Installation

Dependencies

pybaselines requires Python version 3.8 or later and the following libraries:

All of the required libraries should be automatically installed when installing pybaselines using any of the installation methods below.

pybaselines has the following optional dependencies:

Numba (>= 0.49): speeds up calculations used by the following functions:
- loess()
- dietrich()
- golotvin()
- std_distribution()
- fastchrom()
- beads()
- mpspline()
- all functions in pybaselines.spline
pentapy (>= 1.1): provides a faster solver for banded pentadiagonal linear systems, which are used by the following functions (when diff_order=2):
- all functions in pybaselines.whittaker
- mpls()
- jbcd()
- fabc()

pybaselines can be installed from pypi using pip, by running the following command in the terminal:

pip install pybaselines

To also install the optional dependencies when installing pybaselines with pip, run:

pip install pybaselines[full]

pybaselines can alternatively be installed from the conda-forge channel using conda by running:

conda install -c conda-forge pybaselines

If installing with conda, the optional dependencies have to be specified manually.

The sources for pybaselines can be downloaded from the GitHub repo.

To directly install the current version of pybaselines from GitHub, ensure git is installed and then run:

pip install git+https://github.com/derb12/pybaselines.git#egg=pybaselines

Alternatively, to download the entire public repository and install pybaselines, run:

git clone https://github.com/derb12/pybaselines.git
cd pybaselines
pip install .