act_inf_metaanalysis/pyproject.toml at main · ActiveInferenceInstitute/act_inf_metaanalysis · GitHub

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# Active Inference Meta-Analysis Project Configuration
# Inherits workspace settings from root pyproject.toml

[build-system]
requires = ["setuptools>=61.0"]
build-backend = "setuptools.build_meta"

[project]
name = "act_inf_metaanalysis"
version = "2.0.6"
description = "Computational literature meta-analysis of the Active Inference field using probabilistic knowledge graphs"
authors = [
    {name = "Daniel Friedman", email = "daniel@activeinference.institute"},
    {name = "Joel Dietz", email = "jdietz@mit.edu"},
]
requires-python = ">=3.12"
dependencies = [
    "numpy>=1.24.0",
    "scipy>=1.10.0",
    "matplotlib>=3.7.0",
    "pandas>=2.0.0",
    "networkx>=3.0",
    "requests>=2.31.0",
    "rdflib>=7.0.0",
    "pyyaml>=6.0",
    "wordcloud>=1.9.0",
    "scikit-learn>=1.3.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.4.0",
    "pytest-cov>=4.1.0",
    "pytest-httpserver>=1.0.8",
    "ruff>=0.6.0",
    "mypy>=1.10.0",
]
llm = [
    "ollama>=0.1.0",
]

[tool.pytest.ini_options]
pythonpath = ["src"]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_functions = ["test_*"]
addopts = "-v --tb=short --strict-markers"

[tool.coverage.run]
source = ["src"]
branch = true
omit = ["tests/*", "*/__init__.py", "*/test_*.py"]

[tool.coverage.report]
fail_under = 90
show_missing = true
precision = 2
exclude_lines = [
    "pragma: no cover",
    "if __name__ == .__main__.:",
    "raise NotImplementedError",
]

[tool.ruff]
line-length = 100
target-version = "py312"
src = ["src", "scripts", "tests"]

[tool.ruff.lint]
# The documented gate is the classic default set, stated explicitly so a newer
# ruff release cannot silently widen it.
select = ["E4", "E7", "E9", "F"]

# Deliberate exceptions to the default (E4/E7/E9/F) rule set.
[tool.ruff.lint.per-file-ignores]
# Orchestrator scripts import after the sys.path bootstrap by design.
"scripts/*.py" = ["E402"]
# test_variables.py inserts the repo root on sys.path before importing src.
"tests/test_variables.py" = ["E402"]

[tool.mypy]
python_version = "3.12"
mypy_path = "src"
explicit_package_bases = true
ignore_missing_imports = true
disable_error_code = ["import-untyped", "import-not-found"]
check_untyped_defs = true
no_implicit_optional = true
warn_unreachable = false
warn_unused_ignores = false

[project.urls]
Homepage = "https://github.com/ActiveInferenceInstitute/act_inf_metaanalysis"
Documentation = "https://github.com/ActiveInferenceInstitute/act_inf_metaanalysis/tree/main/doc"

[tool.uv]
# Inherits workspace settings from root pyproject.toml