<div dir="ltr">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.<div><br></div><div><a href="https://bitbucket.org/yt_analysis/yt/pull-requests/1663/bugfix-add-support-for-the-fabs-ufunc-to/diff">https://bitbucket.org/yt_analysis/yt/pull-requests/1663/bugfix-add-support-for-the-fabs-ufunc-to/diff</a><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jul 30, 2015 at 11:20 AM, Madison Fitzgerald <span dir="ltr"><<a href="mailto:fitzg152@msu.edu" target="_blank">fitzg152@msu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">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!<div><br></div><div>Thank you so much!<br><div><span class=""><br><div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div>Madison Fitzgerald</div><div><br></div><div>Astrophysics | Lyman Briggs College</div><div>Women’s & Gender Studies | College of Arts & Letters</div><div>LGBTQ and Sexuality Studies Specialization</div><div><div>Women in Science, President</div><div>Undergraduate Teaching Assistant</div><div>Undergraduate Research Assistant</div><div>Department of Physics and Astronomy</div></div><div>Honors College</div><div>Michigan State University</div></div></div></div></div></div></div></div>
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<br></span><div><div class="h5"><div><blockquote type="cite"><div>On Jul 30, 2015, at 11:51 AM, Kacper Kowalik <<a href="mailto:xarthisius.kk@gmail.com" target="_blank">xarthisius.kk@gmail.com</a>> wrote:</div><br><div><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">On 07/30/2015 10:38 AM, Madison Fitzgerald wrote:</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><blockquote type="cite" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Oh! Well, that certainly simplifies things! Thank you! And it does fix<br>my matplotlib error!<br><br>However, I still am seeing an error when I try to run my script (which<br>was what happened to lead me down this insane road with updating yt and<br>breaking matplotlib at the beginning). I’m getting an “Operation not<br>defined” error, but when I create a scratch script to narrow down which<br>part of line 14 is actually the undefined operation, they all work<br>individually.<br><br>Script: <a href="http://paste.yt-project.org/show/5761/" target="_blank">http://paste.yt-project.org/show/5761/</a><br>Error: <a href="http://paste.yt-project.org/show/5760/" target="_blank">http://paste.yt-project.org/show/5760/</a><br><br>Any thoughts?<br></blockquote><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Hi Madison,</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">use np.abs or np.absolute instead of np.fabs for yt arrays.</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Since you also know that all values are negative, I think it'd be faster</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">to just add '-' instead of abs.</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Cheers,</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Kacper</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><blockquote type="cite" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Again, thank you, I really appreciate all of your help.<br><br>Best,<br>Madison<br><br><br><br>Madison Fitzgerald<br><br>Astrophysics | Lyman Briggs College<br>Women’s & Gender Studies | College of Arts & Letters<br>LGBTQ and Sexuality Studies Specialization<br>Women in Science, President<br>Undergraduate Teaching Assistant<br>Undergraduate Research Assistant<br>Department of Physics and Astronomy<br>Honors College<br>Michigan State University<br><br><blockquote type="cite">On Jul 30, 2015, at 11:18 AM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a><br><<a href="mailto:nathan12343@gmail.com" target="_blank">mailto:nathan12343@gmail.com</a>>> wrote:<br><br>"yt update" won't work with the miniconda-based installation. Instead,<br>when we do a new release you'll be able to get the updated yt package<br>by doing "conda update yt".<br><br>You don't need to run an activate script if you're using miniconda's<br>Python, just start Python, import yt, and load your data :)<br><br>Nathan<br><br>On Thursday, July 30, 2015, Madison Fitzgerald <<a href="mailto:fitzg152@msu.edu" target="_blank">fitzg152@msu.edu</a><br><<a href="mailto:fitzg152@msu.edu" target="_blank">mailto:fitzg152@msu.edu</a>>> wrote:<br><br> I figured out that miniconda was having an issue with another<br> version of python, installed when I took a python-based<br> programming class, and I was able to redirect my path to point to<br> miniconda’s version instead, which solved that problem. However, I<br> think my problem now is figuring out how to activate yt with<br> miniconda. By that, I mean, I receive this output after<br> installation and trying to take the first step:<br><br> "Hermione:~ madisonfitzgerald$ yt update<br><br> yt module located at:<br> /Users/madisonfitzgerald/miniconda/lib/python2.7/site-packages<br><br> YT site-packages not in path, so you must<br> update this installation manually by committing and<br> merging your modifications to the code before<br> updating to the newest changeset.”<br><br><br> And I’m not sure what they mean by this.<br><br> Thank you so much for you help and your patience.<br><br> Madison Fitzgerald<br><br> Astrophysics | Lyman Briggs College<br> Women’s & Gender Studies | College of Arts & Letters<br> LGBTQ and Sexuality Studies Specialization<br> Women in Science, President<br> Undergraduate Teaching Assistant<br> Undergraduate Research Assistant<br> Department of Physics and Astronomy<br> Honors College<br> Michigan State University<br><br><blockquote type="cite"> On Jul 30, 2015, at 2:10 AM, Nathan Goldbaum<br> <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a><br> <javascript:_e(%7B%7D,'cvml','<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>');>> wrote:<br><br> Can you explain a little bit more what's going wrong with the<br> miniconda-based installation?<br><br> Unfortunately none of us have been able to reproduce the issue<br> you're having with the install script and since it has something<br> to do with matplotlib, I don't think any of us would know<br> off-hand how to fix it in-place.<br><br> Debugging issues like this over a mailing list is always<br> potentially a frustrating experience, I'm sorry we haven't been<br> able to come up with a suitable solution so far.<br><br> On Wednesday, July 29, 2015, Madison Fitzgerald <<a href="mailto:fitzg152@msu.edu" target="_blank">fitzg152@msu.edu</a><br> <javascript:_e(%7B%7D,'cvml','<a href="mailto:fitzg152@msu.edu" target="_blank">fitzg152@msu.edu</a>');>> wrote:<br><br> Hi everyone,<br><br> Kacper: Sorry, my bad, but no, it didn’t work, unfortunately.<br><br> John and Nathan: Thank you, but I haven’t gotten anything to<br> work, which is especially frustrating because I had a<br> functioning yt just a few days ago. Installing yt with<br> miniconda has only made yt less willing to function, not<br> solve my matplotlib issue.<br><br> Truthfully, I’m really not sure where to go from here. Any<br> thoughts?<br><br> Thank you,<br> Madison<br><br><br> Madison Fitzgerald<br><br> Astrophysics | Lyman Briggs College<br> Women’s & Gender Studies | College of Arts & Letters<br> LGBTQ and Sexuality Studies Specialization<br> Women in Science, President<br> Undergraduate Teaching Assistant<br> Undergraduate Research Assistant<br> Department of Physics and Astronomy<br> Honors College<br> Michigan State University<br><br><blockquote type="cite"> On Jul 29, 2015, at 11:01 PM, John ZuHone<br> <<a href="mailto:jzuhone@gmail.com" target="_blank">jzuhone@gmail.com</a>> wrote:<br><br> A bit late, but I can confirm that I was able to install<br> from the install script on Mac OS 10.10 without any issue.<br><br><blockquote type="cite"> On Jul 29, 2015, at 7:06 PM, Kacper Kowalik<br> <<a href="mailto:xarthisius.kk@gmail.com" target="_blank">xarthisius.kk@gmail.com</a>> wrote:<br><br> Hi again,<br> did setting backend to 'agg' also fail?<br> Cheers,<br> Kacper<br><br> On Jul 29, 2015 5:32 PM, "Nathan Goldbaum"<br> <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:<br><br><br><br> On Wed, Jul 29, 2015 at 5:30 PM, Madison Fitzgerald<br> <<a href="mailto:fitzg152@msu.edu" target="_blank">fitzg152@msu.edu</a>> wrote:<br><br> Hi Nathan,<br><br> I’m still getting the same error when I uninstall<br> and then reinstall matplotlib. How would I be able<br> to use miniconda as a workaround?<br><br><br> Following these instructions:<br><br> <a href="http://yt-project.org/docs/dev/installing.html#installing-yt-using-anaconda" target="_blank">http://yt-project.org/docs/dev/installing.html#installing-yt-using-anaconda</a><br><br> By the way, did you completely erase the old yt<br> installation before rerunning the install script? Not<br> doing so might be the cause of your issue.<br><br><br><br> Thank you,<br> Madison<br><br><br> Madison Fitzgerald<br><br> Astrophysics | Lyman Briggs College<br> Women’s & Gender Studies | College of Arts & Letters<br> LGBTQ and Sexuality Studies Specialization<br> Women in Science, President<br> Undergraduate Teaching Assistant<br> Undergraduate Research Assistant<br> Department of Physics and Astronomy<br> Honors College<br> Michigan State University<br><br><blockquote type="cite"> On Jul 29, 2015, at 5:30 PM, Nathan Goldbaum<br> <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:<br><br><br><br> On Wed, Jul 29, 2015 at 4:19 PM, Madison<br> Fitzgerald <<a href="mailto:fitzg152@msu.edu" target="_blank">fitzg152@msu.edu</a>> wrote:<br><br> Hi everyone,<br><br> I’ve run into an error whenever I try to<br> execute any yt command (see yt_run_error.txt,<br> attached because I can’t use “yt pastebin”).<br> I’ve tried following the steps on the help<br> page, including re-installing yt, and I still<br> get this same error. I just installed the<br> latest stable yt version (I can’t execute the<br> command to give you specific numbers) on Mac<br> OS X 10.10.4.<br><br> Does anyone know where I should start to fix this?<br><br><br> This is happening inside of matplotlib.<span> </span><br><br> Can you try reinstalling the matplotlib that's in<br> the yt environment? You should be able to do that<br> with:<br><br> $ pip uninstall matplotlib<br> $ pip install matplotlib<br><br> And see if that works?<br><br> Failing that, a workaround would be to use a<br> miniconda-based install. <br><br> I'm currently running the install script on my mac<br> laptop to see if I can reproduce your issue.<br><br> -Nathan<br><br><br><br> Thank you,<br> Madison<br><br><br> Madison Fitzgerald<br><br> Astrophysics | Lyman Briggs College<br> Women’s & Gender Studies | College of Arts &<br> Letters<br> LGBTQ and Sexuality Studies Specialization<br> Women in Science, President<br> Undergraduate Teaching Assistant<br> Undergraduate Research Assistant<br> Department of Physics and Astronomy<br> Honors College<br> Michigan State University<br><br><br><br><br><br> _______________________________________________<br> yt-users mailing list<br> <a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br> <a 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