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Merge pull request #3512 from DimitriPapadopoulos/codespell

DOC: Fix typos found by codespell

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THANKS.rst
doc
- _templates
  - indexsidebar.html
  - navbar.html
- devel
  - filename_generation.rst
  - gitwash
nipype
- caching
  - memory.py
- interfaces
  - afni
  - c3.py
  - dcmstack.py
  - freesurfer
    - preprocess.py
  - io.py
  - matlab.py
  - minc
    - minc.py
  - petpvc.py
  - semtools
    - brains
      - segmentation.py
      - utilities.py
    - diffusion
      - diffusion.py
      - gtract.py
      - maxcurvature.py
      - tractography
        commandlineonly.py
        fibertrack.py
        ukftractography.py
    - filtering
      - featuredetection.py
    - legacy
      - registration.py
    - registration
    - segmentation
      - specialized.py
    - testing
      - generateaveragelmkfile.py
    - utilities
      - brains.py
  - slicer
    - generate_classes.py
    - registration
      - brainsfit.py
    - segmentation
      - specialized.py
    - surface.py
  - utility/tests
    - test_wrappers.py
- pipeline/engine
  - report_template.html
  - tests
    - test_join.py
- utils
tools
- feedstock.sh

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48 files changed

+132

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`‎THANKS.rst‎`

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@@ -19,4 +19,3 @@ and `UL1 TR000442 University of Iowa Clinical and Translational Science Program
`19`	`19`
`20`	`20`
`21`	`21`	We would also like to thank `JetBrains <http://www.jetbrains.com/>`__ for providing `Pycharm <http://www.jetbrains.com/pycharm/>`__ licenses.
`22`		`-`

`‎doc/_templates/indexsidebar.html‎`

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`@@ -11,4 +11,4 @@ <h3>{{ _('Links') }}</h3>`
`11`	`11`	`<a href='https://pypi.python.org/pypi/nipype/'><img src='https://img.shields.io/pypi/pyversions/nipype.svg' alt='Python Versions' /></a></li>`
`12`	`12`	`</ul>`
`13`	`13`
`14`		`-{% endblock %}`
	`14`	`+{% endblock %}`

`‎doc/_templates/navbar.html‎`

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`@@ -13,4 +13,3 @@`
`13`	`13`	`<a class="navbar" href="{{pathto('developers')}}">Developers</a> ·`
`14`	`14`	`<a class="navbar" href="{{pathto('about')}}">About</a> ·`
`15`	`15`	`<a class="navbar" href="http://nipy.org">Nipy</a>`
`16`		`-`

`‎doc/devel/filename_generation.rst‎`

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@@ -169,4 +169,3 @@ absolute path is generated and used for the ``cmdline`` when run, but
`169`	`169`
`170`	`170`	`In [80]: res.interface.inputs.outfile`
`171`	`171`	`Out[80]: 'bar.nii'`
`172`		`-`

`‎doc/devel/gitwash/forking_hell.rst‎`

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`@@ -30,4 +30,3 @@ Create your own forked copy of nipype_`
`30`	`30`	`should find yourself at the home page for your own forked copy of nipype_.`
`31`	`31`
`32`	`32`	`.. include:: links.inc`
`33`		`-`

`‎doc/devel/gitwash/git_development.rst‎`

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`@@ -13,4 +13,3 @@ Contents:`
`13`	`13`	`set_up_fork`
`14`	`14`	`configure_git`
`15`	`15`	`development_workflow`
`16`		`-`

`‎doc/devel/gitwash/index.rst‎`

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`@@ -14,5 +14,3 @@ Contents:`
`14`	`14`	`patching`
`15`	`15`	`git_development`
`16`	`16`	`git_resources`
`17`		`-`
`18`		`-`

`‎doc/devel/gitwash/set_up_fork.rst‎`

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`@@ -65,4 +65,3 @@ Just for your own satisfaction, show yourself that you now have a new`
`65`	`65`	`origin git@github.com:your-user-name/nipype.git (push)`
`66`	`66`
`67`	`67`	`.. include:: links.inc`
`68`		`-`

`‎nipype/caching/memory.py‎`

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`@@ -287,7 +287,7 @@ def clear_runs_since(self, day=None, month=None, year=None, warn=True):`
`287`	`287`	`os.remove(log_name)`
`288`	`288`
`289`	`289`	`def _clear_all_but(self, runs, warn=True):`
`290`		`- """Remove all the runs appart from those given to the function`
	`290`	`+ """Remove all the runs apart from those given to the function`
`291`	`291`	`input.`
`292`	`292`	`"""`
`293`	`293`	`rm_all_but(self.base_dir, set(runs.keys()), warn=warn)`

`‎nipype/interfaces/afni/base.py‎`

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`@@ -262,8 +262,8 @@ def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True, ext=None)`
`262`	`262`	`Generate a filename based on the given parameters.`
`263`	`263`
`264`	`264`	`The filename will take the form: cwd/basename<suffix><ext>.`
`265`		`- If change_ext is True, it will use the extentions specified in`
`266`		`- <instance>intputs.output_type.`
	`265`	`+ If change_ext is True, it will use the extensions specified in`
	`266`	`+ <instance>inputs.output_type.`
`267`	`267`
`268`	`268`	`Parameters`
`269`	`269`	`----------`

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