These are chat archives for dereneaton/ipyrad

23rd
Feb 2016
Deren Eaton
@dereneaton
Feb 23 2016 00:06
I think I figured out how to do progress bars
Isaac Overcast
@isaacovercast
Feb 23 2016 03:15
Conda install works for me, at least when i tried earlier around 4pm. Problem is still that conda build will only upload a new package for the platform it's built on, i updated the ticket to see if we can make it build for linux and mac at every conda builld call.
re: progress bars, thats sweet, i think people would appreciate it.
Deren Eaton
@dereneaton
Feb 23 2016 03:37
oh! well we definitely need to get the linux builds caught up. That's what most people will be installing on HPC machines.
yeah, I figured out some new tricks for ipyparallel tonight while working on the svd4tet code. When we get around to it I think we can rewrite a lot of the code so that we catch Engine jobs when they finish and count how many are done and do stuff to the output.
Isaac Overcast
@isaacovercast
Feb 23 2016 03:45
sweet, thx, i'll work on it.
Deren Eaton
@dereneaton
Feb 23 2016 04:11
great
Isaac Overcast
@isaacovercast
Feb 23 2016 04:31
Hm, i don't think there will be a simple way to automate this, especially inside versioner.py. conda convert only works for pure python packages, since we're compiling c, i don't think there's any way around doing a conda build install by hand on at least one or the other of the platforms.
Deren Eaton
@dereneaton
Feb 23 2016 04:42
ok. can you remind me how to build for linux.
we can just remind each other to do it for all major releases.
do I need the user/pass for the anaconda account?
Isaac Overcast
@isaacovercast
Feb 23 2016 04:51
username: ipyrad
password: watwatwat
anaconda login
Then it'll prompt for uname/passwd
then versioner.py will upload. This is still not ideal, but i'll work on simplifyng it.
Deren Eaton
@dereneaton
Feb 23 2016 05:02
oh, btw, does the wQMC binary in the bins dir work for you?
its the quartet-joining program.
They only released a binary that was compiled on linux. I assume it works generally, but we should check.
I guess it probably does since I added it to _cmd_exists() test in __init__
Deren Eaton
@dereneaton
Feb 23 2016 05:11
"solving package specification....." is still really slow. Looking forward to that conda update.
Deren Eaton
@dereneaton
Feb 23 2016 05:19
testing on an HPC cluster ran into this problem:
ValueError: Unable to configure handler 'ipyrad': [Errno 13] Permission denied: '/tmp/ipyrad_debug.txt'
was worried that might happen. I'll write it to re-route to os.devnull if a ValueError is raised.
Isaac Overcast
@isaacovercast
Feb 23 2016 15:33
wQMC binary doesn't work on mac
Deren Eaton
@dereneaton
Feb 23 2016 15:34
Dang. I'll try to get the source.
Deren Eaton
@dereneaton
Feb 23 2016 20:21
This is the only download link listed in the paper: http://research.haifa.ac.il/~ssagi/software/wQMC.tar.gz
Deren Eaton
@dereneaton
Feb 23 2016 21:13
I hit a segfault in step6 when running on a full size RAD data set. My notebook crashed. I wonder if it might have hit a memory limit. I'm investigating.
Deren Eaton
@dereneaton
Feb 23 2016 23:27
I emailed the authors about getting the wQMC source, or a mac compiled version. So close to having it working!
Isaac Overcast
@isaacovercast
Feb 23 2016 23:57
I know dude. i can taste it.
Debugging a problem with step5 on glenn's data. In consens_se.py at like 151:
    ## remove repeat sites from shortcon and stacked
    keeps, consens = zip(*[(i, j) for (i, j) in enumerate(consens) \
                         if i not in ridx])
If consens is empty it throws ValueError: need more than 0 values to unpack