speedup distance computations

[dfolch]

This PR addresses #621.

By turning off generatetree() the time to compute a distance matrix is cut by approximately 90% (ymmv). After turning this off, the code was tested using Network Usage.ipynb. The notebook tests most of the network module including NetworkG, NetworkK and Moran, and ran without problems.

[jlaura]

(1) Tests are failing at line 103 because the tree is being used there. It appears that the tree is not used in the code (only the test). We should confirm that the test coverage is what we want even when the tree is not generated (I think it is).

(2) This PR needs to rebase from master after merging the snapping code.

[dfolch]

1. Thanks for catching that test failure.
2. Is it enough to do a git pull upstream master into my local branch, or is something more sophisticated needed?

[jlaura]

Git fetch upstream master
Git checkout master
Git merge upstream/master

On Saturday, June 20, 2015, David C. Folch notifications@github.com wrote:

1. Thanks for catching that test failure.
   1. Is it enough to do a git pull upstream master into my local
      branch, or is something more sophisticated needed?

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#637 (comment).

[dfolch]

I will reopen this under a new PR since my branch is a total mess.