Fix tutorials (continuation of #1036) #2459

djarecka · 2018-02-22T19:33:56Z

will update and add suggestions from #1036

I'm removing all *.rst files that are not used anymore (e.g. tutorial_101; see also discussion here)

…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

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

…ex page)

effigies · 2018-02-22T19:48:38Z

doc/devel/cmd_interface_devel.rst

@@ -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>`:


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.

effigies · 2018-02-22T19:50:29Z

doc/devel/cmd_interface_devel.rst

@@ -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


I think this change should probably be reverted. There is no documentation for private methods like this.

effigies · 2018-02-22T19:54:40Z

doc/index.rst

        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 


Spaces at the end of lines.

effigies · 2018-02-22T19:56:55Z

examples/fmri_ants_openfmri.py

+    """
+    Return the aparc+aseg.mgz file
+    """
+


I would revert this. I don't see the value in adding newlines. (Could be a bad merge.)

ok, reverted, but this file contains many similar docstrings

effigies · 2018-02-22T20:22:26Z

doc/devel/matlab_interface_devel.rst


+        def _list_outputs(self):
+            outputs = self._outputs().get()
+            return outputs


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

effigies · 2018-02-22T20:24:13Z

doc/devel/cmd_interface_devel.rst

@@ -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`.


This change doesn't do anything. Might as well revert to keep the diff clean, unless there's a good reason to prefer :ref:.

effigies · 2018-02-22T20:26:13Z

doc/users/interface_tutorial.rst

@@ -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


> should be removed. Looks like a bad merge.

effigies · 2018-02-22T20:29:54Z

examples/fmri_ants_openfmri.py

+          `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.


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.

effigies · 2018-02-22T20:30:11Z

examples/fmri_ants_openfmri.py

+          `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.


And this one.

effigies · 2018-02-22T20:34:06Z

examples/rsfmri_vol_surface_preprocessing_nipy.py

+          `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.


And this one.

effigies

LGTM. Will merge tomorrow if no objections.

Mathieu Dubois and others added 30 commits January 30, 2015 18:35

DOC Updated doc/devel/matlab_interface_devel.rst: remove invalid cara…

7aee50d

…cters in example, PEP8-ize examples, language.

Merge remote-tracking branch 'upstream/master' into fix_tutorials

c33285a

DOC Fix typo.

c6d4d06

DOC Fix typo.

552d06d

DOC reworked devel/matlab_interface_devel.rst: move code to external …

ee6c25d

…files and correct output specification in example 2.

DOC add blank line in matlab examples

20a742c

DOC fix literal block issues in nipype/interfaces/fsl/preprocess.py

cb62ced

Merge branch 'fix_tutorials' of https://github.com/duboism/nipype int…

32c4409

…o fix_tutorials

DOC updates in users/tutorial_101: move code in external file (and up…

dbf58c2

…date it), mention that nodes need absolut file path correct typos and add download section.

DOC correct download sections in devel/matlab_interface_devel.rst

343389c

WIP minimal modifications in users/interface_tutorial.rst

4af4773

Merge branch 'master' into fix_tutorials

717555e

DOC correct indentation error in doc/index.rst

7639c66

DOC correct indentation error in doc/users/config.rst

d5d344b

DOC correct references in doc/devel/devel/cmd_interface_devel.rst

54fefed

fix: documentation indentation and highlighting

8b89b73

Merge pull request #1 from nicholsn/docs/rsfmri-example

10b3cc4

fix: documentation indentation and highlighting

DOC minor fix in examples/rsfmri_vol_surface_preprocessing_nipy.py

868b248

DOC fix formatting in examples/fmri_ants_openfmri.py

6d81823

DOC PEP8 edits in examples/fmri_ants_openfmri.py

d67d503

Merge branch 'master' into fix_tutorials

4f5ee8e

Conflicts: examples/fmri_ants_openfmri.py

Merge branch 'master' into fix_tutorials

41b9cd1

Conflicts: examples/fmri_ants_openfmri.py

DOC Added ANTS to the list of wrapped tools.

181255e

Merge branch 'master' into fix_tutorials

e6994e6

Revert "DOC Added ANTS to the list of wrapped tools."

bfb88ba

This reverts commit 181255e.

WIP Updates in examples/fmri_ants_openfmri.py

0eb52cf

Merge branch 'master' of https://github.com/nipy/nipype

a889ad4

Merge branch 'master' into fix_tutorials

20032a2

Merge branch 'master' of https://github.com/nipy/nipype

0434e47

Merge branch 'master' into fix_tutorials

f0c7abd

Mathieu Dubois and others added 22 commits March 1, 2015 19:05

Merge branch 'master' of https://github.com/nipy/nipype

e3d49ea

Merge branch 'master' into fix_tutorials

cb80e24

DOC Updated doc/devel/matlab_interface_devel.rst: remove invalid cara…

346cdc8

…cters in example, PEP8-ize examples, language.

DOC Fix typo.

d2fca1c

DOC reworked devel/matlab_interface_devel.rst: move code to external …

ef6c57c

…files and correct output specification in example 2.

DOC add blank line in matlab examples

2027c70

DOC fix literal block issues in nipype/interfaces/fsl/preprocess.py

55238c1

DOC updates in users/tutorial_101: move code in external file (and up…

e652674

…date it), mention that nodes need absolut file path correct typos and add download section.

WIP minimal modifications in users/interface_tutorial.rst

81fa276

DOC correct indentation error in doc/index.rst

2eeb567

DOC correct indentation error in doc/users/config.rst

bc2bce0

DOC correct references in doc/devel/devel/cmd_interface_devel.rst

0fab2e4

fix: documentation indentation and highlighting

5899dec

DOC minor fix in examples/rsfmri_vol_surface_preprocessing_nipy.py

1044641

DOC PEP8 edits in examples/fmri_ants_openfmri.py

3ff1dbd

DOC Added ANTS to the list of wrapped tools.

fd267ef

Revert "DOC Added ANTS to the list of wrapped tools."

941b7ad

This reverts commit 181255e.

WIP Updates in examples/fmri_ants_openfmri.py

b4d0eee

Merge branch 'fix_tutorials' of https://github.com/duboism/nipype int…

cfb9bc5

…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

DOC remove some leftovers.

8da068c

Merge remote-tracking branch 'upstream/master' into fix_tutorials

611df19

removing tutorials that are not used anymore (not included in the int…

75c7b2a

…ex page)

effigies reviewed Feb 22, 2018

View reviewed changes

djarecka and others added 3 commits February 22, 2018 15:47

updating fmri_abts example

42fe6d5

after comments from Chris

5e13478

STY: Whitespace [skip ci]

d4b05ea

effigies approved these changes Feb 23, 2018

View reviewed changes

effigies added this to the 1.0.1 milestone Feb 23, 2018

effigies merged commit 52efaa0 into nipy:master Feb 23, 2018

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Fix tutorials (continuation of #1036) #2459

Fix tutorials (continuation of #1036) #2459

djarecka commented Feb 22, 2018 •

edited

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Fix tutorials (continuation of #1036) #2459

Fix tutorials (continuation of #1036) #2459

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djarecka commented Feb 22, 2018 • edited

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djarecka commented Feb 22, 2018 •

edited