pyproject.toml

[build-system]
requires = ["setuptools>=61.0", "wheel", "setuptools-scm>=8"]
build-backend = "setuptools.build_meta"

[project]
name = "pnanolocz"
description = "A Python library for AFM, HS-AFM, and Localization AFM data analysis. Based on NanoLocz"
authors = [
    { name = "George Heath", email = "G.R.Heath@leeds.ac.uk" },
    { name = "Daniel E. Rollins", email = "d.e.rollins@leeds.ac.uk" }
]
dynamic = ["version"]
readme = { file = "README.md", content-type = "text/markdown" }
license = { text = "GPL-3.0-or-later" }
requires-python = ">=3.11"
dependencies = [
    "numpy",
    "scipy",
    "ruptures",
    "sknw",
    "scikit-image>=0.26,<0.27",
]
keywords = [
  # Core domain
  "AFM",
  "atomic force microscopy",
  "high-speed AFM",
  "HS-AFM",
  "scanning probe microscopy",
  "SPM",
  "nanoscopy",
  "nanometrology",
  "LAFM",
  "Localization AFM",
  "microscopy",

  # Techniques and data
  "image processing",
  "video processing",
  "image segmentation",
  "image analysis",

  # Scientific software context
  "scientific visualization",
  "data analysis",
  "microscopy data",
  "scientific computing",
  "open science",

  # Target users
  "materials science",
  "biophysics",
  "nanotechnology",
  "biomolecular imaging",
  "surface analysis",

  "nanolocz",
]

classifiers = [
  "Development Status :: 3 - Alpha",
  "Intended Audience :: Science/Research",
  "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
  "Natural Language :: English",
  "Operating System :: OS Independent",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Topic :: Scientific/Engineering :: Image Processing",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0",
    "pytest-cov",
    "pre-commit",
    "isort",
    "ruff",
    "black",
    "codespell>=2.3.0",
    "mypy==1.11.1",
    "nbstripout",
    "setuptools_scm",
]

[project.urls]
Homepage = "https://github.com/derollins/Python-Nanolocz-Library"
Issues = "https://github.com/derollins/Python-Nanolocz-Library/issues"
Changelog = "https://github.com/derollins/Python-Nanolocz-Library/blob/main/CHANGELOG.md"

[project.entry-points."playnano.filters"]
pnanolocz_level = "pnanolocz.level:apply_level"
pnanolocz_level_auto = "pnanolocz.level_auto:apply_level_auto"

[tool.setuptools]
package-dir = { "" = "src" }

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

[tool.setuptools_scm]
write_to = "src/pnanolocz/_version.py"

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

exclude = '''
(
  ^\.git
| ^\.hg
| ^\.mypy_cache
| ^\.tox
| ^\.venv
| ^_build
| ^buck-out
| ^build
| ^dist
| \.ipynb$
)
'''

[tool.isort]
profile = "black"
line_length = 88
multi_line_output = 3
include_trailing_comma = true
force_grid_wrap = 0
combine_as_imports = true
known_first_party = ["pnanolocz"]
known_third_party = ["numpy","scipy","matplotlib","skimage","ruptures","sknw"]

[tool.ruff]
line-length = 88
target-version = "py311"
respect-gitignore = true
src = ["src"]
exclude = ["notebooks", "*.ipynb"]

[tool.ruff.lint]
select = ["E", "F", "I", "B", "C4", "D"]
ignore = ["D100", "D104", "D203", "D212", "D401"]

[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.codespell]
skip = "*.egg-info,*.png,*.jpg,*.jpeg,*.gif,*.bmp,*.svg,*.ico,*.pdf,*.zip,*.gz,*.bz2,*.xz,*.7z,*.mp3,*.wav,*.mp4,*.mov,*.tif,*.tiff,*.ipynb,docs/_build/*,build/*,dist/*,*.html,*.css,*.js"
ignore-words-list = "tabel,crate"
check-filenames = false
check-hidden = false

[tool.mypy]
python_version = "3.11"
mypy_path = ["src"]

# Only check your library code; do not include tests here.
files = ["src"]

# Regular package (you created src/pnanolocz/__init__.py)
explicit_package_bases = false
namespace_packages = false

# Your existing strictness
strict = true
warn_unused_ignores = false
disallow_untyped_defs = true
exclude = '^tests/'

[[tool.mypy.overrides]]
module = [
    "scipy.*",
    "skimage.*",
    "ruptures",
    "sknw",
    "numpy.*"
]
ignore_missing_imports = true

[tool.pytest.ini_options]
addopts = "--cov=pnanolocz --cov-report=term-missing --cov-append"
testpaths = ["tests"]

[tool.coverage.run]
branch = true
source = ["pnanolocz"]

[tool.coverage.report]
exclude_lines = [
  "pragma: no cover",
  "if __name__ == .__main__.:",
  "raise NotImplementedError"
]