pypops - Python Interface to PoPS

This is a Python interface to the PoPS (Pest or Pathogen Spread) model.

Install using pip

Here, we will use a Python virtual environment to separate the pypops package install from the rest of your system. First, create the environment:

python3 -m venv testvenv

Then, active the environment (this will be different for different platfroms and shells):

source testvenv/bin/activate

Before using pip, upgrate it:

python -m pip install --upgrade pip

Install pypops from the GitHub repository:

pip install git+https://github.com/ncsu-landscape-dynamics/pypops

To install from previosly downloaded source code, just use path the source code instead of the URL. If you want to edit the source code and run without installing it, use pip with the --editable flag.

Run tests using pytest

In the virtual environment, install pytest using pip:

pip install pytest

Assuming you are in the pypops project directory (e.g. your Git clone), run the tests:

pytest tests/

Test basic functionality in Python

In the virtual environment, start Python:

python

In Python, import the package and try some basic functions:

>>> import _pypops
>>> _pypops.get_float_raster_scalar_type()
dtype('float64')
>>> _pypops.get_integer_raster_scalar_type()
dtype('int32')

Compile using CMake

For development of pypops, you can use CMake build directly (skipping the installation with pip).

Configure the project and use build directory for configure and build outputs:

cmake -S . -B build -DCMAKE_BUILD_TYPE=Debug

The -DCMAKE_BUILD_TYPE=Debug is for debugging build which will, e.g., show line numbers when executed with gdb. It and can be removed in other cases.

Build the project:

cmake --build build

Run tests:

CTEST_OUTPUT_ON_FAILURE=1 cmake --build build --target test

Optionally, to remove the build directory when you are done, use:

rm -rf build

Run Python code for testing manually

Assuming that you have a build from CMake, to run Python code from tests or any other script, use in the build directory as PYTHONPATH (here, assuming nested build directory under the source tree):

PYTHONPATH="build" python3 tests/test_pypops.py

Run it with Valgrind:

PYTHONPATH="build" valgrind python3 tests/test_simulation_function.py

Run it with GDB:

PYTHONPATH="build" gdb -ex=run --args python3 tests/test_simulation_function.py

Version of PoPS C++ used

Currently, this repository uses cmake-build branch from the PoPS.