[Neuroimaging] Nipy.org new website needs a complete remake

vanessa sochat vsochat at stanford.edu
Mon Jul 27 01:23:57 CEST 2015

Hi guys,

Just to poke in - I think I've gotten us started on this site business :)
More to come in the next few days!



On Sun, Jul 26, 2015 at 4:12 PM, Ariel Rokem <arokem at gmail.com> wrote:

> Hi,
> On Sun, Jul 26, 2015 at 9:53 AM, Eleftherios Garyfallidis <
> garyfallidis at gmail.com> wrote:
>> Hi Ariel,
>> On Sat, Jul 25, 2015 at 10:58 PM, Ariel Rokem <arokem at gmail.com> wrote:
>>> Hi Eleftherios,
>>> I am happy to have you finally chime in on the discussion surrounding
>>> the webpage. The previous email thread was indeed supposed to spur this
>>> discussion, but it did fairly quickly turn into a discussion of github
>>> workflow and technical issues surrounding redirection instead. So - better
>>> late than never!
>> Okay.
>>> As I mentioned in my first email in that previous thread (can't link to
>>> it, because the archives on mail.scipy.org are down...), this redesign
>>> was the result of conversations at the Berkeley coding sprint back in May.
>>> While talking to some relative newcomers, we noticed that the content in
>>> the old webpage was really confusing, and gave a somewhat misleading
>>> picture of the current state of affairs in the nipy community. For example,
>>> I don't think that anyone here really thinks that neuroimaging in Python is
>>> only 6 projects, or that one of the first projects people should try out is
>>> pbrain (which was one of the six previously mentioned on the front page).
>>> So, I don't think that going to the old version of the page is a good
>>> solution.
>> Okay but this new website as it is now is not ready to be online too. It
>> is still misleading and I find it difficult to understand what the portal
>> is about. It needs much more work to be useful.
>>> Like almost everything else around here, the webpage is of course work
>>> in progress. For example, I can relate to the objections regarding the
>>> background image on the front page. I had full intention of replacing the
>>> background image with something (possibly several things rotating?) more
>>> indicative of the subject matter. I just haven't had the time to do that
>>> yet. If someone else wants to jump in and do that, this is the file that
>>> would need to be replaced:
>>> https://github.com/nipy/nipy.github.com/blob/master/images/rect1600x800.png
>>> I think from now on when a new website like this is created which
>> affects other projects it shouldn't replace immediately the existing
>> website but have a link in the existing website saying that there is a new
>> website coming. In that way the transition is smoother and it gives you the
>> developer the time to make the website better and get more feedback.
> The message with the link to the new version of the website went to the
> mailing list on May 18th. The redirection wasn't changed for another 3
> weeks or so. There wasn't anything but positive indications from the list,
> and no reason to think that anyone had any reservations about the new
> format until 2 days ago.
>>> I am sure that a bit of logic could be used to put in several different
>>> attractive images of brain data from which one would be chosen randomly
>>> every time you land on the page.
>>> Yes, you can put a carousel in the website and remove that background
>> with many images. You should also remove the mission with the form it is
>> now. It doesn't communicate.
> I don't know what you are referring to. "Mission"? Are you talking about
> https://github.com/nipy/nipy.github.com/pull/1? That was mentioned in a
> message asking for feedback on the mailing list on May 22nd. Did you get
> any of these messages? Is all this a misunderstanding because the mailing
> list was starting to be a bit flaky at that point? I think that others got
> these messages, considering that a few people did have comments on this PR,
> before it was eventually merged a couple of weeks later.
>>> Concerning choice of design/technology: as Vanessa pointed out, the
>>> technology used for these pages is Jekyll <http://jekyllrb.com/>. It
>>> has the following advantages:
>>> 1. It is the 'native' technology on Github's platform. That means that
>>> we can version control on the markdown from which the site gets generated,
>>> and the site itself gets built on Github, rather than needing to be built
>>> on anyone's machine every time changes are made. This makes it relatively
>>> easy to extend the website, work on it collaboratively using the standard
>>> github workflow, and to add additional content. I've even put some
>>> instructions in http://nipy.org/contribute/ on how to add such content,
>>> especially articles/blog posts. Happy to have people write little articles
>>> in that vein, and make things a little bit more lively. It really doesn't
>>> have to be a dissertation - writing down a few lines reporting on some new
>>> cool project you've seen, or reporting from a conference you've attended
>>> from the nipy point of view would be wonderful.
>>> 2. Reasonably good-looking, with plenty of customization possible. This
>>> is, of course, a matter of taste, so I don't expect anyone to agree with
>>> me. Whether having more colors on a page or not is better is really not
>>> something I expect anyone to agree with me on. I certainly would not object
>>> to changes to the current design that wouldn't be too gaudy. Concerning a
>>> comment Gael made: what does a "structured" layout mean? Is that a
>>> web-design term? I am (surprise!) not a web designer ;-)
>>> The only disadvantage of Jekyll I can see is that it is Ruby-based. I
>>> think that point 1 above outweighs that disadvantage. Point 2 is really a
>>> matter for some discussion, and additional work. By the way, whether to use
>>> Jekyll is also a discussion that has come up in the context of Software
>>> Carpentry. I think that no one in that community regrets choosing jekyll to
>>> manage a much more complicated network of web sites, but we can ask them
>>> for more advice, if someone thinks that would be useful.
>> As I said in my previous e-mail this website can be created using Pelican
>> too or with Sphinx and Bootstrap and it will be more pythonic. About option
>> 2. Jetkyll can be good looking because of bootstrap. We have exactly the
>> same good looks with Sphinx or Pelican. By the way also Pelican supports
>> both markdown and rst.
>> What it seems as advantage is 1. but in practice it is not a big
>> advantage because even if people submit their markdown scripts the website
>> will be updated only when those are merged and still you will need someone
>> checking if they render correctly. I prefer if people who submit content
>> check the final website first in their machine before updating the final
>> website.
> We can still use Jekyll only for the portal but the websites of the rest
>> of the projects will have to use sphinx anyway. So, why bother introducing
>> new tech.
> That's roughly analogous to comparing local test runs to Travis. Another
> case in which additional technology is adopted because it removes barriers
> to collaboration and productivity. Definitely worth it in the case of
> testing/Travis. I think it's worth it here as well.
>> So, my final suggestion is to use Pelican for the portal which supports
>> everything that Jekyll supports and works in github fine. And for the other
>> websites e.g. dipy, nibabel etc. use sphinx with the same or similar theme
>> used in the portal but with some alternations to create a unique look for
>> each project.
>> Some immediate actions:
>> a) For now I think you should at least add this information
>> http://nipy.org/project-directory/ to the first page and explain what is
>> your vision of this portal.
> That's the link in the middle of the front page. Or am I missing
> something? Do you want me to move the entire project directory to the front
> page? That wouldn't look great, I think (but I think we've already
> established that I am not a web designer...).
>> b) Definitely change this background picture maybe add a neuro-related
>> picture. You don't need to wait for others to do that. You can do that by
>> yourself too. I am sure you have many cool pictures around.
> Vanessa offered help earlier in this thread, so maybe she has an image she
> likes? :-)
>> c) Then let's set a meeting together and with other people who want to
>> help and I can show you how Pelican/Bootstrap work so you can then see the
>> benefits by yourself. Don't worry nothing from the content that you added
>> in nipy.org is going to be lost. All these markdowns can also be used
>> with Pelican.
>> I will be available after Wednesday to help you with this.
>> Cheers,
>> Eleftherios
>>> Cheers,
>>> Ariel
>>> On Sat, Jul 25, 2015 at 6:46 AM, Eleftherios Garyfallidis <
>>> garyfallidis at gmail.com> wrote:
>>>> Hi Gael, Vanessa and Ariel,
>>>> Gael I think the previous e-mail thread was about moving the pages into
>>>> github.io and not about the design, the technology or the content of
>>>> nipy.org. This being the portal of all projects needs to communicate
>>>> the ideas better and use libraries that can be used in other projects too.
>>>> Hopefully also be as Pythonic as possible and as useful and attractive as
>>>> possible.
>>>> So, my point is that the new portal, although it has some nice ideas,
>>>> for examle it is using bootstrap which allows for better and more
>>>> responsive viewing
>>>> from different devices, it is not ready for prime time. And it
>>>> shouldn't be online with the form that is now. So, I would recommend to use
>>>> the previous website with updated links to the new github pages until this
>>>> one is in a better form.
>>>> Now about the technology used for creating the website. From my
>>>> understanding Ariel is using the default engine promoted by github which is
>>>> jekyll which at the end is using bootstrap. But bootstrap can be used with
>>>> sphinx and with pelican too which are both Python projects.
>>>> So we could actually have two better options. For the portal we can
>>>> use:
>>>> a) Pelican which is an alternative of Octpress/Jekyll in Python. I used
>>>> it to make my  own website and it is easy to use for creating static
>>>> websites (like the portal). Link here http://garyfallidis.github.io
>>>> and here https://github.com/Garyfallidis/website-dev . Pelican
>>>> supports both markdown and restructuredtext.
>>>> b) It is now possible to use Sphinx with bootstrap directly. See here
>>>> https://readthedocs.org/projects/sphinx-bootstrap-theme/ and here
>>>> https://pypi.python.org/pypi/sphinx-bootstrap-theme/
>>>> The option is possibly the best solution as we could just update our
>>>> template engine (to use bootstrap) and continue using sphinx as before. But
>>>> now we can use any template we want and have a much more responsive website.
>>>> Ideally the portal should have a main theme and then the different
>>>> projects would make some alterations to this theme to create their
>>>> individual image. For example in Dipy our main colors are black and orange
>>>> so we will alternate the theme so we can use mainly those colors is our
>>>> website.
>>>> Vanessa of course I am writing this e-mail because I am willing up to
>>>> my capacity to help Ariel or anyone else who wants to improve the look and
>>>> feel of the organization.
>>>> Ariel in summary, I think the portal is not well designed right now and
>>>> the content needs some more work before it is presented. I am happy to help
>>>> and I think you will find it useful to have a look in the links that I have
>>>> in this e-mail before we meet. In the meantime, I would strongly suggest to
>>>> upload the old portal until we have something more solid. I hope this is
>>>> okay.
>>>> Cheers,
>>>> Eleftherios
>>>> On Sat, Jul 25, 2015 at 4:41 AM, Gael Varoquaux <
>>>> gael.varoquaux at normalesup.org> wrote:
>>>>> On Fri, Jul 24, 2015 at 08:57:48PM -0400, Eleftherios Garyfallidis
>>>>> wrote:
>>>>> > It seems that nipy.org has recently changed. The previous page was
>>>>> much
>>>>> > better from what we have now.
>>>>> I agree with you that the previous page was much better in term of
>>>>> design
>>>>> (more colors, a more structured layout, and an image that looked like a
>>>>> brain clearly visible) and of content (clear list of main projects and
>>>>> subprojects).
>>>>> However, the change was advertised. I understand that you missed it: we
>>>>> all have too much mails and too many things to do.
>>>>> I think that you could make proposals and maybe pull requests to shape
>>>>> the website toward something that you like better. It would be great.
>>>>> Gaël
>>>>> _______________________________________________
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Vanessa Villamia Sochat
Stanford University
(603) 321-0676
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