*.pyc
*cachedir
*.csv
!Experiment/Lewis/Data/all.csv
!Experiment/Lewis/Data/combinatorial_all.csv
!Experiment/Lewis/mech_path/Data/reconstruction_audit/polar-failures.csv
!Experiment/Lewis/mech_path/Data/reconstruction_audit/radical-failures.csv
!Experiment/Lewis/mech_path/Data/reconstruction_audit/radical-arrow-review.csv
*/catboost_info/*


*.pkl.gz
*.pdf

.coverage
dev/*
/debug/
/Test/Conformance/
*.rdf
test_syn_reactor.py

Data/Benchmark/*
!Data/Benchmark/partial_expand/
!Data/Benchmark/partial_expand/**
Data/Benchmark/partial_expand/results/
!Data/Benchmark/mech/
Data/Benchmark/mech/*
!Data/Benchmark/mech/README.md
!Data/Benchmark/mech/polar-failures.csv
!Data/Benchmark/mech/radical-failures.csv
*.json.gz
!Experiment/Lewis/Data/benchmark.json.gz
# *.png

run.sh
docs/*
run_rdcanon.py
Data/Fragment/*
test_partial.py
Data/Benchmark/synthesis/*
Data/USPTO/*
crn/*
test_run.py
Data/Study/CRN/case_formose/*

synkit/Graph/dev/*
*.ipynb
*.json
# Stereo benchmark inputs are versioned for reproducible fresh-clone runs.
# Generated reports stay Git-visible so completed results can be committed
# explicitly, including reports created by the long raw stress stages.
!Experiment/Stereo/Data/**/*.csv
!Experiment/Stereo/Data/**/*.json
!Data/Schema/
!Data/Schema/attribute_propagation_v1_5.json
!/tools/python_file_size_baseline.json
!Data/Mech/polar.json
!Data/Mech/radical.json
!Data/Mech/stereo.json
!Experiment/Lewis/Data/hydrogen.pkl.gz
# Canonical reviewed MechanismBench partitions are executable test data.
!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/electrocyclic_machinery.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/rule_replay/Data/bidirectional-replay/results.json
!Experiment/Lewis/rule_replay/Data/relative-lone-pair/results.json
!Experiment/Stereo/Data/manifest.json
!Experiment/Stereo/Data/Perception/perception_conformance_cases.json
!Experiment/Stereo/Data/Perception/full_detection_report.json
!Test/Synthesis/Reactor/fixtures/small_rewrite_conformance.json
!Data/Conformance/stereomolgraph_graph_conformance.json
!Data/Benchmark/Stereo/
!Data/Benchmark/Stereo/**
*.txt
!LICENSES/*.txt
*.log
/dist/
sprint/
sprint/*
test_syn.py
.gitignore
measure_candidate_stages.py
run_valid_bug_cases.py
paper/*
# Nested standalone Git repository.
/paper/og_paper/

# Fresh benchmark runs are reproducible and can be large. Retained reference
# outputs live inside each experiment's Data directory.
Experiment/Lewis/Runs/

# Generated FLOWER intermediates and long-run evidence. The portable
# full-reaction batch payload is intentionally retained in Git.
Experiment/Lewis/FLOWER/batches/
Experiment/Lewis/FLOWER/full_reactions/
Experiment/Lewis/FLOWER/replay-debug/
Experiment/Lewis/FLOWER/replay-runs/
Experiment/Lewis/FLOWER/replay-results*/
!Experiment/Lewis/FLOWER/full-reaction-batches/manifest.json
!Experiment/Lewis/FLOWER/full-reaction-replay-summary.json

# Keep generated Python bytecode ignored after directory re-inclusions above.
**/__pycache__/
*.py[cod]

# RBL long-run checkpoints are resumable local state, not retained evidence.
Experiment/RBL/*checkpoint*.jsonl
request.md
