andrewkern

#!/usr/bin/osascript
tell application "iTerm2"
    tell current session of current tab of current window
        write text "ssh -X $USERNAME@sesame.uoregon.edu"
        # i generally like to activate a conda environment 
        write text "conda activate stdpopsim"
        write text "jupyter lab --no-browser --port 8088"
        split horizontally with default profile
    end tell
    tell second session of current tab of current window

andrewkern

# fetch the code on a PR
git fetch upstream pull/351/head:pr351
# make sure you got it
git branch -v

# switch to relevant branch
git checkout pr351

# perhaps you need to rebase against
# upstream/master cause the PR is stale

andrewkern

import msprime


import stdpopsim
from stdpopsim import drosophila_melanogaster

chr_str = "chr2L"
genetic_map = stdpopsim.drosophila_melanogaster.Comeron2012_dm6()
genetic_map.download()
chrom = drosophila_melanogaster.genome.chromosomes[chr_str]

andrewkern

import keras
import msprime
import matplotlib
import numpy as np

# generate tree sequence
ts=msprime.simulate(
                Ne=0.5,
                population_configurations=[
                    msprime.PopulationConfiguration(sample_size=1000)],

andrewkern

import time
import msprime
now = time.clock()
theta=2
nsamp=100
m = 0.1
numReps=100
for i in list(range(numReps)):
    ts = msprime.simulate(
        Ne=1/2,