pyproject.toml

[build-system]
requires = ["maturin>=1.0,<2.0"]
build-backend = "maturin"

[project]
name = "piaso-tools"
version = "1.2.3"
description = "Precise Integrative Analysis of Single-cell Omics."
requires-python = ">=3.9"
license = {text = "BSD-3-Clause"}
authors = [
    { name = "Min Dai", email = "dai@broadinstitute.org" }
]
maintainers = [
    { name = "Min Dai", email = "dai@broadinstitute.org" },
    { name = "Vallari Shende", email = "vshende@broadinstitute.org" }
]
readme = "README.md"
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Environment :: Console",
    "Framework :: Jupyter",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Natural Language :: English",
    "Operating System :: MacOS :: MacOS X",
    "Operating System :: Microsoft :: Windows",
    "Operating System :: POSIX :: Linux",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Visualization",
]
dependencies = [
    "anndata>=0.8",
    "numpy>=1.21.6",
    "matplotlib>=3.5.2",
    "pandas>=1.4.4",
    "scipy>=1.7.3",
    "seaborn>=0.11.2",
    "scikit-learn>=1.1",
    "statsmodels>=0.13.2",
    "tqdm",
    "typing-extensions",
    "requests",
    "lz4",
    "zstandard",
    "h5py",
    "umap-learn>=0.5",
    "igraph>=0.10",
    # >=1.1.0, not 1.0.3: runGDR's cytome path calls cosg.run_cosg_cytome,
    # which does not exist before 1.1.0. The import is lazy, so a stale cosg
    # does not break `import piaso` -- it fails partway through a GDR run with
    # ModuleNotFoundError, which is the worst time to find out.
    "cosg>=1.1.2",
    # Required, not optional. PIASO reads cytome datasets throughout tl/pp/pl,
    # and cytome is a 124 KB pure-Python wheel whose own dependencies (numpy,
    # scipy, pandas, lz4) are all already listed above -- so requiring it adds
    # exactly one package and no transitive weight.
    # Upper bound: cytome's public modality API is pinned by its own
    # conformance test, so 0.x minors are safe; the bound exists to stop a
    # future 1.0 API cleanup from reaching installs pinned to this release.
    # Floor raised for 0.3.0's naming invariant: `{modality}_counts` holds raw
    # integer counts or does not exist, and matrix_meta records is_integer.
    # PIASO reads both -- older files still work -- but its error messages and
    # the plotting fallback describe 0.3.0's layout, so an install that pairs
    # this release with an older cytome would be advised about names its files
    # do not use.
    "cytome>=0.3.0,<1.0",
]

# https://docs.pypi.org/project_metadata/#project-urls
[project.urls]
Documentation = "https://piaso.org"
Source = "https://github.com/genecell/PIASO"
Homepage = "https://piaso.org"

[project.optional-dependencies]
# Optional, NOT required. numba's `default` threading layer already resolves to
# omp -- which is thread-safe and is what runGDR's per-batch pool needs -- and
# numba's own wheel ships the omp pool, so the parallel path is on out of the
# box. tbb only matters if something in your environment pins
# NUMBA_THREADING_LAYER='tbb', or you specifically prefer the tbb pool. Note the
# wheel installs shared objects into <prefix>/lib rather than a Python package,
# which resolves under conda but may not under a plain venv.
tbb = [
    "tbb>=2021.0; (platform_machine == 'x86_64' or platform_machine == 'AMD64') and sys_platform != 'darwin'",
]
dev = [
    "pre-commit", # static checking
]
atac = [
    "pysam",
]
harmony = [
    "harmonypy>=0.0.6",
]
leiden = [
    "leidenalg>=0.9",
]
scanpy = [
    "scanpy>=1.9.1",  # optional: for interop with scanpy-based workflows
]

[tool.maturin]
features = ["pyo3/extension-module"]
module-name = "piaso._piaso"