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pyproject.toml
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[project]
name = "medcat2"
version = "2.0.0-dev"
description = "Medical Concept Annotation Toolkit (v2)"
readme = "README.md"
requires-python = ">=3.9"
license = {file = "LICENSE"}
keywords = ["ML", "NLP", "NER+L"]
authors = [
{name = "Z. Kraljevic"},
{name = "A. Shek"},
{name = "T. Searle"},
{name = "X. Bai"},
{name = "M. Ratas"},
]
# This should be your name or the names of the organization who currently
# maintains the project, and a valid email address corresponding to the name
# listed.
maintainers = [
{name = "CogStack", email = "[email protected]" }
]
classifiers = [
# How mature is this project? Common values are
# 3 - Alpha
# 4 - Beta
# 5 - Production/Stable
"Development Status :: 3 - Alpha",
"Intended Audience :: Hospital Trust Technical Management",
"Topic :: Natural Language Processing :: Named Entity Recognition and Linking",
# Specify the Python versions you support here. In particular, ensure
# that you indicate you support Python 3. These classifiers are *not*
# checked by "pip install". See instead "python_requires" below.
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3 :: Only",
]
# This field lists other packages that your project depends on to run.
# Any package you put here will be installed by pip when your project is
# installed, so they must be valid existing projects.
#
# For an analysis of this field vs pip's requirements files see:
# https://packaging.python.org/discussions/install-requires-vs-requirements/
dependencies = [ # Optional
"numpy>2.0",
"dill",
"pandas>=2.2,<3.0",
"tqdm>=4.64,<5.0",
"xxhash>=3.5.0,<4.0",
"pydantic>2.0",
# TODO - others
]
# List additional groups of dependencies here (e.g. development
# dependencies). Users will be able to install these using the "extras"
# syntax, for example:
#
# $ pip install sampleproject[dev]
#
# Similar to `dependencies` above, these must be valid existing
# projects.
[project.optional-dependencies] # Optional
dev = [
"ruff~=0.1.7",
"mypy",
"flake8",
]
spacy = [
"spacy",
"spacy<3.8.4; python_version == '3.9'"
]
meta_cat = [
"peft>0.8.2,<1.0",
"torch>=2.4.0,<3.0",
"scikit-learn>=1.1.3,<2.0",
]
dict_ner = [
"pyahocorasick>=2.1.0,<3.0"
]
deid = [
"datasets>=2.2.2,<3.0.0",
"transformers>=4.41.0,<5.0" # avoid major bump
]
test = [] # TODO - list
[project.urls]
"Homepage" = "https://cogstack.org/"
"Bug Reports" = "https://discourse.cogstack.org/"
"Source" = "https://github.com/CogStack/MedCAT/"
[build-system]
# These are the assumed default build requirements from pip:
# https://pip.pypa.io/en/stable/reference/pip/#pep-517-and-518-support
requires = ["setuptools>=43.0.0", "wheel"]
build-backend = "setuptools.build_meta"