Installation

This page describes how to download and install phyddle and its dependencies.

Python package

phyddle is available as a PyPI package and can be installed using pip.

python3 -m pip install phyddle
# ... install ...
phyddle

Conda package

phyddle is also available as a conda package, and can be installed with the following commands:

conda create -n phyddle -c bioconda -c pytorch -c landismj phyddle
conda install -c bioconda -c pytorch -c landismj phyddle
# ... install ...
conda activate phyddle
phyddle

GitHub repository

To download the phyddle source code to your computer, you can either clone the repository

git clone git@github.com:mlandis/phyddle.git       # using SSH
git clone https://github.com/mlandis/phyddle.git   # using HTTPS
gh repo clone mlandis/phyddle                      # using GitHub CLI

Note, that newer experimental features are stored on the development branch.

git checkout development
git pull

You can also download and unzip the current version of the main branch

wget https://github.com/mlandis/phyddle/archive/refs/heads/main.zip
unzip main.zip

Once cloned, you can build phyddle into a local Python package

cd ~/projects/phyddle
python3 -m pip install -e .
# ... install ...
phyddle

System configuration

phyddle is regularly tested on Mac OS X 14.2.1 (Intel CPU) and Python 3.11.7 (installed with homebrew). phyddle is also intermittently tested on a 64-core Ubuntu LTS 22.04 server using Python 3.xx.xx (aptitude) and similar package versions.

To install required Python packages

python3 -m ensurepip --upgrade
python3 -m pip install --upgrade pip
python3 -m pip install dendropy graphviz h5py keras matplotlib numpy pandas Pillow pydot_ng pypdf scikit-learn scipy torch torchview tqdm

Last tested Python package versions are

dendropy 4.5.2
graphviz 0.20.1
h5py 3.8.0
keras 2.12.0
matplotlib 3.7.1
numpy 1.23.5
pandas 2.0.0
Pillow 10.1.0
pydot_ng 2.0.2
pypdf 3.12.0
scikit-learn 1.2.2
scipy 1.11.4
torch 2.0.0
torchview 0.2.6
tqdm 4.65.0