# Dependencies
node_modules/
# also a node_modules symlink (worktrees link it to a shared install)
node_modules
__pycache__/
*.pyc
.venv/
venv/

# Playwright e2e test artifacts
browser/frontend/test-results/
browser/frontend/playwright-report/
browser/frontend/playwright/.cache/

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

# Logs
*.log
logs/

# Environment
.env
.env.local

# Temp files
*.tmp
*.temp

# Uploads (user data)
browser/uploads/

# Test/data files (don't commit large genomic data)
*.fa
*.fasta
*.bb
*.bigBed
*.bigbed
*.bw
*.bigWig
*.bigwig
*.bam
*.bai
# Small BAM fixtures made by the real tools (fibertools / FiberHMM frame tests)
!tests/fixtures/fibertools_frame/*.bam
!tests/fixtures/fibertools_frame/*.bam.bai
*.gtf
*.gff
*.bed

# BLAST databases
*.nin
*.nsq
*.nhr
*.nsi
# ...but not the Windows installer's NSIS scripts
!packaging/windows/*.nsi
*.nsd
*.nog

# Primer output
primers/

# Local editor and agent settings
.claude/

# macOS app bundle and launch scripts
FiberBrowser.app/
Install.command

# Local Copilot artifacts (private until reviewed/distilled into training data)
data/copilot_dataset/usage_logs/
data/copilot_dataset/transitions/
data/copilot_dataset/shared_usage.jsonl
data/copilot_dataset/mlx/
adapters/
fused_models/

# Demo dataset for the guided tour
!browser/data/demo/napa_ddda.bam
!browser/data/demo/napa_ddda.bam.bai
!browser/data/demo/h1_chr1_insertion.bam
!browser/data/demo/h1_chr1_insertion.bam.bai

# Parsed-annotation caches written next to GTF/GFF files
*.fbcache.json

# Copilot training seed set: generated by scripts/build_copilot_dataset.py
# (byte-identical from data/copilot_dataset/records*.py), ~60 MB.
data/copilot_dataset/seed_v1.jsonl

# Mac app / wheel build output (packaging/macos/build_app.sh, python -m build)
/build/
/dist/

# Local wheels for a Docker build (deploy/wheels/, see docs/deployment/public-server.md)
deploy/wheels/*.whl

# Local list of private terms for tests/test_repo_hygiene.py
.hygiene-denylist
