Merge pull request #1124 from DimitriPapadopoulos/pyupgrade

MAINT: apply suggestions from pyupgrade

mriqc/__main__.py

@@ -28,5 +28,5 @@
 
     # `python -m <module>` typically displays the command as __main__.py
     if "__main__.py" in sys.argv[0]:
-        sys.argv[0] = "%s -m %s" % (sys.executable, module)
+        sys.argv[0] = f"{sys.executable} -m {module}"
     main()

mriqc/bin/abide2bids.py

@@ -127,7 +127,7 @@ def fetch(args: Tuple[str, str, str, str]) -> Tuple[str, str]:
     pkg_id = [u[9:] for u in url.split("/") if u.startswith("NITRC_IR_")][0]
     sub_file = op.join(tmpdir, "%s.zip" % pkg_id)
 
-    cmd = ["curl", "-s", "-u", "%s:%s" % (user, password), "-o", sub_file, url]
+    cmd = ["curl", "-s", "-u", f"{user}:{password}", "-o", sub_file, url]
     sp.check_call(cmd)
     sp.check_call(["unzip", "-qq", "-d", tmpdir, "-u", sub_file])
 

mriqc/bin/fs2gif.py

@@ -130,7 +130,7 @@ def main():
                 tclfp.write("    SetSlice $slice\n")
                 tclfp.write("    RedrawScreen\n")
                 tclfp.write(
-                    '    SaveTIFF [format "%s/%s-' % (tmp_sub, subid)
+                    f'    SaveTIFF [format "{tmp_sub}/{subid}-'
                     + '%03d.tif" $i]\n'
                 )
                 tclfp.write("    incr i\n")
@@ -160,8 +160,8 @@ def main():
                     "10",
                     "-loop",
                     "0",
-                    "%s/%s-*.tif" % (tmp_sub, subid),
-                    "%s/%s.gif" % (out_dir, subid),
+                    f"{tmp_sub}/{subid}-*.tif",
+                    f"{out_dir}/{subid}.gif",
                 ]
             )
 
@@ -236,8 +236,8 @@ def main():
                     "10",
                     "-loop",
                     "0",
-                    "%s/%s-lh-*.tif" % (tmp_sub, subid),
-                    "%s/%s-lh.gif" % (out_dir, subid),
+                    f"{tmp_sub}/{subid}-lh-*.tif",
+                    f"{out_dir}/{subid}-lh.gif",
                 ]
             )
             sp.call(
@@ -247,8 +247,8 @@ def main():
                     "10",
                     "-loop",
                     "0",
-                    "%s/%s-rh-*.tif" % (tmp_sub, subid),
-                    "%s/%s-rh.gif" % (out_dir, subid),
+                    f"{tmp_sub}/{subid}-rh-*.tif",
+                    f"{out_dir}/{subid}-rh.gif",
                 ]
             )
 
@@ -268,10 +268,10 @@ def _xvfb_run(wait=5, server_args="-screen 0, 1600x1200x24", logs=None):
     return [
         "xvfb-run",
         "-a",  # automatically get a free server number
-        "-f {}.out".format(logs),
-        "-e {}.err".format(logs),
-        "--wait={:d}".format(wait),
-        '--server-args="{}"'.format(server_args),
+        f"-f {logs}.out",
+        f"-e {logs}.err",
+        f"--wait={wait:d}",
+        f'--server-args="{server_args}"',
     ]
 
 

mriqc/bin/subject_wrangler.py

@@ -24,7 +24,6 @@
 import glob
 import os.path as op
 from argparse import ArgumentParser, RawTextHelpFormatter
-from builtins import range  # pylint: disable=W0622
 from random import shuffle
 from textwrap import dedent
 

mriqc/config.py

@@ -397,7 +397,7 @@ class execution(_Config):
     """Enable resource monitor."""
     run_id = None
     """Filter input dataset by run identifier."""
-    run_uuid = "%s_%s" % (strftime("%Y%m%d-%H%M%S"), uuid4())
+    run_uuid = "{}_{}".format(strftime("%Y%m%d-%H%M%S"), uuid4())
     """Unique identifier of this particular run."""
     session_id = None
     """Filter input dataset by session identifier."""

mriqc/engine/plugin.py

@@ -133,7 +133,7 @@ class DistributedPluginBase(PluginBase):
 
     def __init__(self, plugin_args=None):
         """Initialize runtime attributes to none."""
-        super(DistributedPluginBase, self).__init__(plugin_args=plugin_args)
+        super().__init__(plugin_args=plugin_args)
         self.procs = None
         self.depidx = None
         self.refidx = None
@@ -419,7 +419,7 @@ def __init__(self, pool=None, plugin_args=None):
         """Initialize the plugin."""
         from mriqc import config
 
-        super(MultiProcPlugin, self).__init__(plugin_args=plugin_args)
+        super().__init__(plugin_args=plugin_args)
         self._taskresult = {}
         self._task_obj = {}
         self._taskid = 0

mriqc/instrumentation/__main__.py

@@ -34,7 +34,7 @@
     args = parser.parse_args()
 
     if "__main__.py" in argparse._sys.argv[0]:  # sys.argv[0]:
-        argparse._sys.argv[0] = "%s -m %s" % (argparse._sys.executable, module)
+        argparse._sys.argv[0] = f"{argparse._sys.executable} -m {module}"
 
     pid = args.name if args.name.isnumeric() else FindProcess(args.name)
 

mriqc/interfaces/bids.py

@@ -59,12 +59,12 @@ class IQMFileSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
     def __setattr__(self, key, value):
         if key not in self.copyable_trait_names():
             if not isdefined(value):
-                super(IQMFileSinkInputSpec, self).__setattr__(key, value)
+                super().__setattr__(key, value)
             self._outputs[key] = value
         else:
             if key in self._outputs:
                 self._outputs[key] = value
-            super(IQMFileSinkInputSpec, self).__setattr__(key, value)
+            super().__setattr__(key, value)
 
 
 class IQMFileSinkOutputSpec(TraitedSpec):
@@ -77,7 +77,7 @@ class IQMFileSink(SimpleInterface):
     expr = re.compile("^root[0-9]+$")
 
     def __init__(self, fields=None, force_run=True, **inputs):
-        super(IQMFileSink, self).__init__(**inputs)
+        super().__init__(**inputs)
 
         if fields is None:
             fields = []

mriqc/interfaces/functional.py

@@ -20,7 +20,6 @@
 #
 #     https://www.nipreps.org/community/licensing/
 #
-from builtins import zip
 from os import path as op
 
 import nibabel as nb

mriqc/interfaces/transitional.py

@@ -84,7 +84,7 @@ class GCOR(CommandLine):
     output_spec = GCOROutputSpec
 
     def _run_interface(self, runtime):
-        runtime = super(GCOR, self)._run_interface(runtime)
+        runtime = super()._run_interface(runtime)
 
         gcor_line = [
             line.strip()

mriqc/qc/functional.py

@@ -244,7 +244,7 @@ def gsr(epi_data, mask, direction="y", ref_file=None, out_file=None):
     direction = direction.lower()
     if direction[-1] not in ["x", "y", "all"]:
         raise Exception(
-            "Unknown direction {}, should be one of x, -x, y, -y, all".format(direction)
+            f"Unknown direction {direction}, should be one of x, -x, y, -y, all"
         )
 
     if direction == "all":
@@ -256,7 +256,7 @@ def gsr(epi_data, mask, direction="y", ref_file=None, out_file=None):
                 if ext == ".gz":
                     fname, ext2 = op.splitext(fname)
                     ext = ext2 + ext
-                ofile = "{0}_{1}{2}".format(fname, newdir, ext)
+                ofile = f"{fname}_{newdir}{ext}"
             result += [gsr(epi_data, mask, newdir, ref_file=ref_file, out_file=ofile)]
         return result
 

mriqc/qc/tests/test_anatomical.py

@@ -23,7 +23,6 @@
 """
 Anatomical tests
 """
-from builtins import object
 from shutil import rmtree
 from tempfile import mkdtemp
 
@@ -35,7 +34,7 @@
 from ..anatomical import art_qi2
 
 
-class GroundTruth(object):
+class GroundTruth:
     def get_data(self, sigma, noise="normal"):
         """Generates noisy 3d data"""
         size = (50, 50, 50)

mriqc/reports/group.py

@@ -21,8 +21,6 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Encapsulates report generation functions."""
-from builtins import object  # pylint: disable=W0622
-from io import open
 from sys import version_info
 
 import pandas as pd
@@ -297,5 +295,5 @@ def _format_labels(row, id_labels):
 
     for col_id, prefix in list(BIDS_COMP.items()):
         if col_id in id_labels:
-            crow.append("%s-%s" % (prefix, row[[col_id]].values[0]))
+            crow.append(f"{prefix}-{row[[col_id]].values[0]}")
     return "_".join(crow)

mriqc/synthstrip/__main__.py

@@ -28,5 +28,5 @@
 
     # `python -m <module>` typically displays the command as __main__.py
     if "__main__.py" in sys.argv[0]:
-        sys.argv[0] = "%s -m %s" % (sys.executable, module)
+        sys.argv[0] = f"{sys.executable} -m {module}"
     main()

mriqc/utils/misc.py

@@ -31,7 +31,7 @@
 try:
     from collections.abc import MutableMapping
 except ImportError:
-    from collections import MutableMapping
+    from collections.abc import MutableMapping
 
 IMTYPES = {
     "T1w": "anat",
@@ -104,25 +104,25 @@ def rotate_files(fname):
     if not op.isfile(fname):
         return
 
-    prev = glob.glob("{}.*{}".format(name, ext))
+    prev = glob.glob(f"{name}.*{ext}")
     prev.insert(0, fname)
-    prev.append("{0}.{1:d}{2}".format(name, len(prev) - 1, ext))
+    prev.append(f"{name}.{len(prev) - 1:d}{ext}")
     for i in reversed(list(range(1, len(prev)))):
         os.rename(prev[i - 1], prev[i])
 
 
 def bids_path(subid, sesid=None, runid=None, prefix=None, out_path=None, ext="json"):
     import os.path as op
 
-    fname = "{}".format(subid)
+    fname = f"{subid}"
     if prefix is not None:
         if not prefix.endswith("_"):
             prefix += "_"
         fname = prefix + fname
     if sesid is not None:
-        fname += "_ses-{}".format(sesid)
+        fname += f"_ses-{sesid}"
     if runid is not None:
-        fname += "_run-{}".format(runid)
+        fname += f"_run-{runid}"
 
     if out_path is not None:
         fname = op.join(out_path, fname)
@@ -139,7 +139,7 @@ def generate_pred(derivatives_dir, output_dir, mod):
         return None
 
     # If some were found, generate the CSV file and group report
-    jsonfiles = list(output_dir.glob("sub-*/**/%s/sub-*_%s.json" % (IMTYPES[mod], mod)))
+    jsonfiles = list(output_dir.glob(f"sub-*/**/{IMTYPES[mod]}/sub-*_{mod}.json"))
     if not jsonfiles:
         return None
 
@@ -178,7 +178,7 @@ def generate_tsv(output_dir, mod):
 
     # If some were found, generate the CSV file and group report
     out_tsv = output_dir / ("group_%s.tsv" % mod)
-    jsonfiles = list(output_dir.glob("sub-*/**/%s/sub-*_%s.json" % (IMTYPES[mod], mod)))
+    jsonfiles = list(output_dir.glob(f"sub-*/**/{IMTYPES[mod]}/sub-*_{mod}.json"))
     if not jsonfiles:
         return None, out_tsv
 

mriqc/workflows/anatomical/base.py

@@ -771,7 +771,7 @@ def _apply_bias_correction(in_file, bias_image, out_file=None):
         if ext == ".gz":
             fname, ext2 = op.splitext(fname)
             ext = ext2 + ext
-        out_file = op.abspath("{}_inu{}".format(fname, ext))
+        out_file = op.abspath(f"{fname}_inu{ext}")
 
     out_img.to_filename(out_file)
     return out_file
@@ -788,7 +788,7 @@ def _binarize(in_file, threshold=0.5, out_file=None):
         if ext == ".gz":
             fname, ext2 = op.splitext(fname)
             ext = ext2 + ext
-        out_file = op.abspath("{}_bin{}".format(fname, ext))
+        out_file = op.abspath(f"{fname}_bin{ext}")
 
     nii = nb.load(in_file)
     data = nii.get_fdata() > threshold

mriqc/workflows/functional/output.py

@@ -330,8 +330,8 @@ def spikes_mask(in_file, in_mask=None, out_file=None):
         if ext == ".gz":
             fname, ext2 = op.splitext(fname)
             ext = ext2 + ext
-        out_file = op.abspath("{}_spmask{}".format(fname, ext))
-        out_plot = op.abspath("{}_spmask.pdf".format(fname))
+        out_file = op.abspath(f"{fname}_spmask{ext}")
+        out_plot = op.abspath(f"{fname}_spmask.pdf")
 
     in_4d_nii = nb.load(in_file)
     orientation = nb.aff2axcodes(in_4d_nii.affine)

mriqc/workflows/utils.py

@@ -21,7 +21,6 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Helper functions for the workflows."""
-from builtins import range
 
 
 def _tofloat(inlist):
@@ -53,7 +52,7 @@ def thresh_image(in_file, thres=0.5, out_file=None):
         if ext == ".gz":
             fname, ext2 = op.splitext(fname)
             ext = ext2 + ext
-        out_file = op.abspath("{}_thresh{}".format(fname, ext))
+        out_file = op.abspath(f"{fname}_thresh{ext}")
 
     im = nb.load(in_file)
     data = np.asanyarray(im.dataobj)