pyproject.toml

[tool.poetry]
name = "stpipeline"
version = "2.0.0"
description = "ST Pipeline: An automated pipeline for spatial mapping of unique transcripts"
authors = ["Jose Fernandez Navarro <jc.fernandez.navarro@gmail.com>"]
license = "MIT"
readme = "README.md"
keywords = ["visium", "analysis", "pipeline", "spatial", "transcriptomics", "toolkit"]
repository = "https://github.com/jfnavarro/st_pipeline"
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "Topic :: Software Development",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Operating System :: Unix",
    "Operating System :: MacOS",
    "Environment :: Console",
]
include = [
    { path = "README.md" },
    { path = "LICENSE" },
    { path = "doc/**" }
]

[tool.poetry.dependencies]
python = ">=3.10,<3.13"
argparse = "^1.4.0"
numpy = "^2.2.1"
pandas = "^2.2.3"
scipy = "^1.15.0"
scikit-learn = "^1.6.0"
regex = "^2024.11.6"
pre-commit = "^4.0.1"
taggd = ">=0.4.0"
htseq = "^2.0.9"
pysam = "^0.22.1"
seaborn = "^0.13.2"
types-regex = "^2024.11.6.20241221"
pandas-stubs = "^2.2.3.241126"
dnaio = "^1.2.3"
distance = "^0.1.3"

# Marked as optional
toml = { version = "^0.10", optional = true }
ruff = { version = "^0.1", optional = true }
isort = { version = "^5.12", optional = true }
pytest = { version = "^7.2", optional = true }
pytest-cov = { version = "^4.0", optional = true }
mkdocs = { version = "^1.4", optional = true }
mkdocs-include-markdown-plugin = { version = "^3.4", optional = true }
mkdocs-material = { version = "^9.1", optional = true }
mkdocstrings = { version = "^0.20", optional = true }
mkdocstrings-python = { version = "^0.9", optional = true }
mkdocs-autorefs = { version = "^0.4", optional = true }
mike = { version = "^1.1", optional = true }
setuptools = { version = "^68", optional = true }
virtualenv = { version = "^20.21", optional = true }

[tool.poetry.scripts]
st_qa = "stpipeline.scripts.st_qa:main"
st_pipeline_run = "stpipeline.scripts.st_pipeline_run:main"
multi_qa = "stpipeline.scripts.multi_qa:main"
merge_fastq = "stpipeline.scripts.merge_fastq:main"
filter_gene_type_matrix = "stpipeline.scripts.filter_gene_type_matrix:main"
convertEnsemblToNames = "stpipeline.scripts.convertEnsemblToNames:main"
adjust_matrix_coordinates = "stpipeline.scripts.adjust_matrix_coordinates:main"

[tool.poetry.extras]

dev = [
    "toml",
    "ruff",
    "isort",
    "pytest",
    "pytest-cov"
    ]

doc = [
    "mkdocs",
    "mkdocs-include-markdown-plugin",
    "mkdocs-material",
    "mkdocstrings",
    "mkdocstrings-python",
    "mkdocs-autorefs",
    "mike",
    "setuptools",
    "virtualenv"
    ]

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

[tool.ruff]
# 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",
    "makefile",
    "docs",
    "docsrc",
    "*.yml",
    "*.yaml",
    "*.md",
    "*.rst",
    "*.ipynb",
    "*.pyx",
    "requirements.txt"
]

# Same as Black.
line-length = 120
indent-width = 4

# Assume Python 3.9
target-version = "py39"

[tool.ruff.lint]
ignore = ["E203","E266","F403","F401"]
select = ["B","C","E","F","W","B9"]
pydocstyle.convention = "google"

# 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]
# 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"

[tool.ruff.lint.mccabe]
max-complexity = 50

[tool.mypy]
# Ensure we know what we do
warn_redundant_casts = true
warn_unused_ignores = true
warn_unused_configs = true

# Imports management
ignore_missing_imports = false

# Ensure full coverage
disallow_untyped_defs = true
#disallow_incomplete_defs = true
disallow_untyped_calls = true
disallow_untyped_decorators = true
# Restrict dynamic typing (a little)
# e.g. `x: List[Any]` or x: List`
disallow_any_generics = true

# Show errors codes
show_error_codes = true

# From functions not declared to return Any
warn_return_any = true

exclude = ["tests", "docsrc"]