[Neuroimaging] Site Contributions

Tue Oct 27 15:04:38 EDT 2015

Hi everyone,

would it be possible to add our neuroimaging project to the nipy website?
https://github.com/neuropoly/spinalcordtoolbox

it is 100% python and notably uses nibabel and dipy.

cheers
julien

--
Julien Cohen-Adad, PhD
Assistant Professor, Polytechnique Montreal
Associate Director, Functional Neuroimaging Unit, University of Montreal
Phone: 514 340 5121 (office: 2264);  Skype: jcohenadad
Web: www.neuro.polymtl.ca

On Tue, Oct 27, 2015 at 2:44 PM, Eleftherios Garyfallidis <
garyfallidis at gmail.com> wrote:

> Epic awesomeness! Thank you Vanessa!
>
> On Tue, Oct 27, 2015 at 2:40 PM, Ariel Rokem <arokem at gmail.com> wrote:
>
>> Great work! Will resubmit my blog-post PR through the new mechanism.
>>
>> On Tue, Oct 27, 2015 at 11:38 AM, vanessa sochat <vsochat at stanford.edu>
>> wrote:
>>
>>> Hi everyone,
>>>
>>> I just added the missing CNAME file, apologies for the oversight, I did
>>> not know it was there :) It looks like nipy.org is working as well now
>>> too - please let me know if you see any issues.
>>>
>>> Circle is expected to have some changes in the next week, so I am going
>>> to wait for the weekend to debug the building of artifacts. Will let you
>>> know when I fix that up!
>>>
>>> Best,
>>>
>>> Vanessa
>>>
>>> On Tue, Oct 27, 2015 at 11:30 AM, vanessa sochat <vsochat at stanford.edu>
>>> wrote:
>>>
>>>> Hi Everyone,
>>>>
>>>> Site is live!
>>>>
>>>> https://nipy.github.io/
>>>>
>>>> Ariel - I'm not sure how to set up the nipy.org. Would you mind taking
>>>> a look and fixing that up?
>>>>
>>>> Circle is having some bugs with the artifact generation, I think I can
>>>> probably fix it, but not during the work week. Ben - I added your
>>>> contribution to the README but didn't get the other comment in time. The
>>>> good news is now anyone and everyone can submit changes as PR. I encourage
>>>> everyone to familiarize yourself with tumblr, and start contributing
>>>> content, PRs to tweak it.
>>>>
>>>> Best,
>>>>
>>>> Vanessa
>>>>
>>>> On Tue, Oct 27, 2015 at 11:10 AM, vanessa sochat <vsochat at stanford.edu>
>>>> wrote:
>>>>
>>>>> Got it! Thanks! :)
>>>>>
>>>>> On Tue, Oct 27, 2015 at 11:07 AM, Ariel Rokem <arokem at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi,
>>>>>> On Tue, Oct 27, 2015 at 10:56 AM, vanessa sochat <
>>>>>> vsochat at stanford.edu> wrote:
>>>>>>
>>>>>>> Hi Ariel,
>>>>>>>
>>>>>>> Please add me as an admin to nipy.github.io, so I can set up circle
>>>>>>> for CI. Thanks!
>>>>>>>
>>>>>>>
>>>>>> I believe I just did that. Let me know how you get on.
>>>>>>
>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Vanessa
>>>>>>>
>>>>>>> On Tue, Oct 27, 2015 at 10:42 AM, vanessa sochat <
>>>>>>> vsochat at stanford.edu> wrote:
>>>>>>>
>>>>>>>> Just as a proof of concept for adding a project - I just added a
>>>>>>>> new entry to the data file (copy pasting basically), copied one file, and
>>>>>>>> the entire process took me like, 48 seconds :)
>>>>>>>>
>>>>>>>> On Tue, Oct 27, 2015 at 10:36 AM, Ben Cipollini <bcipolli at ucsd.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Thanks Vanessa!
>>>>>>>>>
>>>>>>>>> On Tue, Oct 27, 2015 at 10:35 AM, vanessa sochat <
>>>>>>>>> vsochat at stanford.edu> wrote:
>>>>>>>>>
>>>>>>>>>> I will do some tweaks and get the site working. There will be a
>>>>>>>>>> change for the URL so there might be some bugs with my initial release, but
>>>>>>>>>> I'll get it fixed asap. Will send an update later.
>>>>>>>>>>
>>>>>>>>>> On Tue, Oct 27, 2015 at 6:48 AM, Ariel Rokem <arokem at gmail.com>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> Oh, one more:
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Oct 27, 2015 at 6:40 AM, Ariel Rokem <arokem at gmail.com>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Vanessa,
>>>>>>>>>>>>
>>>>>>>>>>>> I have a few comments/suggestions:
>>>>>>>>>>>>
>>>>>>>>>>>> 1. I would rather not have the front page be the project
>>>>>>>>>>>> directory. In my opinion, the front page should instead explain briefly
>>>>>>>>>>>> what this is, and lead visitors to the various other parts of the website.
>>>>>>>>>>>>
>>>>>>>>>>>> 2. There are a few issues with formatting in the Code of
>>>>>>>>>>>> Conduct page (bullet points appear as continued lines)
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> 3. Please include mindboggle in the project directory (it's been
>>>>>>>>>>> recently added!).
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> Other than these two, I think this is ready to be introduced as
>>>>>>>>>>>> a PR against the nipy/nipy.github.com repository (you don't
>>>>>>>>>>>> need any admin rights to do that, but I also just added you to "team blog"
>>>>>>>>>>>> on the github nipy org, so you can even do the merge yourself, if you want).
>>>>>>>>>>>>
>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>
>>>>>>>>>>>> Ariel
>>>>>>>>>>>>
>>>>>>>>>>>> On Mon, Oct 26, 2015 at 12:56 PM, vanessa sochat <
>>>>>>>>>>>> vsochat at stanford.edu> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Eleftherios,
>>>>>>>>>>>>>
>>>>>>>>>>>>> It definitely would be possible! I'm not any sort of admin in
>>>>>>>>>>>>> the nipy space, so the farthest I could take it is having the repo for
>>>>>>>>>>>>> someone to deploy on nipy.github.io. The code is here:
>>>>>>>>>>>>>
>>>>>>>>>>>>> https://github.com/vsoch/nipy-jekyll
>>>>>>>>>>>>>
>>>>>>>>>>>>> and deployment on my github pages:
>>>>>>>>>>>>>
>>>>>>>>>>>>> http://vsoch.github.io/nipy-jekyll/
>>>>>>>>>>>>>
>>>>>>>>>>>>> I mostly stopped working on it because I accomplished all the
>>>>>>>>>>>>> things that I set out to do (jekyll site, preview on continuous integration
>>>>>>>>>>>>> with circle, standard ways to add new content, and an easy way to multiple
>>>>>>>>>>>>> ways to add content a la github
>>>>>>>>>>>>> <http://vsoch.github.io/nipy-jekyll/contribute.html>, or for
>>>>>>>>>>>>> those who aren't comfortable with pushing and pulling, la
>>>>>>>>>>>>> social media <http://neuroimaging.tumblr.com>). I think I had
>>>>>>>>>>>>> suggested moving forward for people to try out tumblr (and start
>>>>>>>>>>>>> contributing content!), and if people were happy, to move it over to the
>>>>>>>>>>>>> nipy repo. If the outcome of the work was not a desired solution, I was
>>>>>>>>>>>>> content to just let it be. However if there is interest, that is definitely
>>>>>>>>>>>>> still a possibility.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Vanessa
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Mon, Oct 26, 2015 at 12:34 PM, Eleftherios Garyfallidis <
>>>>>>>>>>>>> garyfallidis at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Vanessa and all,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Would it be possible to switch to your much nicer new
>>>>>>>>>>>>>> website? I still see the older version being up.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Do you have a plan for this? Or you waiting for some feedback
>>>>>>>>>>>>>> on our side?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Best regards,
>>>>>>>>>>>>>> Eleftherios
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Wed, Sep 2, 2015 at 12:57 PM, Ben Cipollini <
>>>>>>>>>>>>>> bcipolli at ucsd.edu> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I think they're good for mobile sites. I think they're
>>>>>>>>>>>>>>> generally expanded by default on full screens, and compacted on mobile. So
>>>>>>>>>>>>>>> I suggest to keep it, but have a regular menu that's showing on full
>>>>>>>>>>>>>>> screens and hidden on mobile.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Wed, Sep 2, 2015 at 9:51 AM, vanessa sochat <
>>>>>>>>>>>>>>> vsochat at stanford.edu> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> That's a good suggestion, and I'll add as an issue so I can
>>>>>>>>>>>>>>>> find it easily when the next round of changes comes around. Generally,
>>>>>>>>>>>>>>>> these "hamburger" menu things are useless functionality wise, and only
>>>>>>>>>>>>>>>> serve to aesthetically "get rid of the navigation" to have a clean looking
>>>>>>>>>>>>>>>> site. In our case, it is probably just annoying to have the extra clicks.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Wed, Sep 2, 2015 at 8:50 AM, Ben Cipollini <
>>>>>>>>>>>>>>>> bcipolli at ucsd.edu> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> This looks great. It's also cool to see "ask a question"
>>>>>>>>>>>>>>>>> integrated into the website, though we'll still have to hash things out for
>>>>>>>>>>>>>>>>> that.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Rather than open a github issue (which few may see), I'll
>>>>>>>>>>>>>>>>> make a suggestion here: can we have the menu expanded by default when
>>>>>>>>>>>>>>>>> accessing via a full-size screen?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> It feels odd to me to have to expand the menu in order to
>>>>>>>>>>>>>>>>> navigate anywhere, by default. To me, navigation options should be obvious,
>>>>>>>>>>>>>>>>> unless pressed for space.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Sun, Aug 30, 2015 at 1:14 PM, vanessa sochat <
>>>>>>>>>>>>>>>>> vsochat at stanford.edu> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Everyone,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> I've finished work on the "contribute" page with my
>>>>>>>>>>>>>>>>>> thinking for how to contribute various content:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> http://vsoch.github.io/nipy-jekyll/contribute.html
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> and as an example, put up a quick blog post:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> http://neuroimaging.tumblr.com/
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> The old "example" blog posts are hidden (private) and can
>>>>>>>>>>>>>>>>>> be viewed if you are a contributor. I'd like to add anyone and everyone
>>>>>>>>>>>>>>>>>> interested to contribute as "official" contributors via tumblr - if you are
>>>>>>>>>>>>>>>>>> interested please send me your email address. I've already invited some of
>>>>>>>>>>>>>>>>>> you for which I know the email.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Vanessa
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>> Vanessa Villamia Sochat
>>>>>>>>>>>>>>>>>> Stanford University
>>>>>>>>>>>>>>>>>> (603) 321-0676
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>> Vanessa Villamia Sochat
>>>>>>>>>>>>>>>> Stanford University
>>>>>>>>>>>>>>>> (603) 321-0676
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Vanessa Villamia Sochat
>>>>>>>>>>>>> Stanford University
>>>>>>>>>>>>> (603) 321-0676
>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Vanessa Villamia Sochat
>>>>>>>>>> Stanford University
>>>>>>>>>> (603) 321-0676
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Neuroimaging mailing list
>>>>>>>>> Neuroimaging at python.org
>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Vanessa Villamia Sochat
>>>>>>>> Stanford University
>>>>>>>> (603) 321-0676
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Vanessa Villamia Sochat
>>>>>>> Stanford University
>>>>>>> (603) 321-0676
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Neuroimaging mailing list
>>>>>>> Neuroimaging at python.org
>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Neuroimaging mailing list
>>>>>> Neuroimaging at python.org
>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Vanessa Villamia Sochat
>>>>> Stanford University
>>>>> (603) 321-0676
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Vanessa Villamia Sochat
>>>> Stanford University
>>>> (603) 321-0676
>>>>
>>>
>>>
>>>
>>> --
>>> Vanessa Villamia Sochat
>>> Stanford University
>>> (603) 321-0676
>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>>>
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
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