  
  import tomli_w
  
  DEPENDENCIES = "dependencies"
  PROJECT = "project"
  REQUIRES_PYTHON = "requires-python"
  
  DST = Path("bundle.py")
  PYPROJECT = Path("pyproject.toml")
  SRC = Path("main.py")
  
  BUNDLE = Template(
      """
  #! /usr/bin/env -S uv run --quiet --script
  # /// script
  $toml
  # ///
  
  $code
  """.strip()
  )
  
  
  def main() -> None:
      with PYPROJECT.open("rb") as f:
          pyproject = tomllib.load(f)
  
      toml = tomli_w.dumps(
          {
              DEPENDENCIES: pyproject[PROJECT][DEPENDENCIES],
              REQUIRES_PYTHON: pyproject[PROJECT][REQUIRES_PYTHON],
          },
          indent=2,
      )
  
      code = SRC.read_text()
      code = re.sub(r"^#![^\n]+\n", "", code)
  
      bundle = BUNDLE.substitute(
          toml="\n".join(f"# {line}" for line in toml.splitlines()),
          code=code,
      )
  
      DST.write_text(bundle)
  
  
  if __name__ == "__main__":
      main()