Software increasingly functions as part of the scientific instrument itself, making failures in scientific code capable of compromising not only program behavior but also the evidence underlying scientific conclusions. Yet existing evaluations of coding agents largely emphasize aggregate task success, providing limited insight into why agents fail when repairing scientific software. We introduce \textbf{SWE-bench Science}, a repository-level benchmark for scientific software engineering comprising 119 tasks from 98 GitHub repositories across 20 scientific domains. Each task is organized into one of three paradigms: Issue-driven, Expert-exploratory, and Engineering-integration. Even the best-performing agent, \textbf{Claude Code with Opus-5 (max), achieves a pass@1 below 50%}, highlighting the substantial challenges posed by scientific software engineering. We identify four recurring failure mechanisms: deficits in scientific knowledge or abstraction, misguided exploration or surface-level repair, incomplete repair coverage or system integration, and failures to generalize scientific knowledge beyond observed cases in our analysis. We further conduct a paired ablation that removes explicit scientific guidance while preserving the repository and executable engineering context. The results show that scientific knowledge is not uniformly beneficial: well-grounded information can constrain repair and improve average performance and token efficiency, whereas poorly aligned guidance can induce anchoring and does not necessarily improve exact repair success. Together, SWE-bench Science provides a broad testbed for studying both the capabilities and failure mechanisms of coding agents in scientific software engineering.
Repository-level software engineering benchmarks have significantly advanced the evaluation of coding agents, but existing benchmarks primarily measure whether generated patches pass functional tests and overlook review-derived acceptance constraints (review constraints) that often influence whether a patch is acceptable in real-world software development. We introduce SWE-Gate, a repository-level benchmark for software engineering agents that explicitly evaluates review constraint compliance alongside functional correctness. SWE-Gate derives review constraints from real pull request review comments and synthesizes repository-level repair instances around these constraints. Each instance provides separate functional and constraint tests, together with non-compliant and gold patches, enabling explicit separation between issue resolution capability and review constraint compliance. We construct SWE-Gate with 303 repository-level repair instances spanning 75 open-source Python repositories across diverse software domains. Experiments with four LLM backends spanning different capability levels under a common coding-agent scaffold reveal a substantial gap between functional success and success under the complete repair specification: among 644 repairs that pass the functional tests, 221 fail to satisfy the provided review constraints. These findings show that functional-only evaluation overestimates agents' ability to satisfy the full requirements of repository-level repair tasks. The replication package including code, data, and experimental results is available at https://github.com/DeepSoftwareAnalytics/SWE-Gate.
Scientific code repositories encode decades of human knowledge in executable models, methods, and tools. Yet fragmented toolchains, implicit domain conventions, and specialized correctness criteria make this knowledge difficult to convert into reliable learning experience-a challenge we call the scientific experience bottleneck. We introduce ScienceIDE, infrastructure for turning the world's scientific code into programmable environments for scientific agents. Guided by expert-defined scientific cases and acceptance criteria, agents transform repositories into executable environments that support task generation, execution, and scientific verification. These environments provide a shared foundation for supervised fine-tuning, reinforcement learning, and evaluation. Using verified interaction trajectories, we train PhAI-IDE-72B, PhAI-IDE-9B, and PhAI-IDE-4B. The model family shows gains in held-out scientific-code repair and across selected general-purpose benchmarks in code, reasoning, and knowledge, providing evidence of positive transfer from scientific experience to broader capabilities. ScienceIDE lays the foundation for an integrated workspace for agent learning and scientific practice, making humanity's scientific software a shared substrate for developing scientific intelligence. Code: https://github.com/aitofound/ScienceIDE
SWE-Bench Pro has emerged as a standard benchmark for evaluating software engineering agents on challenging repository-level tasks. However, our analysis work show that its evaluation is undermined by two sources of unreliability: reward hacking, enabled by leakage of gold solutions or hidden evaluation information, and task quality issues, including misleading problem statements and improperly scoped tests. These issues can inflate benchmark performance and obscure agents' true coding ability. We present SWE-Bench Pro Verified, a verified version of SWE-Bench Pro that addresses both problems. Our approach combines anti-hacking safeguards that eliminate major leakage channels without disrupting normal agent functionality, with task refinement that minimally corrects inconsistencies within flawed instances. Evaluations on SWE-Bench Pro Verified reveal that some models perform substantially worse than previously evaluated, suggesting that existing results on SWE-Bench Pro may overestimate real software engineering capability. SWE-Bench Pro Verified offers a more trustworthy benchmark for assessing software engineering agents.