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pyproject.toml
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[tool.poetry]
name = "tcr-embeddings"
version = "0.0.1"
description = "Analysis of Expressivity of TCR Embeddings."
authors = ["Rudy Yuen <r.yuen.20@alumni.ucl.ac.uk>"]
license = "MIT"
readme = "README.md"
[tool.poetry.dependencies]
python = "^3.12"
blosum = "2.0.3"
contourpy = "1.3.1"
cycler = "0.12.1"
fonttools = "4.55.2"
fsspec = "2024.10.0"
joblib = "1.4.2"
kiwisolver = "1.4.7"
libtcrlm = "1.0.0.post1"
matplotlib = "3.9.3"
numpy = "1.26.4"
packaging = "24.2"
pandas = "2.2.3"
polars = "1.16.0"
pyparsing = "3.2.0"
python-dateutil = "2.9.0.post0"
pytz = "2024.2"
sceptr = "1.1.0.post1"
scikit-learn = "1.5.2"
scipy = "1.14.1"
seaborn = "0.13.2"
setuptools = "75.1.0"
six = "1.17.0"
sparsemax = "0.1.9"
sympy = "1.13.1"
threadpoolctl = "3.5.0"
tidytcells = "2.1.3.post1"
tqdm = "4.67.1"
tzdata = "2024.2"
wheel = "0.44.0"
jinja2 = "3.1.4"
markupsafe = "3.0.2"
mpmath = "1.3.0"
networkx = "3.4.2"
pillow = "11.0.0"
pip = "24.3.0"
tbb = "2022.0.0"
tcmlib = "1.2.0"
typing-extensions = "4.12.2"
umf = "0.9.1"
filelock = "3.16.1"
intel-cmplr-lib-ur = "2025.0.3"
intel-openmp = "2025.0.3"
[[tool.poetry.source]]
name = "pytorch"
url = "https://download.pytorch.org/whl/cu124"
secondary = true
[tool.poetry.group.dev.dependencies]
mypy = "^1.13.0"
transformers = "^4.47.0"
pyarrow = "^18.1.0"
ipykernel = "^6.29.5"
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"
[tool.isort]
profile = "black"
known_first_party = ["tcr_embeddings", "tests"]
skip_gitignore = true
color_output = true
[tool.black]
target-version = ["py312"]
color = true
skip_magic_trailing_comma = true
[tool.mypy]
exclude = "(logs|output)/"
warn_redundant_casts = true
show_error_codes = true
show_column_numbers = true
check_untyped_defs = true
follow_imports = "silent"
warn_unused_ignores = false
ignore_missing_imports = true
explicit_package_bases = true
modules = [
"matplotlib",
"matplotlib.colours",
"matplotlib.dates",
"matplotlib.pyplot",
"matplotlib.ticker",
"matplotlib.transforms",
"pandas",
"polars",
"tqdm",
"csv",
"torch",
"virtualenv.config.convert"
]
mypy_path = ["."]
[tool.flake8]
max-line-length = 88
extend-ignore = ["E203", "W503", "E501"]