Okay, my git skills are not so good, so definitely not *sure*.  Just tried to check by doing this:

 cd yt-conda/yt
(root) -bash-4.2$ git pull https://github.com/brittonsmith/yt.git clurmps
From https://github.com/brittonsmith/yt
 * branch                clurmps    -> FETCH_HEAD
Already up-to-date.

so...I think yes?
I also just did the same thing in my script and got the same output.
--
Dr. Stephanie Tonnesen
Associate Research Scientist
CCA, Flatiron Institute
New York, NY

stonnes@gmail.com


On Wed, Oct 3, 2018 at 2:56 PM Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Stephanie,

Are you *sure* you pulled britton's pull request? He deleted that entry in yt/analysis_modules/level_sets/api.py, so it looks like you're using a version of that file from before his pull request.

-Nathan

On Wed, Oct 3, 2018 at 1:44 PM Stephanie Tonnesen <stonnes@gmail.com> wrote:
Go it, thanks!

I think I have pulled your update, Britton, and now my code crashes almost immediately with this error.

yt_clump_fingert.py:4: VisibleDeprecationWarning: The level_sets module has been moved to yt.data_objects.level_sets.This import is deprecated and will be 
removed in a future release.Please, change the import in your scripts from 'from yt.analysis_modules.level_sets' to 'from yt.data_objects.level_sets.'.
  from yt.analysis_modules.level_sets.api import *
Traceback (most recent call last):
  File "yt_clump_fingert.py", line 4, in <module>
    from yt.analysis_modules.level_sets.api import *
  File "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/api.py", line 28, in <module>
    from yt.data_objects.level_sets.clump_handling import \
ImportError: cannot import name 'write_clump_index'

I am running:
yt version

yt module located at:
    /mnt/home/stonnesen/yt-conda/yt

The current version of yt is:

---
Version = 3.5.dev0
Changeset = ff956e8708c5
---
This installation CAN be automatically updated.

I am guessing that maybe I didn't include some other necessary update?

Thanks!!
Stephanie
--
Dr. Stephanie Tonnesen
Associate Research Scientist
CCA, Flatiron Institute
New York, NY

stonnes@gmail.com


On Tue, Oct 2, 2018 at 6:54 PM Britton Smith <brittonsmith@gmail.com> wrote:
Hi Stephanie,

While looking into this issue, I found some low hanging refactoring fruit, so I've issued a pull request that cleans things up and takes care of this as well. You can have a look here:

In running the example you attached, I found that the calculation resulted in a single clump comprised of the entire domain, so the clump annotation may be effectively invisible as it will draw a box around the entire figure. If I used a slightly smaller smaller data container, I was able to see the annotation, so I think things are ok. Let me know if it still doesn't seem right.

Britton

On Tue, Oct 2, 2018 at 1:05 PM Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi John,

Thanks!  I *think* it works--here is my only confusion.  If I set c_max to some value less than the max density (say, 1e-24 in the code I attached previously), it doesn't crash anymore but it doesn't actually plot a clump contour either.  If I set c_max to the max density setting (or I guess a bit above, 10**np.floor(np.log10(data_source[field]).max()+1) ), then I get a contour plotted.  Does this seem right to you?  

Also, they both give me this message "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/contour.py:1180: UserWarning: No contour levels w
ere found within the data range.
  warnings.warn("No contour levels were found"
"
Even though I seem to have one central contour in the c_max = 10**np.floor(np.log10(data_source[field]).max()+1) case.

Thanks!
Stephanie

--
Dr. Stephanie Tonnesen
Associate Research Scientist
CCA, Flatiron Institute
New York, NY

stonnes@gmail.com


On Tue, Oct 2, 2018 at 7:38 AM Wise, John H <jwise@physics.gatech.edu> wrote:
Hi Stephanie,

I actually ran into this bug in the past week.  I fixed in for my case
by making this change in clump_handling.py

-            elif (child._validate()):
+            elif ((child.children is not None) and child._validate()):

I haven't had the time to submit a PR. If this works for you, let me
know, and I can I create one this week.

Thanks,
John


On 10/01/2018 09:48 PM, Stephanie Tonnesen wrote:
> Hi,
>
> Sorry about the crazy delay, here is a script that reproduces the error
> with the IsolatedGalaxy dataset!
>
> The script is attached.  I am happy to help someone look into it, or
> look more myself with a bit of extra guidance.
>
> Thanks!!
>
> Stephanie
>
> --
> Dr. Stephanie Tonnesen
> Associate Research Scientist
> CCA, Flatiron Institute
> New York, NY
>
> stonnes@gmail.com <mailto:stonnes@gmail.com>
>
>
> On Fri, Sep 14, 2018 at 6:51 AM Stephanie Tonnesen <stonnes@gmail.com
> <mailto:stonnes@gmail.com>> wrote:
>
>     Hi Britton!
>
>     No, I have not resolved the issue, unfortunately.  I will try and
>     get a script that reproduces the problem up soon.
>
>     Best,
>     Stephanie
>
>     On Thu, Sep 13, 2018 at 7:45 PM Britton Smith
>     <brittonsmith@gmail.com <mailto:brittonsmith@gmail.com>> wrote:
>
>         HI Stephanie,
>
>         Have you managed to resolve this issue? If so, would you be
>         willing to submit a pull request to get this fix in the main
>         repo? If not, could you post a script that could be used to
>         reproduce this error with some of the public data?
>
>         Britton
>
>         On Fri, Sep 7, 2018 at 1:05 PM Nathan Goldbaum
>         <nathan12343@gmail.com <mailto:nathan12343@gmail.com>> wrote:
>
>             Generally an error like this is due to a bug in yt. I don't
>             know enough about the code you're using to provide useful
>             advice, but perhaps we should be checking if `children` is
>             `None` and doing something else. The "workaround" is likely
>             to fix whatever bug you've run into.
>
>             On Fri, Sep 7, 2018 at 2:56 PM, Stephanie Tonnesen
>             <stonnes@gmail.com <mailto:stonnes@gmail.com>> wrote:
>
>                 Hi yt-users!
>
>                 I have been fiddling some more with yt's clump finder
>                 and have another question.  I want to use density to
>                 find clumps, but want my maximum threshold value to be
>                 below the fiducial setting--instead of above the maximum
>                 possible density in the code I just want the finder to
>                 stop searching at, say 3.2e-24.
>
>                 The code was working but running out of memory until I
>                 set the max threshold, and I now get this error:
>
>                 ....lots of pleasant looking output messages....
>                 Updating joins ... :   0%|          | 0/7 [00:00<?, ?it/s]
>                 Updating joins ... : 100%|██████████| 7/7 [00:00<00:00,
>                 48933.55it/s]
>                 yt : [INFO     ] 2018-09-07 14:08:55,007 Investigating 2
>                 children.
>                 yt : [INFO     ] 2018-09-07 14:08:55,007 Finding clumps:
>                 min: 3.200000e-24, max: 3.200000e-24, step: 2.000000
>                 yt : [INFO     ] 2018-09-07 14:08:55,041 Finding clumps:
>                 min: 3.200000e-24, max: 3.200000e-24, step: 2.000000
>                 yt : [INFO     ] 2018-09-07 14:08:55,042 Eliminating
>                 invalid, childless clump with 2 cells.
>                 yt : [INFO     ] 2018-09-07 14:08:55,042 1 of 2 children
>                 survived, linking its children to parent.
>                 Traceback (most recent call last):
>                    File "yt_clump_fingert.py", line 59, in <module>
>                      find_clumps(master_clump, c_min, c_max, step)
>                    File
>                 "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py",
>                 line 444, in find_clumps
>                      find_clumps(child, min_val*d_clump, max_val, d_clump)
>                    File
>                 "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py",
>                 line 438, in find_clumps
>                      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>                    File
>                 "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py",
>                 line 438, in find_clumps
>                      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>                    File
>                 "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py",
>                 line 438, in find_clumps
>                      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>                    File
>                 "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py",
>                 line 461, in find_clumps
>                      for child in clump.children:
>                 TypeError: 'NoneType' object is not iterable
>
>                 I tried to circumvent this error by changing my max to
>                 2e-24 (not a multiple of 2 of 1e-25), and got the same
>                 error when the min was 3.2e-24 and the max was 2e-24 (!).
>
>                 Is there any way I can get around this error and have
>                 the clumpfinder stop looking once it has clump edges at
>                 my maximum density?
>
>                 Thanks!
>                 Stephanie
>                 --
>                 Dr. Stephanie Tonnesen
>                 Associate Research Scientist
>                 CCA, Flatiron Institute
>                 New York, NY
>
>                 stonnes@gmail.com <mailto:stonnes@gmail.com>
>
>                 _______________________________________________
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>
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>
>     --
>     --
>     Dr. Stephanie Tonnesen
>     Associate Research Scientist
>     CCA, Flatiron Institute
>     New York, NY
>
>     stonnes@gmail.com <mailto:stonnes@gmail.com>
>
>
>
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> yt-users mailing list -- yt-users@python.org
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>

--
John Wise
Associate Professor of Physics
Center for Relativistic Astrophysics, Georgia Tech
http://cosmo.gatech.edu
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