• This research provides the first comprehensive systematic literature review on software engineering research specifically targeting Jupyter notebooks, identifying 199 primary studies published up to September 2025 and categorizing them into 11 core software engineering topics. • This research reveals that a large portion of the studies have been published outside traditional software engineering venues, with Human-Computer Interaction conferences like ACM Conference on Human Factors in Computing Systems (CHI) being the top publishing venues, highlighting the interdisciplinary nature of Jupyter Notebook research. • This research identifies a reusability gap in existing research, showing that only 82 out of 199 studies offer usable replication packages, and most are hosted on GitHub instead of permanent repositories, which violates open science best practices. • This research identifies that notebook-specific solutions for software engineering issues such as testing, refactoring, and documentation are relatively underexplored. Future directions include resolving duplicated execution numbers, refactoring inter-notebook clones, and generating grouped documentation for coherent-code cells are future directions derived from our study. • This research proposes the integration of modern AI-based solutions into Jupyter notebooks to support various software engineering topics, including code search and code generation. Additionally, future research should leverage advanced AI techniques (e.g., large language models), to improve conversational AI-powered assistants for automated code generation by multi-step workflow automation in data science notebooks. • Although the paper exceeds the recommended length due to the inclusion of detailed tables, figures, and categorized analyses (covering 11 topics and 21 subtopics), we believe that this extended content is essential for clearly and completely reporting our findings. As the first systematic literature review in this domain, we have carefully structured the paper to ensure readability. We believe the length is justified by the value and breadth of this paper’s contributions. Context : Jupyter Notebook has emerged as a versatile tool that transforms how researchers, developers, and data scientists conduct and communicate their work. As the adoption of Jupyter notebooks continues to rise, so does the interest from the software engineering research community in improving the software engineering practices for Jupyter notebooks. Objective : The purpose of this study is to analyze trends, gaps, and methodologies used in software engineering research on Jupyter notebooks. Method : We selected 199 relevant publications up to September 2025, following established systematic literature review guidelines. We explored publication trends, categorized them based on software engineering topics, and reported findings based on those topics. Results : The most popular venues for publishing software engineering research on Jupyter notebooks are related to human-computer interaction instead of traditional software engineering venues. Researchers have addressed a wide range of software engineering topics on notebooks, such as code reuse, readability, and execution environment. Although reusability is one of the research topics for Jupyter notebooks, only 82 of the 199 studies can be reused based on their provided URLs. Additionally, most replication packages are not hosted on permanent repositories for long-term availability and adherence to open science principles. Conclusion : Solutions specific to notebooks for software engineering issues, including testing, refactoring, and documentation, are underexplored. Future research opportunities exist in automatic testing frameworks, refactoring clones between notebooks, and generating group documentation for coherent code cells.

The popularity of computational notebooks is rapidly increasing because of their interactive code-output visualization and on-demand non-sequential code block execution. These notebook features have made notebooks especially popular with machine learning developers and data scientists. However, as prior work shows, notebooks generally contain low quality code. In this paper, we investigate whether the low quality code is inherent to the programming style in notebooks, or whether it is correlated with the use of machine learning techniques. We present a large-scale empirical analysis of 246,599 opensource notebooks to explore how machine learning code quality in Jupyter Notebooks differs from non-machine learning code, thereby focusing on code style issues. We explored code style issues across the Error, Convention, Warning, and Refactoring categories. We found that machine learning notebooks are of lower quality regarding PEP-8 code standards than non-machine learning notebooks, and their code quality distributions significantly differ with a small effect size. We identified several code style issues with large differences in occurrences between machine learning and non-machine learning notebooks. For example, package and import-related issues are more prevalent in machine learning notebooks. Our study shows that code quality and code style issues differ significantly across machine learning and non-machine learning notebooks.

Comments are the internal documentation of corresponding code blocks, which are essential to understand and maintain a software. In large scale software development, developers need to analyze existing codes, where comments assist better readability. In practice, developers commonly ignore comments' updating with respect to changing codes, which leads the code comment inconsistency. Traditionally researchers detect these inconsistencies based on code-comment tokens. However, sequence ordering in codecomments is ignored in existing solution, as a result inconsistencies for invalid sequences of codes and comments are neglected. This paper solves these inconsistencies using siamese recurrent network which uses word tokens in codes and comments as well as their sequences in corresponding codes or comments. Proposed approach has been evaluated with a benchmark dataset, along with the ability of detecting invalid code comment sequence is examined.

Move Method Refactoring (MMR) is used to place highly coupled methods in appropriate classes for making source code more cohesive. Like other refactoring techniques, it is mandatory that applying MMR will preserve applications’ behaviors. However, traditional MMR techniques failed to meet this essential precondition for Action methods in web-based application and API methods in libraries projects. The reason is that applying MMR on these methods changes the behaviors of the projects by raising Application-breaking issues, for instance, failure of browser requests and compilation errors in client projects. To resolve this problem, developers are suggested to manually check Action and API methods while applying MMR. However, manually inspecting thousands of lines of code for these issues is a time-consuming and hectic task. In this paper, an advanced MMR technique is proposed which automatically identifies Application-breaking MMR suggestions. This technique first takes the initial move method suggestions from the existing prominent MMR techniques e.g. JDeodorant. For each of the suggestions, it parses the source code and construct Abstract Syntax Tree to examine two types of usage. One is whether a suggestion has not been used in any unit test and Regular Class, and another is whether the suggestion has been used in unit test classes only. If any MMR suggestion is found having one of these two types of usage or both, the respective suggestion is marked as Application-breaking. In order to evaluate the proposed technique, several experiments have been conducted on open source projects. The experimental results show that the proposed technique achieved 96.4% Precision, 90% Recall and 93.1% F-score in detecting Application-breaking MMR suggestions, because of considering external dependencies of the MMR suggestions.