mutmut v3 copies source to temp dir, breaking editable-install imports

[dirkenglund]

Description

When using mutmut v3 (3.5.0) on a project installed with pip install -e ., mutations fail because mutmut copies source files to a temporary directory where the editable package's import paths no longer resolve.

Reproduction

Project structure:

my-project/
├── pyproject.toml          # [project] name = "my_project"
├── src/
│   └── my_project/
│       ├── __init__.py
│       └── core.py         # file to mutate
└── tests/
    └── test_core.py        # imports my_project.core

Steps:

1. pip install -e .
2. pytest tests/ — passes
3. mutmut run --paths-to-mutate src/my_project/core.py
4. Mutations fail with ModuleNotFoundError: No module named 'my_project'

Expected behavior

Mutations should run in-place (or with sys.path adjusted) so that editable installs and relative imports continue to work.

Actual behavior

mutmut copies files to /tmp/ (or a mutants/ directory), then runs pytest from that context. The editable install's .pth file points to the original src/ directory, so the mutated code is never imported — or worse, the original un-mutated code is imported instead, producing false "survived" results.

Workaround

Manual mutation testing via subprocess + file patching (mutate in-place, run tests, restore original).

Related

• Mutation testing doesn't work with Django app structure - import path issues ? #456 reports a similar import path issue with Django projects
• mutmut run bombs out during initial test run #485 may also be related (initial test run failure)

Environment

• mutmut 3.5.0 (pip reports 2.4.5, mutmut.__version__ reports 3.5.0)
• Python 3.11.9
• macOS 14 (arm64)
• Project uses src/ layout with pyproject.toml

[boxed]

The mutmut run command is a bit strange. That looks like a mutmut 2.x style invocation, not what mutmut 3.x does. What happens if you run just mutmut run like the docs say?

[Otto-AA]

Can you create a github repo with the minimal example? I could not reproduce it locally.

pip reports 2.4.5

This sounds suspicious 🤔

[raschmitt]

Related failure: copy_src_dir crashes on socket files in CI

We hit a different manifestation of the same copy_src_dir issue on GitHub Actions (Ubuntu runner, Python 3.12).

Error:

FileNotFoundError: [Errno 2] No such file or directory: '/run/user/1001/systemd/units/invocation:gpg-agent-ssh.socket'

Full traceback:

File ".../mutmut/__main__.py", line 208, in copy_src_dir
    shutil.copy2(source_path, target_path)
  File ".../shutil.py", line 475, in copy2
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File ".../shutil.py", line 260, in copyfile
    with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '/run/user/1001/systemd/units/invocation:gpg-agent-ssh.socket'

copy_src_dir is walking too broadly and attempting to copy a systemd socket file, which disappears between the directory listing and the shutil.copy2 call (or simply cannot be opened as a regular file). The fix would be to filter out non-regular files (sockets, pipes, devices) before copying, e.g. with os.path.isfile() or checking stat.S_ISREG.

Workaround: pin to mutmut==2.5.1.

[Otto-AA]

Thanks for reporting this @raschmitt

Could you test if the filter-is-file branch fixes your issue? (#517)

We hit a different manifestation of the same copy_src_dir issue on GitHub Actions (Ubuntu runner, Python 3.12).

I don't understand how it is related to the original issue, to me it seems like an unrelated issue.