partitionfinder
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brettc
Feature/morphology2
This is a pretty big pull request, and includes ALL of Paul's stuff as well as ALL of April's stuff (right @pbfrandsen? @wrightaprilm?).
I wonder if we should wait until the workshop to merge this. There are bound to be a lot of conflicts that would probably be best addressed with Paul, Brett, and myself in the room at the same time!!
So, yes, this is all of my stuff. My code should be easily mergeable with paul_develop (it's mostly model-handling additions), but I'm not able to speak to how paul_develop relates to the rest of the code.
OK, I'm an idiot. I thought this was the big merge into the main branch, now I see you're merging with Paul_develop.
@brettc, what do you think the best way to handle this is?
Given it is not on the main develop branch, I think this is fine as long as a) Paul is happy with it b) all tests pass. We plan to merge the morphology stuff in anyway, as well as Paul's stuff, so having it all in one place might help.
It looks mostly harmless to me from a quick scan, but 2 Questions:
- What is shelve doing in there?
- Why the changes to threadpool?
Brett
- I forgot that call to shelve was there. It's from before I realized I should be pulling from paul_develop and was developing off a branch that used pickle. I'll pull it out.
- I was testing the code out in a virtual session on my department's cluster, but only had one CPU available. I don't know much about threading, but the code choked in that function and tossing in that switch fixed it. That might be enough of a corner case problem that this can be removed.
I think this should be pretty straightforward. I will spend some time running the tests and merging the changes into the paul_develop branch early next week.
Sent from my iPad
On Jan 31, 2015, at 3:20 PM, April Wright [email protected] wrote:
- I forgot that call to shelve was there. It's from before I realized I should be pulling from paul_develop and was developing off a branch that used pickle. I'll pull it out.
- I was testing the code out in a virtual session on my department's cluster, but only had one CPU available. I don't know much about threading, but the code choked in that function and tossing in that switch fixed it. That might be enough of a corner case problem that this can be removed.
— Reply to this email directly or view it on GitHub.
The threading problem sounds odd --- it shouldn't even be called when only a single thread is being used. I'll add this to our list of things to check for v2.0.
Brett - start a new issue for the threading problem.
Paul - good luck!
On 1 February 2015 at 16:07, Brett Calcott [email protected] wrote:
The threading problem sounds odd --- it shouldn't even be called when only a single thread is being used. I'll add this to our list of things to check for v2.0.
— Reply to this email directly or view it on GitHub https://github.com/brettc/partitionfinder/pull/32#issuecomment-72349080.
Rob Lanfear School of Biological Sciences, Macquarie University, Sydney
phone: +61 (0)2 9850 8204
www.robertlanfear.com
Just by way of an update, the paul_develop branch fails a bunch of tests by itself, so I haven't completed the merge. I'm tracking down what is going wrong in paul_develop before I merge in the morphology branch.