@@ -7,19 +7,18 @@ Interface Specifications
77Before you start
88----------------
99
10- Nipype is a young project maintained by an enthusiastic group of developers.
11- Even though the documentation might be sparse or cryptic at times we strongly
12- encourage you to contact us on the official nipype developers mailing list in
13- case of any troubles: nipy-devel@neuroimaging.scipy.org (we are sharing a
14- mailing list with the nipy community therefore please add ``[nipype] `` to the
15- messsage title).
10+ Nipype is maintained by an enthusiastic group of developers, and we're excited to have you join!
11+ In case of trouble, we encourage you to post on `NeuroStars <https://neurostars.org >`_ with the `nipype ` tag.
12+ NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics.
13+ You can also post on the nipype developers mailing list: http://mail.python.org/mailman/listinfo/neuroimaging.
14+ We are sharing a mailing list with the nipy community therefore please add ``[nipype] `` to the message title.
1615
1716
1817Overview
1918--------
2019
21- We're using the `Enthought Traits
22- <http://code .enthought.com/projects/ traits/> `_ package for all of our
20+ We're using the `Traits, formerly known as Enthought Traits
21+ <http://docs .enthought.com/traits/traits_user_manual/intro.html > `_ package for all of our
2322inputs and outputs. Traits allows us to validate user inputs and
2423provides a mechanism to handle all the *special cases * in a simple and
2524concise way though metadata. With the metadata, each input/output can
@@ -37,36 +36,33 @@ Specification, you only need to learn a few of the basics of Traits.
3736Here are a few starting points in the documentation:
3837
3938* What are Traits? The `Introduction in the User Manual
40- <http://code .enthought.com/projects/ traits/docs/html /traits_user_manual/intro.html> `_
39+ <http://docs .enthought.com/traits/traits_user_manual/intro.html> `_
4140 gives a brief description of the functionality traits provides.
4241
4342* Traits and metadata. The `second section of the User Manual
44- <http://code .enthought.com/projects/ traits/docs/html /traits_user_manual/defining.html> `_
43+ <http://docs .enthought.com/traits/traits_user_manual/defining.html> `_
4544 gives more details on traits and how to use them. Plus there a
4645 section describing metadata, including the metadata all traits have.
4746
4847* If your interested in more of a *big picture * overview, `Gael wrote
4948 a good tutorial
50- <http://code .enthought.com/projects/traits/docs/html /tutorials/traits_ui_scientific_app.html> `_
49+ <http://docs .enthought.com/traitsui /tutorials/traits_ui_scientific_app.html> `_
5150 that shows how to write a scientific application using traits for
5251 the benefit of the generated UI components. (For now, Nipype is not
5352 taking advantage of the generated UI feature of traits.)
5453
5554Traits version
5655^^^^^^^^^^^^^^
5756
58- We're using Traits version 3.x which can be install as part of `EPD
59- <http://enthought.com/products/epd.php> `_ or from `pypi
60- <http://pypi.python.org/pypi/Traits/3.3.0> `_
57+ We're using Traits version 4.x which can be installed from `pypi
58+ <https://pypi.python.org/pypi/traits> `_
6159
6260More documentation
6361^^^^^^^^^^^^^^^^^^
6462
6563Not everything is documented in the User Manual, in those cases the
66- `enthought-dev mailing list
67- <https://mail.enthought.com/mailman/listinfo/enthought-dev> `_ or the
68- `API docs
69- <http://code.enthought.com/projects/files/ETS32_API/enthought.traits.html> `_
64+ the `API docs
65+ <http://docs.enthought.com/traits/traits_api_reference/index.html> `_
7066is your next place to look.
7167
7268Nipype Interface Specifications
@@ -80,13 +76,12 @@ the interfaces. For example, Bet has these specs:
8076 - BETOutputSpec
8177
8278Each of these Specs are classes, derived from a base TraitedSpec class
83- (more on these below). The InputSpec consists of attributes which
79+ (more on these below). The InputSpec consists of attributes which
8480correspond to different parameters for the tool they wrap/interface.
8581In the case of a command-line tool like Bet, the InputSpec attributes
8682correspond to the different command-line parameters that can be passed
87- to Bet. If you are familiar with the Nipype 0.2 code-base, these
88- attributes are the same as the keys in the opt_map dictionaries. When
89- an interfaces class is instantiated, the InputSpec is bound to the
83+ to Bet.
84+ When an interfaces class is instantiated, the InputSpec is bound to the
9085``inputs `` attribute of that object. Below is an example of how the
9186``inputs `` appear to a user for Bet::
9287
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