pyproject.toml

[build-system]
requires = ["setuptools>=64", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "mumdia"
version = "0.1.0"
description = "MuMDIA"
readme = "README.md"
requires-python = ">=3.11"
license = "Apache-2.0"
authors = [
    {name = "Robbin Bouwmeester", email = "robbin.bouwmeester@ugent.be"},
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
    # Core scientific computing
    "polars>=0.20.0",
    "pandas>=2.0.0",
    "numpy>=1.24.0",
    "scipy>=1.10.0",
    "scikit-learn>=1.3.0",
    "matplotlib>=3.7.0",
    "numba>=0.57.0",
    
    # System and monitoring
    "psutil>=5.9.0",
    "rich>=13.0.0",
    "tqdm>=4.65.0",
    
    # Machine learning and proteomics
    "mokapot>=0.8.0",
    "tensorflow>=2.13.0",
    "scikeras>=0.12.0",
    
    # Mass spectrometry tools
    "pymzml>=2.5.0",
    "pyopenms>=3.0.0",
    # "rustyms>=0.9.0",
    "rustyms @ git+https://github.com/rodvrees/mzcore-mumdia.git@mumdia-branch#subdirectory=rustyms-py",
    
    # MS prediction tools
    "ms2pip>=4.0.0",
    "psm-utils>=0.4.0",
    "deeplc>=2.0.0",
    
    # Web and data handling
    "requests>=2.31.0",
]

[tool.setuptools.packages.find]
include = [
    "feature_generators*",
    "utilities*", 
    "parsers*",
    "prediction_wrappers*",
    "peptide_search*",
    "sequence*",
    "deconvolution*"
]
exclude = [
    "tests*",
    "notebook_helpers*",
    "configs*",
    "fasta*",
    "results*"
]

[tool.setuptools]
py-modules = [
    "mumdia",
    "run",
    "data_structures",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0",
    "pytest-cov>=4.0",
    "black>=23.0",
    "isort>=5.12",
    "mypy>=1.0",
    "flake8>=6.0",
]

[project.urls]
Homepage = "https://github.com/CompOmics/MuMDIA"
Repository = "https://github.com/CompOmics/MuMDIA.git"
Issues = "https://github.com/CompOmics/MuMDIA/issues"

[tool.pytest.ini_options]
# Pytest configuration for MuMDIA
minversion = "7.0"
testpaths = ["tests"]

# Test discovery patterns
python_files = ["test_*.py", "*_test.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]

# Markers for test categorization
markers = [
    "unit: Unit tests for individual functions/classes",
    "integration: Integration tests for component interaction", 
    "slow: Tests that take a long time to run",
    "fast: Quick tests for CI/CD",
    "fragmentation: Tests related to fragment intensity features",
    "data_validation: Tests for data structure validation",
    "io: Tests for input/output operations",
    "performance: Performance and benchmarking tests",
    "numerical: Tests for numerical accuracy and mathematical functions",
    "memory: Tests for memory usage and resource monitoring",
    "statistical: Tests for statistical methods and analysis",
    "scalability: Tests for scalability and large data handling",
    "complexity: Tests for computational complexity analysis",
    "resource: Tests for resource usage and monitoring"
]

# Output formatting
addopts = [
    "--strict-markers",
    "--tb=short",
    "--disable-warnings",
    "-ra",  # Show summary of all except passed
]

# Filters for warnings
filterwarnings = [
    "ignore::UserWarning",
    "ignore::DeprecationWarning",
    "ignore::PendingDeprecationWarning",
]

# Test timeout (in seconds)
timeout = 300

[tool.coverage.run]
source = [
    "feature_generators",
    "data_structures", 
    "utilities",
    "parsers",
    "prediction_wrappers",
    "peptide_search"
]

omit = [
    "*/tests/*",
    "*/__pycache__/*",
    "*/venv/*",
    "*/env/*",
    "setup.py",
    "conftest.py"
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "if self.debug:",
    "if settings.DEBUG",
    "raise AssertionError",
    "raise NotImplementedError",
    "if 0:",
    "if __name__ == .__main__.:",
    "class .*\\bProtocol\\):",
    "@(abc\\.)?abstractmethod",
]

show_missing = true
precision = 2
skip_covered = false

[tool.coverage.html]
directory = "htmlcov"

[tool.mypy]
python_version = "3.11"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = true
disallow_incomplete_defs = true
check_untyped_defs = true
disallow_untyped_decorators = true
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = true
warn_no_return = true
warn_unreachable = true
strict_equality = true

[tool.black]
line-length = 88
target-version = ['py311']
include = '\.pyi?$'

[tool.isort]
profile = "black"
multi_line_output = 3
line_length = 88
known_first_party = ["mumdia", "feature_generators", "data_structures", "utilities"]