Python package for breeding program numerical optimization and simulation
Project description
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
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:
cyvcf2-0.30.14+
(reading VCFs)cvxpy-1.1.18+
(linear programming)pymoo-0.6.0+
(genetic algorithms)h5py-3.6.0+
(HDF5 file support)matplotlib-3.5.1+
(graphics)numpy-1.22.2+
(matrix storage and algebra)pandas-1.4.1+
(data frames)pytest-7.0.1+
(unit tests)pytest-datadir-1.3.1+
(unit tests)scipy-1.8.0+
(miscellaneous numerical routines)setuptools
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
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