pyproject.toml

[tool.poetry]
name = "modos"
version = "0.2.3"
description = "SMOC Multi-Omics Digital Object System API"
authors = ["SDSC-ORDES"]
license = "Apache-2.0"
readme = "README.md"
packages = [{ include = "modos" }]

[tool.poetry.dependencies]
calamus = "^0.4.2"
modos_schema = "^0.3"
pysam = "^0.22.0"
python = "^3.11"
pyyaml = "^6.0.1"
rdflib = "^6.3"
s3fs = "^2024.3.1"
typer = "^0.9.0"
zarr = "^2.16.1"
pydantic = "^2.8.2"
botocore = "<1.36.0"

pyfuzon = { version = "^0.2", optional = true}
prompt-toolkit = "^3.0.48"
pyteomics = "^4.7.4"
pandas = "^2.2.3"

[tool.poetry.extras]
pyfuzon = ["pyfuzon"]

[tool.poetry.group.dev.dependencies]
pre-commit = "^3.6.0"
black = "^23.12.0"
pytest = "^8.2.2"
pytest-cov = "^4.1.0"
testcontainers = { extras = ["minio"], version = "^4.4.1" }

[tool.poetry.group.docs]
optional = true

[tool.poetry.group.docs.dependencies]
myst-parser = "^2.0.0"
sphinx = "^7.2.6"
pydata-sphinx-theme = "^0.15.2"
sphinx-click = "^5.1.0"
sphinx-autoapi = "^3.0.0"
sphinx-design = "^0.5.0"

[tool.poetry.scripts]
modos = 'modos.cli:cli'

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

# Tooling configuration

[tool.pytest.ini_options]
addopts = ["--doctest-modules"]
testpaths = ["modos", "tests"]

[tool.black]
line-length = 79
target-version = ["py310"]