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pyproject.toml
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pyproject.toml
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# configuration approach followed:
# - whenever possible, prefer pyproject.toml
# - for configurations insufficiently supported by pyproject.toml, use setup.cfg instead
# - setup.py discouraged; minimal stub included only for compatibility with legacy tools
[build-system]
requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
build-backend = "setuptools.build_meta"
[project]
name = "biomed-multi-alignment"
description = "MAMMAL (Molecular Aligned Multi-Modal Architecture and Language), a flexible, multi-domain architecture with an adaptable task prompt syntax."
authors = [
{name="IBM Research"},
{name="Moshe Raboh", email="[email protected]"}
]
version = "0.2.1"
readme = "README.md"
license = {file = "LICENSE.txt"}
# due to how PEP 440 defines version matching, prefer [incl, excl) definitions like below:
requires-python = ">=3.10, <3.13"
dependencies = [
"fuse-med-ml==0.4.0",
"tensorflow>=2.17",
"peft",
"tabulate",
"clearml",
"hydra-core",
"pytest",
]
[project.optional-dependencies]
examples = [
"PyTDC"
]
[project.urls]
repository = "https://github.com/BiomedSciAI/biomed-multi-alignment"
[tool.setuptools.packages]
find = {}
[tool.ruff]
target-version = "py310"
extend-include = ["*.ipynb"]
# Activate all the rules that are pyupgrade-related
lint.select = [
# "UP", # pyupgrade
"D", # pydocstyle
"PT", # pytest style checking
"C4", # comprehensions style checking
"PD", # pandas style checking
"F", # pyflakes: is-literal
"W605", # pycodestyle: invalid-escape-sequence
"I", # isort
]
# On top of the Google convention, disable `D417`, which requires
# documentation for every function parameter.
lint.ignore = [
"D100", # pydocstyle: Missing module docstring
"D101", # pydocstyle: Missing module-level docstring
"D102", # pydocstyle: Missing docstring in public module
"D103", # pydocstyle: Missing class docstring
"D105", # pydocstyle: Missing docstring in magic method
"D107", # pydocstyle: Missing parameter descriptions in the docstring
"D203", # pydocstyle: 1 blank line required before class docstring
"D205", # pydocstyle: 1 blank line required between summary line and description
"D212", # pydocstyle: Multi-line docstring summary should start at the first line
"D401", # pydocstyle: First line should be in imperative mood
"D417", # pydocstyle: Missing argument descriptions in the docstring
"F841", # flake8: unused variable
"PD011", # pandas do not use .values (false positives causing bugs in torch code)
"PD015", # Use .merge method instead of pd.merge function. They have equivalent functionality.
"PT011", #TODO remove
"UP035", # TODO types. remove
]
[lint.per-file-ignores]
"__init__.py" = ["I001"]
[tool.coverage.report]
exclude_lines = ["pragma: no cover", "abc.abstractmethod", "@abstract"]
#[tool.coverage.run]
#omit = ["gene_benchmark/tests/*"]
[tool.mypy]
disable_error_code = [
"index",
"override",
"arg-type",
"union-attr"
]