Bump pyarrow from 13.0.0 to 14.0.1 #501
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Jenkins - ci.inria.fr / Tests / Functional tests / GPU / Train tests Linux
failed
Nov 16, 2023 in 0s
failed: 9, passed: 2
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test_train_ae.test_train_ae[image_ae]
assert False
Stack trace
cmdopt = {'input': '/mnt/data/clinicadl_data_ci/data_ci'}
tmp_path = PosixPath('/local2/ci/tmp/test_train_ae_image_ae_0')
test_name = 'image_ae'
def test_train_ae(cmdopt, tmp_path, test_name):
base_dir = Path(cmdopt["input"])
input_dir = base_dir / "train" / "in"
ref_dir = base_dir / "train" / "ref"
tmp_out_dir = base_dir / "train" / "out"
# tmp_out_dir.mkdir(parents=True)
clean_folder(tmp_out_dir, recreate=True)
labels_path = str(input_dir / "labels_list" / "2_fold")
config_path = str(input_dir / "train_config.toml")
if test_name == "image_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_image"),
"t1-linear_crop-True_mode-image.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
"--split",
"1",
]
elif test_name == "patch_multi_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_patch"),
"t1-linear_crop-True_mode-patch.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
"--multi_network",
]
elif test_name == "roi_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_roi"),
"t1-linear_crop-True_mode-roi.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
]
elif test_name == "slice_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_slice"),
"t1-linear_crop-True_mode-slice.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
]
else:
raise NotImplementedError(f"Test {test_name} is not implemented.")
if tmp_out_dir.is_dir():
shutil.rmtree(tmp_out_dir)
flag_error = not os.system("clinicadl " + " ".join(test_input))
> assert flag_error
E assert False
test_train_ae.py:95: AssertionError
test_train_ae.test_train_ae[patch_multi_ae]
assert False
Stack trace
cmdopt = {'input': '/mnt/data/clinicadl_data_ci/data_ci'}
tmp_path = PosixPath('/local2/ci/tmp/test_train_ae_patch_multi_ae_0')
test_name = 'patch_multi_ae'
def test_train_ae(cmdopt, tmp_path, test_name):
base_dir = Path(cmdopt["input"])
input_dir = base_dir / "train" / "in"
ref_dir = base_dir / "train" / "ref"
tmp_out_dir = base_dir / "train" / "out"
# tmp_out_dir.mkdir(parents=True)
clean_folder(tmp_out_dir, recreate=True)
labels_path = str(input_dir / "labels_list" / "2_fold")
config_path = str(input_dir / "train_config.toml")
if test_name == "image_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_image"),
"t1-linear_crop-True_mode-image.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
"--split",
"1",
]
elif test_name == "patch_multi_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_patch"),
"t1-linear_crop-True_mode-patch.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
"--multi_network",
]
elif test_name == "roi_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_roi"),
"t1-linear_crop-True_mode-roi.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
]
elif test_name == "slice_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_slice"),
"t1-linear_crop-True_mode-slice.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
]
else:
raise NotImplementedError(f"Test {test_name} is not implemented.")
if tmp_out_dir.is_dir():
shutil.rmtree(tmp_out_dir)
flag_error = not os.system("clinicadl " + " ".join(test_input))
> assert flag_error
E assert False
test_train_ae.py:95: AssertionError
test_train_ae.test_train_ae[roi_ae]
assert False
Stack trace
cmdopt = {'input': '/mnt/data/clinicadl_data_ci/data_ci'}
tmp_path = PosixPath('/local2/ci/tmp/test_train_ae_roi_ae_0')
test_name = 'roi_ae'
def test_train_ae(cmdopt, tmp_path, test_name):
base_dir = Path(cmdopt["input"])
input_dir = base_dir / "train" / "in"
ref_dir = base_dir / "train" / "ref"
tmp_out_dir = base_dir / "train" / "out"
# tmp_out_dir.mkdir(parents=True)
clean_folder(tmp_out_dir, recreate=True)
labels_path = str(input_dir / "labels_list" / "2_fold")
config_path = str(input_dir / "train_config.toml")
if test_name == "image_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_image"),
"t1-linear_crop-True_mode-image.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
"--split",
"1",
]
elif test_name == "patch_multi_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_patch"),
"t1-linear_crop-True_mode-patch.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
"--multi_network",
]
elif test_name == "roi_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_roi"),
"t1-linear_crop-True_mode-roi.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
]
elif test_name == "slice_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_slice"),
"t1-linear_crop-True_mode-slice.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
]
else:
raise NotImplementedError(f"Test {test_name} is not implemented.")
if tmp_out_dir.is_dir():
shutil.rmtree(tmp_out_dir)
flag_error = not os.system("clinicadl " + " ".join(test_input))
> assert flag_error
E assert False
test_train_ae.py:95: AssertionError
test_train_ae.test_train_ae[slice_ae]
assert False
Stack trace
cmdopt = {'input': '/mnt/data/clinicadl_data_ci/data_ci'}
tmp_path = PosixPath('/local2/ci/tmp/test_train_ae_slice_ae_0')
test_name = 'slice_ae'
def test_train_ae(cmdopt, tmp_path, test_name):
base_dir = Path(cmdopt["input"])
input_dir = base_dir / "train" / "in"
ref_dir = base_dir / "train" / "ref"
tmp_out_dir = base_dir / "train" / "out"
# tmp_out_dir.mkdir(parents=True)
clean_folder(tmp_out_dir, recreate=True)
labels_path = str(input_dir / "labels_list" / "2_fold")
config_path = str(input_dir / "train_config.toml")
if test_name == "image_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_image"),
"t1-linear_crop-True_mode-image.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
"--split",
"1",
]
elif test_name == "patch_multi_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_patch"),
"t1-linear_crop-True_mode-patch.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
"--multi_network",
]
elif test_name == "roi_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_roi"),
"t1-linear_crop-True_mode-roi.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
]
elif test_name == "slice_ae":
split = [0, 0]
test_input = [
"train",
"reconstruction",
str(input_dir / "caps_slice"),
"t1-linear_crop-True_mode-slice.json",
labels_path,
str(tmp_out_dir),
"-c",
config_path,
]
else:
raise NotImplementedError(f"Test {test_name} is not implemented.")
if tmp_out_dir.is_dir():
shutil.rmtree(tmp_out_dir)
flag_error = not os.system("clinicadl " + " ".join(test_input))
> assert flag_error
E assert False
test_train_ae.py:95: AssertionError
test_train_cnn.test_train_cnn[slice_cnn]
assert False
Stack trace
cmdopt = {'input': '/mnt/data/clinicadl_data_ci/data_ci'}
tmp_path = PosixPath('/local2/ci/tmp/test_train_cnn_slice_cnn_0')
test_name = 'slice_cnn'
def test_train_cnn(cmdopt, tmp_path, test_name):
base_dir = Path(cmdopt["input"])
input_dir = base_dir / "train" / "in"
ref_dir = base_dir / "train" / "ref"
tmp_out_dir = tmp_path / "train" / "out"
tmp_out_dir.mkdir(parents=True)
labels_path = input_dir / "labels_list" / "2_fold"
config_path = input_dir / "train_config.toml"
split = "0"
if test_name == "slice_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_slice"),
"t1-linear_crop-True_mode-slice.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
]
elif test_name == "image_cnn":
split_ref = 1
test_input = [
"train",
"regression",
str(input_dir / "caps_image"),
"t1-linear_crop-True_mode-image.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
]
elif test_name == "patch_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_patch"),
"t1-linear_crop-True_mode-patch.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
"--split",
split,
]
elif test_name == "patch_multi_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_patch"),
"t1-linear_crop-True_mode-patch.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
"--multi_network",
]
elif test_name == "roi_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_roi"),
"t1-linear_crop-True_mode-roi.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
]
else:
raise NotImplementedError(f"Test {test_name} is not implemented.")
if tmp_out_dir.is_dir():
shutil.rmtree(tmp_out_dir)
flag_error = not os.system("clinicadl " + " ".join(test_input))
> assert flag_error
E assert False
test_train_cnn.py:108: AssertionError
test_train_cnn.test_train_cnn[image_cnn]
assert False
Stack trace
cmdopt = {'input': '/mnt/data/clinicadl_data_ci/data_ci'}
tmp_path = PosixPath('/local2/ci/tmp/test_train_cnn_image_cnn_0')
test_name = 'image_cnn'
def test_train_cnn(cmdopt, tmp_path, test_name):
base_dir = Path(cmdopt["input"])
input_dir = base_dir / "train" / "in"
ref_dir = base_dir / "train" / "ref"
tmp_out_dir = tmp_path / "train" / "out"
tmp_out_dir.mkdir(parents=True)
labels_path = input_dir / "labels_list" / "2_fold"
config_path = input_dir / "train_config.toml"
split = "0"
if test_name == "slice_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_slice"),
"t1-linear_crop-True_mode-slice.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
]
elif test_name == "image_cnn":
split_ref = 1
test_input = [
"train",
"regression",
str(input_dir / "caps_image"),
"t1-linear_crop-True_mode-image.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
]
elif test_name == "patch_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_patch"),
"t1-linear_crop-True_mode-patch.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
"--split",
split,
]
elif test_name == "patch_multi_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_patch"),
"t1-linear_crop-True_mode-patch.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
"--multi_network",
]
elif test_name == "roi_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_roi"),
"t1-linear_crop-True_mode-roi.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
]
else:
raise NotImplementedError(f"Test {test_name} is not implemented.")
if tmp_out_dir.is_dir():
shutil.rmtree(tmp_out_dir)
flag_error = not os.system("clinicadl " + " ".join(test_input))
> assert flag_error
E assert False
test_train_cnn.py:108: AssertionError
test_train_cnn.test_train_cnn[patch_cnn]
assert False
Stack trace
cmdopt = {'input': '/mnt/data/clinicadl_data_ci/data_ci'}
tmp_path = PosixPath('/local2/ci/tmp/test_train_cnn_patch_cnn_0')
test_name = 'patch_cnn'
def test_train_cnn(cmdopt, tmp_path, test_name):
base_dir = Path(cmdopt["input"])
input_dir = base_dir / "train" / "in"
ref_dir = base_dir / "train" / "ref"
tmp_out_dir = tmp_path / "train" / "out"
tmp_out_dir.mkdir(parents=True)
labels_path = input_dir / "labels_list" / "2_fold"
config_path = input_dir / "train_config.toml"
split = "0"
if test_name == "slice_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_slice"),
"t1-linear_crop-True_mode-slice.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
]
elif test_name == "image_cnn":
split_ref = 1
test_input = [
"train",
"regression",
str(input_dir / "caps_image"),
"t1-linear_crop-True_mode-image.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
]
elif test_name == "patch_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_patch"),
"t1-linear_crop-True_mode-patch.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
"--split",
split,
]
elif test_name == "patch_multi_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_patch"),
"t1-linear_crop-True_mode-patch.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
"--multi_network",
]
elif test_name == "roi_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_roi"),
"t1-linear_crop-True_mode-roi.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
]
else:
raise NotImplementedError(f"Test {test_name} is not implemented.")
if tmp_out_dir.is_dir():
shutil.rmtree(tmp_out_dir)
flag_error = not os.system("clinicadl " + " ".join(test_input))
> assert flag_error
E assert False
test_train_cnn.py:108: AssertionError
test_train_cnn.test_train_cnn[patch_multi_cnn]
assert False
Stack trace
cmdopt = {'input': '/mnt/data/clinicadl_data_ci/data_ci'}
tmp_path = PosixPath('/local2/ci/tmp/test_train_cnn_patch_multi_cnn0')
test_name = 'patch_multi_cnn'
def test_train_cnn(cmdopt, tmp_path, test_name):
base_dir = Path(cmdopt["input"])
input_dir = base_dir / "train" / "in"
ref_dir = base_dir / "train" / "ref"
tmp_out_dir = tmp_path / "train" / "out"
tmp_out_dir.mkdir(parents=True)
labels_path = input_dir / "labels_list" / "2_fold"
config_path = input_dir / "train_config.toml"
split = "0"
if test_name == "slice_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_slice"),
"t1-linear_crop-True_mode-slice.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
]
elif test_name == "image_cnn":
split_ref = 1
test_input = [
"train",
"regression",
str(input_dir / "caps_image"),
"t1-linear_crop-True_mode-image.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
]
elif test_name == "patch_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_patch"),
"t1-linear_crop-True_mode-patch.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
"--split",
split,
]
elif test_name == "patch_multi_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_patch"),
"t1-linear_crop-True_mode-patch.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
"--multi_network",
]
elif test_name == "roi_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_roi"),
"t1-linear_crop-True_mode-roi.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
]
else:
raise NotImplementedError(f"Test {test_name} is not implemented.")
if tmp_out_dir.is_dir():
shutil.rmtree(tmp_out_dir)
flag_error = not os.system("clinicadl " + " ".join(test_input))
> assert flag_error
E assert False
test_train_cnn.py:108: AssertionError
test_train_cnn.test_train_cnn[roi_cnn]
assert False
Stack trace
cmdopt = {'input': '/mnt/data/clinicadl_data_ci/data_ci'}
tmp_path = PosixPath('/local2/ci/tmp/test_train_cnn_roi_cnn_0')
test_name = 'roi_cnn'
def test_train_cnn(cmdopt, tmp_path, test_name):
base_dir = Path(cmdopt["input"])
input_dir = base_dir / "train" / "in"
ref_dir = base_dir / "train" / "ref"
tmp_out_dir = tmp_path / "train" / "out"
tmp_out_dir.mkdir(parents=True)
labels_path = input_dir / "labels_list" / "2_fold"
config_path = input_dir / "train_config.toml"
split = "0"
if test_name == "slice_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_slice"),
"t1-linear_crop-True_mode-slice.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
]
elif test_name == "image_cnn":
split_ref = 1
test_input = [
"train",
"regression",
str(input_dir / "caps_image"),
"t1-linear_crop-True_mode-image.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
]
elif test_name == "patch_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_patch"),
"t1-linear_crop-True_mode-patch.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
"--split",
split,
]
elif test_name == "patch_multi_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_patch"),
"t1-linear_crop-True_mode-patch.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
"--multi_network",
]
elif test_name == "roi_cnn":
split_ref = 0
test_input = [
"train",
"classification",
str(input_dir / "caps_roi"),
"t1-linear_crop-True_mode-roi.json",
str(labels_path),
str(tmp_out_dir),
"-c",
str(config_path),
]
else:
raise NotImplementedError(f"Test {test_name} is not implemented.")
if tmp_out_dir.is_dir():
shutil.rmtree(tmp_out_dir)
flag_error = not os.system("clinicadl " + " ".join(test_input))
> assert flag_error
E assert False
test_train_cnn.py:108: AssertionError
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