# Python bytecode
__pycache__/
*.py[cod]
*$py.class

# Editor / runtime UI state
imgui.ini

# Build artefacts
build/
dist/
*.egg-info/
.eggs/

# Test / lint caches
.pytest_cache/
.ruff_cache/

# Generated by CI: environment.yml minus the private CNV git dependency
environment-ci.yml

# Derived data caches (regenerated by palms-preprocess)
transcript_cache/

# Per-dataset zarr cache (created next to xenium output)
sdata_cached.zarr/

# Large reference datasets (only metadata/JSON is checked in)
reference_datasets/*.h5ad
reference_datasets/raw/

# Manuscript drafts and planning notes (kept out of the public repo)
manuscript/

# Untracked local data
data/

# Notebook-replay reports (scripts/verify_notebook.py --out): a measurement of
# one dataset on one machine, not a build artefact worth versioning
report.json
verify_report.json
report_*.json
