Merge pull request #1649 from FCP-INDI/style/noqa-specificity

tergeorge · web-flow · commit 5e3c132043a2 · 2022-02-04T16:19:31.000-05:00
🚨 Fix `  # noqa` specificity
diff --git a/CPAC/cwas/tests/test_cwas.py b/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
diff --git a/CPAC/pipeline/cpac_pipeline.py b/CPAC/pipeline/cpac_pipeline.py
@@ -352,7 +352,7 @@ def run_workflow(sub_dict, c, run, pipeline_timing_info=None, p_name=None,
     Setting ANTS/ITK thread usage to {ants_threads}
     Maximum potential number of cores that might be used during this run: {max_cores}
 {random_seed}
-"""  # noqa E501
+"""  # noqa: E501
 
     execution_info = """
 
@@ -367,7 +367,7 @@ def run_workflow(sub_dict, c, run, pipeline_timing_info=None, p_name=None,
         System time of start:      {run_start}
         System time of completion: {run_finish}
 
-"""  # noqa E501
+"""  # noqa: E501
 
     logger.info('%s', information.format(
         run_command=' '.join(['run', *sys.argv[1:]]),
diff --git a/CPAC/pipeline/nipype_pipeline_engine/__init__.py b/CPAC/pipeline/nipype_pipeline_engine/__init__.py
@@ -2,10 +2,10 @@
 See https://fcp-indi.github.io/docs/developer/nodes
 for C-PAC-specific documentation.
 See https://nipype.readthedocs.io/en/latest/api/generated/nipype.pipeline.engine.html
-for Nipype's documentation.'''  # noqa E501
+for Nipype's documentation.'''  # noqa: E501
 from nipype.pipeline import engine as pe
 # import everything in nipype.pipeline.engine.__all__
-from nipype.pipeline.engine import *  # noqa F401
+from nipype.pipeline.engine import *  # noqa: F401,F403
 # import our DEFAULT_MEM_GB and override Node, MapNode
 from .engine import DEFAULT_MEM_GB, get_data_size, Node, MapNode, \
                     UNDEFINED_SIZE, Workflow
diff --git a/CPAC/pipeline/nipype_pipeline_engine/engine.py b/CPAC/pipeline/nipype_pipeline_engine/engine.py
@@ -3,7 +3,7 @@
 for C-PAC-specific documentation.
 See https://nipype.readthedocs.io/en/latest/api/generated/nipype.pipeline.engine.html
 for Nipype's documentation.
-'''  # noqa E501
+'''  # noqa: E501
 import os
 import re
 import warnings
@@ -140,7 +140,7 @@ def __init__(self, *args, mem_gb=DEFAULT_MEM_GB, **kwargs):
             ``mode`` can be any one of
             * 'xyzt' (spatial * temporal) (default if not specified)
             * 'xyz' (spatial)
-            * 't' (temporal)''']))  # noqa E501
+            * 't' (temporal)''']))  # noqa: E501
 
     def _add_flags(self, flags):
         r'''
@@ -415,7 +415,7 @@ def _handle_just_in_time_exception(self, node):
                 self._local_func_scans)  # pylint: disable=no-member
         else:
             # TODO: handle S3 files
-            node._apply_mem_x(UNDEFINED_SIZE)  # noqa W0212
+            node._apply_mem_x(UNDEFINED_SIZE)  # noqa: W0212
 
 
 def get_data_size(filepath, mode='xyzt'):
diff --git a/CPAC/pipeline/nipype_pipeline_engine/plugins/__init__.py b/CPAC/pipeline/nipype_pipeline_engine/plugins/__init__.py
@@ -1,6 +1,6 @@
 """Import Nipype's pipeline plugins and selectively override"""
-from nipype.pipeline.plugins import *  # noqa F401,F403
+from nipype.pipeline.plugins import *  # noqa: F401,F403
 # Override LegacyMultiProc
-from .legacymultiproc import LegacyMultiProcPlugin  # noqa F401
+from .legacymultiproc import LegacyMultiProcPlugin  # noqa: F401
 # Override MultiProc
-from .multiproc import MultiProcPlugin  # noqa F401
+from .multiproc import MultiProcPlugin  # noqa: F401
diff --git a/CPAC/pipeline/nipype_pipeline_engine/plugins/cpac_nipype_custom.py b/CPAC/pipeline/nipype_pipeline_engine/plugins/cpac_nipype_custom.py
@@ -130,7 +130,7 @@ def _send_procs_to_workers(self, updatehash=False, graph=None):
         Sends jobs to workers when system resources are available.
         Customized from https://github.com/nipy/nipype/commit/79e2fdfc38759bc0853e4051b99ba4c37587d65f
         to catch overhead deadlocks
-        """  # noqa E501  # pylint: disable=line-too-long
+        """  # noqa: E501  # pylint: disable=line-too-long
         # pylint: disable=too-many-branches, too-many-statements
         # Check to see if a job is available (jobs with all dependencies run)
         # See https://github.com/nipy/nipype/pull/2200#discussion_r141605722
diff --git a/CPAC/pipeline/random_state/seed.py b/CPAC/pipeline/random_state/seed.py
@@ -162,7 +162,7 @@ def set_up_random_state(seed):
     ValueError: Valid random seeds are positive integers up to 2147483647, "random", or None, not 0
     >>> set_up_random_state(None)
 
-    '''  # noqa E501  # pylint: disable=line-too-long
+    '''  # noqa: E501  # pylint: disable=line-too-long
     if seed is not None:
         if seed == 'random':
             seed = random_random_seed()
diff --git a/CPAC/pipeline/schema.py b/CPAC/pipeline/schema.py
@@ -173,7 +173,7 @@ def permutation_message(key, options):
 
     Returns
     -------
-    msg: str'''  # noqa E501
+    msg: str'''  # noqa: E501
     return f'''
 
 \'{key}\' takes a dictionary with paths to region-of-interest (ROI)
diff --git a/CPAC/qc/xcp.py b/CPAC/qc/xcp.py
@@ -49,7 +49,7 @@
     "Normalization of T1w/Functional to Template:[…] cross correlation" :cite:`cite-Ciri19` :cite:`cite-Penn19`
 normCoverage : float
     "Normalization of T1w/Functional to Template:[…] Coverage index" :cite:`cite-Ciri19` :cite:`cite-Penn19`
-"""  # noqa E501  # pylint: disable=line-too-long
+"""  # noqa: E501  # pylint: disable=line-too-long
 import os
 import re
 from io import BufferedReader
@@ -103,7 +103,7 @@ def calculate_overlap(image_pair):
     (1.0, 1.0, 0.9999999999999998, 1.0)
     >>> tuple(calculate_overlap((a2, a2)).values())
     (1.0, 1.0, 0.9999999999999998, 1.0)
-    '''  # noqa E501  # pylint: disable=line-too-long
+    '''  # noqa: E501  # pylint: disable=line-too-long
     if len(image_pair) != 2:
         raise IndexError('`calculate_overlap` requires 2 images, but '
                          f'{len(image_pair)} were provided')
diff --git a/CPAC/seg_preproc/seg_preproc.py b/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']),
diff --git a/CPAC/seg_preproc/utils.py b/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
diff --git a/CPAC/utils/interfaces/netcorr.py b/CPAC/utils/interfaces/netcorr.py
@@ -189,7 +189,7 @@ class NetCorr(AFNICommand):
     '3dNetCorr -prefix sub0.tp1.ncorr -fish_z -inset functional.nii -in_rois maps.nii -mask mask.nii -ts_wb_Z -ts_wb_corr'
     >>> res = ncorr.run()  # doctest: +SKIP
 
-    """  # noqa E501  # pylint: disable=line-too-long
+    """  # noqa: E501  # pylint: disable=line-too-long
     _cmd = "3dNetCorr"
     input_spec = NetCorrInputSpec
     output_spec = NetCorrOutputSpec
diff --git a/CPAC/utils/monitoring/__init__.py b/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, \
diff --git a/CPAC/utils/utils.py b/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
@@ -1725,7 +1726,7 @@ def list_item_replace(l, old, new):  # noqa E741
     if isinstance(l, list) and old in l:
         l[l.index(old)] = new
     elif isinstance(l, str):
-        l = l.replace(old, new)  # noqa E741
+        l = l.replace(old, new)  # noqa: E741
     return l
 
 
@@ -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())
 
diff --git a/CPAC/utils/yaml_template.py b/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
diff --git a/dev/circleci_data/test_external_utils.py b/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
-
+        import gzip  # noqa: F401
     backup.restore()
