# This repository contains the FlashDeconv package: source, tests, docs,
# examples and the README figure. Everything else is local research workspace.

# --- Python build and cache artifacts ---
__pycache__/
*.py[cod]
*.so
build/
dist/
*.egg-info/
.eggs/

# --- Virtual environments ---
.venv/
venv/

# --- Test, lint and JIT caches ---
.pytest_cache/
.coverage
coverage.xml
htmlcov/
.mypy_cache/
.ruff_cache/
.numba_cache/
.mplcache/
.ipynb_checkpoints/

# --- Editors, OS and logs ---
.idea/
.vscode/
*.swp
.DS_Store
Thumbs.db
*.log

# --- Local assistant and automation state ---
.claude/
.playwright-cli/
.playwright-mcp/
CLAUDE.md
AGENTS.md

# --- Research workspace (manuscript, analyses, data, results) ---
paper/*
!paper/figures/
paper/figures/*
!paper/figures/figure1.svg
!paper/figures/figure1.pdf
validation/
analysis/
results/
data/
promotion/

# --- Large data files anywhere ---
*.h5ad
*.h5
*.pkl
*.pickle

# --- Local development notes (only user-facing guides are tracked) ---
docs/*
!docs/api_reference.md
!docs/reference_data_guide.md
!docs/stereo_seq_guide.md
