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We describe a novel, interdisciplinary, computational methods course that uses Python and associated numerical and visualization libraries to enable students to implement simulations for a number of different course modules. Problems in…
Three object-oriented implementations of a prototype solver of the advection equation are introduced. The presented programs are based on Blitz++ (C++), NumPy (Python), and Fortran's built-in array containers. The solvers include an…
Most of Python and R scientific packages incorporate compiled scientific libraries to speed up the code and reuse legacy libraries. While several semi-automatic solutions exist to wrap these compiled libraries, the process of wrapping a…
The Message-Passing Interface (MPI) and C++ form the backbone of high-performance computing, but MPI only provides C and Fortran bindings. While this offers great language interoperability, high-level programming languages like C++ make…
partycls is a Python framework for cluster analysis of systems of interacting particles. By grouping particles that share similar structural or dynamical properties, partycls enables rapid and unsupervised exploration of the system's…
Machine learning solutions are very popular in the field of chemoinformatics, where they have numerous applications, such as novel drug discovery or molecular property prediction. Molecular fingerprints are algorithms commonly used for…
We present the first public release (v0.1) of the open-source GADGET Dataframe Library: gadfly. The aim of this package is to leverage the capabilities of the broader python scientific computing ecosystem by providing tools for analyzing…
The advent of modern data processing has led to an increasing tendency towards interdisciplinarity, which frequently involves the importation of different technical approaches. Consequently, there is an urgent need for a unified data…
Representing scientific data sets efficiently on external storage usually involves converting them to a byte string representation using specialized reader/writer routines. The resulting storage files are frequently difficult to interpret…
I describe the design, implementation, and usage of galpy, a Python package for galactic-dynamics calculations. At its core, galpy consists of a general framework for representing galactic potentials both in Python and in C (for accelerated…
Python is a particularly appealing language to carry out data analysis, owing in part to its user-friendly character as well as its access to well maintained and powerful libraries like NumPy and SciPy. Still, for the purpose of analyzing…
Data gridding is a common task in astronomy and many other science disciplines. It refers to the resampling of irregularly sampled data to a regular grid. We present cygrid, a library module for the general purpose programming language…
Literate programming - the bringing together of program code and natural language narratives - has become a ubiquitous approach in the realm of data science. This methodology is appealing as well for the domain of Density Functional Theory…
We present the CosmoBolognaLib, a large set of Open Source C++ numerical libraries for cosmological calculations. CosmoBolognaLib is a living project aimed at defining a common numerical environment for cosmological investigations of the…
Massively parallel Fourier transforms are widely used in computational sciences, and specifically in computational fluid dynamics which involves unbounded Poisson problems. In practice the latter is usually the most time-consuming operation…
The growing popularity of generative flow networks (GFlowNets or GFNs) from a range of researchers with diverse backgrounds and areas of expertise necessitates a library that facilitates the testing of new features (e.g., training losses…
We introduce a Python framework designed to automate the most common tasks associated with the extraction and upscaling of the statistics of single-impact crater functions to inform coefficients of continuum equations describing surface…
Conan is a C++ library created for the accurate and efficient modelling, inference and analysis of complex networks. It implements the generation and modification of graphs according to several published models, as well as the unexpensive…
We introduce a tensor network library designed for classical and quantum physics simulations called Cytnx (pronounced as sci-tens). This library provides almost an identical interface and syntax for both C++ and Python, allowing users to…
Open science is a fundamental pillar to promote scientific progress and collaboration, based on the principles of open data, open source and open access. However, the requirements for publishing and sharing open data are in many cases…