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MEG and EEG data analysis with MNE-Python by Gramfort, Alexandre

“… As part of the MNE software suite, MNE-Python is an open-source software package that addresses this challenge by providing state-of-the-art algorithms implemented in Python that cover multiple…”
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Domain Knowledge Matters: Improving Prompts with Fix Templates for Repairing Python Type Errors by Peng, Yun, Gao, Shuzheng, Gao, Cuiyun, Huo, Yintong, Lyu, Michael R.

“…As a dynamic programming language, Python has become increasingly popular in recent years…”
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Discovering Repetitive Code Changes in Python ML Systems by Dilhara, Malinda, Ketkar, Ameya, Sannidhi, Nikhith, Dig, Danny

“… Despite the extraordinary rise in popularity of Python-based ML systems, they do not benefit from these advances…”
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Evaluating Large Language Models in Class-Level Code Generation by Du, Xueying, Liu, Mingwei, Wang, Kaixin, Wang, Hanlin, Liu, Junwei, Chen, Yixuan, Feng, Jiayi, Sha, Chaofeng, Peng, Xin, Lou, Yiling

“…Recently, many large language models (LLMs) have been proposed, showing advanced proficiency in code generation…”
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PyTy: Repairing Static Type Errors in Python by Chow, Yiu Wai, Di Grazia, Luca, Pradel, Michael

“… As more and more code bases get type-annotated, static type checkers detect an increasingly large number of type errors…”
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A Python Instrument Control and Data Acquisition Suite for Reproducible Research by Koerner, Lucas J., Caswell, Thomas A., Allan, Daniel B., Campbell, Stuart I.

“… The National Synchrotron Light Source-II (NSLS-II) has generated an open-source Python data acquisition, management, and analysis software suite that automates X-ray…”
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SpotFlow: Tracking Method Calls and States at Runtime by Hora, Andre

“… In this paper, we propose SpotFlow, a tool to ease the runtime analysis of Python programs. With Spot-Flow, practitioners and researchers can easily extract information…”
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CoverUp: Effective High Coverage Test Generation for Python by Altmayer Pizzorno, Juan, Berger, Emery D.

“… We evaluate our prototype CoverUp implementation across a benchmark of challenging code derived from open-source Python projects and show that CoverUp substantially improves on the state of the art…”
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SNPAAMapper-Python: A highly efficient genome-wide SNP variant analysis pipeline for Next-Generation Sequencing data by Li, Chang, Ma, Kevin, Xu, Nicole, Fu, Chenjian, He, Andrew, Liu, Xiaoming, Bai, Yongsheng

“… In this study, we updated SNPAAMapper, a variant annotation pipeline by converting perl codes to python for generating annotation output with an improved computational efficiency and updated…”
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Bloat beneath Python’s Scales: A Fine-Grained Inter-Project Dependency Analysis by Drosos, Georgios-Petros, Sotiropoulos, Thodoris, Spinellis, Diomidis, Mitropoulos, Dimitris

“… In this work, we conduct a large-scale, fine-grained analysis to understand bloated dependency code in the PyPI ecosystem…”
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Inspect4py: A Knowledge Extraction Framework for Python Code Repositories by Filgueira, Rosa, Garijo, Daniel

“…This work presents inspect4py, a static code analysis framework designed to automatically extract the main features, metadata and documentation of Python code repositories…”
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Unleashing the Giants: Enabling Advanced Testing for Infrastructure as Code by Sokolowski, Daniel, Spielmann, David, Salvaneschi, Guido

“…Infrastructure as Code (IaC) programs are written in imperative programming languages like Python or TypeScript while declar-atively defining the target state of software deployments, which the IaC solution then sets up, e.g…”
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Kubernetes for Developers by Joseph Heck

“… In 'Kubernetes for Developers,' you'll learn essential Kubernetes concepts and master practical skills to containerize, run, and manage your code…”
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Analysis methods and code for very high-precision mass measurements of unstable isotopes by Karthein, J., Atanasov, D., Blaum, K., Lunney, D., Manea, V., Mougeot, M.

“…We present a robust analysis code developed in the Python language and incorporating libraries of the ROOT data analysis framework for the state-of-the-art mass spectrometry method called phase…”
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Restoring Reproducibility of Jupyter Notebooks by Wang, Jiawei, Kuo, Tzu-yang, Li, Li, Zeller, Andreas

“…Jupyter notebooks-documents that contain live code, equations, visualizations, and narrative text-now are among the most popular means to compute, present, discuss and disseminate scientific findings…”
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Computational Tools for the Multiscale Analysis of Hi-C Data in Bacterial Chromosomes by Varoquaux, Nelle, Lioy, Virginia S, Boccard, Frédéric, Junier, Ivan

“… Our objective is twofold. On the one hand, we aim at providing a full, understandable Python/Jupyter-based code which can be used by both computer scientists and biologists with no advanced computational background…”
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A Study of Large Language Models in Detecting Python Code Violations by Mohammed Salih, Hekar A., Sarhan, Qusay I.

“… Common static code analysis tools for Python, such as Pylint and Flake8, are widely used to enforce code quality by detecting coding violations without executing the code…”
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MolProbity: More and better reference data for improved all‐atom structure validation by Williams, Christopher J., Headd, Jeffrey J., Moriarty, Nigel W., Prisant, Michael G., Videau, Lizbeth L., Deis, Lindsay N., Verma, Vishal, Keedy, Daniel A., Hintze, Bradley J., Chen, Vincent B., Jain, Swati, Lewis, Steven M., Arendall, W. Bryan, Snoeyink, Jack, Adams, Paul D., Lovell, Simon C., Richardson, Jane S., Richardson, David C.

“… There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open…”
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Lost in Translation: A Study of Bugs Introduced by Large Language Models While Translating Code by Pan, Rangeet, Ibrahimzada, Ali Reza, Krishna, Rahul, Sankar, Divya, Wassi, Lambert Pougeum, Merler, Michele, Sobolev, Boris, Pavuluri, Raju, Sinha, Saurabh, Jabbarvand, Reyhaneh

“… The prerequisite for advancing the state of LLM-based code translation is to understand their promises and limitations over existing techniques…”
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Detecting and Explaining Anomalies Caused by Web Tamper Attacks via Building Consistency-based Normality by Liao, Yifan, Xu, Ming, Lin, Yun, Teoh, Xiwen, Xie, Xiaofei, Feng, Ruitao, Liauw, Frank, Zhang, Hongyu, Dong, Jin Song

“… However, their frontend can be manipulable by the clients (e.g., the frontend code can be modified to bypass some validation steps…”
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