pyproject.toml

[tool.poetry]
name = "lm-assistant-for-biocatalysis"
version = "0.0.1"
description = "This project focuses on streamlining and automating key tasks in protein modeling, optimization, and the design of experiments for biocatalyzed reactions."
authors = [" Y.G. Nana Teukam <yves.g.nana@zgmail.com>"]
readme = "README.md"
packages = [{include = "lmabc", from="src"}]
include = [
    "lmabc/py.typed",
    "resources/*",
    "resources/*/*",
    "assets/*",
    "tools_setup/*"
    ]

[tool.poetry_bumpversion.file."src/lmabc/__init__.py"]

[[tool.poetry.source]]
name = "PyPI"
priority = "primary"

[tool.poetry.dependencies]
python = ">=3.10,<3.11"
tqdm = "^4.25.0"
# For extras

# For internal packages
# internal-package = { version = "^0.0.1", source = "internal_private" }
python-dotenv = "^1.0.1"

ibm-generative-ai = "^3.0.0"
ipykernel = "^6.29.5"
pydantic-settings = "^2.4.0"
biopython = "^1.84"
rdkit = "^2024.3.5"
loguru = "^0.7.2"
torch = ">=1.0,<=1.12.1"
streamlit = "1.33"
colorama = "^0.4.6"
rxn-aa-mapper = {git = "https://github.com/rxn4chemistry/rxnaamapper.git"}
langchain-unstructured = "^0.1.2"
unstructured = "^0.15.9"
requests = "^2.32.3"
types-requests = "^2.32.0.20240907"
rcsbsearchapi = "^1.6.0"
protobuf = "3.20.3"
importlib-resources = "^6.4.5"
langchain-ibm = "^0.3.1"
langchain = "^0.3.3"
langchain-community = "^0.3.2"
langchain-huggingface = "^0.1.0"
enzeptional = "^1.0.4"
bitsandbytes = "0.42.0"
accelerate = "^1.0.1"
langchain-ollama = "^0.2.0"
pandas = "^2.0.0"

[tool.poetry.scripts]
lmabc = "lmabc.cli:main"
lmabc-app = "lmabc.app.launcher:main"

[tool.poetry.dev-dependencies]
jupyter = "^1.0.0"
mypy = "^1.0.0"
pytest = "^7.4.4"
pytest-cov = "^5.0.0"
ruff = "^0.1.3"
types-setuptools = "^57.4.14"

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

[tool.mypy]
check_untyped_defs = true

ignore_missing_imports = true

[tool.ruff]
# Include also Jupyter notebooks.
extend-include = ["*.ipynb"]
# Exclude a variety of commonly ignored directories.
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".git-rewrite",
    ".hg",
    ".ipynb_checkpoints",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pyenv",
    ".pytest_cache",
    ".pytype",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    ".vscode",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "site-packages",
    "venv",
]

# Same as Black.
line-length = 100
indent-width = 4

target-version = "py310"

[tool.ruff.lint]
# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
# McCabe complexity (`C901`) by default.
preview = true
select = [
    "E4", 
    "E7", 
    "E9", 
    "F", 
    "W291", 
    "W292", 
    "W505", 
    "E721",
    "I",
    "N801",
    "N802",
    "N803",
    "N804",
    "N805",
    "N806",
    "N816",
    "D100",
    "D101",
    "D102",
    "D103",
    "D104",
    "D105",
    "D106",
    "D107",
    "D300",
    "UP010",
    "UP011",
    "UP019",
    "UP032",
    "ARG",
    "PTH",
    "LOG001",
    "LOG002",
]
ignore = []

# Allow fix for all enabled rules (when `--fix`) is provided.
fixable = ["ALL"]
unfixable = []

# Allow unused variables when underscore-prefixed.
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

[tool.ruff.format]
preview = true
# Like Black, use double quotes for strings.
quote-style = "double"

# Like Black, indent with spaces, rather than tabs.
indent-style = "space"

# Like Black, respect magic trailing commas.
skip-magic-trailing-comma = false

# Like Black, automatically detect the appropriate line ending.
line-ending = "auto"

# Enable auto-formatting of code examples in docstrings. Markdown,
# reStructuredText code/literal blocks and doctests are all supported.
#
# This is currently disabled by default, but it is planned for this
# to be opt-out in the future.
docstring-code-format = false

# Set the line length limit used when formatting code snippets in
# docstrings.
#
# This only has an effect when the `docstring-code-format` setting is
# enabled.
docstring-code-line-length = "dynamic"