# os
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
Thumbs.db

# python
__pycache__/
*.py[cod]
*.egg-info/
dist/
build/
.eggs/
*.egg
.venv/
venv/
env/

# jupyter
.ipynb_checkpoints/
*.ipynb_checkpoints

# env
.env
.env.*
!.env.example

# data - large files never committed
data/inputs/
data/embeddings/
data/outputs/
runs/

# ml artifacts
*.pt
*.pth
*.ckpt
*.npy
*.zarr
*.h5
*.h5ad
*.parquet

# ide
.vscode/
.idea/
*.swp
*.swo

# langsmith / api logs
*.log
langsmith_traces/
docs/papers/
knowledge/
notebooks/embeddings/*.html
notebooks/embeddings/*.png
docs/TODO*

docs/tnbc92_summary.pdf
docs/tnbc92_three_hypotheses.pdf

.claude/
notebooks/final/*.html

# scratch workspaces - superseded / one-off work, kept locally as record
design/_scratch
scripts/_scratch/

# manuscript drafts - local until deliberately published
docs/reports/**/discussion.md


design/omicstra-deck-presenter.pdf
design/omicstra-deck.pdf


demo/
docs/deck_v3_plan.md
docs/deck_v4_plan.md
docs/deck_v5_qa.md
docs/talk_content.md
docs/deck_v4_outline.md

scripts/slurm/
projects/tnbc-92/talk/
docs/media/slides_omicstra_2026-08-18.zip
docs/talk_speaker_notes_2026-08-18.md

design/pseudocode/
# site - deployment notes for one institution. never committed.
# the package is site-agnostic by design; anything naming a cluster, a quota,
# an approval or an account belongs here, not in docs/.
site/


# a second venv that was being packaged into the sdist
venv_test/
