molpopgen

pub struct EdgeTableRow {
    pub id: EdgeId,
    pub left: Position,
    pub right: Position,
    pub parent: NodeId,
    pub child: NodeId,
    pub metadata: Option<Vec<u8>>,
}

molpopgen

import demes
import demesdraw
import matplotlib.pyplot as plt
import msprime
import numpy as np
import tskit

dmodel = """
time_units: generations
demes:

molpopgen

import sqlite3
import pickle
import codecs
x = {'a':1,2:'b'}

xp = pickle.dumps(x, -1)
xps = codecs.encode(xp, "base64").decode()

print(xps,type(xps),len(xps))
with sqlite3.connect("test.db") as conn:

molpopgen

// Usage:
// c++ -std=c++11 -o order order.cc
// ./order
//
// A "standard library*"-like implementation of R's order.
// To back-port this to C++98, one would need to
// replace the lambda closures with functors.  But there's no need
// to do such silliness anymore.
//
// The implementation is in terms of sorting iterators and then

molpopgen

# Test code writing fwdpy11
# pop data to hdf5 via PyTables.
# GOAL IS COMPRESSION!!!!
# Instead of using ragged arrays
# (not compressable), we use carrays,
# and simply concacenate gamete data.
# In longer-term, this would be
# abstracted into some sort of GameteTable
# class that interacts with an hdf5 object.

molpopgen

Problem

You want to use Jupyter remotely. X11 forwarding is too slow for this.

Solution

SSH port forwarding!

The recipe

molpopgen

#!sh

##collect the simulation results.  This may have to be run as 'bash collate.sh' on some systems
echo "Simulation L time mem" > results.txt
paste <(find . -name "*.time" -type f ! -size 0 | sed 's/\.\///' | cut -d"." -f 1,2 | sed 's/\./ /') <(find . -name "*.time" -type f ! -size 0 | xargs cat) | sort -n -k 2,3 >> results.txt

molpopgen

library(Rcpp)
Sys.setenv("PKG_CXXFLAGS" = "-std=c++11")
sourceCpp("tuple.cc",verbose=TRUE)

molpopgen

#include <boost/interprocess/sync/file_lock.hpp>
#include <boost/interprocess/sync/scoped_lock.hpp>

#include <fstream>

int main( int argc, char ** argv )
{
  std::ofstream o("monkey.txt",std::ios_base::app);

  boost::interprocess::file_lock ol("monkey.txt");

molpopgen

//////////////////////////////////////////////////////////////////
//                                                              //
//           PLINK (c) 2005-2008 Shaun Purcell                  //
//                                                              //
// This file is distributed under the GNU General Public        //
// License, Version 2.  Please see the file COPYING for more    //
// details                                                      //
//                                                              //
//////////////////////////////////////////////////////////////////