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benchflow
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frontierphysics-pr401-evidence

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params=[
("fitness", RESULTS, "public_submission"),
("growthrate", GROWTH_RESULTS, "growthrate_submission"),
],
)
def public_bundle(request: pytest.FixtureRequest) -> dict[str, Any]:
phenotype, results_root, preserved_name = request.param
> assert SOURCE.is_file() and not SOURCE.is_symlink()
E AssertionError: assert (False)
E + where False = is_file()
E + where is_file = PosixPath('/root/fit_stability_landscape.py').is_file
test_outputs.py:940: AssertionError
_ ERROR at setup of test_hamming_diagnostics_are_data_derived[public_bundle1] __
request = <SubRequest 'public_bundle' for <Function test_public_artifact_and_input_contract[public_bundle1]>>
@pytest.fixture(
scope="session",
params=[
("fitness", RESULTS, "public_submission"),
("growthrate", GROWTH_RESULTS, "growthrate_submission"),
],
)
def public_bundle(request: pytest.FixtureRequest) -> dict[str, Any]:
phenotype, results_root, preserved_name = request.param
> assert SOURCE.is_file() and not SOURCE.is_symlink()
E AssertionError: assert (False)
E + where False = is_file()
E + where is_file = PosixPath('/root/fit_stability_landscape.py').is_file
test_outputs.py:940: AssertionError
___ ERROR at setup of test_optimizer_diagnostics_and_report[public_bundle1] ____
request = <SubRequest 'public_bundle' for <Function test_public_artifact_and_input_contract[public_bundle1]>>
@pytest.fixture(
scope="session",
params=[
("fitness", RESULTS, "public_submission"),
("growthrate", GROWTH_RESULTS, "growthrate_submission"),
],
)
def public_bundle(request: pytest.FixtureRequest) -> dict[str, Any]:
phenotype, results_root, preserved_name = request.param
> assert SOURCE.is_file() and not SOURCE.is_symlink()
E AssertionError: assert (False)
E + where False = is_file()
E + where is_file = PosixPath('/root/fit_stability_landscape.py').is_file
test_outputs.py:940: AssertionError
______________ ERROR at setup of test_cross_phenotype_comparison _______________
@pytest.fixture(scope="session")
def public_bundles_by_phenotype() -> dict[str, dict[str, Any]]:
> assert SOURCE.is_file() and not SOURCE.is_symlink()
E AssertionError: assert (False)
E + where False = is_file()
E + where is_file = PosixPath('/root/fit_stability_landscape.py').is_file
test_outputs.py:965: AssertionError
_ ERROR at setup of test_hidden_replay_is_isolated_generalizes_and_ignores_test_labels _
jail_root = PosixPath('/tmp/protein-stability-jail-akafuob2')
@pytest.fixture(scope="session")
def hidden_bundles(jail_root: Path) -> dict[str, tuple[dict[str, Any], dict[str, Any]]]:
LOG_DIR.mkdir(parents=True, exist_ok=True)
bundles: dict[str, tuple[dict[str, Any], dict[str, Any]]] = {}
for phenotype in ("fitness", "growthrate"):
> original_case = prepare_case(jail_root, f"hidden-original-{phenotype}", INPUT)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
test_outputs.py:1103:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
test_outputs.py:1048: in prepare_case
shutil.copy2(SOURCE, case / "fit_stability_landscape.py")
/usr/local/lib/python3.12/shutil.py:475: in copy2
copyfile(src, dst, follow_symlinks=follow_symlinks)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
src = PosixPath('/root/fit_stability_landscape.py')
dst = PosixPath('/tmp/protein-stability-jail-akafuob2/hidden-original-fitness/fit_stability_landscape.py')
def copyfile(src, dst, *, follow_symlinks=True):
"""Copy data from src to dst in the most efficient way possible.
If follow_symlinks is not set and src is a symbolic link, a new
symlink will be created instead of copying the file it points to.
"""
sys.audit("shutil.copyfile", src, dst)
if _samefile(src, dst):
raise SameFileError("{!r} and {!r} are the same file".format(src, dst))
file_size = 0
for i, fn in enumerate([src, dst]):
try:
st = _stat(fn)