[TEST] update + dependancy to niflow

narps_open/pipelines/team_98BT.py

@@ -325,7 +325,11 @@ def get_preprocessing(self):
 
     def get_preprocessing_outputs(self):
         """ Return the names of the files the preprocessing is supposed to generate. """
+        return []
 
+    def get_run_level_analysis(self):
+        """ No run level analysis has been done by team 98BT """
+        return None
 
     def get_parameters_files(
         parameters_files, wc2_file, motion_corrected_files, subject_id, working_dir):
@@ -351,9 +355,9 @@ def get_parameters_files(
 
         from warnings import simplefilter
         # ignore all future warnings
-        simplefilter(action='ignore', category=FutureWarning)
-        simplefilter(action='ignore', category=UserWarning)
-        simplefilter(action='ignore', category=RuntimeWarning)
+        simplefilter(action = 'ignore', category = FutureWarning)
+        simplefilter(action = 'ignore', category = UserWarning)
+        simplefilter(action = 'ignore', category = RuntimeWarning)
 
         # Load wc2 file and create a mask out of it
         wc2 = load(wc2_file)

narps_open/utils/configuration/testing_config.toml

@@ -3,9 +3,9 @@ title = "Testing configuration for the NARPS open pipelines project"
 config_type = "testing"
 
 [directories]
-dataset = "run/data/ds001734/"
+dataset = "data/original/ds001734/"
 reproduced_results = "run/data/reproduced/"
-narps_results = "run/data/results/"
+narps_results = "data/results/"
 test_data = "tests/test_data/"
 test_runs = "run/"
 

setup.py

@@ -19,7 +19,8 @@
     'networkx>=2.0,<3.0', # a workaround to nipype's bug (issue 3530)
     'nilearn>=0.10.0,<0.11',
     'nipype',
-    'pandas'
+    'pandas',
+    'niflow-nipype1-workflows>=0.0.5,<0.1.0'
 ]
 extras_require = {
     'tests': [

tests/pipelines/test_team_98BT.py

@@ -53,16 +53,16 @@ def test_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_subject_level_outputs()) == 9
+        assert len(pipeline.get_group_level_outputs()) == 84
         assert len(pipeline.get_hypotheses_outputs()) == 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_subject_level_outputs()) == 36
+        assert len(pipeline.get_group_level_outputs()) == 84
         assert len(pipeline.get_hypotheses_outputs()) == 18
 
     @staticmethod