# ====================
# Runtime data (large, never needed in image)
# ====================
workdir/
workdir*
data/
tmp/
benchmarks/
examples/
home/
results/
*_results/
*_report/
figures/
.venv*/
pertpy/
pertpy_demo/
projects/
analysis/
scripts/
notebooks/
fish_image_analysis/
.matplotlib_figs/
cache/
backup/
jetstream_storage/
.uploaded_files/
*.h5ad

# ====================
# Development & CI (not needed at runtime)
# ====================
tests/
.github/
docs/
# Root-level test scripts
/test_*.py
# Root-level markdown files except README
/*.md
!/README.md
# Packaging/docs metadata
MANIFEST.in
.readthedocs.yaml
*.egg-info/
dist/
build/

# ====================
# Environment and secrets
# ====================
.venv/
.env
.env.*

# ====================
# Local dev tooling
# ====================
.git/
.gitignore
.vscode/
.idea/
.clade/
.executor/
.gemini/
.pantheon/
.endpoint-logs/
.pytest_cache/
.mypy_cache/
.notebook_contexts.json
*.notebook_sessions_metadata.json
.pantheon_tasks.json

# ====================
# Python artifacts
# ====================
__pycache__/
*.pyc
*.pyo
*.pyd

# ====================
# Notebooks and large generated files
# ====================
*.ipynb
.ipynb_checkpoints/
