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Command line interface

Requirements

The Python code runs with Python 3. (Python 2.7 is not supported.)

The Python json and csv packages are part of the Python standard library, while the PyYAML package needs to be installed to support YAML, openpyxl to support XLSX, and Pandas together with odfpy to support ODS (all are included as dependencies when the install the popsborder package is installed).

If you do not install the package or modify Python path, you will need to run in from the directory with the popsborder package, i.e., the root directory of the repository. If you install the package using pip, pip will take of the dependencies and it will work in any directory.

Running

The configuration is provided in a file which is specified as a command line parameter --config-file. The configuration format is YAML (extensions .yml or .yaml), JSON (extension .json), XLSX (.xlsx), ODS (.ods), or CSV (.csv).

For spreadsheet (tabular) formats (XLSX, ODS, and CSV), you need specify sheet, key_column, and value_column together with the file name in the --config-file separated by :: from the file name as key-value pairs where key and value are separated by = and individual keys are separated by ,.

Examples

Direct run of the simulation with 1000 consignments repeated 20 times:

python -m popsborder --num-simulations 20 --num-consignments 1000 --config-file config.yml

In the example above, replace config.yml by a full path to the file. Full path may be an absolute path in the file system with all directories (folders) included, a relative path from the current directory to the file, or just the file name as in the example if the file is in the current directory.

Run of the simulation once with 100 consignments with a tabular config in a CSV file where parameter keys and values are in the first (A) and second (B) columns:

python -m popsborder --num-consignments 100 --config-file config.csv::key_column=1,value_column=2

Here we use XLSX specifying a sheet and specifying columns using letters:

python -m popsborder --num-consignments 100 --config-file "config.xlsx::sheet=Sheet 2,key_column=A,value_column=B"

For a sheet with spaces in the name as in the example above, simply quote the whole command-line argument as you would quote spaces in a file name.

Command line options

Get all command line options for the simulation by running:

python -m popsborder --help

Post-processing the output

The following sample script included in the repository shows simple runs of the simulation with predefined values covering both success rate in detection of contaminants and generation of F280 records:

./examples/bash/bash_examples.sh

Next: Consignments