.gitignore

.idea
.vscode
__pycache__
build
dist
*.egg-info
scarf.egg-info
scarf_toolkit.egg-info
.venv
.venv*/
.ruff_cache
# zarr ":memory:" URL materialized as a local directory by older tests
:memory:
:memory:/
*.ipynb_checkpoints
*.ipynb
!docs/.jupyter_cache/executed/**/base.ipynb
docs/.jupyter_cache/_parallel/
docs/.jupyter_cache.backup/
docs/.jupyter_cache.candidate-*/
docs/.jupyter_cache.lock
docs/.jupyter_cache.resume/
docs/.jupyter_cache.work-*/
docs/.ipython/
docs/source/vignettes/README.md
docs/source/vignettes/scarf_datasets
docs/source/vignettes/dev
docs/source/vignettes/*.txt
docs/source/vignettes/*.mtx
docs/build/
docs/_build/
docs/jupyter_execute
# Downloaded/converted notebook datasets (path depends on CWD during execute)
docs/source/scarf_datasets/
docs/source/tutorials/scarf_datasets/
docs/**/scarf_datasets/
*.zarr/
**/*.zarr/
.coverage
coverage.xml
coverage.json
htmlcov/
.pytest_cache
interrogate_badge.svg
tests/datasets/*
!tests/datasets/markers_all_clusters.csv
tests/.env
tests/.env.*
benchmarks/.env
benchmarks/.env.*
!benchmarks/.env.example
profiling/.env
profiling/.env.*
!profiling/.env.example
scarf/agent/.env
scarf/agent/.env.*
!scarf/agent/.env.example
/profiling/config.toml
/profiling/config.*.toml
!/profiling/config.example.toml
# Generated and machine-specific profiling configs.
profiling/layouts/
/profiling/cluster_sources.toml
test_data
# Generated plotting showcase outputs. Curated references live in tests/visual.
/artifacts/
/plotting_showcase/
tests/visual/showcase/*.json
# Generated by setuptools-scm during build/sync.
scarf/_version.py
# Local working notes for countsT strip-shard experiments (tmp Modal hacks).
/performance_reconfig.md
.env
temp/