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.gitignore

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+# --- Python ---
+__pycache__/
+*.py[cod]
+*.egg-info/
+*.egg
+dist/
+build/
+
+# --- Virtual environments ---
+.venv/
+venv/
+env/
+.python-version
+
+# --- Editor / IDE ---
+.vscode/
+.idea/
+*.swp
+*.swo
+
+# --- OS ---
+.DS_Store
+Thumbs.db
+
+# --- Jupyter ---
+.ipynb_checkpoints/
+
+# --- Test / type-check caches ---
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.coverage
+htmlcov/
+
+# --- Logs ---
+*.log
+auto_push.log
+logs/
+
+# --- Environment / secrets ---
+.env
+.env.*
+
+# --- Large data (not versioned) ---
+data/
+data/raw/
+data/processed/
+data/corpus/
+*.h5ad
+*.h5
+*.loom
+
+# --- Intermediate numerical arrays ---
+*.npy
+*.npz
+
+# --- Model checkpoints (large, regenerable) ---
+/models/
+checkpoints/
+checkpoints/*/best_model.pt
+checkpoints/*/training_history.json
+checkpoints/*.pt
+checkpoints/**/*.pt
+
+# --- Legacy artefacts (preserved locally only; 83GB) ---
+
+# --- Figures (regenerable) — but paper + supplement PDFs kept ---
+figures/*
+!figures/*.pdf
+!figures/supplement/
+figures/supplement/*
+!figures/supplement/*.pdf
+
+# --- Generated docs / scratch ---
+presentation/
+results.md
+PLAN.md
+
+# Caches
+__pycache__/
+.pytest_cache/
+*.pyc
+*.pyo
+
+# IDE
+.vscode/
+.idea/
+
+# Logs (volume)
+logs/*.log
+
+# LaTeX build artefacts
+paper/*.aux
+paper/*.log
+paper/*.out
+paper/*.toc