nnUNet Writes Into Current Directory By Default

[ericspod]

This was flagged by Coderabbit and should be addressed. nnUNet will write test data to the current directory during testing, this should be changed to writing to a temporary directory in tests. This avoids leaving a mess in the user's current directory.

⚠️ Potential issue | 🟠 Major | ⚡ Quick win

Keep the generated nnUNet paths inside self.test_dir.

nnUNetV2Runner.__init__ creates nnunet_raw, nnunet_preprocessed, and nnunet_results immediately. With the current ./... values, these tests write into the repo cwd instead of the temp directory, so state leaks across tests and tearDown() does not clean it up.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@tests/integration/test_integration_nnunetv2_runner.py` around lines 110 -
148, The test YAMLs currently use relative paths (./data, ./work, ./nnUNet_raw,
./nnUNet_preprocessed, ./nnUNet_results) so nnUNetV2Runner.__init__ creates
directories in the repo cwd; update the YAML strings (good_yml_content1,
good_yml_content2, injecting_yml_content) to build all generated paths inside
the test temp dir (use self.test_dir) for keys dataroot, datalist, work_dir,
nnunet_raw, nnunet_preprocessed, and nnunet_results so the runner creates those
folders under self.test_dir and tearDown can clean them up (also ensure the
injected dataset_name_or_id test keeps the path substitution to self.test_dir).

Originally posted by @coderabbitai[bot] in #8885 (comment)

[aymuos15]

I’ll add a fix for this tomorrow if that’s okay.