Reformat with new version of black (#1020)

* Run new version of black.

* Run isort.

docs/conf.py

@@ -26,7 +26,6 @@
 
 from github_link import make_linkcode_resolve
 
-
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -55,9 +54,10 @@
     "sphinxcontrib.bibtex",  # for foot-citations
 ]
 
-import sphinx
 from distutils.version import LooseVersion
 
+import sphinx
+
 if LooseVersion(sphinx.__version__) < LooseVersion("1.4"):
     extensions.append("sphinx.ext.pngmath")
 else:

docs/sphinxext/github_link.py

@@ -2,12 +2,13 @@
 This script comes from scikit-learn:
 https://github.com/scikit-learn/scikit-learn/blob/main/doc/sphinxext/github_link.py
 """
-from operator import attrgetter
+
 import inspect
-import subprocess
 import os
+import subprocess
 import sys
 from functools import partial
+from operator import attrgetter
 
 REVISION_CMD = "git rev-parse --short HEAD"
 

tedana/bibtex.py

@@ -1,4 +1,5 @@
 """Utilities for managing the tedana bibliography."""
+
 import logging
 import os.path as op
 import re

tedana/combine.py

@@ -1,4 +1,5 @@
 """Functions to optimally combine data across echoes."""
+
 import logging
 
 import numpy as np

tedana/decay.py

@@ -1,4 +1,5 @@
 """Functions to estimate S0 and T2* from multi-echo data."""
+
 import logging
 
 import numpy as np

tedana/decomposition/ica.py

@@ -1,4 +1,5 @@
 """ICA and related signal decomposition methods for tedana."""
+
 import logging
 import warnings
 

tedana/decomposition/pca.py

@@ -1,4 +1,5 @@
 """PCA and related signal decomposition methods for tedana."""
+
 import logging
 from numbers import Number
 

tedana/docs.py

@@ -1,4 +1,5 @@
 """Documentation to be injected into docstrings."""
+
 import sys
 
 ###################################

tedana/gscontrol.py

@@ -1,4 +1,5 @@
 """Global signal control methods."""
+
 import logging
 
 import numpy as np

tedana/io.py

@@ -4,6 +4,7 @@
 data sources, assist in writing per-echo verbose outputs, or act as helper
 functions for any of the above.
 """
+
 import json
 import logging
 import os

tedana/metrics/_utils.py

@@ -1,4 +1,5 @@
 """Miscellaneous utility functions for metric calculation."""
+
 import logging
 
 import numpy as np

tedana/metrics/collect.py

@@ -1,4 +1,5 @@
 """Tools to collect and generate metrics."""
+
 import logging
 import os.path as op
 

tedana/metrics/dependence.py

@@ -1,4 +1,5 @@
 """Metrics evaluating component TE-dependence or -independence."""
+
 import logging
 
 import numpy as np

tedana/reporting/dynamic_figures.py

@@ -1,4 +1,5 @@
 """Dynamic figures for tedana report."""
+
 from math import pi
 
 import numpy as np

tedana/reporting/html_report.py

@@ -1,4 +1,5 @@
 """Build HTML reports for tedana."""
+
 import logging
 import os
 import re

tedana/reporting/static_figures.py

@@ -1,4 +1,5 @@
 """Functions to creating figures to inspect tedana output."""
+
 import logging
 import os
 

tedana/selection/component_selector.py

@@ -1,4 +1,5 @@
 """Identify and label TE-dependent and TE-independent components."""
+
 import inspect
 import logging
 import os.path as op

tedana/selection/selection_nodes.py

@@ -1,4 +1,5 @@
 """Functions that will be used as steps in a decision tree."""
+
 import logging
 
 import numpy as np
@@ -536,9 +537,9 @@ def dec_variance_lessthan_thresholds(
     if custom_node_label:
         outputs["node_label"] = custom_node_label
     else:
-        outputs[
-            "node_label"
-        ] = f"{var_metric}<{single_comp_threshold}. All variance<{all_comp_threshold}"
+        outputs["node_label"] = (
+            f"{var_metric}<{single_comp_threshold}. All variance<{all_comp_threshold}"
+        )
 
     LGR.info(f"{function_name_idx}: {if_true} if {outputs['node_label']}, else {if_false}")
     if log_extra_info:
@@ -1019,9 +1020,9 @@ def dec_classification_doesnt_exist(
     if custom_node_label:
         outputs["node_label"] = custom_node_label
     elif at_least_num_exist == 1:
-        outputs[
-            "node_label"
-        ] = f"Change {decide_comps} to {new_classification} if {class_comp_exists} doesn't exist"
+        outputs["node_label"] = (
+            f"Change {decide_comps} to {new_classification} if {class_comp_exists} doesn't exist"
+        )
     else:
         outputs["node_label"] = (
             f"Change {decide_comps} to {new_classification} if less than "

tedana/selection/selection_utils.py

@@ -158,9 +158,9 @@ def change_comptable_classifications(
         dont_warn_reclassify=dont_warn_reclassify,
     )
 
-    selector.component_status_table[
-        f"Node {selector.current_node_idx}"
-    ] = selector.component_table["classification"]
+    selector.component_status_table[f"Node {selector.current_node_idx}"] = (
+        selector.component_table["classification"]
+    )
 
     n_true = decision_boolean.sum()
     n_false = np.logical_not(decision_boolean).sum()

tedana/selection/tedica.py

@@ -1,4 +1,5 @@
 """Functions to identify TE-dependent and TE-independent components."""
+
 import logging
 
 from tedana.metrics import collect

tedana/selection/tedpca.py

@@ -1,4 +1,5 @@
 """Functions to identify TE-dependent and TE-independent components."""
+
 import logging
 
 import numpy as np

tedana/stats.py

@@ -1,4 +1,5 @@
 """Statistical functions."""
+
 import logging
 
 import numpy as np

tedana/tests/test_component_selector.py

@@ -1,4 +1,5 @@
 """Tests for the decision tree modularization."""
+
 import glob
 import json
 import os

tedana/tests/test_metrics.py

@@ -1,4 +1,5 @@
 """Tests for tedana.metrics."""
+
 import os.path as op
 
 import numpy as np

tedana/tests/test_reporting.py

@@ -1,4 +1,5 @@
 """Tests for tedana.reporting."""
+
 import numpy as np
 
 from tedana import reporting

tedana/tests/test_selection_nodes.py

@@ -1,4 +1,5 @@
 """Tests for the tedana.selection.selection_nodes module."""
+
 import os
 
 import pytest

tedana/tests/test_selection_utils.py

@@ -1,4 +1,5 @@
 """Tests for the tedana.selection.selection_utils module."""
+
 import os
 
 import numpy as np

tedana/tests/test_stats.py

@@ -1,4 +1,5 @@
 """Tests for the tedana stats module."""
+
 import random
 
 import numpy as np

tedana/tests/test_workflows_parser_utils.py

@@ -1,4 +1,5 @@
 """Test workflow parser utility functions."""
+
 import argparse
 
 import pytest

tedana/utils.py

@@ -1,4 +1,5 @@
 """Utilities for tedana package."""
+
 import logging
 import os.path as op
 import platform

tedana/workflows/ica_reclassify.py

@@ -1,4 +1,5 @@
 """Run the reclassification workflow for a previous tedana run."""
+
 import argparse
 import datetime
 import logging

tedana/workflows/parser_utils.py

@@ -1,4 +1,5 @@
 """Functions for parsers."""
+
 import argparse
 import os.path as op
 

tedana/workflows/t2smap.py

@@ -1,4 +1,5 @@
 """Estimate T2 and S0, and optimally combine data across TEs."""
+
 import argparse
 import logging
 import os

tedana/workflows/tedana.py

@@ -1,4 +1,5 @@
 """Run the "canonical" TE-Dependent ANAlysis workflow."""
+
 import argparse
 import datetime
 import json