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pyproject.toml
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pyproject.toml
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# Poetry pyproject.toml: https://python-poetry.org/docs/pyproject/
[build-system]
requires = ["poetry_core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
[tool.poetry]
name = "foundation-cancer-image-biomarker"
version = "1.0.1a3"
description = "Official repo for Foundation Models for Quantitative Biomarker Discovery in Cancer Imaging [INSERT DOI]"
readme = "README.md"
authors = ["Suraj Pai <bspai@bwh.harvard.edu>"]
license = "MIT"
repository = "https://github.com/AIM-Harvard/foundation-cancer-image-biomarker"
homepage = "https://aim.hms.harvard.edu/foundation-cancer-image-biomarker"
# Keywords description https://python-poetry.org/docs/pyproject/#keywords
keywords = [] #! Update me
packages = [
{ include = "fmcib" },
]
# Pypi classifiers: https://pypi.org/classifiers/
classifiers = [ #! Update me
"Development Status :: 3 - Alpha",
"Intended Audience :: Developers",
"Operating System :: OS Independent",
"Topic :: Software Development :: Libraries :: Python Modules",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
]
[tool.poetry.dependencies]
python = ">=3.9,<3.12"
project-lighter = {version = "0.0.2a19", allow-prereleases = true}
wget = "^3.2"
google-cloud-storage = "^2.9.0"
thedicomsort = "^1.0.1"
dcmrtstruct2nii = "^5"
nibabel = "^5.1.0"
matplotlib = "^3.7.1"
platipy = "0.4.1"
pynrrd = "^1.0.0"
pydicom-seg = "^0.4.1"
pydicom = "^2.4.0"
itk = "^5.3.0"
scipy = "1.10.0"
fonttools = "^4.44.0"
pydantic = "1.10.13"
lightly = "1.4.19"
werkzeug = "^3.0.1"
urllib3 = "^2.1.0"
aiohttp = "^3.9.1"
pip = "^24.0"
tornado = "^6.4"
wandb = "^0.16.3"
mpmath = "1.3.0"
[tool.poetry.group.dev.dependencies]
black = "^24.4.2"
bandit = "^1.7.7"
isort = {extras = ["colors"], version = "^5.10.1"}
mypy = "^0.910"
mypy-extensions = "^0.4.3"
pre-commit = "^2.15.0"
pydocstyle = "^6.1.1"
pylint = "^2.11.1"
pytest = "^6.2.5"
pyupgrade = "^2.29.1"
safety = "^2.3.5"
coverage = "^6.1.2"
coverage-badge = "^1.1.0"
pytest-html = "^3.1.1"
pytest-cov = "^3.0.0"
aiohttp = "^3.9.3"
[tool.black]
# https://github.com/psf/black
target-version = ["py38"]
line-length = 127
color = true
exclude = '''
/(
\.git
| \.hg
| \.mypy_cache
| \.tox
| \.venv
| _build
| buck-out
| build
| dist
| env
| venv
)/
'''
[tool.isort]
# https://github.com/timothycrosley/isort/
py_version = 38
line_length = 127
known_typing = ["typing", "types", "typing_extensions", "mypy", "mypy_extensions"]
sections = ["FUTURE", "TYPING", "STDLIB", "THIRDPARTY", "FIRSTPARTY", "LOCALFOLDER"]
include_trailing_comma = true
profile = "black"
multi_line_output = 3
indent = 4
color_output = true
[tool.mypy]
# https://mypy.readthedocs.io/en/latest/config_file.html#using-a-pyproject-toml-file
python_version = 3.9
pretty = true
show_traceback = true
color_output = true
allow_redefinition = false
check_untyped_defs = true
disallow_any_generics = true
disallow_incomplete_defs = true
ignore_missing_imports = true
implicit_reexport = false
no_implicit_optional = true
show_column_numbers = true
show_error_codes = true
show_error_context = true
strict_equality = true
strict_optional = true
warn_no_return = true
warn_redundant_casts = true
warn_return_any = true
warn_unreachable = true
warn_unused_configs = true
warn_unused_ignores = true
[tool.pytest.ini_options]
# https://docs.pytest.org/en/6.2.x/customize.html#pyproject-toml
# Directories that are not visited by pytest collector:
norecursedirs =["hooks", "*.egg", ".eggs", "dist", "build", "docs", ".tox", ".git", "__pycache__"]
doctest_optionflags = ["NUMBER", "NORMALIZE_WHITESPACE", "IGNORE_EXCEPTION_DETAIL"]
# Extra options:
addopts = [
"--strict-markers",
"--tb=short",
"--doctest-modules",
"--doctest-continue-on-failure",
]
# Markers to categorize tests
markers = [
"slow: marks tests as slow (deselect with '-m \"not slow\"')",
"serial",
]
[tool.coverage.run]
source = ["tests"]
[coverage.paths]
source = "foundation-cancer-image-biomarker"
[coverage.run]
branch = true
[coverage.report]
fail_under = 50
show_missing = true
[tool.pylint.'MESSAGES CONTROL']
max-line-length = 127
disable = """
too-many-arguments,
no-else-return,
missing-module-docstring,
missing-function-docstring,
invalid-name
"""
generated-members = "torch.*"
[tool.pylint.master]
fail-under=8
[tool.poetry_bumpversion.file."version.py"]
[tool.poetry_bumpversion.file."fmcib/__init__.py"]
[tool.bandit]
skips = ["B108", "B301"]