[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

.gitignore

@@ -139,4 +139,3 @@ _version.py
 
 # Mac Garbage
 .DS_Store
-

pydra/tasks/mrtrix3/v3_1/amp2response.py

@@ -86,7 +86,7 @@ class Amp2Response(shell.Task["Amp2Response.Outputs"]):
     shells: list[float] | None = shell.arg(
         default=None,
         argstr="-shells",
-        help="""specify one or more b-values to use during processing, as a comma-separated list of the desired approximate b-values (b-values are clustered to allow for small deviations). Note that some commands are incompatible with multiple b-values, and will report an error if more than one b-value is provided. 
+        help="""specify one or more b-values to use during processing, as a comma-separated list of the desired approximate b-values (b-values are clustered to allow for small deviations). Note that some commands are incompatible with multiple b-values, and will report an error if more than one b-value is provided.
 WARNING: note that, even though the b=0 volumes are never referred to as a 'shell' in the literature, they still have to be explicitly included in the list of b-values as provided to the -shell option! Several algorithms that include the b=0 volumes in their computations may otherwise return an undesired result.""",
         sep=",",
     )

pydra/tasks/mrtrix3/v3_1/amp2sh.py

@@ -95,7 +95,7 @@ class Amp2Sh(shell.Task["Amp2Sh.Outputs"]):
     shells: list[float] | None = shell.arg(
         default=None,
         argstr="-shells",
-        help="""specify one or more b-values to use during processing, as a comma-separated list of the desired approximate b-values (b-values are clustered to allow for small deviations). Note that some commands are incompatible with multiple b-values, and will report an error if more than one b-value is provided. 
+        help="""specify one or more b-values to use during processing, as a comma-separated list of the desired approximate b-values (b-values are clustered to allow for small deviations). Note that some commands are incompatible with multiple b-values, and will report an error if more than one b-value is provided.
 WARNING: note that, even though the b=0 volumes are never referred to as a 'shell' in the literature, they still have to be explicitly included in the list of b-values as provided to the -shell option! Several algorithms that include the b=0 volumes in their computations may otherwise return an undesired result.""",
         sep=",",
     )

pydra/tasks/mrtrix3/v3_1/dirstat.py

@@ -107,7 +107,7 @@ class DirStat(shell.Task["DirStat.Outputs"]):
     shells: list[float] | None = shell.arg(
         default=None,
         argstr="-shells",
-        help="""specify one or more b-values to use during processing, as a comma-separated list of the desired approximate b-values (b-values are clustered to allow for small deviations). Note that some commands are incompatible with multiple b-values, and will report an error if more than one b-value is provided. 
+        help="""specify one or more b-values to use during processing, as a comma-separated list of the desired approximate b-values (b-values are clustered to allow for small deviations). Note that some commands are incompatible with multiple b-values, and will report an error if more than one b-value is provided.
 WARNING: note that, even though the b=0 volumes are never referred to as a 'shell' in the literature, they still have to be explicitly included in the list of b-values as provided to the -shell option! Several algorithms that include the b=0 volumes in their computations may otherwise return an undesired result.""",
         sep=",",
     )

pydra/tasks/mrtrix3/v3_1/dwi2fod.py

@@ -108,7 +108,7 @@ class Dwi2Fod(shell.Task["Dwi2Fod.Outputs"]):
     shells: list[float] | None = shell.arg(
         default=None,
         argstr="-shells",
-        help="""specify one or more b-values to use during processing, as a comma-separated list of the desired approximate b-values (b-values are clustered to allow for small deviations). Note that some commands are incompatible with multiple b-values, and will report an error if more than one b-value is provided. 
+        help="""specify one or more b-values to use during processing, as a comma-separated list of the desired approximate b-values (b-values are clustered to allow for small deviations). Note that some commands are incompatible with multiple b-values, and will report an error if more than one b-value is provided.
 WARNING: note that, even though the b=0 volumes are never referred to as a 'shell' in the literature, they still have to be explicitly included in the list of b-values as provided to the -shell option! Several algorithms that include the b=0 volumes in their computations may otherwise return an undesired result.""",
         sep=",",
     )

pydra/tasks/mrtrix3/v3_1/dwidenoise.py

@@ -83,8 +83,8 @@ class DwiDenoise(shell.Task["DwiDenoise.Outputs"]):
     estimator: str | None = shell.arg(
         default=None,
         argstr="-estimator",
-        help="""Select the noise level estimator (default = Exp2), either: 
-* Exp1: the original estimator used in Veraart et al. (2016), or 
+        help="""Select the noise level estimator (default = Exp2), either:
+* Exp1: the original estimator used in Veraart et al. (2016), or
 * Exp2: the improved estimator introduced in Cordero-Grande et al. (2019).""",
         allowed_values=["exp1", "exp2"],
     )

pydra/tasks/mrtrix3/v3_1/dwiextract.py

@@ -94,7 +94,7 @@ class DwiExtract(shell.Task["DwiExtract.Outputs"]):
     shells: list[float] | None = shell.arg(
         default=None,
         argstr="-shells",
-        help="""specify one or more b-values to use during processing, as a comma-separated list of the desired approximate b-values (b-values are clustered to allow for small deviations). Note that some commands are incompatible with multiple b-values, and will report an error if more than one b-value is provided. 
+        help="""specify one or more b-values to use during processing, as a comma-separated list of the desired approximate b-values (b-values are clustered to allow for small deviations). Note that some commands are incompatible with multiple b-values, and will report an error if more than one b-value is provided.
 WARNING: note that, even though the b=0 volumes are never referred to as a 'shell' in the literature, they still have to be explicitly included in the list of b-values as provided to the -shell option! Several algorithms that include the b=0 volumes in their computations may otherwise return an undesired result.""",
         sep=",",
     )

pydra/tasks/mrtrix3/v3_1/fod2dec.py

@@ -51,7 +51,7 @@ class Fod2Dec(shell.Task["Fod2Dec.Outputs"]):
     contrast: ImageIn | None = shell.arg(
         default=None,
         argstr="-contrast",
-        help="""Weight the computed DEC map by the provided image contrast. If the contrast has a different image grid, the DEC map is first resliced and renormalised. To achieve panchromatic sharpening, provide an image with a higher spatial resolution than the input FOD image; e.g., a T1 anatomical volume. Only the DEC is subject to the mask, so as to allow for partial colouring of the contrast image. 
+        help="""Weight the computed DEC map by the provided image contrast. If the contrast has a different image grid, the DEC map is first resliced and renormalised. To achieve panchromatic sharpening, provide an image with a higher spatial resolution than the input FOD image; e.g., a T1 anatomical volume. Only the DEC is subject to the mask, so as to allow for partial colouring of the contrast image.
 Default when this option is *not* provided: integral of input FOD, subject to the same mask/threshold as used for DEC computation.""",
     )
     lum: bool = shell.arg(

pydra/tasks/mrtrix3/v3_1/mredit.py

@@ -58,13 +58,13 @@ class MrEdit(shell.Task["MrEdit.Outputs"]):
         help="""fill one or more planes on a particular image axis""",
         sep=" ",
     )
-    sphere: MultiInputObj[tuple[list[float], list[float], list[float]]] | None = (
-        shell.arg(
-            default=None,
-            argstr="-sphere",
-            help="""draw a sphere with radius in mm""",
-            sep=" ",
-        )
+    sphere: MultiInputObj[
+        tuple[list[float], list[float], list[float]]
+    ] | None = shell.arg(
+        default=None,
+        argstr="-sphere",
+        help="""draw a sphere with radius in mm""",
+        sep=" ",
     )
     voxel: MultiInputObj[tuple[list[float], list[float]]] | None = shell.arg(
         default=None,

pydra/tasks/mrtrix3/v3_1/mrregister.py

@@ -427,17 +427,17 @@ class Outputs(shell.Outputs):
             path_template="transformed.mif",
             help="""image1 after registration transformed and regridded to the space of image2. Note that -transformed needs to be repeated for each contrast if multi-contrast registration is used.""",
         )
-        transformed_midway: MultiInputObj[tuple[ImageOut, ImageOut]] | bool | None = (
-            shell.outarg(
-                default=None,
-                argstr="-transformed_midway",
-                path_template=(
-                    "transformed_midway0.mif",
-                    "transformed_midway1.mif",
-                ),
-                help="""image1 and image2 after registration transformed and regridded to the midway space. Note that -transformed_midway needs to be repeated for each contrast if multi-contrast registration is used.""",
-                sep=" ",
-            )
+        transformed_midway: MultiInputObj[
+            tuple[ImageOut, ImageOut]
+        ] | bool | None = shell.outarg(
+            default=None,
+            argstr="-transformed_midway",
+            path_template=(
+                "transformed_midway0.mif",
+                "transformed_midway1.mif",
+            ),
+            help="""image1 and image2 after registration transformed and regridded to the midway space. Note that -transformed_midway needs to be repeated for each contrast if multi-contrast registration is used.""",
+            sep=" ",
         )
         rigid: File | bool | None = shell.outarg(
             default=None,