[eval] Add ScienceAgentBench. (#4645)

Co-authored-by: Xingyao Wang <xingyao@all-hands.dev>

.gitignore

@@ -174,6 +174,7 @@ evaluation/bird/data
 evaluation/gaia/data
 evaluation/gorilla/data
 evaluation/toolqa/data
+evaluation/scienceagentbench/benchmark
 
 # frontend
 

evaluation/scienceagentbench/Dockerfile

@@ -0,0 +1,17 @@
+FROM python:3.11-bookworm
+
+
+# For OpenHands agents to explore the dataset directories, please download the full benchmark [here](https://buckeyemailosu-my.sharepoint.com/:u:/g/personal/chen_8336_buckeyemail_osu_edu/EQuA6uJ3CtRHvRfZ2GiN1tYBRVJE4DSUD10MW61fr7HuSQ?e=sCBegG) and unzip it with password `scienceagentbench`.
+# **Please DO NOT redistribute the unzipped data files online.**
+# It will download a benchmark.zip file to the current directory.
+# unzip it and put the benchmark folder under evaluation/scienceagentbench/
+
+RUN mkdir -p /benchmark
+COPY benchmark /benchmark
+
+RUN mkdir -p /workspace
+WORKDIR /workspace
+
+# pushd evaluation/scienceagentbench
+# docker build -t xingyaoww/openhands-eval-scienceagentbench .
+# popd

evaluation/scienceagentbench/Dockerfile.evaluator

@@ -0,0 +1,25 @@
+FROM mambaorg/micromamba:debian12
+
+USER root
+# For https://github.com/OSU-NLP-Group/ScienceAgentBench/tree/main?tab=readme-ov-file#code-generation-with-agents
+
+RUN micromamba create -n sci-agent-eval python=3.10 pip setuptools wheel
+RUN micromamba run -n sci-agent-eval pip install pip-tools
+
+RUN mkdir -p /workspace
+WORKDIR /workspace
+
+RUN apt-get update && apt-get install -y git
+
+RUN git clone https://github.com/OSU-NLP-Group/ScienceAgentBench.git /workspace/
+RUN git checkout 4eddc7db6449a5ade3e37285747c8b208cd54ce7
+
+RUN micromamba create -n sci-agent python=3.10 pip setuptools wheel
+RUN micromamba run -n sci-agent pip install -r requirements.txt
+
+# Replace all occurence of conda with micromamba under the /workspace
+RUN find ./ -type f -exec sed -i 's/conda/micromamba/g' {} \;
+
+# pushd evaluation/scienceagentbench
+# docker build -t xingyaoww/openhands-eval-scienceagentbench-evaluator -f Dockerfile.evaluator .
+# popd

evaluation/scienceagentbench/README.md

@@ -0,0 +1,54 @@
+# ScienceAgentBench Evaluation with OpenHands
+
+This folder contains the evaluation harness for [ScienceAgentBench](https://osu-nlp-group.github.io/ScienceAgentBench/) (paper: https://arxiv.org/abs/2410.05080).
+
+## Setup Environment and LLM Configuration
+
+Please follow instruction [here](../README.md#setup) to setup your local development environment and LLM.
+
+## Setup ScienceAgentBench
+
+To prevent benchmark data contamination, we only provide the annotation sheet on [Huggingface](https://huggingface.co/datasets/osunlp/ScienceAgentBench), which includes all necessary *inputs* to run an agent.
+
+## Run Inference on ScienceAgentBench
+
+```bash
+./evaluation/scienceagentbench/scripts/run_infer.sh [model_config] [git-version] [use_knowledge] [agent] [eval_limit] [max_iter] [num_workers] [dataset] [dataset_split]
+
+# Example
+./evaluation/scienceagentbench/scripts/run_infer.sh llm.eval_gpt4o 0.9.3
+```
+
+where `model_config` is mandatory, and the rest are optional.
+
+- `model_config`, e.g. `eval_gpt4_1106_preview`, is the config group name for your
+LLM settings, as defined in your `config.toml`.
+- `git-version`, e.g. `HEAD`, is the git commit hash of the OpenHands version you would
+like to evaluate. It could also be a release tag like `0.6.2`.
+- `use_knowledge`, e.g. `true`, specifies whether allowing the agent to use expert-provided knowledge as additional input or not. By default, it is set to `false`.
+- `agent`, e.g. `CodeActAgent`, is the name of the agent for benchmarks, defaulting
+to `CodeActAgent`.
+- `eval_limit`, e.g. `10`, limits the evaluation to the first `eval_limit` instances. By
+default, the script evaluates the entire SWE-bench_Lite test set (300 issues). Note:
+in order to use `eval_limit`, you must also set `agent`.
+- `max_iter`, e.g. `20`, is the maximum number of iterations for the agent to run. By
+default, it is set to 30.
+- `num_workers`, e.g. `3`, is the number of parallel workers to run the evaluation. By
+default, it is set to 1.
+
+## Evaluate Generated Programs
+
+### Extract Necessary Information from OpenHands Log
+
+After the inference is completed, you may use the following command to extract necessary information from the output log for evaluation:
+
+```bash
+python post_proc.py [log_fname]
+```
+- `log_fname`, e.g. `evaluation/.../output.jsonl`, is the automatically saved trajectory log of an OpenHands agent.
+
+Output will be write to e.g. `evaluation/.../output.converted.jsonl`
+
+### Run evaluation
+
+Please follow the steps [here](https://github.com/OSU-NLP-Group/ScienceAgentBench/tree/main?tab=readme-ov-file#evaluation-of-generated-code) to evaluate the generated programs.

evaluation/scienceagentbench/post_proc.py

@@ -0,0 +1,30 @@
+import json
+from argparse import ArgumentParser
+
+if __name__ == '__main__':
+    parser = ArgumentParser()
+    parser.add_argument(
+        'log_fname',
+        type=str,
+    )
+    args = parser.parse_args()
+
+    fname = args.log_fname
+    out_fname = args.log_fname.replace('.jsonl', '.converted.jsonl')
+
+    log = [json.loads(line) for line in open(fname)]
+
+    simple_log = [
+        json.dumps(
+            {
+                'instance_id': ex['instance_id'],
+                'instruction': ex['instruction'],
+                'test_result': ex['test_result'],
+                'cost': ex['metrics']['accumulated_cost'],
+            }
+        )
+        for ex in log
+    ]
+
+    with open(out_fname, 'w+', encoding='utf-8') as f:
+        f.write('\n'.join(simple_log))

evaluation/scienceagentbench/run_infer.py

@@ -0,0 +1,292 @@
+import asyncio
+import os
+from typing import Any
+
+import pandas as pd
+from datasets import load_dataset
+from tqdm import tqdm
+
+from evaluation.utils.shared import (
+    EvalMetadata,
+    EvalOutput,
+    codeact_user_response,
+    make_metadata,
+    prepare_dataset,
+    reset_logger_for_multiprocessing,
+    run_evaluation,
+)
+from openhands.controller.state.state import State
+from openhands.core.config import (
+    AppConfig,
+    SandboxConfig,
+    get_llm_config_arg,
+    get_parser,
+)
+from openhands.core.logger import openhands_logger as logger
+from openhands.core.main import create_runtime, run_controller
+from openhands.events.action import CmdRunAction, MessageAction
+from openhands.events.observation import CmdOutputObservation
+from openhands.runtime.base import Runtime
+from openhands.utils.async_utils import call_async_from_sync
+
+AGENT_CLS_TO_FAKE_USER_RESPONSE_FN = {
+    'CodeActAgent': codeact_user_response,
+}
+
+LOCAL_DATASET_PATH = os.path.join(os.path.dirname(__file__), 'benchmark')
+
+
+def format_task_dict(example, use_knowledge):
+    task = {
+        'instance_id': example['instance_id'],
+        'task_inst': example['task_inst'],
+        'dataset_path': '/benchmark/datasets/'
+        + example['dataset_folder_tree'].split('\n')[0][4:],
+        'dataset_folder_tree': example['dataset_folder_tree'],
+        'dataset_preview': example['dataset_preview'],
+        'pred_program_name': 'pred_' + example['gold_program_name'],
+    }
+
+    if use_knowledge:
+        task['task_inst'] += '\n' + str(example['domain_knowledge'])
+
+    return task
+
+
+def get_config(
+    metadata: EvalMetadata,
+    instance_id: str,
+) -> AppConfig:
+    config = AppConfig(
+        default_agent=metadata.agent_class,
+        run_as_openhands=False,
+        runtime=os.environ.get('RUNTIME', 'eventstream'),
+        max_budget_per_task=4,
+        max_iterations=metadata.max_iterations,
+        sandbox=SandboxConfig(
+            base_container_image='docker.io/xingyaoww/openhands-eval-scienceagentbench',
+            enable_auto_lint=True,
+            use_host_network=False,
+            timeout=300,
+            api_key=os.environ.get('ALLHANDS_API_KEY', None),
+            remote_runtime_api_url=os.environ.get('SANDBOX_REMOTE_RUNTIME_API_URL'),
+            keep_remote_runtime_alive=False,
+        ),
+        # do not mount workspace
+        workspace_base=None,
+        workspace_mount_path=None,
+    )
+    config.set_llm_config(metadata.llm_config)
+    if metadata.llm_config.log_completions:
+        metadata.llm_config.log_completions_folder = os.path.join(
+            metadata.eval_output_dir, 'llm_completions', instance_id
+        )
+        logger.info(
+            f'Logging LLM completions for instance {instance_id} to '
+            f'{metadata.llm_config.log_completions_folder}'
+        )
+    return config
+
+
+def initialize_runtime(
+    runtime: Runtime,
+    instance: pd.Series,  # this argument is not required
+):
+    """Initialize the runtime for the agent.
+
+    This function is called before the runtime is used to run the agent.
+    """
+    logger.info(f"{'-' * 50} BEGIN Runtime Initialization Fn {'-' * 50}")
+    obs: CmdOutputObservation
+
+    # Set up workspace directories
+    action = CmdRunAction(command='mkdir -p /workspace/pred_programs')
+    logger.info(action, extra={'msg_type': 'ACTION'})
+    obs = runtime.run_action(action)
+    assert obs.exit_code == 0
+
+    action = CmdRunAction(command='mkdir -p /workspace/pred_results')
+    logger.info(action, extra={'msg_type': 'ACTION'})
+    obs = runtime.run_action(action)
+    assert obs.exit_code == 0
+
+    dataset_name = instance['dataset_folder_tree'].split('\n')[0][4:].rstrip('/')
+
+    # Copy the dataset to the workspace
+    dataset_dir = os.path.join(
+        LOCAL_DATASET_PATH,
+        'datasets',
+        dataset_name,
+    )
+    runtime.copy_to(dataset_dir, '/workspace/benchmark/datasets', recursive=True)
+
+    # Check the dataset exists
+    action = CmdRunAction(
+        command='cd /workspace/benchmark/datasets && ls',
+        keep_prompt=False,
+    )
+    obs = runtime.run_action(action)
+    logger.info(obs, extra={'msg_type': 'OBSERVATION'})
+    assert obs.exit_code == 0
+    assert dataset_name in obs.content
+
+    logger.info(f"{'-' * 50} END Runtime Initialization Fn {'-' * 50}")
+
+
+def complete_runtime(
+    runtime: Runtime,
+    instance: pd.Series,
+) -> dict[str, Any]:
+    """Complete the runtime for the agent.
+
+    This function is called before the runtime is used to run the agent.
+    If you need to do something in the sandbox to get the correctness metric after
+    the agent has run, modify this function.
+    """
+    logger.info(f"{'-' * 50} BEGIN Runtime Completion Fn {'-' * 50}")
+    obs: CmdOutputObservation
+
+    test_result = {}
+
+    action = CmdRunAction(command='cd /workspace')
+    logger.info(action, extra={'msg_type': 'ACTION'})
+    obs = runtime.run_action(action)
+
+    assert obs.exit_code == 0
+
+    action = CmdRunAction(
+        command=f'cat pred_programs/{instance.pred_program_name}',
+        keep_prompt=False,
+    )
+    logger.info(action, extra={'msg_type': 'ACTION'})
+    obs = runtime.run_action(action)
+
+    if obs.exit_code == 0:
+        test_result = {'program': obs.content}
+    else:
+        test_result = {'program': 'ERROR'}
+
+    logger.info(f"{'-' * 50} END Runtime Completion Fn {'-' * 50}")
+    return test_result
+
+
+def process_instance(
+    instance: pd.Series,
+    metadata: EvalMetadata,
+    reset_logger: bool = True,
+) -> EvalOutput:
+    instance_id = instance.instance_id.replace('/', '__')
+    config = get_config(metadata, instance_id)
+
+    # Set up the logger properly, so you can run multi-processing to parallelize the evaluation
+    if reset_logger:
+        log_dir = os.path.join(metadata.eval_output_dir, 'infer_logs')
+        reset_logger_for_multiprocessing(logger, instance_id, log_dir)
+    else:
+        logger.info(f'Starting evaluation for instance {instance_id}.')
+
+    instruction = f"""You are an expert Python programming assistant that helps scientist users to write high-quality code to solve their tasks.
+Given a user request, you are expected to write a complete program that accomplishes the requested task and save any outputs to `/workspace/pred_results/` in the correct format.
+
+Here's the user request you need to work on:
+{instance.task_inst}
+
+You can access the dataset at `{instance.dataset_path}`. Here is the directory structure of the dataset:
+```
+{instance.dataset_folder_tree}
+```
+Here are some helpful previews for the dataset file(s):
+{instance.dataset_preview}
+
+Please save your program as `/workspace/pred_programs/{instance.pred_program_name}`.
+Then, please run the program to check and fix any errors.
+Please do NOT run the program in the background.
+If the program uses some packages that are incompatible, please figure out alternative implementations and do NOT restart the environment.
+
+"""
+
+    runtime = create_runtime(config)
+    call_async_from_sync(runtime.connect)
+    initialize_runtime(runtime, instance)
+
+    # Here's how you can run the agent (similar to the `main` function) and get the final task state
+    state: State | None = asyncio.run(
+        run_controller(
+            config=config,
+            initial_user_action=MessageAction(content=instruction),
+            runtime=runtime,
+            fake_user_response_fn=AGENT_CLS_TO_FAKE_USER_RESPONSE_FN.get(
+                metadata.agent_class
+            ),
+        )
+    )
+
+    # ======= Attempt to evaluate the agent's edits =======
+    test_result = complete_runtime(runtime, instance)
+
+    # If you are working on some simpler benchmark that only evaluates the final model output (e.g., in a MessageAction)
+    # You can simply get the LAST `MessageAction` from the returned `state.history` and parse it for evaluation.
+    if state is None:
+        raise ValueError('State should not be None.')
+    metrics = state.metrics.get() if state.metrics else None
+
+    # history is now available as a stream of events, rather than list of pairs of (Action, Observation)
+    # for compatibility with the existing output format, we can remake the pairs here
+    # remove when it becomes unnecessary
+    histories = state.history.compatibility_for_eval_history_pairs()
+
+    # Save the output
+    output = EvalOutput(
+        instance_id=instance.instance_id,
+        instruction=instruction,
+        metadata=metadata,
+        history=histories,
+        metrics=metrics,
+        error=state.last_error if state and state.last_error else None,
+        test_result=test_result,
+    )
+    return output
+
+
+if __name__ == '__main__':
+    parser = get_parser()
+    parser.add_argument(
+        '--use_knowledge',
+        type=str,
+        default='false',
+        choices=['true', 'false'],
+        help='use expert-provided knowledge or not',
+    )
+    args, _ = parser.parse_known_args()
+
+    sab_dataset = load_dataset('osunlp/ScienceAgentBench', split='validation')
+
+    dataset_processed = []
+    for example in tqdm(sab_dataset):
+        dataset_processed.append(
+            format_task_dict(example, args.use_knowledge == 'true')
+        )
+
+    dataset = pd.DataFrame(dataset_processed)
+
+    llm_config = None
+    if args.llm_config:
+        llm_config = get_llm_config_arg(args.llm_config)
+    if llm_config is None:
+        raise ValueError(f'Could not find LLM config: --llm_config {args.llm_config}')
+
+    metadata = make_metadata(
+        llm_config,
+        'ScienceAgentBench',
+        args.agent_cls,
+        args.max_iterations,
+        args.eval_note,
+        args.eval_output_dir,
+    )
+    output_file = os.path.join(metadata.eval_output_dir, 'output.jsonl')
+    dataset['instance_id'] = dataset['instance_id'].apply(str)
+    instances = prepare_dataset(dataset, output_file, args.eval_n_limit)
+
+    run_evaluation(
+        instances, metadata, output_file, args.eval_num_workers, process_instance
+    )

evaluation/scienceagentbench/scripts/run_infer.sh

@@ -0,0 +1,49 @@
+#!/bin/bash
+set -eo pipefail
+
+source "evaluation/utils/version_control.sh"
+
+MODEL_CONFIG=$1
+COMMIT_HASH=$2
+USE_KNOWLEDGE=$3
+AGENT=$4
+EVAL_LIMIT=$5
+NUM_WORKERS=$6
+
+if [ -z "$NUM_WORKERS" ]; then
+  NUM_WORKERS=1
+  echo "Number of workers not specified, use default $NUM_WORKERS"
+fi
+checkout_eval_branch
+
+if [ -z "$AGENT" ]; then
+  echo "Agent not specified, use default CodeActAgent"
+  AGENT="CodeActAgent"
+fi
+
+if [ -z "$USE_KNOWLEDGE" ]; then
+  echo "Use knowledge not specified, use default False"
+  USE_KNOWLEDGE=false
+fi
+
+get_agent_version
+
+echo "AGENT: $AGENT"
+echo "AGENT_VERSION: $AGENT_VERSION"
+echo "MODEL_CONFIG: $MODEL_CONFIG"
+
+COMMAND="poetry run python evaluation/scienceagentbench/run_infer.py \
+  --agent-cls $AGENT \
+  --llm-config $MODEL_CONFIG \
+  --use_knowledge $USE_KNOWLEDGE \
+  --max-iterations 30 \
+  --eval-num-workers $NUM_WORKERS \
+  --eval-note $AGENT_VERSION" \
+
+if [ -n "$EVAL_LIMIT" ]; then
+  echo "EVAL_LIMIT: $EVAL_LIMIT"
+  COMMAND="$COMMAND --eval-n-limit $EVAL_LIMIT"
+fi
+
+# Run the command
+eval $COMMAND

openhands/runtime/impl/e2b/sandbox.py

@@ -4,9 +4,7 @@ import tarfile
 from glob import glob
 
 from e2b import Sandbox as E2BSandbox
-from e2b.sandbox.exception import (
-    TimeoutException,
-)
+from e2b.sandbox.exception import TimeoutException
 
 from openhands.core.config import SandboxConfig
 from openhands.core.logger import openhands_logger as logger