Cultural transmission models in python using simuPOP, SciPy, and NumPy
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admin
analytics
conf
ctpy
db
doc
simulations
test
.gitignore
.travis.yml
Doxyfile
LICENSE
README.md
install-simupop-for-travis.sh
install-slatkin-tools.sh
required-modules.txt
requirements.txt
run-experiment-sequence.sh
runtests-travis.sh
setup.py

README.md

CTPy

Build Status

Cultural transmission models in python using simuPOP, SciPy, and NumPy. Data storage is currently in a MongoDB instance, which can be local or remote, if simulations are being run on multiple machines.

CTPy is a software layer on top of simuPOP by Bo Peng, currently version 1.X. See http://simupop.sourceforge.net/ for source code, license, and documentation.

Directory Structure

analytics : python scripts which process simulation data from the database, and make entries into the database of their results.

ctpy : python modules and classes used in simulations and analytics

simulations : python scripts which run simuPOP simulations of cultural transmission models, logging samples to the database.

test : unit and functional test scripts

Runtime Dependency

CTPy assumes that there is an instance of MongoDB to which it can log samples and statistical data. The init.py file in the ctpy/sampling directory contains the database initialization, so that remote connections can be substituted for a local development server. This may be more easily configurable in future releases.

CTPy uses the Ming object relational library to connect from Python to MongoDB.

Module Dependencies

find . -name "*.py" | xargs grep -h 'import ' | grep -v ctpy | grep -v simu | sort | cut -d' ' -f2 | uniq > required-modules.txt

Author

Mark E. Madsen Copyright 2012-2013. All rights reserved. This software is made available under the Apache Software License (see file LICENSE), which allows you to use the software for commercial or non-commercial purposes, but you must attribute authorship, and derivatives must allow the user to find the original code and license.

mark@madsenlab.org Website and Lab Notebook