examples from nipype

[djarecka]

@satra , @miykael - should we move these examples to the nipype tutorial?
Should we still point to the "Beginner's Guide"?

You might have already write about it, but can't find it right now.

[miykael]

@djarecka - I'm all for moving the examples to the tutorial, but I have two concerns:

1. Some of those workflows might be out of shape or obsolete. Which ones should we keep? How should we clean them?
2. Having all of them in the nipype_tutorial might increase computation time on circleci too much and also requires to have a much bigger Docker container (accounting for additional dependencies). We might not want that.

I think a better place to put those examples (and to let them be improved by the community) is niflows. What do you think?

I also think that we could eventually improve the "Workflow Example" section on nipype tutorial. At the moment it's just a two different pipelines ("Example" and "Hands-on") that I like to show. But I think we can improve the content there, as well as the layout.

[miykael]

@djarecka - About the beginner's guide... While I'm very attached to it (it was my first own homepage - and it also looks that way), I would be happy to let it slowly disappear. There's no point of having the beginner's guide and the tutorial together, and I currently have not much time to focus on the beginner's guide.

The problem is that the beginner's guide is still more popular than the tutorial:

Site Overview over the last 13 months for the Beginner's Guide

Site Overview over the last 13 months for the Nipype Tutorial

This all might change over the next few months, but for the moment the beginner's guide seems to be useful.

[djarecka]

@miykael - of course, I don't want you to remove something that is useful, but I have to admit it's not clear to me who should be pointed to the Beginner's Guide and and who to the Nipype Tutorial. It seems to me that links to these website are included a bit randomly on Nipype website, but I could be wrong.
I'm not really surprised that it has bigger traffic, since this is the 3rd website that is shown by google, just after github.

If you think that this website is dedicated to different people, that's fine, but maybe we can at least clarify it somewhere. Do we test any examples from the beginner website with the current Nipype?

And about the examples: I'm sure that many of them are out of shape and that's why I started thinking that they should be tested somewhere. Not saying that Nipype Tutorial is the best place, just wanted have discussion where they fit best and how they should be updated/tested.

[miykael]

I'm happy to "hide" the beginner's guide. How could I best do that? I already have an Important banner on the beginner's guide, directing people to the tutorial (http://miykael.github.io/nipype-beginner-s-guide/). Hmm... I just saw that this banner is outdated. I think I will rewrite the text and state very clearly that the beginner's guide content hasn't been updated since April 2016. That should hopefully move people to the tutorial. What do you think @djarecka?

The beginner's example are not tested. And in comparison to the tutorial, I think the only real additional content is the FAQ and Glossary section. And anyhow, their content is to 95% from http://mindhive.mit.edu/node/46 and http://mindhive.mit.edu/node/71. @djarecka and @satra, should I include those two sections in the tutorial as well? Does it make more sense to update the mindhive homepage (many links and references are broken) or should I leave this aside anyhow?

[djarecka]

@miykael - yes, I think it's a good idea to be clear that the examples from the website are not tested (so people don't expect that everything is working), and that the tutorial is tested.

I'm checking now FAQ and Glossary, and you're absolutely right that this can be very useful for the beginners, so we shouldn't hide them.

My main concern was really regarding the nipype code, since there are many sources that people take examples, and they expect that everything should work... And it looks like many examples haven't been really tested for long time (e.g. the pipelines from nipype/examples), but we are not clear about it.

[satra]

a few notes:

1. nipype/examples and workflows should go to niflows
2. mindhive.mit.edu is not really being maintained, so we should not be pointing towards it
3. a single entrypoint is better than two. so perhaps we should take the useful bits of the beginners guide and add it to the tutorial