🚨 Rerun ruff format after upgrading to 0.3.2 (#2083)

.github/scripts/get_package_id.py

@@ -20,6 +20,7 @@
 
 Usage: python get_package_id.py $OWNER $IMAGE_TAG $VERSION_TAG
 """
+
 import os
 import sys
 

.github/scripts/get_pr_base_shas.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Get base SHAs for open PRs."""
+
 import os
 
 from github import Github

CPAC/_entrypoints/__init__.py

@@ -16,4 +16,5 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Entrypoints for C-PAC containers."""
+
 __all__ = []

CPAC/_entrypoints/run.py

@@ -16,6 +16,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Run C-PAC in a container."""
+
 import argparse
 import datetime
 import os
@@ -592,9 +593,9 @@ def run_main():
             c["awsCredentialsFile"] = resolve_aws_credential(args.aws_input_creds)
 
         if args.aws_output_creds:
-            c["pipeline_setup"]["Amazon-AWS"][
-                "aws_output_bucket_credentials"
-            ] = resolve_aws_credential(args.aws_output_creds)
+            c["pipeline_setup"]["Amazon-AWS"]["aws_output_bucket_credentials"] = (
+                resolve_aws_credential(args.aws_output_creds)
+            )
 
         c["pipeline_setup"]["output_directory"]["path"] = os.path.join(
             output_dir, "output"
@@ -610,9 +611,9 @@ def run_main():
             )
 
         if args.mem_gb:
-            c["pipeline_setup"]["system_config"][
-                "maximum_memory_per_participant"
-            ] = float(args.mem_gb)
+            c["pipeline_setup"]["system_config"]["maximum_memory_per_participant"] = (
+                float(args.mem_gb)
+            )
         elif args.mem_mb:
             c["pipeline_setup"]["system_config"]["maximum_memory_per_participant"] = (
                 float(args.mem_mb) / 1024.0
@@ -660,9 +661,9 @@ def run_main():
                 // c["pipeline_setup"]["system_config"]["num_participants_at_once"]
             )
             if c["pipeline_setup"]["system_config"]["max_cores_per_participant"] == 0:
-                c["pipeline_setup"]["system_config"][
-                    "max_cores_per_participant"
-                ] = args.n_cpus
+                c["pipeline_setup"]["system_config"]["max_cores_per_participant"] = (
+                    args.n_cpus
+                )
                 c["pipeline_setup"]["system_config"]["num_participants_at_once"] = 1
 
         if int(args.num_ants_threads) == 0:
@@ -690,13 +691,13 @@ def run_main():
             )
 
         if args.runtime_usage is not None:
-            c["pipeline_setup"]["system_config"]["observed_usage"][
-                "callback_log"
-            ] = args.runtime_usage
+            c["pipeline_setup"]["system_config"]["observed_usage"]["callback_log"] = (
+                args.runtime_usage
+            )
         if args.runtime_buffer is not None:
-            c["pipeline_setup"]["system_config"]["observed_usage"][
-                "buffer"
-            ] = args.runtime_buffer
+            c["pipeline_setup"]["system_config"]["observed_usage"]["buffer"] = (
+                args.runtime_buffer
+            )
 
         if args.save_working_dir is not False:
             c["pipeline_setup"]["working_directory"]["remove_working_dir"] = False

CPAC/anat_preproc/tests/test_anat_preproc.py

@@ -199,9 +199,8 @@ def test_anat_reorient(self):
                         else:
                             assert int(anat_reorient_sform[i][i]) > 0
 
-                    else:
-                        if not (j == 3):
-                            assert int(anat_reorient_sform[i][j]) == 0
+                    elif not (j == 3):
+                        assert int(anat_reorient_sform[i][j]) == 0
 
     def test_anat_skullstrip(self):
         """

CPAC/aroma/aroma_test.py

@@ -21,6 +21,7 @@
 
 @author: nrajamani
 """
+
 import os
 
 import pytest

CPAC/connectome/connectivity_matrix.py

@@ -17,6 +17,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Functions for creating connectome connectivity matrices."""
+
 import os
 from warnings import warn
 

CPAC/cwas/cwas.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """CWAS module for CPAC."""
+
 import os
 
 import numpy as np

CPAC/cwas/tests/test_cwas.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Test the CWAS pipeline."""
+
 from logging import basicConfig, INFO
 
 import pytest

CPAC/cwas/tests/test_pipeline_cwas.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Test the CWAS pipeline."""
+
 from logging import basicConfig, INFO
 import os
 from urllib.error import URLError

CPAC/func_preproc/__init__.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Functional preprocessing."""
+
 from .func_motion import (
     calc_motion_stats,
     func_motion_correct,

CPAC/func_preproc/tests/test_preproc_connections.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Test graph connections for functional preprocessing."""
+
 from itertools import product
 from random import sample
 import re

CPAC/generate_motion_statistics/__init__.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Functions for generating motion statistics."""
+
 from .generate_motion_statistics import (
     calculate_DVARS,
     calculate_FD_J,

CPAC/generate_motion_statistics/generate_motion_statistics.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Functions to calculate motion statistics."""
+
 import os
 import sys
 from typing import Optional

CPAC/generate_motion_statistics/utils.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Utilities for motion parameters."""
+
 from typing import Optional
 
 import numpy as np

CPAC/longitudinal_pipeline/longitudinal_preproc.py

@@ -16,6 +16,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Preprocessing for longitudinal pipelines."""
+
 from collections import Counter
 from multiprocessing.dummy import Pool as ThreadPool
 import os

CPAC/nuisance/utils/__init__.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Utilities for nuisance regression."""
+
 from . import compcor
 from .compcor import calc_compcor_components
 from .utils import (

CPAC/nuisance/utils/utils.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """General utilities for nuisance regression."""
+
 from collections import OrderedDict
 import os
 import re

CPAC/pipeline/check_outputs.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Test to check if all expected outputs were generated."""
+
 from itertools import chain
 from logging import Logger
 import os

CPAC/pipeline/cpac_group_runner.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Run a group-level analysis with C-PAC."""
+
 import fnmatch
 import os
 
@@ -1249,9 +1250,9 @@ def run_feat(group_config_file, feat=True):
     if contrasts_df.shape[0] == 1 and np.count_nonzero(contrasts_df.values[0][1:]) == 0:
         err = (
             "\n\n[!] C-PAC says: It appears you haven't defined any "
-            "contrasts in your contrasts CSV file.\n\nContrasts file:\n{0}"
+            f"contrasts in your contrasts CSV file.\n\nContrasts file:\n{custom_contrasts_csv}"
             "\n\nDefine your contrasts in this file and run again."
-            "\n\n".format(custom_contrasts_csv)
+            "\n\n"
         )
         raise Exception(err)
 
@@ -1923,8 +1924,8 @@ def run_basc(pipeline_config):
                 if df_scan not in scan_inclusion:
                     continue
 
-            basc_config_dct["analysis_ID"] = "{0}_{1}".format(
-                os.path.basename(pipeline_dir), df_scan
+            basc_config_dct["analysis_ID"] = (
+                f"{os.path.basename(pipeline_dir)}_{df_scan}"
             )
 
             # add scan label and nuisance regression strategy label to the
@@ -2161,7 +2162,7 @@ def run_isc(pipeline_config):
     permutations = pipeconfig_dct.get("isc_permutations", 1000)
     std_filter = pipeconfig_dct.get("isc_level_voxel_std_filter", None)
 
-    if std_filter == 0.0:  # noqa: PLR2004
+    if std_filter == 0.0:
         std_filter = None
 
     levels = []

CPAC/pipeline/cpac_pipeline.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Build a pipeline for C-PAC to run on a subject."""
+
 import copy
 import csv
 import faulthandler

CPAC/pipeline/nipype_pipeline_engine/__init__.py

@@ -20,6 +20,7 @@
 See https://nipype.readthedocs.io/en/latest/api/generated/nipype.pipeline.engine.html
 for Nipype's documentation.
 """  # pylint: disable=line-too-long
+
 from nipype.pipeline import engine as pe
 
 # import everything in nipype.pipeline.engine.__all__

CPAC/pipeline/nodeblock.py

@@ -1,4 +1,5 @@
 """Class and decorator for NodeBlock functions."""
+
 from typing import Any, Callable, Dict, List, Optional, Union
 
 

CPAC/pipeline/random_state/__init__.py

@@ -1,4 +1,5 @@
 """Random state for C-PAC."""
+
 from .seed import (
     random_seed,
     random_seed_flags,

CPAC/pipeline/random_state/seed.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Functions to set, check, and log random seed."""
+
 import random
 
 import numpy as np

CPAC/pipeline/test/test_cpac_pipeline.py

@@ -1,4 +1,5 @@
 """Tests for cpac_pipeline.py."""
+
 import pytest
 
 from CPAC.pipeline.cpac_pipeline import run_workflow

CPAC/pipeline/test/test_schema_validation.py

@@ -1,4 +1,5 @@
 """Tests for schema.py."""
+
 from itertools import combinations
 
 import pytest

CPAC/pipeline/utils.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """C-PAC pipeline engine utilities."""
+
 from itertools import chain
 from typing import Union
 

CPAC/qc/xcp.py

@@ -55,6 +55,7 @@
 normCoverage : float
     "Normalization of T1w/Functional to Template:[…] Coverage index" :footcite:`xcp_22,Ciri19`
 """  # pylint: disable=line-too-long
+
 from io import BufferedReader
 import os
 import re

CPAC/randomise/test_randomise.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Test randomise."""
+
 import os
 
 import pytest

CPAC/registration/output_func_to_standard.py

@@ -15,6 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Transform functional images to template space."""
+
 from nipype.interfaces import ants, c3, fsl
 from nipype.interfaces.afni import utils as afni_utils
 import nipype.interfaces.utility as util
@@ -518,9 +519,7 @@ def ants_apply_warps_func_mni(
         # define the node
         collect_transforms = pe.Node(
             util.Merge(num_transforms),
-            name="collect_transforms_{0}_{1}_{2}_{3}".format(
-                output_name, inverse_string, registration_template, num_strat
-            ),
+            name=f"collect_transforms_{output_name}_{inverse_string}_{registration_template}_{num_strat}",
         )
 
         # wire in the various transformations
@@ -540,9 +539,7 @@ def ants_apply_warps_func_mni(
                 output_names=["checked_transform_list", "list_length"],
                 function=check_transforms,
             ),
-            name="check_transforms{0}_{1}_{2}_{3}".format(
-                output_name, inverse_string, registration_template, num_strat
-            ),
+            name=f"check_transforms{output_name}_{inverse_string}_{registration_template}_{num_strat}",
         )
 
         workflow.connect(collect_transforms, "out", check_transform, "transform_list")
@@ -554,9 +551,7 @@ def ants_apply_warps_func_mni(
                 output_names=["inverse_transform_flags"],
                 function=generate_inverse_transform_flags,
             ),
-            name="inverse_transform_flags_{0}_{1}_{2}_{3}".format(
-                output_name, inverse_string, registration_template, num_strat
-            ),
+            name=f"inverse_transform_flags_{output_name}_{inverse_string}_{registration_template}_{num_strat}",
         )
 
         workflow.connect(
@@ -582,19 +577,15 @@ def ants_apply_warps_func_mni(
     if map_node:
         apply_ants_warp = pe.MapNode(
             interface=ants.ApplyTransforms(),
-            name="apply_ants_warp_{0}_mapnode_{1}_{2}_{3}".format(
-                output_name, inverse_string, registration_template, num_strat
-            ),
+            name=f"apply_ants_warp_{output_name}_mapnode_{inverse_string}_{registration_template}_{num_strat}",
             iterfield=["input_image"],
             mem_gb=1,
             mem_x=(1401462037888665 / 2361183241434822606848, "input_image"),
         )
     else:
         apply_ants_warp = pe.Node(
             interface=ants.ApplyTransforms(),
-            name="apply_ants_warp_{0}_{1}_{2}_{3}".format(
-                output_name, inverse_string, registration_template, num_strat
-            ),
+            name=f"apply_ants_warp_{output_name}_{inverse_string}_{registration_template}_{num_strat}",
             mem_gb=1,
             mem_x=(1401462037888665 / 2361183241434822606848, "input_image"),
         )
@@ -628,9 +619,7 @@ def ants_apply_warps_func_mni(
         # write out the composite functional to standard transforms
         write_composite_xfm = pe.Node(
             interface=ants.ApplyTransforms(),
-            name="write_composite_xfm_{0}_{1}_{2}_{3}".format(
-                output_name, inverse_string, registration_template, num_strat
-            ),
+            name=f"write_composite_xfm_{output_name}_{inverse_string}_{registration_template}_{num_strat}",
             mem_gb=8.0,
         )
         write_composite_xfm.inputs.print_out_composite_warp_file = True