LSP rename incorrectly replaces characters with pyrefly

[piotr-ginal]

Summary

When renaming a Python function parameter using LSP rename functionality, with pyrefly configured, the operation incorrectly replaces characters within function calls instead of properly renaming only the variable references.

Note: I'm not entirely sure if this is a Helix issue or a pyrefly issue. The problem only occurs with pyrefly and not with pylsp. Even when using both pyrefly and pylsp together, the issue persists, suggesting that pyrefly's rename may be taking precedence.

Is it possible to disable rename for pyrefly, and use pylsp for that?

---

Tested on 25.01.1-479-g479c3b55 and 25.01.1 (3683cd9e)

Reproduction Steps

Install pyrefly 0.22.0 (with pipx install pyrefly in my case)

Configure pyrefly as the only LSP for python in languages.toml

[language-server.pyrefly]
command = "pyrefly"
args = ["lsp"]

[[language]]
name = "python"
language-servers = [
  "pyrefly",
]

Create a python file with the following contents

def some(A):
    if bar(A):
        pass

Place cursor on the A parameter in the some function definition

Trigger rename operation (default: <space>r)

Type new name a

Confirm the rename

Expected Behavior

The parameter A should be renamed to a only in:

• Function parameter declaration: some(A):
• Function call argument: bar(a)

Final result should be:

def some(a):
    if bar(a):
        pass

Actual Behavior

The rename operation incorrectly replaces characters, resulting in:

def some(a):
    ifaa:
        pass

Notice that bar(A) becomes aa instead of bar(a).

output.mp4

Helix log

No verbose flag

~/.cache/helix/helix.log

2025-07-07T14:40:51.924 helix_lsp::transport [ERROR] pyrefly err <- "starting generic LSP server\n"
2025-07-07T14:40:51.927 helix_lsp::transport [ERROR] pyrefly err <- "Reading messages\n"
2025-07-07T14:41:00.187 helix_lsp::transport [ERROR] pyrefly err <- "Handling non-canceled request textDocument/prepareRename (1)\n"
2025-07-07T14:41:00.747 helix_lsp::transport [ERROR] pyrefly err <- "Handling non-canceled request textDocument/rename (2)\n"

Single verbose flag (-v)

~/.cache/helix/helix.log

2025-07-07T14:43:47.687 helix_lsp::transport [INFO] pyrefly -> {"jsonrpc":"2.0","method":"textDocument/prepareRename","params":{"position":{"character":9,"line":0},"textDocument":{"uri":"file:///home/ginal/main.py"}},"id":1}
2025-07-07T14:43:47.687 helix_lsp::transport [ERROR] pyrefly err <- "Handling non-canceled request textDocument/prepareRename (1)\n"
2025-07-07T14:43:47.687 helix_lsp::transport [INFO] pyrefly <- {"jsonrpc":"2.0","id":1,"result":{"end":{"character":10,"line":0},"start":{"character":9,"line":0}}}
2025-07-07T14:43:48.208 helix_lsp::transport [INFO] pyrefly -> {"jsonrpc":"2.0","method":"textDocument/rename","params":{"newName":"a","position":{"character":9,"line":0},"textDocument":{"uri":"file:///home/ginal/main.py"}},"id":2}
2025-07-07T14:43:48.208 helix_lsp::transport [ERROR] pyrefly err <- "Handling non-canceled request textDocument/rename (2)\n"
2025-07-07T14:43:48.209 helix_lsp::transport [INFO] pyrefly <- {"jsonrpc":"2.0","id":2,"result":{"changes":{"file:///home/ginal/main.py":[{"newText":"a","range":{"end":{"character":10,"line":0},"start":{"character":9,"line":0}}},{"newText":"a","range":{"end":{"character":13,"line":1},"start":{"character":7,"line":1}}},{"newText":"a","range":{"end":{"character":12,"line":1},"start":{"character":11,"line":1}}}]}}}
2025-07-07T14:43:48.210 helix_lsp::transport [INFO] pyrefly -> {"jsonrpc":"2.0","method":"textDocument/didChange","params":{"contentChanges":[{"range":{"end":{"character":10,"line":0},"start":{"character":9,"line":0}},"text":"a"},{"range":{"end":{"character":13,"line":1},"start":{"character":7,"line":1}},"text":"a"},{"range":{"end":{"character":7,"line":1},"start":{"character":6,"line":1}},"text":"a"}],"textDocument":{"uri":"file:///home/ginal/main.py","version":1}}}
2025-07-07T14:43:48.212 helix_lsp::transport [INFO] pyrefly <- {"jsonrpc":"2.0","method":"textDocument/publishDiagnostics","params":{"diagnostics":[{"code":"parse-error","message":"Parse error: Expected an expression","range":{"end":{"character":0,"line":2},"start":{"character":9,"line":1}},"severity":1,"source":"Pyrefly"},{"code":"parse-error","message":"Parse error: Unexpected indentation","range":{"end":{"character":8,"line":2},"start":{"character":0,"line":2}},"severity":1,"source":"Pyrefly"},{"code":"parse-error","message":"Parse error: Expected a statement","range":{"end":{"character":0,"line":3},"start":{"character":0,"line":3}},"severity":1,"source":"Pyrefly"}],"uri":"file:///home/ginal/main.py"}}

Platform

Linux

Terminal Emulator

alacritty 0.16.0-dev (03c2907b)

Installation Method

source

Helix Version

25.01.1-479-g479c3b55

[the-mikedavis]

This is probably a bug in pirefly rather than Helix. You can configure Helix to not use pyrefly for the rename-symbol feature https://docs.helix-editor.com/master/languages.html#configuring-language-servers-for-a-language

[piotr-ginal]

Thank you! This solution worked perfectly.

For anyone else encountering this issue, adding except-features = ["rename-symbol"] to the pyrefly configuration resolves the problem:

[[language]]
name = "python"
language-servers = [
  { name = "pyrefly", except-features = ["rename-symbol"] },
  "ruff",
  "pylsp",
]