pyproject.toml

[tool.poetry]
name = "protein_metamorphisms_is"
version = "2.3.0"
description = "Comprehensive Python Module for Protein Data Management: Designed for streamlined integration and processing of protein information from both UniProt and PDB. Equipped with features for concurrent data fetching, robust error handling, and database synchronization."
authors = ["frapercan <frapercan1@alum.us.es>"]
readme = "README.md"

[tool.poetry.dependencies]
python = "^3.10"
docopt = "^0.6.2"
bio = "^1.6.0"
biopython = "^1.81"
sqlalchemy = "^2.0.23"
pyyaml = "^6.0.1"
py-cdhit = "^0.8.0"
psycopg2-binary = "^2.9.9"
pyarrow = "^15.0.0"
goatools = "^1.3.11"
pgvector = "^0.2.5"
networkx = "^3.3"
obonet = "^1.0.0"
scikit-learn = "^1.5.0"
transformers = "^4.41.1"
torch = "^2.3.0"
tokenizer = "^3.4.3"
mini3di = "^0.1.1"
matplotlib = "^3.9.0"
pika = "^1.3.2"
retry = "^0.9.2"
gemmi = "^0.6.7"
sentencepiece = "^0.2.0"
rcsb-api = "^0.5.0"
rcsbsearchapi = "^2.0.0"
fastobo = "^0.12.3"
responses = "^0.25.3"
h5py = "^3.12.1"
esm = "^3.1.1"
pandas = "^2.2.3"
zstd = "1.5.6.1"



[tool.poetry.group.dev.dependencies]
pytest = "^7.2.2"
coverage = {extras = ["toml"], version = "^7.2.1"}
flake8 = "^6.0.0"
flake8-bugbear = "^23.2.13"
taskipy = "^1.10.3"
sphinx = "^7.2.6"
sphinx-rtd-theme = "^1.2.0"
autopep8 = "^2.0.4"
black = "^23.11.0"
sqlalchemy-schemadisplay = "^1.3"
pytest-order = "^1.3.0"
sphinx-copybutton = "^0.5.2"






[tool.taskipy.tasks]
html_docs = "make html -C docs"
lint = "poetry run flake8 protein_metamorphisms_is"
autopep = "autopep8 --in-place --recursive . --max-line-length=79"
coverage = "poetry run coverage run -m --source=protein_metamorphisms_is pytest tests && poetry run coverage report -m"



[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"