Overhaul PyDesigner Code 2 #52
7 fail, 119 pass in 12s
Annotations
Check warning on line 0 in tests.test_preprocessing_mrpreproc
github-actions / Test Results
test_degibbs_output_failure (tests.test_preprocessing_mrpreproc) failed
test_results/results.xml [took 0s]
Raw output
pydesigner.system.errors.FileExtensionError: Input file (/src/tests/data/hifi/hifi_splenium_4vox.nii) does not posses the required .mif extension.
tmp_path = PosixPath('/tmp/pytest-of-root/pytest-0/test_degibbs_output_failure0')
def test_degibbs_output_failure(tmp_path):
"""Test whether function `degibbs` fails when return code is non-zero"""
output_nii = str(tmp_path / "output.nii")
with patch("subprocess.run") as mock_subprocess:
mock_subprocess.return_value = MagicMock(
returncode=1, stderr="stderr"
)
with pytest.raises(MRTrixError) as exc:
> mrpreproc.degibbs(PATH_DWI, output_nii)
tests/test_preprocessing_mrpreproc.py:207:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pydesigner/preprocessing/mrpreproc.py:272: in degibbs
input=input_path_validator(input, ".mif"),
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
path = '/src/tests/data/hifi/hifi_splenium_4vox.nii', ctype = '.mif'
def input_path_validator(path: str, ctype: str = None):
"""Validates a provided input path
Parameters
----------
path : str
Path to input file
ctype : str
File extension to enfore on input path
Returns
-------
str
Sanitized path
See Also
--------
output_path_validator
"""
opts = modelmrtrix(input=path)
if ctype is not None:
if not isinstance(ctype, str):
msg = f"ctype variable (ctype={ctype}) needs to be a valid string."
raise (TypeError(msg))
if ctype:
if op.splitext(op.basename(opts.input))[-1] != ctype:
msg = f"Input file ({path}) does not posses the required {ctype} extension."
> raise FileExtensionError(msg)
E pydesigner.system.errors.FileExtensionError: Input file (/src/tests/data/hifi/hifi_splenium_4vox.nii) does not posses the required .mif extension.
pydesigner/system/models.py:93: FileExtensionError
Check warning on line 0 in tests.test_preprocessing_mrpreproc
github-actions / Test Results
test_degibbs_output_success[None-None-None] (tests.test_preprocessing_mrpreproc) failed
test_results/results.xml [took 0s]
Raw output
pydesigner.system.errors.FileExtensionError: Input file (/src/tests/data/hifi/hifi_splenium_4vox.nii) does not posses the required .mif extension.
tmp_path = PosixPath('/tmp/pytest-of-root/pytest-0/test_degibbs_output_success_No0')
nthreads = None, force = None, verbose = None
@pytest.mark.parametrize(
"nthreads, force, verbose",
[
(None, None, None),
(1, None, None),
(None, True, None),
(None, False, None),
(None, None, True),
(None, None, False),
]
)
def test_degibbs_output_success(tmp_path, nthreads, force, verbose):
"""Test whether function `degibbs` fails when return code is non-zero"""
output_mif = str(tmp_path / "output.mif")
> mrpreproc.degibbs(PATH_DWI, output_mif, nthreads=nthreads, force=force, verbose=verbose)
tests/test_preprocessing_mrpreproc.py:225:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pydesigner/preprocessing/mrpreproc.py:272: in degibbs
input=input_path_validator(input, ".mif"),
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
path = '/src/tests/data/hifi/hifi_splenium_4vox.nii', ctype = '.mif'
def input_path_validator(path: str, ctype: str = None):
"""Validates a provided input path
Parameters
----------
path : str
Path to input file
ctype : str
File extension to enfore on input path
Returns
-------
str
Sanitized path
See Also
--------
output_path_validator
"""
opts = modelmrtrix(input=path)
if ctype is not None:
if not isinstance(ctype, str):
msg = f"ctype variable (ctype={ctype}) needs to be a valid string."
raise (TypeError(msg))
if ctype:
if op.splitext(op.basename(opts.input))[-1] != ctype:
msg = f"Input file ({path}) does not posses the required {ctype} extension."
> raise FileExtensionError(msg)
E pydesigner.system.errors.FileExtensionError: Input file (/src/tests/data/hifi/hifi_splenium_4vox.nii) does not posses the required .mif extension.
pydesigner/system/models.py:93: FileExtensionError
Check warning on line 0 in tests.test_preprocessing_mrpreproc
github-actions / Test Results
test_degibbs_output_success[1-None-None] (tests.test_preprocessing_mrpreproc) failed
test_results/results.xml [took 0s]
Raw output
pydesigner.system.errors.FileExtensionError: Input file (/src/tests/data/hifi/hifi_splenium_4vox.nii) does not posses the required .mif extension.
tmp_path = PosixPath('/tmp/pytest-of-root/pytest-0/test_degibbs_output_success_1_0')
nthreads = 1, force = None, verbose = None
@pytest.mark.parametrize(
"nthreads, force, verbose",
[
(None, None, None),
(1, None, None),
(None, True, None),
(None, False, None),
(None, None, True),
(None, None, False),
]
)
def test_degibbs_output_success(tmp_path, nthreads, force, verbose):
"""Test whether function `degibbs` fails when return code is non-zero"""
output_mif = str(tmp_path / "output.mif")
> mrpreproc.degibbs(PATH_DWI, output_mif, nthreads=nthreads, force=force, verbose=verbose)
tests/test_preprocessing_mrpreproc.py:225:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pydesigner/preprocessing/mrpreproc.py:272: in degibbs
input=input_path_validator(input, ".mif"),
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
path = '/src/tests/data/hifi/hifi_splenium_4vox.nii', ctype = '.mif'
def input_path_validator(path: str, ctype: str = None):
"""Validates a provided input path
Parameters
----------
path : str
Path to input file
ctype : str
File extension to enfore on input path
Returns
-------
str
Sanitized path
See Also
--------
output_path_validator
"""
opts = modelmrtrix(input=path)
if ctype is not None:
if not isinstance(ctype, str):
msg = f"ctype variable (ctype={ctype}) needs to be a valid string."
raise (TypeError(msg))
if ctype:
if op.splitext(op.basename(opts.input))[-1] != ctype:
msg = f"Input file ({path}) does not posses the required {ctype} extension."
> raise FileExtensionError(msg)
E pydesigner.system.errors.FileExtensionError: Input file (/src/tests/data/hifi/hifi_splenium_4vox.nii) does not posses the required .mif extension.
pydesigner/system/models.py:93: FileExtensionError
Check warning on line 0 in tests.test_preprocessing_mrpreproc
github-actions / Test Results
test_degibbs_output_success[None-True-None] (tests.test_preprocessing_mrpreproc) failed
test_results/results.xml [took 0s]
Raw output
pydesigner.system.errors.FileExtensionError: Input file (/src/tests/data/hifi/hifi_splenium_4vox.nii) does not posses the required .mif extension.
tmp_path = PosixPath('/tmp/pytest-of-root/pytest-0/test_degibbs_output_success_No1')
nthreads = None, force = True, verbose = None
@pytest.mark.parametrize(
"nthreads, force, verbose",
[
(None, None, None),
(1, None, None),
(None, True, None),
(None, False, None),
(None, None, True),
(None, None, False),
]
)
def test_degibbs_output_success(tmp_path, nthreads, force, verbose):
"""Test whether function `degibbs` fails when return code is non-zero"""
output_mif = str(tmp_path / "output.mif")
> mrpreproc.degibbs(PATH_DWI, output_mif, nthreads=nthreads, force=force, verbose=verbose)
tests/test_preprocessing_mrpreproc.py:225:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pydesigner/preprocessing/mrpreproc.py:272: in degibbs
input=input_path_validator(input, ".mif"),
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
path = '/src/tests/data/hifi/hifi_splenium_4vox.nii', ctype = '.mif'
def input_path_validator(path: str, ctype: str = None):
"""Validates a provided input path
Parameters
----------
path : str
Path to input file
ctype : str
File extension to enfore on input path
Returns
-------
str
Sanitized path
See Also
--------
output_path_validator
"""
opts = modelmrtrix(input=path)
if ctype is not None:
if not isinstance(ctype, str):
msg = f"ctype variable (ctype={ctype}) needs to be a valid string."
raise (TypeError(msg))
if ctype:
if op.splitext(op.basename(opts.input))[-1] != ctype:
msg = f"Input file ({path}) does not posses the required {ctype} extension."
> raise FileExtensionError(msg)
E pydesigner.system.errors.FileExtensionError: Input file (/src/tests/data/hifi/hifi_splenium_4vox.nii) does not posses the required .mif extension.
pydesigner/system/models.py:93: FileExtensionError
Check warning on line 0 in tests.test_preprocessing_mrpreproc
github-actions / Test Results
test_degibbs_output_success[None-False-None] (tests.test_preprocessing_mrpreproc) failed
test_results/results.xml [took 0s]
Raw output
pydesigner.system.errors.FileExtensionError: Input file (/src/tests/data/hifi/hifi_splenium_4vox.nii) does not posses the required .mif extension.
tmp_path = PosixPath('/tmp/pytest-of-root/pytest-0/test_degibbs_output_success_No2')
nthreads = None, force = False, verbose = None
@pytest.mark.parametrize(
"nthreads, force, verbose",
[
(None, None, None),
(1, None, None),
(None, True, None),
(None, False, None),
(None, None, True),
(None, None, False),
]
)
def test_degibbs_output_success(tmp_path, nthreads, force, verbose):
"""Test whether function `degibbs` fails when return code is non-zero"""
output_mif = str(tmp_path / "output.mif")
> mrpreproc.degibbs(PATH_DWI, output_mif, nthreads=nthreads, force=force, verbose=verbose)
tests/test_preprocessing_mrpreproc.py:225:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pydesigner/preprocessing/mrpreproc.py:272: in degibbs
input=input_path_validator(input, ".mif"),
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
path = '/src/tests/data/hifi/hifi_splenium_4vox.nii', ctype = '.mif'
def input_path_validator(path: str, ctype: str = None):
"""Validates a provided input path
Parameters
----------
path : str
Path to input file
ctype : str
File extension to enfore on input path
Returns
-------
str
Sanitized path
See Also
--------
output_path_validator
"""
opts = modelmrtrix(input=path)
if ctype is not None:
if not isinstance(ctype, str):
msg = f"ctype variable (ctype={ctype}) needs to be a valid string."
raise (TypeError(msg))
if ctype:
if op.splitext(op.basename(opts.input))[-1] != ctype:
msg = f"Input file ({path}) does not posses the required {ctype} extension."
> raise FileExtensionError(msg)
E pydesigner.system.errors.FileExtensionError: Input file (/src/tests/data/hifi/hifi_splenium_4vox.nii) does not posses the required .mif extension.
pydesigner/system/models.py:93: FileExtensionError
Check warning on line 0 in tests.test_preprocessing_mrpreproc
github-actions / Test Results
test_degibbs_output_success[None-None-True] (tests.test_preprocessing_mrpreproc) failed
test_results/results.xml [took 0s]
Raw output
pydesigner.system.errors.FileExtensionError: Input file (/src/tests/data/hifi/hifi_splenium_4vox.nii) does not posses the required .mif extension.
tmp_path = PosixPath('/tmp/pytest-of-root/pytest-0/test_degibbs_output_success_No3')
nthreads = None, force = None, verbose = True
@pytest.mark.parametrize(
"nthreads, force, verbose",
[
(None, None, None),
(1, None, None),
(None, True, None),
(None, False, None),
(None, None, True),
(None, None, False),
]
)
def test_degibbs_output_success(tmp_path, nthreads, force, verbose):
"""Test whether function `degibbs` fails when return code is non-zero"""
output_mif = str(tmp_path / "output.mif")
> mrpreproc.degibbs(PATH_DWI, output_mif, nthreads=nthreads, force=force, verbose=verbose)
tests/test_preprocessing_mrpreproc.py:225:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pydesigner/preprocessing/mrpreproc.py:272: in degibbs
input=input_path_validator(input, ".mif"),
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
path = '/src/tests/data/hifi/hifi_splenium_4vox.nii', ctype = '.mif'
def input_path_validator(path: str, ctype: str = None):
"""Validates a provided input path
Parameters
----------
path : str
Path to input file
ctype : str
File extension to enfore on input path
Returns
-------
str
Sanitized path
See Also
--------
output_path_validator
"""
opts = modelmrtrix(input=path)
if ctype is not None:
if not isinstance(ctype, str):
msg = f"ctype variable (ctype={ctype}) needs to be a valid string."
raise (TypeError(msg))
if ctype:
if op.splitext(op.basename(opts.input))[-1] != ctype:
msg = f"Input file ({path}) does not posses the required {ctype} extension."
> raise FileExtensionError(msg)
E pydesigner.system.errors.FileExtensionError: Input file (/src/tests/data/hifi/hifi_splenium_4vox.nii) does not posses the required .mif extension.
pydesigner/system/models.py:93: FileExtensionError
Check warning on line 0 in tests.test_preprocessing_mrpreproc
github-actions / Test Results
test_degibbs_output_success[None-None-False] (tests.test_preprocessing_mrpreproc) failed
test_results/results.xml [took 0s]
Raw output
pydesigner.system.errors.FileExtensionError: Input file (/src/tests/data/hifi/hifi_splenium_4vox.nii) does not posses the required .mif extension.
tmp_path = PosixPath('/tmp/pytest-of-root/pytest-0/test_degibbs_output_success_No4')
nthreads = None, force = None, verbose = False
@pytest.mark.parametrize(
"nthreads, force, verbose",
[
(None, None, None),
(1, None, None),
(None, True, None),
(None, False, None),
(None, None, True),
(None, None, False),
]
)
def test_degibbs_output_success(tmp_path, nthreads, force, verbose):
"""Test whether function `degibbs` fails when return code is non-zero"""
output_mif = str(tmp_path / "output.mif")
> mrpreproc.degibbs(PATH_DWI, output_mif, nthreads=nthreads, force=force, verbose=verbose)
tests/test_preprocessing_mrpreproc.py:225:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pydesigner/preprocessing/mrpreproc.py:272: in degibbs
input=input_path_validator(input, ".mif"),
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
path = '/src/tests/data/hifi/hifi_splenium_4vox.nii', ctype = '.mif'
def input_path_validator(path: str, ctype: str = None):
"""Validates a provided input path
Parameters
----------
path : str
Path to input file
ctype : str
File extension to enfore on input path
Returns
-------
str
Sanitized path
See Also
--------
output_path_validator
"""
opts = modelmrtrix(input=path)
if ctype is not None:
if not isinstance(ctype, str):
msg = f"ctype variable (ctype={ctype}) needs to be a valid string."
raise (TypeError(msg))
if ctype:
if op.splitext(op.basename(opts.input))[-1] != ctype:
msg = f"Input file ({path}) does not posses the required {ctype} extension."
> raise FileExtensionError(msg)
E pydesigner.system.errors.FileExtensionError: Input file (/src/tests/data/hifi/hifi_splenium_4vox.nii) does not posses the required .mif extension.
pydesigner/system/models.py:93: FileExtensionError