pyproject.toml

[project]
name = "pixelgen-pixelator"
dynamic = ["version"]
description = "A command-line tool and library to process and analyze data generated from technologies from Pixelgen Technologies."
authors = [
    { name = "Pixelgen Technologies AB", email = "developers@pixelgen.com" },
]
requires-python = ">=3.10,<3.14"
readme = "README.md"
license = "MIT"
maintainers = [
    { name = "Johan Dahlberg", email = "johan.dahlberg@pixelgen.com" },
    { name = "Adrien Coulier", email = "adrien.coulier@pixelgen.com" },
    { name = "Pouria Tajvar", email = "pouria.tajvar@pixelgen.com" }
]
keywords = [
    "protein",
    "single-cell",
    "molecular-pixelation",
    "spatial",
    "proteomics",
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "License :: OSI Approved :: MIT License",
    "Natural Language :: English",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
]

dependencies = [
    "click<8.3", # Click 8.3 breaks `--output` in `test_cli_invocation_info`
    "cutadapt>=4.2",
    "xopen[zstd]", # Required by cutadapt
    "pyfastx",
    "yappi",
    "pandas>=2.0.0,<3.0.0",
    "numpy>=2.0.0,<3.0.0",
    "annoy<=1.17.0",
    "xxhash",
    "anndata>=0.8.0",
    "numba>=0.56.4",
    "scanpy",
    "typing_extensions",
    "scipy>=1.11.0,<2.0.0",
    "pyarrow>=14",
    "semver>=3.0.0,<4",
    "ruamel-yaml>=0.17.21,<0.18",
    "pydantic>=2.12.4,<3.0",
    "polars>=1.0.0,<2.0.0",
    "importlib-resources>=5.12.0,<6",
    "fsspec",
    "plotly",
    "graspologic-native>=1.2.4,<2",
    "duckdb>=1.4.2,<2",
    "faiss-cpu>=1.10.0,<2",
    "levenshtein>=0.27.3",
    "pixelgen-pixelator-core>=0.1.0,<0.2",
    "requests>=2.32.5",
]

[project.urls]
Homepage = "https://github.com/PixelgenTechnologies/pixelator"
Repository = "https://github.com/PixelgenTechnologies/pixelator"
Documentation = "https://software.pixelgen.com"

[dependency-groups]
dev = [
    "ruff",
    "pre-commit",
    "coverage",
    "invoke",
    "isort",
    "pytest",
    "pytest-mpl",
    "mypy",
    "pytest-snapshot",
    "pytest-cov",
    "pytest-mock",
    "pytest-dependency",
    "pytest-benchmark",
    "pytest-playwright",
    "pytest-watcher",
    "ipython",
    "types-requests>=2.32.4.20260107",
    "line-profiler>=5.0.2",
    "ipykernel>=7.2.0",
]


[project.scripts]
pixelator = "pixelator.cli:main_cli"

[tool.hatch.build.targets.sdist]
include = ["src/pixelator"]

[tool.hatch.build.targets.wheel]
include = ["src/pixelator"]

[tool.hatch.build.targets.wheel.sources]
"src/pixelator" = "pixelator"

[tool.hatch.version]
source = "vcs"

[tool.hatch.version.raw-options]
version_scheme = "no-guess-dev"
fallback_version = "0.0.0"

[build-system]
requires = ["hatchling>=1.25.0", "hatch-vcs>=0.5.0"]
build-backend = "hatchling.build"

[tool.pytest.ini_options]
pythonpath = ["src"]
testpaths = ["tests"]
markers = [
    "integration_test: Marks a test as an integration test, which is often slow (deselect with '-m \"not integration_test\"')",
    "workflow_test: Marks a test as a complete pixelator workflow, which is extremely slow (deselect with '-m \"not workflow_test\"')",
    "external_workflow_test: Marks a test as a complete pixelator workflow that requires external data, which is extremely slow and requires additional setup before running (deselect with '-m \"not external_workflow_test\"')",
    "web_test: Marks a test as a browser integration test, which requires a playwright browser to be installed (deselect with '-m \"not web_tests\"')",
    "slow: Marks a test as being slow (deselect with '-m \"not slow\"')",
]
mpl-results-path = "tests/reports_mpl"
mpl-generate-summary = "html"
addopts = [
    "--mpl",
    "-p no:pytest-workflow",
    "-m not workflow_test and not web_test",
    "--benchmark-disable",
]
filterwarnings = ["ignore::DeprecationWarning"]

[tool.ruff.lint]
select = [
    # pycodestyle
    "E",
    # pydocstyle
    "D",
    # isort,
    "I",
]
# Allow fix for all enabled rules (when `--fix`) is provided.
fixable = ["ALL"]
unfixable = []
ignore = ["E501", "E402", "E203", "D213", "D203"]
exclude = ["docs/conf.py"]

[tool.ruff.lint.pydocstyle]
convention = "google"

[tool.ruff.lint.per-file-ignores]
# Click command modules keep short help strings for CLI generation.
"src/pixelator/mpx/cli/**" = ["D200", "D212", "D400", "D415"]
# Tests document fixtures in conftest; keep lint focused on production code.
"**/tests/**" = [
    "D100",
    "D101",
    "D102",
    "D103",
    "D105",
    "D107",
    "D200",
    "D202",
    "D205",
    "D212",
    "D400",
    "D401",
    "D403",
    "D404",
    "D415",
    "D417",
]