Merge pull request #167 from effigies/mnt/deprecations

MNT: BIDSLayout.get() parameter "extensions" deprecated

fitlins/interfaces/bids.py

@@ -232,7 +232,7 @@ def _run_interface(self, runtime):
         selectors = self.inputs.selectors
 
         analysis = Analysis(model=self.inputs.model, layout=layout)
-        analysis.setup(drop_na=False, desc='preproc', **selectors)
+        analysis.setup(drop_na=False, **selectors)
         self._load_level1(runtime, analysis)
         self._load_higher_level(runtime, analysis)
 
@@ -263,7 +263,7 @@ def _load_level1(self, runtime, analysis):
             if space is None:
                 spaces = analysis.layout.get_spaces(
                     suffix='bold',
-                    extensions=['.nii', '.nii.gz'])
+                    extension=['.nii', '.nii.gz'])
                 if spaces:
                     spaces = sorted(spaces)
                     space = spaces[0]
@@ -413,8 +413,7 @@ def _run_interface(self, runtime):
         mask_files = []
         entities = []
         for ents in self.inputs.entities:
-            selectors = {**self.inputs.selectors, **ents}
-            bold_file = layout.get(extensions=['.nii', '.nii.gz'], **selectors)
+            bold_file = layout.get(**self.inputs.selectors, **ents)
 
             if len(bold_file) == 0:
                 raise FileNotFoundError(
@@ -435,7 +434,8 @@ def _run_interface(self, runtime):
             bold_ents = layout.parse_file_entities(bold_file[0].path)
             bold_ents['suffix'] = 'mask'
             bold_ents['desc'] = 'brain'
-            mask_file = layout.get(extensions=['.nii', '.nii.gz'], **bold_ents)
+            bold_ents['extension'] = ['.nii', '.nii.gz']
+            mask_file = layout.get(**bold_ents)
             bold_ents.pop('suffix')
             bold_ents.pop('desc')
 

fitlins/viz/reports.py

@@ -45,11 +45,11 @@ def build_report_dict(deriv_dir, work_dir, analysis):
     wd_layout = BIDSLayout(
         Path(work_dir) / 'reportlets' / 'fitlins',
         validate=False)
-    all_pngs = fl_layout.get(extensions='.png')
+    all_pngs = fl_layout.get(extension='.png')
     fig_dirs = set(
         (png.dirname, tuple(ent for ent in png.entities.items()
                             if ent[0] not in ('suffix', 'contrast')))
-        for png in fl_layout.get(extensions='.png'))
+        for png in fl_layout.get(extension='.png'))
 
     report = {
         'dataset': {
@@ -67,7 +67,8 @@ def build_report_dict(deriv_dir, work_dir, analysis):
         report['steps'].append(report_step)
         for _, _, ents in step.get_design_matrix():
             contrasts = step.get_contrasts(**ents)[0]
-            for key in ('datatype', 'desc', 'suffix'):
+            for key in ('datatype', 'desc', 'suffix', 'extension',
+                        'RepetitionTime', 'SkullStripped', 'TaskName'):
                 ents.pop(key, None)
 
             analysis = {
@@ -78,18 +79,18 @@ def build_report_dict(deriv_dir, work_dir, analysis):
                 'contrasts': [
                     {'name': displayify(contrast.name),
                      'glassbrain': fl_layout.get(contrast=snake_to_camel(contrast.name),
-                                                 suffix='ortho', extensions='png', **ents)[0].path}
+                                                 suffix='ortho', extension='png', **ents)[0].path}
                     for contrast in contrasts]
                 }
 
             report_step['analyses'].append(analysis)
 
             # Space doesn't apply to design/contrast matrices
             ents.pop('space', None)
-            design_matrix = fl_layout.get(suffix='design', extensions='svg', **ents)
-            correlation_matrix = fl_layout.get(suffix='corr', extensions='svg', **ents)
-            contrast_matrix = fl_layout.get(suffix='contrasts', extensions='svg', **ents)
-            warning = wd_layout.get(extensions='.html', suffix='snippet', **ents)
+            design_matrix = fl_layout.get(suffix='design', extension='svg', **ents)
+            correlation_matrix = fl_layout.get(suffix='corr', extension='svg', **ents)
+            contrast_matrix = fl_layout.get(suffix='contrasts', extension='svg', **ents)
+            warning = wd_layout.get(extension='.html', suffix='snippet', **ents)
             if design_matrix:
                 analysis['design_matrix'] = design_matrix[0].path
             if correlation_matrix:

fitlins/workflows/base.py

@@ -37,7 +37,9 @@ def init_fitlins_wf(bids_dir, derivatives, out_dir, analysis_level, space,
     loader = pe.Node(
         LoadBIDSModel(bids_dir=bids_dir,
                       derivatives=derivatives,
-                      model=model_dict),
+                      model=model_dict,
+                      selectors={'desc': desc,
+                                 'space': space}),
         name='loader')
 
     if ignore is not None:
@@ -46,17 +48,12 @@ def init_fitlins_wf(bids_dir, derivatives, out_dir, analysis_level, space,
         loader.inputs.force_index = force_index
     if participants is not None:
         loader.inputs.selectors['subject'] = participants
-    if space is not None:
-        loader.inputs.selectors['space'] = space
 
     # Select preprocessed BOLD series to analyze
     getter = pe.Node(
         BIDSSelect(
             bids_dir=bids_dir, derivatives=derivatives,
-            selectors={
-                'suffix': 'bold',
-                'desc': desc,
-                'space': space}),
+            selectors={'suffix': 'bold'}),
         name='getter')
 
     if smoothing:

setup.cfg

@@ -39,7 +39,7 @@ docs =
     sphinx
     sphinxcontrib-apidoc
     sphinx-argparse
-    sphinx-nbexamples @ git+https://github.com/Chilipp/sphinx-nbexamples@5b6070ab30fb3f263c0326d7b17a9291ec65f6b6
+    sphinx-nbexamples >=0.4.0
     texext
     m2r
 all =