Fix tutorials (continuation of #1036) #2459
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…cters in example, PEP8-ize examples, language.
…files and correct output specification in example 2.
…o fix_tutorials
…date it), mention that nodes need absolut file path correct typos and add download section.
fix: documentation indentation and highlighting
Conflicts: examples/fmri_ants_openfmri.py
Conflicts: examples/fmri_ants_openfmri.py
This reverts commit 181255e.
…cters in example, PEP8-ize examples, language.
…files and correct output specification in example 2.
…date it), mention that nodes need absolut file path correct typos and add download section.
This reverts commit 181255e.
…o fix_tutorials Conflicts: doc/devel/cmd_interface_devel.rst doc/devel/matlab_interface_devel.rst doc/users/tutorial_101.rst examples/fmri_ants_openfmri.py examples/rsfmri_vol_surface_preprocessing_nipy.py
effigies
reviewed
Feb 22, 2018
doc/devel/cmd_interface_devel.rst
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| @@ -80,7 +80,7 @@ symbols. For an input defined in InputSpec to be included into the executed | |||
| commandline ``argstr`` has to be included. Additionally inside the main | |||
| interface class you need to specify the name of the executable by assigning it | |||
| to the ``_cmd`` field. Also the main interface class needs to inherit from | |||
| :class:`nipype.interfaces.base.CommandLine`: | |||
| :class:`CommandLine <nipype.interfaces.base.CommandLine>`: | |||
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This currently does not link. We should verify that it does after this change. If not, may want to change :class: to :ref:.
Or possibly it should now be nipype.interfaces.base.core.CommandLine.
doc/devel/cmd_interface_devel.rst
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| @@ -92,7 +92,7 @@ to the ``_cmd`` field. Also the main interface class needs to inherit from | |||
| There is one more thing we need to take care of. When the executable finishes | |||
| processing it will presumably create some output files. We need to know which | |||
| files to look for, check if they exist and expose them to whatever node would | |||
| like to use them. This is done by implementing ``_list_outputs`` method in the | |||
| like to use them. This is done by implementing :func:`_list_outputs <nipype.interfaces.base.BaseInterface._list_outputs>` method in the | |||
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I think this change should probably be reverted. There is no documentation for private methods like this.
doc/index.rst
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| Slicer_), eases the design of workflows within and between packages, and | ||
| reduces the learning curve necessary to use different packages. Nipype is | ||
| creating a collaborative platform for neuroimaging software development | ||
| creating a collaborative platform for neuroimaging software development |
examples/fmri_ants_openfmri.py
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| """ | ||
| Return the aparc+aseg.mgz file | ||
| """ | ||
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I would revert this. I don't see the value in adding newlines. (Could be a bad merge.)
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ok, reverted, but this file contains many similar docstrings
doc/devel/matlab_interface_devel.rst
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| def _list_outputs(self): | ||
| outputs = self._outputs().get() | ||
| return outputs |
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Lines 29-79 have been superseded by line 82 and should be removed. https://387-59325098-gh.circle-artifacts.com/0/home/circleci/work/docs/devel/matlab_interface_devel.html#example-2
doc/devel/cmd_interface_devel.rst
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| @@ -39,7 +39,7 @@ above example we have used the ``desc`` metadata which holds human readable | |||
| description of the input. The ``mandatory`` flag forces Nipype to throw an | |||
| exception if the input was not set. ``exists`` is a special flag that works only | |||
| for ``File traits`` and checks if the provided file exists. More details can be | |||
| found at :doc:`interface_specs`. | |||
| found at :ref:`interface_specs`. | |||
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This change doesn't do anything. Might as well revert to keep the diff clean, unless there's a good reason to prefer :ref:.
doc/users/interface_tutorial.rst
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| @@ -10,7 +10,8 @@ Specifying input settings | |||
| The nipype interface modules provide a Python interface to external | |||
| packages like FSL_ and SPM_. Within the module are a series of Python | |||
| classes which wrap specific package functionality. For example, in | |||
| the fsl module, the class :class:`nipype.interfaces.fsl.BET` wraps the | |||
| the :ref:`fsl <nipype.interfaces.fsl>` module, the class | |||
| :class:`nipype.interfaces.fsl.BET>` wraps the | |||
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> should be removed. Looks like a bad merge.
examples/fmri_ants_openfmri.py
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| `newAntsExample.sh <https://github.com/stnava/ANTs/blob/master/Scripts/newAntsExample.sh>`_ | ||
| * This is currently set to perform a very quick registration. However,\ | ||
| the registration can be made significantly more accurate for cortical\ | ||
| structures by increasing the number of iterations. |
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This is part of a docstring. It doesn't look very good. https://387-59325098-gh.circle-artifacts.com/0/home/circleci/work/docs/users/examples/fmri_ants_openfmri.html
I'd say revert this block.
examples/fmri_ants_openfmri.py
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| `newAntsExample.sh <https://github.com/stnava/ANTs/blob/master/Scripts/newAntsExample.sh>`_ | ||
| * This is currently set to perform a very quick registration. However,\ | ||
| the registration can be made significantly more accurate for cortical\ | ||
| structures by increasing the number of iterations. |
| `newAntsExample.sh <https://github.com/stnava/ANTs/blob/master/Scripts/newAntsExample.sh>`_ | ||
| * This is currently set to perform a very quick registration. However,\ | ||
| the registration can be made significantly more accurate for cortical\ | ||
| structures by increasing the number of iterations. |
effigies
approved these changes
Feb 23, 2018
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will update and add suggestions from #1036
I'm removing all
*.rstfiles that are not used anymore (e.g. tutorial_101; see also discussion here)