These are chat archives for dereneaton/ipyrad

20th
Nov 2017
joqb
@joqb
Nov 20 2017 08:31
Hi @dereneaton oops! I found it there http://nbviewer.jupyter.org/github/dereneaton/ipyrad/blob/master/tests/cookbook-abba-baba.ipynb
Very much looking forward to use it to it's full extent!
joqb
@joqb
Nov 20 2017 16:46

Hi @dereneaton , on Friday the abba baba test was working fine. Today I wanted to run some more tests partlythe same ones but I'm getting an error I don't understand:
cc.run(ipyclient)

IPyradError                               Traceback (most recent call last)
<ipython-input-11-0d42ba703e53> in <module>()
      1 ## run all tests linked to bb
----> 2 cc.run(ipyclient)

/home/brassac/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/baba.pyc in run(self, ipyclient)
    120             An ipyparallel client object to distribute jobs to a cluster.
    121         """
--> 122         self.results_table, self.results_boots = batch(self, ipyclient)
    123         self.results_table.nloci = np.nan_to_num(self.results_table.nloci)\
    124                                                  .astype(int)

/home/brassac/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/baba.pyc in batch(baba, ipyclient)
    276                 if not asyncs[job].successful():
    277                     raise IPyradWarningExit(\
--> 278                         " error: {}: {}".format(job, asyncs[job].exception()))
    279                 ## enter results for successful jobs
    280                 else:

/home/brassac/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/util.pyc in __init__(self, *args, **kwargs)
     50     def __init__(self, *args, **kwargs):
     51         if ipyrad.__interactive__:
---> 52             raise IPyradError(*args, **kwargs)
     53         else:
     54             SystemExit.__init__(self, *args, **kwargs)

IPyradError:  error: 0: ImportError(cannot import name load)

Any suggestions?

Deren Eaton
@dereneaton
Nov 20 2017 17:35
Hi @joqb , did you update the code? I'm not sure what would have changed since Friday. I just ran it with the current release and did not see an error. Perhaps try restarting your notebook and ipcluster instance.
joqb
@joqb
Nov 20 2017 17:53

@dereneaton I just killed everything, updated ipyrad and rerun the notebook but this time it triggered this error

IPyradError:  error: 0: ValueError(Unable to configure handler 'ipyrad': [Errno 13] Permission denied: '/ipyrad_log.txt')

The ipyrad_log.txt is in the folder, it is empty and I have all rights on it...

Deren Eaton
@dereneaton
Nov 20 2017 17:55
Oh, it seems wherever you are running this from, you don't have permission to write into that current directory.
ergh, or it is trying to write the ipyrad log file to root, actually.
joqb
@joqb
Nov 20 2017 17:56
but if I rerun the same commands I get the previous error ImportError(cannot import name load)
Deren Eaton
@dereneaton
Nov 20 2017 17:57
It might be that when it imports ipyrad it tries to write the version information to the log file, and that raises an import error.
try changing your current directory to somewhere else, like $HOME, and then running it.
if that's the problem it's good to know, we could change this to raise a warning and avoid logging, instead of raising an error.
joqb
@joqb
Nov 20 2017 18:08
I changed directory to my HOME. I got the same error, I tried the .generate_tests_from_tree function, tests are being created but ImportError(cannot import name load) pops up when I want to run the tests
Deren Eaton
@dereneaton
Nov 20 2017 19:46
@joqb I'm trying to figure it out. Did you restart the ipcluster instance as well?
joqb
@joqb
Nov 20 2017 20:43
Yes I also restarted ipcluster