pyproject.toml

################################################################################
# Project Configuration
################################################################################
[project]
name = "snakemake-orcestrator"
version = "0.1.0"
description = "Add a short description here"
authors = [
  { name = "Jermiah Joseph", email = "jermiah.joseph@uhn.ca" },
  { name = "Matthew Boccolon", email = "matthew.boccolon@uhn.ca" },
  { name = "Shahbano" },
]
requires-python = ">= 3.10"

################################################################################
# PIXI Configuration
################################################################################

[tool.pixi.project]
name = "snakemake-orcestrator"
version = "0.1.0"
channels = ["conda-forge", "bioconda"]
platforms = ["osx-arm64", "linux-aarch64"]

[tool.pixi.dependencies]
snakemake = "==7.32.4"
gitpython = ">=3.1.43,<3.2"
aiohttp = ">=3.9.5,<3.10"
git = ">=2.45.1,<2.46"
python-json-logger = ">=2.0.7,<2.1"
pydantic = ">=2.7.4,<2.8"
fastapi = ">=0.111.0,<0.112"
motor = ">=3.4.0,<3.5"
uvicorn = ">=0.30.1,<0.31"
google-cloud-logging = ">=3.10.0,<3.11"
conda = ">=24.5.0,<24.6"
mamba = ">=1.5.8,<1.6"

[tool.pixi.pypi-dependencies]
snakemake-orcestrator = { path = ".", editable = true }
fastapi-cache2 = { extras = ["redis"], version = "*" }

[tool.pixi.environments]
dev = { features = ["test", "style", "docs"], solve-group = "default" }
prod = { features = ["prod"], solve-group = "default" }
release = { features = ["build", "release"], solve-group = "default" }

[tool.pixi.tasks.serve-api]
cmd = "docker compose up"
description = "Serve the API using docker compose. Use '-d' to run in background"

############################################## TEST ################################################
[tool.pixi.feature.test.dependencies]
pytest = "*"
pytest-cov = "*"
pytest-xdist = "*"
pytest-asyncio = ">=0.23.7,<0.24"
jq = ">=1.7.1,<1.8"
python = "==3.11.0"
httpx = ">=0.27.0,<0.28"
mongomock = ">=4.0.0,<4.1"
pytest-dependency = ">=0.5.1,<0.6"

[tool.pixi.feature.test.tasks.test]
cmd = [
  "pytest",
  "-s",
  "--verbose",
  "--cov=src/orcestrator",
  "--cov-report=xml:coverage-report/coverage.xml",
  "--cov-config=config/coverage.toml",
]
inputs = ["src", "tests", "config/coverage.toml"]
outputs = ["coverage-report/coverage.xml"]
description = "Run the test suite"

[tool.pixi.feature.test.tasks.coverage]
cmd = "coverage report --rcfile=config/coverage.toml --show-missing"
inputs = ["coverage-report/coverage.xml", "config/coverage.toml"]
depends-on = ["test"]
description = "Generate a coverage report after running the test suite"

############################################## STYLE ###############################################
# See config/ruff.toml for the configuration
[tool.pixi.feature.style.dependencies]
ruff = ">=0.4.4"
pre-commit = ">=3.7.1,<3.8"

[tool.pixi.feature.style.tasks.lint]
cmd = "ruff check --config=config/ruff.toml src"
inputs = ["src", "config/ruff.toml"]

[tool.pixi.feature.style.tasks.format]
cmd = "ruff format --config=config/ruff.toml src"
inputs = ["src", "config/ruff.toml"]

############################################## DOCS ################################################
# Available tasks: doc-build, doc-serve, doc-deploy
# See config/mkdocs.yaml for the configuration
[tool.pixi.feature.docs.dependencies]
mkdocs = "*"

[tool.pixi.feature.docs.tasks.doc-build]
cmd = "mkdocs build -f config/mkdocs.yaml"
inputs = ["docs", "config/mkdocs.yaml"]
outputs = ["site"]
description = "Build the documentation"

[tool.pixi.feature.docs.tasks.doc-serve]
cmd = "mkdocs serve -f config/mkdocs.yaml"
inputs = ["docs", "config/mkdocs.yaml"]
description = "Serve the documentation locally"

[tool.pixi.feature.docs.tasks.doc-deploy]
cmd = "mkdocs gh-deploy -f config/mkdocs.yaml --force"
inputs = ["docs", "config/mkdocs.yaml"]
depends-on = ["doc-build"]
description = "Deploy the documentation to GitHub Pages"

#################################### RELEASE & BUILD ###############################################

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

[tool.hatch.build.targets.wheel]
packages = ["src/orcestrator"]

[tool.pixi.feature.build.dependencies]
build = "*"
hatchling = "*"
hatch = "*"

[tool.pixi.feature.build.tasks.build]
cmd = "hatch build --clean"
inputs = ["src", "config/hatch.toml", "pyproject.toml"]
outputs = ["dist"]
env = { HATCH_CONFIG = "config/hatch.toml" }
description = "Build the package"

[tool.pixi.feature.release.dependencies]
python-semantic-release = ">=8.5.1"

[tool.pixi.feature.release.tasks.nextversion]
cmd = 'echo "Next Version is: $(semantic-release -c config/releaserc.toml version --print)"'
inputs = ["src", "config/releaserc.toml"]
description = "Print the next version"

[tool.pixi.feature.release.tasks.release]
cmd = "semantic-release -c config/releaserc.toml"

################################### PROD ###########################################################7
[tool.pixi.feature.prod.host-dependencies]
pip = "*"

[tool.pixi.feature.prod.dependencies]
python = ">=3.10"

[tool.pixi.feature.prod.tasks.install-dist]
cmd = "pip install --no-deps --disable-pip-version-check dist/*.whl"
depends-on = ["build"]
description = "Install the package in production mode"