[PEP8] some linting + including the narps_open/pipelines dir to pylint

.github/workflows/code_quality.yml

@@ -46,7 +46,7 @@ jobs:
 
     - name: Analyse the code with pylint
       run: |
-        pylint --fail-under 8 --ignore-paths narps_open/pipelines/ narps_open > pylint_report_narps_open.txt
+        pylint --fail-under 8 narps_open > pylint_report_narps_open.txt
         pylint --fail-under 8 tests > pylint_report_tests.txt
 
     - name: Archive pylint results

narps_open/pipelines/team_0I4U_debug.py

@@ -1,3 +1,4 @@
+# pylint: skip-file
 from nipype.interfaces.spm import (Coregister, Smooth, OneSampleTTestDesign, EstimateModel, EstimateContrast, 
                                    Level1Design, TwoSampleTTestDesign, RealignUnwarp, FieldMap, NewSegment, 
                                    Normalize12, Reslice)

narps_open/pipelines/team_1KB2_debug.py

@@ -1,3 +1,4 @@
+# pylint: skip-file
 from nipype.interfaces.fsl import (BET, FAST, MCFLIRT, FLIRT, FNIRT, ApplyWarp, SUSAN, 
                                    Info, ImageMaths, IsotropicSmooth, Threshold, Level1Design, FEATModel, 
                                    L2Model, Merge, FLAMEO, ContrastMgr,Cluster,  FILMGLS, Randomise, MultipleRegressDesign)

narps_open/pipelines/team_43FJ_debug.py

@@ -1,3 +1,4 @@
+# pylint: skip-file
 from nipype.interfaces.fsl import (BET, FAST, MCFLIRT, FLIRT, FNIRT, ApplyWarp, SUSAN, MotionOutliers,
                                    Info, ImageMaths, IsotropicSmooth, Threshold, Level1Design, FEATModel, 
                                    L2Model, Merge, FLAMEO, ContrastMgr, FILMGLS, Randomise, MultipleRegressDesign)

narps_open/pipelines/team_4TQ6_wip.py

@@ -1,3 +1,4 @@
+# pylint: skip-file
 from nipype.interfaces.fsl import (BET, ICA_AROMA, FAST, MCFLIRT, FLIRT, FNIRT, ApplyWarp, SUSAN, 
                                    Info, ImageMaths, IsotropicSmooth, Threshold, Level1Design, FEATModel, 
                                    L2Model, Merge, FLAMEO, ContrastMgr,Cluster,  FILMGLS, Randomise, MultipleRegressDesign)

narps_open/pipelines/team_98BT.py

@@ -1,3 +1,4 @@
+# pylint: skip-file
 from nipype.interfaces.spm import (Coregister, Smooth, OneSampleTTestDesign, EstimateModel, EstimateContrast, 
                                    Level1Design, TwoSampleTTestDesign, RealignUnwarp, NewSegment, SliceTiming,
                                   DARTEL, DARTELNorm2MNI, FieldMap)

narps_open/pipelines/team_Q6O0.py

@@ -468,11 +468,14 @@ def get_subject_level_outputs(self):
             )
 
         # Formatting templates and returning it as a list of files
-        output_files = [contrast_map_template.format(**dict(zip(parameters.keys(), parameter_values)))\
+        output_files = [
+            contrast_map_template.format(**dict(zip(parameters.keys(), parameter_values)))\
             for parameter_values in parameter_sets]
-        output_files += [mat_file_template.format(**dict(zip(parameters.keys(), parameter_values)))\
+        output_files += [
+            mat_file_template.format(**dict(zip(parameters.keys(), parameter_values)))\
             for parameter_values in parameter_sets]
-        output_files += [spmt_file_template.format(**dict(zip(parameters.keys(), parameter_values)))\
+        output_files += [
+            spmt_file_template.format(**dict(zip(parameters.keys(), parameter_values)))\
             for parameter_values in parameter_sets]
 
         return output_files
@@ -698,23 +701,41 @@ def get_hypotheses_outputs(self):
         """ Return all hypotheses output file names. """
         nb_sub = len(self.subject_list)
         files = [
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_gain', 'spmT_0001.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_gain', 'spmT_0001.nii'),
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_gain', 'spmT_0001.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_gain', 'spmT_0001.nii'),
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_loss', '_threshold1', 'spmT_0002_thr.nii'),
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_loss', 'spmT_0002.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_loss', '_threshold1', 'spmT_0002_thr.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_loss', 'spmT_0002.nii'),
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_loss', '_threshold0', 'spmT_0001_thr.nii'),
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_loss', 'spmT_0001.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_loss', '_threshold0', 'spmT_0001_thr.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_loss', 'spmT_0001.nii'),
-            join(f'l2_analysis_groupComp_nsub_{nb_sub}', '_model_type_loss', '_threshold0', 'spmT_0001_thr.nii'),
-            join(f'l2_analysis_groupComp_nsub_{nb_sub}', '_model_type_loss', 'spmT_0001.nii')
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_gain', 'spmT_0001.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_gain', 'spmT_0001.nii'),
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_gain', 'spmT_0001.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_gain', 'spmT_0001.nii'),
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_loss', '_threshold1', 'spmT_0002_thr.nii'),
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_loss', 'spmT_0002.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_loss', '_threshold1', 'spmT_0002_thr.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_loss', 'spmT_0002.nii'),
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_loss', '_threshold0', 'spmT_0001_thr.nii'),
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_loss', 'spmT_0001.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_loss', '_threshold0', 'spmT_0001_thr.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_loss', 'spmT_0001.nii'),
+            join(f'l2_analysis_groupComp_nsub_{nb_sub}',
+                '_model_type_loss', '_threshold0', 'spmT_0001_thr.nii'),
+            join(f'l2_analysis_groupComp_nsub_{nb_sub}',
+                '_model_type_loss', 'spmT_0001.nii')
         ]
         return [join(self.directories.output_dir, f) for f in files]

narps_open/pipelines/team_R9K3_wip.py

@@ -1,3 +1,4 @@
+# pylint: skip-file
 # THIS IS A TEMPLATE THAT CAN BE USE TO REPRODUCE A NEW PIPELINE
 
 import os

narps_open/pipelines/team_V55J.py

@@ -1,3 +1,4 @@
+# pylint: skip-file
 from nipype.interfaces.spm import (Coregister, Smooth, OneSampleTTestDesign, EstimateModel, EstimateContrast, 
                                    Level1Design, TwoSampleTTestDesign, RealignUnwarp, 
                                    Normalize12, NewSegment, FieldMap)

narps_open/pipelines/team_X19V.py

@@ -1,3 +1,4 @@
+# pylint: skip-file
 from nipype.interfaces.fsl import (Info, ImageMaths, IsotropicSmooth, Threshold, Level1Design, FEATModel, 
                                    L2Model, Merge, FLAMEO, ContrastMgr, FILMGLS, MultipleRegressDesign, Cluster, BET, SmoothEstimate)
 from nipype.algorithms.modelgen import SpecifyModel

tests/conftest.py

@@ -10,6 +10,7 @@
 from os.path import join, isfile
 from shutil import rmtree
 
+from numpy import isclose
 from pytest import helpers
 from pathvalidate import is_valid_filepath
 
@@ -23,6 +24,15 @@
 # Init configuration, to ensure it is in testing mode
 Configuration(config_type='testing')
 
+@helpers.register
+def compare_float_2d_arrays(array_1, array_2):
+    """ Assert array_1 and array_2 are close enough """
+
+    assert len(array_1) == len(array_2)
+    for reference_array, test_array in zip(array_1, array_2):
+        assert len(reference_array) == len(test_array)
+        assert isclose(reference_array, test_array).all()
+
 @helpers.register
 def test_pipeline_outputs(pipeline: Pipeline, number_of_outputs: list):
     """ Test the outputs of a Pipeline.

tests/core/test_common.py

@@ -59,7 +59,7 @@ def test_remove_file(remove_test_dir):
 
         # Check file is removed
         assert not exists(test_file_path)
-    
+
     @staticmethod
     @mark.unit_test
     def test_remove_directory(remove_test_dir):
@@ -396,7 +396,7 @@ def test_node_list_to_file_1():
 
         # Check file was created
         assert exists(out_file)
- 
+
         # Check file was created
         with open(out_file, 'r', encoding = 'utf-8') as file:
             for list_element, file_element in zip(out_list, file.read().split('\n')):
@@ -429,9 +429,8 @@ def test_node_list_to_file_2():
 
         # Check file was created
         assert exists(out_file)
- 
+
         # Check file was created
         with open(out_file, 'r', encoding = 'utf-8') as file:
             for list_element, file_element in zip(out_list, file.read().split('\n')):
                 assert list_element == file_element
-

tests/data/test_results.py

@@ -12,8 +12,7 @@
 """
 
 from os.path import isdir, join
-from shutil import rmtree, move, copytree
-from time import sleep
+from shutil import rmtree, copytree
 
 from checksumdir import dirhash
 from pytest import mark
@@ -74,7 +73,8 @@ def fake_get_uid(_):
 
         # Mock the results path
         results_directory = Configuration()['directories']['narps_results']
-        Configuration()['directories']['narps_results'] = Configuration()['directories']['test_runs']
+        Configuration()[
+            'directories']['narps_results'] = Configuration()['directories']['test_runs']
 
         # Init & download the collection
         collection = ResultsCollection('2T6S')

tests/data/test_task.py

@@ -15,7 +15,7 @@
 from pytest import mark, fixture
 
 from narps_open.utils.configuration import Configuration
-import narps_open.data.task as task
+from narps_open.data import task
 
 @fixture(scope='function', autouse=True)
 def mock_task_data(mocker):
@@ -50,7 +50,7 @@ def test_singleton():
     @mark.unit_test
     def test_derived():
         """ Test the derived values of a TaskInformation object """
-        
+
         task_info = task.TaskInformation()
         assert task_info['NumberOfSlices'] == 6
         assert task_info['AcquisitionTime'] == 1 / 6

tests/pipelines/test_team_08MQ.py

@@ -57,19 +57,11 @@ def test_outputs():
         pipeline = PipelineTeam08MQ()
         # 1 - 1 subject outputs
         pipeline.subject_list = ['001']
-        assert len(pipeline.get_preprocessing_outputs()) == 4*4
-        assert len(pipeline.get_run_level_outputs()) == 8+4*3*4
-        assert len(pipeline.get_subject_level_outputs()) == 4*3
-        assert len(pipeline.get_group_level_outputs()) == 0
-        assert len(pipeline.get_hypotheses_outputs()) == 18
+        helpers.test_pipeline_ouputs(pipeline, [4*4, 8+4*3*4, 4*3, 0, 18])
 
         # 2 - 4 subjects outputs
         pipeline.subject_list = ['001', '002', '003', '004']
-        assert len(pipeline.get_preprocessing_outputs()) == 4*4*4
-        assert len(pipeline.get_run_level_outputs()) == (8+4*3*4)*4
-        assert len(pipeline.get_subject_level_outputs()) == 4*3*4
-        assert len(pipeline.get_group_level_outputs()) == 0
-        assert len(pipeline.get_hypotheses_outputs()) == 18
+        helpers.test_pipeline_ouputs(pipeline, [4*4*4, (8+4*3*4)*4, 4*3*4, 0, 18])
 
     @staticmethod
     @mark.unit_test
@@ -130,10 +122,10 @@ def test_two_sample_t_test_regressors():
             ['002', '004'], # equalIndifference group
             ['001', '002', '003', '004'] # all subjects
             )
-        assert regressors == dict(
-                equalRange = [1, 0, 1, 0],
-                equalIndifference = [0, 1, 0, 1]
-            )
+        assert regressors == {
+                'equalRange' : [1, 0, 1, 0],
+                'equalIndifference' : [0, 1, 0, 1]
+            }
         assert groups == [1, 2, 1, 2]
 
     @staticmethod

tests/pipelines/test_team_2T6S.py

@@ -47,19 +47,11 @@ def test_outputs():
         pipeline = PipelineTeam2T6S()
         # 1 - 1 subject outputs
         pipeline.subject_list = ['001']
-        assert len(pipeline.get_preprocessing_outputs()) == 0
-        assert len(pipeline.get_run_level_outputs()) == 0
-        assert len(pipeline.get_subject_level_outputs()) == 7
-        assert len(pipeline.get_group_level_outputs()) == 63
-        assert len(pipeline.get_hypotheses_outputs()) == 18
+        helpers.test_pipeline_outputs(pipeline, [0, 0, 7, 63, 18])
 
         # 2 - 4 subjects outputs
         pipeline.subject_list = ['001', '002', '003', '004']
-        assert len(pipeline.get_preprocessing_outputs()) == 0
-        assert len(pipeline.get_run_level_outputs()) == 0
-        assert len(pipeline.get_subject_level_outputs()) == 28
-        assert len(pipeline.get_group_level_outputs()) == 63
-        assert len(pipeline.get_hypotheses_outputs()) == 18
+        helpers.test_pipeline_outputs(pipeline, [0, 0, 28, 63, 18])
 
     @staticmethod
     @mark.pipeline_test

tests/pipelines/test_team_C88N.py

@@ -52,27 +52,20 @@ def test_outputs():
         pipeline = PipelineTeamC88N()
         # 1 - 1 subject outputs
         pipeline.subject_list = ['001']
-        assert len(pipeline.get_preprocessing_outputs()) == 0
-        assert len(pipeline.get_run_level_outputs()) == 0
-        assert len(pipeline.get_subject_level_outputs()) == 8
-        assert len(pipeline.get_group_level_outputs()) == 53
-        assert len(pipeline.get_hypotheses_outputs()) == 18
+        helpers.test_pipeline_outputs(pipeline, [0, 0, 8, 53, 18])
 
         # 2 - 4 subjects outputs
         pipeline.subject_list = ['001', '002', '003', '004']
-        assert len(pipeline.get_preprocessing_outputs()) == 0
-        assert len(pipeline.get_run_level_outputs()) == 0
-        assert len(pipeline.get_subject_level_outputs()) == 32
-        assert len(pipeline.get_group_level_outputs()) == 53
-        assert len(pipeline.get_hypotheses_outputs()) == 18
+        helpers.test_pipeline_outputs(pipeline, [0, 0, 32, 53, 18])
 
     @staticmethod
     @mark.unit_test
     def test_subject_information():
         """ Test the get_subject_information method """
 
         # Test with 'gain'
-        test_event_file = join(Configuration()['directories']['test_data'], 'pipelines', 'events.tsv')
+        test_event_file = join(
+            Configuration()['directories']['test_data'], 'pipelines', 'events.tsv')
         information = PipelineTeamC88N.get_subject_information(
             [test_event_file, test_event_file],
             'gain'
@@ -103,7 +96,8 @@ def test_subject_information():
             assert isclose(reference_array, test_array).all()
 
         # Test with 'loss'
-        test_event_file = join(Configuration()['directories']['test_data'], 'pipelines', 'events.tsv')
+        test_event_file = join(
+            Configuration()['directories']['test_data'], 'pipelines', 'events.tsv')
         information = PipelineTeamC88N.get_subject_information(
             [test_event_file, test_event_file],
             'loss'