Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2310.00960

A pragmatic workflow for research software engineering in computational science

Tomislav Marić·Dennis Gläser·Jan-Patrick Lehr·Ioannis Papagiannidis·Benjamin Lambie·Christian Bischof·Dieter Bothe
View original source ↗Read source document ↗Export metadata ↓

Abstract

University research groups in Computational Science and Engineering (CSE) generally lack dedicated funding and personnel for Research Software Engineering (RSE), which, combined with the pressure to maximize the number of scientific publications, shifts the focus away from sustainable research software development and reproducible results. The neglect of RSE in CSE at University research groups negatively impacts the scientific output: research data - including research software - related to a CSE publication cannot be found, reproduced, or re-used, different ideas are not combined easily into new ideas, and published methods must very often be re-implemented to be investigated further. This slows down CSE research significantly, resulting in considerable losses in time and, consequentially, public funding. We propose a RSE workflow for Computational Science and Engineering (CSE) that addresses these challenges, that improves the quality of research output in CSE. Our workflow applies established software engineering practices adapted for CSE: software testing, result visualization, and periodical cross-linking of software with reports/publications and data, timed by milestones in the scientific publication process. The workflow introduces minimal work overhead, crucial for university research groups, and delivers modular and tested software linked to publications whose results can easily be reproduced. We define research software quality from a perspective of a pragmatic researcher: the ability to quickly find the publication, data, and software related to a published research idea, quickly reproduce results, understand or re-use a CSE method, and finally extend the method with new research ideas.

Explore related subjects

cs.SE

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Tomislav Marić, Dennis Gläser, Jan-Patrick Lehr, Ioannis Papagiannidis, Benjamin Lambie, Christian Bischof, Dieter Bothe. 2023-10-02. A pragmatic workflow for research software engineering in computational science. https://arxiv.org/abs/2310.00960

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Combining Type Inference and Automated Unit Test Generation for Python

Automated unit test generation is an established research field that has so far focused on statically-typed programming languages. The lack of type information in dynamically-typed programming languages, such as Python, inhibits test generators, which heavily rely on information about parameter and return types of functions to select suitable arguments when constructing test cases. Since automated test generators inherently rely on frequent execution of candidate tests, we make use of these frequent executions to address this problem by introducing type tracing, which extracts type-related information during execution and gradually refines the available type information. We implement type tracing as an extension of the Pynguin test-generation framework for Python, allowing it (i) to infer parameter types by observing how parameters are used during runtime, (ii) to record the types of values that function calls return, and (iii) to use this type information to increase code coverage. The approach leads to up to 87.8 % more branch coverage, improved mutation scores, and to type information of similar quality to that produced by other state-of-the-art type-inference tools.

cs.SE↗
arXiv2026

MigrateLib: a tool for end-to-end Python library migration

Library migration is the process of replacing a library with a similar one in a software project. Manual library migration is time consuming and error prone, as it requires developers to understand the Application Programming Interfaces (API) of both libraries, map equivalent APIs, and perform the necessary code transformations. Due to the difficulty of the library migration process, most of the existing automated techniques and tooling stop at the API mapping stage or support a limited set of libraries and code transformations. In this paper, we develop an end-to-end solution that can automatically migrate code between any arbitrary pair of Python libraries that provide similar functionality. Due to the promising capabilities of Large Language Models (LLMs) in code generation and transformation, we use LLMs as the primary engine for migration. Before building the tool, we first study the capabilities of LLMs for library migration on a benchmark of 321 real-world library migrations. We find that LLMs can effectively perform library migration, but some post-processing steps can further improve the performance. Based on this, we develop MigrateLib, a command line application that combines the power of LLMs, static analysis, and dynamic analysis to provide accurate library migration. We evaluate MigrateLib on 717 real-world Python applications that are not from our benchmark. We find that MigrateLib can migrate 32% of the migrations with complete correctness. Of the remaining migrations, only 14% of the migration-related changes are left for developers to fix for more than half of the projects.

cs.SE↗
arXiv2026

Constraint Decay: The Fragility of LLM Agents in Backend Code Generation

Large Language Model (LLM) agents demonstrate strong performance in autonomous code generation under loose specifications. However, production-grade software requires strict adherence to structural constraints, such as architectural patterns, databases, and object-relational mappings. Existing benchmarks often overlook these non-functional requirements, rewarding functionally correct but structurally arbitrary solutions. We present a systematic study evaluating how well agents handle structural constraints in multi-file backend generation. By fixing a unified API contract across 80 greenfield generation tasks and 20 feature-implementation tasks spanning eight web frameworks, we isolate the effect of structural complexity using a dual evaluation with end-to-end behavioral tests and static verifiers. Our findings reveal a phenomenon of constraint decay: as structural requirements accumulate, agent performance exhibits a substantial decline. Evaluated configurations lose 27.28 points on average in assertion pass rates from baseline to fully specified tasks. Framework sensitivity analysis exposes performance disparities: mid-tier models succeed in minimal, explicit frameworks (e.g., Flask) but perform substantially worse on average in convention-heavy environments (e.g., FastAPI, Django). Finally, error analysis identifies data-layer defects (e.g., incorrect query composition and ORM runtime violations) as the leading root causes. This work highlights that jointly satisfying functional and structural requirements remains a key open challenge for coding agents.

cs.SE↗