# Python
__pycache__/
*.py[cod]
*$py.class
.pytest_cache/
.mypy_cache/
.ruff_cache/
.coverage
htmlcov/
*.egg-info/
.eggs/
dist/
build/
*.egg

# Virtual environments
.venv/
venv/
.mamba/

# IDE
.vscode/
.idea/
*.swp
*.swo

# OS
.DS_Store
Thumbs.db

# Project-specific
resources/*
!resources/.gitkeep
results/*
!results/.gitkeep
log/*
!log/.gitkeep
*.log
progress.json
progress.jsonl
.abi/
abi_workspace/
workspace/
work/
.nextflow/
.nextflow.log*
nextflow_work/
nf_work/
job_store.json
jobs.json

# Ignore user data by default, but keep curated small examples.
data/*
!data/examples/
!data/examples/**

# Large sequencing or archive inputs should not be committed by default.
*.bam
*.bai
*.sam
*.cram
*.fastq
*.fq
*.fastq.gz
*.fq.gz
*.fasta.gz
*.fa.gz
*.tar
*.tar.gz
*.tgz
*.zip
*.7z

# Keep intentionally tiny test fixtures.
!examples/fixtures/**
!tests/fixtures/**

# CMake (if used)
CMakeCache.txt
CMakeFiles/
cmake_install.cmake
Makefile
CTestTestfile.cmake
Testing/

# Demo execution artifacts
data/e_coli_demo/
results/e_coli_demo/
smoke_test/

# Benchmark results (generated)
bench/results/
bench/Bench_1/bench/results/
metrics.tsv

# Historical planning docs (auto-generated, not for repo)
Rebuild.md
Development_Status.md
Engineering_Roadmap.md
demo_plan.md
autoplasm_DAG.md
docs/experiments/abi_final_development_plan.md
docs/experiments/abi_final_development_plan_zh.md

# Figure output (generated by pipeline, not source)
figures/*.png
figures/*.svg
figures/*.html
figures/*.pdf

# Report artifacts (generated)
report/report.md
report/report.html
report/report_summary.json
report/methods.md
report/limitations.md
report/citations.md

# Resource manifest caches (generated per-run)
resource_manifest.json
resource_manifest_cache.json

# Plugin demo results
results/plasmid_demo/
results/rnaseq_demo/
results/wgs_bacteria_demo/
results/amplicon_16s_demo/
results/metatranscriptomics_demo/
results/rnaseq_expression_demo/

# Benchmark datasets (large, not for repo)
data/benchmark/
data/validation/

# Plugin development artifacts (auto-generated during dev)
plugins/*/figures/*
plugins/*/report/*

# Jupyter notebook checkpoints
.ipynb_checkpoints/

# Temporary analysis outputs
tmp/
temp/
scratch/

# Container / environment
*.sif
*.img
Singularity.lock
environment.lock.yml
conda.lock

# Claude Code project files
.claude/
!.claude/settings.json
!.claude/settings.local.jsondocs/_build/
.readthedocs-cache/
docs/_build/
