nipy · effigies · Apr 5, 2023 · Apr 5, 2023 · Apr 5, 2023 · Apr 5, 2023
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -1,19 +1,80 @@
-# Commits with messages like "STY: black" or "run black"
+# Wed Apr 5 14:01:05 2023 -0400 - effigies@gmail.com - STY: black [ignore-rev]
+a9ce9b78a402ebacf7726ad6454bb75b1447f52f
+# Wed Sep 14 14:12:07 2022 -0400 - mathiasg@stanford.edu - STY: Black
+f4a779223c6b0dffa47138d24ec9ef378c7164a9
+# Tue Apr 19 14:09:31 2022 -0400 - markiewicz@stanford.edu - STY: black [ignore-rev]
+b9716ebd46541f7fb1b96a94cc35b5e2ea6c3bba
+# Fri Apr 15 06:59:48 2022 -0700 - markiewicz@stanford.edu - STY: black [ignore-rev]
+d223fbccda6dee0ef39e00084296a3292f2ccf87
+# Fri Apr 8 21:34:43 2022 -0400 - markiewicz@stanford.edu - STY: black [ignore-rev]
+e3f56da124fd58041018c2e70d16a130ef189a66
+# Sun Apr 3 10:27:07 2022 -0400 - markiewicz@stanford.edu - STY: black [ignore-rev]
+988c382ebfc7df964874b6287b9d9e27e274a4a4
+# Sat Apr 2 21:32:56 2022 -0400 - markiewicz@stanford.edu - STY: black [ignore-rev]
+230fac6149d4dfbd5da669a983332a1fe318ef57
+# Sat Apr 2 12:49:15 2022 -0400 - markiewicz@stanford.edu - STY/TEST: Make specs and run black [ignore-rev]
+2ba8dacb8cc1f6f9c5b15b1cfb7b0395d45dcfb3
+# Sun Mar 20 21:19:39 2022 -0400 - markiewicz@stanford.edu - STY: black [ignore-rev]
+87cc1b54981113024ec3fd594881f72cf67513fb
+# Wed Dec 8 17:02:09 2021 -0500 - markiewicz@stanford.edu - STY: black [ignore-rev]
+5ac2f18ac116832d81a13f0c83e0a6aeda1457cf
+# Thu Dec 2 09:30:42 2021 -0500 - markiewicz@stanford.edu - STY: black
+ee50279ebf061a70ff502e7d2e51385b285cfda4
+# Tue Oct 26 11:18:02 2021 +0200 - code@oscaresteban.es - sty: run black
+5d9adbbb77b7047b9b47cd2fa079dee0094cfc91
+# Wed Oct 20 12:07:15 2021 +0200 - fabio.bernardoni@uniklinikum-dresden.de - run black on the preprocess.py file to improve formatting
+674e9b0eeca082efb5322b61fea57ee89a3e4a24
+# Wed Oct 13 16:08:23 2021 -0400 - markiewicz@stanford.edu - ENH: Add expected steps for FreeSurfer 7 recon-all (#3389)
+8f7c0bf2ec9c819844a2736a9ae2f6eef19a8e7f
+# Wed Oct 13 14:26:48 2021 -0400 - markiewicz@stanford.edu - STY: black
+d8dbc6f7b6a5385535e2fa53b7c6af7aa1370f46
+# Wed Sep 29 16:53:54 2021 +0200 - code@oscaresteban.es - sty: run black on affected files
+5f280da629bb7b5dce908633d2deea85b55dd67b
+# Thu Jun 24 17:43:22 2021 +0200 - code@oscaresteban.es - sty: run black
+135ce497a18adbe0811441c2b720910ec549aa6f
+# Thu Sep 23 08:56:28 2021 -0400 - markiewicz@stanford.edu - STY: black
+f69b3fb09560616822737764bb07272cd587e4a0
+# Fri Apr 30 17:19:55 2021 -0400 - markiewicz@stanford.edu - STY: black
+04718ac71436b6f283af7575dda0f6998b64f893
+# Fri Apr 30 16:50:00 2021 -0400 - markiewicz@stanford.edu - STY: black
 12deb959cccc431fb8222cc5854f1c92a0080021
+# Thu Apr 1 12:26:08 2021 -0400 - markiewicz@stanford.edu - STY: black
 f64bf338f630a9ee5cbe7a3ec98c68292897e720
+# Thu Dec 3 09:24:05 2020 +1100 - tom.g.close@gmail.com - run black over touched files
+c81259bc3b28baa1f18f95f6b056c228c6bfd115
+# Fri Aug 14 17:15:15 2020 -0400 - markiewicz@stanford.edu - STY: Black
 83358d7f17aac07cb90d0330f11ea2322e2974d8
+# Sat Mar 14 12:44:20 2020 -0400 - markiewicz@stanford.edu - STY: black
 faef7d0f93013a700c882f709e98fb3cd36ebb03
+# Sun Mar 8 15:05:28 2020 +0100 - 3453485+daniel-ge@users.noreply.github.com - FIX: get length of generator + STY: Black
+02991da67458b879d7c6360aa6457eb3c1bd5a07
+# Wed Mar 4 16:30:39 2020 -0500 - markiewicz@stanford.edu - STY: black
 d50c1858564c0b3073fb23c54886a0454cb66afa
+# Thu Feb 27 15:08:42 2020 -0800 - code@oscaresteban.es - sty: black
 417b8897a116fcded5000e21e2b6ccbe29452a52
+# Thu Jan 2 11:29:05 2020 -0800 - code@oscaresteban.es - sty: black
 aaf677a87f64c485f3e305799e4a5dc73b69e5fb
+# Sun Dec 29 17:47:51 2019 -0800 - code@oscaresteban.es - sty: black
 f763008442d88d8ce00ec266698268389415f8d6
+# Thu Jan 2 11:29:05 2020 -0800 - code@oscaresteban.es - sty: black
 b1eccafd4edc8503b02d715f5b5f6f783520fdf9
+# Sun Dec 29 17:47:51 2019 -0800 - code@oscaresteban.es - sty: black
 70db90349598cc7f26a4a513779529fba7d0a797
+# Thu Dec 19 09:22:22 2019 -0500 - markiewicz@stanford.edu - STY: Black
 6c1d91d71f6f0db0e985bd2adc34206442b0653d
+# Thu Dec 19 15:51:11 2019 -0500 - markiewicz@stanford.edu - STY: Black
 97bdbd5f48ab242de5288ba4715192a27619a803
+# Fri Nov 15 14:38:10 2019 -0500 - steve@steventilley.com - run black
 78fa360f5b785224349b8b85b07e510d2233bb63
+# Fri Nov 15 14:34:03 2019 -0500 - steve@steventilley.com - run black
 7f85f43a34de8bff8e634232c939b17cee8e8fc5
+# Thu Nov 14 11:14:51 2019 -0500 - markiewicz@stanford.edu - Merge pull request #3096 from effigies/sty/black
+1a869991adc024577536689d557fc748c764f15d
+# Thu Nov 14 09:15:20 2019 -0500 - markiewicz@stanford.edu - STY: Black setup.py
 9c50b5daa797def5672dd057155b0e2c658853e2
+# Thu Nov 14 09:14:38 2019 -0500 - markiewicz@stanford.edu - STY: Black for tools/
 47194993ae14aceeec436cfb3769def667196668
+# Wed Nov 13 23:41:15 2019 -0500 - markiewicz@stanford.edu - STY: Black
 75653feadc6667d5313d83e9c62a5d5819771a9c
+# Tue Nov 12 09:43:34 2019 -0500 - markiewicz@stanford.edu - STY: Black files pre-merge
 497b44d680eee0892fa59c6aaaae22a17d70a536
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -105,13 +105,13 @@ jobs:
             depends: REQUIREMENTS
             deb-depends: true
             nipype-extras: doc,tests,profiler,duecredit,ssh
-          - os: ubuntu-20.04
-            python-version: 3.8
-            check: test
-            pip-flags: ''
-            depends: NUMPY123
-            deb-depends: true
-            nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
+          # - os: ubuntu-20.04
+          #   python-version: 3.8
+          #   check: test
+          #   pip-flags: ''
+          #   depends: NUMPY123
+          #   deb-depends: true
+          #   nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
     env:
       DEPENDS: ${{ matrix.depends }}
       CHECK_TYPE: ${{ matrix.check }}

diff --git a/Makefile b/Makefile
@@ -9,6 +9,10 @@ PYTHON ?= python
 zipdoc: html
 	zip documentation.zip doc/_build/html
 
+.git-blame-ignore-revs: .git/HEAD
+	git log --grep "\[ignore-rev\]\|STY: black\|run black" -i --pretty=format:"# %ad - %ae - %s%n%H" > .git-blame-ignore-revs
+	echo >> .git-blame-ignore-revs
+
 sdist: zipdoc
 	@echo "Building source distribution..."
 	$(PYTHON) setup.py sdist

diff --git a/nipype/algorithms/misc.py b/nipype/algorithms/misc.py
@@ -968,7 +968,6 @@ class CalculateNormalizedMoments(BaseInterface):
     output_spec = CalculateNormalizedMomentsOutputSpec
 
     def _run_interface(self, runtime):
-
         self._moments = calc_moments(self.inputs.timeseries_file, self.inputs.moment)
         return runtime
 

diff --git a/nipype/algorithms/tests/test_ErrorMap.py b/nipype/algorithms/tests/test_ErrorMap.py
@@ -10,7 +10,6 @@
 
 
 def test_errormap(tmpdir):
-
     # Single-Spectual
     # Make two fake 2*2*2 voxel volumes
     # John von Neumann's birthday

diff --git a/nipype/algorithms/tests/test_misc.py b/nipype/algorithms/tests/test_misc.py
@@ -13,7 +13,6 @@
 
 
 def test_CreateNifti(create_analyze_pair_file_in_directory):
-
     filelist, outdir = create_analyze_pair_file_in_directory
 
     create_nifti = misc.CreateNifti()
@@ -35,7 +34,6 @@ def test_CreateNifti(create_analyze_pair_file_in_directory):
 
 
 def test_CalculateMedian(create_analyze_pair_file_in_directory):
-
     mean = misc.CalculateMedian()
 
     with pytest.raises(TypeError):

diff --git a/nipype/algorithms/tests/test_normalize_tpms.py b/nipype/algorithms/tests/test_normalize_tpms.py
@@ -16,7 +16,6 @@
 
 
 def test_normalize_tpms(tmpdir):
-
     in_mask = example_data("tpms_msk.nii.gz")
     mskdata = np.asanyarray(nb.load(in_mask).dataobj)
     mskdata[mskdata > 0.0] = 1.0

diff --git a/nipype/conftest.py b/nipype/conftest.py
@@ -27,7 +27,6 @@ def _docdir(request):
     # Trigger ONLY for the doctests.
     doctest_plugin = request.config.pluginmanager.getplugin("doctest")
     if isinstance(request.node, doctest_plugin.DoctestItem):
-
         # Get the fixture dynamically by its name.
         tmpdir = pp.local(data_dir)
 

diff --git a/nipype/external/cloghandler.py b/nipype/external/cloghandler.py
@@ -151,7 +151,9 @@ def __init__(
                 )
         try:
             BaseRotatingHandler.__init__(self, filename, mode, encoding)
-        except TypeError:  # Due to a different logging release without encoding support  (Python 2.4.1 and earlier?)
+        except (
+            TypeError
+        ):  # Due to a different logging release without encoding support  (Python 2.4.1 and earlier?)
             BaseRotatingHandler.__init__(self, filename, mode)
             self.encoding = encoding
 

diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py
@@ -1133,7 +1133,6 @@ class ClipLevel(AFNICommandBase):
     output_spec = ClipLevelOutputSpec
 
     def aggregate_outputs(self, runtime=None, needed_outputs=None):
-
         outputs = self._outputs()
 
         outfile = os.path.join(os.getcwd(), "stat_result.json")
@@ -2295,7 +2294,6 @@ class Seg(AFNICommandBase):
     output_spec = AFNICommandOutputSpec
 
     def aggregate_outputs(self, runtime=None, needed_outputs=None):
-
         import glob
 
         outputs = self._outputs()

diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py
@@ -302,7 +302,6 @@ class BrickStat(AFNICommandBase):
     output_spec = BrickStatOutputSpec
 
     def aggregate_outputs(self, runtime=None, needed_outputs=None):
-
         outputs = self._outputs()
 
         outfile = os.path.join(os.getcwd(), "stat_result.json")
@@ -2595,7 +2594,6 @@ def _format_arg(self, name, spec, value):
 
 
 class ResampleInputSpec(AFNICommandInputSpec):
-
     in_file = File(
         desc="input file to 3dresample",
         argstr="-inset %s",

diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py
@@ -389,7 +389,6 @@ def run(self, cwd=None, ignore_exception=None, **inputs):
         self._check_version_requirements(self.inputs)
 
         with rtc(self, cwd=cwd, redirect_x=self._redirect_x) as runtime:
-
             # Grab inputs now, as they should not change during execution
             inputs = self.inputs.get_traitsfree()
             outputs = None

diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py
@@ -405,7 +405,6 @@ class MultiObject(traits.List):
     """Abstract class - shared functionality of input and output MultiObject"""
 
     def validate(self, objekt, name, value):
-
         # want to treat range and other sequences (except str) as list
         if not isinstance(value, (str, bytes)) and isinstance(value, Sequence):
             value = list(value)

diff --git a/nipype/interfaces/brainsuite/brainsuite.py b/nipype/interfaces/brainsuite/brainsuite.py
@@ -19,7 +19,6 @@
 
 
 class BseInputSpec(CommandLineInputSpec):
-
     inputMRIFile = File(mandatory=True, argstr="-i %s", desc="input MRI volume")
     outputMRIVolume = File(
         desc="output brain-masked MRI volume. If unspecified, output file name will be auto generated.",

diff --git a/nipype/interfaces/cat12/preprocess.py b/nipype/interfaces/cat12/preprocess.py
@@ -537,7 +537,6 @@ def _list_outputs(self):
         ]
 
         for tidx, tissue in enumerate(["gm", "wm", "csf"]):
-
             for image, prefix in [("modulated", "mw"), ("dartel", "r"), ("native", "")]:
                 outtype = f"{tissue}_output_{image}"
                 if isdefined(getattr(self.inputs, outtype)) and getattr(
@@ -594,7 +593,6 @@ def _list_outputs(self):
 
 
 class CAT12SANLMDenoisingInputSpec(SPMCommandInputSpec):
-
     in_files = InputMultiPath(
         ImageFileSPM(exists=True),
         field="data",
@@ -679,7 +677,6 @@ class CAT12SANLMDenoisingInputSpec(SPMCommandInputSpec):
 
 
 class CAT12SANLMDenoisingOutputSpec(TraitedSpec):
-
     out_file = File(desc="out file")
 
 

diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py
@@ -272,7 +272,6 @@ def cmat(
 
     dis = 0
     for i in range(endpoints.shape[0]):
-
         # ROI start => ROI end
         try:
             startROI = int(

diff --git a/nipype/interfaces/dcm2nii.py b/nipype/interfaces/dcm2nii.py
@@ -119,7 +119,8 @@ class Dcm2nii(CommandLine):
     >>> converter.inputs.gzip_output = True
     >>> converter.inputs.output_dir = '.'
     >>> converter.cmdline  # doctest: +ELLIPSIS
-    'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n functional_1.dcm'"""
+    'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n functional_1.dcm'
+    """
 
     input_spec = Dcm2niiInputSpec
     output_spec = Dcm2niiOutputSpec

diff --git a/nipype/interfaces/freesurfer/model.py b/nipype/interfaces/freesurfer/model.py
@@ -449,7 +449,6 @@ class GLMFitInputSpec(FSTraitedSpec):
 
 
 class GLMFitOutputSpec(TraitedSpec):
-
     glm_dir = Directory(exists=True, desc="output directory")
     beta_file = File(exists=True, desc="map of regression coefficients")
     error_file = File(desc="map of residual error")

diff --git a/nipype/interfaces/freesurfer/petsurfer.py b/nipype/interfaces/freesurfer/petsurfer.py
@@ -24,7 +24,6 @@
 
 
 class GTMSegInputSpec(FSTraitedSpec):
-
     subject_id = traits.String(argstr="--s %s", desc="subject id", mandatory=True)
 
     xcerseg = traits.Bool(
@@ -136,7 +135,6 @@ def _list_outputs(self):
 
 
 class GTMPVCInputSpec(FSTraitedSpec):
-
     in_file = File(
         exists=True,
         argstr="--i %s",
@@ -422,7 +420,6 @@ class GTMPVCInputSpec(FSTraitedSpec):
 
 
 class GTMPVCOutputSpec(TraitedSpec):
-
     pvc_dir = Directory(desc="output directory")
     ref_file = File(desc="Reference TAC in .dat")
     hb_nifti = File(desc="High-binding TAC in nifti")

diff --git a/nipype/interfaces/freesurfer/preprocess.py b/nipype/interfaces/freesurfer/preprocess.py
@@ -1833,7 +1833,6 @@ class BBRegister(FSCommand):
     output_spec = BBRegisterOutputSpec
 
     def _list_outputs(self):
-
         outputs = self.output_spec().get()
         _in = self.inputs
 
@@ -1893,7 +1892,6 @@ def _format_arg(self, name, spec, value):
         return super(BBRegister, self)._format_arg(name, spec, value)
 
     def _gen_filename(self, name):
-
         if name == "out_reg_file":
             return self._list_outputs()[name]
         return None
@@ -2180,7 +2178,6 @@ def _gen_filename(self, name):
 
 
 class RobustRegisterInputSpec(FSTraitedSpec):
-
     source_file = File(
         exists=True, mandatory=True, argstr="--mov %s", desc="volume to be registered"
     )
@@ -2302,7 +2299,6 @@ class RobustRegisterInputSpec(FSTraitedSpec):
 
 
 class RobustRegisterOutputSpec(TraitedSpec):
-
     out_reg_file = File(exists=True, desc="output registration file")
     registered_file = File(exists=True, desc="output image with registration applied")
     weights_file = File(exists=True, desc="image of weights used")
@@ -2388,7 +2384,6 @@ def _list_outputs(self):
 
 
 class FitMSParamsInputSpec(FSTraitedSpec):
-
     in_files = traits.List(
         File(exists=True),
         argstr="%s",
@@ -2408,7 +2403,6 @@ class FitMSParamsInputSpec(FSTraitedSpec):
 
 
 class FitMSParamsOutputSpec(TraitedSpec):
-
     t1_image = File(exists=True, desc="image of estimated T1 relaxation values")
     pd_image = File(exists=True, desc="image of estimated proton density values")
     t2star_image = File(exists=True, desc="image of estimated T2* values")
@@ -2466,7 +2460,6 @@ def _gen_filename(self, name):
 
 
 class SynthesizeFLASHInputSpec(FSTraitedSpec):
-
     fixed_weighting = traits.Bool(
         position=1,
         argstr="-w",
@@ -2495,7 +2488,6 @@ class SynthesizeFLASHInputSpec(FSTraitedSpec):
 
 
 class SynthesizeFLASHOutputSpec(TraitedSpec):
-
     out_file = File(exists=True, desc="synthesized FLASH acquisition")
 
 

diff --git a/nipype/interfaces/freesurfer/tests/test_FSSurfaceCommand.py b/nipype/interfaces/freesurfer/tests/test_FSSurfaceCommand.py
@@ -35,7 +35,6 @@ def test_associated_file(tmpdir):
         ("./lh.white", "./lh.pial"),
         (fsavginfo["white"], fsavginfo["pial"]),
     ]:
-
         # Unspecified paths, possibly with missing hemisphere information,
         # are equivalent to using the same directory and hemisphere
         for name in ("pial", "lh.pial", pial):
-Original file line number
+Diff line change
@@ Expand Up / @@ -272,7 +272,6 @@ def cmat( @@
         dis = 0
         for i in range(endpoints.shape[0]):
             # ROI start => ROI end
             try:
                 startROI = int(
@@ Expand Down @@