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Abstract Analysis on HEP data is an iterative process in which the results of one step often inform the next. In an exploratory analysis, it is common to perform one computation on a collection of events, then view the results (often with histograms) to decide what to try next. Awkward Array is a Scikit-HEP Python package that enables data analysis with array-at-a-time operations to implement cuts as slices, combinatorics as composable functions, etc. However, most C++ HEP libraries, such as FastJet, have an imperative, one-particle-at-a-time interface, which would be inefficient in Python and goes against the grain of the array-at-a-time logic of scientific Python. Therefore, we developed fastjet, a pip-installable Python package that provides FastJet C++ binaries, the classic (particle-at-a-time) Python interface, and the new array-oriented interface for use with Awkward Array. The new interface streamlines interoperability with scientific Python software beyond HEP, such as machine learning. In one case, adopting this library along with other array-oriented tools accelerated HEP analysis code by a factor of 20. It was designed to be easily integrated with libraries in the Scikit-HEP ecosystem, including Uproot (file I/O), hist (histogramming), Vector (Lorentz vectors), and Coffea (high-level glue). We discuss the design of the fastjet Python library, integrating the classic interface with the array oriented interface and with the Vector library for Lorentz vector operations. The new interface was developed as open source.
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This content will become publicly available on July 16, 2026
piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE
piqtree is an easy to use, open-source Python package that directly exposes IQ-TREE’s phylogenetic inference engine. It offers Python functions for performing many of IQ-TREE’s capabilities including phylogenetic reconstruction, ultrafast bootstrapping, branch length optimisation, ModelFinder, rapid neighbour-joining, and more. By exposing IQ-TREE’s algorithms within Python, piqtree greatly simplifies the development of new phylogenetic workflows through seamless interoperability with other Python libraries and tools mediated by the cogent3 package. It also enables users to perform interactive analyses with IQ-TREE through, for instance, Jupyter notebooks. We present the key features available in the piqtree library and a small case study that showcases its interoperability. The piqtree library can be installed withpip install piqtree, with the documentation available at https://piqtree.readthedocs.io and source at https://github.com/iqtree/piqtree.
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- Award ID(s):
- 2333243
- PAR ID:
- 10621351
- Publisher / Repository:
- bioRxiv
- Date Published:
- Format(s):
- Medium: X
- Institution:
- bioRxiv
- Sponsoring Org:
- National Science Foundation
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