# The image should hold what Git tracks, without the Git history. These rules
# follow .gitignore, which Docker does not read, and keep credentials, local
# configs, downloaded data and build output out of the build context.
.git

# Credentials.
**/.env
**/.env.*
!**/.env.example

# Machine-specific profiling configs.
profiling/config.toml
profiling/config.*.toml
!profiling/config.example.toml
profiling/cluster_sources.toml
profiling/layouts

# Environments, caches and build output.
.venv
.venv*
**/__pycache__
**/*.py[cod]
.mypy_cache
.pytest_cache
.ruff_cache
**/.ipynb_checkpoints
**/build
**/dist
**/*.egg-info
cytearc/_version.py
.coverage
coverage.xml
coverage.json
htmlcov
interrogate_badge.svg

# Downloaded datasets and generated outputs.
tests/datasets
tests/visual/showcase/*.json
**/cytearc_datasets
**/*.zarr
**/test_data
docs/build
docs/source/_build
docs/.ipython
docs/source/**/*.tmp
artifacts
plotting_showcase
:memory:

# Untracked notebooks outside the documentation sources.
**/*.ipynb
!docs/source/**/*.ipynb

# Local working directories and notes.
.idea
.vscode
.agents
.codex
**/.cache
**/temp
**/notebook
**/review
**/ideas
**/PR
modal_cytearc
cellxgene_cytebase/datasets
cytebase_analysis
cytearc/cytebase/collection
cytearc/cytebase/README.md
performance_reconfig.md
