# Python bytecode, environments, and tool caches
**/__pycache__/
*.py[cod]
.coverage
.mypy_cache/
.pytest_cache/
.ruff_cache/
.tox/
.venv/
venv/
*cachedir
*/catboost_info/

# Build and generated documentation output
/build/
/dist/
/docs/
*.egg-info/

# Generated logs, reports, notebooks, and data files
*.log
*.pdf
*.rdf
*.ipynb
*.csv
*.json
*.json.gz
*.pkl.gz
*.txt

# Package resources and repository evidence retained despite the broad rules
!LICENSES/*.txt
!synkit/CRN/Benchmark/data/kegg_modules.json
!Data/Conformance/stereomolgraph_graph_conformance.json
!Data/Mech/polar.json
!Data/Mech/radical.json
!Data/Mech/stereo.json
!Data/Schema/
!Data/Schema/attribute_propagation_v1_5.json
!/tools/python_file_size_baseline.json
!Test/Synthesis/Reactor/fixtures/small_rewrite_conformance.json

# Lewis benchmark inputs and reviewed evidence
!Experiment/Lewis/Data/all.csv
!Experiment/Lewis/Data/benchmark.json.gz
!Experiment/Lewis/Data/combinatorial_all.csv
!Experiment/Lewis/Data/hydrogen.pkl.gz
!Experiment/Lewis/mech_path/Data/MechanismBench/electrocyclic_machinery.json
!Experiment/Lewis/mech_path/Data/MechanismBench/polar.json
!Experiment/Lewis/mech_path/Data/MechanismBench/radical.json
!Experiment/Lewis/mech_path/Data/MechanismBench/stereo.json
!Experiment/Lewis/mech_path/Data/MechanismBench/stereo_branch_coverage.json
!Experiment/Lewis/mech_path/Data/MechanismBench/stereo_couplings.json
!Experiment/Lewis/mech_path/Data/MechanismBench/evidence/mechanismbench_evidence.json
!Experiment/Lewis/mech_path/Data/reconstruction_audit/polar-failures.csv
!Experiment/Lewis/mech_path/Data/reconstruction_audit/radical-arrow-review.csv
!Experiment/Lewis/mech_path/Data/reconstruction_audit/radical-failures.csv
!Experiment/Lewis/rule_replay/Data/bidirectional-replay/results.json
!Experiment/Lewis/rule_replay/Data/relative-lone-pair/results.json

# Stereo benchmark inputs and reproducible reports
!Experiment/Stereo/Data/**/*.csv
!Experiment/Stereo/Data/**/*.json
!Experiment/Stereo/Data/manifest.json
!Experiment/Stereo/Data/Perception/full_detection_report.json
!Experiment/Stereo/Data/Perception/perception_conformance_cases.json

# Large or reproducible data products
/Data/Benchmark/*
!/Data/Benchmark/mech/
/Data/Benchmark/mech/*
!/Data/Benchmark/mech/README.md
!/Data/Benchmark/mech/polar-failures.csv
!/Data/Benchmark/mech/radical-failures.csv
!/Data/Benchmark/partial_expand/
!/Data/Benchmark/partial_expand/**
/Data/Benchmark/partial_expand/results/
!/Data/Benchmark/Stereo/
!/Data/Benchmark/Stereo/**
/Data/Fragment/*
/Data/Study/CRN/case_formose/*
/Data/USPTO/*
/Experiment/Lewis/Runs/

# Generated FLOWER intermediates and long-run evidence
/Experiment/Lewis/FLOWER/batches/
/Experiment/Lewis/FLOWER/full_reactions/
/Experiment/Lewis/FLOWER/replay-debug/
/Experiment/Lewis/FLOWER/replay-results*/
/Experiment/Lewis/FLOWER/replay-runs/
!Experiment/Lewis/FLOWER/full-reaction-batches/manifest.json
!Experiment/Lewis/FLOWER/full-reaction-replay-summary.json

# Resumable local benchmark state
/Experiment/RBL/*checkpoint*.jsonl

# Development and scratch paths
/Test/Conformance/
/crn/
/debug/
/dev/
/paper/*
/sprint/
/synkit/Graph/dev/

# Local one-off scripts and prompts
.gitignore
measure_candidate_stages.py
request.md
run.sh
run_rdcanon.py
run_valid_bug_cases.py
test_partial.py
test_run.py
test_syn.py
test_syn_reactor.py
