pyproject.toml

[project]
name = "gemmology-crystal-geometry"
version = "2.0.0"
description = "3D crystal geometry engine for crystallographic visualization"
readme = "README.md"
license = { text = "MIT" }
requires-python = ">=3.10"
authors = [
    { name = "Bissbert", email = "fabian@gemmology.dev" }
]
maintainers = [
    { name = "Bissbert", email = "fabian@gemmology.dev" }
]
keywords = [
    "crystallography",
    "mineralogy",
    "gemmology",
    "geometry",
    "polyhedra",
    "crystal",
    "visualization",
    "3d"
]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Education",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Chemistry",
    "Topic :: Scientific/Engineering :: Visualization",
    "Typing :: Typed"
]
dependencies = [
    "gemmology-cdl-parser>=2.0.0",
    "numpy>=1.20.0",
    "scipy>=1.7.0",
]

[project.urls]
Homepage = "https://crystal-geometry.gemmology.dev"
Documentation = "https://crystal-geometry.gemmology.dev/docs"
Repository = "https://github.com/gemmology-dev/crystal-geometry"
Issues = "https://github.com/gemmology-dev/crystal-geometry/issues"
Changelog = "https://github.com/gemmology-dev/crystal-geometry/blob/main/CHANGELOG.md"

[project.optional-dependencies]
dev = [
    "pytest>=7.0",
    "pytest-cov>=4.0",
    "ruff>=0.1.0",
    "mypy>=1.0"
]
docs = [
    "mkdocs>=1.5",
    "mkdocs-material>=9.0",
    "mkdocstrings[python]>=0.24"
]
native = [
    # Native acceleration is built from source via scikit-build-core
    # No runtime dependencies needed (Eigen is header-only)
]

[build-system]
requires = [
    "scikit-build-core>=0.5",
    "pybind11>=2.11",
]
build-backend = "scikit_build_core.build"

[tool.scikit-build]
# Use editable installs for development
wheel.packages = ["src/crystal_geometry"]
cmake.build-type = "Release"
cmake.minimum-version = "3.15"
build-dir = "build/{wheel_tag}"
# Allow cmake to fail gracefully (pure Python fallback)
strict-config = false
cmake.verbose = false

[tool.scikit-build.cmake.define]
# Default options, can be overridden with CMAKE_ARGS env var
USE_OPENMP = "OFF"

# cibuildwheel configuration for cross-platform wheel building
[tool.cibuildwheel]
# Build for Python 3.10-3.13
build = "cp310-* cp311-* cp312-* cp313-*"
# Skip musllinux (Alpine), PyPy, and 32-bit Linux (i686)
skip = "*-musllinux* pp* *_i686"
# Skip in-container tests (CI runs the full test suite separately).
# Testing inside cibuildwheel fails because scipy needs OpenBLAS in manylinux.
test-skip = "*"

[tool.cibuildwheel.linux]
before-all = "(yum install -y epel-release && yum install -y eigen3-devel openblas-devel) || (apt-get update && apt-get install -y libeigen3-dev libopenblas-dev) || true"
repair-wheel-command = "auditwheel repair -w {dest_dir} {wheel}"

[tool.cibuildwheel.macos]
before-all = "brew install eigen"
repair-wheel-command = "delocate-wheel -w {dest_dir} {wheel}"

[tool.cibuildwheel.windows]
before-all = "choco install eigen -y"
environment = { CMAKE_PREFIX_PATH = "C:\\ProgramData\\chocolatey\\lib\\eigen\\share\\eigen3\\cmake" }

# Fallback to setuptools if scikit-build-core not available
[tool.setuptools]
packages = ["crystal_geometry"]
package-dir = {"" = "src"}

[tool.setuptools.package-data]
crystal_geometry = ["py.typed"]

[tool.ruff]
line-length = 100
target-version = "py310"
exclude = ["benchmarks/"]

[tool.ruff.lint]
select = [
    "E",   # pycodestyle errors
    "W",   # pycodestyle warnings
    "F",   # pyflakes
    "I",   # isort
    "B",   # flake8-bugbear
    "C4",  # flake8-comprehensions
    "UP",  # pyupgrade
]
ignore = [
    "E501",  # line too long
    "E741",  # ambiguous variable name (h, k, l and I are standard crystallographic notation)
]

[tool.ruff.lint.isort]
known-first-party = ["crystal_geometry", "cdl_parser"]

[tool.mypy]
python_version = "3.10"
strict = true
warn_return_any = false  # numpy operations often return Any
warn_unused_ignores = true
ignore_missing_imports = true  # scipy stubs not always available
disable_error_code = ["type-arg"]  # numpy ndarray type parameters

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "-v --tb=short"

[tool.coverage.run]
source = ["src/crystal_geometry"]
branch = true
omit = [
    "*/tests/*",
    "*/__pycache__/*",
]

[tool.coverage.report]
# Target: 80% coverage (current: ~62%)
# Incrementally increase as coverage improves
fail_under = 60
show_missing = true
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise NotImplementedError",
    "if TYPE_CHECKING:",
    "if __name__ == .__main__.:",
]

# Semantic Release configuration
[tool.semantic_release]
version_toml = ["pyproject.toml:project.version"]
branch = "main"
upload_to_pypi = false  # We use separate pypi-publish workflow
upload_to_release = true
build_command = "pip install build && python -m build"

[tool.semantic_release.commit_parser_options]
allowed_tags = [
    "build",
    "chore",
    "ci",
    "docs",
    "feat",
    "fix",
    "perf",
    "refactor",
    "style",
    "test",
]
minor_tags = ["feat"]
patch_tags = ["fix", "perf"]

[tool.semantic_release.changelog]
template_dir = ".github/templates"
changelog_file = "CHANGELOG.md"

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

# Bandit security configuration
[tool.bandit]
exclude_dirs = ["tests", "benchmarks"]
skips = ["B101"]  # Skip assert warnings (we use assert in tests)