Tools for running and analyzing ATN simulation data from ATN Simulator or World of Balance.
I wrote this code for my master's thesis work, and I make no guarantees about its general usefulness.
- Clone the atn-tools git repository.
- Install Miniconda.
- Set up the atn-tools Conda environment:
cd atn-tools conda env create -f environment.yml - Activate the environment:
source activate atn-tools - Install the atn-tools package:
python setup.py install - Copy
atn-tools.conf.exampleto$HOME/atn-tools/atn-tools.confand edit as desired.
After making any changes to the code or any updates, repeat step 5 to update the installed version.
atn-tools provides a number commands implemented as Python scripts.
They are installed into the bin directory of the Conda environment.
Each script is prefixed with atn-.
A good way to see the list of commands is by using tab-completion,
typing atn-(tab) in a shell.
Each command is somewhat documented -- provide the -h argument to see the help.
For example:
(atn-tools) atn-tools $ atn-generate-food-web.py -h
usage: atn-generate-food-web.py [-h] [--parent-dir PARENT_DIR]
[--figsize FIGSIZE FIGSIZE] [--dpi DPI]
{generate,regenerate,from-node-ids} ...
Generates a plot and JSON file describing a food web. Files are stored in a
directory named based on the species in the food web. If --parent-dir is not
specified, the parent directory is determined automatically based on
DATA_HOME.
positional arguments:
{generate,regenerate,from-node-ids}
generate Generate a new food web and save plot and JSON
regenerate Regenerate files in existing food web directory
from-node-ids Generate plot and JSON from given node IDs
optional arguments:
-h, --help show this help message and exit
--parent-dir PARENT_DIR
Parent directory to use instead of automatically-
determined directory under DATA_HOME
--figsize FIGSIZE FIGSIZE
Width and height of the food web plot, in inches
(combine with --dpi)
--dpi DPI Image resolution (dots per inch)
Ben Saylor