🚨 Add \ # pylint: disable\ comments to \ # noqa:\s

[skip ci]

Author: shnizzedy

CPAC/cwas/tests/test_cwas.py

@@ -78,7 +78,8 @@ def run_cwas(self):
 
         # Read in list of subject functionals
         subjects_list = [
-            l.strip().strip('"') for l in open(sfile).readlines()  # noqa: E741
+            l.strip().strip('"') for  # noqa: E741
+            l in open(sfile).readlines()  # pylint: disable=consider-using-with
         ]
 
         # Read in design/regressor file
@@ -93,7 +94,7 @@ def run_cwas(self):
         c.inputs.inputspec.f_samples = nperms
         c.inputs.inputspec.parallel_nodes = 4
         # c.base_dir = op.join(obase, 'results_fs%i_pn%i' % \
-        #                (c.inputs.inputspec.f_samples, c.inputs.inputspec.parallel_nodes))  # noqa: E501
+        #                (c.inputs.inputspec.f_samples, c.inputs.inputspec.parallel_nodes))  # noqa: E501  # pylint: disable=line-too-long
         c.base_dir = op.join(self.base, "results_%s.py" % self.name)
 
         # export MKL_NUM_THREADS=X # in command line

CPAC/seg_preproc/seg_preproc.py

@@ -136,7 +136,8 @@ def process_segment_map(wf_name, use_priors, use_custom_threshold, reg_tool):
         :width: 1100
         :height: 480
 
-    """  # noqa:
+    """
+    # pylint: disable=import-outside-toplevel,redefined-outer-name,reimported
     import nipype.interfaces.utility as util
 
     preproc = pe.Workflow(name=wf_name)
@@ -457,7 +458,7 @@ def create_seg_preproc_freesurfer(config=None,
 
         outputspec.wm_mask : string (nifti file)
             outputs White Matter mask
-    """  # noqa:
+    """
     preproc = pe.Workflow(name=wf_name)
 
     inputnode = pe.Node(util.IdentityInterface(fields=['subject_dir']),

CPAC/seg_preproc/utils.py

@@ -46,7 +46,7 @@ def pick_wm_prob_0(probability_maps):
 
     file : string
         Path to segment_prob_0.nii.gz is returned
-    """  # noqa:
+    """
     if isinstance(probability_maps, list):
         if len(probability_maps) == 1:
             probability_maps = probability_maps[0]
@@ -70,7 +70,7 @@ def pick_wm_prob_1(probability_maps):
 
     file : string
         Path to segment_prob_1.nii.gz is returned
-    """  # noqa:
+    """
     if isinstance(probability_maps, list):
         if len(probability_maps) == 1:
             probability_maps = probability_maps[0]
@@ -94,7 +94,7 @@ def pick_wm_prob_2(probability_maps):
 
     file : string
         Path to segment_prob_2.nii.gz is returned
-    """  # noqa:
+    """
     if isinstance(probability_maps, list):
         if len(probability_maps) == 1:
             probability_maps = probability_maps[0]
@@ -118,7 +118,7 @@ def pick_wm_class_0(tissue_class_files):
 
     file : string
         Path to segment_seg_0.nii.gz is returned
-    """  # noqa:
+    """
     if isinstance(tissue_class_files, list):
         if len(tissue_class_files) == 1:
             tissue_class_files = tissue_class_files[0]
@@ -142,7 +142,7 @@ def pick_wm_class_1(tissue_class_files):
 
     file : string
         Path to segment_seg_1.nii.gz is returned
-    """  # noqa:
+    """
     if isinstance(tissue_class_files, list):
         if len(tissue_class_files) == 1:
             tissue_class_files = tissue_class_files[0]
@@ -166,7 +166,7 @@ def pick_wm_class_2(tissue_class_files):
 
     file : string
         Path to segment_seg_2.nii.gz is returned
-    """  # noqa:
+    """
     if isinstance(tissue_class_files, list):
         if len(tissue_class_files) == 1:
             tissue_class_files = tissue_class_files[0]
@@ -363,11 +363,15 @@ def hardcoded_antsJointLabelFusion(anatomical_brain, anatomical_brain_mask,
     bash_cmd = str.join(cmd)
 
     try:
-        retcode = subprocess.check_output(bash_cmd, shell=True)  # noqa: F841
-    except Exception as e:
+        retcode = subprocess.check_output(bash_cmd, shell=True) \
+            # noqa: F841  # pylint: disable=unused-variable
+    except Exception as e:  # pylint: disable=broad-except,invalid-name
+        # pylint: disable=raise-missing-from
         raise Exception('[!] antsJointLabel segmentation method did not '
                         'complete successfully.\n\nError '
-                        'details:\n{0}\n{1}\n'.format(e, e.output))
+                        'details:\n{0}\n{1}\n'.format(
+                            e,
+                            getattr(e, 'output', '')))
 
     multiatlas_Intensity = None
     multiatlas_Labels = None
@@ -414,7 +418,8 @@ def pick_tissue_from_labels_file(multiatlas_Labels, csf_label=[4,14,15,24,43],
     gm_mask : string (nifti file)
 
     wm_mask : string (nifti file)
-    """  # noqa:
+    """
+    # pylint: disable=import-outside-toplevel,redefined-outer-name,reimported
     import os
     import nibabel as nb
     import numpy as np

CPAC/utils/monitoring/__init__.py

@@ -1,7 +1,7 @@
 '''Module to customize Nipype's process monitoring for use in C-PAC
 
 See https://fcp-indi.github.io/docs/developer/nodes for C-PAC-specific documentation.
-See https://nipype.readthedocs.io/en/latest/api/generated/nipype.utils.profiler.html for Nipype's documentation.'''  # noqa: E501
+See https://nipype.readthedocs.io/en/latest/api/generated/nipype.utils.profiler.html for Nipype's documentation.'''  # noqa: E501  # pylint: disable=line-too-long
 from .custom_logging import set_up_logger
 from .monitoring import LoggingHTTPServer, LoggingRequestHandler, \
                         log_nodes_cb, log_nodes_initial, monitor_server, \

CPAC/utils/utils.py

@@ -251,8 +251,8 @@ def get_zscore(map_node=False, wf_name='z_score'):
     >>> wf.inputs.inputspec.input_file = '/home/data/graph_working_dir/calculate_centrality/degree_centrality_binarize.nii.gz'
     >>> wf.inputs.inputspec.mask_file = '/home/data/graphs/GraphGeneration/new_mask_3m.nii.gz'
     >>> wf.run()  # doctest: +SKIP
-    """  # noqa:
-
+    """  # noqa: E501  # pylint: disable=line-too-long
+    # pylint: disable=import-outside-toplevel,redefined-outer-name,reimported
     from CPAC.pipeline import nipype_pipeline_engine as pe
     import nipype.interfaces.utility as util
     import nipype.interfaces.fsl as fsl
@@ -1666,7 +1666,7 @@ def dct_diff(dct1, dct2):
     ...     'pipeline_config_fmriprep-options.yml')
     >>> dct_diff(pipeline, pipeline2)['pipeline_setup']['pipeline_name']
     ('cpac-default-pipeline', 'cpac_fmriprep-options')
-    '''  # noqa:
+    '''
     diff = {}
     for key in dct1:
         if isinstance(dct1[key], dict):
@@ -1697,7 +1697,8 @@ def dct_diff(dct1, dct2):
     return {}
 
 
-def list_item_replace(l, old, new):  # noqa: E741
+def list_item_replace(l,  # noqa: E741  # pylint: disable=invalid-name
+                      old, new):
     '''Function to replace an item in a list
 
     Parameters
@@ -1917,14 +1918,15 @@ def update_config_dict(old_dict):
 
     Examples
     --------
-    >>> a, b, c = update_config_dict({'pipelineName': 'example-pipeline', '2': None})
+    >>> a, b, c = update_config_dict({
+    ...     'pipelineName': 'example-pipeline', '2': None})
     >>> a
     {'pipeline_setup': {'pipeline_name': 'example-pipeline'}}
     >>> b
     {'2': None}
     >>> c
     {'pipeline_setup': {'pipeline_name': 'example-pipeline'}, '2': None}
-    ''' # noqa:
+    '''
     def _append_to_list(current_value, new_value):
         '''Helper function to add new_value to the current_value list
         or create a list if one does not exist. Skips falsy elements
@@ -2288,7 +2290,7 @@ def update_nested_dict(d_base, d_update, fully_specified=False):
     ...     '/cpac_templates/aal_mask_pad.nii.gz': 'Voxel'
     ... }, 'realignment': 'ROI_to_func'}})
     True
-    """  # noqa:
+    """  # noqa: E501  # pylint: disable=line-too-long
 
     # short-circuit if d_update has `*_roi_paths` and
     # `roi_paths_fully_specified` children
@@ -2330,8 +2332,9 @@ def update_pipeline_values_1_8(d_old):
     >>> update_pipeline_values_1_8({'segmentation': {'tissue_segmentation': {
     ...     'using': ['FSL-FAST Thresholding']}}})
     {'segmentation': {'tissue_segmentation': {'using': ['FSL-FAST'], 'FSL-FAST': {'thresholding': {'use': 'Auto'}}}}}
-    '''  # noqa:
-    from CPAC.pipeline.schema import valid_options
+    '''  # noqa: E501  # pylint: disable=line-too-long
+    from CPAC.pipeline.schema import valid_options \
+        # pylint: disable=import-outside-toplevel
 
     d = replace_in_strings(d_old.copy())
 

CPAC/utils/yaml_template.py

@@ -76,7 +76,7 @@ def _create_import_dict(diff):
         ...         'run': ([True], False),
         ...         'using': (['3dSkullStrip'], ['niworkflows-ants'])}}}})
         {'anatomical_preproc': {'brain_extraction': {'extraction': {'run': False, 'using': ['niworkflows-ants']}}}}
-        '''  # noqa:
+        '''  # noqa: E501  # pylint: disable=line-too-long
         if isinstance(diff, tuple) and len(diff) == 2:
             return diff[1]
         if isinstance(diff, dict):
@@ -112,7 +112,8 @@ def _format_key(key, level):
         '''
         return f'\n{" " * level * 2}{key}: '
 
-    def _format_list_items(l, line_level):  # noqa: E741
+    def _format_list_items(l,  # noqa: E741  # pylint:disable=invalid-name
+                           line_level):
         '''Helper method to handle lists in the YAML
 
         Parameters
@@ -131,11 +132,11 @@ def _format_list_items(l, line_level):  # noqa: E741
         '  - 1\n  - 2\n  - nested: 3'
         >>> _format_list_items([1, 2, {'nested': [3, {'deep': [4]}]}], 1)
         '    - 1\n    - 2\n    - nested:\n      - 3\n      - deep:\n        - 4'
-        '''  # noqa:
+        '''  # noqa: E501  # pylint: disable=line-too-long
         # keep short, simple lists in square brackets
-        if all([any([isinstance(item, item_type) for item_type in {
+        if all(any(isinstance(item, item_type) for item_type in {
             str, bool, int, float
-        }]) for item in l]):
+        }) for item in l):
             if len(str(l)) < 50:
                 return str(l).replace("'", '').replace('"', '')
         # list long or complex lists on lines with indented '-' lead-ins

dev/circleci_data/test_external_utils.py

@@ -7,7 +7,8 @@
 sys.path.append(CPAC_DIR)
 DATA_DIR = os.path.join(CPAC_DIR, 'dev', 'circleci_data')
 
-from CPAC.__main__ import utils as CPAC_main_utils  # noqa: E402
+from CPAC.__main__ import utils as CPAC_main_utils \
+    # noqa: E402  # pylint: disable=wrong-import-position
 
 
 def test_build_data_config(cli_runner):
@@ -103,8 +104,8 @@ def _delete_test_yaml(test_yaml):
 
 
 def _test_repickle(pickle_path, gzipped=False):
+    # pylint: disable=import-outside-toplevel,unused-import
     backup = _Backup(pickle_path)
     if gzipped:
         import gzip  # noqa: F401
-
     backup.restore()