diff --git a/tasks/task_041/task.toml b/tasks/task_041/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..f90dd350fc342556bf3db2baf9174269f04f4c6d --- /dev/null +++ b/tasks/task_041/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-041" +description = "Repair an inconsistent near-Earth vector conversion" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "041" +language = "python" +base_commit_hash = "470d13491dd2c2a9440b3c657af33373ca8d47c1" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-041:v0.1.0@sha256:2d7000ea85b0ce1a1df141d46ccce61e3edcd53e86e9d5136a1b26096799aa77" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_041" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-041:v0.1.0@sha256:7e3b7b1a0ab181ed010a5bdb2bde149d115188f96418edea77331caf6e20b00a" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_041" + +[[verifier.collect]] +command = "cd /app/task_041 && git config --global --add safe.directory /app/task_041 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_041/tests/Dockerfile b/tasks/task_041/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..7cfc5fc9a4d72267afc1ba367a10b30800bbe5d2 --- /dev/null +++ b/tasks/task_041/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-041:v0.1.0@sha256:7e3b7b1a0ab181ed010a5bdb2bde149d115188f96418edea77331caf6e20b00a +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_041/tests/test.sh b/tasks/task_041/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_041/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_042/environment/Dockerfile b/tasks/task_042/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..c209521272f075aae1daba39ebe5e2ae36ffda8b --- /dev/null +++ b/tasks/task_042/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.12-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_042 +COPY repo/ /app/task_042/source/ +COPY public/ /app/task_042/ +COPY requirements.lock /app/task_042/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_042:/app/task_042/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_042/instruction.md b/tasks/task_042/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..2af0b2dc266b4165d2c904d235e0d9241ea34e94 --- /dev/null +++ b/tasks/task_042/instruction.md @@ -0,0 +1,29 @@ +# Repair an inconsistent solar-coordinate archive workflow + +A solar-observation catalogue uses the supplied scientific package to attach +coordinate objects to a table before archiving the catalogue for later +analysis. The coordinates describe a short sequence of features observed from +changing locations. Object construction and the in-memory analysis are valid, +but the archive/reload workflow does not yield a catalogue that can be reused +consistently in the same downstream analysis. + +Reproduce the problem, inspect the source and public workflow, and repair the +implementation so that valid solar-observation +catalogues retain their scientific meaning through supported archive +workflows. The repair must generalize beyond the supplied catalogue. Do not +replace scientific objects with fixed outputs, special-case the supplied data, +or change the public reproduction to hide a failure. + +Work only under this task directory. The evaluation environment is Linux and +has no network access. You may modify files under `source/`; do not modify the +task statement, reproduction, fixtures, workflow, or evaluation infrastructure. + +Run the public smoke test with: + +```bash +python reproduce.py +``` + +The command returns `1` when the untouched source reproduces the scientific +archive failure, `0` after a successful repair, and `2` for a runner or +environment failure. diff --git a/tasks/task_042/metadata.json b/tasks/task_042/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..9ac4e26fe4118049637b6daf7613b91ad848bf1e --- /dev/null +++ b/tasks/task_042/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "042", + "title": "Repair an inconsistent solar-coordinate archive workflow", + "domain": "solar-physics-scientific-data-semantics", + "language": "python", + "source_repository": "https://github.com/sunpy/sunpy", + "source_commit": "c961a1507a83b9dab24ccce12ab92a53b30359d7", + "source_license": "UNKNOWN", + "license_source": "LICENSE.rst", + "gpl_family": false, + "public_payload_sha256": "2b237d17e4f9409c1a9f77b47e60d782df91ca4aa81205bb312c597781819fe9" +} diff --git a/tasks/task_042/task.toml b/tasks/task_042/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..25e675ffb63ca988d6297729bf0cd949168a1e4c --- /dev/null +++ b/tasks/task_042/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-042" +description = "Repair an inconsistent solar-coordinate archive workflow" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "042" +language = "python" +base_commit_hash = "c961a1507a83b9dab24ccce12ab92a53b30359d7" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-042:v0.1.0@sha256:38b71d095fa30606c636c19aa2145fde1f74993809cff837b6da5e5597895181" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_042" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-042:v0.1.0@sha256:133f5154d63c2614e6e754d68ca91bef2a8ea4af1210de147a794c570c06d8f9" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_042" + +[[verifier.collect]] +command = "cd /app/task_042 && git config --global --add safe.directory /app/task_042 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_042/tests/Dockerfile b/tasks/task_042/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..f4263adc3410fcf539ad919f6b1f74910b2ac665 --- /dev/null +++ b/tasks/task_042/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-042:v0.1.0@sha256:133f5154d63c2614e6e754d68ca91bef2a8ea4af1210de147a794c570c06d8f9 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_042/tests/test.sh b/tasks/task_042/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_042/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_043/environment/Dockerfile b/tasks/task_043/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..7dfc62bd28407119a29ddb334c1e3a2f35e41cb0 --- /dev/null +++ b/tasks/task_043/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_043 +COPY repo/ /app/task_043/source/ +COPY public/ /app/task_043/ +COPY requirements.lock /app/task_043/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_043:/app/task_043/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_043/instruction.md b/tasks/task_043/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..92bfa756dde7225270eca400beea819624fc7489 --- /dev/null +++ b/tasks/task_043/instruction.md @@ -0,0 +1,19 @@ +# Repair an inconsistent porous-volume characterization + +A porous-media research group is reprocessing segmented X-ray tomography +data from sandstone with this historical PoreSpy source snapshot. The +supplied offline workflow completes normally, but the summaries produced from +the supplied segmented volume and an explicit axis-permuted representation of +that same volume are not mutually consistent. A radial two-point +characterization should not depend on which array axis stores a physical +direction. + +Run the reproduction, inspect the supplied sample data and project source, and +repair the implementation so the +scientific characterization is consistent with the definitions supported by +the project. The repair must generalize to other valid segmented images and +documented analysis options. + +Do not hard-code the supplied volume, permutation, any public observation, +fixed dimensions, or filename-specific behavior. Do not modify the scientific +input, workflow, public observations, or generated reports. diff --git a/tasks/task_043/metadata.json b/tasks/task_043/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..85d89071251b98f0588ec481e6dce3062d804d92 --- /dev/null +++ b/tasks/task_043/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "043", + "title": "Repair an inconsistent porous-volume characterization", + "domain": "porous-media-image-analysis", + "language": "python", + "source_repository": "https://github.com/PMEAL/porespy", + "source_commit": "f2360a52bc77ec917aa07ce0cf6128dc7687ea64", + "source_license": "MIT", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "dc0ef803237a7f1beab83b5eeaa8fe68fb3c39a553bb28ce9acde348e912b0be" +} diff --git a/tasks/task_043/task.toml b/tasks/task_043/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..44c533936ff9f80df9e686b3276d343402e54788 --- /dev/null +++ b/tasks/task_043/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-043" +description = "Repair an inconsistent porous-volume characterization" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "043" +language = "python" +base_commit_hash = "f2360a52bc77ec917aa07ce0cf6128dc7687ea64" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-043:v0.1.0@sha256:3e82e859587bdd681272bac9ecb4a415e77fe9f2160afe76a9f0bc641cf7096f" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_043" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-043:v0.1.0@sha256:c9a3a93ea8eca723583d471b478202553f011baaaee8411063a1aabec7c1651e" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_043" + +[[verifier.collect]] +command = "cd /app/task_043 && git config --global --add safe.directory /app/task_043 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_043/tests/Dockerfile b/tasks/task_043/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..30465cd9c4e5b10e414ba5156f2f1d983ddd40aa --- /dev/null +++ b/tasks/task_043/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-043:v0.1.0@sha256:c9a3a93ea8eca723583d471b478202553f011baaaee8411063a1aabec7c1651e +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_043/tests/test.sh b/tasks/task_043/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_043/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_044/environment/Dockerfile b/tasks/task_044/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..22534130dfc7cebcdb87d21a9ddfebdab6a11712 --- /dev/null +++ b/tasks/task_044/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_044 +COPY repo/ /app/task_044/source/ +COPY public/ /app/task_044/ +COPY requirements.lock /app/task_044/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_044:/app/task_044/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_044/instruction.md b/tasks/task_044/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..20159a4011e02fa23674af6b6d4a46ae6a7d83d4 --- /dev/null +++ b/tasks/task_044/instruction.md @@ -0,0 +1,17 @@ +# Repair inconsistent battery-model predictions + +A battery-modeling group is using this historical PyBaMM snapshot to study a +realistic lithium-ion cell parameterised for the supplied study. A +valid offline discharge workflow completes, but its scientific output does not +satisfy the discharge behavior required by the model and protocol. + +Run the supplied reproduction, inspect the complete project source and task +workflow. Diagnose the cause of the inconsistent battery prediction and repair +the implementation so that the documented scientific workflow is correct for +supported inputs. + +The repair must be general. Do not hard-code the supplied result, parameter +names, model class, protocol, or file paths. Do not modify the scientific +inputs, workflow, reproduction, or generated reports. +Validate your change with additional legal parameter values and model paths, +not only the public run. diff --git a/tasks/task_044/metadata.json b/tasks/task_044/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..fb10499f5edecafeec526acada3260130db76661 --- /dev/null +++ b/tasks/task_044/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "044", + "title": "Repair inconsistent lithium-ion discharge predictions", + "domain": "electrochemical-battery-modeling", + "language": "python", + "source_repository": "https://github.com/pybamm-team/PyBaMM", + "source_commit": "a42d7a92dd9a2c63240c8ccb6f240e5c3c42de46", + "source_license": "BSD-3-Clause", + "license_source": "LICENSE.txt", + "gpl_family": false, + "public_payload_sha256": "735b90c38de21e5576b5f999f18e125f63adcef3b45423c2115fea41665d1bff" +} diff --git a/tasks/task_044/task.toml b/tasks/task_044/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..0cb271e2308625aa2ec0e0489f545ff16f920b37 --- /dev/null +++ b/tasks/task_044/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-044" +description = "Repair inconsistent lithium-ion discharge predictions" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "044" +language = "python" +base_commit_hash = "a42d7a92dd9a2c63240c8ccb6f240e5c3c42de46" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-044:v0.1.0@sha256:513707a2950f87958370d940ca542603b5a4b83443e5c712c916abd1cc37eeb0" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_044" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-044:v0.1.0@sha256:61f22d5c7943225471bcdeed86f32470249eaefe57453989c3af1314811f3671" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_044" + +[[verifier.collect]] +command = "cd /app/task_044 && git config --global --add safe.directory /app/task_044 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_044/tests/Dockerfile b/tasks/task_044/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..f67315ed1af44f96a4d26e4071558fb4b5711523 --- /dev/null +++ b/tasks/task_044/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-044:v0.1.0@sha256:61f22d5c7943225471bcdeed86f32470249eaefe57453989c3af1314811f3671 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_044/tests/test.sh b/tasks/task_044/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_044/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_045/environment/Dockerfile b/tasks/task_045/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..abcca601dac322f45f1314c2b3da06bc1b8bef4e --- /dev/null +++ b/tasks/task_045/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_045 +COPY repo/ /app/task_045/source/ +COPY public/ /app/task_045/ +COPY requirements.lock /app/task_045/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_045:/app/task_045/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_045/instruction.md b/tasks/task_045/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..a66fe7e63f21a45c430c7437e7015df71fa254fc --- /dev/null +++ b/tasks/task_045/instruction.md @@ -0,0 +1,35 @@ +# Repair inconsistent finite-volume operations on a connected multi-face grid + +An ocean-modeling group is post-processing a tracer field from a global +finite-volume calculation. The supplied grid is represented as several +logically rectangular faces that meet at rotated edges. Interpolation and +differencing across those edges are part of the same diagnostic workflow used +to form transport and mixing budgets. + +The workflow completes and returns finite arrays, but a connected padding call +can reorder the local dimensions. Values occupying the expected connected-halo +positions then no longer come from the neighboring face declared by the +cubed-sphere topology. The result can also depend on process-level ordering +even though the physical grid and field are unchanged. A connected edge is a +geometric interface: padding must preserve the input dimension order, and for a +scalar face-label field every non-corner halo position in that layout must have +the label of the declared neighboring face, independent of process hash seed. + +Inspect the complete source snapshot, the finite-volume references, the grid +description, and the public reproduction. Repair the implementation so that +connected-face operations are geometrically consistent for valid inputs +supported by the project. The repair must remain correct for other connected +multi-face grids, fields, widths, orientations, and valid scientific workflows, +not only for the supplied probes. + +Do not hard-code the supplied field, face count, process seeds, edge probes, +array values, or fixture path. Do not change the scientific input or public +report to hide a failure. Preserve existing behavior for ordinary single-face +grids and valid disconnected boundaries. + +Run `python reproduce.py` before and after your repair. The command checks a +small, transparent subset of connected edges by deriving each required +neighbor directly from the public `face_connections` table. It also reports a +dimension-order comparison as a non-authoritative observation. Hidden tests +cover the complete topology and broader field and operation families, so the +public observations are not the complete correctness oracle. diff --git a/tasks/task_045/metadata.json b/tasks/task_045/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..16f32b5d12a7973049ab9494eb4d2ca1da62fc38 --- /dev/null +++ b/tasks/task_045/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "045", + "title": "Repair inconsistent finite-volume operations on a connected multi-face grid", + "domain": "computational-oceanography-finite-volume-grids", + "language": "python", + "source_repository": "https://github.com/xgcm/xgcm", + "source_commit": "3831b46accbff35f06e4ed3831600d71d5d8da18", + "source_license": "MIT", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "f7e001f18305b0978520b26cb621a76014f6e5d030992ae0bc4f03f76f4ad82b" +} diff --git a/tasks/task_045/task.toml b/tasks/task_045/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..4f68ae5a62463894b1ca0d89b2ccce2999382c19 --- /dev/null +++ b/tasks/task_045/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-045" +description = "Repair inconsistent finite-volume operations on a connected multi-face grid" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "045" +language = "python" +base_commit_hash = "3831b46accbff35f06e4ed3831600d71d5d8da18" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-045:v0.1.0@sha256:bdf7ecf2141952410df47d69d36d45b662047a720f6ff26ceeef1c33486b3fa0" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_045" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-045:v0.1.0@sha256:a3cd9863966518102f06bbf956ddfa7b6578debf5bcf92ccfbe0d1252c3a4b20" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_045" + +[[verifier.collect]] +command = "cd /app/task_045 && git config --global --add safe.directory /app/task_045 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_045/tests/Dockerfile b/tasks/task_045/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..934fbf2ecdece6512df5fc2b8049f5310ebf0d57 --- /dev/null +++ b/tasks/task_045/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-045:v0.1.0@sha256:a3cd9863966518102f06bbf956ddfa7b6578debf5bcf92ccfbe0d1252c3a4b20 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_045/tests/test.sh b/tasks/task_045/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_045/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_046/environment/Dockerfile b/tasks/task_046/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..6c23341e6c9676fcf19f5d21a4dd02561926d207 --- /dev/null +++ b/tasks/task_046/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_046 +COPY repo/ /app/task_046/source/ +COPY public/ /app/task_046/ +COPY requirements.lock /app/task_046/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_046:/app/task_046/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_046/instruction.md b/tasks/task_046/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..339a8de93480d8817ac74923d190ab401f0425f8 --- /dev/null +++ b/tasks/task_046/instruction.md @@ -0,0 +1,16 @@ +# Repair an inconsistent X-ray spectral-timing analysis + +An X-ray timing group is replaying a two-band quality-control observation with +the historical scientific-software source supplied in this task. The +observation loads successfully and the Fourier calculation completes, but the +returned frequency-dependent products do not satisfy the statistical behavior +described by the supplied method material. + +Run the offline reproduction, inspect the complete observation and historical +source, and repair the implementation so the reconstructed analysis agrees +with the required observation semantics. The repair must generalize to +other valid simultaneous light-curve inputs supported by the project. + +Do not hard-code this observation, a filename-specific result, or report +fields. Do not modify the supplied observation, public reproduction, or +generated reports. diff --git a/tasks/task_046/metadata.json b/tasks/task_046/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..00e4b5f240ec55a5f8b7e919faba6b1783a9834d --- /dev/null +++ b/tasks/task_046/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "046", + "title": "Repair an inconsistent X-ray spectral-timing analysis", + "domain": "astrophysical-xray-spectral-timing", + "language": "python", + "source_repository": "https://github.com/StingraySoftware/stingray", + "source_commit": "79b8f9bb9d122bd0176bb37f48f0fd4926eb9afb", + "source_license": "MIT", + "license_source": "LICENSE.rst", + "gpl_family": false, + "public_payload_sha256": "f358c234dfb9d428b07da73956df43b4e327aa28922de1f7380efd56563d9435" +} diff --git a/tasks/task_046/task.toml b/tasks/task_046/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..82aefc10a3e209553e99208908739918867867d5 --- /dev/null +++ b/tasks/task_046/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-046" +description = "Repair an inconsistent X-ray spectral-timing analysis" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "046" +language = "python" +base_commit_hash = "79b8f9bb9d122bd0176bb37f48f0fd4926eb9afb" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-046:v0.1.0@sha256:5113cc358a6f5df25d7b7c09e02cb5b9bd9964248f2d51ead28308c90febd15d" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_046" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-046:v0.1.0@sha256:73e5bc8338655f2d15e7dd871c42544ec9e7d16af3f24e6ecb69030f71edefbf" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_046" + +[[verifier.collect]] +command = "cd /app/task_046 && git config --global --add safe.directory /app/task_046 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_046/tests/Dockerfile b/tasks/task_046/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..c9988ab98bd534e77cf4dea77f97825f746dd30f --- /dev/null +++ b/tasks/task_046/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-046:v0.1.0@sha256:73e5bc8338655f2d15e7dd871c42544ec9e7d16af3f24e6ecb69030f71edefbf +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_046/tests/test.sh b/tasks/task_046/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_046/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_047/environment/Dockerfile b/tasks/task_047/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..05c5f75cdd9af76212f639aac04d68ccfc675037 --- /dev/null +++ b/tasks/task_047/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_047 +COPY repo/ /app/task_047/source/ +COPY public/ /app/task_047/ +COPY requirements.lock /app/task_047/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_047:/app/task_047/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_047/instruction.md b/tasks/task_047/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..be9796385d871fac747c71353c98a96aadc93fb6 --- /dev/null +++ b/tasks/task_047/instruction.md @@ -0,0 +1,20 @@ +# Repair an inconsistent broadband microwave composite + +I am replaying a lossy two-port measurement workflow with the supplied +historical scientific-library source, two measured microstrip records, and a +declared replay configuration. The calculation completes, the frequency sweep +is nonempty, and the reported response is finite. However, the end-to-end +network behavior is not scientifically consistent with the supplied material +for the same records and configuration. + +Run `python reproduce.py` to reproduce the observation. Inspect the complete +source tree and public measurement records, then repair the +library implementation so this workflow and related supported network +workflows are scientifically consistent. Preserve the established public APIs. +The repair must generalize beyond the supplied records, frequencies, and replay +values; do not hard-code the public fixture or replace the scientific +calculation with stored output. + +The task is fully offline. The Touchstone files are authentic upstream +measurement examples. The replay configuration is a fixed input record, not +code under repair. diff --git a/tasks/task_047/metadata.json b/tasks/task_047/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..dd3b10c3ad73bcb22313272d7995399f741516e3 --- /dev/null +++ b/tasks/task_047/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "047", + "title": "Repair an inconsistent broadband microwave composite", + "domain": "microwave-network-analysis", + "language": "python", + "source_repository": "https://github.com/scikit-rf/scikit-rf", + "source_commit": "a6dae181dbcf76fc738fc7fbc03d7de0a6c22634", + "source_license": "BSD-3-Clause", + "license_source": "LICENSE.txt", + "gpl_family": false, + "public_payload_sha256": "fa85f0105f3ab7a955fd95d203fbe54b220508b0f1d04065e60bc9bb1aac505b" +} diff --git a/tasks/task_047/task.toml b/tasks/task_047/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..4e9057ef99780cf1d001453d18b17f3b783d93b8 --- /dev/null +++ b/tasks/task_047/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-047" +description = "Repair an inconsistent broadband microwave composite" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "047" +language = "python" +base_commit_hash = "a6dae181dbcf76fc738fc7fbc03d7de0a6c22634" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-047:v0.1.0@sha256:a94de21354f66e978943e80946546812dbf404c4468baf12a84d23c34720e3d6" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_047" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-047:v0.1.0@sha256:8529979be314893a77f9c51cf5d2c0d6266d6f9df10fb33d332eb242f38953db" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_047" + +[[verifier.collect]] +command = "cd /app/task_047 && git config --global --add safe.directory /app/task_047 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_047/tests/Dockerfile b/tasks/task_047/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..e827cc085dad3d1d0d53d56a0a5be38918da2056 --- /dev/null +++ b/tasks/task_047/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-047:v0.1.0@sha256:8529979be314893a77f9c51cf5d2c0d6266d6f9df10fb33d332eb242f38953db +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_047/tests/test.sh b/tasks/task_047/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_047/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_048/environment/Dockerfile b/tasks/task_048/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..289dcd33c377615c12c678a2c8c0c916d9816849 --- /dev/null +++ b/tasks/task_048/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_048 +COPY repo/ /app/task_048/source/ +COPY public/ /app/task_048/ +COPY requirements.lock /app/task_048/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_048:/app/task_048/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_048/instruction.md b/tasks/task_048/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..51bc6e76ba27ca6aa62eb345489137caf94e63e6 --- /dev/null +++ b/tasks/task_048/instruction.md @@ -0,0 +1,27 @@ +# Repair an inconsistent alloy equilibrium assessment + +A materials-thermodynamics group is replaying literature-linked alloy studies +with the supplied historical pycalphad source and databases. The calculations +complete and return finite datasets, but several observations no longer agree +with the group's archived results: + +- a composition-temperature phase boundary moves when an equivalent database + representation is admitted to the same assessment; +- the associated phase fractions and internal-state evolution cease to form a + physically consistent transition; +- chemical-potential and heat-response curves disagree with the corresponding + baseline calculation; and +- the equilibrium topology depends on a representation that should not create + a new thermodynamic state for the requested components. + +Run the offline workflow, inspect the databases and source snapshot, and repair +the scientific +implementation. Determine the common cause rather than treating the symptoms +independently. The repair must generalize to other valid CALPHAD database +representations and supported phase states while preserving public APIs and +unrelated model behavior. + +Do not hard-code the supplied grids or generated artifacts, and do not modify +the scientific input files. The public workflow only establishes that the real +project calculation runs and saves results; correctness is evaluated on +independent scientific cases. diff --git a/tasks/task_048/metadata.json b/tasks/task_048/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..164092e3aecf515a7090d6c050f31d203af36dac --- /dev/null +++ b/tasks/task_048/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "048", + "title": "Repair an inconsistent alloy equilibrium assessment", + "domain": "computational-thermodynamics-calphad", + "language": "python", + "source_repository": "", + "source_commit": "", + "source_license": "MIT", + "license_source": "LICENSE.txt", + "gpl_family": false, + "public_payload_sha256": "5a22842c3c77c8730dca22e3e922c35f6b0018b981a092d0ef6752cd92855917" +} diff --git a/tasks/task_048/task.toml b/tasks/task_048/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..a0669aa3769527add7524c8bf0cb9944ed3e933b --- /dev/null +++ b/tasks/task_048/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-048" +description = "Repair an inconsistent alloy equilibrium assessment" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "048" +language = "python" +base_commit_hash = "" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-048:v0.1.0@sha256:38893d5510a1f2c722c39dc851c1f4c0698c52602753e0e9a0531ea466ee9a4b" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_048" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-048:v0.1.0@sha256:66acaa226780910a92acf5076beb045a8f521ec7f222277fb4fa1e37296d46da" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_048" + +[[verifier.collect]] +command = "cd /app/task_048 && git config --global --add safe.directory /app/task_048 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_048/tests/Dockerfile b/tasks/task_048/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..8c16404eadff669dfd9ccbb64c6cdf5785f1d80c --- /dev/null +++ b/tasks/task_048/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-048:v0.1.0@sha256:66acaa226780910a92acf5076beb045a8f521ec7f222277fb4fa1e37296d46da +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_048/tests/test.sh b/tasks/task_048/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_048/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_049/environment/Dockerfile b/tasks/task_049/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..ae008f4b262b629cceabba0d527786fd973d13f4 --- /dev/null +++ b/tasks/task_049/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_049 +COPY repo/ /app/task_049/source/ +COPY public/ /app/task_049/ +COPY requirements.lock /app/task_049/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_049:/app/task_049/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_049/instruction.md b/tasks/task_049/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..aaaa5f99560960e61e257484dc961d12af0090f2 --- /dev/null +++ b/tasks/task_049/instruction.md @@ -0,0 +1,31 @@ +# Restore the stochastic sampling and discretization contract + +A computational physics group is maintaining the supplied historical py-pde +source. Complete stochastic `PDE.solve()` calculations remain numerically +stable because the current implementation compensates one scaling choice with +another. The defect is instead at the reusable interface between Gaussian +sampling and spatial discretization. + +The backend Gaussian primitive is a standard-normal sampling service. For the +same backend, seed, dtype, and array shape, its draw must not change when only +the physical grid measure changes. Cell volumes belong to the discretization +of a stochastic field: a variance-based solver converts continuum noise +variance to a cell increment using the inverse cell measure. Keeping these +responsibilities separate lets the primitive remain reusable across fields and +backends while solvers consistently interpret the public noise variance. + +The package also documents a lower-level direct-realization interface. A user +who chooses that route supplies the complete spatially discretized realization, +including any required measure factor. That does not change the contract of the +backend standard-normal primitive used by variance-based solvers. + +Run the offline reproduction, inspect the task context and complete source +snapshot, and repair the implementation so that both sides of this contract +hold for all supported valid inputs. Preserve deterministic PDE +behavior, public APIs, stochastic interpretations, supported backends, device +and dtype behavior, and unrelated functionality. + +Do not hard-code the public grids, seeds, controlled draw, lifecycle status, or +generated report. The public experiment states the architecture being studied +but does not name a target source file or prescribe a patch shape. Hidden tests +vary geometry, backend, solver, noise interpretation, and realization route. diff --git a/tasks/task_049/metadata.json b/tasks/task_049/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..765b289ca93dbf716f5c26fea7d59a6fd7ea591a --- /dev/null +++ b/tasks/task_049/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "049", + "title": "Restore consistent stochastic-field behavior on nonuniform grids", + "domain": "finite-difference-stochastic-partial-differential-equations", + "language": "python", + "source_repository": "https://github.com/zwicker-group/py-pde", + "source_commit": "a9f8256c1b4b48ac73f3df35b3e570993501b333", + "source_license": "MIT", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "2102d49be26585ee8217bb375347adb25a008f36d62c783554d2a4e930489433" +} diff --git a/tasks/task_049/task.toml b/tasks/task_049/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..fce46a7be7bd22fa4727d63333faca22e1cb42d8 --- /dev/null +++ b/tasks/task_049/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-049" +description = "Restore consistent stochastic-field behavior on nonuniform grids" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "049" +language = "python" +base_commit_hash = "a9f8256c1b4b48ac73f3df35b3e570993501b333" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-049:v0.1.0@sha256:5d2c93c90c190f69ed1f8bb05014f34d900f4c68ca483cf428399caa5c80f339" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_049" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-049:v0.1.0@sha256:7a8babe7c3e8d6121a1fff866e0e6ae5871de381c8e759897a4b40244b6b76b6" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_049" + +[[verifier.collect]] +command = "cd /app/task_049 && git config --global --add safe.directory /app/task_049 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_049/tests/Dockerfile b/tasks/task_049/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..4c8cbefc71051eb1f27b72a7efcfc65366eeefe4 --- /dev/null +++ b/tasks/task_049/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-049:v0.1.0@sha256:7a8babe7c3e8d6121a1fff866e0e6ae5871de381c8e759897a4b40244b6b76b6 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_049/tests/test.sh b/tasks/task_049/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_049/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_050/environment/Dockerfile b/tasks/task_050/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..99dd5281cca84c1f210e65fded6dfe6f426459ae --- /dev/null +++ b/tasks/task_050/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_050 +COPY repo/ /app/task_050/source/ +COPY public/ /app/task_050/ +COPY requirements.lock /app/task_050/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_050:/app/task_050/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_050/instruction.md b/tasks/task_050/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..dde1efbe6dab744fe593d2a401b5d295c9918f78 --- /dev/null +++ b/tasks/task_050/instruction.md @@ -0,0 +1,17 @@ +# Repair an inconsistent tensor-network state calculation + +A quantum many-body group is replaying a tensor-network calculation with the +supplied historical source snapshot. The workflow finishes and produces finite +results, but the reported state quantity is not reproducible across +mathematically equivalent executions of the same calculation. + +Run the offline reproduction, read the accompanying primary material, inspect +the complete source snapshot, and repair the implementation so that the +scientific calculation is consistent for valid tensor networks. The repair +must generalize beyond the supplied workload and preserve ordinary public APIs +and unrelated tensor-network behavior. + +Do not hard-code the supplied input, output, or reproduction status. Do not +edit the scientific input. The public reproduction is only a smoke test; use +the references and source to establish the general invariant and validate the +repair on additional valid calculations. diff --git a/tasks/task_050/metadata.json b/tasks/task_050/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..bfe78d37015fb47101f6187f340e6a055988ac0c --- /dev/null +++ b/tasks/task_050/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "050", + "title": "Repair an inconsistent tensor-network state calculation", + "domain": "quantum-information-many-body-tensor-networks", + "language": "python", + "source_repository": "https://github.com/jcmgray/quimb", + "source_commit": "", + "source_license": "Apache-2.0", + "license_source": "LICENSE.txt", + "gpl_family": false, + "public_payload_sha256": "860d67a6ca8a5631f9b564aaf11e06bc1bec2dc388f996ce265d1fd31cd00771" +} diff --git a/tasks/task_050/task.toml b/tasks/task_050/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..27833fc401a887e8564c42dcab3015d908c3cfe4 --- /dev/null +++ b/tasks/task_050/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-050" +description = "Repair an inconsistent tensor-network state calculation" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "050" +language = "python" +base_commit_hash = "" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-050:v0.1.0@sha256:6f1421184ec5bd40580757a5b684b53519b2fb9044b900320b822fbffcc3ed7d" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_050" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-050:v0.1.0@sha256:74fe72ef3a7fe8749cbc7de11f80303278c83e89adfc60dfa00338059b3b0561" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_050" + +[[verifier.collect]] +command = "cd /app/task_050 && git config --global --add safe.directory /app/task_050 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_050/tests/Dockerfile b/tasks/task_050/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..c2710e57151fbd88f12cecd2b4120ea9a0011bcd --- /dev/null +++ b/tasks/task_050/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-050:v0.1.0@sha256:74fe72ef3a7fe8749cbc7de11f80303278c83e89adfc60dfa00338059b3b0561 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_050/tests/test.sh b/tasks/task_050/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_050/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_051/environment/Dockerfile b/tasks/task_051/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..7be7452c78f62fb60a53af62a8b65c013f3b6534 --- /dev/null +++ b/tasks/task_051/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=1 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_051 +COPY repo/ /app/task_051/source/ +COPY public/ /app/task_051/ +COPY requirements.lock /app/task_051/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_051:/app/task_051/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_051/instruction.md b/tasks/task_051/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..26cbf92b39787b1dd4986b70765436b7806a50ef --- /dev/null +++ b/tasks/task_051/instruction.md @@ -0,0 +1,17 @@ +# Repair an inconsistent planetary gradient-tensor calculation + +A planetary-science group is reprocessing an archived magnetic-field model with +this historical SHTOOLS source snapshot. In their analysis, two complete +second-order field calculations based on equivalent representations of the same +spherical-harmonic potential produced smooth finite maps that were not +physically consistent after being expressed in a common Cartesian frame. + +Run the offline Mars field study as a realistic project workflow, inspect its +raw products, the complete source, and coefficient model, and repair the +implementation so equivalent +representations of a supported potential produce the same physical tensor +field. The repair must generalize to other supported coefficient models, +truncation degrees, grid modes, and both gravitational and magnetic tensor +workflows. Do not hard-code the supplied model, a reported status, or a +fixture-specific result, and do not modify the scientific input or the +generated report. diff --git a/tasks/task_051/metadata.json b/tasks/task_051/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..a0653278927ae8ff71fe529b9155985fb1e09d6b --- /dev/null +++ b/tasks/task_051/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "051", + "title": "Repair an inconsistent planetary gradient-tensor calculation", + "domain": "planetary-geodesy-and-geomagnetism", + "language": "fortran", + "source_repository": "https://github.com/SHTOOLS/SHTOOLS", + "source_commit": "7f7d91474509acb597071eb789661b1f0cc304ca", + "source_license": "BSD-3-Clause", + "license_source": "LICENSE.txt", + "gpl_family": false, + "public_payload_sha256": "623104b002867b3f7a57e24a85ce03cc84c897607d507cfafe5d93a423415325" +} diff --git a/tasks/task_051/task.toml b/tasks/task_051/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..2fc5bbea2ce991a19c3cdb1bbdc059dc1f33a60f --- /dev/null +++ b/tasks/task_051/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-051" +description = "Repair an inconsistent planetary gradient-tensor calculation" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "051" +language = "fortran" +base_commit_hash = "7f7d91474509acb597071eb789661b1f0cc304ca" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-fortran-task-051:v0.1.0@sha256:8235525555c16d48f6e12019ba6239fc99569358183a444cb0251b72dfd99de4" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_051" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-fortran-task-051:v0.1.0@sha256:cc4ffda89baf3ef1fed6903ff06b194b1ef2f992413574aa6032451e09e653fb" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_051" + +[[verifier.collect]] +command = "cd /app/task_051 && git config --global --add safe.directory /app/task_051 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_051/tests/Dockerfile b/tasks/task_051/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..1582cef3bb0dac2a2e064a458e5140d7f92d343c --- /dev/null +++ b/tasks/task_051/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-fortran-task-051:v0.1.0@sha256:cc4ffda89baf3ef1fed6903ff06b194b1ef2f992413574aa6032451e09e653fb +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_051/tests/test.sh b/tasks/task_051/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_051/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_052/environment/Dockerfile b/tasks/task_052/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..cf0866d2ff166824661dc81a94289cd7eba32f97 --- /dev/null +++ b/tasks/task_052/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_052 +COPY repo/ /app/task_052/source/ +COPY public/ /app/task_052/ +COPY requirements.lock /app/task_052/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_052:/app/task_052/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_052/instruction.md b/tasks/task_052/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..18fac5d4ea07823bd61a470fba6a89db66d992d6 --- /dev/null +++ b/tasks/task_052/instruction.md @@ -0,0 +1,17 @@ +# Restore the scientific workflow + +A materials-modeling workflow in the supplied FiPy source behaves consistently +on its long-standing control mesh, but the archived polycrystal study cannot +complete when the same coupled finite-volume calculation uses a valid +orthogonal mesh with graded cell sizes. The study cannot produce a usable +phase-field update. + +Reproduce the problem with `python reproduce.py`. Read the supplied method +material and inspect the complete source snapshot. Repair the scientific +implementation so that the coupled workflow behaves coherently for the +archived input and for other valid meshes, while preserving existing uniform- +mesh behavior. + +Make a general source repair. Do not replace the archived input, bypass the +scientific calculation, or hard-code the public report. The evaluator will run +independent finite-volume studies that are not included in the public payload. diff --git a/tasks/task_052/metadata.json b/tasks/task_052/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..64452332741cca103f9c9f41662409a46d642d6f --- /dev/null +++ b/tasks/task_052/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "052", + "title": "Restore a nonuniform finite-volume phase-field workflow", + "domain": "computational-materials-finite-volume-pde", + "language": "python", + "source_repository": "https://github.com/usnistgov/fipy", + "source_commit": "11e5c6ae26207a60e223d46473ac364b352ac982", + "source_license": "UNKNOWN", + "license_source": "LICENSE.rst", + "gpl_family": false, + "public_payload_sha256": "3ee5dcafe311d965bdf99f2208a383202baec7279b4668f0486fa9efabaf78fe" +} diff --git a/tasks/task_052/task.toml b/tasks/task_052/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..6dec092f8e9244b8788038d5afbfe9e84871a551 --- /dev/null +++ b/tasks/task_052/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-052" +description = "Restore a nonuniform finite-volume phase-field workflow" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "052" +language = "python" +base_commit_hash = "11e5c6ae26207a60e223d46473ac364b352ac982" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-052:v0.1.0@sha256:7f5ea002c9963e322dd2ffc1b1c3d2669b511a74391f4ace0d1151207efec376" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_052" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-052:v0.1.0@sha256:d0fa3032421f94d1f0e43986f33125ab48af349eb26e5b68a1e86b372342b7bf" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_052" + +[[verifier.collect]] +command = "cd /app/task_052 && git config --global --add safe.directory /app/task_052 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_052/tests/Dockerfile b/tasks/task_052/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..7ab9beaacbffee46f5f164d017a76f9f1960a049 --- /dev/null +++ b/tasks/task_052/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-052:v0.1.0@sha256:d0fa3032421f94d1f0e43986f33125ab48af349eb26e5b68a1e86b372342b7bf +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_052/tests/test.sh b/tasks/task_052/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_052/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_053/environment/Dockerfile b/tasks/task_053/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..81c639b8dabc5044ed0b956d213a620cf36acde1 --- /dev/null +++ b/tasks/task_053/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_053 +COPY repo/ /app/task_053/source/ +COPY public/ /app/task_053/ +COPY requirements.lock /app/task_053/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_053:/app/task_053/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_053/instruction.md b/tasks/task_053/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..10e94b1724982e90a59d0a29dc6e9d02f4c00845 --- /dev/null +++ b/tasks/task_053/instruction.md @@ -0,0 +1,11 @@ +# Repair a physical surface-overlap calculation + +You are working on a scientific image-analysis workflow built from the supplied MONAI source snapshot. The workflow compares an automated segmentation with a reference segmentation using a normalized surface-overlap score. The supplied paper explains why this kind of score is useful for contour-based evaluation in radiotherapy and why the tolerance is a physical distance. + +Run the public reproduction and inspect the source and paper. The command completes on the supplied inputs, but the finite score changes too much when the same physical study is represented on two different voxel grids. This is a scientific consistency problem, not an installation or syntax problem. + +Repair the implementation so that the metric has a physically meaningful interpretation for supported 2-D and 3-D binary, one-hot, batch-first inputs. Preserve the normal public API, distance choices, reduction behavior, batch handling, and well-defined empty-class behavior. Keep a compatible unit-grid or legacy behavior when the caller has not requested a physical-spacing measurement. + +Do not hard-code the supplied arrays, score values, grid shapes, or tolerance. The repair must generalize to new geometries, spacing orders, thresholds, and input batches. Use the accompanying paper and the source's existing abstractions to determine the correct scientific behavior. Do not modify the public reproduction to conceal a failing result or bypass the metric implementation. + +The source snapshot includes a small import-compatibility layer so that the relevant MONAI metric path runs in the offline task environment. Do not turn package initialization or unrelated optional MONAI modules into a separate task. diff --git a/tasks/task_053/metadata.json b/tasks/task_053/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..cac1510b653468b6b45cc74509bdbd93da3b9167 --- /dev/null +++ b/tasks/task_053/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "053", + "title": "Repair a representation-dependent physical surface Dice workflow", + "domain": "medical-image-segmentation-geometry", + "language": "python", + "source_repository": "https://github.com/Project-MONAI/MONAI", + "source_commit": "18daff1d8b26002b02de526cc19b92a9a4907f89", + "source_license": "UNKNOWN", + "license_source": "not-detected", + "gpl_family": false, + "public_payload_sha256": "1919cce5250d098fee5cb4ebead74a679efde0904619518a436697b3dec04030" +} diff --git a/tasks/task_053/task.toml b/tasks/task_053/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..83c79b5a2e1b22332e88bcc23950fdfe9e1d5330 --- /dev/null +++ b/tasks/task_053/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-053" +description = "Repair a representation-dependent physical surface Dice workflow" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "053" +language = "python" +base_commit_hash = "18daff1d8b26002b02de526cc19b92a9a4907f89" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-053:v0.1.0@sha256:9763fa42d9a9e025dbb4470db64ad48b4d21549219f0938e746aadb5aa77dcc3" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_053" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-053:v0.1.0@sha256:10656f4e5cfb69d613c2442050f34691fe3264e4d03ee6bfa2f98d3529098ab6" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_053" + +[[verifier.collect]] +command = "cd /app/task_053 && git config --global --add safe.directory /app/task_053 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_053/tests/Dockerfile b/tasks/task_053/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..ab9973b57ee19c666a3958277c3f55bd344d5d90 --- /dev/null +++ b/tasks/task_053/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-053:v0.1.0@sha256:10656f4e5cfb69d613c2442050f34691fe3264e4d03ee6bfa2f98d3529098ab6 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_053/tests/test.sh b/tasks/task_053/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_053/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_054/environment/Dockerfile b/tasks/task_054/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..ae0214faf854897af828b7967376a03e0ffed8f5 --- /dev/null +++ b/tasks/task_054/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_054 +COPY repo/ /app/task_054/source/ +COPY public/ /app/task_054/ +COPY requirements.lock /app/task_054/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_054:/app/task_054/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_054/instruction.md b/tasks/task_054/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..1a706f3d3a06673ee977415ed9bbd5e5e57a7476 --- /dev/null +++ b/tasks/task_054/instruction.md @@ -0,0 +1,19 @@ +# Repair an inconsistent tandem-mass spectral similarity workflow + +A mass-spectrometry group is comparing a small library of complete tandem mass +spectra using the historical `matchms` source snapshot supplied with this +task. The workflow finishes and returns finite values, but the resulting +similarity matrix is not consistent with the scientific interpretation of an +entropy-based MS/MS similarity: a self-comparison is not a reliable reference +point, and the aggregate scores can leave the valid similarity range. + +Run the offline reproduction, inspect the complete source snapshot and the +scientific references, and repair the implementation so the public similarity +workflow agrees with the method definition for valid tandem spectra. The +repair must remain correct for other molecular spectra, mass tolerances, and +the project's pairwise and matrix calculation routes. Preserve the existing +public API and keep the implementation usable for large library comparisons. + +Do not hard-code the supplied molecules, the displayed aggregate values, a +single peak list, or a filename-specific result. Do not modify the supplied +scientific inputs or generated reports. diff --git a/tasks/task_054/metadata.json b/tasks/task_054/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..07eb09e9314ddee817b324036db4e1041ff0de60 --- /dev/null +++ b/tasks/task_054/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "054", + "title": "Repair an inconsistent tandem-mass spectral similarity workflow", + "domain": "mass-spectrometry-spectral-similarity", + "language": "python", + "source_repository": "https://github.com/matchms/matchms", + "source_commit": "9f27ba89d8c485e6a2fa2db4756e3fe3aec05151", + "source_license": "Apache-2.0", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "c1a33e4bda2aaf121eb0df8edbfb0c902ceaf32766cdc4a96ff9ef2aba6390a1" +} diff --git a/tasks/task_054/task.toml b/tasks/task_054/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..73340007599dbde2e701a7d9e9d0b1b0bff057a5 --- /dev/null +++ b/tasks/task_054/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-054" +description = "Repair an inconsistent tandem-mass spectral similarity workflow" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "054" +language = "python" +base_commit_hash = "9f27ba89d8c485e6a2fa2db4756e3fe3aec05151" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-054:v0.1.0@sha256:a9e8dedaf3d63ada395f497d35092465a56a34c0862794ee20216f46d70ec98c" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_054" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-054:v0.1.0@sha256:60b1bd49880f5e1bab44cd13d5986b57b055f1ed3b30ff19801ff3232f93cfda" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_054" + +[[verifier.collect]] +command = "cd /app/task_054 && git config --global --add safe.directory /app/task_054 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_054/tests/Dockerfile b/tasks/task_054/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..4d10cc97a30e599f3f20a94ae9b2f9e630b348e1 --- /dev/null +++ b/tasks/task_054/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-054:v0.1.0@sha256:60b1bd49880f5e1bab44cd13d5986b57b055f1ed3b30ff19801ff3232f93cfda +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_054/tests/test.sh b/tasks/task_054/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_054/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_055/environment/Dockerfile b/tasks/task_055/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..43e610f9957c6a92586f07509c69f22464a15c4c --- /dev/null +++ b/tasks/task_055/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_055 +COPY repo/ /app/task_055/source/ +COPY public/ /app/task_055/ +COPY requirements.lock /app/task_055/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_055:/app/task_055/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_055/instruction.md b/tasks/task_055/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..6be8f5cdc5dd5913a000bfc2c446bc53162c881c --- /dev/null +++ b/tasks/task_055/instruction.md @@ -0,0 +1,18 @@ +# Restore a scientific template-comparison workflow + +An astronomy group is comparing an archived extraction of a real SDSS DR16 +observation with a lower-resolution local template through the project's +template-comparison workflow. The command runs to completion, but the +comparison does not produce a usable result consistent with the archived +analysis. + +Inspect the supplied scientific paper, the project documentation, the complete +source snapshot, and the offline reproduction. Repair the implementation so +that the workflow behaves correctly for valid spectra and remains compatible +with the project's public APIs. + +The supplied SDSS case is evidence of a real workflow failure, not the complete +specification. Do not hard-code the dataset, wavelength values, archived +score, or a filename-specific result. Use the scientific material and the +source's existing semantics to make a general repair. Do not modify the +supplied scientific inputs or generated reports. diff --git a/tasks/task_055/metadata.json b/tasks/task_055/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..4b2e15832395b730201727d8f4df251cae01ee83 --- /dev/null +++ b/tasks/task_055/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "055", + "title": "Restore a scientific template-comparison workflow", + "domain": "astronomical-spectroscopy", + "language": "python", + "source_repository": "https://github.com/astropy/specutils", + "source_commit": "0613ba1ba86fd7ae79e9d89c8ffd24004a891aee", + "source_license": "BSD-3-Clause", + "license_source": "LICENSE.rst", + "gpl_family": false, + "public_payload_sha256": "900f504762e2ea9497cc7f4600e112e0a84757ba37e1c3403073fceb8c2ab4ad" +} diff --git a/tasks/task_055/task.toml b/tasks/task_055/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..e9f0a897877429f48bb654bd02770c0f10156f37 --- /dev/null +++ b/tasks/task_055/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-055" +description = "Restore a scientific template-comparison workflow" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "055" +language = "python" +base_commit_hash = "0613ba1ba86fd7ae79e9d89c8ffd24004a891aee" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-055:v0.1.0@sha256:74325f6a3477680f5302abf9e5fd622b90be8d28ca9e01b87697b8cf480dba53" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_055" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-055:v0.1.0@sha256:f1b514a04de8a991bbe7af6591cdf6a260f6a89afa22105e90895e3529bd46d4" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_055" + +[[verifier.collect]] +command = "cd /app/task_055 && git config --global --add safe.directory /app/task_055 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_055/tests/Dockerfile b/tasks/task_055/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..51f916970bb914daedb035c2e27695973d77aef2 --- /dev/null +++ b/tasks/task_055/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-055:v0.1.0@sha256:f1b514a04de8a991bbe7af6591cdf6a260f6a89afa22105e90895e3529bd46d4 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_055/tests/test.sh b/tasks/task_055/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_055/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_056/environment/Dockerfile b/tasks/task_056/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..6cf2301fc98b4086983b1d9694b966cd34a66443 --- /dev/null +++ b/tasks/task_056/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.10-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_056 +COPY repo/ /app/task_056/source/ +COPY public/ /app/task_056/ +COPY requirements.lock /app/task_056/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_056:/app/task_056/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_056/instruction.md b/tasks/task_056/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..157c58e3ec4a52e6d75d1bde4ed215fe04c50bc7 --- /dev/null +++ b/tasks/task_056/instruction.md @@ -0,0 +1,36 @@ +# Restore the scientific meaning of an exported orbital history + +A mission-analysis workflow starts from a valid osculating two-body state and +exports a bounded history for event analysis and visualization. The supplied +historical scientific-software snapshot completes the export, but downstream +users report that the physical meaning of the resulting history is not +consistent with the definitions in the supplied scientific material. + +Use the complete paper, the official project documentation in `source/`, the +full source snapshot, the fixture, and the project-native summaries produced by +the public reproduction to investigate the inconsistency and repair the +implementation. + +Keep the repair focused on the documented semantics of an orbit-history export: +the exported history must remain a faithful time-indexed representation of the +same physical two-body motion. The behavior must generalize beyond the supplied +numbers to valid supported inputs while preserving the existing public API and +other documented ways of creating an ephemeris. Do not hard-code the fixture, +workflow output, or filenames, and do not alter generated reports. + +Do not modify the supplied fixture or generated reports. Do not hard-code the +public input, workflow output, or filenames. A successful repair should make +the scientific representations mutually consistent, not merely suppress an +exception or change the public report. + +Run the offline scientific reproduction while investigating: + +```bash +python reproduce.py +``` + +The source snapshot is intentionally pre-fix. The public command is an +execution smoke test: both the untouched and repaired source should be able to +produce the documented artifacts, while infrastructure failures are reported +separately. The public case is only one legal input; the repair must generalize +and must not depend on the public report or a particular patch shape. diff --git a/tasks/task_056/metadata.json b/tasks/task_056/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..607f52e6919558ed4fb191fc248a2f89eb58ead5 --- /dev/null +++ b/tasks/task_056/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "056", + "title": "Repair a physically inconsistent orbital history export", + "domain": "astrodynamics-and-orbital-mechanics", + "language": "python", + "source_repository": "https://github.com/poliastro/poliastro", + "source_commit": "0583b33091b07229abe2027bccdc596ba3c5033b0", + "source_license": "MIT", + "license_source": "COPYING", + "gpl_family": false, + "public_payload_sha256": "0c40a39f1a705c60ae6088941ee2549c10a86b5886dbe1b9b6689b0557d68830" +} diff --git a/tasks/task_056/task.toml b/tasks/task_056/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..6ec21658717b86154051f3442785e8a0080a689f --- /dev/null +++ b/tasks/task_056/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-056" +description = "Repair a physically inconsistent orbital history export" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "056" +language = "python" +base_commit_hash = "0583b33091b07229abe2027bccdc596ba3c5033b0" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-056:v0.1.0@sha256:2909a24d72bf5161604c65e846c94058d0318cb92e4b86b29a77aff46dea3a70" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_056" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-056:v0.1.0@sha256:3cf9ed1c78f08940105a8155526ab20272bdb2640eaf0f9af03526aac677887a" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_056" + +[[verifier.collect]] +command = "cd /app/task_056 && git config --global --add safe.directory /app/task_056 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_056/tests/Dockerfile b/tasks/task_056/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..6eba4b91e42a3482f388c84d93abf399eeaa36ec --- /dev/null +++ b/tasks/task_056/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-056:v0.1.0@sha256:3cf9ed1c78f08940105a8155526ab20272bdb2640eaf0f9af03526aac677887a +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_056/tests/test.sh b/tasks/task_056/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_056/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_057/environment/Dockerfile b/tasks/task_057/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..15197b6d14c8efe5bf5d70fa48625a2de5534b0f --- /dev/null +++ b/tasks/task_057/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_057 +COPY repo/ /app/task_057/source/ +COPY public/ /app/task_057/ +COPY requirements.lock /app/task_057/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_057:/app/task_057/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_057/instruction.md b/tasks/task_057/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..80762e0d97697e19159cc4125b39849226f0c287 --- /dev/null +++ b/tasks/task_057/instruction.md @@ -0,0 +1,26 @@ +# Investigate a periodic trajectory-processing anomaly + +A researcher is using the supplied historical MDTraj snapshot to prepare an +archived molecular-dynamics coordinate frame for downstream structural +analysis. The input is accepted, its topology and periodic-cell metadata are +available, and the preparation command produces finite coordinates. However, +inspection of the processed structure reveals local molecular dimensions that +are not credible for the chemical structure described by the input. + +Reproduce the observation, study the supplied scientific context and source +snapshot, then determine and repair the underlying project behavior. The repair +must preserve the documented public API, coordinate units, input semantics, and +normal behavior for valid trajectory data. It must be a general repair rather +than a special case for the supplied molecule or coordinate file. + +Do not modify the supplied fixture, supporting task context, or generated +reports, and do not special-case the archived input. + +Run the offline public diagnostic before and after your changes: + +```bash +python reproduce.py +``` + +The diagnostic provides an inspectable scientific observation rather than a +complete correctness oracle. diff --git a/tasks/task_057/metadata.json b/tasks/task_057/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..ceb7065c141eaafc2da2c1273abbdb3b140c7147 --- /dev/null +++ b/tasks/task_057/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "057", + "title": "Investigate a periodic trajectory-processing anomaly", + "domain": "molecular-dynamics-trajectory-analysis", + "language": "python", + "source_repository": "https://github.com/mdtraj/mdtraj", + "source_commit": "b963d4f01290fef66cca714e4a53f4891096b69a", + "source_license": "LGPL-2.1-family", + "license_source": "LICENSE", + "gpl_family": true, + "public_payload_sha256": "0274c5f903a8b34858e57c8d192eb528d3610c6be05065ef78c5ebbd27498b83" +} diff --git a/tasks/task_057/task.toml b/tasks/task_057/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..5b3fc0f5cfba6462ca73e0715c4e156a9a7b626e --- /dev/null +++ b/tasks/task_057/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-057" +description = "Investigate a periodic trajectory-processing anomaly" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "057" +language = "python" +base_commit_hash = "b963d4f01290fef66cca714e4a53f4891096b69a" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-057:v0.1.0@sha256:0a86aec644a934e46f0ebaaa25220b8fe0d792d942e15aab2dda03dae893eb80" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_057" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-057:v0.1.0@sha256:3a837ea554c65947e01e90be6998b561e6d5a0c64e6c29119e156026e4f5ce56" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_057" + +[[verifier.collect]] +command = "cd /app/task_057 && git config --global --add safe.directory /app/task_057 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_057/tests/Dockerfile b/tasks/task_057/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..2d228042214b4a3301032146803242c99c60b5bb --- /dev/null +++ b/tasks/task_057/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-057:v0.1.0@sha256:3a837ea554c65947e01e90be6998b561e6d5a0c64e6c29119e156026e4f5ce56 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_057/tests/test.sh b/tasks/task_057/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_057/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_058/environment/Dockerfile b/tasks/task_058/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..269f3180161d3b91502efa67014bd352c1ce4ecd --- /dev/null +++ b/tasks/task_058/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.12-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=1 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_058 +COPY repo/ /app/task_058/source/ +COPY public/ /app/task_058/ +COPY requirements.lock /app/task_058/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_058:/app/task_058/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_058/instruction.md b/tasks/task_058/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..eb77f03d19f855f61e9e4382713856eccea0c931 --- /dev/null +++ b/tasks/task_058/instruction.md @@ -0,0 +1,30 @@ +# Repair a valid OpenMC fixed-source workflow + +You are repairing a historical source snapshot of OpenMC, a Monte Carlo +particle-transport code used in reactor, shielding, detector, and other +radiation-transport studies. + +A research workflow exports the supplied fixed-source model successfully, but +the transport calculation terminates without producing a usable scientific +result. A separate minimal calculation in the same environment completes, so +the reported behavior is not explained by a missing compiler, an unavailable +Python package, or absent online nuclear data. + +Reproduce the observation, inspect the complete source snapshot, and use the +bundled paper and official documentation to determine why this valid model is +not handled correctly. Repair the underlying implementation while preserving +the documented OpenMC input model, public Python API, and behavior of other +supported calculations. The repair must describe and implement a general +scientific/numerical rule; it must not special-case the supplied files or their +literal values. + +Run the public observation with: + +```bash +python reproduce.py +``` + +The public command is a smoke test, not a complete oracle. Generated files are +written below `outputs/`. Do not edit the fixtures, the reproduction program, +or generated reports to claim success. Changes should be made in `source/` and +must remain buildable and runnable without network access. diff --git a/tasks/task_058/metadata.json b/tasks/task_058/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..3811bbd888e9dd78c9a8624b14c2e90ed44fd919 --- /dev/null +++ b/tasks/task_058/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "058", + "title": "Repair a valid OpenMC fixed-source workflow", + "domain": "monte-carlo-particle-transport", + "language": "python-cpp", + "source_repository": "", + "source_commit": "", + "source_license": "MIT", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "b630748484220716e8abd0185080b07930f00d71b51c1cef8e052642220fc750" +} diff --git a/tasks/task_058/task.toml b/tasks/task_058/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..000873fbd04f951c09026ea8cdd863b5f05df58d --- /dev/null +++ b/tasks/task_058/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-058" +description = "Repair a valid OpenMC fixed-source workflow" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "058" +language = "python-cpp" +base_commit_hash = "" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-cpp-task-058:v0.1.0@sha256:7e911bae59ef2a509e72cc8cc5454ae94d1fcf2cf560613de773aae3b419b78a" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_058" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-cpp-task-058:v0.1.0@sha256:e2b0260ac34ef381c86af8c808838ddb9a1ccc2cc4ece1b52c3cadf25625abfc" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_058" + +[[verifier.collect]] +command = "cd /app/task_058 && git config --global --add safe.directory /app/task_058 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_058/tests/Dockerfile b/tasks/task_058/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..e3e06238ac3bdcc881944627c597bd5be10c8e96 --- /dev/null +++ b/tasks/task_058/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-cpp-task-058:v0.1.0@sha256:e2b0260ac34ef381c86af8c808838ddb9a1ccc2cc4ece1b52c3cadf25625abfc +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_058/tests/test.sh b/tasks/task_058/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_058/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_059/environment/Dockerfile b/tasks/task_059/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..a65bdfbf986850f3284a75b5aa1971233556cfce --- /dev/null +++ b/tasks/task_059/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_059 +COPY repo/ /app/task_059/source/ +COPY public/ /app/task_059/ +COPY requirements.lock /app/task_059/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_059:/app/task_059/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_059/instruction.md b/tasks/task_059/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..2c0c5ba55635c32b8742101ef3cb07786eaeaa5b --- /dev/null +++ b/tasks/task_059/instruction.md @@ -0,0 +1,28 @@ +# Restore physical consistency in a calibrated cell measurement workflow + +I am validating a quantitative-phase microscopy workflow. The supplied image +is a real cell image, and the workflow segments it and measures the resulting +region through the project's ordinary measurement API. The same kind of object +can be represented on a sampling grid whose intervals are different along the +two image axes. The program completes, but the resulting shape record is not +consistent with the physical-coordinate interpretation described by the +provided scientific material. + +Please inspect the supplied method paper, the image-data reference, the source +snapshot, and the public reproduction. Determine why the calibrated +measurements are inconsistent and repair the source so that the scientific +behavior is correct for valid inputs in general. Preserve the public API and +backwards-compatible behavior for ordinary unit sampling. The repair must work +for other masks, intensities, dimensionalities, coordinate origins, and valid +sampling intervals; do not hard-code the supplied image, threshold, dimensions, +or recorded output values. + +The public command is: + +```bash +python reproduce.py +``` + +The public reproduction is only a workflow smoke test over one complete +measurement record. Use it to inspect the project behavior, then trace the +complete scientific computation and validate your repair on new inputs. diff --git a/tasks/task_059/metadata.json b/tasks/task_059/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..48d20c5cee63a440d972f3d7d6f9ae3940007c5c --- /dev/null +++ b/tasks/task_059/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "059", + "title": "Restore physical consistency in calibrated cell morphometry", + "domain": "microscopy-image-analysis", + "language": "python", + "source_repository": "https://github.com/scikit-image/scikit-image", + "source_commit": "e4e3ab682f0ff13460877624ecf068b9652ae071", + "source_license": "BSD-3-Clause", + "license_source": "LICENSE.txt", + "gpl_family": false, + "public_payload_sha256": "901ed621baea7c793b6ec8f1278ce8a570ffd0d08cdef7aacda99e36258ae651" +} diff --git a/tasks/task_059/task.toml b/tasks/task_059/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..2a27e05dc1e82358229ee077cf31ef99d85b0cdd --- /dev/null +++ b/tasks/task_059/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-059" +description = "Restore physical consistency in calibrated cell morphometry" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "059" +language = "python" +base_commit_hash = "e4e3ab682f0ff13460877624ecf068b9652ae071" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-059:v0.1.0@sha256:dec04a1b4fb9014d3f4f70f06966546d3d6055b56a3f1d4ffb8066152d8cff44" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_059" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-059:v0.1.0@sha256:2dda66b63502d81c2e09a7b0311ca76b3796dc1cd28349f9ece060a35795c8b0" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_059" + +[[verifier.collect]] +command = "cd /app/task_059 && git config --global --add safe.directory /app/task_059 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_059/tests/Dockerfile b/tasks/task_059/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..8ee054c5e0392b3c162f94fbb39c1194dd4e4b5e --- /dev/null +++ b/tasks/task_059/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-059:v0.1.0@sha256:2dda66b63502d81c2e09a7b0311ca76b3796dc1cd28349f9ece060a35795c8b0 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_059/tests/test.sh b/tasks/task_059/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_059/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_060/environment/Dockerfile b/tasks/task_060/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..9e0fed025e81144396dac0515da279be03e3fad3 --- /dev/null +++ b/tasks/task_060/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_060 +COPY repo/ /app/task_060/source/ +COPY public/ /app/task_060/ +COPY requirements.lock /app/task_060/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_060:/app/task_060/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_060/instruction.md b/tasks/task_060/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..c734deb6ea30cde656e502864db1bc2eb9662f46 --- /dev/null +++ b/tasks/task_060/instruction.md @@ -0,0 +1,15 @@ +# Restore a complete cross-band drift-correction recording + +An electrophysiology group archived the Neuropixels AP and LF streams and the +registration track supplied with this task. The track is used with the LF +acquisition context to correct a region of the AP recording before downstream +spike analysis. All inputs load through the historical SpikeInterface source +snapshot, but the complete corrected recording cannot be materialized into a +scientifically usable result. + +Run the offline reproduction, inspect the full source, real acquisition +metadata, project manuals, and papers, and repair the implementation so this +normal workflow completes. The repair must preserve the intended physical +registration for other valid recordings and registration tracks supported by +the project. Do not hard-code this session, its channel region, its track, or +the public report, and do not modify the supplied scientific inputs. diff --git a/tasks/task_060/metadata.json b/tasks/task_060/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..298807820b1f77ee7991c4e68d1a03c511b46e6e --- /dev/null +++ b/tasks/task_060/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "060", + "title": "Restore a complete cross-band drift-correction recording", + "domain": "high-density-extracellular-electrophysiology", + "language": "python", + "source_repository": "https://github.com/SpikeInterface/spikeinterface", + "source_commit": "3fd3d97164c6e85c2897ce8b13ba6aace81c2811", + "source_license": "MIT", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "d172cc3adb3c04d7f5cdcac22ceae69e26c0d3d3b429fd08a70725fbf50781c2" +} diff --git a/tasks/task_060/task.toml b/tasks/task_060/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..1e2062d3350d109568d60ea6423b4c6381561c19 --- /dev/null +++ b/tasks/task_060/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-060" +description = "Restore a complete cross-band drift-correction recording" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "060" +language = "python" +base_commit_hash = "3fd3d97164c6e85c2897ce8b13ba6aace81c2811" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-060:v0.1.0@sha256:61af28db733eec1188ad8b90a4a78404e88b7bfb17cf99800b543292c9545747" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_060" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-060:v0.1.0@sha256:d1a95a1456b922044d1cfa9156bf33ba40628a3115b2ff25b4d6b149dfd1f4bf" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_060" + +[[verifier.collect]] +command = "cd /app/task_060 && git config --global --add safe.directory /app/task_060 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_060/tests/Dockerfile b/tasks/task_060/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..f2cd8bb7fdb62e58ce15e86414eb07c0b340133e --- /dev/null +++ b/tasks/task_060/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-060:v0.1.0@sha256:d1a95a1456b922044d1cfa9156bf33ba40628a3115b2ff25b4d6b149dfd1f4bf +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_060/tests/test.sh b/tasks/task_060/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_060/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_061/environment/Dockerfile b/tasks/task_061/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..6a31ddf3dc7957cad695d2895abc184f257037b5 --- /dev/null +++ b/tasks/task_061/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_061 +COPY repo/ /app/task_061/source/ +COPY public/ /app/task_061/ +COPY requirements.lock /app/task_061/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_061:/app/task_061/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_061/instruction.md b/tasks/task_061/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..5fc0c58cccf8e9ac8ad7059717c0ea0c87f6c53c --- /dev/null +++ b/tasks/task_061/instruction.md @@ -0,0 +1,38 @@ +# Repair inconsistent celestial image representation in a mosaic + +A calibrated FITS cutout is being placed onto a different valid celestial grid +and combined through the project's documented conservative mosaicking +workflow. The operation completes and the generated arrays are finite, but the +source measurement and resolved image are not consistent with the scientific +meaning that the accompanying material assigns to this representation change. +The target frame covers the supplied cutout; this is not an out-of-bounds or +missing-data case. + +Use the complete source snapshot, the supplied scientific material, the FITS +fixtures, and the public reproduction to investigate the inconsistency. Repair +the implementation so that supported celestial images and WCS representations +preserve the documented scientific meaning of the data. + +Do not modify the supplied fixtures or generated reports. Do not hard-code the +public image, its dimensions, sky position, pixel values, WCS coefficients, or +the observed disagreement. Preserve documented public behavior and the APIs +used by existing workflows. + +Run the smoke reproduction before and after your changes: + +```bash +python reproduce.py +``` + +The command reports the scientific observation rather than deciding whether a +repair is correct; use the measurements together with the supplied method +material and the complete source. + +After changing the supplied package source, rebuild it before rerunning the +reproduction: + +```bash +cd source +python setup.py build_ext --inplace +cd .. +``` diff --git a/tasks/task_061/metadata.json b/tasks/task_061/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..af65927100ff01a923463f90bebdc0a1d751585d --- /dev/null +++ b/tasks/task_061/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "061", + "title": "Repair inconsistent celestial image representation in a mosaic", + "domain": "astronomical-image-processing", + "language": "python-c", + "source_repository": "https://github.com/astropy/reproject", + "source_commit": "62a0d3f037024d4dcf67857fb83d392f2e099ec0", + "source_license": "BSD-3-Clause", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "3545f63f2d7b0f876e372badde8358dd51214f78bf0aa2e1a226547b0c480ce4" +} diff --git a/tasks/task_061/task.toml b/tasks/task_061/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..a64ce4a20cd1fb2d9a5567eda68b147c2541a4f4 --- /dev/null +++ b/tasks/task_061/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-061" +description = "Repair inconsistent celestial image representation in a mosaic" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "061" +language = "python-c" +base_commit_hash = "62a0d3f037024d4dcf67857fb83d392f2e099ec0" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-c-task-061:v0.1.0@sha256:a69139dfab9d10122d07187ba52e0218c8c3f8350e3d44926c5813c8700bbcbf" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_061" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-c-task-061:v0.1.0@sha256:c0c05b7f3e36a5a4ede6443d7ce6f26522e8ae09db9baf5b14c16741039a7e07" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_061" + +[[verifier.collect]] +command = "cd /app/task_061 && git config --global --add safe.directory /app/task_061 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_061/tests/Dockerfile b/tasks/task_061/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..710cea1c1dfb9c789ad241a79ee2db73fbf3a8a5 --- /dev/null +++ b/tasks/task_061/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-c-task-061:v0.1.0@sha256:c0c05b7f3e36a5a4ede6443d7ce6f26522e8ae09db9baf5b14c16741039a7e07 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_061/tests/test.sh b/tasks/task_061/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_061/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_062/environment/Dockerfile b/tasks/task_062/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..c30f67debd607615d7a25975c0474fb7a0bc6d65 --- /dev/null +++ b/tasks/task_062/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_062 +COPY repo/ /app/task_062/source/ +COPY public/ /app/task_062/ +COPY requirements.lock /app/task_062/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_062:/app/task_062/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_062/instruction.md b/tasks/task_062/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..43dd56de5d5db211d1e8bd5190abc9f7afdc2cc0 --- /dev/null +++ b/tasks/task_062/instruction.md @@ -0,0 +1,19 @@ +# Repair an inconsistent archived elasticity workflow + +A computational-materials group is replaying the complete archived silicon +campaign supplied with this task. The historical workflow parses every +calculation and produces a finite elasticity document, but a downstream +scientific audit cannot reconcile the recorded campaign and fitted response +with the stress-strain method governing the supplied workflow. Repeating the +workflow does not change the discrepancy, and no archived first-principles +calculation reports a runtime failure. + +Run the offline reproduction, inspect the ordinary project output, complete +source snapshot, and task context, then repair the implementation so that +supported elasticity campaigns produce scientifically consistent records and +fitted responses. The repair must generalize to other valid crystal structures, +loading schedules, and coordinate representations supported by the project. + +Do not hard-code silicon, archived numeric results, calculation identifiers, or +fixture paths. Do not replace the workflow with a fabricated document, and do +not modify the supplied scientific inputs or generated reports. diff --git a/tasks/task_062/metadata.json b/tasks/task_062/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..62640466ba6b0ae3ffbd3a6d06f7c916c90bb296 --- /dev/null +++ b/tasks/task_062/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "062", + "title": "Repair an inconsistent archived elasticity workflow", + "domain": "computational-materials-science", + "language": "python", + "source_repository": "https://github.com/materialsproject/atomate2", + "source_commit": "95b15d576f47923e1f200c0894915a8f46675291", + "source_license": "BSD-3-Clause", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "a848f093dd0e16bc9b440ab1cda38b126cdc559d1261b5acc095292febc7eaac" +} diff --git a/tasks/task_062/task.toml b/tasks/task_062/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..4de6ba7af706b3fad2bb20bf89de799f9485dc3b --- /dev/null +++ b/tasks/task_062/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-062" +description = "Repair an inconsistent archived elasticity workflow" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "062" +language = "python" +base_commit_hash = "95b15d576f47923e1f200c0894915a8f46675291" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-062:v0.1.0@sha256:71b7a7f56a39dc1f3fa7d2ee034dbde903e373cc231b6584e542bb1eac6d8e9c" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_062" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-062:v0.1.0@sha256:b40392404273078f316aafdbee792923cdea10b8023ea733abe38ebb8ab5582a" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_062" + +[[verifier.collect]] +command = "cd /app/task_062 && git config --global --add safe.directory /app/task_062 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_062/tests/Dockerfile b/tasks/task_062/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..3bce1b7d134c9d8a58bc6f1dd4d02d5fafa923a2 --- /dev/null +++ b/tasks/task_062/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-062:v0.1.0@sha256:b40392404273078f316aafdbee792923cdea10b8023ea733abe38ebb8ab5582a +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_062/tests/test.sh b/tasks/task_062/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_062/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_063/environment/Dockerfile b/tasks/task_063/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..650c14111349beb6629ef4b6a21510343bf9a7b0 --- /dev/null +++ b/tasks/task_063/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_063 +COPY repo/ /app/task_063/source/ +COPY public/ /app/task_063/ +COPY requirements.lock /app/task_063/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_063:/app/task_063/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_063/instruction.md b/tasks/task_063/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..989fa32ff6bf89a13482caea65ea327944fb1d76 --- /dev/null +++ b/tasks/task_063/instruction.md @@ -0,0 +1,24 @@ +# Task 063 + +A population-genetics consortium is auditing two frozen exports of the same +cohort after a routine archive-curation operation. Both exports load, pass the +project's structural validation, retain the same samples and recorded +genealogical relationships, and produce finite reports. However, the inferred +population-history profiles disagree even though the curation was intended to +preserve the represented scientific study. + +Run the supplied offline audit, then investigate both exports, the historical +source, original papers, and supplied documentation. Repair the scientific +implementation under `source/` so that the ordinary cohort workflow is +consistent with the documented tree-sequence model. The repair must generalize +to other valid tree sequences and supported population-history analyses. + +Do not replace either export, hard-code this cohort, or bypass the workflow. +The public reproduction is one end-to-end diagnostic case; the scientific +behavior must generalize beyond it. + +Run: + +```bash +python reproduce.py +``` diff --git a/tasks/task_063/metadata.json b/tasks/task_063/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..10743bea077c042f6996154300644115a457cc04 --- /dev/null +++ b/tasks/task_063/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "063", + "title": "Repair inconsistent population-history estimates after archive curation", + "domain": "population-genetics-tree-sequence-statistics", + "language": "c-python", + "source_repository": "https://github.com/tskit-dev/tskit", + "source_commit": "", + "source_license": "MIT", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "05453c091458a8e2993e55e7114290a7e6aace041b41c59d8adae6ad38a2b926" +} diff --git a/tasks/task_063/task.toml b/tasks/task_063/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..31d9f9c95e82c1c944df4e2784eb51695312eb5d --- /dev/null +++ b/tasks/task_063/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-063" +description = "Repair inconsistent population-history estimates after archive curation" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "063" +language = "c-python" +base_commit_hash = "" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-c-python-task-063:v0.1.0@sha256:77cb395977290ee08c9d9abd184bcb8d874d8b78a5d55119ad8832b912b58e7e" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_063" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-c-python-task-063:v0.1.0@sha256:1f0346e1c5241487bb858955411ebf920e9bd53b37dcbb8aef37abd4c6dbe550" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_063" + +[[verifier.collect]] +command = "cd /app/task_063 && git config --global --add safe.directory /app/task_063 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_063/tests/Dockerfile b/tasks/task_063/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..ce7e9fb10c52c7abac4af7b5b5fb96459e028864 --- /dev/null +++ b/tasks/task_063/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-c-python-task-063:v0.1.0@sha256:1f0346e1c5241487bb858955411ebf920e9bd53b37dcbb8aef37abd4c6dbe550 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_063/tests/test.sh b/tasks/task_063/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_063/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_064/environment/Dockerfile b/tasks/task_064/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..08ea07e82e9f3f03a4d46d2c14a5d9f25a3d5350 --- /dev/null +++ b/tasks/task_064/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_064 +COPY repo/ /app/task_064/source/ +COPY public/ /app/task_064/ +COPY requirements.lock /app/task_064/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_064:/app/task_064/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_064/instruction.md b/tasks/task_064/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..52a60518340e3989842ce19af8a075e732b3c4ec --- /dev/null +++ b/tasks/task_064/instruction.md @@ -0,0 +1,15 @@ +# Task 064 + +Run the supplied offline reproduction first: + +```bash +python reproduce.py +``` + +Then inspect the real calculation log, the supplied scientific method note, the common data model, and the parser workflow. The visible symptom is a finite but scientifically inconsistent energy interpretation, not a parser crash. Determine which records in the program output describe the same physical calculation and how an optional pairwise correction should participate in the canonical result. + +Repair the source snapshot under `source/`. Keep the public API usable for callers that use the normal top-level parser entry point. The implementation should generalize across supported output versions and calculation modes of the supplied program family: equivalent scientific quantities may appear more than once in a calculation, and one logfile may contain more than one ordered calculation record. + +Your change must preserve the documented sign and unit conventions, keep records associated with their calculation, and leave ordinary calculations without the optional contribution unchanged. Do not hard-code the supplied molecule, input filename, output values, or one exact line layout. Do not modify the fixture to hide the symptom and do not bypass the parser with a task-specific script. + +Use the supplied paper note and source documentation as the offline scientific references. You may add small local tests while investigating, but the final repair should be in the source library rather than in `reproduce.py`. diff --git a/tasks/task_064/metadata.json b/tasks/task_064/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..3571a5ed071828e5f4c8e9c1b8a63f0ab717b313 --- /dev/null +++ b/tasks/task_064/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "064", + "title": "Repair inconsistent molecular-energy interpretation in a quantum-chemistry log parser", + "domain": "computational-chemistry-scientific-data-parsing", + "language": "python", + "source_repository": "https://github.com/cclib/cclib", + "source_commit": "593f0d67cf6a76f4a047f9a4856125c05947cff4", + "source_license": "BSD-3-Clause", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "0b96d317b1b43ecc2a8d1727fd30caf20ac76ad01657eb178e8c18394806b734" +} diff --git a/tasks/task_064/task.toml b/tasks/task_064/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..d524d4b516bcc28cba9d7293fadc4029ee7c1ce1 --- /dev/null +++ b/tasks/task_064/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-064" +description = "Repair inconsistent molecular-energy interpretation in a quantum-chemistry log parser" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "064" +language = "python" +base_commit_hash = "593f0d67cf6a76f4a047f9a4856125c05947cff4" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-064:v0.1.0@sha256:fce98569a3f9c8039892d8411355e49e07633af201083c67501c8fb69f9844a1" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_064" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-064:v0.1.0@sha256:b5b5a01003841af0fd902d84d9b78cc6208d641b22503bff9c325de16c113dbb" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_064" + +[[verifier.collect]] +command = "cd /app/task_064 && git config --global --add safe.directory /app/task_064 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_064/tests/Dockerfile b/tasks/task_064/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..151f8eb2e092d6532e1e88169f72c6712bd3f0c3 --- /dev/null +++ b/tasks/task_064/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-064:v0.1.0@sha256:b5b5a01003841af0fd902d84d9b78cc6208d641b22503bff9c325de16c113dbb +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_064/tests/test.sh b/tasks/task_064/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_064/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_065/environment/Dockerfile b/tasks/task_065/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..2d99599b90e6d7db427f209015cc1434b86005f2 --- /dev/null +++ b/tasks/task_065/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_065 +COPY repo/ /app/task_065/source/ +COPY public/ /app/task_065/ +COPY requirements.lock /app/task_065/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_065:/app/task_065/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_065/instruction.md b/tasks/task_065/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..4c948bd8b482af35d36d9e3a5aa20a5cc5ff9b68 --- /dev/null +++ b/tasks/task_065/instruction.md @@ -0,0 +1,22 @@ +# Task 065 + +The supplied project is used to inspect fields reconstructed from particles in +hydrodynamic simulations. A normal analysis workflow completes on the bundled +workload and produces finite observations, but a reported scientific quantity +can change when the same particle data are used through another valid numerical +representation. This can affect comparisons between otherwise compatible +analyses rather than merely changing the appearance of a plot. + +Read the accompanying method material and the local visualization notes. Run +the public reproduction first, then inspect the historical source and trace the +ordinary public workflows that load the particle data and construct the +observations. Repair the implementation so that the documented scientific +quantity is correct and stable for supported representations of the same +physical input. + +The change must be a general repair to the project under `source/`. Do not +replace the workload, edit the public reproduction to hide the observation, or +hard-code its values. Use the supplied scientific definitions and the source's +public API to investigate the discrepancy, and validate the repair with input +variations of your own. Keep the public API usable and preserve valid behavior +outside the reported case. diff --git a/tasks/task_065/metadata.json b/tasks/task_065/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..95b81d60e1db1df082c1ca5bca1707abe4364f6b --- /dev/null +++ b/tasks/task_065/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "065", + "title": "Repair inconsistent particle-field visualization results", + "domain": "astrophysical hydrodynamics and particle-based field visualization", + "language": "python", + "source_repository": "https://github.com/yt-project/yt", + "source_commit": "c86781b8cbdeea8002c7846d37dc1250045146e6", + "source_license": "BSD-3-Clause", + "license_source": "COPYING.txt", + "gpl_family": false, + "public_payload_sha256": "05e8764a37e3a9fe27c6802af7806b2b394b54c801c88ee9f929e90102959500" +} diff --git a/tasks/task_065/task.toml b/tasks/task_065/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..4e04f5850e6b317199ff312ff2b4589218e3f8dd --- /dev/null +++ b/tasks/task_065/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-065" +description = "Repair inconsistent particle-field visualization results" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "065" +language = "python" +base_commit_hash = "c86781b8cbdeea8002c7846d37dc1250045146e6" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-065:v0.1.0@sha256:5c8c8b8c130b06f1871f1c74a2b0ca0f453519e94d50b6cd3e08b9d873b7d3c9" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_065" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-065:v0.1.0@sha256:2ef10bcb562ab83a9b5641f22a91a4e4a607d231ea8f58194795cb4a324a5efe" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_065" + +[[verifier.collect]] +command = "cd /app/task_065 && git config --global --add safe.directory /app/task_065 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_065/tests/Dockerfile b/tasks/task_065/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..61bcf8fa46895db583f4b4baab9b24b0214b0510 --- /dev/null +++ b/tasks/task_065/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-065:v0.1.0@sha256:2ef10bcb562ab83a9b5641f22a91a4e4a607d231ea8f58194795cb4a324a5efe +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_065/tests/test.sh b/tasks/task_065/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_065/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_066/environment/Dockerfile b/tasks/task_066/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..5bea08dfcc5104b96412077b32be1fd664ece840 --- /dev/null +++ b/tasks/task_066/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_066 +COPY repo/ /app/task_066/source/ +COPY public/ /app/task_066/ +COPY requirements.lock /app/task_066/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_066:/app/task_066/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_066/instruction.md b/tasks/task_066/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..ba35dcb460654ec42dfdebf2f13d6815b4a6151d --- /dev/null +++ b/tasks/task_066/instruction.md @@ -0,0 +1,28 @@ +# Repair an inconsistent regional climate-validation workflow + +A climate-data group is validating a regional precipitation event against the +supplied station observations. The model field loads, remains finite, and has +the expected shape, but the completed regional validation is inconsistent with +the observations. The supplied model and station files are valid inputs for +this workflow. + +Run the public reproduction, study the supplied CF and project material, and +inspect the complete historical source snapshot. Repair the implementation so +that the scientific workflow behaves consistently for valid inputs rather than +only the supplied case. + +Do not hard-code the supplied dimensions, values, file name, or report outcome. +Do not modify the fixture, task statement, workflow, or evaluation +infrastructure. Work only under this task directory and modify the source +snapshot as needed. + +Run the public smoke test from the task root with: + +```bash +python reproduce.py +``` + +The untouched source is expected to produce a finite but inconsistent +scientific result. A correct repair should make the public validation +consistent. Import, fixture, dependency, and unrelated execution failures must +remain distinct from the scientific result. diff --git a/tasks/task_066/metadata.json b/tasks/task_066/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..8d435bcabdd2185dd02bb6407ec7a6f79e42968e --- /dev/null +++ b/tasks/task_066/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "066", + "title": "Restore regional climate-model validation consistency", + "domain": "earth-science-data-semantics", + "language": "python", + "source_repository": "https://github.com/SciTools/iris", + "source_commit": "0b569cdfad5e67f4aec3562bb26460020c7c7354", + "source_license": "AGPL-family", + "license_source": "COPYING", + "gpl_family": true, + "public_payload_sha256": "fbd0a732b640ea057c4f339c9c9de0d96c17f7e8a93a68e178f37df5471defc6" +} diff --git a/tasks/task_066/task.toml b/tasks/task_066/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..095fc5484ee6991ed97053f28bd11e2ab1959abf --- /dev/null +++ b/tasks/task_066/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-066" +description = "Restore regional climate-model validation consistency" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "066" +language = "python" +base_commit_hash = "0b569cdfad5e67f4aec3562bb26460020c7c7354" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-066:v0.1.0@sha256:16eacda2003745c9ea63286b07df5be4ba9bdf27b737761abf3ab0cfe8b6be34" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_066" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-066:v0.1.0@sha256:bf551e3cb78adb7a896b69485af7688c98815988094971978b7b41a2ae89c548" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_066" + +[[verifier.collect]] +command = "cd /app/task_066 && git config --global --add safe.directory /app/task_066 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_066/tests/Dockerfile b/tasks/task_066/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..8d7fae1c770ec6d39b0f12af45939da3a28a465a --- /dev/null +++ b/tasks/task_066/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-066:v0.1.0@sha256:bf551e3cb78adb7a896b69485af7688c98815988094971978b7b41a2ae89c548 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_066/tests/test.sh b/tasks/task_066/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_066/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_067/environment/Dockerfile b/tasks/task_067/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..d9894f9d0f2c65e92875c99f3e9fb563e74640e5 --- /dev/null +++ b/tasks/task_067/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_067 +COPY repo/ /app/task_067/source/ +COPY public/ /app/task_067/ +COPY requirements.lock /app/task_067/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_067:/app/task_067/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_067/instruction.md b/tasks/task_067/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..a4264a96d5f7c3a25d01a3e858c93f34d1f3ccf0 --- /dev/null +++ b/tasks/task_067/instruction.md @@ -0,0 +1,30 @@ +# Repair a seasonal fire-weather calculation + +A climate-analysis group is reproducing a seasonal fire-weather workflow from +the complete historical source snapshot in `source/`. The workflow completes +on the supplied station histories and returns finite arrays, but its seasonal +trajectory is not consistent with the task's scientific definitions. + +Use the source snapshot, `fixtures/seasonal_weather_case.json`, task context, +and the public reproduction to investigate the discrepancy. Run +`python reproduce.py` before and after your changes. Repair the project +implementation, not the scientific input or the public experiment. + +Your solution must: + +- preserve the documented public xarray-facing workflow and supported unit + conversions; +- preserve the stateful interpretation of the FWI method when a seasonal mask + changes over time; +- remain correct for other valid seasonal histories, initial states, masks, + time layouts, and small spatial arrays; +- preserve ordinary continuous-season calculations when no seasonal gap is + present; and +- avoid hard-coding this fixture, dates, station names, output values, or source + filenames. + +Inspect the scientific inputs and references, form and test your own +hypotheses, and repair the underlying implementation rather than manufacturing +agreement in the fixture, public experiment, or generated report. Do not +modify `fixtures/`, `reproduce.py`, or generated reports to hide a +source defect. diff --git a/tasks/task_067/metadata.json b/tasks/task_067/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..859ccf61b25454c4311363dbd9a7431b2d7e2e72 --- /dev/null +++ b/tasks/task_067/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "067", + "title": "Repair a seasonal fire-weather state transition", + "domain": "climate-fire-weather", + "language": "python", + "source_repository": "https://github.com/Ouranosinc/xclim", + "source_commit": "d1e654cf59a5d5761f5586bca1102a1590ae6e32", + "source_license": "Apache-2.0", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "c92bab50be2064b2be6a92409c8b291f4c4187ddbe02bde1c154b45dc361c15d" +} diff --git a/tasks/task_067/task.toml b/tasks/task_067/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..2025ba0435f5123e699a500d73f9eb4d430a82b8 --- /dev/null +++ b/tasks/task_067/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-067" +description = "Repair a seasonal fire-weather state transition" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "067" +language = "python" +base_commit_hash = "d1e654cf59a5d5761f5586bca1102a1590ae6e32" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-067:v0.1.0@sha256:293c50d411ea2c322e9b62189e5bf325abbb814682b1eb4dabec9555d035c78e" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_067" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-067:v0.1.0@sha256:fbbdf79e55e67535ee836f497be5aaf61412c5fe68b6856959217589e144e71c" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_067" + +[[verifier.collect]] +command = "cd /app/task_067 && git config --global --add safe.directory /app/task_067 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_067/tests/Dockerfile b/tasks/task_067/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..78223ec1dd4d196bcb0cbacc86ddb7811cbeda4f --- /dev/null +++ b/tasks/task_067/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-067:v0.1.0@sha256:fbbdf79e55e67535ee836f497be5aaf61412c5fe68b6856959217589e144e71c +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_067/tests/test.sh b/tasks/task_067/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_067/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_068/environment/Dockerfile b/tasks/task_068/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..ce4123729a2213a82e25f37404a7472082f7168d --- /dev/null +++ b/tasks/task_068/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=1 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_068 +COPY repo/ /app/task_068/source/ +COPY public/ /app/task_068/ +COPY requirements.lock /app/task_068/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_068:/app/task_068/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_068/instruction.md b/tasks/task_068/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..30a2aebf71af613b689a93c78cfa73f5baec308c --- /dev/null +++ b/tasks/task_068/instruction.md @@ -0,0 +1,15 @@ +# Restore biologically consistent retrieval from a VCF archive + +A cohort-analysis workflow stores a local VCF archive and retrieves records by +genomic region. The supplied archive slice is accepted by the command-line +workflow, but a record that should be relevant to an interior genomic location +is absent from the result. A nearby control query still returns a record, so +the run looks superficially healthy while changing the biological interpretation +of the archive search. + +Run the supplied reproduction, inspect the source snapshot, and use the local +VCF specifications to repair the implementation. The corrected software must +give biologically consistent behavior for valid supported records, not merely +for the supplied archive slice. Do not hard-code the example's chromosome, +coordinates, record count, or a fixed output. + diff --git a/tasks/task_068/metadata.json b/tasks/task_068/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..6cfad4b5534b6c3fb31214f2b5ac66825cd133ae --- /dev/null +++ b/tasks/task_068/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "068", + "title": "Restore biologically consistent retrieval from a VCF archive", + "domain": "genomic-variant-data-semantics", + "language": "c", + "source_repository": "https://github.com/samtools/htslib", + "source_commit": "a4dde3f93c75dff09e9a1ddaf0db2e54c91ac5e3", + "source_license": "BSD-3-Clause", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "200dced78b8f36c974b68150c631e9247accbaf38a5b7ccea50c46cee503252a" +} diff --git a/tasks/task_068/task.toml b/tasks/task_068/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..9f81b0de2f0f1de368b481cfca6e3c20582110a1 --- /dev/null +++ b/tasks/task_068/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-068" +description = "Restore biologically consistent retrieval from a VCF archive" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "068" +language = "c" +base_commit_hash = "a4dde3f93c75dff09e9a1ddaf0db2e54c91ac5e3" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-c-task-068:v0.1.0@sha256:f08ff570bf57595b94e6fb3bc0f603e76d7b6de53f6c7c76199a099eee12fdd3" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_068" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-c-task-068:v0.1.0@sha256:333ed6fc1e4953d3abe1517a2871c1a2fb19ca0996d8d91bca6406898dac57ad" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_068" + +[[verifier.collect]] +command = "cd /app/task_068 && git config --global --add safe.directory /app/task_068 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_068/tests/Dockerfile b/tasks/task_068/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..98d6f527fd3a58f0fd1c27d9254f43eef76273ad --- /dev/null +++ b/tasks/task_068/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-c-task-068:v0.1.0@sha256:333ed6fc1e4953d3abe1517a2871c1a2fb19ca0996d8d91bca6406898dac57ad +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_068/tests/test.sh b/tasks/task_068/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_068/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_069/environment/Dockerfile b/tasks/task_069/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..c9ae8b1ef54a9996ee8dc6d09bc0d2b2dcd05aec --- /dev/null +++ b/tasks/task_069/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_069 +COPY repo/ /app/task_069/source/ +COPY public/ /app/task_069/ +COPY requirements.lock /app/task_069/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_069:/app/task_069/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_069/instruction.md b/tasks/task_069/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..9cdf4cde37ee40bdb6ba8b993b4f0983a2ea58c4 --- /dev/null +++ b/tasks/task_069/instruction.md @@ -0,0 +1,18 @@ +# Restore a complete Hi-C contact-decay analysis + +A chromatin-conformation group is replaying an archived Hi-C contact map from +an experiment whose later bin-level annotations were not retained with the +interaction archive. The group needs the usual intrachromosomal +distance-dependent contact analysis as a baseline for subsequent work. + +The supplied map is a valid offline archive and the included workflow is an +ordinary project workflow. On the historical source, however, that workflow +does not produce a complete scientific report. This is inconsistent with the +contact-map interpretation described in the supplied scientific material. + +Run the reproduction, inspect the source and the reference material, and repair +the implementation so that the intended analysis is scientifically consistent +for valid inputs. The repair must generalise: do not hard-code the supplied +archive, a chromosome name, a map resolution, a count pattern, or a fixed +numeric result. Do not modify fixtures, the reproduction harness, generated +reports, task metadata, or task instructions. diff --git a/tasks/task_069/metadata.json b/tasks/task_069/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..35dbf3066a7e106fdd06117751697cb90a3cc58b --- /dev/null +++ b/tasks/task_069/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "069", + "title": "Restore a complete Hi-C contact-decay analysis", + "domain": "genomics-contact-map-analysis", + "language": "python", + "source_repository": "https://github.com/open2c/cooltools", + "source_commit": "ba2be42c714fffb6b62ea13e7ecfbecb5f4a4d9a", + "source_license": "MIT", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "ed9582b82d4025b1253ad670bf256d2a1e402152a08828511804b787c2299d21" +} diff --git a/tasks/task_069/task.toml b/tasks/task_069/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..b174734678c6b848dd0859eedf2736de4f690661 --- /dev/null +++ b/tasks/task_069/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-069" +description = "Restore a complete Hi-C contact-decay analysis" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "069" +language = "python" +base_commit_hash = "ba2be42c714fffb6b62ea13e7ecfbecb5f4a4d9a" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-069:v0.1.0@sha256:104bacda92f0419c80454a4bd632d472b6ef53ac89c24c176266d226c3bfd7ba" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_069" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-069:v0.1.0@sha256:d879cd88dc547a45e25105bb4aec34c8c1acaf22d97bc858719692283e547819" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_069" + +[[verifier.collect]] +command = "cd /app/task_069 && git config --global --add safe.directory /app/task_069 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_069/tests/Dockerfile b/tasks/task_069/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..fff6a5326a199b21a7457447f21fe644bae6f991 --- /dev/null +++ b/tasks/task_069/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-069:v0.1.0@sha256:d879cd88dc547a45e25105bb4aec34c8c1acaf22d97bc858719692283e547819 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_069/tests/test.sh b/tasks/task_069/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_069/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_070/environment/Dockerfile b/tasks/task_070/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..b8e00d24c782e8fcced1fffd216f6de87fd3b700 --- /dev/null +++ b/tasks/task_070/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_070 +COPY repo/ /app/task_070/source/ +COPY public/ /app/task_070/ +COPY requirements.lock /app/task_070/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_070:/app/task_070/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_070/instruction.md b/tasks/task_070/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..4f86466153bc576af5a017c3f9cb35040a4e2de0 --- /dev/null +++ b/tasks/task_070/instruction.md @@ -0,0 +1,19 @@ +# Restore chemically consistent proteoform ion annotations + +A proteomics curation group is replaying a small offline precursor-annotation +batch supplied with this task. Every record is intended to be legal under the +included ProForma material, and the historical source can parse the batch. +However, the workflow does not yield a complete table of usable precursor +observations. The reproduction records the candidate precursor measurements it +does obtain, as well as unavailable observations. A present measurement is +evidence from the historical workflow, not by itself a correctness certificate. + +Run the offline reproduction, inspect the source and the supplied scientific +material, and repair the implementation so that valid annotations are handled +consistently with the ProForma definition. The repair must generalize across +valid inputs supported by the project, not merely make the supplied records +finish. + +Do not hard-code a record identifier, annotation string, output count, or fixed +numeric result. Do not modify the supplied fixtures, reproduction script, or +generated reports. diff --git a/tasks/task_070/metadata.json b/tasks/task_070/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..3f89ea4315a79973ca4b636d4d74207dde8c0514 --- /dev/null +++ b/tasks/task_070/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "070", + "title": "Restore chemically consistent proteoform ion annotations", + "domain": "proteomics", + "language": "python", + "source_repository": "https://github.com/levitsky/pyteomics", + "source_commit": "f509b761a5231e9f108780c88c2b3781266e7b90", + "source_license": "Apache-2.0", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "3245e11806859843e00f907068319bf7bda844f2ef96396de5f571f8062aa7db" +} diff --git a/tasks/task_070/task.toml b/tasks/task_070/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..a749e2bcd8779a0d8c71019b9676486da37b4e85 --- /dev/null +++ b/tasks/task_070/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-070" +description = "Restore chemically consistent proteoform ion annotations" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "070" +language = "python" +base_commit_hash = "f509b761a5231e9f108780c88c2b3781266e7b90" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-070:v0.1.0@sha256:a54e1623ce467ff3366a5c064753a7f72c27e2443e5bc14d075ce42bf65768de" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_070" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-070:v0.1.0@sha256:65428a9c41233b574b2d31746f8968a2d3387bad708ec99f7e142256461d17a3" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_070" + +[[verifier.collect]] +command = "cd /app/task_070 && git config --global --add safe.directory /app/task_070 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_070/tests/Dockerfile b/tasks/task_070/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..d1486820257e2bca519264a396a766921a33f593 --- /dev/null +++ b/tasks/task_070/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-070:v0.1.0@sha256:65428a9c41233b574b2d31746f8968a2d3387bad708ec99f7e142256461d17a3 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_070/tests/test.sh b/tasks/task_070/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_070/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_071/environment/Dockerfile b/tasks/task_071/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..11061f83820d7442a00a79eac37186b26eb709bb --- /dev/null +++ b/tasks/task_071/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_071 +COPY repo/ /app/task_071/source/ +COPY public/ /app/task_071/ +COPY requirements.lock /app/task_071/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_071:/app/task_071/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_071/instruction.md b/tasks/task_071/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..e1d768fa5ee77aea3064c6a6206aeee0a90bb726 --- /dev/null +++ b/tasks/task_071/instruction.md @@ -0,0 +1,17 @@ +# Repair an orientation-sensitive fiber-scattering reduction + +A grazing-incidence/fiber diffraction reduction was run on a detector-panel +acquisition whose fiber-axis orientation convention is recorded in the +experimental setup. The workflow completes, but changing that supported +acquisition setting produces a reciprocal-space observation whose movement is +inconsistent with the supplied scattering geometry for an asymmetric panel. +That makes it difficult to interpret whether observed features are in-plane or +out-of-plane. + +Use the supplied offline source, scientific material, and reproduction +workbench to investigate the discrepancy and repair the implementation. The +orientation value in this task belongs to the project's Fiber/sample-axis +workflow; it is not the separate detector metadata enum. The repair must work +for the supported Fiber orientation conventions generally, not only for the +provided panel. Do not modify task metadata, fixtures, the public runner, or +the evaluation harness. Place your solution in `artifacts/model.patch`. diff --git a/tasks/task_071/metadata.json b/tasks/task_071/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..01c31281703a99ae24d60e715fb83fb221707948 --- /dev/null +++ b/tasks/task_071/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "071", + "title": "Repair an orientation-sensitive fiber-scattering reduction", + "domain": "grazing-incidence-and-fiber-x-ray-scattering", + "language": "python", + "source_repository": "https://github.com/silx-kit/pyFAI", + "source_commit": "3a7adedc45c9a94585ec19bbd4622ac9f483ab9c", + "source_license": "UNKNOWN", + "license_source": "not-detected", + "gpl_family": false, + "public_payload_sha256": "a594aff3f42be0d163e6fc22059215b3192da8418a22bb76724ae9799f7f36b0" +} diff --git a/tasks/task_071/task.toml b/tasks/task_071/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..1601b8dd45a5dcc65ef6fb0a3d7d3c67ba6aae82 --- /dev/null +++ b/tasks/task_071/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-071" +description = "Repair an orientation-sensitive fiber-scattering reduction" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "071" +language = "python" +base_commit_hash = "3a7adedc45c9a94585ec19bbd4622ac9f483ab9c" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-071:v0.1.0@sha256:08968262336c765e8d683cc867e2e0c3db50a99cee923ea8fa000bf4523a843d" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_071" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-071:v0.1.0@sha256:0039c955ffd15cd0020334c375dd24e6c41c1b1b2a6b59b392c647db32c47882" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_071" + +[[verifier.collect]] +command = "cd /app/task_071 && git config --global --add safe.directory /app/task_071 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_071/tests/Dockerfile b/tasks/task_071/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..424973a2c094369a7a50ebad355497df4c1cd1e6 --- /dev/null +++ b/tasks/task_071/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-071:v0.1.0@sha256:0039c955ffd15cd0020334c375dd24e6c41c1b1b2a6b59b392c647db32c47882 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_071/tests/test.sh b/tasks/task_071/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_071/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_072/environment/Dockerfile b/tasks/task_072/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..fab5cfbbd583dbd94dcdc88c9f9c194525e16a47 --- /dev/null +++ b/tasks/task_072/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_072 +COPY repo/ /app/task_072/source/ +COPY public/ /app/task_072/ +COPY requirements.lock /app/task_072/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_072:/app/task_072/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_072/instruction.md b/tasks/task_072/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..2c8f3312c68b7f337378a20876d3f505e7632245 --- /dev/null +++ b/tasks/task_072/instruction.md @@ -0,0 +1,16 @@ +# Repair an incomplete DICOM color image presentation workflow + +A medical-imaging research workflow is replaying a small local suite of color +objects through the historical source snapshot. The objects are local, valid +for the workbench, and their stored color samples can be decoded into finite +numeric arrays. However, the normal scientific presentation suite does not +complete with consistent color-image representations for all objects. + +Run the public reproduction, inspect the source code and the supplied DICOM and +pixel-data reference material, and repair the implementation so that supported +DICOM color images are interpreted consistently by the public pixel workflow. +The repair must generalize beyond the supplied files and must not hard-code a +filename, array shape, sample value, or fixed output. + +Do not modify the fixture, public reproduction script, generated reports, or +task metadata. diff --git a/tasks/task_072/metadata.json b/tasks/task_072/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..3b86c5fcbb7e6e137dfafafee345f8dbef8731e3 --- /dev/null +++ b/tasks/task_072/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "072", + "title": "Repair an incomplete DICOM color image presentation workflow", + "domain": "medical-imaging-color-pixel-semantics", + "language": "python", + "source_repository": "https://github.com/pydicom/pydicom", + "source_commit": "b69de21c8610853493bc81d3eac79644554e4bda", + "source_license": "MIT", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "c918fcb63e5730461495bdda55df23582e82cb3a33361cc7a15f54e2a039d9b0" +} diff --git a/tasks/task_072/task.toml b/tasks/task_072/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..c6be63b49c4e61b34a13dc2865e6ce5d18b0bbf5 --- /dev/null +++ b/tasks/task_072/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-072" +description = "Repair an incomplete DICOM color image presentation workflow" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "072" +language = "python" +base_commit_hash = "b69de21c8610853493bc81d3eac79644554e4bda" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-072:v0.1.0@sha256:c9746b594a561e16a92a0718356d2bde20f564a61d882bbce1af3bcd1658dad3" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_072" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-072:v0.1.0@sha256:8683aa3c574011f36df457c54a443457cd37078c2ca48f85fcb46015c431b31d" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_072" + +[[verifier.collect]] +command = "cd /app/task_072 && git config --global --add safe.directory /app/task_072 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_072/tests/Dockerfile b/tasks/task_072/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..a0bb595cbdf53e5bcb1fa40174f5f2bb3889a066 --- /dev/null +++ b/tasks/task_072/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-072:v0.1.0@sha256:8683aa3c574011f36df457c54a443457cd37078c2ca48f85fcb46015c431b31d +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_072/tests/test.sh b/tasks/task_072/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_072/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_073/environment/Dockerfile b/tasks/task_073/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..3dcb8666c04e68c4097b9ebec4277913685c0dc7 --- /dev/null +++ b/tasks/task_073/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_073 +COPY repo/ /app/task_073/source/ +COPY public/ /app/task_073/ +COPY requirements.lock /app/task_073/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_073:/app/task_073/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_073/instruction.md b/tasks/task_073/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..382d5be56506995d533544d7d8d1597eec205e45 --- /dev/null +++ b/tasks/task_073/instruction.md @@ -0,0 +1,15 @@ +You are investigating a Biotite PDBx/mmCIF structure-loading workflow. + +The supplied local structure is a valid biomolecular input, but the public +reproduction completes with an unexpectedly fragmented connectivity summary. + +Run `python reproduce.py` from this task directory, inspect the source snapshot +and the accompanying structural-biology notes, and repair the implementation so +that the supported PDBx/mmCIF structure-loading workflows produce scientifically +consistent atom and connectivity observations for valid inputs. The repair must +generalize beyond the provided structure, residue numbers, atom indices, and one +fixed bond count. + +Preserve the documented meanings of the loader's supported options and +representations, so that returned atoms and connectivity remain interpretable +for the requested PDBx/mmCIF workflow rather than only for this one fixture. diff --git a/tasks/task_073/metadata.json b/tasks/task_073/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..7a881c9702e4085fe175091a961790ce62c1cb30 --- /dev/null +++ b/tasks/task_073/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "073", + "title": "Repair inconsistent alternate-conformer structure connectivity", + "domain": "structural-biology-pdbx-macromolecular-connectivity", + "language": "python", + "source_repository": "https://github.com/biotite-dev/biotite", + "source_commit": "f8c3b8aa5473e078f91c86dcee7340eb9ed3eb97", + "source_license": "BSD-3-Clause", + "license_source": "LICENSE.rst", + "gpl_family": false, + "public_payload_sha256": "4750773214e103b4927e1cfa74f838b86bd0b9fcf3e9f49a25844b17e06b6e24" +} diff --git a/tasks/task_073/task.toml b/tasks/task_073/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..1f96cb6de848f18dab3690f7dc95e2e74b7a7377 --- /dev/null +++ b/tasks/task_073/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-073" +description = "Repair inconsistent alternate-conformer structure connectivity" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "073" +language = "python" +base_commit_hash = "f8c3b8aa5473e078f91c86dcee7340eb9ed3eb97" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-073:v0.1.0@sha256:fca7d2514acb9214baf529a5d4bfddbe5e165ba24cbea63cb4d380f5f5bea483" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_073" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-073:v0.1.0@sha256:6041a2f1f781e1e02e908984c07c6de7a1e2edd67a3ce90529522ebc2e72aee8" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_073" + +[[verifier.collect]] +command = "cd /app/task_073 && git config --global --add safe.directory /app/task_073 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_073/tests/Dockerfile b/tasks/task_073/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..2603c1fea4f78e20d36028df29173c8ffd837f21 --- /dev/null +++ b/tasks/task_073/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-073:v0.1.0@sha256:6041a2f1f781e1e02e908984c07c6de7a1e2edd67a3ce90529522ebc2e72aee8 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_073/tests/test.sh b/tasks/task_073/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_073/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_074/environment/Dockerfile b/tasks/task_074/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..43188682130f3f9fed3076f57cd94105cb991c4d --- /dev/null +++ b/tasks/task_074/environment/Dockerfile @@ -0,0 +1,70 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_074 +COPY repo/ /app/task_074/source/ +COPY public/ /app/task_074/ +COPY requirements.lock /app/task_074/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && env -u HTTP_PROXY -u HTTPS_PROXY -u ALL_PROXY \ + -u http_proxy -u https_proxy -u all_proxy \ + python -m pip install --no-cache-dir \ + --index-url https://download.pytorch.org/whl/cpu \ + torch==2.5.1+cpu \ + && python -m pip install --no-cache-dir -r requirements.lock \ + && env -u HTTP_PROXY -u HTTPS_PROXY -u ALL_PROXY \ + -u http_proxy -u https_proxy -u all_proxy \ + python -m pip install --no-cache-dir \ + --find-links https://data.pyg.org/whl/torch-2.5.0+cpu.html \ + torch-scatter==2.1.2 +ENV PYTHONPATH=/app/task_074:/app/task_074/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_074/instruction.md b/tasks/task_074/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..872f9683b272eec18f8faa39101497a9566540d3 --- /dev/null +++ b/tasks/task_074/instruction.md @@ -0,0 +1,36 @@ +# Repair an ill-conditioned overlap band-postprocessing workflow + +A materials post-processing workflow uses the supplied scientific package to +compute band energies for a non-orthogonal tight-binding model. The input +matrices are Hermitian and represent a valid inference-time case where the +overlap basis contains nearly redundant modes. The workflow should still return +finite, reusable band data and a downstream Fermi-level estimate for the +physical states it can resolve. + +Study the supplied paper notes, source snapshot, and public reproduction. Repair +the implementation so that the post-processing workflow preserves the scientific +meaning of generalized eigenvalues when the overlap basis becomes poorly +conditioned. The repair must generalize beyond the bundled matrices and must not +replace the calculation with fixed outputs, special-case the fixture, or change +the public reproduction to hide a failure. + +Treat this as an explicitly requested handling mode for the supplied workflow. +Ordinary calls that do not request this treatment should keep their existing +behavior rather than silently reclassifying unresolved overlap modes as usable +band states. Any metadata used by downstream consumers to distinguish resolved +states from dense padding should correspond one-to-one with the returned band +entries. + +Work only under this task directory. The evaluation environment is Linux and +has no network access. You may modify files under `source/`; do not modify the +task statement, reproduction, fixtures, workflow, or evaluation infrastructure. + +Run the public smoke test with: + +```bash +python reproduce.py +``` + +The command returns `1` when the untouched source reproduces the scientific +post-processing failure, `0` after a successful repair, and `2` for a runner or +environment failure. diff --git a/tasks/task_074/metadata.json b/tasks/task_074/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..740a8a4c9d96b5fbf44318e5d08841c8a6d369f1 --- /dev/null +++ b/tasks/task_074/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "074", + "title": "Repair an ill-conditioned overlap band-postprocessing workflow", + "domain": "electronic-structure-nonorthogonal-eigenproblems", + "language": "python", + "source_repository": "https://github.com/deepmodeling/DeePTB", + "source_commit": "e365079ea71190aaa0dc96d22253d3888c47abf9", + "source_license": "LGPL-3.0-family", + "license_source": "LICENSE", + "gpl_family": true, + "public_payload_sha256": "ad672fdf766b9ec695c2a3fc0ef10ff87623c0c0ca31d0dcef02fcc67b8bb9ae" +} diff --git a/tasks/task_074/task.toml b/tasks/task_074/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..3cfe19422ba19602886c95953335b8a042272c40 --- /dev/null +++ b/tasks/task_074/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-074" +description = "Repair an ill-conditioned overlap band-postprocessing workflow" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "074" +language = "python" +base_commit_hash = "e365079ea71190aaa0dc96d22253d3888c47abf9" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-074:v0.1.0@sha256:717c4de698523729922644dc8f42dbf98071dbe48c25cf1016d425d2ceb0e49f" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_074" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-074:v0.1.0@sha256:874067a5199b4db19f575c074b7cd51c1eddf03f7aa13c97810ea2873c917d86" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_074" + +[[verifier.collect]] +command = "cd /app/task_074 && git config --global --add safe.directory /app/task_074 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_074/tests/Dockerfile b/tasks/task_074/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..6f457f9bbf9704eb3cfa45daae06d3cd2a65ffaa --- /dev/null +++ b/tasks/task_074/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-074:v0.1.0@sha256:874067a5199b4db19f575c074b7cd51c1eddf03f7aa13c97810ea2873c917d86 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_074/tests/test.sh b/tasks/task_074/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_074/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_075/environment/Dockerfile b/tasks/task_075/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..b874214000d04df91842bb77d9d6ff0caf1aab4b --- /dev/null +++ b/tasks/task_075/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=1 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_075 +COPY repo/ /app/task_075/source/ +COPY public/ /app/task_075/ +COPY requirements.lock /app/task_075/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_075:/app/task_075/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_075/instruction.md b/tasks/task_075/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..0e06dd2c39c13347fd0b5a59eaa9e79784405249 --- /dev/null +++ b/tasks/task_075/instruction.md @@ -0,0 +1,29 @@ +# Restore consistent compressed Deep Potential tabulation + +A molecular-simulation group is evaluating a compressed Deep Potential +workflow using the supplied C++ source snapshot. The calculation completes and +returns finite descriptor contributions and finite sensitivity values, but a +small sweep of compressed-table observations is not consistent with the +energy-force relationship described by the supplied scientific material. + +Run the public reproduction, study the supplied paper and method material, and +inspect the complete source snapshot. The public command is a diagnostic +workbench: read its finite observations rather than treating process success as +scientific correctness. Repair the implementation so that valid +compressed-model tabulation workflows preserve the same scientific meaning for +descriptor values and their sensitivities across supported descriptor families +and valid table configurations. + +The repair must generalize beyond the public probe. Do not hard-code the +public coefficients, coordinates, report values, descriptor family, or generated +driver. Do not replace the scientific calculation with a fixed report or change +the task material to hide the inconsistency. + +Work only under this task directory. The evaluation environment is Linux, +offline, and provides a C++ compiler. You may modify files under `source/`. + +Run the public diagnostic with: + +```bash +python reproduce.py +``` diff --git a/tasks/task_075/metadata.json b/tasks/task_075/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..f240bce1ffa650e66c62dae634f90f4a07380bbd --- /dev/null +++ b/tasks/task_075/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "075", + "title": "Restore consistent compressed Deep Potential tabulation", + "domain": "molecular-dynamics-machine-learning-potentials", + "language": "c++", + "source_repository": "https://github.com/deepmodeling/deepmd-kit", + "source_commit": "a9bcbc505de7d905dbc2a598b10c17a49e0131d8", + "source_license": "LGPL-3.0-family", + "license_source": "LICENSE", + "gpl_family": true, + "public_payload_sha256": "086c38f2b97dbfebbece51b6f558f80eb85378ff99409b964ffc36f4c082ef3e" +} diff --git a/tasks/task_075/task.toml b/tasks/task_075/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..443de0f521dfdcaf8d6c372c632f90c5eb95b50b --- /dev/null +++ b/tasks/task_075/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-075" +description = "Restore consistent compressed Deep Potential tabulation" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "075" +language = "c++" +base_commit_hash = "a9bcbc505de7d905dbc2a598b10c17a49e0131d8" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-c-task-075:v0.1.0@sha256:7beaf3765d9cf49e2d3f647833f63266dfa15bc9978b753755050a66a7ec15dc" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_075" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-c-task-075:v0.1.0@sha256:c50d05f06eee0035eb02e057017cbdbfae6a9855a900ac819bb90b937285a022" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_075" + +[[verifier.collect]] +command = "cd /app/task_075 && git config --global --add safe.directory /app/task_075 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_075/tests/Dockerfile b/tasks/task_075/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..b8fda75a112e0f383b8a3accc26e421b5158c456 --- /dev/null +++ b/tasks/task_075/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-c-task-075:v0.1.0@sha256:c50d05f06eee0035eb02e057017cbdbfae6a9855a900ac819bb90b937285a022 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_075/tests/test.sh b/tasks/task_075/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_075/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_076/environment/Dockerfile b/tasks/task_076/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..4edd07c6e67b90b9a0116fb519f110f467b3fe6c --- /dev/null +++ b/tasks/task_076/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_076 +COPY repo/ /app/task_076/source/ +COPY public/ /app/task_076/ +COPY requirements.lock /app/task_076/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_076:/app/task_076/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_076/instruction.md b/tasks/task_076/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..d48d92dfd8606f679deaee9c706a0e25db685047 --- /dev/null +++ b/tasks/task_076/instruction.md @@ -0,0 +1,24 @@ +# Repair a batched parametric tracking workflow + +A small tracking model uses reusable array-shaped data to represent a sequence +of linear dynamics terms. The supplied source can construct the model, but the +public smoke test does not complete on the untouched source. + +Study the supplied paper and docs, reproduce the failure, and repair the +implementation so the same valid tracking workflow compiles and solves +consistently for the public fixture and related supported cases. Keep the fix +general: do not flatten the model into a different scientific formulation, +hard-code the fixture, or replace the solved trajectory with canned outputs. + +Work only under this task directory. The evaluation environment is Linux and +has no network access. You may modify files under `source/`; do not modify the +task statement, reproduction, fixtures, workflow, or evaluation infrastructure. + +Run the public smoke test with: + +```bash +python reproduce.py +``` + +The command returns `1` when the untouched source reproduces the failure, `0` +after a successful repair, and `2` for a runner or environment failure. diff --git a/tasks/task_076/metadata.json b/tasks/task_076/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..1bb0e24895059b5b6e888039de218734c95ab000 --- /dev/null +++ b/tasks/task_076/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "076", + "title": "Repair a batched parametric tracking workflow", + "domain": "convex-optimization-parametric-workflows", + "language": "python", + "source_repository": "https://github.com/cvxpy/cvxpy", + "source_commit": "5f57b6408864caab207c28f773a14c6261689abe", + "source_license": "Apache-2.0", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "c2303ccea73430e7cca4a82672bdf8c5ea7465237e18f465358267c979f4cb4d" +} diff --git a/tasks/task_076/task.toml b/tasks/task_076/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..b2c18fe8548d47596a5456a3c44d1fdae3305e0a --- /dev/null +++ b/tasks/task_076/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-076" +description = "Repair a batched parametric tracking workflow" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "076" +language = "python" +base_commit_hash = "5f57b6408864caab207c28f773a14c6261689abe" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-076:v0.1.0@sha256:1a50e20a9caf81566ac7f3f9d356b04b8352a7eb3532f8a5543307ef3f0670fe" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_076" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-076:v0.1.0@sha256:c40da6ce2cafe0194e2d74ca0380587b696890713c163a17624a855c86247404" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_076" + +[[verifier.collect]] +command = "cd /app/task_076 && git config --global --add safe.directory /app/task_076 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_076/tests/Dockerfile b/tasks/task_076/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..27509d8b071b8b169c9c09525684660f3de66037 --- /dev/null +++ b/tasks/task_076/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-076:v0.1.0@sha256:c40da6ce2cafe0194e2d74ca0380587b696890713c163a17624a855c86247404 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_076/tests/test.sh b/tasks/task_076/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_076/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_077/environment/Dockerfile b/tasks/task_077/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..cf62c8d6fb68e232332bffdfd0689d2d95ed8537 --- /dev/null +++ b/tasks/task_077/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_077 +COPY repo/ /app/task_077/source/ +COPY public/ /app/task_077/ +COPY requirements.lock /app/task_077/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_077:/app/task_077/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_077/instruction.md b/tasks/task_077/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..413b2575b37462aa6784815b79d283f7277977bc --- /dev/null +++ b/tasks/task_077/instruction.md @@ -0,0 +1,27 @@ +# Repair an inconsistent oriented-envelope fallback workflow + +The supplied point-cloud workflow runs without an exception, but one of its +geometry-engine routes returns rectangles that are not consistent with the +documented minimum-area meaning of an oriented envelope. The same API is used +both for individual point clouds and for NumPy-compatible geometry batches. + +Repair the supplied implementation so the public geometry API remains +offline, deterministic, and geometrically consistent for scalar and batch +workflows. Preserve the property aliases, degenerate point and line results, +and the shape, output-buffer, and container behavior expected by +NumPy-compatible array-like inputs. + +Valid inputs may use coordinates with large but finite magnitudes, including +shapes far from the origin. A uniform scaling of an input must yield a +correspondingly scaled, finite result; intermediate arithmetic must not make a +valid finite computation fail. + +Do not modify the fixtures or generated reports. Do not hard-code the public +sample or its derived geometry. Use the supplied source snapshot and public +reproduction to investigate the inconsistency. + +Run the public diagnostic with: + +```bash +python reproduce.py +``` diff --git a/tasks/task_077/metadata.json b/tasks/task_077/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..845adefad85747f9dff6fc88828e0d34ac811885 --- /dev/null +++ b/tasks/task_077/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "077", + "title": "Repair an inconsistent oriented-envelope fallback workflow", + "domain": "computational-geometry", + "language": "python", + "source_repository": "https://github.com/shapely/shapely", + "source_commit": "d2872f6c4d7c99b16f8a71d99cd56d0a5fe54695", + "source_license": "UNKNOWN", + "license_source": "not-detected", + "gpl_family": false, + "public_payload_sha256": "281a98b13117b5df40f97a7237a835fd669856b82c6afb0913e700dc35f33055" +} diff --git a/tasks/task_077/task.toml b/tasks/task_077/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..30ebd5ef802fc719f337069c83a791ef61c846b0 --- /dev/null +++ b/tasks/task_077/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-077" +description = "Repair an inconsistent oriented-envelope fallback workflow" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "077" +language = "python" +base_commit_hash = "d2872f6c4d7c99b16f8a71d99cd56d0a5fe54695" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-077:v0.1.0@sha256:c0164a3b9503d40d28bdb96503976e673fd0a29c924cfb24e198cd2698d1a2e8" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_077" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-077:v0.1.0@sha256:f9f3eb576dd41c94b0407e0a0395e1df75d6cad627be53a028bc995d4f66e633" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_077" + +[[verifier.collect]] +command = "cd /app/task_077 && git config --global --add safe.directory /app/task_077 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_077/tests/Dockerfile b/tasks/task_077/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..dbf41d78ab5955f77bb8dd208288c5cb8d6908c4 --- /dev/null +++ b/tasks/task_077/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-077:v0.1.0@sha256:f9f3eb576dd41c94b0407e0a0395e1df75d6cad627be53a028bc995d4f66e633 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_077/tests/test.sh b/tasks/task_077/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_077/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_078/environment/Dockerfile b/tasks/task_078/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..0f99d8be7c415a7eebcbe473282d561220fd987d --- /dev/null +++ b/tasks/task_078/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_078 +COPY repo/ /app/task_078/source/ +COPY public/ /app/task_078/ +COPY requirements.lock /app/task_078/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_078:/app/task_078/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_078/instruction.md b/tasks/task_078/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..727a6ee4acad6c4fee292a59262c588ecfc5048f --- /dev/null +++ b/tasks/task_078/instruction.md @@ -0,0 +1,27 @@ +# Repair an inconsistent astronomical aperture workflow + +An astronomical image-analysis workflow runs equivalent observation workloads +on several calibrated image grids. The calculations complete, but a normalized +scientific quantity changes when only the coordinate representation changes. + +Study the supplied scientific material and source snapshot. Run the public +workload survey, inspect the implementation, and repair the underlying +representation handling so the same physical workload gives the same +normalized quantity across finite, nonsingular calibrated maps, within normal +sampling and floating-point variation. The repair must generalize beyond the +supplied survey and must not hard-code a particular grid, angle, center, scale, +workload, or fixed numeric output. + +Work only under this task directory. The evaluation environment is offline; all +required Python dependencies and source material are provided. + +Run the public diagnostic with: + +```bash +python reproduce.py +``` + +The command returns `0` after producing a finite measurement survey and `2` +for an import, path, dependency, or other runner failure. The public report is +an observational workbench rather than a correctness oracle; the verifier +checks broader scientific consistency cases. diff --git a/tasks/task_078/metadata.json b/tasks/task_078/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..74248a7e4b69f871b3667e77752d64d232671f75 --- /dev/null +++ b/tasks/task_078/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "078", + "title": "Repair an inconsistent astronomical aperture workflow", + "domain": "astronomical-image-analysis-and-wcs-aperture-photometry", + "language": "python", + "source_repository": "", + "source_commit": "", + "source_license": "BSD-3-Clause", + "license_source": "LICENSE.rst", + "gpl_family": false, + "public_payload_sha256": "842e8b9cc90cfc2fa565d985ad1d43d880025e8237e60838f0d164d37f50f906" +} diff --git a/tasks/task_078/task.toml b/tasks/task_078/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..a2b819a7c2bcb4bb4ea919fbd251d33be2e0bacd --- /dev/null +++ b/tasks/task_078/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-078" +description = "Repair an inconsistent astronomical aperture workflow" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "078" +language = "python" +base_commit_hash = "" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-078:v0.1.0@sha256:5b91a58b57d7fd6c87dbbeab4daf50ef8f9deb08db5c5d8063d77eb67dcd93b1" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_078" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-078:v0.1.0@sha256:9a64793e10d20c2c0b719ae87a72d795435b24f5efb8577071b693ec88b6f882" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_078" + +[[verifier.collect]] +command = "cd /app/task_078 && git config --global --add safe.directory /app/task_078 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_078/tests/Dockerfile b/tasks/task_078/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..b49d9bae017a2e7ef025261c05566022a6509c06 --- /dev/null +++ b/tasks/task_078/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-078:v0.1.0@sha256:9a64793e10d20c2c0b719ae87a72d795435b24f5efb8577071b693ec88b6f882 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_078/tests/test.sh b/tasks/task_078/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_078/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_079/environment/Dockerfile b/tasks/task_079/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..8adc5c0fe9b3b1bf667ace4ccb61b948069bdf69 --- /dev/null +++ b/tasks/task_079/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_079 +COPY repo/ /app/task_079/source/ +COPY public/ /app/task_079/ +COPY requirements.lock /app/task_079/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_079:/app/task_079/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_079/instruction.md b/tasks/task_079/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..33ab86c71f3797cd612b0b81be6e1e9252446093 --- /dev/null +++ b/tasks/task_079/instruction.md @@ -0,0 +1,29 @@ +# Repair molecular-string translation for catalogue workflows + +A molecular-screening workflow uses the supplied source package to translate +SMILES strings into SELFIES and decode them back to concrete SMILES strings for +later processing. Several chemically varied catalogue entries complete this +workflow, but one library scaffold cannot be processed even though it follows +the documented surface API. + +Study the supplied paper notes, reproduce the failure, inspect the source, and +repair the implementation so that valid project molecules can pass through the +SMILES-to-SELFIES-to-SMILES workflow without losing their molecular meaning. +The repair must generalize beyond the supplied fixture. Do not return fixed +molecular strings, special-case the public inputs, loosen all scientific +constraints indiscriminately, or change the public reproduction to hide a +failure. + +Work only under this task directory. The evaluation environment is Linux and +has no network access. You may modify files under `source/`; do not modify the +task statement, fixtures, reproduction script, or evaluation infrastructure. + +Run the public smoke test with: + +```bash +python reproduce.py +``` + +The command returns `1` when the untouched source reproduces the molecular +translation failure, `0` after a successful repair, and `2` for a runner or +environment failure. diff --git a/tasks/task_079/metadata.json b/tasks/task_079/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..b9565124510d23249edeeca09b778be333cfcaff --- /dev/null +++ b/tasks/task_079/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "079", + "title": "Repair molecular-string translation for catalogue workflows", + "domain": "computational-chemistry-molecular-representations", + "language": "python", + "source_repository": "https://github.com/aspuru-guzik-group/selfies", + "source_commit": "55f4e3437b6fb68deafa533cb00277b119e6eb8a", + "source_license": "Apache-2.0", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "a4dd29c213c064d6ebe5d7024b329032ab8da4aedf0287da8de36c8964403d1f" +} diff --git a/tasks/task_079/task.toml b/tasks/task_079/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..aeabfec9182ff995cf5adbb574542bab25816d28 --- /dev/null +++ b/tasks/task_079/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-079" +description = "Repair molecular-string translation for catalogue workflows" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "079" +language = "python" +base_commit_hash = "55f4e3437b6fb68deafa533cb00277b119e6eb8a" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-079:v0.1.0@sha256:700ef06ac1ce8d1550984b274b58f9440ca378a240bdc3064e51ab1d302fcad6" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_079" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-079:v0.1.0@sha256:243dfa0eb24b77c5c08a9141b632177711d7f438177f0f737c0c2d453c14f7f4" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_079" + +[[verifier.collect]] +command = "cd /app/task_079 && git config --global --add safe.directory /app/task_079 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_079/tests/Dockerfile b/tasks/task_079/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..9a3218b3bb34801ec28ba851f54d10b618b7c265 --- /dev/null +++ b/tasks/task_079/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-079:v0.1.0@sha256:243dfa0eb24b77c5c08a9141b632177711d7f438177f0f737c0c2d453c14f7f4 +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_079/tests/test.sh b/tasks/task_079/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_079/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_080/environment/Dockerfile b/tasks/task_080/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..5070d3bdb78666b2e6cfc24fd7ef6656ba02d66b --- /dev/null +++ b/tasks/task_080/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_080 +COPY repo/ /app/task_080/source/ +COPY public/ /app/task_080/ +COPY requirements.lock /app/task_080/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_080:/app/task_080/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_080/instruction.md b/tasks/task_080/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..1c60ebb5bd68f9e0dbadaea4f6bc01f1db0c6316 --- /dev/null +++ b/tasks/task_080/instruction.md @@ -0,0 +1,23 @@ +# Task + +The source tree contains a pre-fix snapshot of xarray-spatial. A small +georeferenced surface and several clipped target views are included as an +offline workbench for the normal raster reprojection workflow. + +Run the public reproduction, study the supplied project material and source, +and repair the implementation so valid raster remapping respects the coordinate +geometry, nodata convention, and requested sampling method for supported input +grids. The repair must generalize to rasters and target views beyond the +included case. + +Work only in this task directory. You may modify files under `source/`. Do not +special-case the included raster, view names, report fields, or fixture values. + +Use: + +```bash +python reproduce.py +``` + +The report is a finite workflow observation. Evaluation uses additional +behavioral checks. diff --git a/tasks/task_080/metadata.json b/tasks/task_080/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..19a974318476fc26af056c077f4cc1ffbc28572a --- /dev/null +++ b/tasks/task_080/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "080", + "title": "Repair inconsistent geospatial raster remapping", + "domain": "geospatial-raster-reprojection", + "language": "python", + "source_repository": "https://github.com/xarray-contrib/xarray-spatial", + "source_commit": "7d252520dbf81b168a2789a6aedfb75d04a21061", + "source_license": "MIT", + "license_source": "LICENSE.txt", + "gpl_family": false, + "public_payload_sha256": "2e7d63a1052c7b94245de245deed7e14e20169bb0ad2447c854e4f1d6026fa6e" +} diff --git a/tasks/task_080/task.toml b/tasks/task_080/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..f3ccf501792a831b70e972095e140a9f92bb6108 --- /dev/null +++ b/tasks/task_080/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-080" +description = "Repair inconsistent geospatial raster remapping" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "080" +language = "python" +base_commit_hash = "7d252520dbf81b168a2789a6aedfb75d04a21061" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-080:v0.1.0@sha256:bd33e55e04ded03f1911abe6f673e4217c4fed04e14db72be630c1503cd10735" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_080" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-080:v0.1.0@sha256:0bd2b80b544ce97b0ecbab0c397a5d68014ee7cb2c3133be648db3d3ca0045ed" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_080" + +[[verifier.collect]] +command = "cd /app/task_080 && git config --global --add safe.directory /app/task_080 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_080/tests/Dockerfile b/tasks/task_080/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..6fa265481ff7e69261dda7ade1eae0385b53b31c --- /dev/null +++ b/tasks/task_080/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-080:v0.1.0@sha256:0bd2b80b544ce97b0ecbab0c397a5d68014ee7cb2c3133be648db3d3ca0045ed +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_080/tests/test.sh b/tasks/task_080/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_080/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_081/environment/Dockerfile b/tasks/task_081/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..b222870b3c94f78c068d86823957730819f04fc3 --- /dev/null +++ b/tasks/task_081/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_081 +COPY repo/ /app/task_081/source/ +COPY public/ /app/task_081/ +COPY requirements.lock /app/task_081/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_081:/app/task_081/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_081/instruction.md b/tasks/task_081/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..f53d7d31ee2aef2d98042ee27ed717d86032d641 --- /dev/null +++ b/tasks/task_081/instruction.md @@ -0,0 +1,24 @@ +# Repair Local Study Workflow + +You are working with a local snapshot of `anndata`, a Python package for +annotated single-cell data matrices. A small offline workflow under `fixtures/` + and `workflow/` processes multiple local study shards from the same experiment. + +Run the public workbench: + +```bash +python reproduce.py +``` + +Users have reported inconsistent behavior when the workflow output is passed +into later analysis steps. The public workbench runs a compact observation pass +over the local result. Repair the local source so the workflow produces +reliable outputs for small and large studies. + +Keep the fix inside `source/`. Do not modify the public fixtures, reproduction +script, or task metadata. Your repair should generalize beyond the supplied +files and should remain practical on larger studies. + +Do not hard-code values derived from the supplied inputs. Do not download +external data or use network access; all information needed for the public +workbench is already in this task directory. diff --git a/tasks/task_081/metadata.json b/tasks/task_081/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..34ea333378b3e8c642a49daec81a52bc95444366 --- /dev/null +++ b/tasks/task_081/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "081", + "title": "Repair local study workflow", + "domain": "single-cell-annotated-data-containers", + "language": "python", + "source_repository": "https://github.com/scverse/anndata", + "source_commit": "", + "source_license": "BSD-3-Clause", + "license_source": "LICENSE", + "gpl_family": false, + "public_payload_sha256": "d0c8f80b09a6b76fe96ceb4bb7c2fbccf23feb16a911a23d5aa81234e9f6cf7c" +} diff --git a/tasks/task_081/task.toml b/tasks/task_081/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..c7015c51cd33005cfff047b3b87222cfe81f0019 --- /dev/null +++ b/tasks/task_081/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-081" +description = "Repair local study workflow" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "081" +language = "python" +base_commit_hash = "" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-081:v0.1.0@sha256:6114de7210e1f47c1ad558a9ca8886105a5ecf5af6a8453a9c7732ac415a7431" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_081" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-081:v0.1.0@sha256:3a3f4428f0129a1302f743125649b4bea7445e57912bdd734ad3452389003efa" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_081" + +[[verifier.collect]] +command = "cd /app/task_081 && git config --global --add safe.directory /app/task_081 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_081/tests/Dockerfile b/tasks/task_081/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..f9091e46058969dfaeeaabc1a6a8b729d8962f34 --- /dev/null +++ b/tasks/task_081/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-081:v0.1.0@sha256:3a3f4428f0129a1302f743125649b4bea7445e57912bdd734ad3452389003efa +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_081/tests/test.sh b/tasks/task_081/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_081/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_082/environment/Dockerfile b/tasks/task_082/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..1bb3b5e6dbcb116369ca65c762ee5e0668398022 --- /dev/null +++ b/tasks/task_082/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_082 +COPY repo/ /app/task_082/source/ +COPY public/ /app/task_082/ +COPY requirements.lock /app/task_082/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_082:/app/task_082/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"] diff --git a/tasks/task_082/instruction.md b/tasks/task_082/instruction.md new file mode 100644 index 0000000000000000000000000000000000000000..57c9ce1f05f42db46f975116b33c5b1f8dc36016 --- /dev/null +++ b/tasks/task_082/instruction.md @@ -0,0 +1,12 @@ +# Task + +I am replaying a DP-GEN active-learning setup with the supplied source snapshot +and a small LAMMPS template. A valid settings record should produce consistent +generated input in the public workflow. + +Run `python reproduce.py` to inspect the observation. Repair the implementation +so the public workflow stays consistent across the documented settings +combinations. + +Do not hard-code the public fixture, a particular graph list, a specific +template line, or any fixed output text from the reproduction. diff --git a/tasks/task_082/metadata.json b/tasks/task_082/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..c1b309de0c96edbeba0425b14c5a18adc40ba356 --- /dev/null +++ b/tasks/task_082/metadata.json @@ -0,0 +1,12 @@ +{ + "task_id": "082", + "title": "Repair a workflow consistency bug", + "domain": "atomistic-machine-learning-and-molecular-simulation", + "language": "python", + "source_repository": "https://github.com/deepmodeling/dpgen", + "source_commit": "02a442c6bd7da9b5b2c9f958d3a103f5d6cd2a27", + "source_license": "UNKNOWN", + "license_source": "not-detected", + "gpl_family": false, + "public_payload_sha256": "2385deedff3d0a8ef16754877f091f473675d1dabfd7a965bd63a5d15ad6e987" +} diff --git a/tasks/task_082/task.toml b/tasks/task_082/task.toml new file mode 100644 index 0000000000000000000000000000000000000000..a9fe5d4cc6172f77b5ebeb40918a879ddf177fb0 --- /dev/null +++ b/tasks/task_082/task.toml @@ -0,0 +1,44 @@ +schema_version = "1.3" +artifacts = ["/logs/artifacts/model.patch"] + +[task] +name = "openmoss/swe-bench-science-082" +description = "Repair a workflow consistency bug" +authors = [] +keywords = ["scientific-computing", "software-engineering"] + +[metadata] +task_id = "082" +language = "python" +base_commit_hash = "02a442c6bd7da9b5b2c9f958d3a103f5d6cd2a27" + +[agent] +network_mode = "no-network" +timeout_sec = 5400.0 + +[environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-environment-python-task-082:v0.1.0@sha256:ff25e7997b4194fb53e3df8b71d48e8db25d299bf632ebebdb6a162925e73204" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_082" + +[verifier] +network_mode = "no-network" +environment_mode = "separate" +timeout_sec = 1800.0 + +[verifier.environment] +docker_image = "docker.io/kevinxulearning/swe-bench-science-verifier-python-task-082:v0.1.0@sha256:a829af72c8e716a904d83a590a865d07a7b9a31a8d4b7083afbf90b6611a937c" +os = "linux" +allow_internet = false +cpus = 2 +memory_mb = 8192 +storage_mb = 20480 +workdir = "/app/task_082" + +[[verifier.collect]] +command = "cd /app/task_082 && git config --global --add safe.directory /app/task_082 && baseline=$(git rev-list --max-parents=0 --reverse HEAD | head -n 1) && git add -A && git diff --cached --binary \"$baseline\" > /logs/artifacts/model.patch" +timeout_sec = 300.0 diff --git a/tasks/task_082/tests/Dockerfile b/tasks/task_082/tests/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..234208ad10d7ee9ba872afe72fb704d24f0e7bbb --- /dev/null +++ b/tasks/task_082/tests/Dockerfile @@ -0,0 +1,2 @@ +ARG VERIFIER_IMAGE=docker.io/kevinxulearning/swe-bench-science-verifier-python-task-082:v0.1.0@sha256:a829af72c8e716a904d83a590a865d07a7b9a31a8d4b7083afbf90b6611a937c +FROM ${VERIFIER_IMAGE} diff --git a/tasks/task_082/tests/test.sh b/tasks/task_082/tests/test.sh new file mode 100644 index 0000000000000000000000000000000000000000..714959da692677fd78953da0372dfeb595111b19 --- /dev/null +++ b/tasks/task_082/tests/test.sh @@ -0,0 +1,6 @@ +#!/bin/sh +set -eu + +# Pier requires a public tests entrypoint when loading a local task. In +# separate-verifier mode the executable grader remains inside the verifier image. +exec python /tests/grader.py diff --git a/tasks/task_083/environment/Dockerfile b/tasks/task_083/environment/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..d2ae7aaa3aaee7b5f70029d60bb53b249cc60dc8 --- /dev/null +++ b/tasks/task_083/environment/Dockerfile @@ -0,0 +1,60 @@ +ARG BASE_IMAGE=python:3.11-slim +FROM ${BASE_IMAGE} + +ARG DEBIAN_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian +ARG DEBIAN_SECURITY_MIRROR=https://mirrors.tuna.tsinghua.edu.cn/debian-security +ARG PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple +ARG INSTALL_FORTRAN=0 +ARG INSTALL_OCTAVE=0 +ENV DEBIAN_FRONTEND=noninteractive \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_INDEX_URL=${PIP_INDEX_URL} \ + PIP_NO_CACHE_DIR=1 \ + PYTHONDONTWRITEBYTECODE=1 + +RUN sed -i \ + -e "s|http://deb.debian.org/debian-security|${DEBIAN_SECURITY_MIRROR}|g" \ + -e "s|http://deb.debian.org/debian|${DEBIAN_MIRROR}|g" \ + /etc/apt/sources.list.d/debian.sources + +RUN apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + git \ + ripgrep \ + && rm -rf /var/lib/apt/lists/* + +RUN if [ "${INSTALL_FORTRAN}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends gfortran \ + && rm -rf /var/lib/apt/lists/*; \ + fi \ + && if [ "${INSTALL_OCTAVE}" = "1" ]; then \ + apt-get -o Acquire::Retries=10 update \ + && apt-get -o Acquire::Retries=10 install -y --no-install-recommends octave \ + && rm -rf /var/lib/apt/lists/*; \ + fi + +WORKDIR /app/task_083 +COPY repo/ /app/task_083/source/ +COPY public/ /app/task_083/ +COPY requirements.lock /app/task_083/requirements.lock + +RUN python -m pip install --no-cache-dir --upgrade pip \ + && python -m pip install --no-cache-dir -r requirements.lock +ENV PYTHONPATH=/app/task_083:/app/task_083/source + +RUN git init \ + && git checkout -b main \ + && git config user.email science-bench@example.invalid \ + && git config user.name "SWE-bench Science baseline" \ + && git add -A \ + && GIT_AUTHOR_DATE=2025-01-01T00:00:00Z \ + GIT_COMMITTER_DATE=2025-01-01T00:00:00Z \ + git commit -m baseline \ + && git reflog expire --expire=now --all \ + && git gc --prune=now + +CMD ["bash"]