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The increasing importance of Computational Science and Engineering has highlighted the need for high-quality scientific software. However, research software development is often hindered by limited funding, time, staffing, and technical…
Protecting software supply chains from malicious packages is paramount in the evolving landscape of software development. Attacks on the software supply chain involve attackers injecting harmful software into commonly used packages or…
Open-source licenses establish the legal foundation for software reuse, yet license variants, including both modified standard licenses and custom-created alternatives, introduce significant compliance complexities. Despite their prevalence…
We introduce API Pack, a massive multi-programming language dataset containing over one million instruction-API calls for improving the API call generation capabilities of large language models. Our evaluation highlights three key findings:…
Understanding how the brain functions is one of the biggest challenges of our time. The analysis of experimentally recorded neural firing patterns (spike trains) plays a crucial role in addressing this problem. Here, the PySpike library is…
Malicious code in open-source repositories such as PyPI poses a growing threat to software supply chains. Traditional rule-based tools often overlook the semantic patterns in source code that are crucial for identifying adversarial…
Security policies, such as SECURITY.md files, are now common in open-source projects. They help guide responsible vulnerability reporting and build trust among users and contributors. Despite their growing use, it is still unclear how these…
Academic publications have been evaluated in terms of their impact on research communities based on many metrics, such as the number of citations. On the other hand, the impact of academic publications on industry has been rarely studied.…
Software systems rely heavily on open source software (OSS) libraries, which offer benefits but also pose risks. When vulnerabilities arise, the OSS community may struggle to address them due to inactivity or lack of resources. Research…
Context: Over the last decades, open-source software has pervaded the software industry and has become one of the key pillars in software engineering. The incomparable growth of open source reflected that pervasion: Prior work described…
Scientific inference is often undermined by the vast but rarely explored "multiverse" of defensible modelling choices, which can generate results as variable as the phenomena under study. We introduce RobustiPy, an open-source Python…
There has been a long-standing hypothesis that a software's popularity is related to its security or insecurity in both research and popular discourse. There are also a few empirical studies that have examined the hypothesis, either…
The reliance of popular programming languages such as Python and JavaScript on centralized package repositories and open-source software, combined with the emergence of code-generating Large Language Models (LLMs), has created a new type of…
Python libraries are widely used for machine learning and scientific computing tasks today. APIs in Python libraries are deprecated due to feature enhancements and bug fixes in the same way as in other languages. These deprecated APIs are…
We present HaPy-Bug, a curated dataset of 793 Python source code commits associated with bug fixes, with each line of code annotated by three domain experts. The annotations offer insights into the purpose of modified files, changes at the…
Maintaining software is an ongoing process that stretches beyond the initial release. Stable software versions continuously evolve to fix bugs, add improvements, address security issues, and ensure compatibility. This ongoing support…
GitHub is the largest code hosting platform, with millions of repositories spanning multiple technologies. Despite this, little is known about the actual contents of GitHub's repositories in the wild. This paper presents an initial…
The recomputability and reproducibility of results from scientific software requires access to both the source code and all associated input and output data. However, the full collection of these resources often does not accompany the key…
AI systems rest on software with low integrity mechanisms, leaving AI systems exposed across every stage from data acquisition to final inference. This paper makes the AI supply chain a first-class object of analysis, decomposing it across…
Software Heritage is the largest public archive of software source code and associated development history, as captured by modern version control systems. As of July 2023, it has archived more than 16 billion unique source code files coming…