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 FitzgeraldAstrophysics | Lyman Briggs CollegeWomen’s & Gender Studies | College of Arts & LettersLGBTQ and Sexuality Studies SpecializationWomen in Science, PresidentUndergraduate Teaching AssistantUndergraduate Research AssistantDepartment of Physics and AstronomyHonors CollegeMichigan State UniversityOn 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,
KacperAgain, 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 UniversityOn 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 UniversityOn 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 UniversityOn 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 UniversityOn 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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