[DATALAD RUNCMD] Run codespell throughout

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

Author: yarikoptic

doc/changelog/0.X.X-changelog.rst

@@ -15,7 +15,7 @@
 * ENH: Generate Dockerfiles with neurodocker (https://github.com/nipy/nipype/pull/2202)
 * ENH: FLAIR options for recon-all (https://github.com/nipy/nipype/pull/2279)
 * ENH: Config option for setting maxtasksperchild when multiprocessing (https://github.com/nipy/nipype/pull/2284)
-* FIX: Testing maintainance and improvements (https://github.com/nipy/nipype/pull/2252)
+* FIX: Testing maintenance and improvements (https://github.com/nipy/nipype/pull/2252)
 * ENH: Add elapsed_time and final metric_value to ants.Registration (https://github.com/nipy/nipype/pull/1985)
 * ENH: Improve terminal_output feature (https://github.com/nipy/nipype/pull/2209)
 * ENH: Simple interface to FSL std2imgcoords (https://github.com/nipy/nipype/pull/2209, prev #1398)
@@ -39,7 +39,7 @@
 * ENH: Add cosine-basis high-pass-filter to CompCor, allow skip of initial volumes (https://github.com/nipy/nipype/pull/2107, https://github.com/nipy/nipype/pull/#2122)
 * FIX: Catch more dcm2niix DTI conversions (https://github.com/nipy/nipype/pull/2110)
 * FIX: Retrieve aseg + wmparc stats properly (https://github.com/nipy/nipype/pull/2117)
-* ENH: ANTs MeasureImageSimilarity Inteface (https://github.com/nipy/nipype/pull/2128)
+* ENH: ANTs MeasureImageSimilarity Interface (https://github.com/nipy/nipype/pull/2128)
 * FIX: CompCor filter_basis of correct size, pre-filter column headers (https://github.com/nipy/nipype/pull/2136, https://github.com/nipy/nipype/pull/2138)
 * ENH: FreeSurfer lta_convert and mri_coreg interfaces (https://github.com/nipy/nipype/pull/2140, https://github.com/nipy/nipype/pull/2172)
 * ENH: Speed up S3DataGrabber (https://github.com/nipy/nipype/pull/2143)
@@ -311,7 +311,7 @@ Release 0.11.0 (September 15, 2015)
 Release 0.10.0 (October 10, 2014)
 =================================
 
-* ENH: New miscelaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
+* ENH: New miscellaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
        to enable parallel processing of very large images.
 * ENH: Updated FSL interfaces: BEDPOSTX and XFibres, former interfaces are still
        available with the version suffix: BEDPOSTX4 and XFibres4. Added gpu
@@ -320,7 +320,7 @@ Release 0.10.0 (October 10, 2014)
 * ENH: New dipy interfaces: Denoise, Resample
 * ENH: New Freesurfer interfaces: Tkregister2 (for conversion of fsl style matrices to freesurfer format), MRIPretess
 * ENH: New FSL interfaces: WarpPoints, WarpPointsToStd, EpiReg, ProbTrackX2, WarpUtils, ConvertWarp
-* ENH: New miscelaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise
+* ENH: New miscellaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise
 * ENH: New AFNI interfaces:  Eval, Means, SVMTest, SVMTrain
 * ENH: FUGUE interface has been refactored to use the name_template system, 3 examples
        added to doctests, some bugs solved.
@@ -510,7 +510,7 @@ Release 0.5 (Mar 10, 2012)
 * API: By default inputs are removed from Node working directory
 * API: InterfaceResult class is now versioned and stores class type not instance
 * API: Added FIRST interface
-* API: Added max_jobs paramter to plugin_args. limits the number of jobs
+* API: Added max_jobs parameter to plugin_args. limits the number of jobs
        executing at any given point in time
 * API: crashdump_dir is now a config execution option
 * API: new config execution options for controlling hash checking, execution and

doc/changelog/1.X.X-changelog.rst

@@ -426,7 +426,7 @@ Python 1.2.3 will be the last version to support Python 3.4.
 
   * FIX: ANTS LaplacianThickness cmdline opts fixed up (https://github.com/nipy/nipype/pull/2846)
   * FIX: Resolve LinAlgError during SVD (https://github.com/nipy/nipype/pull/2838)
-  * ENH: Add interfaces wrapping DIPY worflows (https://github.com/nipy/nipype/pull/2830)
+  * ENH: Add interfaces wrapping DIPY workflows (https://github.com/nipy/nipype/pull/2830)
   * ENH: Update BIDSDataGrabber for pybids 0.7 (https://github.com/nipy/nipype/pull/2737)
   * ENH: Add FSL `eddy_quad` interface (https://github.com/nipy/nipype/pull/2825)
   * ENH: Support tckgen -select in MRtrix3 v3+ (https://github.com/nipy/nipype/pull/2823)

nipype/algorithms/icc.py

@@ -150,8 +150,8 @@ def ICC_rep_anova(Y, projection_matrix=None):
     SSR = SST - SSC - SSE
     MSR = SSR / dfr
 
-    # ICC(3,1) = (mean square subjeT - mean square error) /
-    #            (mean square subjeT + (k-1)*-mean square error)
+    # ICC(3,1) = (mean square subject - mean square error) /
+    #            (mean square subject + (k-1)*-mean square error)
     ICC = (MSR - MSE) / (MSR + dfc * MSE)
 
     e_var = MSE  # variance of error

nipype/interfaces/ants/segmentation.py

@@ -1009,10 +1009,10 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
         runtime = super(BrainExtraction, self)._run_interface(runtime)
 
         # Still, double-check if it didn't found N4
-        if "we cant find" in runtime.stdout:
+        if "we can't find" in runtime.stdout:
             for line in runtime.stdout.split("\n"):
-                if line.strip().startswith("we cant find"):
-                    tool = line.strip().replace("we cant find the", "").split(" ")[0]
+                if line.strip().startswith("we can't find"):
+                    tool = line.strip().replace("we can't find the", "").split(" ")[0]
                     break
 
             errmsg = (

nipype/interfaces/base/specs.py

@@ -177,7 +177,7 @@ def get_traitsfree(self, **kwargs):
         return out
 
     def _clean_container(self, objekt, undefinedval=None, skipundefined=False):
-        """Convert a traited obejct into a pure python representation."""
+        """Convert a traited object into a pure python representation."""
         if isinstance(objekt, TraitDictObject) or isinstance(objekt, dict):
             out = {}
             for key, val in list(objekt.items()):

nipype/interfaces/spm/tests/test_utils.py

@@ -23,7 +23,7 @@ def test_coreg():
     _, tgt, _ = split_filename(target)
     mat = os.path.join(pth, "%s_to_%s.mat" % (mov, tgt))
     invmat = fname_presuffix(mat, prefix="inverse_")
-    scrpt = coreg._make_matlab_command(None)
+    script = coreg._make_matlab_command(None)
     assert coreg.inputs.mat == mat
     assert coreg.inputs.invmat == invmat
 
@@ -35,11 +35,11 @@ def test_apply_transform():
     assert applymat.inputs.matlab_cmd == "mymatlab"
     applymat.inputs.in_file = moving
     applymat.inputs.mat = mat
-    scrpt = applymat._make_matlab_command(None)
+    script = applymat._make_matlab_command(None)
     expected = "[p n e v] = spm_fileparts(V.fname);"
-    assert expected in scrpt
+    assert expected in script
     expected = "V.mat = transform.M * V.mat;"
-    assert expected in scrpt
+    assert expected in script
 
 
 def test_reslice():

nipype/interfaces/tests/test_io.py

@@ -708,10 +708,10 @@ def _mock_get_ssh_client(self):
 
 
 def test_ExportFile(tmp_path):
-    testin = tmp_path / "in.txt"
-    testin.write_text("test string", encoding='utf-8')
+    testing = tmp_path / "in.txt"
+    testing.write_text("test string", encoding='utf-8')
     i = nio.ExportFile()
-    i.inputs.in_file = str(testin)
+    i.inputs.in_file = str(testing)
     i.inputs.out_file = str(tmp_path / "out.tsv")
     i.inputs.check_extension = True
     with pytest.raises(RuntimeError):

tools/ex2rst

@@ -98,7 +98,7 @@ def exfile2rst(filename):
             proc_line = None
             # handle doc start
             if not indocs:
-                # guarenteed to start with """
+                # guaranteed to start with """
                 if len(cleanline) > 3 \
                   and (cleanline.endswith('"""') \
                        or cleanline.endswith("'''")):