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Statistical models serve as the cornerstone for hypothesis testing in empirical studies. This paper introduces a new cross-platform Python-based package designed to utilise different likelihood prescriptions via a flexible plug-in system.…
The characterization of exoplanet requires reliable determination of the fundamental parameters of their host stars. Spectral fitting plays an important role in this process. For the majority of stellar parameters matching synthetic spectra…
The emergence of data-driven computational materials science offers unprecedented opportunities to explore complex material landscapes, complementing experimental research with the discovery of novel compounds. To enable these developments,…
{\mu}Manager, an open-source microscopy acquisition software, has been an essential tool for many microscopy experiments over the past 15 years, but is not easy to use for experiments in which image acquisition and analysis are closely…
CurvPy is an open-source Python library for automated curve fitting and regression analysis, aiming to make advanced statistical and machine learning techniques more accessible. This paper explores the mathematical foundations and…
There are numerous approaches to building analysis applications across the high-energy physics community. Among them are Python-based, or at least Python-driven, analysis workflows. We aim to ease the adoption of a Python-based analysis…
Histopathology, the current gold standard for cancer diagnosis, involves the manual examination of tissue samples after chemical staining, a time-consuming process requiring expert analysis. Raman spectroscopy is an alternative, stain-free…
Single molecule F\"orster resonance energy transfer (smFRET) is a powerful experimental technique for studying the properties of individual biological molecules in solution. However, as adoption of smFRET techniques becomes more widespread,…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…
This paper describes the design and use of the graph-based parsing framework and toolkit UniParse, released as an open-source python software package. UniParse as a framework novelly streamlines research prototyping, development and…
Integrated information theory provides a mathematical framework to fully characterize the cause-effect structure of a physical system. Here, we introduce PyPhi, a Python software package that implements this framework for causal analysis…
Data analysis in fundamental sciences nowadays is an essential process that pushes frontiers of our knowledge and leads to new discoveries. At the same time we can see that complexity of those analyses increases fast due to a)~enormous…
Since Lorenz's seminal work on a simplified weather model, the numerical analysis of nonlinear dynamical systems has become one of the main subjects of research in physics. Despite of that, there remains a need for accessible, efficient,…
We announce ChromaStarPy, an integrated general stellar atmospheric modeling and spectrum synthesis code written entirely in python V. 3. ChromaStarPy is a direct port of the ChromaStarServer (CSServ) Java modeling code described in earlier…
The adoption of large language models (LLMs) as rerankers in multi-stage retrieval systems has gained significant traction in academia and industry. These models refine a candidate list of retrieved documents, often through carefully…
Mayavi is an open-source, general-purpose, 3D scientific visualization package. It seeks to provide easy and interactive tools for data visualization that fit with the scientific user's workflow. For this purpose, Mayavi provides several…
PySCF is a general-purpose electronic structure platform designed from the ground up to emphasize code simplicity, both to aid new method development, as well as for flexibility in computational workflow. The package provides a wide range…
We present kikuchipy, an open-source toolbox for analysis of electron backscatter diffraction patterns, written in Python. The software is capable of both Hough and dictionary indexing and orientation and/or projection center refinement of…
Many research groups aspire to make data and code FAIR and reproducible, yet struggle because the data and code life cycles are disconnected, executable environments are often missing from published work, and technical skill requirements…
Despite impressive success of machine learning algorithms in clinical natural language processing (cNLP), rule-based approaches still have a prominent role. In this paper, we introduce medspaCy, an extensible, open-source cNLP library based…