Switch to new simplify

[petrelharp]

Here's an initial (untested) implementation of the new set-up, which:

• allows for sequential simplification
• keeps track of a tree sequence and some lists rather than the less efficient ordered dict
• does most everything with numpy arrays

TO-DO:

• actually use the new simplify() (else this won't work)
• test
• implement automatic sequential simplification
• allow initialization with a tree sequence

[ashander]

Note this is still failing on the CircleCI due to the test in tests/unit, line: https://github.com/ashander/ftprime/blob/589c9a9be6670d2c9b0c37fb98145cba78bafbec/tests/unit/test_arg_recorder.py#L5

[ashander]

Also: it will continue to fail there till an appropriate msprime version is subbed in here: https://github.com/ashander/ftprime/blob/master/environment.yml#L32

[petrelharp]

Ok. Will have to remember to sub that in when it exists.

On Fri, Jul 28, 2017 at 11:50 AM, ashander notifications@github.com wrote:

Also: it will continue to fail there till an appropriate msprime version is subbed in here: https://github.com/ashander/ftprime/blob/master/environment.yml#L32

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ashander/ftprime/pull/34#issuecomment-318734135, or mute the thread https://github.com/notifications/unsubscribe-auth/AA_26bFP3oFhsBSSjUm_p-VfWLO1qZDCks5sSi11gaJpZM4OanCv .

[ashander]

I've subbed in the current correct version of msprime in environment.yml, but this will need to be changed later to something in https://github.com/jeromekelleher/msprime once the code is merged there. It's working now via conda on Circle (I had to remove some config that assumed tests/unit existed in 634cafe)

[codecov[bot]]

Codecov Report

Merging #34 into master will decrease coverage by 15.41%. The diff coverage is 79.19%.

@@             Coverage Diff             @@
##           master      #34       +/-   ##
===========================================
- Coverage   98.13%   82.72%   -15.42%     
===========================================
  Files           3        3               
  Lines         161      191       +30     
===========================================
  Hits          158      158               
- Misses          3       33       +30

Flag	Coverage Δ
#unit	?

Impacted Files	Coverage Δ
ftprime/argrecorder.py	76.86% <76.8%> (-21.2%)	:arrow_down:
ftprime/recomb_collector.py	96.36% <91.66%> (-1.86%)	:arrow_down:

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 008e40a...e3dafc1. Read the comment docs.

[ashander]

once this is merged:

• closes #34
• 8ab3de9 closes #36