Unable to patch binary in Python environment with uv

[dmarcoux]

In another issue, I wrote about how to patch the ruff binary in a Python virtual environment relying on venv.

This was my devenv.nix:

  (...)

  languages.python = {
    enable = true;
    version = "3.12.7";
    venv = {
      enable = true;
      requirements = ./requirements.txt;
    };
  };

  tasks = {
    # Patch ruff to make it runnable
    "venv:patchelf" = {
      exec = "${lib.getExe pkgs.patchelf} --set-interpreter ${pkgs.stdenv.cc.bintools.dynamicLinker} $VIRTUAL_ENV/bin/ruff";
      after = [ "devenv:python:virtualenv" ]; # Runs after this
      before = [ "devenv:enterShell" ]; # Runs before this
    };
  };

Since then, I've migrated to uv and I am now unable to patch the ruff binary. devenv.nix is now like this:

(...)

  languages.python = {
    enable = true;
    version = "3.12.7";
    # Enable uv, an extremely fast Python package and project manager - https://docs.astral.sh/uv/
    uv = {
      enable = true;
      package = pkgs-unstable.uv;
      # Sync the project's dependencies (from `pyproject.toml`) with the virtual environment
      sync.enable = true;
    };
    # Enable Python virtual environment. It's created with `uv venv`.
    venv.enable = true;
  };

  tasks = {
    "venv:patchelf-ruff" = {
      description = "Patch ruff binary. It is dynamically linked to ld, which will not work with Nix";
      exec = "${lib.getExe pkgs.patchelf} --set-interpreter ${pkgs.stdenv.cc.bintools.dynamicLinker} $VIRTUAL_ENV/bin/ruff";
      after = [ "devenv:python:uv" ]; # Our task runs after this
      before = [ "devenv:enterShell" ]; # Our task runs before this
    };
  };

I don't know why, but I cannot execute the ruff binary anymore. uv run ruff errors out with cannot execute binary file. Executing ruff directly (it's in the $PATH), results in zsh: exec format error: ruff.

So somehow, setting up the Python virtual environment with uv changes something... but what exactly?

Thank you for your help!

[dmarcoux]

In a devenv where both uv and venv are enabled, the virtual environment will be created with uv env. This is where it's implemented.

devenv/src/modules/languages/python.nix

Lines 73 to 75 in 24f0aac

	${if cfg.uv.enable then ''
	echo uv venv -p ${package.interpreter} "$VENV_PATH"
	uv venv -p ${package.interpreter} "$VENV_PATH"

I wonder if the issue I am hitting is exactly the same as this one in upstream uv. I am thinking this since the ruff binary is callable (and runnable after patching it with patchelf) when using only venv. This is however not even possible with uv venv.

[dmarcoux]

I ended up deleting uv.lock, and it nows works... which I don't understand. Here are the diffs from uv.lock after it's been recreated.

uv.lock diffs

diff --git a/uv.lock b/uv.lock
index c5eb410..c6379a6 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,9 +1,5 @@
 version = 1
 requires-python = ">=3.12"
-resolution-markers = [
-    "python_full_version < '3.13'",
-    "python_full_version >= '3.13'",
-]
 
 [[package]]
 name = "annotated-types"
@@ -81,16 +77,16 @@ wheels = [
 
 [[package]]
 name = "fastapi"
-version = "0.115.4"
+version = "0.115.5"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "pydantic" },
     { name = "starlette" },
     { name = "typing-extensions" },
 ]
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+sdist = { url = "https://files.pythonhosted.org/packages/ae/29/f71316b9273b6552a263748e49cd7b83898dc9499a663d30c7b9cb853cb8/fastapi-0.115.5.tar.gz", hash = "sha256:0e7a4d0dc0d01c68df21887cce0945e72d3c48b9f4f79dfe7a7d53aa08fbb289", size = 301047 }
 wheels = [
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 ]
 
 [package.optional-dependencies]
@@ -132,15 +128,15 @@ wheels = [
 
 [[package]]
 name = "httpcore"
-version = "1.0.6"
+version = "1.0.7"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
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     { name = "h11" },
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+sdist = { url = "https://files.pythonhosted.org/packages/6a/41/d7d0a89eb493922c37d343b607bc1b5da7f5be7e383740b4753ad8943e90/httpcore-1.0.7.tar.gz", hash = "sha256:8551cb62a169ec7162ac7be8d4817d561f60e08eaa485234898414bb5a8a0b4c", size = 85196 }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/06/89/b161908e2f51be56568184aeb4a880fd287178d176fd1c860d2217f41106/httpcore-1.0.6-py3-none-any.whl", hash = "sha256:27b59625743b85577a8c0e10e55b50b5368a4f2cfe8cc7bcfa9cf00829c2682f", size = 78011 },
+    { url = "https://files.pythonhosted.org/packages/87/f5/72347bc88306acb359581ac4d52f23c0ef445b57157adedb9aee0cd689d2/httpcore-1.0.7-py3-none-any.whl", hash = "sha256:a3fff8f43dc260d5bd363d9f9cf1830fa3a458b332856f34282de498ed420edd", size = 78551 },
 ]
 
 [[package]]
@@ -290,51 +286,55 @@ wheels = [
 
 [[package]]
 name = "pydantic"
-version = "2.9.2"
+version = "2.10.1"
 source = { registry = "https://pypi.org/simple" }
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     { name = "pydantic-core" },
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 ]
 
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 name = "pydantic-core"
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+version = "2.27.1"
 source = { registry = "https://pypi.org/simple" }
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I guess this can be marked as solved now....