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⬢ HIVE-PROTOCOL ⬢ RESEARCH SOFTWARE CONTAINMENT STANDARD
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THE DEFINITIVE PROTOCOL FOR PYTHON IN COMPUTATIONAL BIOLOGY
PROTOCOL-001 | v1.0.0
⚠ WARNING: Unstructured research code detected
→ SOLUTION: Deploy HIVE-PROTOCOL
Transform research scripts into production-grade software.
PROTOCOL COMPONENTS:
[✓] Dependency Management [✓] Code Quality
[✓] Testing Framework [✓] CI/CD Pipeline
[✓] Type Safety [✓] Documentation
[✓] Configuration [✓] Reproducibility
# 1. CLONE
git clone https://github.com/cbg-ethz/hive-protocol.git
cd hive-protocol
# 2. INSTALL PIXI (if not present)
curl -fsSL https://pixi.sh/install.sh | bash
# 3. INITIALIZE ENVIRONMENT
pixi install
# 4. VERIFY DEPLOYMENT
pixi run testSTATUS: Environment operational.
| Category | Old Protocol | Modern Protocol | Improvement |
|---|---|---|---|
| Package Management | pip + requirements.txt | pixi | 10-100x faster |
| Code Quality | Black + flake8 + isort | Ruff | 30-100x faster |
| Data Processing | pandas | Polars | 5-50x faster |
| Notebooks | Jupyter | Quarto | Git-friendly |
| Testing | unittest | pytest + Hypothesis | Property-based |
| Configuration | argparse / dict | Pydantic | Auto-validation |
| Type Checking | None | mypy + Pyright | Static analysis |
hive-protocol/
├── src/hive_protocol/ # SOURCE CODE (src layout)
│ ├── inference/ # Kalman filter + diagnostics
│ └── data/ # Data simulation
├── tests/ # PYTEST + HYPOTHESIS
├── notebooks/ # QUARTO TUTORIALS
│ ├── 01_introduction.qmd
│ ├── 02_kalman_filter.qmd
│ └── 03_diagnostics.qmd
├── workflow/ # SNAKEMAKE PIPELINE
│ ├── Snakefile
│ └── config/params.yaml
├── docs/ # WORKSHOP MATERIALS
├── pyproject.toml # SINGLE SOURCE OF TRUTH
├── pixi.toml # ENVIRONMENT SPEC
└── .pre-commit-config.yaml # QUALITY HOOKS
# TESTING
pixi run test # Run test suite
pixi run test-cov # Run with coverage report
# CODE QUALITY
pixi run lint # Check code style
pixi run lint-fix # Auto-fix issues
pixi run format # Format code
# TYPE CHECKING
pixi run typecheck # Pyright (fast, local)
pixi run typecheck-ci # mypy (stable, CI)
# DOCUMENTATION
pixi run docs # Render notebooks
pixi run slides # Render presentation
# WORKFLOW
pixi run workflow # Execute Snakemake pipeline
pixi run workflow-dry # Dry run (preview)
# MAINTENANCE
pixi run check # Run ALL quality checks
pixi run hooks # Install pre-commit hooks- FORK this repository
- RENAME
hive_protocol→your_project - UPDATE
pyproject.tomlmetadata - REPLACE Kalman filter with your domain logic
- RETAIN testing + CI patterns
[✓] src/ layout [✓] pyproject.toml structure
[✓] Test organization [✓] CI/CD workflows
[✓] Pre-commit config [✓] Quarto notebooks pattern
CBG Retreat 2026 | ETH Zurich | January 21-23, 2026
| Resource | Location |
|---|---|
| Slides | docs/slides.qmd |
| Tutorial | docs/TUTORIAL.md |
| Render | pixi run slides |
| Tool | Documentation |
|---|---|
| Pixi | pixi.sh |
| Ruff | docs.astral.sh/ruff |
| Pydantic | docs.pydantic.dev |
| Hypothesis | hypothesis.readthedocs.io |
| Quarto | quarto.org |
| PyMC | pymc.io |
# 1. Fork repository
# 2. Create feature branch
git checkout -b feature/enhancement
# 3. Make changes
# 4. Verify compliance
pixi run check
# 5. Commit (pre-commit enforces standards)
git commit -m "feat: add enhancement"
# 6. Push and create PR
git push -u origin feature/enhancementMIT License — see LICENSE
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HIVE-PROTOCOL | RESEARCH SOFTWARE CONTAINMENT STANDARD | STATUS: OPERATIONAL
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Built with modern Python for computational biology
CBG-ETH Zurich