Make sure temporary directories are cleaned up in tests

[marcuscollins]

This got flagged by code rabbit in PR #274

# Must be set before any `import protpardelle...` happens. Respect an
# externally configured directory (e.g. when real weights are available).
os.environ.setdefault(
    "PROTPARDELLE_MODEL_PARAMS", tempfile.mkdtemp(prefix="protpardelle_model_params_")
)

and again in test_protpardelle_wrapper.py.

To resolve this issue, make any necessary changes to make sure the temp directories are cleaned up after tests are completed. If no changes are needed, just add that to the comments that the directories are cleaned up, and how that is known (something in pytest, somewhere else in the code) just so this doesn't get flagged again.

[manzuoni-astera]

PR up: #297 (targets mdc/add-protpardelle). The os.environ.setdefault(..., tempfile.mkdtemp(...)) leaked a temp dir on every run (setdefault evaluates the default eagerly even when the var is already set). Now guards on the var being unset and registers atexit cleanup with shutil.rmtree(..., ignore_errors=True), in both conftest and the test module.

[xraymemory]

Status: implemented, pending merge to main.

Fixed by #297 ("support bare require_* decorators; clean up protpardelle temp dirs", branch michaelanzuoni/protpardelle-p1-quickwins), which is merged into the protpardelle feature branch mdc/add-protpardelle — not into main, so GitHub never auto-closed this despite the "Fixes #286" in that PR. (The flagged code isn't in main yet because protpardelle itself isn't.)

The code lands in main via #300. I've added Closes #286 to #300's description, so this will close automatically when protpardelle merges. Leaving it open until then.