Toolbox that provides functions and data structures to generate and handle ultrametric matrices.
Project description
Ultrametric matrix tools
This toolbox provides functions and data structures to construct and handle ultrametric matrices in Rust and Python. The aim of the project is to provide efficient tools for ultrametric matrices and ultrametric trees. Currently, the project has the following features.
Features:
- Generate a random ultrametric matrix
- Test ultramtic matrix property
- Construct the ultrametric tree from the ultrametric matrix
- Get properties of ultrametric tree
- Fast multiplication of ultrametric matrix with vector
The implementation is written in Rust and can be cross-compiled to Python.
Table of Contents
Quickstart
Quickstart Rust
Add the following to the Cargo.toml
file:
[dependencies]
# TODO: replace the * by the latest version.
ultrametric_matrix_tools = "*"
An example of the usage of is:
use ultrametric_matrix_tools::na::{DMatrix, DVector};
use ultrametric_matrix_tools::UltrametricTree;
fn main() {
let matrix = DMatrix::from_vec(
4,
4,
vec![
0.0, 1.0, 3.0, 1.0, 1.0, 3.0, 1.0, 1.0, 3.0, 1.0, 5.0, 1.0, 1.0, 1.0, 1.0, 1.0,
],
);
let vector = DVector::from_vec(vec![4.0, 2.0, 7.0, 5.0]);
let tree = UltrametricTree::from_matrix(&matrix);
let product = tree * vector;
}
More examples can be found in ./examples/
.
Quickstart Python
You can install the current release by running:
pip install ultrametric_matrix_tools
An example of the construction of the ultrametric tree and multiplication with it is:
from ultrametric_matrix_tools import UltrametricTree
import numpy as np
matrix = np.array([[0.0, 1.0, 3.0, 1.0], [1.0, 3.0, 1.0, 1.0], [
3.0, 1.0, 5.0, 1.0], [1.0, 1.0, 1.0, 1.0]])
vector = np.array([4.0, 2.0, 7.0, 5.0])
tree = UltrametricTree(matrix)
product = tree.mult(vector)
More examples can be found in ./examples/
.
Build
Build Rust Library
The Rust library is build by running:
cargo build --release
The compiled Rust library is located in ./target/release/
and can be copied from there.
Build Python Module
The Python module is build from the Rust code using the PyO3. To build the Python module, you need to install Cargo and run:
cargo build --release
The compiled Python module is located in ./target/release/
and can be copied from there.
To export the Python wheels from a Linux host system run the following commands:
Linux (requires docker):
docker run --rm -v $(pwd):/io konstin2/maturin build --release
Windows (requires mingw32-python and mingw64-python):
make python_package_windows
Currently, cross-compiling to macOS is not supported.
Examples
Rust Example
You can try out the Rust examples, you need to install Cargo. You can try out the Python examples located in ./examples/
by running the following command:
cargo run --release --example [example_name]
E.g. to run the multiplication example run:
cargo run --release --example multiplication
Python Example
To run the Python examples, you need to install Cargo. You can try out the Python examples located in ./examples/
by running the following command:
make python_example name=[example_name]
E.g. to run the multiplication example run:
make python_example name=multiplication
Alternatively, if you have the Python package already installed via pip, then you can run the examples directly:
python [example_name].py
License
This project is under the Apache-2.0 license.
Benchmarks
The benchmarks use criterion
for cargo
, which can be installed by running:
cargo install cargo-criterion
The benchmarks can be found in ./benches
and are run by:
cargo criterion --bench [benchmark_name]
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