To close this discussion, I've opened a pull request to add support for the fabs ufunc to YTArray. I've also made the error message a bit nicer and less mysterious.

https://bitbucket.org/yt_analysis/yt/pull-requests/1663/bugfix-add-support-for-the-fabs-ufunc-to/diff

On Thu, Jul 30, 2015 at 11:20 AM, Madison Fitzgerald <fitzg152@msu.edu> wrote:
Omgiod thank you! I don’t know why it was returning an undefined error, which was the source of my confusion, but I’m glad it was such a simple fix!

Thank you so much!

Madison Fitzgerald

Astrophysics | Lyman Briggs College
Women’s & Gender Studies | College of Arts & Letters
LGBTQ and Sexuality Studies Specialization
Women in Science, President
Undergraduate Teaching Assistant
Undergraduate Research Assistant
Department of Physics and Astronomy
Honors College
Michigan State University

On Jul 30, 2015, at 11:51 AM, Kacper Kowalik <xarthisius.kk@gmail.com> wrote:

On 07/30/2015 10:38 AM, Madison Fitzgerald wrote:
Oh! Well, that certainly simplifies things! Thank you! And it does fix
my matplotlib error!

However, I still am seeing an error when I try to run my script (which
was what happened to lead me down this insane road with updating yt and
breaking matplotlib at the beginning). I’m getting an “Operation not
defined” error, but when I create a scratch script to narrow down which
part of line 14 is actually the undefined operation, they all work
individually.

Script: http://paste.yt-project.org/show/5761/
Error: http://paste.yt-project.org/show/5760/

Any thoughts?

Hi Madison,
use np.abs or np.absolute instead of np.fabs for yt arrays.
Since you also know that all values are negative, I think it'd be faster
to just add '-' instead of abs.
Cheers,
Kacper

Again, thank you, I really appreciate all of your help.

Best,
Madison



Madison Fitzgerald

Astrophysics | Lyman Briggs College
Women’s & Gender Studies | College of Arts & Letters
LGBTQ and Sexuality Studies Specialization
Women in Science, President
Undergraduate Teaching Assistant
Undergraduate Research Assistant
Department of Physics and Astronomy
Honors College
Michigan State University

On Jul 30, 2015, at 11:18 AM, Nathan Goldbaum <nathan12343@gmail.com
<mailto:nathan12343@gmail.com>> wrote:

"yt update" won't work with the miniconda-based installation. Instead,
when we do a new release you'll be able to get the updated yt package
by doing "conda update yt".

You don't need to run an activate script if you're using miniconda's
Python, just start Python, import yt, and load your data :)

Nathan

On Thursday, July 30, 2015, Madison Fitzgerald <fitzg152@msu.edu
<mailto:fitzg152@msu.edu>> wrote:

   I figured out that miniconda was having an issue with another
   version of python, installed when I took a python-based
   programming class, and I was able to redirect my path to point to
   miniconda’s version instead, which solved that problem. However, I
   think my problem now is figuring out how to activate yt with
   miniconda. By that, I mean, I receive this output after
   installation and trying to take the first step:

   "Hermione:~ madisonfitzgerald$ yt update

   yt module located at:
       /Users/madisonfitzgerald/miniconda/lib/python2.7/site-packages

   YT site-packages not in path, so you must
   update this installation manually by committing and
   merging your modifications to the code before
   updating to the newest changeset.”


   And I’m not sure what they mean by this.

   Thank you so much for you help and your patience.

   Madison Fitzgerald

   Astrophysics | Lyman Briggs College
   Women’s & Gender Studies | College of Arts & Letters
   LGBTQ and Sexuality Studies Specialization
   Women in Science, President
   Undergraduate Teaching Assistant
   Undergraduate Research Assistant
   Department of Physics and Astronomy
   Honors College
   Michigan State University

   On Jul 30, 2015, at 2:10 AM, Nathan Goldbaum
   <nathan12343@gmail.com
   <javascript:_e(%7B%7D,'cvml','nathan12343@gmail.com');>> wrote:

   Can you explain a little bit more what's going wrong with the
   miniconda-based installation?

   Unfortunately none of us have been able to reproduce the issue
   you're having with the install script and since it has something
   to do with matplotlib, I don't think any of us would know
   off-hand how to fix it in-place.

   Debugging issues like this over a mailing list is always
   potentially a frustrating experience, I'm sorry we haven't been
   able to come up with a suitable solution so far.

   On Wednesday, July 29, 2015, Madison Fitzgerald <fitzg152@msu.edu
   <javascript:_e(%7B%7D,'cvml','fitzg152@msu.edu');>> wrote:

       Hi everyone,

       Kacper: Sorry, my bad, but no, it didn’t work, unfortunately.

       John and Nathan: Thank you, but I haven’t gotten anything to
       work, which is especially frustrating because I had a
       functioning yt just a few days ago. Installing yt with
       miniconda has only made yt less willing to function, not
       solve my matplotlib issue.

       Truthfully, I’m really not sure where to go from here. Any
       thoughts?

       Thank you,
       Madison


       Madison Fitzgerald

       Astrophysics | Lyman Briggs College
       Women’s & Gender Studies | College of Arts & Letters
       LGBTQ and Sexuality Studies Specialization
       Women in Science, President
       Undergraduate Teaching Assistant
       Undergraduate Research Assistant
       Department of Physics and Astronomy
       Honors College
       Michigan State University

       On Jul 29, 2015, at 11:01 PM, John ZuHone
       <jzuhone@gmail.com> wrote:

       A bit late, but I can confirm that I was able to install
       from the install script on Mac OS 10.10 without any issue.

       On Jul 29, 2015, at 7:06 PM, Kacper Kowalik
       <xarthisius.kk@gmail.com> wrote:

       Hi again,
       did setting backend to 'agg' also fail?
       Cheers,
       Kacper

       On Jul 29, 2015 5:32 PM, "Nathan Goldbaum"
       <nathan12343@gmail.com> wrote:



           On Wed, Jul 29, 2015 at 5:30 PM, Madison Fitzgerald
           <fitzg152@msu.edu> wrote:

               Hi Nathan,

               I’m still getting the same error when I uninstall
               and then reinstall matplotlib. How would I be able
               to use miniconda as a workaround?


           Following these instructions:

           http://yt-project.org/docs/dev/installing.html#installing-yt-using-anaconda

           By the way, did you completely erase the old yt
           installation before rerunning the install script? Not
           doing so might be the cause of your issue.



               Thank you,
               Madison


               Madison Fitzgerald

               Astrophysics | Lyman Briggs College
               Women’s & Gender Studies | College of Arts & Letters
               LGBTQ and Sexuality Studies Specialization
               Women in Science, President
               Undergraduate Teaching Assistant
               Undergraduate Research Assistant
               Department of Physics and Astronomy
               Honors College
               Michigan State University

               On Jul 29, 2015, at 5:30 PM, Nathan Goldbaum
               <nathan12343@gmail.com> wrote:



               On Wed, Jul 29, 2015 at 4:19 PM, Madison
               Fitzgerald <fitzg152@msu.edu> wrote:

                   Hi everyone,

                   I’ve run into an error whenever I try to
                   execute any yt command (see yt_run_error.txt,
                   attached because I can’t use “yt pastebin”).
                   I’ve tried following the steps on the help
                   page, including re-installing yt, and I still
                   get this same error. I just installed the
                   latest stable yt version (I can’t execute the
                   command to give you specific numbers) on Mac
                   OS X 10.10.4.

                   Does anyone know where I should start to fix this?


               This is happening inside of matplotlib. 

               Can you try reinstalling the matplotlib that's in
               the yt environment? You should be able to do that
               with:

               $ pip uninstall matplotlib
               $ pip install matplotlib

               And see if that works?

               Failing that, a workaround would be to use a
               miniconda-based install.  

               I'm currently running the install script on my mac
               laptop to see if I can reproduce your issue.

               -Nathan



                   Thank you,
                   Madison


                   Madison Fitzgerald

                   Astrophysics | Lyman Briggs College
                   Women’s & Gender Studies | College of Arts &
                   Letters
                   LGBTQ and Sexuality Studies Specialization
                   Women in Science, President
                   Undergraduate Teaching Assistant
                   Undergraduate Research Assistant
                   Department of Physics and Astronomy
                   Honors College
                   Michigan State University





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