pybrops 1.0.3

Python package for breeding program numerical optimization and simulation

PyBrOpS

Python Breeding Optimizer and Simulator: A Python library for simulating breeding programs and optimizing breeding-related problems.

Detailed Documentation

A full website hosting all documentation can be found at the project GitHub Pages website. Please consult the documentation to learn how to use PyBrOpS.

General installation requirements

1. Python 3.8.0+

Notes on Linux installation requirements

You will need to install Python developmental headers in addition to Python 3.8.0+. Even though PyBrOpS is written in pure Python, some of its dependencies require compilation.

Commands for installing Python developmental headers:

Linux Distro	Command
Fedora	sudo dnf install python3-devel
Ubuntu	sudo apt install python3-dev

Python package dependencies

PyBrOpS relies on several dependencies. They are:

1. cyvcf2-0.30.14+ (reading VCFs)
2. cvxpy-1.1.18+ (linear programming)
3. pymoo-0.6.0+ (genetic algorithms)
4. h5py-3.6.0+ (HDF5 file support)
5. matplotlib-3.5.1+ (graphics)
6. numpy-1.22.2+ (matrix storage and algebra)
7. pandas-1.4.1+ (data frames)
8. pytest-7.0.1+ (unit tests)
9. pytest-datadir-1.3.1+ (unit tests)
10. scipy-1.8.0+ (miscellaneous numerical routines)
11. setuptools
12. wheel

Developmental version installation

To install first clone the repository:

git clone https://github.com/rzshrote/pybrops.git

It is a best practice to create a virtual environment where PyBrOpS dependencies can be installed. To do this, you can use the Makefile:

make install-devel

Alternatively, this may be done manually using the following commands:

python3 -m venv env
. env/bin/activate
python3 -m pip install --editable .

Next, you must activate the virtual environment using either the . command (for sh) or the source command (for bash):

. env/bin/activate

or

source env/bin/activate

Now that the virtual environment is activated, you can access pybrops through the python3 command-line interface prompt and through script execution.

Documentation generation

Non-exhaustive list for building

source env/bin/activate

pip3 install sphinx-autodoc-typehints sphinx_rtd_theme pydata_sphinx_theme