pyproject.toml

[build-system]
requires = ["setuptools>=64.0.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "pamica"
version = "0.4.1.dev1"
description = "pAMICA: Python implementation of the Adaptive Mixture ICA algorithm"
readme = "README.md"
authors = [
    {name = "Seyed Yahya Shirazi", email = "shirazi@ieee.org"},
]
maintainers = [
    {name = "Seyed Yahya Shirazi", email = "shirazi@ieee.org"},
]
license = {text = "BSD-3-Clause"}
classifiers = [
    "Development Status :: 3 - Alpha",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Operating System :: OS Independent",
    "Programming Language :: Python",
    "Topic :: Scientific/Engineering"
]
requires-python = ">=3.12"
dependencies = [
    "numpy",
    "scipy",
    "matplotlib",
    "tqdm",
    "json5",
    "torch>=2.12.1",
    "threadpoolctl>=3",
]

# Optional Apple-Silicon GPU backend (AMICAMLXNG). MLX is Apple-only, so it is
# NOT a core dependency; install with `uv pip install mlx` or `pip install
# pamica[mlx]`. `import pamica` never requires it (mlx_impl is imported lazily).
[project.optional-dependencies]
mlx = ["mlx>=0.32"]
# Documentation stack (MkDocs Material + mkdocstrings). Built and deployed to
# GitHub Pages by .github/workflows/docs.yml via `uv sync --extra docs`.
docs = [
    "mkdocs-material>=9.5",
    "mkdocstrings[python]>=0.26",
    "mkdocs-git-revision-date-localized-plugin>=1.2",
]
# Visualization for the benchmark sweeps: MNE builds the scalp-map montage for
# the IC topomaps and (issue #91) the distributed channel-subset positions.
viz = ["mne>=1.6"]
# MNE-Python compatibility layer (AMICAICA, issue #139). MNE is not a core
# dependency, so install with `pip install pamica[mne]`; `import pamica` never
# requires it (pamica.mne_compat is imported lazily, same pattern as mlx).
mne = ["mne>=1.6"]

[project.urls]
Homepage = "https://github.com/sccn/pAMICA"
Repository = "https://github.com/sccn/pAMICA"
Documentation = "https://eeglab.org/pAMICA/"
Changelog = "https://eeglab.org/pAMICA/changelog/"

[tool.setuptools]
# List subpackages explicitly so the wheel is deterministic across platforms
# (a bare ["pamica"] dropped torch_impl/ on some setuptools versions).
packages = ["pamica", "pamica.numpy_impl", "pamica.torch_impl", "pamica.mlx_impl", "pamica.metrics", "pamica.native", "pamica.mne_compat"]
# numpy_impl/params.json is the NumPy backend's default parameter file, loaded at
# runtime via importlib/__file__, so it must ship in the wheel.
package-data = {"pamica.numpy_impl" = ["params.json"]}

[dependency-groups]
dev = [
    "pre-commit>=4.0",
    "pytest>=9.1.1",
    "pytest-cov>=7.1.0",
    "pytest-xdist>=3.6.1",
    "ruff>=0.15.0",
    "ty>=0.0.57",
]

[tool.coverage.run]
source = ["pamica"]
branch = true
omit = [
    "pamica/tests/*",
    # argparse CLI entrypoint: exercised via subprocess, not unit-covered here.
    "pamica/numpy_impl/cli.py",
    # Optional MLX backend (Apple Silicon only): its tests require MLX + an Apple
    # GPU. The `test-macos` job does now run them for real (issue #246), but it
    # runs with --no-cov, so the coverage total still comes only from the ubuntu
    # `test` job -- where mlx is absent and this package always measures 0%. The
    # omission stays required until coverage is combined across both runners.
    "pamica/mlx_impl/*",
    # Optional MNE compatibility layer (issue #139): imports mne, absent from the
    # base test env, so the base coverage run always measures 0%. Exercised by
    # the dedicated `test-mne` CI job (uv sync --extra mne) on real sample EEG.
    "pamica/mne_compat/*",
]

[tool.coverage.report]
show_missing = true
precision = 1
exclude_lines = [
    "pragma: no cover",
    "if __name__ == .__main__.:",
    "if TYPE_CHECKING:",
    "raise NotImplementedError",
    "@(abc\\.)?abstractmethod",
]

[tool.ty.src]
# .context/ holds point-in-time investigation/debugging artifacts (per
# AGENTS.md): frozen reproduction/prototype scripts for closed issues (e.g.
# issue-21/corrected_mstep_prototype.py, marked "do not ship as-is"), not
# maintained production code, so it is out of scope for type checking. Live
# analysis scripts that ARE tested (loaded via importlib from the test suite)
# were fixed on their own merits rather than excluded. (issue #122)
exclude = [".context/**"]

[tool.ty.rules]
# Optional-extra lazy imports (mne: benchmarks/benchmark_decompose.py; mlx:
# pamica/mlx_impl/core.py, benchmarks/benchmark_dimsweep.py) carry
# `# ty: ignore[unresolved-import]` comments, since CI's base env (no extras,
# matching the other jobs) can't resolve either. Whether such a comment is
# "used" or "unused" then depends on whether the local env happens to have the
# extra installed, so this rule would otherwise flip between a false pass and
# a false "unused-ignore-comment" warning depending on the developer's own
# environment rather than the code. Disabled project-wide rather than per-line
# since there's no per-environment suppression for the checker itself.
unused-ignore-comment = "ignore"