pyproject.toml

[tool.poetry]
name = "tnfr"
version = "0.0.3.5"
description = "TNFR (Resonant Fractal Nature Theory): a mathematical framework for modeling coherent patterns in complex systems through resonance-based dynamics on networks."
readme = "README.md"
authors = ["F. F. Martinez Gamo"]
license = "MIT"
packages = [{include = "tnfr", from = "src"}]

[project]
name = "tnfr"
version = "0.0.3.5"
description = "TNFR (Resonant Fractal Nature Theory): a mathematical framework for modeling coherent patterns in complex systems through resonance-based dynamics on networks."
readme = "README.md"
requires-python = ">=3.10"
license = "MIT"
license-files = ["LICENSE.md"]
authors = [{ name = "F. F. Martinez Gamo" }]
dependencies = [
  "numpy>=1.24",
  "networkx>=2.6,<4.0",
  "cachetools>=5.0,<7.0",
  "mpmath>=1.3,<2.0",
]

[tool.poetry.dependencies]
python = "^3.10"
# Minimal core - truly minimal for primality testing
networkx = {version = "^2.6", optional = true}
cachetools = {version = "^5.0", optional = true}
mpmath = {version = "^1.3", optional = true}
numpy = {version = "^1.24", optional = true}
scipy = {version = "^1.9", optional = true}
sympy = {version = "^1.10", optional = true}

[tool.poetry.extras]
full = ["numpy", "scipy", "networkx", "cachetools", "sympy", "mpmath"]
math = ["sympy"]
tnfr = ["networkx", "cachetools", "mpmath"]
dev = ["pytest", "black", "flake8", "mypy"]

[tool.poetry.scripts]
tnfr-primality = "tnfr_primality.cli:main"

[tool.tnfr.metadata]
# ORCID retained outside PEP 621 authors block to satisfy strict validators
primary_author_orcid = "0009-0007-6116-0613"
keywords = [
  "TNFR", "Resonant Fractal Nature Theory", "complex systems", "fractals", "resonance", 
  "networks", "structural dynamics", "structural operators", "coherence theory",
  "physics simulation", "emergence", "synchronization", "zenodo", "doi"
]
classifiers = [
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Operating System :: OS Independent",
  "Intended Audience :: Science/Research",
  "Topic :: Scientific/Engineering",
  "Topic :: Scientific/Engineering :: Information Analysis",
  "Topic :: Scientific/Engineering :: Mathematics"
]
dependencies = [
  "networkx>=2.6,<4.0",
  "cachetools>=5.0,<7.0",
  "mpmath>=1.3,<2.0",
]

[project.optional-dependencies]
# Computational backends
compute-jax = ["jax>=0.4,<1.0"]
compute-torch = ["torch>=2.1,<3.0"]

# Serialization formats
serialization = ["pyyaml>=6.0,<7.0", "orjson>=3,<4"]

# Visualization
viz-basic = ["matplotlib>=3.7,<4.0", "sympy>=1.12,<2.0"]

# Legacy compatibility aliases (for backward compatibility with existing workflows)
# Note: numpy is now a core dependency, so this extra installs nothing additional
numpy = []  # Empty - numpy is now in core dependencies
jax = ["jax>=0.4,<1.0"]
torch = ["torch>=2.1,<3.0"]
yaml = ["pyyaml>=6.0,<7.0"]
orjson = ["orjson>=3,<4"]
viz = ["matplotlib>=3.7,<4.0"]
docs = [
  "sphinx>=7.2",
  "sphinx-autodoc-typehints>=1.25",
  "myst-parser>=2.0",
  "nbsphinx>=0.9",
  "sphinx-rtd-theme>=1.3",
  "sphinxcontrib-mermaid>=0.9",
  "ipykernel>=6",
  "nbconvert>=7.16",
  "pypandoc-binary>=1.14",
  "mkdocs>=1.5",
  "mkdocs-material>=9.4",
  "mkdocs-jupyter>=0.24",
]
# Testing - modular groups
test-unit = [
  "pytest>=7,<10",
  "pytest-cov>=4,<8",
  "pytest-timeout>=2,<3",
]
test-property = [
  "hypothesis>=6,<7",
  "hypothesis-networkx>=0.3,<1.0",
]
test-performance = [
  "pytest-benchmark>=4,<6",
]
test-parallel = [
  "pytest-xdist>=3,<4",
]
test-quality = [
  "pydocstyle>=6,<7",
  "flake8>=5,<8",
  "flake8-pyproject>=1.2,<2.0",
  "vulture>=2,<3",
]
test-all = [
  "pytest>=7,<10",
  "pytest-cov>=4,<8",
  "pytest-timeout>=2,<3",
  "hypothesis>=6,<7",
  "hypothesis-networkx>=0.3,<1.0",
  "pytest-benchmark>=4,<6",
  "pytest-xdist>=3,<4",
  "pydocstyle>=6,<7",
  "flake8>=5,<8",
  "flake8-pyproject>=1.2,<2.0",
  "vulture>=2,<3",
  "matplotlib>=3.7,<4.0",
  "scipy>=1.9",
  "sympy>=1.10",
]
test = [  # Legacy alias
  "pytest>=7,<10",
  "pytest-cov>=4,<8",
  "pytest-timeout>=2,<3",
  "hypothesis>=6,<7",
  "hypothesis-networkx>=0.3,<1.0",
  "pytest-benchmark>=4,<6",
  "pytest-xdist>=3,<4",
  "pydocstyle>=6,<7",
  "flake8>=5,<8",
  "flake8-pyproject>=1.2,<2.0",
  "vulture>=2,<3",
  "matplotlib>=3.7,<4.0",
  "scipy>=1.9",
  "sympy>=1.10",
]

# Type checking
typecheck = [
  "mypy>=1.8,<2.0",
  "pyright>=1.1.350,<1.2.0",
  "networkx-stubs>=0.0.1",
  "types-cachetools>=6.0.0.0",
]
# Development environment groups
dev-minimal = [
  "mypy>=1.8,<2.0",
  "black>=23,<26",
  "pytest>=7,<10",
  "pytest-cov>=4,<8",
  "pytest-timeout>=2,<3",
]
dev-full = [
  "pytest>=7,<10",
  "pytest-cov>=4,<8",
  "pytest-timeout>=2,<3",
  "hypothesis>=6,<7",
  "hypothesis-networkx>=0.3,<1.0",
  "pytest-benchmark>=4,<6",
  "pytest-xdist>=3,<4",
  "pydocstyle>=6,<7",
  "flake8>=5,<8",
  "flake8-pyproject>=1.2,<2.0",
  "vulture>=2,<3",
  "matplotlib>=3.7,<4.0",
  "jax>=0.4,<1.0",
  "mypy>=1.8,<2.0",
  "pyright>=1.1.350,<1.2.0",
  "networkx-stubs>=0.0.1",
  "types-cachetools>=6.0.0.0",
]

# Release tooling
release = [
  "python-semantic-release>=10.4,<11",
  "setuptools-scm>=8,<10",
  "build>=1,<2",
  "towncrier>=23,<26",
]

[project.scripts]
tnfr = "tnfr.cli:main"
tnfr-is-prime = "tnfr.tools.tnfr_is_prime_cli:main"

[project.urls]
Homepage = "https://github.com/fermga/TNFR-Python-Engine"
Repository = "https://github.com/fermga/TNFR-Python-Engine"
PyPI = "https://pypi.org/project/tnfr/"
Citation = "https://doi.org/10.5281/zenodo.17602860"
Zenodo = "https://zenodo.org/records/17602860"
Issues = "https://github.com/fermga/TNFR-Python-Engine/issues"
Documentation = "https://fermga.github.io/TNFR-Python-Engine/"
GPT = "https://chatgpt.com/g/g-67abc78885a88191b2d67f94fd60dc97-tnfr-resonant-fractal-nature-theory"

[tool.setuptools.package-data]
tnfr = ["py.typed", "schemas/*.json"]

[tool.setuptools.packages.find]
# Ensure all tnfr subpackages (including newly added modules like 'physics')
# are included in builds and editable installs.
where = ["src"]
include = ["tnfr", "tnfr.*"]

[tool.setuptools_scm]
tag_regex = '^v(?P<version>[0-9]+\.[0-9]+\.[0-9]+)$'
local_scheme = "no-local-version"
write_to = "src/tnfr/_generated_version.py"
fallback_version = "0.0.1"

[tool.semantic_release]
version_source = "tag"
commit_parser = "conventional"
allow_zero_version = false
major_on_zero = false
tag_format = "v{version}"

[tool.semantic_release.branches.main]
match = "^main$"
prerelease = false

[tool.semantic_release.changelog]
template_dir = "meta/semantic_release/templates"
mode = "update"

[tool.semantic_release.changelog.default_templates]
mask_initial_release = true
changelog_file = ""

[tool.semantic_release.commit_parser_options]
minor_tags = ["feat", "structure"]
patch_tags = ["fix", "perf", "refactor", "docs", "test", "build", "ci", "style", "chore"]
other_allowed_tags = ["revert", "docs", "test", "build", "ci", "style", "refactor", "perf", "chore"]
allowed_tags = ["feat", "fix", "perf", "refactor", "docs", "test", "build", "ci", "style", "chore", "structure", "revert"]
default_bump_level = 0
parse_squash_commits = true
ignore_merge_commits = true

[tool.black]
line-length = 88
target-version = ["py39", "py310", "py311", "py312", "py313"]

[tool.isort]
profile = "black"
line_length = 88
skip = ["benchmarks"]

[tool.flake8]
max-line-length = 88
# extend-ignore keeps flake8's black-compatible defaults (E704, E226, ...) and
# adds E203/E501/W503 (black) plus E402 (intentional post-setup imports in the
# scientific modules) and F841 (unused locals are tolerated in numeric kernels).
extend-ignore = ["E203", "E501", "W503", "E402", "F841"]
# Package __init__ files re-export the public API (intentional "unused" imports).
per-file-ignores = ["__init__.py:F401"]
exclude = ["benchmarks/"]

[tool.pydocstyle]
convention = "numpy"
add-ignore = [
  "D202",  # Allow blank line after docstring where needed for readability.
]

[tool.tnfr.language_check]
exclude = [
  "TNFR.pdf",
  "benchmarks/**/*.pdf",
]

[tool.pytest.ini_options]
pythonpath = ["src"]
testpaths = ["tests"]
addopts = "-m 'not slow'"
markers = [
  "slow: marks tests as slow (deselect with '-m \"not slow\"')",
  "benchmarks: run with 'pytest benchmarks --benchmark-only' to execute the benchmark suite",
  "stress: high-load deterministic stress coverage (select with '-m \"stress\"')",
  "val: Tests specific to VAL (Expansion) operator",
  "canonical: Tests validating canonical TNFR invariants",
  "nodal_equation: Tests validating fundamental nodal equation",
  "fractality: Tests validating fractal preservation",
  "integration: Integration tests that touch IO or external boundaries",
]

[tool.mypy]
python_version = "3.9"
warn_unused_configs = true
warn_return_any = false
no_implicit_optional = false
strict_equality = false
disallow_any_unimported = false
show_error_codes = true
follow_imports = "skip"
allow_redefinition = true
allow_untyped_defs = false
allow_untyped_calls = false
allow_untyped_globals = false

[[tool.mypy.overrides]]
module = ["networkx", "networkx.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["yaml", "yaml.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["numpy", "numpy.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["matplotlib", "matplotlib.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["jsonschema", "jsonschema.*"]
ignore_missing_imports = true


[build-system]
requires = ["setuptools>=78.1.1", "wheel"]
build-backend = "setuptools.build_meta"