# --- Python build artifacts ---
site/
env/
build/
dist/
.eggs/
*.egg-info/
*.eggs
*.pyc
*.pyo
__pycache__/
!**/site-packages/

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

# --- Jupyter ---
.ipynb_checkpoints/

# --- Large data / model files ---
*.h5ad
*.h5
*.hdf5
*.pkl
*.pickle
*.loom
*.lz4
*.tar.gz
*.tar.bz2
*.zarr
*.bak

# --- Docs output and large assets ---
docs/_build/
docs/autoapi/
*.gif
docs/my_topometry_report.pdf
docs/topometry_revised.pdf
docs/topometry_revised.txt
docs/GSE126480_Raw_counts.txt
docs/DentateGyrus.loom
docs/filtered_matrices_mex/
docs/*.pdf

# --- LLM / AI tool configuration ---
.claude/

# --- Integration module (WIP) ---
topo/integration/
topo/integration_tests/

# --- Claude blueprints (not for public Git) ---
api_notes.md
topometry_integration_blueprint.md
cca_integration_blueprint.md
cca_integration_blueprint_final.md
cca_implementation_report.md

# --- Test / cache ---
.pytest_cache/
data/
!data/.gitkeep

# --- Private docs (not for public Git) ---
docs/LBO_Review/

# --- IDE and OS ---
.vscode/
.idea/
.DS_Store
Thumbs.db
*.swp
*.swo

# Scrach files
scratch/

# repomix
*repomix*.xml

# Agents
GEMINI.md
CLAUDE.md
.agents
.prompt.md
.github/prompts/
.github/copilot-instructions.md

# --- Secrets ---
.pypi-token
