CultureMech/pyproject.toml at main · CultureBotAI/CultureMech · GitHub

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[project]
name = "culturemech"
version = "0.1.0"
description = "Knowledge base for microbial growth media recipes and formulations"
authors = [
    {name = "CultureMech Contributors"}
]
readme = "README.md"
license = {text = "CC0-1.0"}
requires-python = ">=3.10"
keywords = [
    "microbiology",
    "growth media",
    "culture media",
    "ontology",
    "knowledge graph",
    "linkml"
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
]

dependencies = [
    "linkml>=1.7.0",
    "linkml-runtime>=1.7.0",
    "linkml-term-validator>=0.1.0",  # Validates ontology term references
    "linkml-reference-validator>=0.1.0",  # Validates evidence snippets against PMIDs
    "oaklib>=0.5.0",
    "pyyaml>=6.0",
    "jinja2>=3.1.0",
    "click>=8.1.0",
    "requests>=2.31.0",
    "biolink-model>=4.0.0",
    "beautifulsoup4>=4.12.0",
    "bacdive>=1.0.0",
    "sqlparse>=0.4.0",  # For parsing KOMODO and MediaDB SQL dumps
    "openpyxl>=3.1.0",  # For parsing KOMODO Excel supplementary files
    "PyPDF2>=3.0.0",  # For PDF text extraction in literature verification
    "numpy>=1.24.0",  # Array operations for embeddings
    "pandas>=2.0.0",  # DataFrame for UMAP coordinates
    "umap-learn>=0.5.0",  # UMAP dimensionality reduction
    "tqdm>=4.66.0",  # Progress bars for embedding loading
    "scikit-learn>=1.3.0",  # Required by umap-learn
    "rapidfuzz>=3.0.0",  # Fuzzy string matching for ingredient name matching
]

[project.optional-dependencies]
dev = [
    "pytest>=7.4.0",
    "pytest-cov>=4.1.0",
    "black>=23.0.0",
    "ruff>=0.1.0",
    "mypy>=1.5.0",
]
koza = [
    "koza>=0.6.0",
]

[project.urls]
Homepage = "https://github.com/KG-Hub/CultureMech"
Repository = "https://github.com/KG-Hub/CultureMech"
Documentation = "https://kg-hub.github.io/CultureMech"

[project.scripts]
culturemech = "culturemech.cli:cli"

[build-system]
requires = ["setuptools>=68.0", "wheel"]
build-backend = "setuptools.build_meta"

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools.package-data]
culturemech = ["schema/*.yaml", "templates/*.j2", "templates/*.html"]

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
addopts = [
    "--strict-markers",
    "--cov=culturemech",
    "--cov-report=term-missing",
    "--cov-report=html",
]

[tool.black]
line-length = 100
target-version = ["py310", "py311", "py312"]
include = '\.pyi?$'
exclude = '''
/(
    \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | _build
  | buck-out
  | build
  | dist
)/
'''

[tool.ruff]
line-length = 100
target-version = "py310"
select = [
    "E",   # pycodestyle errors
    "W",   # pycodestyle warnings
    "F",   # pyflakes
    "I",   # isort
    "B",   # flake8-bugbear
    "C4",  # flake8-comprehensions
    "UP",  # pyupgrade
]
ignore = [
    "E501",  # line too long (handled by black)
    "B008",  # do not perform function calls in argument defaults
    "C901",  # too complex
]

[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = true
disallow_incomplete_defs = true
check_untyped_defs = true
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = true
strict_equality = true