Installation

PLASTRO can be installed via pip or conda. We recommend using conda for easier dependency management.

Requirements

PLASTRO requires Python 3.10 or higher and the following core dependencies:

PLASTRO requires pybind11 to be installed first for building essential dependencies:

pip install pybind11
pip install plastro

To install with all optional dependencies:

pip install pybind11
pip install plastro[all]

For development, clone the repository and install in editable mode:

git clone https://github.com/dpeerlab/PLASTRO.git
cd PLASTRO
pip install pybind11
pip install -e ".[dev]"

We provide environment files for easy setup:

Using conda:

conda env create -f environment.yml
conda activate plastro

Using pip:

pip install -r requirements.txt

Some features require additional packages:

Lineage Tracing:

pip install cassiopeia-lineage

Development Tools:

pip install plastro[dev]

Documentation:

pip install plastro[docs]

Test your installation:

import plastro
print(plastro.__version__)

# Test basic functionality
print("Available functions:", dir(plastro))

Common Issues:

ETE3 Installation Problems

If you encounter issues with ETE3:
```
conda install -c etetoolkit ete3
```
Graph-Walker Build Issues

If graph-walker fails to build, ensure pybind11 is installed first:
```
pip install pybind11
pip install graph-walker
```
Memory Issues with Large Datasets

For large datasets, consider:
- Using a machine with more RAM
- Processing data in chunks
- Using sparse matrix representations

Getting Help:

If you encounter issues: