pyproject.toml

[build-system]
requires = [
    "setuptools>=42, <74",
    "wheel>=0.38.4",
    "build>=0.10.0",
    "cython>=0.29.0",
    "numpy>=1.19.0",
    "mako",
]

build-backend = "setuptools.build_meta"

[project]
# For an example see REF: https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
name = "nanopyx"
description = "Nanoscopy Python library (NanoPyx, the successor to NanoJ) - focused on light microscopy and super-resolution imaging"
readme = "README.md"
requires-python = ">=3.9,<3.13"
license = { file = "LICENSE.txt" }
keywords = [
    "NanoJ",
    "Super-Resolution Microscopy",
    "Fluorescence",
    "BioImage Analysis",
]
authors = [
    { name = "Ricardo Henriques", email = "ricardo.jv.henriques@gmail.com" },
    { name = "Bruno Saraiva", email = "bruno.msaraiva2@gmail.com" },
    { name = "Inês Cunha", email = "inescunha200@gmail.com" },
    { name = "António Brito", email = "antmsbrito95@gmail.com" },
]
maintainers = [{ name = "Bruno Saraiva", email = "bruno.msaraiva2@gmail.com" }]
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
]
dependencies = [
    "liquid_engine",
    "mako>=1.3.0",
    "cython>=0.29.32",
    "numpy>=1.22,<2",
    "scipy>=1.8",
    "tifffile>=2022.5.4",
    "scikit-image>=0.19.2",
    "pyyaml>=6.0",
    "onedrivedownloader>=1.1.3",
    "gdown>=4.7.3",
    "tqdm>=4.64.1",
    "lmfit>=1.1.0",
    "opencv-python>=4.7.0.68",
    "pyopencl>=2022.3.1",
    "scikit-learn>=1.1.0",
    "matplotlib>=3.5",
    "importlib-resources",
]
dynamic = ["version"] # changed in setup.py

# [project.scripts]
# nanopyx-pyx2pxd = "scripts.pyx2pxd:main"
# nanopyx-c2cl = "scripts.c2cl:main"

[project.optional-dependencies]
all = ["nanopyx[developer,test,jupyter,doc, optional]"]
developer = ["pyx2pxd>=0.1.1", "black>=23.1.0", "flake8>=6.0.0"]
test = [
    "nox>=2022.11.21",
    "pytest==7.2", # required to work with pytest-cython (https://github.com/lgpage/pytest-cython/issues/58)
    "pytest-cov>= 4.0.0",
    "pytest-icdiff>=0.6",    # https://github.com/hjwp/pytest-icdiff
    "pytest-clarity>=1.0.1", # https://pypi.org/project/pytest-clarity/
    "pytest-timeout>=2.1.0",
    "pytest-plt>=1.1.0",
    "pytest-xdist>=3.1.0",
    "pytest-sugar>=0.9.6",
    "pytest-cython>=0.2.0",
    "nanopyx[jupyter]",
    "nanopyx[optional]",
]
optional=["numba", "dask", "dask_image", "transonic"]
cuda = ["cupy"] # should be manually installed by users according to their CUDA version https://docs.cupy.dev/en/stable/install.html
jupyter = [
    "nbformat>=4.2.0",
    "seaborn>=0.12.1",
    "celluloid>=0.2.0",  # https://towardsdatascience.com/the-simplest-way-of-making-gifs-and-math-videos-with-python-aec41da74c6e
    "jupyterlab>=3.5.3",
    "ipywidgets>=8.0.0",
    "nbmake>=1.3.5",
    "ipyfilechooser>=0.6.0", 
    "ipympl>=0.9.3",
    "stackview>=0.6.1",
    "ipycanvas>=0.13",
]
colab = [
    "stackview>=0.6.1",
    "ipycanvas==0.11.0",
]
doc = ["pdoc>=12.3.1", "nanopyx[jupyter,developer]"]

[project.urls]
homepage = "https://github.com/HenriquesLab/NanoPyx"
documentation = "https://henriqueslab.github.io/nanopyx"
repository = "https://github.com/HenriquesLab/NanoPyx"
#changelog = "https://github.com/me/spam/blob/master/CHANGELOG.md"
bug_tracker = "https://github.com/HenriquesLab/NanoPyx/issues"

[tool.setuptools]
include-package-data = true

[tool.setuptools.package-data]
"*" = ["*.yaml", "*.jpg", "*.cl"]

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

[tool.black]
exclude = '''
/(
    \.eggs
  | \.git
  | \.venv
  | build
  | dist
)/
'''
line-length = 120
import-order = ["stdlib", "thirdparty", "local"]
py37 = true

[tool.flake8]
# https://pypi.org/project/Flake8-pyproject/
# https://flake8.pycqa.org/en/latest/user/configuration.html
filename = [".py", "*.pyx", "*.px*"]
exclude = [".eggs", "*.egg,build"]
ignore = ["E901", "E225", "E226", "E227", "W503", "F401"]
max-line-length = 120

[tool.pyright]
reportUndefinedVariable = false
reportMissingImports = false

[tool.pytest.ini_options]
addopts = "--cov=nanopyx --plots --doctest-modules --doctest-cython --ignore-glob=run*Tools.py --ignore=setup.py --ignore=notebooks/ --ignore=src/scripts --ignore=src/notebookchef --ignore=tests/notebooks --cov-report term-missing"
timeout = 6001
plt_dirname = "tests_plots"
doctest_encoding = "latin1"
doctest_optionflags = "NORMALIZE_WHITESPACE ELLIPSIS"
# Filters are standard python warning filters as described here:
# https://docs.python.org/3/library/warnings.html#the-warnings-filter
filterwarnings = [
    "ignore:.*distutils.*:DeprecationWarning:.*",
    "ignore:.*distutils.*:UserWarning:.*",
    "ignore:.*The 'u' format is deprecated.*:DeprecationWarning:pywintypes",
    "ignore:.*Deprecated NumPy.*:DeprecationWarning:.*",
]
testpaths = ["tests", "src/nanopyx"]

[tool.coverage.run]
plugins = ["Cython.Coverage"]
source = ["src/nanopyx"]
omit = [
    "tests",
    "src/nanopyx/core/utils/benchmark.py",
    "src/nanopyx/core/templates",
    "*__init__.py",
    "*__*.py"
]

[tool.cibuildwheel]
# https://cibuildwheel.readthedocs.io/en/stable/options/
skip = ["pp*", "*musllinux*"]
build = ["cp39-*", "cp310-*", "cp311-*"]
# it is not possible to test arm64 and the arm64 part of a universal2 wheel on this CI platform
test-skip = ["*arm64"]
# build-frontend = "pip"
# config-settings = {}
# dependency-versions = "pinned"
# environment = {}
# environment-pass = []

# # An number from 1 to 3 to increase the level of verbosity (corresponding to invoking pip with -v, -vv, and -vvv),
# # between -1 and -3 (-q, -qq, and -qqq), or just 0 (default verbosity)
build-verbosity = 0

# before-all = ""
# before-build = ["git status"]
# repair-wheel-command = ""

test-command = "pytest {project}/tests"
test-requires = ["nanopyx[test]"]
# test-extras = []

[tool.cibuildwheel.linux]
# archs = ["x86_64"]
manylinux-x86_64-image = "manylinux2014"
# before-all = "yum install opencv opencv-devel opencv-python"
# before-all = "yum install opencv-python"
# repair-wheel-command = "auditwheel repair -w {dest_dir} {wheel}"

[tool.cibuildwheel.macos]
archs = ["x86_64", "arm64"]
before-all = ["brew install llvm libomp"]
test-requires = ["nanopyx[test]"]
#test-command = "pytest -n=1 --timeout=1200 {project}/tests"
# #repair-wheel-command = "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}"
# repair-wheel-command = "delocate-wheel -w {dest_dir} -v {wheel}"

# [tool.cibuildwheel.macos.environment]
# CMAKE_OSX_ARCHITECTURES = "arm64;x86_64"
# MACOSX_DEPLOYMENT_TARGET = "11"
# LDFLAGS="-L/usr/local/lib"
# CXX="/usr/local/opt/llvm/bin/clang++"
# CC="/usr/local/opt/llvm/bin/clang"

[tool.cibuildwheel.windows]
archs = ["AMD64"]
test-requires = ["nanopyx[test]"]
#test-command = "pytest -n=0 --timeout=1200 {project}\\tests"
# before-build = "pip install delvewheel"
# repair-wheel-command = "delvewheel repair -w {dest_dir} {wheel}"

# [tool.cibuildwheel.windows.environment]
# SETUPTOOLS_USE_DISTUTILS = "stdlib"