Quickstart

Installation

conda env create -f environment.yml
conda activate offtarget-benchmark-repro
pip install -e .

This environment is used by both the benchmark runner and the Quarto notebooks.

CLI check

offtarget-benchmark paths
python scripts/run_manuscript_benchmark.py --help

offtarget-benchmark paths reports the resolved repository paths used by the public CLI. The benchmark wrapper exposes the canonical rerun command with the default manuscript inputs.

Staged prediction contracts

Place the standardized tool outputs under:

  • data/zenodo/standard_tool_predictions/

The expected filenames are listed in:

  • config/tool_output_manifest.example.yml
  • docs/06_tool_setup_reference.qmd

Benchmark rerun

python scripts/run_manuscript_benchmark.py

This command writes the benchmark tables used by the documentation site under results/benchmark_runs/manuscript_primary/.

Site render

python scripts/render_docs.py

This command executes the notebooks in docs/ and writes the rendered site to docs/_site/.