publish SWE-bench Science release
Browse filesThis view is limited to 50 files because it contains too many changes. See raw diff
- README.md +165 -0
- data/statistics.md +145 -0
- data/tasks.csv +120 -0
- manifests/tasks.jsonl +0 -0
- profiles/codex.env.example +7 -0
- selections/all-119.json +124 -0
- selections/default-107.json +112 -0
- tasks/task_001/environment/Dockerfile +60 -0
- tasks/task_001/instruction.md +13 -0
- tasks/task_001/metadata.json +12 -0
- tasks/task_001/task.toml +44 -0
- tasks/task_001/tests/Dockerfile +2 -0
- tasks/task_001/tests/test.sh +6 -0
- tasks/task_002/environment/Dockerfile +60 -0
- tasks/task_002/instruction.md +10 -0
- tasks/task_002/metadata.json +12 -0
- tasks/task_002/task.toml +44 -0
- tasks/task_002/tests/Dockerfile +2 -0
- tasks/task_002/tests/test.sh +6 -0
- tasks/task_003/environment/Dockerfile +60 -0
- tasks/task_003/instruction.md +28 -0
- tasks/task_003/metadata.json +12 -0
- tasks/task_003/task.toml +44 -0
- tasks/task_003/tests/Dockerfile +2 -0
- tasks/task_003/tests/test.sh +6 -0
- tasks/task_004/environment/Dockerfile +60 -0
- tasks/task_004/instruction.md +28 -0
- tasks/task_004/metadata.json +12 -0
- tasks/task_004/task.toml +44 -0
- tasks/task_004/tests/Dockerfile +2 -0
- tasks/task_004/tests/test.sh +6 -0
- tasks/task_005/environment/Dockerfile +60 -0
- tasks/task_005/instruction.md +19 -0
- tasks/task_005/metadata.json +12 -0
- tasks/task_005/task.toml +44 -0
- tasks/task_005/tests/Dockerfile +2 -0
- tasks/task_005/tests/test.sh +6 -0
- tasks/task_006/environment/Dockerfile +60 -0
- tasks/task_006/instruction.md +5 -0
- tasks/task_006/metadata.json +12 -0
- tasks/task_006/task.toml +44 -0
- tasks/task_006/tests/Dockerfile +2 -0
- tasks/task_006/tests/test.sh +6 -0
- tasks/task_007/environment/Dockerfile +60 -0
- tasks/task_007/instruction.md +25 -0
- tasks/task_007/metadata.json +12 -0
- tasks/task_007/task.toml +44 -0
- tasks/task_007/tests/Dockerfile +2 -0
- tasks/task_007/tests/test.sh +6 -0
- tasks/task_008/environment/Dockerfile +60 -0
README.md
ADDED
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| 1 |
+
---
|
| 2 |
+
pretty_name: SWE-bench Science
|
| 3 |
+
language:
|
| 4 |
+
- en
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| 5 |
+
task_categories:
|
| 6 |
+
- text-generation
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| 7 |
+
tags:
|
| 8 |
+
- software-engineering
|
| 9 |
+
- code-agents
|
| 10 |
+
- scientific-computing
|
| 11 |
+
- benchmark
|
| 12 |
+
---
|
| 13 |
+
|
| 14 |
+
# SWE-bench Science
|
| 15 |
+
|
| 16 |
+
> Generated from the canonical 119-row release manifest. All task environment
|
| 17 |
+
> and verifier references point to immutable `linux/amd64` Docker Hub digests.
|
| 18 |
+
|
| 19 |
+
SWE-bench Science evaluates coding agents on software-engineering problems from
|
| 20 |
+
scientific computing repositories. Each task is paired with an isolated task
|
| 21 |
+
environment and a separate verifier environment. Agent harnesses are selected
|
| 22 |
+
at evaluation time through Pier and are not baked into per-task release images.
|
| 23 |
+
|
| 24 |
+
## Dataset Summary
|
| 25 |
+
|
| 26 |
+
| Metric | Value |
|
| 27 |
+
| --- | ---: |
|
| 28 |
+
| Total tasks | 119 |
|
| 29 |
+
| Default non-GPL-family tasks | 107 |
|
| 30 |
+
| GPL/LGPL/AGPL-family opt-in tasks | 12 |
|
| 31 |
+
| Task environment images | 119 Docker Hub digests |
|
| 32 |
+
| Separate verifier images | 119 Docker Hub digests |
|
| 33 |
+
| linux/amd64 coverage | 119/119 |
|
| 34 |
+
|
| 35 |
+
Domain, language, license, and verifier-status tables will be generated from
|
| 36 |
+
`data/tasks.csv`; they will not be maintained manually. `UNKNOWN` is retained
|
| 37 |
+
when a sparse upstream source has no machine-detectable license; such rows need
|
| 38 |
+
manual review before final publication.
|
| 39 |
+
|
| 40 |
+
## Task Format
|
| 41 |
+
|
| 42 |
+
Each row records a stable task id, title, scientific domain, implementation
|
| 43 |
+
language, upstream repository and base commit, source license, GPL-family gate,
|
| 44 |
+
task environment image, verifier image, and local Pier task path.
|
| 45 |
+
|
| 46 |
+
The downloadable task bundle follows the Harbor-compatible format consumed by
|
| 47 |
+
Pier. The task environment and verifier run in separate containers. A trial
|
| 48 |
+
exports the agent's Git diff as `model.patch`; the verifier applies it to a
|
| 49 |
+
fresh baseline, rebuilds the project, and runs the grading contract offline.
|
| 50 |
+
|
| 51 |
+
Pier currently runs local task directories rather than downloading this Hugging
|
| 52 |
+
Face dataset directly. The release therefore includes a small materialization
|
| 53 |
+
tool that resolves an explicit selection into a local `tasks-selected/`
|
| 54 |
+
directory before `pier run -p tasks-selected`.
|
| 55 |
+
|
| 56 |
+
## Quick Start
|
| 57 |
+
|
| 58 |
+
A clean user can run the following after downloading this private dataset:
|
| 59 |
+
|
| 60 |
+
```bash
|
| 61 |
+
python3 -m pip install "huggingface_hub[cli]"
|
| 62 |
+
hf auth login
|
| 63 |
+
hf download <organization>/<dataset-repo> \
|
| 64 |
+
--repo-type dataset --local-dir swe-bench-science
|
| 65 |
+
cd swe-bench-science
|
| 66 |
+
|
| 67 |
+
uv venv --python 3.12 .venv
|
| 68 |
+
uv pip install "git+https://github.com/datacurve-ai/pier.git"
|
| 69 |
+
|
| 70 |
+
# Default: the fixed 107-task non-GPL selection.
|
| 71 |
+
python3 tools/materialize.py --output tasks-selected
|
| 72 |
+
|
| 73 |
+
# Arbitrary explicit batch. A GPL-family id still requires --allow-GPL.
|
| 74 |
+
python3 tools/materialize.py --task-id 002 --task-id 019 \
|
| 75 |
+
--output tasks-selected-small
|
| 76 |
+
|
| 77 |
+
# Pull both prebuilt images per task as linux/amd64, then run Pier.
|
| 78 |
+
python3 tools/run_batch.py --path tasks-selected-small \
|
| 79 |
+
--pier-bin .venv/bin/pier --agent nop --n-concurrent 2
|
| 80 |
+
```
|
| 81 |
+
|
| 82 |
+
To materialize all tasks, including the 12 GPL-family tasks:
|
| 83 |
+
|
| 84 |
+
```bash
|
| 85 |
+
python3 tools/materialize.py --allow-GPL --output tasks-selected-all
|
| 86 |
+
```
|
| 87 |
+
|
| 88 |
+
The materializer writes the exact task ids to `selection.json`. The batch runner
|
| 89 |
+
hashes that list, pulls the environment and verifier images, writes a redacted
|
| 90 |
+
`batch-run.json`, and invokes Pier with `--no-force-build --no-delete`. It never
|
| 91 |
+
uses runner-side random sampling. The selected `--platform` is also exported as
|
| 92 |
+
`DOCKER_DEFAULT_PLATFORM` so Pier's ephemeral environment+agent image stays
|
| 93 |
+
compatible with the prebuilt image architecture on an arm64 host.
|
| 94 |
+
|
| 95 |
+
## Codex Gateway Profile
|
| 96 |
+
|
| 97 |
+
Keep credentials outside the dataset checkout. Start from
|
| 98 |
+
`profiles/codex.env.example`, place the real profile in a user-only directory,
|
| 99 |
+
and select it per run:
|
| 100 |
+
|
| 101 |
+
```bash
|
| 102 |
+
python3 tools/run_batch.py --path tasks-selected-small \
|
| 103 |
+
--pier-bin .venv/bin/pier --agent codex \
|
| 104 |
+
--env-file ~/.config/swe-bench-science/openai.env \
|
| 105 |
+
--n-concurrent 2 --n-attempts 1
|
| 106 |
+
```
|
| 107 |
+
|
| 108 |
+
| Field | Purpose |
|
| 109 |
+
| --- | --- |
|
| 110 |
+
| `MODEL` | Model sent to Codex; CLI `--model` overrides it |
|
| 111 |
+
| `OPENAI_API_KEY` | Gateway credential; never written to run metadata |
|
| 112 |
+
| `CODEX_BASE_URL` | Selected relay or OpenAI-compatible endpoint |
|
| 113 |
+
| `CODEX_WIRE_API` | `responses` or `chat` |
|
| 114 |
+
| `CODEX_VERSION` | Installed `@openai/codex` version |
|
| 115 |
+
| `CODEX_REASONING_EFFORT` | Codex reasoning effort |
|
| 116 |
+
|
| 117 |
+
The runner translates these fields into Pier's native Codex `config_toml` and
|
| 118 |
+
derives the network allowlist from the endpoint. Switching relay, protocol, or
|
| 119 |
+
credential means selecting another env file; task files and images do not
|
| 120 |
+
change. It also uses a runtime-only Codex adapter to install npm's optional
|
| 121 |
+
linux-x64 package correctly; no agent binary is placed in task images. Advanced
|
| 122 |
+
users can disable these defaults with `--no-auto-provider` and
|
| 123 |
+
`--no-auto-agent-adapter`, then pass repeated `--agent-kwarg` / `--agent-env` values directly to Pier.
|
| 124 |
+
Provider-qualified model names are preserved through Codex's
|
| 125 |
+
`command_model_name`; this matters for gateways that route `provider/model-name`
|
| 126 |
+
differently from the unqualified `model-name`. An explicit
|
| 127 |
+
`--agent-kwarg command_model_name=...` still takes precedence.
|
| 128 |
+
For a short smoke, add `--agent-timeout-multiplier 0.0223` (approximately 120
|
| 129 |
+
seconds against the default task timeout); verifier timeout remains separate.
|
| 130 |
+
|
| 131 |
+
## Agent Harnesses
|
| 132 |
+
|
| 133 |
+
Codex, Claude Code, mini-swe-agent, and other Pier-supported harnesses are trial
|
| 134 |
+
configuration. They are not dataset columns and are not published once per
|
| 135 |
+
task. Reproducible evaluation records pin the Pier version, agent/version,
|
| 136 |
+
model/provider configuration, installation fingerprint, and both image digests.
|
| 137 |
+
|
| 138 |
+
## GPL-family Tasks
|
| 139 |
+
|
| 140 |
+
The default download selection contains 107 tasks. Use the project download
|
| 141 |
+
tool's explicit `--allow-GPL` option to materialize all 119 tasks. This option
|
| 142 |
+
is a distribution selection and does not replace compliance with the upstream
|
| 143 |
+
license of each source repository.
|
| 144 |
+
|
| 145 |
+
## Security and Leakage Policy
|
| 146 |
+
|
| 147 |
+
The dataset does not distribute reference-answer patches, oracle solutions,
|
| 148 |
+
author notes, credentials, or previous agent trajectories. Verifier material is
|
| 149 |
+
never mounted into the agent environment. The verifier disclosure policy is
|
| 150 |
+
pending final confirmation by the dataset owners.
|
| 151 |
+
|
| 152 |
+
## Images
|
| 153 |
+
|
| 154 |
+
Image references will point to immutable Docker Hub digests after the owners
|
| 155 |
+
provide the final namespace and complete per-task validation. Blank image fields
|
| 156 |
+
mean unpublished, not "use a default image".
|
| 157 |
+
|
| 158 |
+
## Citation
|
| 159 |
+
|
| 160 |
+
Pending the final paper citation.
|
| 161 |
+
|
| 162 |
+
## License
|
| 163 |
+
|
| 164 |
+
Dataset metadata license: pending owner confirmation. Each task row records the
|
| 165 |
+
license of its upstream source repository separately.
|
data/statistics.md
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| 1 |
+
# Generated Release Statistics
|
| 2 |
+
|
| 3 |
+
Canonical rows: **119**; default non-GPL rows: **107**; GPL-family rows: **12**.
|
| 4 |
+
|
| 5 |
+
Environment image references: **119/119**; verifier image references: **119/119**.
|
| 6 |
+
|
| 7 |
+
### Domain
|
| 8 |
+
|
| 9 |
+
| Value | Count |
|
| 10 |
+
| --- | ---: |
|
| 11 |
+
| `ai-chemistry-reaction-property-learning` | 1 |
|
| 12 |
+
| `ai4science-nmr-structure-elucidation` | 1 |
|
| 13 |
+
| `astrodynamics-and-orbital-mechanics` | 1 |
|
| 14 |
+
| `astronomical-image-analysis-and-wcs-aperture-photometry` | 1 |
|
| 15 |
+
| `astronomical-image-processing` | 1 |
|
| 16 |
+
| `astronomical-spectroscopy` | 1 |
|
| 17 |
+
| `astrophysical hydrodynamics and particle-based field visualization` | 1 |
|
| 18 |
+
| `astrophysical-xray-spectral-timing` | 1 |
|
| 19 |
+
| `atmospheric-science-isentropic-interpolation` | 1 |
|
| 20 |
+
| `atomistic thermodynamic integration and free-energy calculation` | 1 |
|
| 21 |
+
| `atomistic-machine-learning-and-molecular-simulation` | 2 |
|
| 22 |
+
| `atomistic-machine-learning-data` | 1 |
|
| 23 |
+
| `atomistic-machine-learning-potentials` | 1 |
|
| 24 |
+
| `boundary-aggregation` | 1 |
|
| 25 |
+
| `chemoinformatics-molecular-fingerprints` | 1 |
|
| 26 |
+
| `chromatin-accessibility peak calling` | 1 |
|
| 27 |
+
| `climate-fire-weather` | 1 |
|
| 28 |
+
| `computational-chemistry` | 1 |
|
| 29 |
+
| `computational-chemistry-and-solvation` | 1 |
|
| 30 |
+
| `computational-chemistry-molecular-representations` | 1 |
|
| 31 |
+
| `computational-chemistry-scientific-data-parsing` | 1 |
|
| 32 |
+
| `computational-chemistry-spectroscopy` | 1 |
|
| 33 |
+
| `computational-crystallography-and-materials-symmetry` | 1 |
|
| 34 |
+
| `computational-electromagnetics-and-geophysical-forward-modeling` | 1 |
|
| 35 |
+
| `computational-geometry` | 1 |
|
| 36 |
+
| `computational-high-energy-molecular-chemistry-periodic-models` | 1 |
|
| 37 |
+
| `computational-materials-finite-volume-pde` | 1 |
|
| 38 |
+
| `computational-materials-science` | 1 |
|
| 39 |
+
| `computational-mathematics-special-functions` | 1 |
|
| 40 |
+
| `computational-mechanics-and-soft-filament-dynamics` | 1 |
|
| 41 |
+
| `computational-oceanography-and-spherical-geometry` | 1 |
|
| 42 |
+
| `computational-oceanography-finite-volume-grids` | 1 |
|
| 43 |
+
| `computational-thermodynamics-calphad` | 1 |
|
| 44 |
+
| `computer-algebra` | 1 |
|
| 45 |
+
| `condensed-matter-magnetism-and-magnetic-symmetry` | 1 |
|
| 46 |
+
| `convex-optimization-parametric-workflows` | 1 |
|
| 47 |
+
| `crystallography-file-format-semantics` | 1 |
|
| 48 |
+
| `density-functional-theory` | 2 |
|
| 49 |
+
| `diffusion-mri-denoising` | 1 |
|
| 50 |
+
| `drug-discovery-cheminformatics` | 1 |
|
| 51 |
+
| `earth-science-data-semantics` | 1 |
|
| 52 |
+
| `earth-surface-dynamics-and-river-sediment-transport` | 1 |
|
| 53 |
+
| `edited-magnetic-resonance-spectroscopy-workflow` | 1 |
|
| 54 |
+
| `electrochemical-battery-modeling` | 1 |
|
| 55 |
+
| `electronic-structure-nonorthogonal-eigenproblems` | 1 |
|
| 56 |
+
| `energy-materials-and-finite-volume-transport` | 1 |
|
| 57 |
+
| `epigenomics-atac-seq-hmm` | 1 |
|
| 58 |
+
| `finite-difference-stochastic-partial-differential-equations` | 1 |
|
| 59 |
+
| `gamma-ray-astronomy-dark-matter` | 1 |
|
| 60 |
+
| `genomic-variant-data-semantics` | 1 |
|
| 61 |
+
| `genomics-contact-map-analysis` | 1 |
|
| 62 |
+
| `genomics-interval-statistics` | 1 |
|
| 63 |
+
| `genomics-sequence-annotation` | 1 |
|
| 64 |
+
| `geospatial-raster-reprojection` | 1 |
|
| 65 |
+
| `grazing-incidence-and-fiber-x-ray-scattering` | 1 |
|
| 66 |
+
| `high-density-extracellular-electrophysiology` | 1 |
|
| 67 |
+
| `high-performance-fibers-and-composites` | 4 |
|
| 68 |
+
| `lithium-ion-battery-modeling` | 1 |
|
| 69 |
+
| `magnetic-resonance-spectroscopy` | 1 |
|
| 70 |
+
| `magnetic-resonance-spectroscopy-processing` | 1 |
|
| 71 |
+
| `magnetic-resonance-spin-dynamics` | 1 |
|
| 72 |
+
| `magnetism-and-spin-models` | 1 |
|
| 73 |
+
| `mass-spectrometry-spectral-similarity` | 1 |
|
| 74 |
+
| `materials-science-scientific-data-semantics` | 1 |
|
| 75 |
+
| `materials-science-volumetric-data-semantics` | 1 |
|
| 76 |
+
| `medical-image-processing` | 1 |
|
| 77 |
+
| `medical-image-segmentation-geometry` | 1 |
|
| 78 |
+
| `medical-imaging` | 1 |
|
| 79 |
+
| `medical-imaging-color-pixel-semantics` | 1 |
|
| 80 |
+
| `microscopy-image-analysis` | 1 |
|
| 81 |
+
| `microwave-network-analysis` | 1 |
|
| 82 |
+
| `molecular-dynamics-machine-learning-potentials` | 1 |
|
| 83 |
+
| `molecular-dynamics-periodic-boundary-analysis` | 1 |
|
| 84 |
+
| `molecular-dynamics-trajectory-analysis` | 1 |
|
| 85 |
+
| `molecular-simulation` | 1 |
|
| 86 |
+
| `monte-carlo-particle-transport` | 1 |
|
| 87 |
+
| `neuroimaging` | 1 |
|
| 88 |
+
| `neurophysiology-signal-processing` | 1 |
|
| 89 |
+
| `new-energy-materials` | 1 |
|
| 90 |
+
| `nuclear-magnetic-resonance-spectroscopy` | 1 |
|
| 91 |
+
| `numerical-analysis-and-chemical-kinetics` | 1 |
|
| 92 |
+
| `periodic-electronic-structure` | 1 |
|
| 93 |
+
| `planetary-geodesy-and-geomagnetism` | 1 |
|
| 94 |
+
| `plasma-stability` | 7 |
|
| 95 |
+
| `polymer-coordinate-generation` | 1 |
|
| 96 |
+
| `population-genetics-tree-sequence-statistics` | 1 |
|
| 97 |
+
| `porous-media-image-analysis` | 1 |
|
| 98 |
+
| `power-system-energy-storage` | 1 |
|
| 99 |
+
| `probabilistic-scientific-computing` | 1 |
|
| 100 |
+
| `proteomics` | 1 |
|
| 101 |
+
| `quantum-chemistry-reaction-paths` | 1 |
|
| 102 |
+
| `quantum-information-many-body-tensor-networks` | 1 |
|
| 103 |
+
| `remote-sensing-and-geostationary-geolocation` | 1 |
|
| 104 |
+
| `renewable-energy-modelling` | 1 |
|
| 105 |
+
| `reticular-chemistry-and-framework-geometry` | 1 |
|
| 106 |
+
| `rna-seq-genomic-interval-semantics` | 1 |
|
| 107 |
+
| `satellite-navigation-and-gnss-positioning` | 1 |
|
| 108 |
+
| `single-cell-annotated-data-containers` | 1 |
|
| 109 |
+
| `single-cell-chromatin-accessibility` | 1 |
|
| 110 |
+
| `single-cell-perturbation-response-modeling` | 1 |
|
| 111 |
+
| `solar-physics-scientific-data-semantics` | 1 |
|
| 112 |
+
| `space-physics-coordinate-systems` | 1 |
|
| 113 |
+
| `stochastic-numerical-analysis` | 1 |
|
| 114 |
+
| `structural-biology-pdbx-macromolecular-connectivity` | 1 |
|
| 115 |
+
| `structural-engineering-and-disaster-resilience` | 1 |
|
| 116 |
+
| `structural-engineering-disaster-resilience` | 1 |
|
| 117 |
+
| `structural-engineering-finite-element-resilience` | 1 |
|
| 118 |
+
| `tropical-cyclone-hazard-monitoring` | 1 |
|
| 119 |
+
|
| 120 |
+
### Language
|
| 121 |
+
|
| 122 |
+
| Value | Count |
|
| 123 |
+
| --- | ---: |
|
| 124 |
+
| `c` | 2 |
|
| 125 |
+
| `c++` | 3 |
|
| 126 |
+
| `c-python` | 1 |
|
| 127 |
+
| `fortran` | 2 |
|
| 128 |
+
| `matlab-octave` | 3 |
|
| 129 |
+
| `python` | 103 |
|
| 130 |
+
| `python-c` | 1 |
|
| 131 |
+
| `python-cpp` | 2 |
|
| 132 |
+
| `python-cython` | 2 |
|
| 133 |
+
|
| 134 |
+
### Source License
|
| 135 |
+
|
| 136 |
+
| Value | Count |
|
| 137 |
+
| --- | ---: |
|
| 138 |
+
| `AGPL-family` | 4 |
|
| 139 |
+
| `Apache-2.0` | 10 |
|
| 140 |
+
| `BSD-3-Clause` | 37 |
|
| 141 |
+
| `LGPL-2.1-family` | 2 |
|
| 142 |
+
| `LGPL-3.0-family` | 6 |
|
| 143 |
+
| `LGPL-family` | 1 |
|
| 144 |
+
| `MIT` | 38 |
|
| 145 |
+
| `UNKNOWN` | 21 |
|
data/tasks.csv
ADDED
|
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|
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|
|
|
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|
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|
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|
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|
|
|
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|
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|
|
|
|
|
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|
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|
|
|
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|
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|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
task_id,title,domain,language,repository_url,base_commit,source_license,gpl_family,environment_image,verifier_image,image_platform,task_path,status
|
| 2 |
+
001,Repair omega-dependent range-separated PBE workflow in a real PySCF STRSF repository,density-functional-theory,python,https://github.com/aditisingh4812/simplified_tuned_range_separated,f794ca5265d38906782506f1ac4e197b4e273fc4,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-001:v0.1.0@sha256:ba7befeae4625761cb107ea17ff7962f0d7fd45a71eb25cf75369dc93da8f9d3,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-001:v0.1.0@sha256:3cf671ebe637b067246b05330c0c95c82bd0e1445fafaa3de1b6c1c4d1d7cd64,linux/amd64,tasks/task_001,dockerhub-published
|
| 3 |
+
002,Repair an inconsistent reduced validation workflow,density-functional-theory,python,https://github.com/aditisingh4812/simplified_tuned_range_separated,f794ca5265d38906782506f1ac4e197b4e273fc4,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-002:v0.1.0@sha256:13e8c428f486c685ec92b031e46f3520bac3d4e26b6bdd83fde9826a488b7761,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-002:v0.1.0@sha256:a863b98f920e1e9b1aede8bd0460d039628aab19a413cce3dad7417028e1bd1a,linux/amd64,tasks/task_002,dockerhub-published
|
| 4 |
+
003,Repair extxyz stress and virial tensor-label preservation,atomistic-machine-learning-data,python,https://github.com/deepmodeling/dpdata,4d8048b51ee0cc00caa4854844c28b7f892fd908,LGPL-3.0-family,True,docker.io/kevinxulearning/swe-bench-science-environment-python-task-003:v0.1.0@sha256:f161a1e658abd71c5c3abda59b61814a2c5bf140a4826b5598a917d62a258f4e,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-003:v0.1.0@sha256:4d2e13b726b99a0c9d302ba913cdaa727c49fdc403b65b68918ec70c1713a790,linux/amd64,tasks/task_003,dockerhub-published
|
| 5 |
+
004,Repair split-read exon-overlap filtering,rna-seq-genomic-interval-semantics,c++,https://github.com/arq5x/bedtools2,0f45761e8ef6ffc093f649b0145788577a62ed33,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-c-task-004:v0.1.0@sha256:290695ddb1d2a160142311b604ccb61ff5d51d9500b6d218c56b43cbb94d9620,docker.io/kevinxulearning/swe-bench-science-verifier-c-task-004:v0.1.0@sha256:2553def59dc88f1886ad281da1d561600560a6f8391f177d33bb9f4975e7cc4f,linux/amd64,tasks/task_004,dockerhub-published
|
| 6 |
+
005,Repair edited MRS subspectrum polarity handling,magnetic-resonance-spectroscopy-processing,matlab-octave,,,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-matlab-octave-task-005:v0.1.0@sha256:a2c49556f75e3dc3fd7f186e6309b2af8def8b724a950abe28fec9c317043440,docker.io/kevinxulearning/swe-bench-science-verifier-matlab-octave-task-005:v0.1.0@sha256:a7504e832bbcdd27a696ef1a476ae48afae9b470fcb38037c5eb24fd30ccf3b0,linux/amd64,tasks/task_005,dockerhub-published
|
| 7 |
+
006,Repair inconsistent genomic interval enrichment counts,genomics-interval-statistics,c++,https://github.com/arq5x/bedtools2,ac6b252a3a6df2498757d76190b2b164cc591453,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-c-task-006:v0.1.0@sha256:f740af3206582652b34972f662852a98c370ab94b5e4c1fccb88d065f8abae04,docker.io/kevinxulearning/swe-bench-science-verifier-c-task-006:v0.1.0@sha256:21e0cc23312edf271bb76b5cb35e61125952ff0056813c8e15c52713b6a2e5f9,linux/amd64,tasks/task_006,dockerhub-published
|
| 8 |
+
007,Repair unstable spectral registration for drifted MRS transients,magnetic-resonance-spectroscopy,python,https://github.com/openmrslab/suspect,2254ab2ae6194b41487c933039c5f2ea204e5107,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-007:v0.1.0@sha256:3d7361fdd902b7603b13befdaee0d7a2bcfb2d1f3f970633c981bd5b975103ec,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-007:v0.1.0@sha256:ba9b6eeba1b6ac397d7878bff2d920b1137caf4fda6909422fa9001aab26b24b,linux/amd64,tasks/task_007,dockerhub-published
|
| 9 |
+
008,Establish first vacuum-plus-wall external-region capability in the TERPSICHORE-native path,plasma-stability,python,https://github.com/PlasmaControl/DESC,ab1c5a33031a2e64581f5e663ef8e2f6203a5220,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-008:v0.1.0@sha256:e65d078c640c84fcd915c520a99d477b3c650ec137056a552ea8aa505d0a19ec,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-008:v0.1.0@sha256:5f02708ac41337aa21e611a45fc0b398613378833718f2900a18ae753808974a,linux/amd64,tasks/task_008,dockerhub-published
|
| 10 |
+
009,Enable projection-wall external-region support in the TERPSICHORE-native path,plasma-stability,python,https://github.com/PlasmaControl/DESC,ab1c5a33031a2e64581f5e663ef8e2f6203a5220,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-009:v0.1.0@sha256:a40f148e84915c6a8b0cf89b8cf6ce27d7aedb4451c4bcaee715a55b295831e4,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-009:v0.1.0@sha256:73746f77074cfc0a1b7abaebf7f95d877a883a454eb8e4e48ef5db52c5ccceac,linux/amd64,tasks/task_009,dockerhub-published
|
| 11 |
+
010,Complete alternate perturbation-representation support,plasma-stability,python,https://github.com/PlasmaControl/DESC,ab1c5a33031a2e64581f5e663ef8e2f6203a5220,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-010:v0.1.0@sha256:647be22b8cc7a897a02a21d624e72a02f3ee49ff44f6524e85d6e244ecb677a7,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-010:v0.1.0@sha256:fe5b09f4a5b92039fc793cd50a3feb28c9828eed93a42e4392fb2ea0d0402d11,linux/amd64,tasks/task_010,dockerhub-published
|
| 12 |
+
011,Complete the Missing Response Capability,plasma-stability,python,https://github.com/PlasmaControl/DESC,ab1c5a33031a2e64581f5e663ef8e2f6203a5220,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-011:v0.1.0@sha256:9ad40bda1a487a22ba30afd79d7c99cc16533444404a653f74c21c189855acbc,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-011:v0.1.0@sha256:a2cce1bf22739b0728b7de005fb8bf8473fd95cc362409fc529a918dd4ca87b7,linux/amd64,tasks/task_011,dockerhub-published
|
| 13 |
+
012,Complete 3-D Cross-n FOURIN Spectral Coupling,plasma-stability,python,https://github.com/PlasmaControl/DESC,ab1c5a33031a2e64581f5e663ef8e2f6203a5220,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-012:v0.1.0@sha256:4b4284b2dddfead4001e9be44b2dc8807b7b30043dff03541cbfe925bf44b066,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-012:v0.1.0@sha256:3ccc8ecdaed2fce6d60b926a927315995930a3f75a1713470564b11f2622e47c,linux/amd64,tasks/task_012,dockerhub-published
|
| 14 |
+
013,Establish boundary-regime operator and energy closure in the TERPSICHORE-native path,plasma-stability,python,https://github.com/PlasmaControl/DESC,ab1c5a33031a2e64581f5e663ef8e2f6203a5220,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-013:v0.1.0@sha256:440fac5af67d594f3353b77e800fd23a0b0b57c6ce8b491cfa96fa70f8386ae6,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-013:v0.1.0@sha256:f68b8c823724cca42f43145922859e183a018c5ea9c4205fe5b61e3ecebac878,linux/amd64,tasks/task_013,dockerhub-published
|
| 15 |
+
014,Complete the native multi-equilibrium TERPSICHORE workflow,plasma-stability,python,https://github.com/PlasmaControl/DESC,ab1c5a33031a2e64581f5e663ef8e2f6203a5220,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-014:v0.1.0@sha256:d43ca8fee4244a69302cb5c69bbefa88e6ded15761589ed73c56f2e6077ffb10,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-014:v0.1.0@sha256:9d4ec1597ff0ea20e8355f790a4d8fcb0198dec12a7ccfefe6a18cdd205b7362,linux/amd64,tasks/task_014,dockerhub-published
|
| 16 |
+
015,Restore thermal-equilibrium invariants in a Liouville-space relaxation workflow,magnetic-resonance-spin-dynamics,matlab-octave,https://github.com/IlyaKuprov/Spinach,,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-matlab-octave-task-015:v0.1.0@sha256:b7ff9bd36cb3192e650ec44bf8e67c759a2082b0c7e4e75ed482995d476ba25b,docker.io/kevinxulearning/swe-bench-science-verifier-matlab-octave-task-015:v0.1.0@sha256:c177454ee8a6507ed2decf46b803a405d92b326da3d7de660197e125ff273699,linux/amd64,tasks/task_015,dockerhub-published
|
| 17 |
+
016,Repair HMMRATAC peak refinement under sparse signal resolution,chromatin-accessibility peak calling,python-cython,https://github.com/macs3-project/MACS,a341a2f0ede26735f744d6d5e3b0f7ac1861cfe9,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-cython-task-016:v0.1.0@sha256:6d34aa3b31fbe05c100f041765d9a80c9a389db4a58dd3dec6d051cf756b9ff3,docker.io/kevinxulearning/swe-bench-science-verifier-python-cython-task-016:v0.1.0@sha256:9b8e3efae0b9f9978ac842d43bcb7ac279f98d5a5c8ad91bc06286d55b60116d,linux/amd64,tasks/task_016,dockerhub-published
|
| 18 |
+
017,Repair dark-matter line-of-sight maps in Gammapy,gamma-ray-astronomy-dark-matter,python,https://github.com/gammapy/gammapy,,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-017:v0.1.0@sha256:8dd3e5daae6c78f1bcf4a9713aa983048d6ed8a25a221792a6c09d5b0b6e8628,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-017:v0.1.0@sha256:d5e1f280d98ae2142f4a5a88f2203681710ecffa75544f59464f87d1b0de6fda,linux/amd64,tasks/task_017,dockerhub-published
|
| 19 |
+
018,Restore blacklist semantics in an HMMRATAC chromatin-accessibility workflow,epigenomics-atac-seq-hmm,python-cython,https://github.com/macs3-project/MACS,f01cb680e239192484ab672b9e34531b1403eb3d,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-cython-task-018:v0.1.0@sha256:89e99d411185696887e7f538559b5b6b7e96ef80826e567686b38a7c236ba0e6,docker.io/kevinxulearning/swe-bench-science-verifier-python-cython-task-018:v0.1.0@sha256:8b1dd5120cf838ae85b5b2824d2d9fdf419b830b49127d10e3c0d34ef38ead8e,linux/amd64,tasks/task_018,dockerhub-published
|
| 20 |
+
019,Complete robust topic-to-cistrome binarization for independent probability matrices,single-cell-chromatin-accessibility,python,https://github.com/aertslab/pycisTopic,cb5f54111d2affd89ad732c20c14dab6138026f0,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-019:v0.1.0@sha256:2640cbaa3fbd5ede86dd353b7f48173230d80448581bbacc6d434b9a13f9966c,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-019:v0.1.0@sha256:ffba9cf85dd9585323f72ac3e160da993c4f9ebb66846aa95071a62346e62330,linux/amd64,tasks/task_019,dockerhub-published
|
| 21 |
+
020,Complete an edge-graph geometry and force/virial capability for atomistic models,atomistic-machine-learning-and-molecular-simulation,python,https://github.com/deepmodeling/deepmd-kit,44f44acb2b9a56f55609ec7f0594d9b6fa01cb92,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-020:v0.1.0@sha256:da151294981c7487cd2b48c3b2f95eee3a66afca3ff00e2ea1e8bc4e24dc8443,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-020:v0.1.0@sha256:373d19decc97090d881cd8c39d3e9b8eeb9481ec4f7d2dfdda10b29ec11b92f6,linux/amd64,tasks/task_020,dockerhub-published
|
| 22 |
+
021,Complete a missing atomic-liquid thermodynamic-integration capability,atomistic thermodynamic integration and free-energy calculation,python,https://github.com/deepmodeling/dpti,9d90fd83c1eec85b7e204bb87f281df0b592623a,LGPL-3.0-family,True,docker.io/kevinxulearning/swe-bench-science-environment-python-task-021:v0.1.0@sha256:67e1047313c9010d69249bed758dfad28ef6108ac3627b3ae39149fcbb90a00e,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-021:v0.1.0@sha256:4556f2a24cf62743731721b1c2e36f82a08ca5c173f639e47b305e93bcd2013d,linux/amd64,tasks/task_021,dockerhub-published
|
| 23 |
+
022,Repair an inconsistent volume-to-surface projection,neuroimaging,python,https://github.com/nilearn/nilearn,fefa4d30c262384ebda0f1123a1691abf466a9f0,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-022:v0.1.0@sha256:0c0ed46caaa7b0d52a862dad6461ebdc165396fe7f96e8e50df3e4fed8155cf2,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-022:v0.1.0@sha256:ae3adfc761d0744164c6e5e45f686cd766b5ceb1ac17c8c590ce074e0dee938e,linux/amd64,tasks/task_022,dockerhub-published
|
| 24 |
+
023,Restore continuous NPT periodic-boundary unwrapping,molecular-dynamics-periodic-boundary-analysis,python,https://github.com/MDAnalysis/mdanalysis,2acd594449c02c2a354b07291031d89b50b52186,AGPL-family,True,docker.io/kevinxulearning/swe-bench-science-environment-python-task-023:v0.1.0@sha256:26adc2c4f41e400af9bd961ffbfd52711abd2f7a1856deac6eb462d4c6ebf8f9,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-023:v0.1.0@sha256:20999504b153a946750db97cc28b7458975f6399b7e146350955a1532ad140f4,linux/amd64,tasks/task_023,dockerhub-published
|
| 25 |
+
024,Restore coherent inference in a centered factorial-effects model,probabilistic-scientific-computing,python,https://github.com/pymc-devs/pymc,9ee5d84b5048aea0690bba2629ece684656ad186,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-024:v0.1.0@sha256:6432ca66d7b714d23f5ce315cc1b3ce39dcf7937046d46be4bb470d059c92dcd,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-024:v0.1.0@sha256:e641ce128a4db3c75da315e0b85872c2f65a064badbb5e05a972fc4a71b2c30b,linux/amd64,tasks/task_024,dockerhub-published
|
| 26 |
+
025,Repair inconsistent cross-protocol Osprey validation reports,edited-magnetic-resonance-spectroscopy-workflow,matlab-octave,https://github.com/schorschinho/osprey,24e89ec3ac278cc642ce06cbbe30321155435e0b,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-matlab-octave-task-025:v0.1.0@sha256:eebf7a8137f4a36b5d7f27d49bf52596cf342700ca016f003c723f1affab8626,docker.io/kevinxulearning/swe-bench-science-verifier-matlab-octave-task-025:v0.1.0@sha256:8da94067fe1009753dc73eaf8410b8fe743212c8c1929cc43cb450d3292aac01,linux/amd64,tasks/task_025,dockerhub-published
|
| 27 |
+
026,Restore isentropic interpolation for terrain-following model data,atmospheric-science-isentropic-interpolation,python,https://github.com/Unidata/MetPy,34d14b293c9e75dfff5422c0461d48731916d773,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-026:v0.1.0@sha256:425b952ba92036d8fe6b7a240e0ee7a57ceafc456e68e8297d8d814e06988593,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-026:v0.1.0@sha256:46fadf320df6b6adca39a81c2e83a3f16f8fa486a2adfefdc56a0518edb5db45,linux/amd64,tasks/task_026,dockerhub-published
|
| 28 |
+
027,Restore consistent NMR peak-set encoding under batch padding,ai4science-nmr-structure-elucidation,python,https://github.com/little1d/NMRTrans,9e59a111d201c1c3aee6db079fe1ea2c6a2d8ba8,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-027:v0.1.0@sha256:a0b2b795f21ebf2107c72a04657c3f5dedf1ef816974bedf0e765e8f3d1feafe,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-027:v0.1.0@sha256:7553e8b9d60ddba9b86ee74d4f200929dfaed195b79a7e29efa3713f93e5a656,linux/amd64,tasks/task_027,dockerhub-published
|
| 29 |
+
028,Repair control-referenced relative responses in a single-cell perturbation workflow,single-cell-perturbation-response-modeling,python,https://github.com/JialongJiang/DSPIN,cbedc58e2127d912895defa95c65a623fa2f67d6,Apache-2.0,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-028:v0.1.0@sha256:c9ed2829a11ec5fc42b54d30bbcd8e2b51f82061a7c0476564d073ed66f3d915,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-028:v0.1.0@sha256:4c4ec965b94251ab9b163fe1294a4e863dc5a2b0a005dabb51dbaa5a5d6c95fe,linux/amd64,tasks/task_028,dockerhub-published
|
| 30 |
+
029,Restore annotation equivalence after circular-record orientation normalization,genomics-sequence-annotation,python,https://github.com/biopython/biopython,fb0e7f522d714d76eec42f5fd428eb7942a11dde,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-029:v0.1.0@sha256:ef7e5c2b118cfb635fe2a38a96a3e74a8b8ccad4f45c4420a262224cde2aed3d,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-029:v0.1.0@sha256:bf60c02145e60447a42aa0e8205c11851bafae01fb38da1969c8ca9697ab119f,linux/amd64,tasks/task_029,dockerhub-published
|
| 31 |
+
030,Repair format-conformant SHELX/AIRSS .res export in a crystallographic IO workflow,crystallography-file-format-semantics,python,https://github.com/materialsproject/pymatgen,585bb673c4aa222669c4b0d72ffeec3dbf092630,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-030:v0.1.0@sha256:78f08b2d5abbea8a230c26ba7870f472e7888a8a99bf8a7a860164bbd77f0e95,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-030:v0.1.0@sha256:c2f2d33b4f3eac896abeb9dff00a81386b8e763f5aea124aedac4b9f6a8e9a60,linux/amd64,tasks/task_030,dockerhub-published
|
| 32 |
+
031,Restore documented average-reference semantics for mixed-modality recordings,neurophysiology-signal-processing,python,https://github.com/mne-tools/mne-python,3b3f3afb0e46a6ac6b97e6ecfbc2414497ea9a3a,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-031:v0.1.0@sha256:d4140ef5964abbe2f30c6df0ce3348263ae7696d2e1bd45fa022a63165439437,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-031:v0.1.0@sha256:11198de9a24cc54ef854642f96d3106d3e50e5e69f86e3d1e88da26254cea4be,linux/amd64,tasks/task_031,dockerhub-published
|
| 33 |
+
032,Repair an inconsistent peptide energy after topology import,molecular-simulation,python,https://github.com/openmm/openmm,d2f76949b3ccac1139f0a0a0d1459aa47e2f0a98,LGPL-family,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-032:v0.1.0@sha256:1f1e710ff121fc590e1a1bcc0d6e35b6b20488b67b4ff2ea9e088c5ed5b3c617,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-032:v0.1.0@sha256:b33b42c56351b94f8e871921d9c51b3edba1f2317186ec51db8d0e7a49c1a0c4,linux/amd64,tasks/task_032,dockerhub-published
|
| 34 |
+
033,Repair inconsistent energies across equivalent periodic representations,periodic-electronic-structure,python,https://github.com/pyscf/pyscf,802cd37e9dc6abb52f30d84bb422b6ee15493fc9,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-033:v0.1.0@sha256:44845aa0036b539e82cf042b31b278ab3e4dba56dd5d0abe1da426466a4d1c49,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-033:v0.1.0@sha256:02bd79559d1d6180dbcc19db90b316567798ba192fed39d51bc1f5c20adca064,linux/amd64,tasks/task_033,dockerhub-published
|
| 35 |
+
034,Repair an inconsistent stochastic trajectory calculation,stochastic-numerical-analysis,python,https://github.com/patrick-kidger/diffrax,56d78e1acbdc9c1493caef17a34777931430f3bf,Apache-2.0,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-034:v0.1.0@sha256:7059fdb21c925acab3c847faecece53d294086745e3f4e373473aab44b180edb,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-034:v0.1.0@sha256:232f4698c8988c515640b1225e1a25b275b3a3bcc0658c08697e37dfdb740a64,linux/amd64,tasks/task_034,dockerhub-published
|
| 36 |
+
035,Repair an incomplete stiff-kinetics campaign,numerical-analysis-and-chemical-kinetics,python,https://github.com/scipy/scipy,c4e7f1146556f4b038bfbfc0912ac3843e844c55,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-035:v0.1.0@sha256:ade094c8b37641bf91ee9e09c12b5dcd6ff0f0251613c73c73b7e0f0109a170f,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-035:v0.1.0@sha256:5bdf5079219dab4d67b255724888338b3d5602d4dd24df83723b27a699f578b9,linux/amd64,tasks/task_035,dockerhub-published
|
| 37 |
+
036,Repair inconsistent sampling on a spherical curvilinear ocean grid,computational-oceanography-and-spherical-geometry,python,https://github.com/Parcels-code/Parcels,439ea290f9a75c3cbd66d79333fed475f92aeb00,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-036:v0.1.0@sha256:85db05aa83f3c2408533a237892331b08af27cdbc4a380e772eb5810fcd7c8d4,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-036:v0.1.0@sha256:c0bab454078f7f8f8fb3474977e6be7f057aecb040e936a92d95ececdb091d29,linux/amd64,tasks/task_036,dockerhub-published
|
| 38 |
+
037,Repair an inconsistent multiframe MR reconstruction,medical-imaging,python,https://github.com/nipy/nibabel,5d10c5b8bb09576e24e9d316da1019fb909d7d32,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-037:v0.1.0@sha256:526eaf4f7800f715fda24e8c515162d91a2e89d46c6a7228fa9f13706e6f3c63,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-037:v0.1.0@sha256:adcfa1988d7786568e96018c91ca4d73f12c409e2d81af2fb416e868ff304881,linux/amd64,tasks/task_037,dockerhub-published
|
| 39 |
+
038,Repair inconsistent crystal classification across equivalent representations,computational-crystallography-and-materials-symmetry,c,https://github.com/spglib/spglib,,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-c-task-038:v0.1.0@sha256:41ba231d44d2445f621ed17c3a5f881a41941b79d2f297b49bd66e9e8145a8fb,docker.io/kevinxulearning/swe-bench-science-verifier-c-task-038:v0.1.0@sha256:511507351b10162103c5f48282142f8b767230784456e9952c943657beddb7a9,linux/amd64,tasks/task_038,dockerhub-published
|
| 40 |
+
039,Repair a river-network sediment transport calculation,earth-surface-dynamics-and-river-sediment-transport,python,https://github.com/landlab/landlab,546bc11054cff5e12808c7122b3e8b38f1ef555f,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-039:v0.1.0@sha256:3ed83c8573077b62d1c7b2a498bc9dca044d772a6f930ef5c570feccbbb0b43f,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-039:v0.1.0@sha256:f6e72d3a31b0d1321a608fb1f33ddbdd6ca30eb0da862eebce3590b27c4650a4,linux/amd64,tasks/task_039,dockerhub-published
|
| 41 |
+
040,Restore consistent magnetic-dipole electromagnetic predictions,computational-electromagnetics-and-geophysical-forward-modeling,python,https://github.com/simpeg/simpeg,3cc6605c54b0f6062c1a139ece2ecf69cddc829,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-040:v0.1.0@sha256:a052d87111542518755781c8d49a50de5d7ed6e3f75b2132fc1d8418dba89e85,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-040:v0.1.0@sha256:2f4ad5a63994c9ff62b9ad0b21e24da4a2130a337f20839ff97dccd4016aebd6,linux/amd64,tasks/task_040,dockerhub-published
|
| 42 |
+
041,Repair an inconsistent near-Earth vector conversion,space-physics-coordinate-systems,python,https://github.com/sunpy/sunpy,470d13491dd2c2a9440b3c657af33373ca8d47c1,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-041:v0.1.0@sha256:2d7000ea85b0ce1a1df141d46ccce61e3edcd53e86e9d5136a1b26096799aa77,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-041:v0.1.0@sha256:7e3b7b1a0ab181ed010a5bdb2bde149d115188f96418edea77331caf6e20b00a,linux/amd64,tasks/task_041,dockerhub-published
|
| 43 |
+
042,Repair an inconsistent solar-coordinate archive workflow,solar-physics-scientific-data-semantics,python,https://github.com/sunpy/sunpy,c961a1507a83b9dab24ccce12ab92a53b30359d7,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-042:v0.1.0@sha256:38b71d095fa30606c636c19aa2145fde1f74993809cff837b6da5e5597895181,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-042:v0.1.0@sha256:133f5154d63c2614e6e754d68ca91bef2a8ea4af1210de147a794c570c06d8f9,linux/amd64,tasks/task_042,dockerhub-published
|
| 44 |
+
043,Repair an inconsistent porous-volume characterization,porous-media-image-analysis,python,https://github.com/PMEAL/porespy,f2360a52bc77ec917aa07ce0cf6128dc7687ea64,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-043:v0.1.0@sha256:3e82e859587bdd681272bac9ecb4a415e77fe9f2160afe76a9f0bc641cf7096f,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-043:v0.1.0@sha256:c9a3a93ea8eca723583d471b478202553f011baaaee8411063a1aabec7c1651e,linux/amd64,tasks/task_043,dockerhub-published
|
| 45 |
+
044,Repair inconsistent lithium-ion discharge predictions,electrochemical-battery-modeling,python,https://github.com/pybamm-team/PyBaMM,a42d7a92dd9a2c63240c8ccb6f240e5c3c42de46,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-044:v0.1.0@sha256:513707a2950f87958370d940ca542603b5a4b83443e5c712c916abd1cc37eeb0,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-044:v0.1.0@sha256:61f22d5c7943225471bcdeed86f32470249eaefe57453989c3af1314811f3671,linux/amd64,tasks/task_044,dockerhub-published
|
| 46 |
+
045,Repair inconsistent finite-volume operations on a connected multi-face grid,computational-oceanography-finite-volume-grids,python,https://github.com/xgcm/xgcm,3831b46accbff35f06e4ed3831600d71d5d8da18,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-045:v0.1.0@sha256:bdf7ecf2141952410df47d69d36d45b662047a720f6ff26ceeef1c33486b3fa0,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-045:v0.1.0@sha256:a3cd9863966518102f06bbf956ddfa7b6578debf5bcf92ccfbe0d1252c3a4b20,linux/amd64,tasks/task_045,dockerhub-published
|
| 47 |
+
046,Repair an inconsistent X-ray spectral-timing analysis,astrophysical-xray-spectral-timing,python,https://github.com/StingraySoftware/stingray,79b8f9bb9d122bd0176bb37f48f0fd4926eb9afb,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-046:v0.1.0@sha256:5113cc358a6f5df25d7b7c09e02cb5b9bd9964248f2d51ead28308c90febd15d,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-046:v0.1.0@sha256:73e5bc8338655f2d15e7dd871c42544ec9e7d16af3f24e6ecb69030f71edefbf,linux/amd64,tasks/task_046,dockerhub-published
|
| 48 |
+
047,Repair an inconsistent broadband microwave composite,microwave-network-analysis,python,https://github.com/scikit-rf/scikit-rf,a6dae181dbcf76fc738fc7fbc03d7de0a6c22634,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-047:v0.1.0@sha256:a94de21354f66e978943e80946546812dbf404c4468baf12a84d23c34720e3d6,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-047:v0.1.0@sha256:8529979be314893a77f9c51cf5d2c0d6266d6f9df10fb33d332eb242f38953db,linux/amd64,tasks/task_047,dockerhub-published
|
| 49 |
+
048,Repair an inconsistent alloy equilibrium assessment,computational-thermodynamics-calphad,python,,,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-048:v0.1.0@sha256:38893d5510a1f2c722c39dc851c1f4c0698c52602753e0e9a0531ea466ee9a4b,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-048:v0.1.0@sha256:66acaa226780910a92acf5076beb045a8f521ec7f222277fb4fa1e37296d46da,linux/amd64,tasks/task_048,dockerhub-published
|
| 50 |
+
049,Restore consistent stochastic-field behavior on nonuniform grids,finite-difference-stochastic-partial-differential-equations,python,https://github.com/zwicker-group/py-pde,a9f8256c1b4b48ac73f3df35b3e570993501b333,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-049:v0.1.0@sha256:5d2c93c90c190f69ed1f8bb05014f34d900f4c68ca483cf428399caa5c80f339,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-049:v0.1.0@sha256:7a8babe7c3e8d6121a1fff866e0e6ae5871de381c8e759897a4b40244b6b76b6,linux/amd64,tasks/task_049,dockerhub-published
|
| 51 |
+
050,Repair an inconsistent tensor-network state calculation,quantum-information-many-body-tensor-networks,python,https://github.com/jcmgray/quimb,,Apache-2.0,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-050:v0.1.0@sha256:6f1421184ec5bd40580757a5b684b53519b2fb9044b900320b822fbffcc3ed7d,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-050:v0.1.0@sha256:74fe72ef3a7fe8749cbc7de11f80303278c83e89adfc60dfa00338059b3b0561,linux/amd64,tasks/task_050,dockerhub-published
|
| 52 |
+
051,Repair an inconsistent planetary gradient-tensor calculation,planetary-geodesy-and-geomagnetism,fortran,https://github.com/SHTOOLS/SHTOOLS,7f7d91474509acb597071eb789661b1f0cc304ca,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-fortran-task-051:v0.1.0@sha256:8235525555c16d48f6e12019ba6239fc99569358183a444cb0251b72dfd99de4,docker.io/kevinxulearning/swe-bench-science-verifier-fortran-task-051:v0.1.0@sha256:cc4ffda89baf3ef1fed6903ff06b194b1ef2f992413574aa6032451e09e653fb,linux/amd64,tasks/task_051,dockerhub-published
|
| 53 |
+
052,Restore a nonuniform finite-volume phase-field workflow,computational-materials-finite-volume-pde,python,https://github.com/usnistgov/fipy,11e5c6ae26207a60e223d46473ac364b352ac982,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-052:v0.1.0@sha256:7f5ea002c9963e322dd2ffc1b1c3d2669b511a74391f4ace0d1151207efec376,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-052:v0.1.0@sha256:d0fa3032421f94d1f0e43986f33125ab48af349eb26e5b68a1e86b372342b7bf,linux/amd64,tasks/task_052,dockerhub-published
|
| 54 |
+
053,Repair a representation-dependent physical surface Dice workflow,medical-image-segmentation-geometry,python,https://github.com/Project-MONAI/MONAI,18daff1d8b26002b02de526cc19b92a9a4907f89,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-053:v0.1.0@sha256:9763fa42d9a9e025dbb4470db64ad48b4d21549219f0938e746aadb5aa77dcc3,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-053:v0.1.0@sha256:10656f4e5cfb69d613c2442050f34691fe3264e4d03ee6bfa2f98d3529098ab6,linux/amd64,tasks/task_053,dockerhub-published
|
| 55 |
+
054,Repair an inconsistent tandem-mass spectral similarity workflow,mass-spectrometry-spectral-similarity,python,https://github.com/matchms/matchms,9f27ba89d8c485e6a2fa2db4756e3fe3aec05151,Apache-2.0,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-054:v0.1.0@sha256:a9e8dedaf3d63ada395f497d35092465a56a34c0862794ee20216f46d70ec98c,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-054:v0.1.0@sha256:60b1bd49880f5e1bab44cd13d5986b57b055f1ed3b30ff19801ff3232f93cfda,linux/amd64,tasks/task_054,dockerhub-published
|
| 56 |
+
055,Restore a scientific template-comparison workflow,astronomical-spectroscopy,python,https://github.com/astropy/specutils,0613ba1ba86fd7ae79e9d89c8ffd24004a891aee,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-055:v0.1.0@sha256:74325f6a3477680f5302abf9e5fd622b90be8d28ca9e01b87697b8cf480dba53,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-055:v0.1.0@sha256:f1b514a04de8a991bbe7af6591cdf6a260f6a89afa22105e90895e3529bd46d4,linux/amd64,tasks/task_055,dockerhub-published
|
| 57 |
+
056,Repair a physically inconsistent orbital history export,astrodynamics-and-orbital-mechanics,python,https://github.com/poliastro/poliastro,0583b33091b07229abe2027bccdc596ba3c5033b0,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-056:v0.1.0@sha256:2909a24d72bf5161604c65e846c94058d0318cb92e4b86b29a77aff46dea3a70,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-056:v0.1.0@sha256:3cf9ed1c78f08940105a8155526ab20272bdb2640eaf0f9af03526aac677887a,linux/amd64,tasks/task_056,dockerhub-published
|
| 58 |
+
057,Investigate a periodic trajectory-processing anomaly,molecular-dynamics-trajectory-analysis,python,https://github.com/mdtraj/mdtraj,b963d4f01290fef66cca714e4a53f4891096b69a,LGPL-2.1-family,True,docker.io/kevinxulearning/swe-bench-science-environment-python-task-057:v0.1.0@sha256:0a86aec644a934e46f0ebaaa25220b8fe0d792d942e15aab2dda03dae893eb80,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-057:v0.1.0@sha256:3a837ea554c65947e01e90be6998b561e6d5a0c64e6c29119e156026e4f5ce56,linux/amd64,tasks/task_057,dockerhub-published
|
| 59 |
+
058,Repair a valid OpenMC fixed-source workflow,monte-carlo-particle-transport,python-cpp,,,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-cpp-task-058:v0.1.0@sha256:7e911bae59ef2a509e72cc8cc5454ae94d1fcf2cf560613de773aae3b419b78a,docker.io/kevinxulearning/swe-bench-science-verifier-python-cpp-task-058:v0.1.0@sha256:e2b0260ac34ef381c86af8c808838ddb9a1ccc2cc4ece1b52c3cadf25625abfc,linux/amd64,tasks/task_058,dockerhub-published
|
| 60 |
+
059,Restore physical consistency in calibrated cell morphometry,microscopy-image-analysis,python,https://github.com/scikit-image/scikit-image,e4e3ab682f0ff13460877624ecf068b9652ae071,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-059:v0.1.0@sha256:dec04a1b4fb9014d3f4f70f06966546d3d6055b56a3f1d4ffb8066152d8cff44,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-059:v0.1.0@sha256:2dda66b63502d81c2e09a7b0311ca76b3796dc1cd28349f9ece060a35795c8b0,linux/amd64,tasks/task_059,dockerhub-published
|
| 61 |
+
060,Restore a complete cross-band drift-correction recording,high-density-extracellular-electrophysiology,python,https://github.com/SpikeInterface/spikeinterface,3fd3d97164c6e85c2897ce8b13ba6aace81c2811,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-060:v0.1.0@sha256:61af28db733eec1188ad8b90a4a78404e88b7bfb17cf99800b543292c9545747,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-060:v0.1.0@sha256:d1a95a1456b922044d1cfa9156bf33ba40628a3115b2ff25b4d6b149dfd1f4bf,linux/amd64,tasks/task_060,dockerhub-published
|
| 62 |
+
061,Repair inconsistent celestial image representation in a mosaic,astronomical-image-processing,python-c,https://github.com/astropy/reproject,62a0d3f037024d4dcf67857fb83d392f2e099ec0,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-c-task-061:v0.1.0@sha256:a69139dfab9d10122d07187ba52e0218c8c3f8350e3d44926c5813c8700bbcbf,docker.io/kevinxulearning/swe-bench-science-verifier-python-c-task-061:v0.1.0@sha256:c0c05b7f3e36a5a4ede6443d7ce6f26522e8ae09db9baf5b14c16741039a7e07,linux/amd64,tasks/task_061,dockerhub-published
|
| 63 |
+
062,Repair an inconsistent archived elasticity workflow,computational-materials-science,python,https://github.com/materialsproject/atomate2,95b15d576f47923e1f200c0894915a8f46675291,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-062:v0.1.0@sha256:71b7a7f56a39dc1f3fa7d2ee034dbde903e373cc231b6584e542bb1eac6d8e9c,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-062:v0.1.0@sha256:b40392404273078f316aafdbee792923cdea10b8023ea733abe38ebb8ab5582a,linux/amd64,tasks/task_062,dockerhub-published
|
| 64 |
+
063,Repair inconsistent population-history estimates after archive curation,population-genetics-tree-sequence-statistics,c-python,https://github.com/tskit-dev/tskit,,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-c-python-task-063:v0.1.0@sha256:77cb395977290ee08c9d9abd184bcb8d874d8b78a5d55119ad8832b912b58e7e,docker.io/kevinxulearning/swe-bench-science-verifier-c-python-task-063:v0.1.0@sha256:1f0346e1c5241487bb858955411ebf920e9bd53b37dcbb8aef37abd4c6dbe550,linux/amd64,tasks/task_063,dockerhub-published
|
| 65 |
+
064,Repair inconsistent molecular-energy interpretation in a quantum-chemistry log parser,computational-chemistry-scientific-data-parsing,python,https://github.com/cclib/cclib,593f0d67cf6a76f4a047f9a4856125c05947cff4,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-064:v0.1.0@sha256:fce98569a3f9c8039892d8411355e49e07633af201083c67501c8fb69f9844a1,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-064:v0.1.0@sha256:b5b5a01003841af0fd902d84d9b78cc6208d641b22503bff9c325de16c113dbb,linux/amd64,tasks/task_064,dockerhub-published
|
| 66 |
+
065,Repair inconsistent particle-field visualization results,astrophysical hydrodynamics and particle-based field visualization,python,https://github.com/yt-project/yt,c86781b8cbdeea8002c7846d37dc1250045146e6,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-065:v0.1.0@sha256:5c8c8b8c130b06f1871f1c74a2b0ca0f453519e94d50b6cd3e08b9d873b7d3c9,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-065:v0.1.0@sha256:2ef10bcb562ab83a9b5641f22a91a4e4a607d231ea8f58194795cb4a324a5efe,linux/amd64,tasks/task_065,dockerhub-published
|
| 67 |
+
066,Restore regional climate-model validation consistency,earth-science-data-semantics,python,https://github.com/SciTools/iris,0b569cdfad5e67f4aec3562bb26460020c7c7354,AGPL-family,True,docker.io/kevinxulearning/swe-bench-science-environment-python-task-066:v0.1.0@sha256:16eacda2003745c9ea63286b07df5be4ba9bdf27b737761abf3ab0cfe8b6be34,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-066:v0.1.0@sha256:bf551e3cb78adb7a896b69485af7688c98815988094971978b7b41a2ae89c548,linux/amd64,tasks/task_066,dockerhub-published
|
| 68 |
+
067,Repair a seasonal fire-weather state transition,climate-fire-weather,python,https://github.com/Ouranosinc/xclim,d1e654cf59a5d5761f5586bca1102a1590ae6e32,Apache-2.0,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-067:v0.1.0@sha256:293c50d411ea2c322e9b62189e5bf325abbb814682b1eb4dabec9555d035c78e,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-067:v0.1.0@sha256:fbbdf79e55e67535ee836f497be5aaf61412c5fe68b6856959217589e144e71c,linux/amd64,tasks/task_067,dockerhub-published
|
| 69 |
+
068,Restore biologically consistent retrieval from a VCF archive,genomic-variant-data-semantics,c,https://github.com/samtools/htslib,a4dde3f93c75dff09e9a1ddaf0db2e54c91ac5e3,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-c-task-068:v0.1.0@sha256:f08ff570bf57595b94e6fb3bc0f603e76d7b6de53f6c7c76199a099eee12fdd3,docker.io/kevinxulearning/swe-bench-science-verifier-c-task-068:v0.1.0@sha256:333ed6fc1e4953d3abe1517a2871c1a2fb19ca0996d8d91bca6406898dac57ad,linux/amd64,tasks/task_068,dockerhub-published
|
| 70 |
+
069,Restore a complete Hi-C contact-decay analysis,genomics-contact-map-analysis,python,https://github.com/open2c/cooltools,ba2be42c714fffb6b62ea13e7ecfbecb5f4a4d9a,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-069:v0.1.0@sha256:104bacda92f0419c80454a4bd632d472b6ef53ac89c24c176266d226c3bfd7ba,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-069:v0.1.0@sha256:d879cd88dc547a45e25105bb4aec34c8c1acaf22d97bc858719692283e547819,linux/amd64,tasks/task_069,dockerhub-published
|
| 71 |
+
070,Restore chemically consistent proteoform ion annotations,proteomics,python,https://github.com/levitsky/pyteomics,f509b761a5231e9f108780c88c2b3781266e7b90,Apache-2.0,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-070:v0.1.0@sha256:a54e1623ce467ff3366a5c064753a7f72c27e2443e5bc14d075ce42bf65768de,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-070:v0.1.0@sha256:65428a9c41233b574b2d31746f8968a2d3387bad708ec99f7e142256461d17a3,linux/amd64,tasks/task_070,dockerhub-published
|
| 72 |
+
071,Repair an orientation-sensitive fiber-scattering reduction,grazing-incidence-and-fiber-x-ray-scattering,python,https://github.com/silx-kit/pyFAI,3a7adedc45c9a94585ec19bbd4622ac9f483ab9c,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-071:v0.1.0@sha256:08968262336c765e8d683cc867e2e0c3db50a99cee923ea8fa000bf4523a843d,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-071:v0.1.0@sha256:0039c955ffd15cd0020334c375dd24e6c41c1b1b2a6b59b392c647db32c47882,linux/amd64,tasks/task_071,dockerhub-published
|
| 73 |
+
072,Repair an incomplete DICOM color image presentation workflow,medical-imaging-color-pixel-semantics,python,https://github.com/pydicom/pydicom,b69de21c8610853493bc81d3eac79644554e4bda,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-072:v0.1.0@sha256:c9746b594a561e16a92a0718356d2bde20f564a61d882bbce1af3bcd1658dad3,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-072:v0.1.0@sha256:8683aa3c574011f36df457c54a443457cd37078c2ca48f85fcb46015c431b31d,linux/amd64,tasks/task_072,dockerhub-published
|
| 74 |
+
073,Repair inconsistent alternate-conformer structure connectivity,structural-biology-pdbx-macromolecular-connectivity,python,https://github.com/biotite-dev/biotite,f8c3b8aa5473e078f91c86dcee7340eb9ed3eb97,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-073:v0.1.0@sha256:fca7d2514acb9214baf529a5d4bfddbe5e165ba24cbea63cb4d380f5f5bea483,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-073:v0.1.0@sha256:6041a2f1f781e1e02e908984c07c6de7a1e2edd67a3ce90529522ebc2e72aee8,linux/amd64,tasks/task_073,dockerhub-published
|
| 75 |
+
074,Repair an ill-conditioned overlap band-postprocessing workflow,electronic-structure-nonorthogonal-eigenproblems,python,https://github.com/deepmodeling/DeePTB,e365079ea71190aaa0dc96d22253d3888c47abf9,LGPL-3.0-family,True,docker.io/kevinxulearning/swe-bench-science-environment-python-task-074:v0.1.0@sha256:717c4de698523729922644dc8f42dbf98071dbe48c25cf1016d425d2ceb0e49f,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-074:v0.1.0@sha256:874067a5199b4db19f575c074b7cd51c1eddf03f7aa13c97810ea2873c917d86,linux/amd64,tasks/task_074,dockerhub-published
|
| 76 |
+
075,Restore consistent compressed Deep Potential tabulation,molecular-dynamics-machine-learning-potentials,c++,https://github.com/deepmodeling/deepmd-kit,a9bcbc505de7d905dbc2a598b10c17a49e0131d8,LGPL-3.0-family,True,docker.io/kevinxulearning/swe-bench-science-environment-c-task-075:v0.1.0@sha256:7beaf3765d9cf49e2d3f647833f63266dfa15bc9978b753755050a66a7ec15dc,docker.io/kevinxulearning/swe-bench-science-verifier-c-task-075:v0.1.0@sha256:c50d05f06eee0035eb02e057017cbdbfae6a9855a900ac819bb90b937285a022,linux/amd64,tasks/task_075,dockerhub-published
|
| 77 |
+
076,Repair a batched parametric tracking workflow,convex-optimization-parametric-workflows,python,https://github.com/cvxpy/cvxpy,5f57b6408864caab207c28f773a14c6261689abe,Apache-2.0,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-076:v0.1.0@sha256:1a50e20a9caf81566ac7f3f9d356b04b8352a7eb3532f8a5543307ef3f0670fe,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-076:v0.1.0@sha256:c40da6ce2cafe0194e2d74ca0380587b696890713c163a17624a855c86247404,linux/amd64,tasks/task_076,dockerhub-published
|
| 78 |
+
077,Repair an inconsistent oriented-envelope fallback workflow,computational-geometry,python,https://github.com/shapely/shapely,d2872f6c4d7c99b16f8a71d99cd56d0a5fe54695,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-077:v0.1.0@sha256:c0164a3b9503d40d28bdb96503976e673fd0a29c924cfb24e198cd2698d1a2e8,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-077:v0.1.0@sha256:f9f3eb576dd41c94b0407e0a0395e1df75d6cad627be53a028bc995d4f66e633,linux/amd64,tasks/task_077,dockerhub-published
|
| 79 |
+
078,Repair an inconsistent astronomical aperture workflow,astronomical-image-analysis-and-wcs-aperture-photometry,python,,,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-078:v0.1.0@sha256:5b91a58b57d7fd6c87dbbeab4daf50ef8f9deb08db5c5d8063d77eb67dcd93b1,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-078:v0.1.0@sha256:9a64793e10d20c2c0b719ae87a72d795435b24f5efb8577071b693ec88b6f882,linux/amd64,tasks/task_078,dockerhub-published
|
| 80 |
+
079,Repair molecular-string translation for catalogue workflows,computational-chemistry-molecular-representations,python,https://github.com/aspuru-guzik-group/selfies,55f4e3437b6fb68deafa533cb00277b119e6eb8a,Apache-2.0,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-079:v0.1.0@sha256:700ef06ac1ce8d1550984b274b58f9440ca378a240bdc3064e51ab1d302fcad6,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-079:v0.1.0@sha256:243dfa0eb24b77c5c08a9141b632177711d7f438177f0f737c0c2d453c14f7f4,linux/amd64,tasks/task_079,dockerhub-published
|
| 81 |
+
080,Repair inconsistent geospatial raster remapping,geospatial-raster-reprojection,python,https://github.com/xarray-contrib/xarray-spatial,7d252520dbf81b168a2789a6aedfb75d04a21061,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-080:v0.1.0@sha256:bd33e55e04ded03f1911abe6f673e4217c4fed04e14db72be630c1503cd10735,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-080:v0.1.0@sha256:0bd2b80b544ce97b0ecbab0c397a5d68014ee7cb2c3133be648db3d3ca0045ed,linux/amd64,tasks/task_080,dockerhub-published
|
| 82 |
+
081,Repair local study workflow,single-cell-annotated-data-containers,python,https://github.com/scverse/anndata,,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-081:v0.1.0@sha256:6114de7210e1f47c1ad558a9ca8886105a5ecf5af6a8453a9c7732ac415a7431,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-081:v0.1.0@sha256:3a3f4428f0129a1302f743125649b4bea7445e57912bdd734ad3452389003efa,linux/amd64,tasks/task_081,dockerhub-published
|
| 83 |
+
082,Repair a workflow consistency bug,atomistic-machine-learning-and-molecular-simulation,python,https://github.com/deepmodeling/dpgen,02a442c6bd7da9b5b2c9f958d3a103f5d6cd2a27,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-082:v0.1.0@sha256:ff25e7997b4194fb53e3df8b71d48e8db25d299bf632ebebdb6a162925e73204,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-082:v0.1.0@sha256:a829af72c8e716a904d83a590a865d07a7b9a31a8d4b7083afbf90b6611a937c,linux/amd64,tasks/task_082,dockerhub-published
|
| 84 |
+
083,Repair bond-order species reporting,computational-chemistry,python,https://github.com/deepmodeling/reacnetgenerator,37b0bef6fd9d5945f1b752ac82d4f8564728cd8b,LGPL-3.0-family,True,docker.io/kevinxulearning/swe-bench-science-environment-python-task-083:v0.1.0@sha256:9483e6962b892e928f5f1e1c608d646d2d35c5899da15f57fa7bc8c23bd2e14f,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-083:v0.1.0@sha256:a1c0f1dabd6d4c334c815cb398eda399fbb8b7739b7b5ec60ea8abb1882b7727,linux/amd64,tasks/task_083,dockerhub-published
|
| 85 |
+
084,Repair ABACUS relaxation archive/reload semantics,materials-science-scientific-data-semantics,python,https://github.com/deepmodeling/dpdata,80abfc5037876c0e883dcb58cd96521397e3fe36,LGPL-3.0-family,True,docker.io/kevinxulearning/swe-bench-science-environment-python-task-084:v0.1.0@sha256:735e7ece88fa49a77257cfb2a59b435ed6ef511e99cc1739e24b366ea129836b,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-084:v0.1.0@sha256:8cbe4554c727f25c1584f79c48f574a3d08e1fcf6d3c4cb32df36a7d8482216a,linux/amd64,tasks/task_084,dockerhub-published
|
| 86 |
+
085,Inconsistent archived observables,computational-chemistry-and-solvation,fortran,https://github.com/dftbplus/dftbplus,d4da8c5027b643291f3a6295efd4340ce79d6a36,AGPL-family,True,docker.io/kevinxulearning/swe-bench-science-environment-fortran-task-085:v0.1.0@sha256:c4613c3e94fefc6cd721075d314d4fc463269cdd92cf7f6d0b656078a838a7cd,docker.io/kevinxulearning/swe-bench-science-verifier-fortran-task-085:v0.1.0@sha256:e68ac55c7cfb257756103351c305b97789d72f1e79203305d2aa7fa39e657eb1,linux/amd64,tasks/task_085,dockerhub-published
|
| 87 |
+
086,Repair a silent MatGL fine-tuning incompatibility,atomistic-machine-learning-potentials,python,https://github.com/materialyzeai/matgl,02b415ba8bb25244bc5e3ad970491f0fbbea0292,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-086:v0.1.0@sha256:7a54bd7e811a51abdd7571abbc03213eece0310016b174bfa52dcbe4ad171476,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-086:v0.1.0@sha256:fb47312ac7443db59115807334c5d2345e3a2fb7a8f83d89bc8bfb48f7ce4bac,linux/amd64,tasks/task_086,dockerhub-published
|
| 88 |
+
087,Repair a silent diffusion-MRI denoising inconsistency,diffusion-mri-denoising,python,https://github.com/dipy/dipy,ee6016ab81dd649ab40439d75212f35669302810,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-087:v0.1.0@sha256:5a00e4d7a825618ba70259ef5c5e229f7ba2549ab7648ead6fc91fce31256793,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-087:v0.1.0@sha256:b1ce39c75913bccef5f09acfd2b989857c071fc64c7fdc0dbff092e14dc5270f,linux/amd64,tasks/task_087,dockerhub-published
|
| 89 |
+
088,Repair a boundary aggregation failure,boundary-aggregation,python,https://github.com/pydata/xarray,0b071e369a88f6672accc2a99c40d3b4b334f2f9,Apache-2.0,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-088:v0.1.0@sha256:c98a81a135c210d7681b57574c8f39a00f1a92778e458dc5300a7f2775e2ba6f,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-088:v0.1.0@sha256:9f8a00b079fb998f0672f57af8f75628dabc8582122a294f2b20cd304503ac6e,linux/amd64,tasks/task_088,dockerhub-published
|
| 90 |
+
089,Repair inconsistent ORCA excited-state oscillator strengths,computational-chemistry-spectroscopy,python,https://github.com/cclib/cclib,6ba33bdd48bf336a81400147d2870323b241e457,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-089:v0.1.0@sha256:87e8b70f8d192990fe5a0f5d1773dcb304ab1bf5074a187236f2e0bd041ba356,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-089:v0.1.0@sha256:66ee7d7df906e3cad4e9d27664f1c6ea9bd6673ef36d5ddd61f5aaa75c88db60,linux/amd64,tasks/task_089,dockerhub-published
|
| 91 |
+
090,Restore multidimensional NMR acquisition grids,nuclear-magnetic-resonance-spectroscopy,python,,,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-090:v0.1.0@sha256:a2a7d3de4b603c2e170a1ea679103aeefdd43c1503f5c2210f32fec9f51e3efa,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-090:v0.1.0@sha256:8ba7b5dff3e7bd208683b7d457ebfe6277ce4bdd218bea4d2e0ea322f49a5007,linux/amd64,tasks/task_090,dockerhub-published
|
| 92 |
+
091,Repair a workflow regression,materials-science-volumetric-data-semantics,python,https://github.com/materialsproject/pymatgen-core,c8cfee71f3ce5d92c5b5f6ca3d363f8f3a9f4495,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-091:v0.1.0@sha256:e99b9784d9297b360713e12ff77833dfa629f31298f504322fa3ee98dc833ed8,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-091:v0.1.0@sha256:274078dbc1df8898a9f4d704e0e833c21b54447ff33e78314d2cc6e8c2e16435,linux/amd64,tasks/task_091,dockerhub-published
|
| 93 |
+
092,Repair inconsistent Chemprop reaction observations,ai-chemistry-reaction-property-learning,python,https://github.com/chemprop/chemprop,1f367d55d1bac14dd6b9e0cd5746574fcfab9a59,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-092:v0.1.0@sha256:43ddc1b17809459d59ff0d6eaf8886368305e6164d7076d81a1660685a8dfac5,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-092:v0.1.0@sha256:6eac8072686557e2a87b94a3600cdb5e6e1a94862c97c69cdf34a916ea0d7c83,linux/amd64,tasks/task_092,dockerhub-published
|
| 94 |
+
093,Repair a patient-space round trip in MONAI,medical-image-processing,python,https://github.com/Project-MONAI/MONAI,5a644e4edcc37e5c963e52fda6fab4c85b3ff02e,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-093:v0.1.0@sha256:5a60042d49b60549e07475ed0d0f717e1ceddac7c1e7832cec4803a8c5647e6a,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-093:v0.1.0@sha256:1a0872591921ff43bf480d6d6daa9e99f8f30c94d74f308337235ca21fe08e26,linux/amd64,tasks/task_093,dockerhub-published
|
| 95 |
+
094,Repair magnetic-space-group operations across archived settings,condensed-matter-magnetism-and-magnetic-symmetry,python,https://github.com/materialsproject/pymatgen,,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-094:v0.1.0@sha256:29e3fa554e2177b07fb0e7f1cc9b470dd310202d31612af2e75baef512ae97e4,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-094:v0.1.0@sha256:0b8980bec95351d787ad34347fde67096254dbe62b04ceb69b5d4fd0f8ea86df,linux/amd64,tasks/task_094,dockerhub-published
|
| 96 |
+
095,Repair a repeated porous-electrode transport workflow,new-energy-materials,python,https://github.com/PMEAL/OpenPNM,d8efaa211ea6721cc4a718890f11fb60b8b43326,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-095:v0.1.0@sha256:08fb28caff95e4cc11459e4bc8d21965e2b52cfa2ad1829e98aa440eba3f47be,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-095:v0.1.0@sha256:9e1febafa3ee120cd3fdf92d8882fc81ac9c1f6215094130cc8f58de53fd82f9,linux/amd64,tasks/task_095,dockerhub-published
|
| 97 |
+
096,Repair a wrapped tropical-cyclone hazard workflow,tropical-cyclone-hazard-monitoring,python,https://github.com/CLIMADA-project/climada_python,104dfdb64ed00fce6c49a5d67be371f4fca016dd,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-096:v0.1.0@sha256:b5d83702d5a8bf8b17ce88fe6c95847eaf8b4ad5132e037fbaf6727154256a5f,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-096:v0.1.0@sha256:f83195b4ce577c453e2228e642418f22e935ebd835db2a0c168b8b7c93be28d9,linux/amd64,tasks/task_096,dockerhub-published
|
| 98 |
+
097,Repair spin-model consistency in DeePMD-kit,magnetism-and-spin-models,python,https://github.com/deepmodeling/deepmd-kit,6c3b985cbc6e2dec51976a20ae51214186c693b5,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-097:v0.1.0@sha256:d568b716103abb844e7d5f8e92693fc9bda65f9329fa82628da0433f52660de2,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-097:v0.1.0@sha256:f3cb6aea78fe4974c5f9fa31a55c02cec54773666d27857bfa0c1d9b79856ba1,linux/amd64,tasks/task_097,dockerhub-published
|
| 99 |
+
098,Repair inconsistent satellite parallax geolocation,remote-sensing-and-geostationary-geolocation,python,,,UNKNOWN,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-098:v0.1.0@sha256:7749c5504674fd868d0c9f318caa3bddbc2eb7beaa77fc4b92822b0c19ced514,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-098:v0.1.0@sha256:60c92aee990b8ff7809aa094f99a6ada0935ac7fe605bfa6f90345912e56e598,linux/amd64,tasks/task_098,dockerhub-published
|
| 100 |
+
099,Repair an inconsistent GNSS point solution,satellite-navigation-and-gnss-positioning,python,https://github.com/Stanford-NavLab/gnss_lib_py,9a4e467ba06e636ffa4de6ceee302cefee8b2a34,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-099:v0.1.0@sha256:99a563d1d49d0ae4fcff3a709bf6eadb46e5c1514ec902545d7c4fa7b11c529a,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-099:v0.1.0@sha256:821dfafb1035f4ffe52e58226ae63be3d779edcdd077cd1e2890b9916b67a97b,linux/amd64,tasks/task_099,dockerhub-published
|
| 101 |
+
100,Repair calibrated framework embedding relaxation,reticular-chemistry-and-framework-geometry,python,https://github.com/DCoupry/autografs,c2f22341f2b1eb2f619b76534cf4abe2e5e6b3a3,LGPL-2.1-family,True,docker.io/kevinxulearning/swe-bench-science-environment-python-task-100:v0.1.0@sha256:9bfa2b87a911734bd13a90d76db6e6fc482793b851cfe9e37e2616368eb4ea8b,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-100:v0.1.0@sha256:24d7057aa54c241cb71822a31b12711ad36c6d13c53d58af790290752df9ef84,linux/amd64,tasks/task_100,dockerhub-published
|
| 102 |
+
101,Repair an inconsistent battery-model reproduction,lithium-ion-battery-modeling,python,https://github.com/pybamm-team/PyBaMM,1e9fbcea25b78a0a633face62b077dae1f92bf62,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-101:v0.1.0@sha256:fd4bfc3ad2bcdaa12f1e2c7f8451646b14175f70bfd76a5066b06fbc8fa775b6,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-101:v0.1.0@sha256:d87a3417f48574040b26cf616241f4f448f766aac2c04b1945ad05392ec04840,linux/amd64,tasks/task_101,dockerhub-published
|
| 103 |
+
102,Repair an inconsistent polymer coordinate workflow,polymer-coordinate-generation,python,https://github.com/marrink-lab/polyply_1.0,160e9707d844ad1b108e1d8184152050d16088a0,Apache-2.0,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-102:v0.1.0@sha256:961828d6d0051e381646dc093bc531e80659fb62b7bda3181e6d624aa381efba,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-102:v0.1.0@sha256:efc0d2d6b049ecc34b2272455392e8eaec4e82f52d340a1b944597cbbb00342b,linux/amd64,tasks/task_102,dockerhub-published
|
| 104 |
+
103,Repair symmetric composite laminate ABD calculations,high-performance-fibers-and-composites,python,https://github.com/SteveDoyle2/pyNastran,bdff2bb616847a058960c56328b68e36ab3764e3,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-103:v0.1.0@sha256:8b1934f764347452d72e5a136b8925daf6002803df163fdda7285f9757831467,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-103:v0.1.0@sha256:6eee1cc75c6043694dc04e4d6de95a09eb4300c684c9901cb64fde126651ef29,linux/amd64,tasks/task_103,dockerhub-published
|
| 105 |
+
104,Repair inconsistent finite-volume advection edge states,energy-materials-and-finite-volume-transport,python,https://github.com/pybamm-team/PyBaMM,4cf09f36bb4afb42c661e8765e14b4527581eff7,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-104:v0.1.0@sha256:0d857f3eb3f235360133e7ac9f179871788984cc44ad877c33592de25b9a6d55,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-104:v0.1.0@sha256:255bdf4c710228c19cbdb1ae9add8b9740edc29edc129361dc83e13bd1c07e6e,linux/amd64,tasks/task_104,dockerhub-published
|
| 106 |
+
105,Restore a stereo-preserving tautomer workflow,drug-discovery-cheminformatics,python-cpp,,,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-cpp-task-105:v0.1.0@sha256:c300da3c9e6851ebd49f1aaee9d30b11edfb3ff0d116687fd6d648d1dc237f9b,docker.io/kevinxulearning/swe-bench-science-verifier-python-cpp-task-105:v0.1.0@sha256:f1db6d0edacb4e211696f3e954c59bccbe2beb5ef28ea730dc73ee2bbb041d69,linux/amd64,tasks/task_105,dockerhub-published
|
| 107 |
+
106,Reproduce and extend a version-pinned MAP4/MAPC retrieval protocol,chemoinformatics-molecular-fingerprints,python,https://github.com/MLCIL/scikit-fingerprints,839001468ba8f8da64ba9d54b33fa33c795ed3c5,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-106:v0.1.0@sha256:06c0ff508ca79a201a203fbdba027bc4325e83a9d66ea6da91dc6edb5a3bfc70,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-106:v0.1.0@sha256:1cd49e20a456955be7217fb7d096e81562c9bbc081931055fd3e719ee9eaf111,linux/amd64,tasks/task_106,dockerhub-published
|
| 108 |
+
107,Repair a public symbolic workflow,computer-algebra,python,,,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-107:v0.1.0@sha256:0d36982015454e5d48e5d6f24a8964813386dfc86bd7d2bb6b89c5183b18a289,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-107:v0.1.0@sha256:dfc6b902fd30de1a96bf83fc929da8a7fd05d2bdbbc9ca9b0a4dce53107363f9,linux/amd64,tasks/task_107,dockerhub-published
|
| 109 |
+
108,Restore stable Jacobi theta evaluations across difficult regimes,computational-mathematics-special-functions,python,https://github.com/mpmath/mpmath,5e683847c782a4c38ec71b8a88e6b1fbd903548f,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-108:v0.1.0@sha256:27ee5433771c81d7c81fe8dd421f6be77525f2970022969db930273d2c361cc0,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-108:v0.1.0@sha256:c7d2a5a47ab0b41c8da2154568fc37a12cd8da33569e1e73c41ddd2556550bf5,linux/amd64,tasks/task_108,dockerhub-published
|
| 110 |
+
109,Repair paired wrinkle FE analysis,high-performance-fibers-and-composites,python,https://github.com/elhajjar1/wrinkleFE,e81538d9a2ab5031559d0dd74b742ded5465406c,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-109:v0.1.0@sha256:28e18df47f0a3b6a207c6c8ecfc9c13ecf92888acf3abd19c8bb172636b9934a,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-109:v0.1.0@sha256:401e19dafcba0c5e8d08b55e01eca2380927e41be82c2144d9e99e3a86968d9b,linux/amd64,tasks/task_109,dockerhub-published
|
| 111 |
+
110,Restore consistent cross-section analysis results,high-performance-fibers-and-composites,python,,,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-110:v0.1.0@sha256:31221c81a3b4eecab2d2a678620d800acdb02f804093d809656ad695b4e667d6,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-110:v0.1.0@sha256:f73746797050455f54de4c5aef6c2d50ad43601623072479fda97d9d80bbece7,linux/amd64,tasks/task_110,dockerhub-published
|
| 112 |
+
111,Restore consistent tapered-filament free response,computational-mechanics-and-soft-filament-dynamics,python,https://github.com/GazzolaLab/PyElastica,46ad665fb84bda0c2d9b3392b6f2ef2388af1358,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-111:v0.1.0@sha256:3ffa5e7326116f513a3a357db186b3c1d115e7b95328eec5a0c7646530eabf72,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-111:v0.1.0@sha256:3babb2ab453edfca93f09d4a4c2412a8eed02c686db64d4f122b656cb04be6cb,linux/amd64,tasks/task_111,dockerhub-published
|
| 113 |
+
112,Repair an inconsistent hybrid-section plastic capacity workflow,high-performance-fibers-and-composites,python,,,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-112:v0.1.0@sha256:cf1d158d5fff8dc097eb9656e900a1db377e2d117cbcdd1f974abd1fd19c97d9,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-112:v0.1.0@sha256:30342a49f647f500a584e94e70157d8fde2a5f444c2d2c6f85eaf5cbf40ee421,linux/amd64,tasks/task_112,dockerhub-published
|
| 114 |
+
113,Repair an inconsistent solar-resource workflow,renewable-energy-modelling,python,,,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-113:v0.1.0@sha256:ed2da0d993479cb7e2468edd003d7e0995b64c12f531af018f1e6342bd7b6298,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-113:v0.1.0@sha256:9cc086c8edab07c617306a43a0e2bf7e2e2f70003734287d40e84138fdd73c11,linux/amd64,tasks/task_113,dockerhub-published
|
| 115 |
+
114,Repair an implausible storage history at a planning-epoch boundary,power-system-energy-storage,python,https://github.com/PyPSA/PyPSA,895bc26c721abbb826d7f8caf51587a66c69f15d,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-114:v0.1.0@sha256:d00e869c664e260a5f304cefea76ebc24b7771534511614557b49dabff377790,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-114:v0.1.0@sha256:413bf5a0fb0be52e587cf96314cfa625a9a55c8214506562b79d74aa5221074e,linux/amd64,tasks/task_114,dockerhub-published
|
| 116 |
+
115,Restore physically meaningful structural stability checks,structural-engineering-and-disaster-resilience,python,https://github.com/JWock82/Pynite,147c7aa24ec30b1c6a4d4820446915380752877b,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-115:v0.1.0@sha256:b1349937225fba8160651c9b9b218d1c8eef9c8c0f38e2a97620ac6f69d285e8,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-115:v0.1.0@sha256:a1b79491c7ee62a7541fe24e1053d2094f439d23b7b1fadff3f2086f9044b3ed,linux/amd64,tasks/task_115,dockerhub-published
|
| 117 |
+
116,Repair mode-dependent structural analysis observations,structural-engineering-finite-element-resilience,python,https://github.com/JWock82/Pynite,,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-116:v0.1.0@sha256:915ef0a612a06d17d0dae56aa1481524f7ff3a522e8373acf846faf6e5bd9423,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-116:v0.1.0@sha256:0f6df9acdb29e887cbcce79b2fe207237fee4edfbf825459002da778c7ccf90f,linux/amd64,tasks/task_116,dockerhub-published
|
| 118 |
+
117,Repair inconsistent lateral-frame member observations,structural-engineering-disaster-resilience,python,https://github.com/JWock82/Pynite,573e51689fe5fe54f279a7a875e431a35355fe73,MIT,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-117:v0.1.0@sha256:194616d6aabade2a36d9d1076a2628f50790c9a88beccd353de1a508b3a5f417,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-117:v0.1.0@sha256:4bff5cf1692b605c6de4c67fcaa834de3c63bcece3857dfb0074aee990b8a7ca,linux/amd64,tasks/task_117,dockerhub-published
|
| 119 |
+
118,Repair inconsistent periodic molecular energy representations,computational-high-energy-molecular-chemistry-periodic-models,python,,,AGPL-family,True,docker.io/kevinxulearning/swe-bench-science-environment-python-task-118:v0.1.0@sha256:d368971b40f90dbf4197b0a285dd19086c66fb8287bc96f8c4601be5b2c0f95b,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-118:v0.1.0@sha256:1e5311b58eae5b34988b4a7b193b50e3dae7e6037605b1deaeb2c854a3de4cd5,linux/amd64,tasks/task_118,dockerhub-published
|
| 120 |
+
119,Repair a molecular curvature workflow for reaction-path analysis,quantum-chemistry-reaction-paths,python,https://github.com/MolSSI/QCEngine,dd5eec6bfefa11ffe0ec81e2c4018003e8e39f2b,BSD-3-Clause,False,docker.io/kevinxulearning/swe-bench-science-environment-python-task-119:v0.1.0@sha256:bd74671fe69b403be15607d8f221b5e2528cb8fac5ea76561542af3ac3421bdc,docker.io/kevinxulearning/swe-bench-science-verifier-python-task-119:v0.1.0@sha256:17807f4660a135d0d24a77e806d34f7fb1708117ab490bcdd0c4711ef5c5b560,linux/amd64,tasks/task_119,dockerhub-published
|
manifests/tasks.jsonl
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
profiles/codex.env.example
ADDED
|
@@ -0,0 +1,7 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# Keep the real file outside the repository and pass it with --env-file.
|
| 2 |
+
MODEL=gpt-5
|
| 3 |
+
OPENAI_API_KEY=replace-with-your-key
|
| 4 |
+
CODEX_BASE_URL=https://api.openai.com/v1
|
| 5 |
+
CODEX_WIRE_API=responses
|
| 6 |
+
CODEX_VERSION=latest
|
| 7 |
+
CODEX_REASONING_EFFORT=high
|
selections/all-119.json
ADDED
|
@@ -0,0 +1,124 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"task_ids": [
|
| 3 |
+
"001",
|
| 4 |
+
"002",
|
| 5 |
+
"003",
|
| 6 |
+
"004",
|
| 7 |
+
"005",
|
| 8 |
+
"006",
|
| 9 |
+
"007",
|
| 10 |
+
"008",
|
| 11 |
+
"009",
|
| 12 |
+
"010",
|
| 13 |
+
"011",
|
| 14 |
+
"012",
|
| 15 |
+
"013",
|
| 16 |
+
"014",
|
| 17 |
+
"015",
|
| 18 |
+
"016",
|
| 19 |
+
"017",
|
| 20 |
+
"018",
|
| 21 |
+
"019",
|
| 22 |
+
"020",
|
| 23 |
+
"021",
|
| 24 |
+
"022",
|
| 25 |
+
"023",
|
| 26 |
+
"024",
|
| 27 |
+
"025",
|
| 28 |
+
"026",
|
| 29 |
+
"027",
|
| 30 |
+
"028",
|
| 31 |
+
"029",
|
| 32 |
+
"030",
|
| 33 |
+
"031",
|
| 34 |
+
"032",
|
| 35 |
+
"033",
|
| 36 |
+
"034",
|
| 37 |
+
"035",
|
| 38 |
+
"036",
|
| 39 |
+
"037",
|
| 40 |
+
"038",
|
| 41 |
+
"039",
|
| 42 |
+
"040",
|
| 43 |
+
"041",
|
| 44 |
+
"042",
|
| 45 |
+
"043",
|
| 46 |
+
"044",
|
| 47 |
+
"045",
|
| 48 |
+
"046",
|
| 49 |
+
"047",
|
| 50 |
+
"048",
|
| 51 |
+
"049",
|
| 52 |
+
"050",
|
| 53 |
+
"051",
|
| 54 |
+
"052",
|
| 55 |
+
"053",
|
| 56 |
+
"054",
|
| 57 |
+
"055",
|
| 58 |
+
"056",
|
| 59 |
+
"057",
|
| 60 |
+
"058",
|
| 61 |
+
"059",
|
| 62 |
+
"060",
|
| 63 |
+
"061",
|
| 64 |
+
"062",
|
| 65 |
+
"063",
|
| 66 |
+
"064",
|
| 67 |
+
"065",
|
| 68 |
+
"066",
|
| 69 |
+
"067",
|
| 70 |
+
"068",
|
| 71 |
+
"069",
|
| 72 |
+
"070",
|
| 73 |
+
"071",
|
| 74 |
+
"072",
|
| 75 |
+
"073",
|
| 76 |
+
"074",
|
| 77 |
+
"075",
|
| 78 |
+
"076",
|
| 79 |
+
"077",
|
| 80 |
+
"078",
|
| 81 |
+
"079",
|
| 82 |
+
"080",
|
| 83 |
+
"081",
|
| 84 |
+
"082",
|
| 85 |
+
"083",
|
| 86 |
+
"084",
|
| 87 |
+
"085",
|
| 88 |
+
"086",
|
| 89 |
+
"087",
|
| 90 |
+
"088",
|
| 91 |
+
"089",
|
| 92 |
+
"090",
|
| 93 |
+
"091",
|
| 94 |
+
"092",
|
| 95 |
+
"093",
|
| 96 |
+
"094",
|
| 97 |
+
"095",
|
| 98 |
+
"096",
|
| 99 |
+
"097",
|
| 100 |
+
"098",
|
| 101 |
+
"099",
|
| 102 |
+
"100",
|
| 103 |
+
"101",
|
| 104 |
+
"102",
|
| 105 |
+
"103",
|
| 106 |
+
"104",
|
| 107 |
+
"105",
|
| 108 |
+
"106",
|
| 109 |
+
"107",
|
| 110 |
+
"108",
|
| 111 |
+
"109",
|
| 112 |
+
"110",
|
| 113 |
+
"111",
|
| 114 |
+
"112",
|
| 115 |
+
"113",
|
| 116 |
+
"114",
|
| 117 |
+
"115",
|
| 118 |
+
"116",
|
| 119 |
+
"117",
|
| 120 |
+
"118",
|
| 121 |
+
"119"
|
| 122 |
+
],
|
| 123 |
+
"allow_gpl": true
|
| 124 |
+
}
|
selections/default-107.json
ADDED
|
@@ -0,0 +1,112 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"task_ids": [
|
| 3 |
+
"001",
|
| 4 |
+
"002",
|
| 5 |
+
"004",
|
| 6 |
+
"005",
|
| 7 |
+
"006",
|
| 8 |
+
"007",
|
| 9 |
+
"008",
|
| 10 |
+
"009",
|
| 11 |
+
"010",
|
| 12 |
+
"011",
|
| 13 |
+
"012",
|
| 14 |
+
"013",
|
| 15 |
+
"014",
|
| 16 |
+
"015",
|
| 17 |
+
"016",
|
| 18 |
+
"017",
|
| 19 |
+
"018",
|
| 20 |
+
"019",
|
| 21 |
+
"020",
|
| 22 |
+
"022",
|
| 23 |
+
"024",
|
| 24 |
+
"025",
|
| 25 |
+
"026",
|
| 26 |
+
"027",
|
| 27 |
+
"028",
|
| 28 |
+
"029",
|
| 29 |
+
"030",
|
| 30 |
+
"031",
|
| 31 |
+
"032",
|
| 32 |
+
"033",
|
| 33 |
+
"034",
|
| 34 |
+
"035",
|
| 35 |
+
"036",
|
| 36 |
+
"037",
|
| 37 |
+
"038",
|
| 38 |
+
"039",
|
| 39 |
+
"040",
|
| 40 |
+
"041",
|
| 41 |
+
"042",
|
| 42 |
+
"043",
|
| 43 |
+
"044",
|
| 44 |
+
"045",
|
| 45 |
+
"046",
|
| 46 |
+
"047",
|
| 47 |
+
"048",
|
| 48 |
+
"049",
|
| 49 |
+
"050",
|
| 50 |
+
"051",
|
| 51 |
+
"052",
|
| 52 |
+
"053",
|
| 53 |
+
"054",
|
| 54 |
+
"055",
|
| 55 |
+
"056",
|
| 56 |
+
"058",
|
| 57 |
+
"059",
|
| 58 |
+
"060",
|
| 59 |
+
"061",
|
| 60 |
+
"062",
|
| 61 |
+
"063",
|
| 62 |
+
"064",
|
| 63 |
+
"065",
|
| 64 |
+
"067",
|
| 65 |
+
"068",
|
| 66 |
+
"069",
|
| 67 |
+
"070",
|
| 68 |
+
"071",
|
| 69 |
+
"072",
|
| 70 |
+
"073",
|
| 71 |
+
"076",
|
| 72 |
+
"077",
|
| 73 |
+
"078",
|
| 74 |
+
"079",
|
| 75 |
+
"080",
|
| 76 |
+
"081",
|
| 77 |
+
"082",
|
| 78 |
+
"086",
|
| 79 |
+
"087",
|
| 80 |
+
"088",
|
| 81 |
+
"089",
|
| 82 |
+
"090",
|
| 83 |
+
"091",
|
| 84 |
+
"092",
|
| 85 |
+
"093",
|
| 86 |
+
"094",
|
| 87 |
+
"095",
|
| 88 |
+
"096",
|
| 89 |
+
"097",
|
| 90 |
+
"098",
|
| 91 |
+
"099",
|
| 92 |
+
"101",
|
| 93 |
+
"102",
|
| 94 |
+
"103",
|
| 95 |
+
"104",
|
| 96 |
+
"105",
|
| 97 |
+
"106",
|
| 98 |
+
"107",
|
| 99 |
+
"108",
|
| 100 |
+
"109",
|
| 101 |
+
"110",
|
| 102 |
+
"111",
|
| 103 |
+
"112",
|
| 104 |
+
"113",
|
| 105 |
+
"114",
|
| 106 |
+
"115",
|
| 107 |
+
"116",
|
| 108 |
+
"117",
|
| 109 |
+
"119"
|
| 110 |
+
],
|
| 111 |
+
"allow_gpl": false
|
| 112 |
+
}
|
tasks/task_001/environment/Dockerfile
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ARG BASE_IMAGE=python:3.11-slim
|
| 2 |
+
FROM ${BASE_IMAGE}
|
| 3 |
+
|
| 4 |
+
ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian
|
| 5 |
+
ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security
|
| 6 |
+
ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple
|
| 7 |
+
ARG INSTALL_FORTRAN=0
|
| 8 |
+
ARG INSTALL_OCTAVE=0
|
| 9 |
+
ENV DEBIAN_FRONTEND=noninteractive \
|
| 10 |
+
PIP_DISABLE_PIP_VERSION_CHECK=1 \
|
| 11 |
+
PIP_INDEX_URL=${PIP_INDEX_URL} \
|
| 12 |
+
PIP_NO_CACHE_DIR=1 \
|
| 13 |
+
PYTHONDONTWRITEBYTECODE=1
|
| 14 |
+
|
| 15 |
+
RUN sed -i \
|
| 16 |
+
-e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \
|
| 17 |
+
-e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \
|
| 18 |
+
/etc/apt/sources.list.d/debian.sources
|
| 19 |
+
|
| 20 |
+
RUN apt-get -o Acquire::Retries=10 update \
|
| 21 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends \
|
| 22 |
+
build-essential \
|
| 23 |
+
ca-certificates \
|
| 24 |
+
curl \
|
| 25 |
+
git \
|
| 26 |
+
ripgrep \
|
| 27 |
+
&& rm -rf /var/lib/apt/lists/*
|
| 28 |
+
|
| 29 |
+
RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \
|
| 30 |
+
apt-get -o Acquire::Retries=10 update \
|
| 31 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \
|
| 32 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 33 |
+
fi \
|
| 34 |
+
&& if [ "${INSTALL_OCTAVE}" = "1" ]; then \
|
| 35 |
+
apt-get -o Acquire::Retries=10 update \
|
| 36 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \
|
| 37 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 38 |
+
fi
|
| 39 |
+
|
| 40 |
+
WORKDIR /app/task_001
|
| 41 |
+
COPY repo/ /app/task_001/source/
|
| 42 |
+
COPY public/ /app/task_001/
|
| 43 |
+
COPY requirements.lock /app/task_001/requirements.lock
|
| 44 |
+
|
| 45 |
+
RUN python -m pip install --no-cache-dir --upgrade pip \
|
| 46 |
+
&& python -m pip install --no-cache-dir -r requirements.lock
|
| 47 |
+
ENV PYTHONPATH=/app/task_001:/app/task_001/source
|
| 48 |
+
|
| 49 |
+
RUN git init \
|
| 50 |
+
&& git checkout -b main \
|
| 51 |
+
&& git config user.email science-bench@example.invalid \
|
| 52 |
+
&& git config user.name "SWE-bench Science baseline" \
|
| 53 |
+
&& git add -A \
|
| 54 |
+
&& GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \
|
| 55 |
+
GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \
|
| 56 |
+
git commit -m baseline \
|
| 57 |
+
&& git reflog expire --expire=now --all \
|
| 58 |
+
&& git gc --prune=now
|
| 59 |
+
|
| 60 |
+
CMD ["bash"]
|
tasks/task_001/instruction.md
ADDED
|
@@ -0,0 +1,13 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
The included repository implements a tuned range-separated DFT workflow. The
|
| 2 |
+
baseline calculation runs, and the
|
| 3 |
+
workflow reports a tuned range-separation parameter. However, the final
|
| 4 |
+
calculation does not show the kind of change one would expect after a successful
|
| 5 |
+
tuning step.
|
| 6 |
+
|
| 7 |
+
Inspect the source code and public reproduction workflow, and repair
|
| 8 |
+
the implementation so that the reported tuning step has a real effect on the
|
| 9 |
+
final scientific calculation. Do not hard-code a single molecule, a single
|
| 10 |
+
parameter value, or a fixed expected output.
|
| 11 |
+
|
| 12 |
+
The task is about diagnosing why the reproduced tuned workflow still behaves too
|
| 13 |
+
much like its untuned baseline.
|
tasks/task_001/metadata.json
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"task_id": "001",
|
| 3 |
+
"title": "Repair omega-dependent range-separated PBE workflow in a real PySCF STRSF repository",
|
| 4 |
+
"domain": "density-functional-theory",
|
| 5 |
+
"language": "python",
|
| 6 |
+
"source_repository": "https://github.com/aditisingh4812/simplified_tuned_range_separated",
|
| 7 |
+
"source_commit": "f794ca5265d38906782506f1ac4e197b4e273fc4",
|
| 8 |
+
"source_license": "BSD-3-Clause",
|
| 9 |
+
"license_source": "LICENSE",
|
| 10 |
+
"gpl_family": false,
|
| 11 |
+
"public_payload_sha256": "9ed895761e11ebcd5d3d383429d1b50b2039969eab6be3369298f32077d581dd"
|
| 12 |
+
}
|
tasks/task_001/task.toml
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
schema_version = "1.3"
|
| 2 |
+
artifacts = ["/logs/artifacts/model.patch"]
|
| 3 |
+
|
| 4 |
+
[task]
|
| 5 |
+
name = "openmoss/swe-bench-science-001"
|
| 6 |
+
description = "Repair omega-dependent range-separated PBE workflow in a real PySCF STRSF repository"
|
| 7 |
+
authors = []
|
| 8 |
+
keywords = ["scientific-computing", "software-engineering"]
|
| 9 |
+
|
| 10 |
+
[metadata]
|
| 11 |
+
task_id = "001"
|
| 12 |
+
language = "python"
|
| 13 |
+
base_commit_hash = "f794ca5265d38906782506f1ac4e197b4e273fc4"
|
| 14 |
+
|
| 15 |
+
[agent]
|
| 16 |
+
network_mode = "no-network"
|
| 17 |
+
timeout_sec = 5400.0
|
| 18 |
+
|
| 19 |
+
[environment]
|
| 20 |
+
docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-001:v0.1.0@sha256:ba7befeae4625761cb107ea17ff7962f0d7fd45a71eb25cf75369dc93da8f9d3"
|
| 21 |
+
os = "linux"
|
| 22 |
+
allow_internet = false
|
| 23 |
+
cpus = 2
|
| 24 |
+
memory_mb = 8192
|
| 25 |
+
storage_mb = 20480
|
| 26 |
+
workdir = "/app/task_001"
|
| 27 |
+
|
| 28 |
+
[verifier]
|
| 29 |
+
network_mode = "no-network"
|
| 30 |
+
environment_mode = "separate"
|
| 31 |
+
timeout_sec = 1800.0
|
| 32 |
+
|
| 33 |
+
[verifier.environment]
|
| 34 |
+
docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-001:v0.1.0@sha256:3cf671ebe637b067246b05330c0c95c82bd0e1445fafaa3de1b6c1c4d1d7cd64"
|
| 35 |
+
os = "linux"
|
| 36 |
+
allow_internet = false
|
| 37 |
+
cpus = 2
|
| 38 |
+
memory_mb = 8192
|
| 39 |
+
storage_mb = 20480
|
| 40 |
+
workdir = "/app/task_001"
|
| 41 |
+
|
| 42 |
+
[[verifier.collect]]
|
| 43 |
+
command = "cd /app/task_001 && git config --global --add safe.directory /app/task_001 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch"
|
| 44 |
+
timeout_sec = 300.0
|
tasks/task_001/tests/Dockerfile
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-001:v0.1.0@sha256:3cf671ebe637b067246b05330c0c95c82bd0e1445fafaa3de1b6c1c4d1d7cd64
|
| 2 |
+
FROM ${VERIFIER_IMAGE}
|
tasks/task_001/tests/test.sh
ADDED
|
@@ -0,0 +1,6 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
#!/bin/sh
|
| 2 |
+
set -eu
|
| 3 |
+
|
| 4 |
+
# Pier requires a public tests entrypoint when loading a local task. In
|
| 5 |
+
# separate-verifier mode the executable grader remains inside the verifier image.
|
| 6 |
+
exec python /tests/grader.py
|
tasks/task_002/environment/Dockerfile
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ARG BASE_IMAGE=python:3.11-slim
|
| 2 |
+
FROM ${BASE_IMAGE}
|
| 3 |
+
|
| 4 |
+
ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian
|
| 5 |
+
ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security
|
| 6 |
+
ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple
|
| 7 |
+
ARG INSTALL_FORTRAN=0
|
| 8 |
+
ARG INSTALL_OCTAVE=0
|
| 9 |
+
ENV DEBIAN_FRONTEND=noninteractive \
|
| 10 |
+
PIP_DISABLE_PIP_VERSION_CHECK=1 \
|
| 11 |
+
PIP_INDEX_URL=${PIP_INDEX_URL} \
|
| 12 |
+
PIP_NO_CACHE_DIR=1 \
|
| 13 |
+
PYTHONDONTWRITEBYTECODE=1
|
| 14 |
+
|
| 15 |
+
RUN sed -i \
|
| 16 |
+
-e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \
|
| 17 |
+
-e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \
|
| 18 |
+
/etc/apt/sources.list.d/debian.sources
|
| 19 |
+
|
| 20 |
+
RUN apt-get -o Acquire::Retries=10 update \
|
| 21 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends \
|
| 22 |
+
build-essential \
|
| 23 |
+
ca-certificates \
|
| 24 |
+
curl \
|
| 25 |
+
git \
|
| 26 |
+
ripgrep \
|
| 27 |
+
&& rm -rf /var/lib/apt/lists/*
|
| 28 |
+
|
| 29 |
+
RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \
|
| 30 |
+
apt-get -o Acquire::Retries=10 update \
|
| 31 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \
|
| 32 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 33 |
+
fi \
|
| 34 |
+
&& if [ "${INSTALL_OCTAVE}" = "1" ]; then \
|
| 35 |
+
apt-get -o Acquire::Retries=10 update \
|
| 36 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \
|
| 37 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 38 |
+
fi
|
| 39 |
+
|
| 40 |
+
WORKDIR /app/task_002
|
| 41 |
+
COPY repo/ /app/task_002/source/
|
| 42 |
+
COPY public/ /app/task_002/
|
| 43 |
+
COPY requirements.lock /app/task_002/requirements.lock
|
| 44 |
+
|
| 45 |
+
RUN python -m pip install --no-cache-dir --upgrade pip \
|
| 46 |
+
&& python -m pip install --no-cache-dir -r requirements.lock
|
| 47 |
+
ENV PYTHONPATH=/app/task_002:/app/task_002/source
|
| 48 |
+
|
| 49 |
+
RUN git init \
|
| 50 |
+
&& git checkout -b main \
|
| 51 |
+
&& git config user.email science-bench@example.invalid \
|
| 52 |
+
&& git config user.name "SWE-bench Science baseline" \
|
| 53 |
+
&& git add -A \
|
| 54 |
+
&& GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \
|
| 55 |
+
GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \
|
| 56 |
+
git commit -m baseline \
|
| 57 |
+
&& git reflog expire --expire=now --all \
|
| 58 |
+
&& git gc --prune=now
|
| 59 |
+
|
| 60 |
+
CMD ["bash"]
|
tasks/task_002/instruction.md
ADDED
|
@@ -0,0 +1,10 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
The bundled repository implements a published computational workflow.
|
| 2 |
+
The reduced reproduction completes normally and returns finite observations, but
|
| 3 |
+
the values do not agree quantitatively with the corresponding validation data.
|
| 4 |
+
|
| 5 |
+
Determine why the reduced path drifts from the intended calculation and repair
|
| 6 |
+
the implementation across the related bundled cases. Use the source, public
|
| 7 |
+
workflow, and generated observations as the basis for the correction.
|
| 8 |
+
|
| 9 |
+
Do not hard-code case names, sequence positions, expected values, or the visible
|
| 10 |
+
default selection.
|
tasks/task_002/metadata.json
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"task_id": "002",
|
| 3 |
+
"title": "Repair an inconsistent reduced validation workflow",
|
| 4 |
+
"domain": "density-functional-theory",
|
| 5 |
+
"language": "python",
|
| 6 |
+
"source_repository": "https://github.com/aditisingh4812/simplified_tuned_range_separated",
|
| 7 |
+
"source_commit": "f794ca5265d38906782506f1ac4e197b4e273fc4",
|
| 8 |
+
"source_license": "BSD-3-Clause",
|
| 9 |
+
"license_source": "LICENSE",
|
| 10 |
+
"gpl_family": false,
|
| 11 |
+
"public_payload_sha256": "413aae9a4fa7428016b80984ed9c66d8b5e9e3af97d9588571f64fcac7a1dc46"
|
| 12 |
+
}
|
tasks/task_002/task.toml
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
schema_version = "1.3"
|
| 2 |
+
artifacts = ["/logs/artifacts/model.patch"]
|
| 3 |
+
|
| 4 |
+
[task]
|
| 5 |
+
name = "openmoss/swe-bench-science-002"
|
| 6 |
+
description = "Repair an inconsistent reduced validation workflow"
|
| 7 |
+
authors = []
|
| 8 |
+
keywords = ["scientific-computing", "software-engineering"]
|
| 9 |
+
|
| 10 |
+
[metadata]
|
| 11 |
+
task_id = "002"
|
| 12 |
+
language = "python"
|
| 13 |
+
base_commit_hash = "f794ca5265d38906782506f1ac4e197b4e273fc4"
|
| 14 |
+
|
| 15 |
+
[agent]
|
| 16 |
+
network_mode = "no-network"
|
| 17 |
+
timeout_sec = 5400.0
|
| 18 |
+
|
| 19 |
+
[environment]
|
| 20 |
+
docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-002:v0.1.0@sha256:13e8c428f486c685ec92b031e46f3520bac3d4e26b6bdd83fde9826a488b7761"
|
| 21 |
+
os = "linux"
|
| 22 |
+
allow_internet = false
|
| 23 |
+
cpus = 2
|
| 24 |
+
memory_mb = 8192
|
| 25 |
+
storage_mb = 20480
|
| 26 |
+
workdir = "/app/task_002"
|
| 27 |
+
|
| 28 |
+
[verifier]
|
| 29 |
+
network_mode = "no-network"
|
| 30 |
+
environment_mode = "separate"
|
| 31 |
+
timeout_sec = 1800.0
|
| 32 |
+
|
| 33 |
+
[verifier.environment]
|
| 34 |
+
docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-002:v0.1.0@sha256:a863b98f920e1e9b1aede8bd0460d039628aab19a413cce3dad7417028e1bd1a"
|
| 35 |
+
os = "linux"
|
| 36 |
+
allow_internet = false
|
| 37 |
+
cpus = 2
|
| 38 |
+
memory_mb = 8192
|
| 39 |
+
storage_mb = 20480
|
| 40 |
+
workdir = "/app/task_002"
|
| 41 |
+
|
| 42 |
+
[[verifier.collect]]
|
| 43 |
+
command = "cd /app/task_002 && git config --global --add safe.directory /app/task_002 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch"
|
| 44 |
+
timeout_sec = 300.0
|
tasks/task_002/tests/Dockerfile
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-002:v0.1.0@sha256:a863b98f920e1e9b1aede8bd0460d039628aab19a413cce3dad7417028e1bd1a
|
| 2 |
+
FROM ${VERIFIER_IMAGE}
|
tasks/task_002/tests/test.sh
ADDED
|
@@ -0,0 +1,6 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
#!/bin/sh
|
| 2 |
+
set -eu
|
| 3 |
+
|
| 4 |
+
# Pier requires a public tests entrypoint when loading a local task. In
|
| 5 |
+
# separate-verifier mode the executable grader remains inside the verifier image.
|
| 6 |
+
exec python /tests/grader.py
|
tasks/task_003/environment/Dockerfile
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ARG BASE_IMAGE=python:3.11-slim
|
| 2 |
+
FROM ${BASE_IMAGE}
|
| 3 |
+
|
| 4 |
+
ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian
|
| 5 |
+
ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security
|
| 6 |
+
ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple
|
| 7 |
+
ARG INSTALL_FORTRAN=0
|
| 8 |
+
ARG INSTALL_OCTAVE=0
|
| 9 |
+
ENV DEBIAN_FRONTEND=noninteractive \
|
| 10 |
+
PIP_DISABLE_PIP_VERSION_CHECK=1 \
|
| 11 |
+
PIP_INDEX_URL=${PIP_INDEX_URL} \
|
| 12 |
+
PIP_NO_CACHE_DIR=1 \
|
| 13 |
+
PYTHONDONTWRITEBYTECODE=1
|
| 14 |
+
|
| 15 |
+
RUN sed -i \
|
| 16 |
+
-e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \
|
| 17 |
+
-e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \
|
| 18 |
+
/etc/apt/sources.list.d/debian.sources
|
| 19 |
+
|
| 20 |
+
RUN apt-get -o Acquire::Retries=10 update \
|
| 21 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends \
|
| 22 |
+
build-essential \
|
| 23 |
+
ca-certificates \
|
| 24 |
+
curl \
|
| 25 |
+
git \
|
| 26 |
+
ripgrep \
|
| 27 |
+
&& rm -rf /var/lib/apt/lists/*
|
| 28 |
+
|
| 29 |
+
RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \
|
| 30 |
+
apt-get -o Acquire::Retries=10 update \
|
| 31 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \
|
| 32 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 33 |
+
fi \
|
| 34 |
+
&& if [ "${INSTALL_OCTAVE}" = "1" ]; then \
|
| 35 |
+
apt-get -o Acquire::Retries=10 update \
|
| 36 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \
|
| 37 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 38 |
+
fi
|
| 39 |
+
|
| 40 |
+
WORKDIR /app/task_003
|
| 41 |
+
COPY repo/ /app/task_003/source/
|
| 42 |
+
COPY public/ /app/task_003/
|
| 43 |
+
COPY requirements.lock /app/task_003/requirements.lock
|
| 44 |
+
|
| 45 |
+
RUN python -m pip install --no-cache-dir --upgrade pip \
|
| 46 |
+
&& python -m pip install --no-cache-dir -r requirements.lock
|
| 47 |
+
ENV PYTHONPATH=/app/task_003:/app/task_003/source
|
| 48 |
+
|
| 49 |
+
RUN git init \
|
| 50 |
+
&& git checkout -b main \
|
| 51 |
+
&& git config user.email science-bench@example.invalid \
|
| 52 |
+
&& git config user.name "SWE-bench Science baseline" \
|
| 53 |
+
&& git add -A \
|
| 54 |
+
&& GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \
|
| 55 |
+
GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \
|
| 56 |
+
git commit -m baseline \
|
| 57 |
+
&& git reflog expire --expire=now --all \
|
| 58 |
+
&& git gc --prune=now
|
| 59 |
+
|
| 60 |
+
CMD ["bash"]
|
tasks/task_003/instruction.md
ADDED
|
@@ -0,0 +1,28 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# Repair extxyz tensor-label preservation for atomistic ML data
|
| 2 |
+
|
| 3 |
+
You are working on a pinned snapshot of `deepmodeling/dpdata`, a data conversion
|
| 4 |
+
library used in atomistic simulation and machine-learning potential workflows.
|
| 5 |
+
|
| 6 |
+
A collaborator is converting extended XYZ datasets produced by ASE/QUIP-style
|
| 7 |
+
tools into dpdata/DeepMD-style labeled systems. Energies, cells, coordinates,
|
| 8 |
+
and forces survive the conversion, but an important cell-level tensor label used
|
| 9 |
+
for stress/virial training is missing or not preserved for common extxyz files.
|
| 10 |
+
This is dangerous because downstream training can silently proceed with an
|
| 11 |
+
incomplete label set.
|
| 12 |
+
|
| 13 |
+
Inspect the source tree and repair the implementation so that
|
| 14 |
+
extxyz datasets following common ASE-style conventions preserve the physically
|
| 15 |
+
equivalent tensor information needed by dpdata. Your fix should be general; do
|
| 16 |
+
not hard-code the public fixture, molecule, cell size, or numeric output.
|
| 17 |
+
Consider the public extxyz read and write paths that users naturally exercise
|
| 18 |
+
through dpdata's format APIs, not only the single public reproduction script.
|
| 19 |
+
|
| 20 |
+
You can run the public reproduction workflow:
|
| 21 |
+
|
| 22 |
+
```bash
|
| 23 |
+
python reproduce.py
|
| 24 |
+
```
|
| 25 |
+
|
| 26 |
+
Keep generated files out of your patch. Do not modify task metadata. Existing
|
| 27 |
+
QUIP/GAP extxyz files that already provide virial-like labels should continue to
|
| 28 |
+
work.
|
tasks/task_003/metadata.json
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"task_id": "003",
|
| 3 |
+
"title": "Repair extxyz stress and virial tensor-label preservation",
|
| 4 |
+
"domain": "atomistic-machine-learning-data",
|
| 5 |
+
"language": "python",
|
| 6 |
+
"source_repository": "https://github.com/deepmodeling/dpdata",
|
| 7 |
+
"source_commit": "4d8048b51ee0cc00caa4854844c28b7f892fd908",
|
| 8 |
+
"source_license": "LGPL-3.0-family",
|
| 9 |
+
"license_source": "LICENSE",
|
| 10 |
+
"gpl_family": true,
|
| 11 |
+
"public_payload_sha256": "1f00289f07104c48c4894348dc606860079c7e5647e213570bb613d52603927e"
|
| 12 |
+
}
|
tasks/task_003/task.toml
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
schema_version = "1.3"
|
| 2 |
+
artifacts = ["/logs/artifacts/model.patch"]
|
| 3 |
+
|
| 4 |
+
[task]
|
| 5 |
+
name = "openmoss/swe-bench-science-003"
|
| 6 |
+
description = "Repair extxyz stress and virial tensor-label preservation"
|
| 7 |
+
authors = []
|
| 8 |
+
keywords = ["scientific-computing", "software-engineering"]
|
| 9 |
+
|
| 10 |
+
[metadata]
|
| 11 |
+
task_id = "003"
|
| 12 |
+
language = "python"
|
| 13 |
+
base_commit_hash = "4d8048b51ee0cc00caa4854844c28b7f892fd908"
|
| 14 |
+
|
| 15 |
+
[agent]
|
| 16 |
+
network_mode = "no-network"
|
| 17 |
+
timeout_sec = 5400.0
|
| 18 |
+
|
| 19 |
+
[environment]
|
| 20 |
+
docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-003:v0.1.0@sha256:f161a1e658abd71c5c3abda59b61814a2c5bf140a4826b5598a917d62a258f4e"
|
| 21 |
+
os = "linux"
|
| 22 |
+
allow_internet = false
|
| 23 |
+
cpus = 2
|
| 24 |
+
memory_mb = 8192
|
| 25 |
+
storage_mb = 20480
|
| 26 |
+
workdir = "/app/task_003"
|
| 27 |
+
|
| 28 |
+
[verifier]
|
| 29 |
+
network_mode = "no-network"
|
| 30 |
+
environment_mode = "separate"
|
| 31 |
+
timeout_sec = 1800.0
|
| 32 |
+
|
| 33 |
+
[verifier.environment]
|
| 34 |
+
docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-003:v0.1.0@sha256:4d2e13b726b99a0c9d302ba913cdaa727c49fdc403b65b68918ec70c1713a790"
|
| 35 |
+
os = "linux"
|
| 36 |
+
allow_internet = false
|
| 37 |
+
cpus = 2
|
| 38 |
+
memory_mb = 8192
|
| 39 |
+
storage_mb = 20480
|
| 40 |
+
workdir = "/app/task_003"
|
| 41 |
+
|
| 42 |
+
[[verifier.collect]]
|
| 43 |
+
command = "cd /app/task_003 && git config --global --add safe.directory /app/task_003 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch"
|
| 44 |
+
timeout_sec = 300.0
|
tasks/task_003/tests/Dockerfile
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-003:v0.1.0@sha256:4d2e13b726b99a0c9d302ba913cdaa727c49fdc403b65b68918ec70c1713a790
|
| 2 |
+
FROM ${VERIFIER_IMAGE}
|
tasks/task_003/tests/test.sh
ADDED
|
@@ -0,0 +1,6 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
#!/bin/sh
|
| 2 |
+
set -eu
|
| 3 |
+
|
| 4 |
+
# Pier requires a public tests entrypoint when loading a local task. In
|
| 5 |
+
# separate-verifier mode the executable grader remains inside the verifier image.
|
| 6 |
+
exec python /tests/grader.py
|
tasks/task_004/environment/Dockerfile
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ARG BASE_IMAGE=python:3.11-slim
|
| 2 |
+
FROM ${BASE_IMAGE}
|
| 3 |
+
|
| 4 |
+
ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian
|
| 5 |
+
ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security
|
| 6 |
+
ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple
|
| 7 |
+
ARG INSTALL_FORTRAN=1
|
| 8 |
+
ARG INSTALL_OCTAVE=0
|
| 9 |
+
ENV DEBIAN_FRONTEND=noninteractive \
|
| 10 |
+
PIP_DISABLE_PIP_VERSION_CHECK=1 \
|
| 11 |
+
PIP_INDEX_URL=${PIP_INDEX_URL} \
|
| 12 |
+
PIP_NO_CACHE_DIR=1 \
|
| 13 |
+
PYTHONDONTWRITEBYTECODE=1
|
| 14 |
+
|
| 15 |
+
RUN sed -i \
|
| 16 |
+
-e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \
|
| 17 |
+
-e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \
|
| 18 |
+
/etc/apt/sources.list.d/debian.sources
|
| 19 |
+
|
| 20 |
+
RUN apt-get -o Acquire::Retries=10 update \
|
| 21 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends \
|
| 22 |
+
build-essential \
|
| 23 |
+
ca-certificates \
|
| 24 |
+
curl \
|
| 25 |
+
git \
|
| 26 |
+
ripgrep \
|
| 27 |
+
&& rm -rf /var/lib/apt/lists/*
|
| 28 |
+
|
| 29 |
+
RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \
|
| 30 |
+
apt-get -o Acquire::Retries=10 update \
|
| 31 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \
|
| 32 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 33 |
+
fi \
|
| 34 |
+
&& if [ "${INSTALL_OCTAVE}" = "1" ]; then \
|
| 35 |
+
apt-get -o Acquire::Retries=10 update \
|
| 36 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \
|
| 37 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 38 |
+
fi
|
| 39 |
+
|
| 40 |
+
WORKDIR /app/task_004
|
| 41 |
+
COPY repo/ /app/task_004/source/
|
| 42 |
+
COPY public/ /app/task_004/
|
| 43 |
+
COPY requirements.lock /app/task_004/requirements.lock
|
| 44 |
+
|
| 45 |
+
RUN python -m pip install --no-cache-dir --upgrade pip \
|
| 46 |
+
&& python -m pip install --no-cache-dir -r requirements.lock
|
| 47 |
+
ENV PYTHONPATH=/app/task_004:/app/task_004/source
|
| 48 |
+
|
| 49 |
+
RUN git init \
|
| 50 |
+
&& git checkout -b main \
|
| 51 |
+
&& git config user.email science-bench@example.invalid \
|
| 52 |
+
&& git config user.name "SWE-bench Science baseline" \
|
| 53 |
+
&& git add -A \
|
| 54 |
+
&& GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \
|
| 55 |
+
GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \
|
| 56 |
+
git commit -m baseline \
|
| 57 |
+
&& git reflog expire --expire=now --all \
|
| 58 |
+
&& git gc --prune=now
|
| 59 |
+
|
| 60 |
+
CMD ["bash"]
|
tasks/task_004/instruction.md
ADDED
|
@@ -0,0 +1,28 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# Repair Split-Read Exon-Overlap Filtering
|
| 2 |
+
|
| 3 |
+
You are working with a pinned BEDTools source snapshot used in an RNA-seq
|
| 4 |
+
quality-control workflow.
|
| 5 |
+
|
| 6 |
+
The workflow asks which aligned reads have enough support inside annotated
|
| 7 |
+
exons. A junction-spanning alignment is visible when the analysis accepts any
|
| 8 |
+
exonic contact, but it disappears when the documented fractional-overlap filter
|
| 9 |
+
is enabled. A comparable contiguous alignment remains present. This changes the
|
| 10 |
+
count of biologically valid spliced reads even though the input records are
|
| 11 |
+
well-formed and sorted consistently.
|
| 12 |
+
|
| 13 |
+
Inspect the source's format handling, public fixtures, and reproduction. Repair
|
| 14 |
+
the implementation so discontinuous genomic records are
|
| 15 |
+
handled consistently with the documented interval semantics. Preserve ordinary
|
| 16 |
+
non-split intersection behavior and unrelated command-line behavior.
|
| 17 |
+
|
| 18 |
+
Your repair must be general. Do not hard-code the public coordinates, record
|
| 19 |
+
names, chromosome, threshold, block count, option order, or output mode.
|
| 20 |
+
|
| 21 |
+
Run the public reproduction with:
|
| 22 |
+
|
| 23 |
+
```bash
|
| 24 |
+
python reproduce.py
|
| 25 |
+
```
|
| 26 |
+
|
| 27 |
+
The verifier will build the repaired source and exercise additional genomic
|
| 28 |
+
layouts and intersection modes in a fresh offline workspace.
|
tasks/task_004/metadata.json
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"task_id": "004",
|
| 3 |
+
"title": "Repair split-read exon-overlap filtering",
|
| 4 |
+
"domain": "rna-seq-genomic-interval-semantics",
|
| 5 |
+
"language": "c++",
|
| 6 |
+
"source_repository": "https://github.com/arq5x/bedtools2",
|
| 7 |
+
"source_commit": "0f45761e8ef6ffc093f649b0145788577a62ed33",
|
| 8 |
+
"source_license": "MIT",
|
| 9 |
+
"license_source": "LICENSE",
|
| 10 |
+
"gpl_family": false,
|
| 11 |
+
"public_payload_sha256": "8cc8d65610e3d79b5906805b086ce8163a7f03a586bfcbc62badbe9c62d8c555"
|
| 12 |
+
}
|
tasks/task_004/task.toml
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
schema_version = "1.3"
|
| 2 |
+
artifacts = ["/logs/artifacts/model.patch"]
|
| 3 |
+
|
| 4 |
+
[task]
|
| 5 |
+
name = "openmoss/swe-bench-science-004"
|
| 6 |
+
description = "Repair split-read exon-overlap filtering"
|
| 7 |
+
authors = []
|
| 8 |
+
keywords = ["scientific-computing", "software-engineering"]
|
| 9 |
+
|
| 10 |
+
[metadata]
|
| 11 |
+
task_id = "004"
|
| 12 |
+
language = "c++"
|
| 13 |
+
base_commit_hash = "0f45761e8ef6ffc093f649b0145788577a62ed33"
|
| 14 |
+
|
| 15 |
+
[agent]
|
| 16 |
+
network_mode = "no-network"
|
| 17 |
+
timeout_sec = 5400.0
|
| 18 |
+
|
| 19 |
+
[environment]
|
| 20 |
+
docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-c-task-004:v0.1.0@sha256:290695ddb1d2a160142311b604ccb61ff5d51d9500b6d218c56b43cbb94d9620"
|
| 21 |
+
os = "linux"
|
| 22 |
+
allow_internet = false
|
| 23 |
+
cpus = 2
|
| 24 |
+
memory_mb = 8192
|
| 25 |
+
storage_mb = 20480
|
| 26 |
+
workdir = "/app/task_004"
|
| 27 |
+
|
| 28 |
+
[verifier]
|
| 29 |
+
network_mode = "no-network"
|
| 30 |
+
environment_mode = "separate"
|
| 31 |
+
timeout_sec = 1800.0
|
| 32 |
+
|
| 33 |
+
[verifier.environment]
|
| 34 |
+
docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-c-task-004:v0.1.0@sha256:2553def59dc88f1886ad281da1d561600560a6f8391f177d33bb9f4975e7cc4f"
|
| 35 |
+
os = "linux"
|
| 36 |
+
allow_internet = false
|
| 37 |
+
cpus = 2
|
| 38 |
+
memory_mb = 8192
|
| 39 |
+
storage_mb = 20480
|
| 40 |
+
workdir = "/app/task_004"
|
| 41 |
+
|
| 42 |
+
[[verifier.collect]]
|
| 43 |
+
command = "cd /app/task_004 && git config --global --add safe.directory /app/task_004 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch"
|
| 44 |
+
timeout_sec = 300.0
|
tasks/task_004/tests/Dockerfile
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-c-task-004:v0.1.0@sha256:2553def59dc88f1886ad281da1d561600560a6f8391f177d33bb9f4975e7cc4f
|
| 2 |
+
FROM ${VERIFIER_IMAGE}
|
tasks/task_004/tests/test.sh
ADDED
|
@@ -0,0 +1,6 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
#!/bin/sh
|
| 2 |
+
set -eu
|
| 3 |
+
|
| 4 |
+
# Pier requires a public tests entrypoint when loading a local task. In
|
| 5 |
+
# separate-verifier mode the executable grader remains inside the verifier image.
|
| 6 |
+
exec python /tests/grader.py
|
tasks/task_005/environment/Dockerfile
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ARG BASE_IMAGE=python:3.11-slim
|
| 2 |
+
FROM ${BASE_IMAGE}
|
| 3 |
+
|
| 4 |
+
ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian
|
| 5 |
+
ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security
|
| 6 |
+
ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple
|
| 7 |
+
ARG INSTALL_FORTRAN=0
|
| 8 |
+
ARG INSTALL_OCTAVE=1
|
| 9 |
+
ENV DEBIAN_FRONTEND=noninteractive \
|
| 10 |
+
PIP_DISABLE_PIP_VERSION_CHECK=1 \
|
| 11 |
+
PIP_INDEX_URL=${PIP_INDEX_URL} \
|
| 12 |
+
PIP_NO_CACHE_DIR=1 \
|
| 13 |
+
PYTHONDONTWRITEBYTECODE=1
|
| 14 |
+
|
| 15 |
+
RUN sed -i \
|
| 16 |
+
-e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \
|
| 17 |
+
-e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \
|
| 18 |
+
/etc/apt/sources.list.d/debian.sources
|
| 19 |
+
|
| 20 |
+
RUN apt-get -o Acquire::Retries=10 update \
|
| 21 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends \
|
| 22 |
+
build-essential \
|
| 23 |
+
ca-certificates \
|
| 24 |
+
curl \
|
| 25 |
+
git \
|
| 26 |
+
ripgrep \
|
| 27 |
+
&& rm -rf /var/lib/apt/lists/*
|
| 28 |
+
|
| 29 |
+
RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \
|
| 30 |
+
apt-get -o Acquire::Retries=10 update \
|
| 31 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \
|
| 32 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 33 |
+
fi \
|
| 34 |
+
&& if [ "${INSTALL_OCTAVE}" = "1" ]; then \
|
| 35 |
+
apt-get -o Acquire::Retries=10 update \
|
| 36 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \
|
| 37 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 38 |
+
fi
|
| 39 |
+
|
| 40 |
+
WORKDIR /app/task_005
|
| 41 |
+
COPY repo/ /app/task_005/source/
|
| 42 |
+
COPY public/ /app/task_005/
|
| 43 |
+
COPY requirements.lock /app/task_005/requirements.lock
|
| 44 |
+
|
| 45 |
+
RUN python -m pip install --no-cache-dir --upgrade pip \
|
| 46 |
+
&& python -m pip install --no-cache-dir -r requirements.lock
|
| 47 |
+
ENV PYTHONPATH=/app/task_005:/app/task_005/source
|
| 48 |
+
|
| 49 |
+
RUN git init \
|
| 50 |
+
&& git checkout -b main \
|
| 51 |
+
&& git config user.email science-bench@example.invalid \
|
| 52 |
+
&& git config user.name "SWE-bench Science baseline" \
|
| 53 |
+
&& git add -A \
|
| 54 |
+
&& GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \
|
| 55 |
+
GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \
|
| 56 |
+
git commit -m baseline \
|
| 57 |
+
&& git reflog expire --expire=now --all \
|
| 58 |
+
&& git gc --prune=now
|
| 59 |
+
|
| 60 |
+
CMD ["bash"]
|
tasks/task_005/instruction.md
ADDED
|
@@ -0,0 +1,19 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
You are working with a pinned snapshot of Osprey/FID-A, a magnetic resonance
|
| 2 |
+
spectroscopy processing pipeline. A collaborator is processing edited MRS data
|
| 3 |
+
with multiple subspectra. In a reduced synthetic reproduction, one acquisition
|
| 4 |
+
condition has a 180 degree polarity relationship to the others, and the current
|
| 5 |
+
pipeline produces an inconsistent aligned/combined result.
|
| 6 |
+
|
| 7 |
+
Run `python reproduce.py` and repair the source under
|
| 8 |
+
`source/` so that edited subspectra are handled consistently before alignment
|
| 9 |
+
and combination. The repair should be general across edited MRS datasets and
|
| 10 |
+
ordinary load/process workflows.
|
| 11 |
+
|
| 12 |
+
The symptom may come from inconsistent semantics between data loading and later
|
| 13 |
+
processing, not only from the final alignment routine.
|
| 14 |
+
|
| 15 |
+
Do not hard-code the public fixture, a particular sample count, a particular
|
| 16 |
+
ppm grid, a particular subspectrum count, or fixed expected numbers from the
|
| 17 |
+
public reproduction. Existing behavior for workflows that intentionally preserve
|
| 18 |
+
the original acquisition polarity should remain distinct from workflows that
|
| 19 |
+
need polarity-consistent spectra for alignment.
|
tasks/task_005/metadata.json
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"task_id": "005",
|
| 3 |
+
"title": "Repair edited MRS subspectrum polarity handling",
|
| 4 |
+
"domain": "magnetic-resonance-spectroscopy-processing",
|
| 5 |
+
"language": "matlab-octave",
|
| 6 |
+
"source_repository": "",
|
| 7 |
+
"source_commit": "",
|
| 8 |
+
"source_license": "MIT",
|
| 9 |
+
"license_source": "LICENSE.md",
|
| 10 |
+
"gpl_family": false,
|
| 11 |
+
"public_payload_sha256": "dafbff8689114068d979e814bece33e26c954a846a4ce816e3ee4614552ae813"
|
| 12 |
+
}
|
tasks/task_005/task.toml
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
schema_version = "1.3"
|
| 2 |
+
artifacts = ["/logs/artifacts/model.patch"]
|
| 3 |
+
|
| 4 |
+
[task]
|
| 5 |
+
name = "openmoss/swe-bench-science-005"
|
| 6 |
+
description = "Repair edited MRS subspectrum polarity handling"
|
| 7 |
+
authors = []
|
| 8 |
+
keywords = ["scientific-computing", "software-engineering"]
|
| 9 |
+
|
| 10 |
+
[metadata]
|
| 11 |
+
task_id = "005"
|
| 12 |
+
language = "matlab-octave"
|
| 13 |
+
base_commit_hash = ""
|
| 14 |
+
|
| 15 |
+
[agent]
|
| 16 |
+
network_mode = "no-network"
|
| 17 |
+
timeout_sec = 5400.0
|
| 18 |
+
|
| 19 |
+
[environment]
|
| 20 |
+
docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-matlab-octave-task-005:v0.1.0@sha256:a2c49556f75e3dc3fd7f186e6309b2af8def8b724a950abe28fec9c317043440"
|
| 21 |
+
os = "linux"
|
| 22 |
+
allow_internet = false
|
| 23 |
+
cpus = 2
|
| 24 |
+
memory_mb = 8192
|
| 25 |
+
storage_mb = 20480
|
| 26 |
+
workdir = "/app/task_005"
|
| 27 |
+
|
| 28 |
+
[verifier]
|
| 29 |
+
network_mode = "no-network"
|
| 30 |
+
environment_mode = "separate"
|
| 31 |
+
timeout_sec = 1800.0
|
| 32 |
+
|
| 33 |
+
[verifier.environment]
|
| 34 |
+
docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-matlab-octave-task-005:v0.1.0@sha256:a7504e832bbcdd27a696ef1a476ae48afae9b470fcb38037c5eb24fd30ccf3b0"
|
| 35 |
+
os = "linux"
|
| 36 |
+
allow_internet = false
|
| 37 |
+
cpus = 2
|
| 38 |
+
memory_mb = 8192
|
| 39 |
+
storage_mb = 20480
|
| 40 |
+
workdir = "/app/task_005"
|
| 41 |
+
|
| 42 |
+
[[verifier.collect]]
|
| 43 |
+
command = "cd /app/task_005 && git config --global --add safe.directory /app/task_005 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch"
|
| 44 |
+
timeout_sec = 300.0
|
tasks/task_005/tests/Dockerfile
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-matlab-octave-task-005:v0.1.0@sha256:a7504e832bbcdd27a696ef1a476ae48afae9b470fcb38037c5eb24fd30ccf3b0
|
| 2 |
+
FROM ${VERIFIER_IMAGE}
|
tasks/task_005/tests/test.sh
ADDED
|
@@ -0,0 +1,6 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
#!/bin/sh
|
| 2 |
+
set -eu
|
| 3 |
+
|
| 4 |
+
# Pier requires a public tests entrypoint when loading a local task. In
|
| 5 |
+
# separate-verifier mode the executable grader remains inside the verifier image.
|
| 6 |
+
exec python /tests/grader.py
|
tasks/task_006/environment/Dockerfile
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ARG BASE_IMAGE=python:3.11-slim
|
| 2 |
+
FROM ${BASE_IMAGE}
|
| 3 |
+
|
| 4 |
+
ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian
|
| 5 |
+
ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security
|
| 6 |
+
ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple
|
| 7 |
+
ARG INSTALL_FORTRAN=1
|
| 8 |
+
ARG INSTALL_OCTAVE=0
|
| 9 |
+
ENV DEBIAN_FRONTEND=noninteractive \
|
| 10 |
+
PIP_DISABLE_PIP_VERSION_CHECK=1 \
|
| 11 |
+
PIP_INDEX_URL=${PIP_INDEX_URL} \
|
| 12 |
+
PIP_NO_CACHE_DIR=1 \
|
| 13 |
+
PYTHONDONTWRITEBYTECODE=1
|
| 14 |
+
|
| 15 |
+
RUN sed -i \
|
| 16 |
+
-e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \
|
| 17 |
+
-e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \
|
| 18 |
+
/etc/apt/sources.list.d/debian.sources
|
| 19 |
+
|
| 20 |
+
RUN apt-get -o Acquire::Retries=10 update \
|
| 21 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends \
|
| 22 |
+
build-essential \
|
| 23 |
+
ca-certificates \
|
| 24 |
+
curl \
|
| 25 |
+
git \
|
| 26 |
+
ripgrep \
|
| 27 |
+
&& rm -rf /var/lib/apt/lists/*
|
| 28 |
+
|
| 29 |
+
RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \
|
| 30 |
+
apt-get -o Acquire::Retries=10 update \
|
| 31 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \
|
| 32 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 33 |
+
fi \
|
| 34 |
+
&& if [ "${INSTALL_OCTAVE}" = "1" ]; then \
|
| 35 |
+
apt-get -o Acquire::Retries=10 update \
|
| 36 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \
|
| 37 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 38 |
+
fi
|
| 39 |
+
|
| 40 |
+
WORKDIR /app/task_006
|
| 41 |
+
COPY repo/ /app/task_006/source/
|
| 42 |
+
COPY public/ /app/task_006/
|
| 43 |
+
COPY requirements.lock /app/task_006/requirements.lock
|
| 44 |
+
|
| 45 |
+
RUN python -m pip install --no-cache-dir --upgrade pip \
|
| 46 |
+
&& python -m pip install --no-cache-dir -r requirements.lock
|
| 47 |
+
ENV PYTHONPATH=/app/task_006:/app/task_006/source
|
| 48 |
+
|
| 49 |
+
RUN git init \
|
| 50 |
+
&& git checkout -b main \
|
| 51 |
+
&& git config user.email science-bench@example.invalid \
|
| 52 |
+
&& git config user.name "SWE-bench Science baseline" \
|
| 53 |
+
&& git add -A \
|
| 54 |
+
&& GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \
|
| 55 |
+
GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \
|
| 56 |
+
git commit -m baseline \
|
| 57 |
+
&& git reflog expire --expire=now --all \
|
| 58 |
+
&& git gc --prune=now
|
| 59 |
+
|
| 60 |
+
CMD ["bash"]
|
tasks/task_006/instruction.md
ADDED
|
@@ -0,0 +1,5 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
Inspect the BEDTools source tree and the public reproduction workflow. A small genomic interval-enrichment analysis becomes unstable when the database/background interval set is augmented with valid intervals that cannot overlap the query intervals.
|
| 2 |
+
|
| 3 |
+
Those appended background intervals should not create new observed overlaps, but they are still part of the statistical sample used by the Fisher exact test table. Repair the implementation so that interval-enrichment output uses complete summary state for valid BED and genome inputs. The fix should preserve the behavior of ordinary interval-overlap commands and should not hard-code the public fixture, file names, chromosome names, counts, p-values, or coordinates.
|
| 4 |
+
|
| 5 |
+
Run `python reproduce.py` from this task directory to build the local source and reproduce the public failure.
|
tasks/task_006/metadata.json
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"task_id": "006",
|
| 3 |
+
"title": "Repair inconsistent genomic interval enrichment counts",
|
| 4 |
+
"domain": "genomics-interval-statistics",
|
| 5 |
+
"language": "c++",
|
| 6 |
+
"source_repository": "https://github.com/arq5x/bedtools2",
|
| 7 |
+
"source_commit": "ac6b252a3a6df2498757d76190b2b164cc591453",
|
| 8 |
+
"source_license": "MIT",
|
| 9 |
+
"license_source": "LICENSE",
|
| 10 |
+
"gpl_family": false,
|
| 11 |
+
"public_payload_sha256": "13d72d9ddbb69f144a85b474cae6106efe5bb7198ab09e144771589a4639ebc3"
|
| 12 |
+
}
|
tasks/task_006/task.toml
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
schema_version = "1.3"
|
| 2 |
+
artifacts = ["/logs/artifacts/model.patch"]
|
| 3 |
+
|
| 4 |
+
[task]
|
| 5 |
+
name = "openmoss/swe-bench-science-006"
|
| 6 |
+
description = "Repair inconsistent genomic interval enrichment counts"
|
| 7 |
+
authors = []
|
| 8 |
+
keywords = ["scientific-computing", "software-engineering"]
|
| 9 |
+
|
| 10 |
+
[metadata]
|
| 11 |
+
task_id = "006"
|
| 12 |
+
language = "c++"
|
| 13 |
+
base_commit_hash = "ac6b252a3a6df2498757d76190b2b164cc591453"
|
| 14 |
+
|
| 15 |
+
[agent]
|
| 16 |
+
network_mode = "no-network"
|
| 17 |
+
timeout_sec = 5400.0
|
| 18 |
+
|
| 19 |
+
[environment]
|
| 20 |
+
docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-c-task-006:v0.1.0@sha256:f740af3206582652b34972f662852a98c370ab94b5e4c1fccb88d065f8abae04"
|
| 21 |
+
os = "linux"
|
| 22 |
+
allow_internet = false
|
| 23 |
+
cpus = 2
|
| 24 |
+
memory_mb = 8192
|
| 25 |
+
storage_mb = 20480
|
| 26 |
+
workdir = "/app/task_006"
|
| 27 |
+
|
| 28 |
+
[verifier]
|
| 29 |
+
network_mode = "no-network"
|
| 30 |
+
environment_mode = "separate"
|
| 31 |
+
timeout_sec = 1800.0
|
| 32 |
+
|
| 33 |
+
[verifier.environment]
|
| 34 |
+
docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-c-task-006:v0.1.0@sha256:21e0cc23312edf271bb76b5cb35e61125952ff0056813c8e15c52713b6a2e5f9"
|
| 35 |
+
os = "linux"
|
| 36 |
+
allow_internet = false
|
| 37 |
+
cpus = 2
|
| 38 |
+
memory_mb = 8192
|
| 39 |
+
storage_mb = 20480
|
| 40 |
+
workdir = "/app/task_006"
|
| 41 |
+
|
| 42 |
+
[[verifier.collect]]
|
| 43 |
+
command = "cd /app/task_006 && git config --global --add safe.directory /app/task_006 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch"
|
| 44 |
+
timeout_sec = 300.0
|
tasks/task_006/tests/Dockerfile
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-c-task-006:v0.1.0@sha256:21e0cc23312edf271bb76b5cb35e61125952ff0056813c8e15c52713b6a2e5f9
|
| 2 |
+
FROM ${VERIFIER_IMAGE}
|
tasks/task_006/tests/test.sh
ADDED
|
@@ -0,0 +1,6 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
#!/bin/sh
|
| 2 |
+
set -eu
|
| 3 |
+
|
| 4 |
+
# Pier requires a public tests entrypoint when loading a local task. In
|
| 5 |
+
# separate-verifier mode the executable grader remains inside the verifier image.
|
| 6 |
+
exec python /tests/grader.py
|
tasks/task_007/environment/Dockerfile
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ARG BASE_IMAGE=python:3.11-slim
|
| 2 |
+
FROM ${BASE_IMAGE}
|
| 3 |
+
|
| 4 |
+
ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian
|
| 5 |
+
ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security
|
| 6 |
+
ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple
|
| 7 |
+
ARG INSTALL_FORTRAN=0
|
| 8 |
+
ARG INSTALL_OCTAVE=0
|
| 9 |
+
ENV DEBIAN_FRONTEND=noninteractive \
|
| 10 |
+
PIP_DISABLE_PIP_VERSION_CHECK=1 \
|
| 11 |
+
PIP_INDEX_URL=${PIP_INDEX_URL} \
|
| 12 |
+
PIP_NO_CACHE_DIR=1 \
|
| 13 |
+
PYTHONDONTWRITEBYTECODE=1
|
| 14 |
+
|
| 15 |
+
RUN sed -i \
|
| 16 |
+
-e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \
|
| 17 |
+
-e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \
|
| 18 |
+
/etc/apt/sources.list.d/debian.sources
|
| 19 |
+
|
| 20 |
+
RUN apt-get -o Acquire::Retries=10 update \
|
| 21 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends \
|
| 22 |
+
build-essential \
|
| 23 |
+
ca-certificates \
|
| 24 |
+
curl \
|
| 25 |
+
git \
|
| 26 |
+
ripgrep \
|
| 27 |
+
&& rm -rf /var/lib/apt/lists/*
|
| 28 |
+
|
| 29 |
+
RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \
|
| 30 |
+
apt-get -o Acquire::Retries=10 update \
|
| 31 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \
|
| 32 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 33 |
+
fi \
|
| 34 |
+
&& if [ "${INSTALL_OCTAVE}" = "1" ]; then \
|
| 35 |
+
apt-get -o Acquire::Retries=10 update \
|
| 36 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \
|
| 37 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 38 |
+
fi
|
| 39 |
+
|
| 40 |
+
WORKDIR /app/task_007
|
| 41 |
+
COPY repo/ /app/task_007/source/
|
| 42 |
+
COPY public/ /app/task_007/
|
| 43 |
+
COPY requirements.lock /app/task_007/requirements.lock
|
| 44 |
+
|
| 45 |
+
RUN python -m pip install --no-cache-dir --upgrade pip \
|
| 46 |
+
&& python -m pip install --no-cache-dir -r requirements.lock
|
| 47 |
+
ENV PYTHONPATH=/app/task_007:/app/task_007/source
|
| 48 |
+
|
| 49 |
+
RUN git init \
|
| 50 |
+
&& git checkout -b main \
|
| 51 |
+
&& git config user.email science-bench@example.invalid \
|
| 52 |
+
&& git config user.name "SWE-bench Science baseline" \
|
| 53 |
+
&& git add -A \
|
| 54 |
+
&& GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \
|
| 55 |
+
GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \
|
| 56 |
+
git commit -m baseline \
|
| 57 |
+
&& git reflog expire --expire=now --all \
|
| 58 |
+
&& git gc --prune=now
|
| 59 |
+
|
| 60 |
+
CMD ["bash"]
|
tasks/task_007/instruction.md
ADDED
|
@@ -0,0 +1,25 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
Inspect the Suspect source code, run the public
|
| 2 |
+
reproduction workflow, and repair the dynamic-registration implementation so
|
| 3 |
+
that spectral registration improves drifted magnetic-resonance spectroscopy
|
| 4 |
+
transients.
|
| 5 |
+
|
| 6 |
+
The public reproduction uses a small dynamic MRS-like series. The current
|
| 7 |
+
workflow should build or use a common reference, estimate frequency/phase drift
|
| 8 |
+
for each transient in the stable spectral region, compensate that drift before
|
| 9 |
+
averaging, and keep unusable transients from polluting the reported average.
|
| 10 |
+
The reported quality metrics show that the processed series is still not
|
| 11 |
+
behaving as a scientifically meaningful drift correction should.
|
| 12 |
+
|
| 13 |
+
Your repair should be general. Do not hard-code the public fixture, point
|
| 14 |
+
count, dwell time, peak frequency, or a fixed set of numeric outputs. The
|
| 15 |
+
correct behavior should hold for other drift directions, spectral windows,
|
| 16 |
+
noise levels, and sampling settings.
|
| 17 |
+
|
| 18 |
+
Run:
|
| 19 |
+
|
| 20 |
+
```bash
|
| 21 |
+
python reproduce.py
|
| 22 |
+
```
|
| 23 |
+
|
| 24 |
+
The script writes `outputs/reproduction_report.json` and prints the same report
|
| 25 |
+
to stdout.
|
tasks/task_007/metadata.json
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"task_id": "007",
|
| 3 |
+
"title": "Repair unstable spectral registration for drifted MRS transients",
|
| 4 |
+
"domain": "magnetic-resonance-spectroscopy",
|
| 5 |
+
"language": "python",
|
| 6 |
+
"source_repository": "https://github.com/openmrslab/suspect",
|
| 7 |
+
"source_commit": "2254ab2ae6194b41487c933039c5f2ea204e5107",
|
| 8 |
+
"source_license": "MIT",
|
| 9 |
+
"license_source": "LICENSE",
|
| 10 |
+
"gpl_family": false,
|
| 11 |
+
"public_payload_sha256": "212b3be3c819f1587ea5e3bed18c94872ce7325e527a521f51ab37680bbfb004"
|
| 12 |
+
}
|
tasks/task_007/task.toml
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
schema_version = "1.3"
|
| 2 |
+
artifacts = ["/logs/artifacts/model.patch"]
|
| 3 |
+
|
| 4 |
+
[task]
|
| 5 |
+
name = "openmoss/swe-bench-science-007"
|
| 6 |
+
description = "Repair unstable spectral registration for drifted MRS transients"
|
| 7 |
+
authors = []
|
| 8 |
+
keywords = ["scientific-computing", "software-engineering"]
|
| 9 |
+
|
| 10 |
+
[metadata]
|
| 11 |
+
task_id = "007"
|
| 12 |
+
language = "python"
|
| 13 |
+
base_commit_hash = "2254ab2ae6194b41487c933039c5f2ea204e5107"
|
| 14 |
+
|
| 15 |
+
[agent]
|
| 16 |
+
network_mode = "no-network"
|
| 17 |
+
timeout_sec = 5400.0
|
| 18 |
+
|
| 19 |
+
[environment]
|
| 20 |
+
docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-007:v0.1.0@sha256:3d7361fdd902b7603b13befdaee0d7a2bcfb2d1f3f970633c981bd5b975103ec"
|
| 21 |
+
os = "linux"
|
| 22 |
+
allow_internet = false
|
| 23 |
+
cpus = 2
|
| 24 |
+
memory_mb = 8192
|
| 25 |
+
storage_mb = 20480
|
| 26 |
+
workdir = "/app/task_007"
|
| 27 |
+
|
| 28 |
+
[verifier]
|
| 29 |
+
network_mode = "no-network"
|
| 30 |
+
environment_mode = "separate"
|
| 31 |
+
timeout_sec = 1800.0
|
| 32 |
+
|
| 33 |
+
[verifier.environment]
|
| 34 |
+
docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-007:v0.1.0@sha256:ba9b6eeba1b6ac397d7878bff2d920b1137caf4fda6909422fa9001aab26b24b"
|
| 35 |
+
os = "linux"
|
| 36 |
+
allow_internet = false
|
| 37 |
+
cpus = 2
|
| 38 |
+
memory_mb = 8192
|
| 39 |
+
storage_mb = 20480
|
| 40 |
+
workdir = "/app/task_007"
|
| 41 |
+
|
| 42 |
+
[[verifier.collect]]
|
| 43 |
+
command = "cd /app/task_007 && git config --global --add safe.directory /app/task_007 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch"
|
| 44 |
+
timeout_sec = 300.0
|
tasks/task_007/tests/Dockerfile
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-007:v0.1.0@sha256:ba9b6eeba1b6ac397d7878bff2d920b1137caf4fda6909422fa9001aab26b24b
|
| 2 |
+
FROM ${VERIFIER_IMAGE}
|
tasks/task_007/tests/test.sh
ADDED
|
@@ -0,0 +1,6 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
#!/bin/sh
|
| 2 |
+
set -eu
|
| 3 |
+
|
| 4 |
+
# Pier requires a public tests entrypoint when loading a local task. In
|
| 5 |
+
# separate-verifier mode the executable grader remains inside the verifier image.
|
| 6 |
+
exec python /tests/grader.py
|
tasks/task_008/environment/Dockerfile
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ARG BASE_IMAGE=python:3.11-slim
|
| 2 |
+
FROM ${BASE_IMAGE}
|
| 3 |
+
|
| 4 |
+
ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian
|
| 5 |
+
ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security
|
| 6 |
+
ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple
|
| 7 |
+
ARG INSTALL_FORTRAN=0
|
| 8 |
+
ARG INSTALL_OCTAVE=0
|
| 9 |
+
ENV DEBIAN_FRONTEND=noninteractive \
|
| 10 |
+
PIP_DISABLE_PIP_VERSION_CHECK=1 \
|
| 11 |
+
PIP_INDEX_URL=${PIP_INDEX_URL} \
|
| 12 |
+
PIP_NO_CACHE_DIR=1 \
|
| 13 |
+
PYTHONDONTWRITEBYTECODE=1
|
| 14 |
+
|
| 15 |
+
RUN sed -i \
|
| 16 |
+
-e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \
|
| 17 |
+
-e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \
|
| 18 |
+
/etc/apt/sources.list.d/debian.sources
|
| 19 |
+
|
| 20 |
+
RUN apt-get -o Acquire::Retries=10 update \
|
| 21 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends \
|
| 22 |
+
build-essential \
|
| 23 |
+
ca-certificates \
|
| 24 |
+
curl \
|
| 25 |
+
git \
|
| 26 |
+
ripgrep \
|
| 27 |
+
&& rm -rf /var/lib/apt/lists/*
|
| 28 |
+
|
| 29 |
+
RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \
|
| 30 |
+
apt-get -o Acquire::Retries=10 update \
|
| 31 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \
|
| 32 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 33 |
+
fi \
|
| 34 |
+
&& if [ "${INSTALL_OCTAVE}" = "1" ]; then \
|
| 35 |
+
apt-get -o Acquire::Retries=10 update \
|
| 36 |
+
&& apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \
|
| 37 |
+
&& rm -rf /var/lib/apt/lists/*; \
|
| 38 |
+
fi
|
| 39 |
+
|
| 40 |
+
WORKDIR /app/task_008
|
| 41 |
+
COPY repo/ /app/task_008/source/
|
| 42 |
+
COPY public/ /app/task_008/
|
| 43 |
+
COPY requirements.lock /app/task_008/requirements.lock
|
| 44 |
+
|
| 45 |
+
RUN python -m pip install --no-cache-dir --upgrade pip \
|
| 46 |
+
&& python -m pip install --no-cache-dir -r requirements.lock
|
| 47 |
+
ENV PYTHONPATH=/app/task_008:/app/task_008/source
|
| 48 |
+
|
| 49 |
+
RUN git init \
|
| 50 |
+
&& git checkout -b main \
|
| 51 |
+
&& git config user.email science-bench@example.invalid \
|
| 52 |
+
&& git config user.name "SWE-bench Science baseline" \
|
| 53 |
+
&& git add -A \
|
| 54 |
+
&& GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \
|
| 55 |
+
GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \
|
| 56 |
+
git commit -m baseline \
|
| 57 |
+
&& git reflog expire --expire=now --all \
|
| 58 |
+
&& git gc --prune=now
|
| 59 |
+
|
| 60 |
+
CMD ["bash"]
|