Installation

Installation#

Python package#

pip#

The easiest way to install the standard Python package is using pip:

pip install phylo2vec

Several optimization schemes based on Phylo2Vec are also available, but require extra dependencies. (See this notebook for a demo). To avoid bloating the standard package, these dependencies must be installed separately. To do so, run:

pip install phylo2vec[opt]

Manual installation#

  • We recommend setting up pixi package management tool.

  • Clone the repository and install using pixi:

git clone https://github.com/sbhattlab/phylo2vec.git
cd phylo2vec
pixi run -e py-phylo2vec install-python

This will compile and install the package as the core functionality is written in Rust.

R package#

Install a release (Windows, Mac, Ubuntu >= 22.04)#

Retrieve one of the compiled binaries from the releases that fits your OS. Once the file is downloaded, simply run install.packages in your R command line.

install.packages("/path/to/package_file", repos = NULL, type = 'source')

devtools#

⚠️ This requires installing Rust to build the core package.

devtools::install_github("sbhattlab/phylo2vec", subdir="./r-phylo2vec", build = FALSE)

Note: to download a specific version, use:

devtools::install_github("sbhattlab/phylo2vec@vX.Y.Z", subdir="./r-phylo2vec", build = FALSE)

Manual installation#

⚠️ This requires installing Rust to build the core package.

Clone the repository and run the following install.packages in your R command line.

Note: to download a specific version, you can use git checkout to a desired tag.

git clone https://github.com/sbhattlab/phylo2vec
cd phylo2vec

install.packages("./r-phylo2vec", repos = NULL, type = 'source')