pyproject.toml

[project]
name = "pycashier"
description = "cash in on expressed barcode tags"
authors = [{ name = "Daylin Morgan", email = "daylinmorgan@gmail.com" }]
dependencies = [
  "rich>=12.0.0",
  "tomlkit>=0.10.1",
  "click-rich-help>=22.1.0",
  "click>=8.1.0",
  "polars>=1.10.0",
]
requires-python = ">=3.9"
readme = "README.md"
license = { text = "MIT" }
dynamic = ["version"]

[project.urls]
repository = "https://github.com/brocklab/pycashier/"
documentation = "https://docs.brocklab.com/pycashier"

[project.scripts]
pycashier = "pycashier.cli:main"

[build-system]
requires = ["setuptools>=64", "setuptools_scm>=8"]
build-backend = "setuptools.build_meta"

[tool.setuptools_scm]

[tool.mypy]
check_untyped_defs = true
disallow_untyped_defs = true
disallow_incomplete_defs = true
disallow_untyped_decorators = true
disallow_any_unimported = true
no_implicit_optional = true
warn_return_any = true
warn_no_return = false
warn_unused_ignores = true
show_error_codes = true
ignore_missing_imports = true

[tool.ruff]
select = [
  # Pyflakes
  "F",
  # Pycodestyle
  "E",
  "W",
  # isort
  "I001",
]
# docstrings are longer because of formatting
# ruff will handle the code formatting for us
ignore = ["E501"]

[tool.coverage.run]
omit = ["tests/", "env/"]

[tool.pixi]

[tool.pixi.project]
name = "pycashier"
authors = ["Daylin Morgan <daylinmorgan@gmail.com>"]
channels = ["conda-forge", "bioconda"]
platforms = ["linux-64"]


[tool.pixi.environments]
dev = [
  "base",
  "bioconda",
  "dev",
  "pycashier",
  "build",
  "docs",
  "tutorial",
  "test",
]
docs = ["base", "pycashier", "docs", "tutorial"]
prod = ["base", "bioconda", "prod"]
build = ["base", "build"]
test = ["base", "bioconda", "dev", "test", "pycashier", "prod"]
test39 = ["base", "bioconda", "dev", "test", "pycashier", "prod", "test39"]
test310 = ["base", "bioconda", "dev", "test", "pycashier", "prod", "test310"]
test311 = ["base", "bioconda", "dev", "test", "pycashier", "prod", "test311"]
test312 = ["base", "bioconda", "dev", "test", "pycashier", "prod", "test312"]


[tool.pixi.host-dependencies]
pip = "*"

[tool.pixi.feature.base.dependencies]
python = ">=3.9,<3.13" # https://bioconda.github.io/faqs.html#what-versions-are-supported
# when pixi add polars to pypi-dependencies it was trying to build it with cargo
# adding it here to use pre-built objects from conda-forge
polars = ">=1.10.0"

[tool.pixi.feature.docs.dependencies]
sphinx = "*"
sphinx-autobuild = "*"
sphinx-copybutton = "*"
sphinx-inline-tabs = "*"
myst-parser = "*"
shibuya = "*"


[tool.pixi.feature.pycashier.pypi-dependencies]
pycashier = { path = ".", editable = true }

[tool.pixi.feature.dev.dependencies]
pre-commit = ">=3"
mypy = ">=0.982"

[tool.pixi.feature.prod.dependencies]
rich = ">=12.0.0"
tomlkit = ">=0.10.1"
click-rich-help = ">=22.1.0"
click = ">=8.1.0"
polars = ">=1.10.0"

[tool.pixi.feature.bioconda.dependencies]
cutadapt = ">=4.6,<5"
starcode = ">=1.4,<2"
fastp = ">=0.23.4,<0.24"
pysam = ">=0.22.0,<0.23"

[tool.pixi.feature.test.dependencies]
pytest = ">=7.2.0"
pytest-cov = ">=4.1.0"

[tool.pixi.feature.tutorial.dependencies]
ipykernel = "*"

[tool.pixi.feature.test39.dependencies]
python = "3.9.*"
[tool.pixi.feature.test310.dependencies]
python = "3.10.*"
[tool.pixi.feature.test311.dependencies]
python = "3.11.*"
[tool.pixi.feature.test312.dependencies]
python = "3.12.*"

[tool.pixi.feature.build.dependencies]
python-build = ">=1.2.1,<2"
setuptools = "*"
setuptools_scm = "*"
git = "*"                   # for scm-versioning with setuptools_scm

[tool.pixi.feature.build.tasks]
build-wheel = "python -m build --no-isolation --wheel ."

[tool.pixi.feature.prod.tasks]
postinstall-production = "pip install --no-deps --disable-pip-version-check dist/pycashier-*.whl"