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FIX: Mark strings containing regex escapes as raw #3106

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Merged
merged 1 commit into from
Dec 12, 2019
Merged

FIX: Mark strings containing regex escapes as raw #3106

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8 changes: 4 additions & 4 deletions nipype/interfaces/diffusion_toolkit/odf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,11 +96,11 @@ class HARDIMat(CommandLine):

def _create_gradient_matrix(self, bvecs_file, bvals_file):
_gradient_matrix_file = "gradient_matrix.txt"
bvals = [val for val in re.split("\s+", open(bvals_file).readline().strip())]
bvals = [val for val in re.split(r"\s+", open(bvals_file).readline().strip())]
bvecs_f = open(bvecs_file)
bvecs_x = [val for val in re.split("\s+", bvecs_f.readline().strip())]
bvecs_y = [val for val in re.split("\s+", bvecs_f.readline().strip())]
bvecs_z = [val for val in re.split("\s+", bvecs_f.readline().strip())]
bvecs_x = [val for val in re.split(r"\s+", bvecs_f.readline().strip())]
bvecs_y = [val for val in re.split(r"\s+", bvecs_f.readline().strip())]
bvecs_z = [val for val in re.split(r"\s+", bvecs_f.readline().strip())]
bvecs_f.close()
gradient_matrix_f = open(_gradient_matrix_file, "w")
for i in range(len(bvals)):
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4 changes: 2 additions & 2 deletions nipype/interfaces/dipy/base.py
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Expand Up @@ -158,7 +158,7 @@ def create_interface_specs(class_name, params=None, BaseClass=TraitedSpec):
attr[name] = traits_type(desc=desc[-1], mandatory=is_mandatory)
else:
attr[name] = traits_type(
p[3], desc=desc[-1], exists=True, usedefault=True,
p[3], desc=desc[-1], exists=True, usedefault=True
)

newclass = type(str(class_name), (BaseClass,), attr)
Expand Down Expand Up @@ -189,7 +189,7 @@ def dipy_to_nipype_interface(cls_name, dipy_flow, BaseClass=DipyBaseInterface):
parser = IntrospectiveArgumentParser()
flow = dipy_flow()
parser.add_workflow(flow)
default_values = inspect.getargspec(flow.run).defaults
default_values = inspect.getfullargspec(flow.run).defaults
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Guess I fixed another deprecation warning. This works for all Py3.

optional_params = [
args + (val,) for args, val in zip(parser.optional_parameters, default_values)
]
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16 changes: 8 additions & 8 deletions nipype/interfaces/elastix/utils.py
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Expand Up @@ -85,7 +85,7 @@ class EditTransform(BaseInterface):
input_spec = EditTransformInputSpec
output_spec = EditTransformOutputSpec
_out_file = ""
_pattern = '\((?P<entry>%s\s"?)([-\.\s\w]+)("?\))'
_pattern = r'\((?P<entry>%s\s"?)([-\.\s\w]+)("?\))'

_interp = {"nearest": 0, "linear": 1, "cubic": 3}

Expand All @@ -103,14 +103,14 @@ def _run_interface(self, runtime):
p = re.compile(
(self._pattern % "ResultImagePixelType").decode("string-escape")
)
rep = "(\g<entry>%s\g<3>" % self.inputs.output_type
rep = r"(\g<entry>%s\g<3>" % self.inputs.output_type
contents = p.sub(rep, contents)

if isdefined(self.inputs.output_format):
p = re.compile(
(self._pattern % "ResultImageFormat").decode("string-escape")
)
rep = "(\g<entry>%s\g<3>" % self.inputs.output_format
rep = r"(\g<entry>%s\g<3>" % self.inputs.output_format
contents = p.sub(rep, contents)

if isdefined(self.inputs.interpolation):
Expand All @@ -119,7 +119,7 @@ def _run_interface(self, runtime):
"string-escape"
)
)
rep = "(\g<entry>%s\g<3>" % self._interp[self.inputs.interpolation]
rep = r"(\g<entry>%s\g<3>" % self._interp[self.inputs.interpolation]
contents = p.sub(rep, contents)

if isdefined(self.inputs.reference_image):
Expand All @@ -130,17 +130,17 @@ def _run_interface(self, runtime):

size = " ".join(["%01d" % s for s in im.shape])
p = re.compile((self._pattern % "Size").decode("string-escape"))
rep = "(\g<entry>%s\g<3>" % size
rep = r"(\g<entry>%s\g<3>" % size
contents = p.sub(rep, contents)

index = " ".join(["0" for s in im.shape])
p = re.compile((self._pattern % "Index").decode("string-escape"))
rep = "(\g<entry>%s\g<3>" % index
rep = r"(\g<entry>%s\g<3>" % index
contents = p.sub(rep, contents)

spacing = " ".join(["%0.4f" % f for f in im.header.get_zooms()])
p = re.compile((self._pattern % "Spacing").decode("string-escape"))
rep = "(\g<entry>%s\g<3>" % spacing
rep = r"(\g<entry>%s\g<3>" % spacing
contents = p.sub(rep, contents)

itkmat = np.eye(4)
Expand All @@ -156,7 +156,7 @@ def _run_interface(self, runtime):
# contents = p.sub(rep, contents)

p = re.compile((self._pattern % "Origin").decode("string-escape"))
rep = "(\g<entry>%s\g<3>" % orig
rep = r"(\g<entry>%s\g<3>" % orig
contents = p.sub(rep, contents)

with open(self._get_outfile(), "w") as of:
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6 changes: 3 additions & 3 deletions nipype/interfaces/freesurfer/utils.py
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Expand Up @@ -1017,7 +1017,7 @@ def _format_arg(self, name, spec, value):
# extension strings
if value.endswith(".annot"):
value = value[:-6]
if re.match("%s[\.\-_]" % self.inputs.hemi, value[:3]):
if re.match(r"%s[\.\-_]" % self.inputs.hemi, value[:3]):
value = value[3:]
return "-annotation %s" % value
return super(SurfaceSnapshots, self)._format_arg(name, spec, value)
Expand Down Expand Up @@ -1145,7 +1145,7 @@ class ImageInfo(FSCommand):
output_spec = ImageInfoOutputSpec

def info_regexp(self, info, field, delim="\n"):
m = re.search("%s\s*:\s+(.+?)%s" % (field, delim), info)
m = re.search(r"%s\s*:\s+(.+?)%s" % (field, delim), info)
if m:
return m.group(1)
else:
Expand Down Expand Up @@ -1175,7 +1175,7 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
outputs.ph_enc_dir = self.info_regexp(info, "PhEncDir")

# File format and datatype are both keyed by "type"
ftype, dtype = re.findall("%s\s*:\s+(.+?)\n" % "type", info)
ftype, dtype = re.findall(r"%s\s*:\s+(.+?)\n" % "type", info)
outputs.file_format = ftype
outputs.data_type = dtype

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9 changes: 5 additions & 4 deletions nipype/interfaces/spm/model.py
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Expand Up @@ -474,15 +474,16 @@ def _make_matlab_command(self, _):
script += "condnames=names;\n"
else:
if self.inputs.use_derivs:
script += "pat = 'Sn\([0-9]*\) (.*)';\n"
script += r"pat = 'Sn\([0-9]*\) (.*)';" "\n"
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Hopefully we test these. I'm less comfortable with these, since they need to work when written to MATLAB scripts.

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as long as we are still running the spm workflows.

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Codecov doesn't seem to hit them.

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I've tested:

>>> a = ""
>>> a += r"\s+" "\nnextline"                                                                   
>>> print(a)                                                                                   
\s+
nextline

So rawstring/string concatenation works fine, and the += is lower precedence, so I'm reasonably confident in this change.

Merging.

else:
script += (
"pat = 'Sn\([0-9]*\) (.*)\*bf\(1\)|Sn\([0-9]*\) "
".*\*bf\([2-9]\)|Sn\([0-9]*\) (.*)';\n"
r"pat = 'Sn\([0-9]*\) (.*)\*bf\(1\)|Sn\([0-9]*\) "
r".*\*bf\([2-9]\)|Sn\([0-9]*\) (.*)';"
"\n"
)
script += "t = regexp(names,pat,'tokens');\n"
# get sessidx for columns
script += "pat1 = 'Sn\(([0-9].*)\)\s.*';\n"
script += r"pat1 = 'Sn\(([0-9].*)\)\s.*';" "\n"
script += "t1 = regexp(names,pat1,'tokens');\n"
script += (
"for i0=1:numel(t),condnames{i0}='';condsess(i0)=0;if "
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4 changes: 2 additions & 2 deletions nipype/pipeline/plugins/tests/test_tools.py
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Expand Up @@ -21,12 +21,12 @@ def test_report_crash():
mock_node = mock.MagicMock(name="mock_node")
mock_node._id = "an_id"
mock_node.config = {
"execution": {"crashdump_dir": ".", "crashfile_format": "pklz",}
"execution": {"crashdump_dir": ".", "crashfile_format": "pklz"}
}

actual_crashfile = report_crash(mock_node)

expected_crashfile = re.compile(".*/crash-.*-an_id-[0-9a-f\-]*.pklz")
expected_crashfile = re.compile(r".*/crash-.*-an_id-[0-9a-f\-]*.pklz")

assert (
expected_crashfile.match(actual_crashfile).group() == actual_crashfile
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2 changes: 1 addition & 1 deletion nipype/sphinxext/plot_workflow.py
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Expand Up @@ -314,7 +314,7 @@ def remove_coding(text):
"""
Remove the coding comment, which exec doesn't like.
"""
sub_re = re.compile("^#\s*-\*-\s*coding:\s*.*-\*-$", flags=re.MULTILINE)
sub_re = re.compile(r"^#\s*-\*-\s*coding:\s*.*-\*-$", flags=re.MULTILINE)
return sub_re.sub("", text)


Expand Down