refractoring

Author: GalKepler

doc/devel/matlab_example1.py

@@ -1,13 +1,17 @@
 from nipype.interfaces.matlab import MatlabCommand
-from nipype.interfaces.base import TraitedSpec, \
-    BaseInterface, BaseInterfaceInputSpec, File
+from nipype.interfaces.base import (
+    TraitedSpec,
+    BaseInterface,
+    BaseInterfaceInputSpec,
+    File,
+)
 import os
 from string import Template
 
 
 class ConmapTxt2MatInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True)
-    out_file = File('cmatrix.mat', usedefault=True)
+    out_file = File("cmatrix.mat", usedefault=True)
 
 
 class ConmapTxt2MatOutputSpec(TraitedSpec):
@@ -19,14 +23,15 @@ class ConmapTxt2Mat(BaseInterface):
     output_spec = ConmapTxt2MatOutputSpec
 
     def _run_interface(self, runtime):
-        d = dict(in_file=self.inputs.in_file,
-                 out_file=self.inputs.out_file)
+        d = dict(in_file=self.inputs.in_file, out_file=self.inputs.out_file)
         # This is your MATLAB code template
-        script = Template("""in_file = '$in_file';
+        script = Template(
+            """in_file = '$in_file';
                              out_file = '$out_file';
                              ConmapTxt2Mat(in_file, out_file);
                              exit;
-                          """).substitute(d)
+                          """
+        ).substitute(d)
 
         # mfile = True  will create an .m file with your script and executed.
         # Alternatively
@@ -43,5 +48,5 @@ def _run_interface(self, runtime):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        outputs['out_file'] = os.path.abspath(self.inputs.out_file)
+        outputs["out_file"] = os.path.abspath(self.inputs.out_file)
         return outputs

doc/devel/matlab_example2.py

@@ -4,8 +4,7 @@
 
 
 class HelloWorldInputSpec(MatlabInputSpec):
-    name = traits.Str(mandatory=True,
-                      desc='Name of person to say hello to')
+    name = traits.Str(mandatory=True, desc="Name of person to say hello to")
 
 
 class HelloWorldOutputSpec(TraitedSpec):
@@ -29,6 +28,7 @@ class HelloWorld(MatlabCommand):
     >>> out = hello.run()
     >>> print out.outputs.matlab_output
     """
+
     input_spec = HelloWorldInputSpec
     output_spec = HelloWorldOutputSpec
 
@@ -37,7 +37,9 @@ def _my_script(self):
         script = """
         disp('Hello %s Python')
         two = 1 + 1
-        """ % (self.inputs.name)
+        """ % (
+            self.inputs.name
+        )
         return script
 
     def run(self, **inputs):

nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py

@@ -44,6 +44,16 @@ def test_MRConvert_inputs():
             mandatory=True,
             position=-2,
         ),
+        json_export=dict(
+            argstr="-json_export %s",
+            extensions=None,
+            mandatory=False,
+        ),
+        json_import=dict(
+            argstr="-json_import %s",
+            extensions=None,
+            mandatory=False,
+        ),
         nthreads=dict(
             argstr="-nthreads %d",
             nohash=True,
@@ -73,6 +83,9 @@ def test_MRConvert_inputs():
 
 def test_MRConvert_outputs():
     output_map = dict(
+        json_export=dict(
+            extensions=None,
+        ),
         out_file=dict(
             extensions=None,
         ),

nipype/interfaces/mrtrix3/utils.py

@@ -678,6 +678,7 @@ class MRConvert(MRTrix3Base):
     def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs["out_file"] = op.abspath(self.inputs.out_file)
+        outputs["json_export"] = op.abspath(self.inputs.json_export)
         return outputs
 
 

tools/checkspecs.py

@@ -13,8 +13,7 @@
 
 # Functions and classes
 class InterfaceChecker(object):
-    """Class for checking all interface specifications
-    """
+    """Class for checking all interface specifications"""
 
     def __init__(
         self,
@@ -23,7 +22,7 @@ def __init__(
         module_skip_patterns=None,
         class_skip_patterns=None,
     ):
-        r""" Initialize package for parsing
+        r"""Initialize package for parsing
 
         Parameters
         ----------
@@ -113,14 +112,14 @@ def _uri2path(self, uri):
         return path
 
     def _path2uri(self, dirpath):
-        """ Convert directory path to uri """
+        """Convert directory path to uri"""
         relpath = dirpath.replace(self.root_path, self.package_name)
         if relpath.startswith(os.path.sep):
             relpath = relpath[1:]
         return relpath.replace(os.path.sep, ".")
 
     def _parse_module(self, uri):
-        """ Parse module defined in *uri* """
+        """Parse module defined in *uri*"""
         filename = self._uri2path(uri)
         if filename is None:
             # nothing that we could handle here.
@@ -131,7 +130,7 @@ def _parse_module(self, uri):
         return functions, classes
 
     def _parse_lines(self, linesource, module):
-        """ Parse lines of text for functions and classes """
+        """Parse lines of text for functions and classes"""
         functions = []
         classes = []
         for line in linesource:
@@ -387,7 +386,7 @@ def test_specs(self, uri):
         return bad_specs
 
     def _survives_exclude(self, matchstr, match_type):
-        """ Returns True if *matchstr* does not match patterns
+        """Returns True if *matchstr* does not match patterns
 
         ``self.package_name`` removed from front of string if present
 
@@ -429,7 +428,7 @@ def _survives_exclude(self, matchstr, match_type):
         return True
 
     def discover_modules(self):
-        """ Return module sequence discovered from ``self.package_name``
+        """Return module sequence discovered from ``self.package_name``
 
 
         Parameters

tools/gitwash_dumper.py

@@ -50,9 +50,7 @@ def cp_files(in_path, globs, out_path):
 
 
 def filename_search_replace(sr_pairs, filename, backup=False):
-    """ Search and replace for expressions in files
-
-    """
+    """Search and replace for expressions in files"""
     in_txt = open(filename, "rt").read(-1)
     out_txt = in_txt[:]
     for in_exp, out_exp in sr_pairs:
@@ -94,7 +92,7 @@ def make_link_targets(
     url=None,
     ml_url=None,
 ):
-    """ Check and make link targets
+    """Check and make link targets
 
     If url is None or ml_url is None, check if there are links present for
     these in `known_link_fname`.  If not, raise error.  The check is:

tools/run_examples.py

@@ -4,9 +4,15 @@
 
 
 if __name__ == "__main__":
-    print(dedent("""Nipype examples have been moved to niflow-nipype1-examples.
+    print(
+        dedent(
+            """Nipype examples have been moved to niflow-nipype1-examples.
 
-Install with: pip install niflow-nipype1-examples"""))
+Install with: pip install niflow-nipype1-examples"""
+        )
+    )
     if sys.argv[1:]:
-        print("Run this command with: niflow-nipype1-examples " + " ".join(sys.argv[1:]))
+        print(
+            "Run this command with: niflow-nipype1-examples " + " ".join(sys.argv[1:])
+        )
     sys.exit(1)

tools/toollib.py

@@ -31,7 +31,9 @@ def sh(cmd):
 def compile_tree():
     """Compile all Python files below current directory."""
     vstr = ".".join(map(str, sys.version_info[:2]))
-    stat = os.system("%s %s/lib/python%s/compileall.py ." % (sys.executable, sys.prefix, vstr))
+    stat = os.system(
+        "%s %s/lib/python%s/compileall.py ." % (sys.executable, sys.prefix, vstr)
+    )
     if stat:
         msg = "*** ERROR: Some Python files in tree do NOT compile! ***\n"
         msg += "See messages above for the actual file that produced it.\n"