Merge pull request #3549 from yarikoptic/enh-codespell

codespell: config, workflow, typos fixed

Author: effigies

.codespellrc

@@ -0,0 +1,12 @@
+[codespell]
+skip = .git,*.pdf,*.svg,external
+# nd,nam - import module short
+# fith - oddness coming from AFNI
+# whos - smth used in matlab things
+# SMAL - Stanford CNI MRS Library
+# Suh - name
+# noo,crasher - field/var name used
+# Reson - short journal name
+# ALS, FWE - neuroimaging specific abbrevs
+# Comision - foreign word used
+ignore-words-list = te,inport,objekt,jist,nd,hel,inout,fith,whos,fot,ue,shs,smal,nam,filetest,suh,noo,reson,als,fwe,crasher,comision

.github/workflows/codespell.yml

@@ -0,0 +1,19 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v1

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)
@@ -311,16 +311,16 @@ 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
        versions of BEDPOSTX: BEDPOSTXGPU, BEDPOSTX5GPU, and BEDPOSTX4GPU
-* ENH: Added experimental support for MIPAV algorithms thorugh JIST plugins
+* ENH: Added experimental support for MIPAV algorithms through JIST plugins
 * 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

@@ -443,7 +443,7 @@ 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/registration.py

@@ -865,7 +865,7 @@ class Registration(ANTSCommand):
 --write-composite-transform 0'
 
     One can use multiple similarity metrics in a single registration stage.The Node below first
-    performs a linear registation using only the Mutual Information ('Mattes')-metric.
+    performs a linear registration using only the Mutual Information ('Mattes')-metric.
     In a second stage, it performs a non-linear registration ('Syn') using both a
     Mutual Information and a local cross-correlation ('CC')-metric. Both metrics are weighted
     equally ('metric_weight' is .5 for both). The Mutual Information- metric uses 32 bins.

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/base/tests/test_core.py

@@ -288,28 +288,28 @@ class WithoutInput(WithInput):
         _version = "0.6"
 
     has = WithInput()
-    hasnt = WithoutInput()
+    hasnot = WithoutInput()
     trying_anyway = WithoutInput(foo=3)
     assert has.inputs.foo == 3
-    assert not nib.isdefined(hasnt.inputs.foo)
+    assert not nib.isdefined(hasnot.inputs.foo)
     assert trying_anyway.inputs.foo == 3
 
     has.run()
-    hasnt.run()
+    hasnot.run()
     with pytest.raises(Exception):
         trying_anyway.run()
 
     # Still settable
     has.inputs.foo = 4
-    hasnt.inputs.foo = 4
+    hasnot.inputs.foo = 4
     trying_anyway.inputs.foo = 4
     assert has.inputs.foo == 4
-    assert hasnt.inputs.foo == 4
+    assert hasnot.inputs.foo == 4
     assert trying_anyway.inputs.foo == 4
 
     has.run()
     with pytest.raises(Exception):
-        hasnt.run()
+        hasnot.run()
     with pytest.raises(Exception):
         trying_anyway.run()
 

nipype/interfaces/cmtk/nx.py

@@ -542,8 +542,8 @@ def _run_interface(self, runtime):
             "Saving extra measure file to %s in Pickle format",
             op.abspath(out_pickled_extra_measures),
         )
-        with open(out_pickled_extra_measures, "w") as fo:
-            pickle.dump(dict_measures, fo)
+        with open(out_pickled_extra_measures, "w") as f:
+            pickle.dump(dict_measures, f)
 
         iflogger.info("Saving MATLAB measures as %s", matlab)
 

nipype/interfaces/freesurfer/longitudinal.py

@@ -73,7 +73,7 @@ class RobustTemplateInputSpec(FSTraitedSpecOpenMP):
     )
     initial_timepoint = traits.Int(
         argstr="--inittp %d",
-        desc="use TP# for spacial init (default random), 0: no init",
+        desc="use TP# for special init (default random), 0: no init",
     )
     fixed_timepoint = traits.Bool(
         default_value=False,

nipype/interfaces/fsl/model.py

@@ -2026,7 +2026,7 @@ class ClusterInputSpec(FSLCommandInputSpec):
         argstr="--stdvol=%s", desc="filename for standard-space volume"
     )
     num_maxima = traits.Int(argstr="--num=%d", desc="no of local maxima to report")
-    warpfield_file = File(argstr="--warpvol=%s", desc="file contining warpfield")
+    warpfield_file = File(argstr="--warpvol=%s", desc="file containing warpfield")
 
 
 class ClusterOutputSpec(TraitedSpec):

nipype/interfaces/fsl/preprocess.py

@@ -376,12 +376,12 @@ class FAST(FSLCommand):
     Examples
     --------
     >>> from nipype.interfaces import fsl
-    >>> fastr = fsl.FAST()
-    >>> fastr.inputs.in_files = 'structural.nii'
-    >>> fastr.inputs.out_basename = 'fast_'
-    >>> fastr.cmdline
+    >>> fast = fsl.FAST()
+    >>> fast.inputs.in_files = 'structural.nii'
+    >>> fast.inputs.out_basename = 'fast_'
+    >>> fast.cmdline
     'fast -o fast_ -S 1 structural.nii'
-    >>> out = fastr.run()  # doctest: +SKIP
+    >>> out = fast.run()  # doctest: +SKIP
 
     """
 

nipype/interfaces/io.py

@@ -1678,7 +1678,7 @@ class FSSourceOutputSpec(TraitedSpec):
         File(exists=True), desc="Inflated surface meshes", loc="surf"
     )
     pial = OutputMultiPath(
-        File(exists=True), desc="Gray matter/pia mater surface meshes", loc="surf"
+        File(exists=True), desc="Gray matter/pia matter surface meshes", loc="surf"
     )
     area_pial = OutputMultiPath(
         File(exists=True),

nipype/interfaces/mrtrix/tracking.py

@@ -388,14 +388,14 @@ class StreamlineTrack(CommandLine):
     -------
 
     >>> import nipype.interfaces.mrtrix as mrt
-    >>> strack = mrt.StreamlineTrack()
-    >>> strack.inputs.inputmodel = 'SD_PROB'
-    >>> strack.inputs.in_file = 'data.Bfloat'
-    >>> strack.inputs.seed_file = 'seed_mask.nii'
-    >>> strack.inputs.mask_file = 'mask.nii'
-    >>> strack.cmdline
+    >>> streamtrack = mrt.StreamlineTrack()
+    >>> streamtrack.inputs.inputmodel = 'SD_PROB'
+    >>> streamtrack.inputs.in_file = 'data.Bfloat'
+    >>> streamtrack.inputs.seed_file = 'seed_mask.nii'
+    >>> streamtrack.inputs.mask_file = 'mask.nii'
+    >>> streamtrack.cmdline
     'streamtrack -mask mask.nii -seed seed_mask.nii SD_PROB data.Bfloat data_tracked.tck'
-    >>> strack.run()                                    # doctest: +SKIP
+    >>> streamtrack.run()                                    # doctest: +SKIP
     """
 
     _cmd = "streamtrack"
@@ -423,10 +423,10 @@ class DiffusionTensorStreamlineTrack(StreamlineTrack):
     -------
 
     >>> import nipype.interfaces.mrtrix as mrt
-    >>> dtstrack = mrt.DiffusionTensorStreamlineTrack()
-    >>> dtstrack.inputs.in_file = 'data.Bfloat'
-    >>> dtstrack.inputs.seed_file = 'seed_mask.nii'
-    >>> dtstrack.run()                                  # doctest: +SKIP
+    >>> dtstreamtrack = mrt.DiffusionTensorStreamlineTrack()
+    >>> dtstreamtrack.inputs.in_file = 'data.Bfloat'
+    >>> dtstreamtrack.inputs.seed_file = 'seed_mask.nii'
+    >>> dtstreamtrack.run()                                  # doctest: +SKIP
     """
 
     input_spec = DiffusionTensorStreamlineTrackInputSpec

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

@@ -707,10 +707,10 @@ def _mock_get_ssh_client(self):
 
 
 def test_ExportFile(tmp_path):
-    testin = tmp_path / "in.txt"
-    testin.write_text("test string", encoding='utf-8')
+    test_in = tmp_path / "in.txt"
+    test_in.write_text("test string", encoding='utf-8')
     i = nio.ExportFile()
-    i.inputs.in_file = str(testin)
+    i.inputs.in_file = str(test_in)
     i.inputs.out_file = str(tmp_path / "out.tsv")
     i.inputs.check_extension = True
     with pytest.raises(RuntimeError):

nipype/utils/profiler.py

@@ -44,7 +44,7 @@ def stop(self):
 
 class ResourceMonitor(threading.Thread):
     """
-    A ``Thread`` to monitor a specific PID with a certain frequence
+    A ``Thread`` to monitor a specific PID with a certain frequency
     to a file
     """
 

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("'''")):