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Fix example.ipynb in the tutorial folder #27

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Fix example.ipynb in the tutorial folder #27

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92f5c3d
fix: update tutorial notebook configuration and fix paths
Apr 22, 2026
7da12fe
Update README links to point to the Finch repository
ghareea Apr 22, 2026
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8 changes: 4 additions & 4 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,8 @@ The agent was used to produce the trajectories for the [BixBench benchmark](http

```bash
# Clone the repository
git clone https://github.com/Future-House/data-analysis-crow.git
cd data-analysis-crow
git clone https://github.com/Future-House/finch.git
cd finch

# Install dependencies
pip install -e .
Expand All @@ -46,7 +46,7 @@ ANTHROPIC_API_KEY = "your-anthropic-api-key"

## Using the Agent

The agent works by taking a dataset and a prompt, then iteratively building a Jupyter notebook to answer the question. Visit the [tutorial](https://github.com/Future-House/data-analysis-crow/blob/main/tutorial/example.ipynb) for a simple step-by-step guide on how to use the agent.
The agent works by taking a dataset and a prompt, then iteratively building a Jupyter notebook to answer the question. Visit the [tutorial](https://github.com/Future-House/finch/blob/main/tutorial/example.ipynb) for a simple step-by-step guide on how to use the agent.

## Advanced Usage
For advanced evaluations, you can configure `server.yaml` and `runner.yaml` in the `src/scripts/bixbench_evaluation` directory and then run the evaluation script:
Expand All @@ -62,7 +62,7 @@ This will:

Results are saved in the output directory specified in your configuration file.

Note that the dataset and environment configuration must be updated appropriately. For an example, see [dataset.py](https://github.com/Future-House/data-analysis-crow/blob/main/src/fhda/dataset.py) which includes the capsule dataset configuration used for the BixBench benchmark.
Note that the dataset and environment configuration must be updated appropriately. For an example, see [dataset.py](https://github.com/Future-House/finch/blob/main/src/fhda/dataset.py) which includes the capsule dataset configuration used for the BixBench benchmark.

We also recommend visiting the BixBench repository where we share a full evaluation harness for the agent.

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12 changes: 6 additions & 6 deletions tutorial/example.ipynb
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Expand Up @@ -75,7 +75,6 @@
" language=language,\n",
" system_prompt=prompts.CAPSULE_SYSTEM_PROMPT_QUERY,\n",
" use_tmp_work_dir=False,\n",
" run_notebook_on_edit=True if cfg.USE_DOCKER else False,\n",
" )\n",
" return dae"
]
Expand All @@ -94,11 +93,11 @@
"# If using docker, be sure to pull the image from docker hub first\n",
"# docker pull futurehouse/bixbench:aviary-notebook-env\n",
"# This image includes many bioinformatics and data science packages\n",
"cfg.USE_DOCKER = False\n",
"cfg.USE_DOCKER = True\n",
"# This can be R or PYTHON in Docker or with a local kernel if you have R installed\n",
"LANGUAGE = NBLanguage.PYTHON\n",
"MAX_STEPS = 3\n",
"MODEL_NAME = \"claude-3-7-sonnet-latest\""
"MAX_STEPS = 20\n",
"MODEL_NAME = \"claude-sonnet-4-5-20250929\""
]
},
{
Expand Down Expand Up @@ -173,7 +172,7 @@
"outputs": [],
"source": [
"# VANILLA ROLLOUT - this is a simple version of the what the rollout Manager does\n",
"dataset_folder = Path(\"dataset\")\n",
"dataset_folder = Path(\"datasets/brain_size_data.csv\")\n",
"query = \"Analyze the dataset and give me an in depth analysis using pretty plots. I am particularly interested in crows.\"\n",
"environment = setup_data_analysis_env(query, dataset_folder)\n",
"\n",
Expand Down Expand Up @@ -222,7 +221,8 @@
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3"
"pygments_lexer": "ipython3",
"version": "3.13.2"
}
},
"nbformat": 4,
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