pixi.toml

# pixi.toml - Modern package management for conda + PyPI
# Pixi is the recommended tool for computational biology because it handles
# both conda packages (samtools, bedtools, etc.) and PyPI packages seamlessly.
#
# See: https://pixi.sh/
#
# Quick start:
#   pixi install          # Create environment and install dependencies
#   pixi run test         # Run tests
#   pixi run lint         # Check code style
#   pixi shell            # Activate environment

[workspace]
name = "hive-protocol"
version = "0.1.0"
description = "The definitive protocol for Python in computational biology"
authors = ["CBG-ETH Zurich <cbg@ethz.ch>"]
channels = ["conda-forge"]
platforms = ["linux-64", "osx-64", "osx-arm64"]

# =============================================================================
# Dependencies
# =============================================================================

[dependencies]
# Python version
python = ">=3.10,<3.13"

# Scientific computing core (from conda-forge for optimized builds)
numpy = ">=1.24"
scipy = ">=1.10"

# Bayesian inference
pymc = ">=5.0"
arviz = ">=0.15"

# Data manipulation
polars = ">=0.20"

# Data validation
pydantic = ">=2.0"

# Visualization
matplotlib = ">=3.7"
seaborn = ">=0.12"

# Development tools (available on conda-forge)
pytest = ">=7.0"
pytest-cov = ">=4.0"
hypothesis = ">=6.0"
ruff = ">=0.8.0"
pre-commit = ">=3.0"

# Documentation
quarto = ">=1.4"
ipykernel = ">=6.0"    # Required for Quarto to find Python kernel
jupyter = ">=1.0"
pyyaml = ">=6.0"       # Required by Quarto's jupyter integration

# Type checking
mypy = ">=1.0"      # Used in CI/pre-commit for stability
pyright = ">=1.1"   # Used locally for fast feedback

# =============================================================================
# PyPI-only dependencies
# =============================================================================

[pypi-dependencies]
# Install the package itself in editable mode
hive-protocol = { path = ".", editable = true }

# Snakemake from PyPI (more reliable cross-platform than conda)
snakemake = ">=8.0"

# Docstring coverage checker
interrogate = ">=1.5"

# =============================================================================
# Tasks - Custom commands accessible via `pixi run <task>`
# =============================================================================

[tasks]
# Run tests
test = "pytest tests/ -v"

# Run tests with coverage
test-cov = "pytest tests/ --cov=src/hive_protocol --cov-report=term-missing"

# Run linter
lint = "ruff check src/ tests/"

# Auto-fix lint issues
lint-fix = "ruff check src/ tests/ --fix"

# Format code
format = "ruff format src/ tests/"

# Check formatting without changing files
format-check = "ruff format src/ tests/ --check"

# Type checking - pyright for local dev (fast), mypy for CI (stable)
typecheck = "pyright src/"           # Default: fast local feedback
typecheck-strict = "pyright src/ --level strict"  # Stricter checking
typecheck-ci = "mypy src/"           # Used in CI/pre-commit

# Docstring coverage
docstring-cov = "interrogate src/ -v --fail-under=80"

# Run all quality checks (uses mypy for CI compatibility)
check = { depends-on = ["lint", "format-check", "typecheck-ci", "docstring-cov", "test"] }

# Install pre-commit hooks
hooks = "pre-commit install"

# Run pre-commit on all files
hooks-all = "pre-commit run --all-files"

# Register Jupyter kernel for Quarto
kernel = "python -m ipykernel install --user --name python3 --display-name 'Python 3 (hive-protocol)'"

# Render Quarto notebooks and copy to docs/tutorials
docs = { cmd = "quarto render notebooks/ && rm -rf docs/tutorials && mv notebooks/_site docs/tutorials", depends-on = ["kernel"] }

# Render presentation slides
slides = "quarto render docs/slides.qmd"

# Publish documentation to GitHub Pages
docs-publish = "quarto publish gh-pages docs/ --no-prompt"

# Run Snakemake workflow (dry run)
workflow-dry = "snakemake -n --snakefile workflow/Snakefile"

# Run Snakemake workflow
workflow = "snakemake --cores 4 --snakefile workflow/Snakefile"

# Clean generated files
clean = "rm -rf results/*.parquet docs/*.html .pytest_cache .mypy_cache .ruff_cache"

# =============================================================================
# Activation
# =============================================================================

[activation.env]
# Ensure reproducible PyMC behavior
PYTENSOR_FLAGS = "device=cpu,floatX=float64"

# =============================================================================
# Platform-specific configuration
# =============================================================================

[target.osx-arm64.dependencies]
# ARM Mac specific - use accelerate for faster linear algebra
libblas = { version = "*", build = "*accelerate" }

[target.linux-64.dependencies]
# Linux specific - use OpenBLAS
libblas = { version = "*", build = "*openblas" }