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pyproject.toml
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[tool.poetry]
name = "medem"
version = "0.0.0"
description = "Medical_Embedding_Transfer"
authors = ["Matthieu Doutreligne <[email protected]>"]
license = "EUPL-v1.2"
readme = "README.md"
repository = "https://github.com/soda-inria/predictive-ehr-benchmark"
homepage = "https://github.com/soda-inria/predictive-ehr-benchmark"
include = ["bin"]
keywords = []
classifiers = [
"Intended Audience :: Developers",
"Natural Language :: English",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: Implementation :: CPython",
"Programming Language :: Python",
"Topic :: Software Development :: Libraries :: Python Modules",
]
# [tool.poetry.urls]
[tool.poetry.dependencies]
python = ">=3.8, <3.11"
# Project-Specific
click = "^8.0.4"
# Jupyter Notebook
jupyter = "^1.0.0"
matplotlib = "^3.5.1"
jupytext = "^1.13.7"
python-dotenv = "^0.15.0"
scikit-learn = "^1.0.0"
importlib-metadata = "^4.11.3"
Sphinx = "^4.4.0"
sphinx-click = "^3.1.0"
sphinxcontrib-apidoc = "^0.3.0"
pydata-sphinx-theme = "^0.12.0"
sphinx-autodoc-typehints = "^1.17.0"
Pygments = "^2.11.2"
myst-parser = "^0.17.0"
seaborn = "^0.12.2"
tabulate = "^0.9.0"
openpyxl = "^3.1.2"
tqdm = "^4.65.0"
schemdraw = {version="^0.16", python=">=3.8"}
#eds-scikit = { version = "^0.1.5", optional = true, python = ">=3.7.1, <3.8"}
loguru = "0.6.0"
polars = "^0.18.0"
pyarrow = "^11.0.0"
tableone = "^0.7.12"
moepy = "^1.1.4"
event2vec = ">=0.0.44"
[tool.poetry.dev-dependencies]
# Testing
pytest = "^7.1.1"
pytest-cov = "^3.0.0"
pytest-mock = "^3.7.0"
pytest-sugar = "^0.9.4"
pytest-xdist = "^2.5.0"
# Linting
## Type Checking and Data Validation
mypy = "^0.942" # Static type checker
## Code formatting
black = "^22.1.0" # see: https://black.readthedocs.io/en/stable/editor_integration.html
## Code quality
isort = "^5.10.1"
pylint = "^2.13.0"
## Automation and management
pre-commit = "^2.17.0"
# Documentation
[tool.poetry.group.docs]
optional = true
[tool.poetry.group.docs.dependencies]
importlib-metadata = { version = "^4.11.3", optional = true }
myst-parser = { version = "^0.17.0", optional = true }
pygments = { version = "^2.11.2", optional = true }
sphinx = { version = "^4.4.0", optional = true }
sphinx-autodoc-typehints = { version = "^1.17.0", optional = true }
pydata-sphinx-theme = { version = "^0.12.0", optional = true }
sphinxcontrib-apidoc = { version = "^0.3.0", optional = true }
sphinx-click = { version = "^3.1.0", optional = true }
# see: https://github.com/sphinx-doc/sphinx/issues/10291
jinja2 = { version = "<3.1", optional = true}
#eds = ["eds-scikit"]
[tool.poetry.scripts]
cli = "bin.cli:cli"
#################################################################################
# Tooling configs #
#################################################################################
[tool.poetry.group.dev.dependencies]
pylint = "^2.16.2"
ipdb = "^0.13.11"
[tool.black]
line-length = 79
[tool.coverage.run]
branch = true
concurrency = ["multiprocessing"]
parallel = true
source = ["medem"]
[tool.coverage.report]
exclude_lines =[
"pragma: no cover",
"raise AssertionError",
"raise NotImplementedError",
"if __name__ == .__main__.:",
]
fail_under = 70
show_missing = true
skip_covered = true
[tool.isort]
profile = "black"
atomic = "true"
combine_as_imports = "true"
line_length = 79
[tool.mypy]
disallow_untyped_defs = false
files = ["medem/*.py","bin/*.py"]
exclude = "notebooks/config.py"
ignore_missing_imports = true
pretty = true
show_column_numbers = true
show_error_context = true
show_error_codes = true
[tool.pylint.basic]
good-names-rgxs = ["^Test_.*$", "logger"]
[tool.pylint.messages_control]
disable = [
# Explicitly document only as needed
"missing-module-docstring",
"missing-class-docstring",
"missing-function-docstring",
# Black & Flake8 purview
"line-too-long",
#"bad-continuation",
"c-extension-no-member",
# Ignore errors resulting from Jupyter notebook-style programming
"invalid-name",
"redefined-outer-name",
"reimported",
"ungrouped-imports",
"wrong-import-order",
"wrong-import-position",
]
[tool.pylint.similarities]
# Ignore imports when computing similarities.
ignore-imports = "yes"
[tool.cruft]
skip = [
".git",
"README.md",
]
[tool.pytest.ini_options]
addopts = ["-rfsxX", "-l", "--tb=short", "--strict-markers", "-vv", "-pno:warnings"]
log_cli = 1
log_cli_level = "ERROR"
xfail_strict = "true"
testpaths = ["tests",]
norecursedirs = [".*", "*.egg", "build", "dist",]
[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"