snkmt/pyproject.toml at main · cademirch/snkmt · GitHub

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[project]
name = "snkmt"
version = "0.3.0"
description = "Realtime monitoring of Snakemake workflows"
readme = "README.md"
authors = [{ name = "Cade Mirchandani", email = "cmirchan@ucsc.edu" }]
requires-python = ">=3.11"
dependencies = [
    "textual>=3.1.1",
    "typer>=0.15.3",
    "sqlalchemy>=2.0.38",
    "alembic>=1.16.1,<2",
    "platformdirs>=4.3.8,<5",
    "loguru>=0.7.3,<0.8", "aiosqlite>=0.21.0,<0.22",
    "beaupy>=3.0.0,<4",
]

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

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.pixi.workspace]
channels = ["conda-forge", "bioconda"]
platforms = ["osx-arm64", "linux-64"]

[tool.pixi.environments]
dev = { features = ["dev"] }
publish = { features = ["publish"] }

[tool.pixi.pypi-dependencies]
snkmt = { path = ".", editable = true }
textual-dev = ">=1.7.0"


[tool.pixi.feature.dev.pypi-dependencies]
snkmt = { path = ".", editable = true }
snakemake-logger-plugin-snkmt = { git = "https://github.com/cademirch/snakemake-logger-plugin-snkmt.git", editable = true, branch="dev" }

[tool.pixi.feature.dev.dependencies]
pytest = ">=8.3.5,<9"
ruff = ">=0.10.0,<0.11"
mypy = ">=1.15.0,<2"
pytest-cov = ">=6.0.0,<7"
snakemake = ">=9.9.0,<10"

[tool.pixi.feature.dev.tasks]
demo = {cmd = "./run.sh", cwd="demo"}
cleanup-demo ={cmd = "rm -r results", cwd="demo"}
console = {cmd = "textual run --dev -c snkmt console"}
dev-console = {cmd = "textual console -x SYSTEM -x EVENT -x WORKER"}
format = "ruff format src"
lint = "ruff check"
type-check = "mypy src/"
qc = { depends-on = ["format", "lint", ] }
db-migrate = {cmd = "alembic revision --autogenerate -m", cwd="src/snkmt/core/db"}
db-upgrade = {cmd = "alembic upgrade head", cwd="src/snkmt/core/db"}

[tool.pixi.feature.dev.tasks.test]
cmd = [
  "pytest",
  "--cov=snkmt",
  "--cov-report=xml:coverage-report/coverage.xml",
  "--cov-report=term-missing",
]

# Publish
[tool.pixi.feature.publish.dependencies]
twine = ">=6.1.0,<7"
python-build = ">=1.2.2,<2"

[tool.pixi.feature.publish.tasks]
build = { cmd = "python -m build", description = "Build the package into the dist/ directory" }
check-build = { cmd = "python -m twine check dist/*", depends-on = [
  "build",
], description = "Check that the package can be uploaded" }


[tool.mypy]
ignore_missing_imports = true # Temporary until https://github.com/snakemake/snakemake-interface-common/pull/55
disallow_untyped_defs = true
warn_no_return = true

[tool.ruff]
exclude = ["tests/*"]

[tool.pyright]
include = ["src"]
extraPaths = ["src"]
typeCheckingMode = "basic"

[dependency-groups]
dev = ["pytest-asyncio>=1.1.0,<2", "greenlet>=3.2.4,<4", "pytest-loguru>=0.4.0,<0.5"]