pyproject.toml

[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "qbiocode"
dynamic = ["version", "dependencies"]
description = "A comprehensive suite of computational resources for quantum computing applications in healthcare and life science data analysis"
readme = "README.md"
requires-python = ">=3.10,<3.13"
license = {text = "Apache License 2.0"}
authors = [
    {name = "Bryan Raubenolt", email = "raubenb@ccf.org"},
    {name = "Aritra Bose", email = "a.bose@ibm.com"},
    {name = "Kahn Rhrissorrakrai", email = "krhriss@us.ibm.com"},
    {name = "Filippo Utro", email = "futro@us.ibm.com"},
    {name = "Akhil Mohan", email = "mohana2@ccf.org"},
    {name = "Daniel Blankenberg", email = "blanked2@ccf.org"},
    {name = "Laxmi Parida", email = "parida@us.ibm.com"},
]
maintainers = [
    {name = "IBM Research"},
]
keywords = [
    "quantum machine learning",
    "quantum computing",
    "qiskit",
    "bioinformatics",
    "healthcare",
    "life sciences",
    "omics",
    "genomics",
    "proteomics",
    "metabolomics",
    "data complexity",
    "model profiling",
    "model selection",
    "oracle",
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Healthcare Industry",
    "Intended Audience :: Developers",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Physics",
    "Topic :: Software Development :: Libraries :: Python Modules",
    "License :: OSI Approved :: Apache Software License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3 :: Only",
    "Operating System :: OS Independent",
    "Natural Language :: English",
]

[project.urls]
Homepage = "https://github.com/IBM/qbiocode"
Documentation = "https://ibm.github.io/QBioCode/"
Repository = "https://github.com/IBM/qbiocode"
"Bug Tracker" = "https://github.com/IBM/qbiocode/issues"

[project.optional-dependencies]
# Mirrors of the tiered files in requirements/ -- tests/test_requirements_consistency.py
# asserts that `quvine` and `docs` here match requirements-quvine.txt and
# requirements-docs.txt exactly, so the two cannot drift apart.
apps = [
    "hydra-core",
    "joblib",
]
# QuVINE embedding app (qbiocode.apps.quvine). One all-or-nothing extra: with it
# installed, every `get_embeddings("quvine_*", ...)` method resolves; without it,
# `import qbiocode` and all classical embeddings still work.
quvine = [
    # node2vec imports the deprecated `pkg_resources`, removed in setuptools>=81.
    "setuptools<81",
    # gensim>=4.4 drops `scipy.triu` (removed in scipy 1.13); an older gensim would
    # force numpy<2.0, conflicting with qiskit-machine-learning==0.9.0 (numpy>=2.0).
    "gensim>=4.4",
    "hiperwalk",
    "node2vec",
    "omegaconf",
    "python-louvain",
    "ripser",
    "torch-geometric",
]
# `pandoc` is intentionally not listed: it is a system binary, not a Python
# package. Install it with brew/apt -- see requirements/requirements-docs.txt.
docs = [
    "sphinx",
    "sphinx-autodoc-typehints",
    "sphinx_rtd_theme",
    "sphinx-design",
    "myst_parser",
    "myst_nb",
    "nbsphinx",
    "better_apidoc",
    "furo",
    "pydata-sphinx-theme",
]
dev = [
    "pytest>=7.0",
    "pytest-cov>=4.0",
    # tests/integration/test_notebook_execution.py executes every tracked
    # notebook through these two. Undeclared, they were reached by
    # ``pytest.importorskip`` and 21 notebook tests skipped silently in any
    # environment that happened not to have them.
    "nbclient>=0.7",
    "nbformat>=5.0",
    # tests/integration/test_distribution_contents.py builds a real sdist and wheel
    # and inspects what they carry. It guards on `build` and says the [dev] extra
    # provides it -- which was not true until this line, so the guard could only
    # ever skip.
    "build>=1.0",
    "black>=23.0",
    "isort>=5.0",
    "flake8>=6.0",
    "mypy>=1.0",
    "types-PyYAML",
]
# Union of every extra above. Keep in sync when adding to any tier.
all = [
    "qbiocode[apps,quvine,docs,dev]",
]

[project.scripts]
qprofiler = "qbiocode.apps.qprofiler.cli:main"
qprofiler-batch = "qbiocode.apps.qprofiler.qprofiler_batchmode:main"
qsage = "qbiocode.apps.sage.sage:main"
quvine = "qbiocode.apps.quvine.cli:main"

[tool.setuptools]
include-package-data = true

[tool.setuptools.packages.find]
where = ["."]
include = ["qbiocode*"]
exclude = ["tests*", "docs*", "archive*"]

[tool.setuptools.dynamic]
version = {attr = "qbiocode.version.__version__"}
dependencies = {file = ["requirements/requirements-base.txt"]}

[tool.setuptools.package-data]
# No `qbiocode = ["py.typed"]` here. The marker was declared and the file has
# never existed, so setuptools silently shipped nothing -- but had anyone created
# it to "fix" the declaration, the claim would have been false: py.typed tells a
# consumer's type checker that this package's annotations are complete and
# authoritative, and `disallow_untyped_defs = false` below says they are not.
# Downstream users would then get confident `error:` lines derived from `Any`.
# Add the marker when the tree is fully annotated, not before.
"qbiocode.apps.qprofiler" = ["configs/*.yaml"]
"qbiocode.apps.quvine" = ["configs/*.yaml"]

[tool.black]
line-length = 100
target-version = ['py310', 'py311', 'py312']
include = '\.pyi?$'

[tool.isort]
profile = "black"
line_length = 100

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
# No --cov here on purpose: it made a bare `pytest` fail outright in any
# environment without pytest-cov, which is every environment that installed
# qbiocode rather than the [dev] extra. CI passes --cov explicitly.
# The default deselection keeps the matrix fast; run the excluded tiers with
#   pytest -m slow            (notebook execution)
#   pytest -m requires_quantum (anything needing a real backend)
addopts = "-v -m 'not slow and not requires_quantum'"

markers = [
    "slow: minutes-long tests, e.g. executing a tutorial notebook end to end",
    "requires_quantum: needs a real quantum backend and network credentials",
]

[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = false
ignore_missing_imports = true