pyproject.toml

[build-system]
requires = ["setuptools>=61.2", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "affinivae"
version = "0.0.1"
description = "Affinity-VAE"
authors = [{name = "Alan R. Lowe", email = "alowe@turing.ac.uk"}]
license = {text = "BSD 3-Clause"}
classifiers = [
    "Programming Language :: Python",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.10",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Image Recognition",
    "Operating System :: POSIX",
    "Operating System :: Unix",
    "Operating System :: MacOS",
]
requires-python = ">=3.10"

dependencies = [
    "altair",
    "click",
    "mrcfile",
    "matplotlib",
    "numpy",
    "scipy",
    "pillow",
    "pandas",
    "pyyaml",
    "requests",
    "scikit-image",
    "scikit-learn",
    "tensorboard",
    "umap-learn",
    "caked@git+https://github.com/alan-turing-institute/caked/" #to be changed when caked is in pypi.
]

[project.readme]
file = "README.md"
content-type = "text/markdown"

[project.urls]
Homepage = "https://github.com/alan-turing-institute/affinity-vae"

[tool.hatch]
version.path = "avae/__init__.py"
envs.default.dependencies = [
  "pytest",
  "pytest-cov",
]



[project.optional-dependencies]
all = ["torch",
    "torchvision",
    "pydantic>2",
    "lightning",
    ]

test = [
    "affinivae[all]",
    "pytest >=6",
    "pytest-cov >=3",
    "lightning",
]

baskerville = [
    "pydantic>2",
     "lightning",

]
napari = [
    "napari[all]",
    "torch",
    "torchvision",
    "pydantic<2", # latest napari version is incompatible with napari, napari demo doesnt use pydantic.
]

[tool.pytest.ini_options]
minversion = "6.0"
addopts = ["-ra", "--showlocals"]#, "--strict-markers", "--strict-config"]
xfail_strict = true
filterwarnings = [ # NEED TO FIX THESE WARNINGS ISSUE X
    "error",
    "ignore:jsonschema.RefResolver is deprecated as of v4.18.0, in favor of the:DeprecationWarning",
    "ignore:The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator.",
    "ignore:Tensorflow not installed; ParametricUMAP will be unavailable",
    "ignore:pkg_resources is deprecated as an API",
    "ignore:Deprecated call to `pkg_resources.declare_namespace('mpl_toolkits')`",
    "ignore:The get_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later.",
    "ignore:Maximum iterations (500) reached and the optimization hasn't converged yet", # FIX THESE WARNINGS ISSUE x
    "ignore:Could not initialize NNPACK!.",
    "ignore:Mean of empty slice.",
    "ignore:invalid value encountered in divide",
    "ignore:Degrees of freedom <= 0 for slice",
    "ignore:Scoring failed. The score on this train-test partition for these parameters will be set to nan.",
    "ignore:One or more of the test scores are non-finite:",
]

log_cli_level = "INFO"
testpaths = [
  "tests",
]
[tool.setuptools]
include-package-data = true
license-files = ["LICENSE.md"]

[tool.setuptools.packages]
find = {namespaces = false}

[tool.tox]
isolated_build = "true"

[tool.tox.envlist]
extend-ignore = [
  "PLR",    # Design related pylint codes
  "E501",   # Line too long
]

src = ["avae"]
unfixable = [
  "F841", # Would remove unused variables
]
exclude = []
flake8-unused-arguments.ignore-variadic-names = true

[tool.black]
target-version = ['py38', 'py39', 'py310']
line-length = 79
skip-string-normalization = true
include = '\.pyi?$'
exclude = '''
(
  /(
      \.eggs
    | \.git
    | \.hg
    | \.mypy_cache
    | \.tox
    | \.venv
    | _build
    | build
    | dist
    | examples
  )/
)
'''

[tool.isort]
profile = "black"
line_length = 79