atn-tools

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.

Installation

1. Clone the atn-tools git repository.
2. Install Miniconda.
3. Set up the atn-tools Conda environment:

   cd atn-tools
   conda env create -f environment.yml
   

4. Activate the environment:

   source activate atn-tools
   

5. Install the atn-tools package:

   python setup.py install
   

6. Copy atn-tools.conf.example to $HOME/atn-tools/atn-tools.conf and edit as desired.

After making any changes to the code or any updates, repeat step 5 to update the installed version.

Commands

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)

Author

Ben Saylor