pyproject.toml

[project]
name = "minisim"
dynamic = ["version"]
description = "Physically-driven synthetic 1-photon miniscope data: a forward-model generator and teaching tool, the inverse of the minian analysis pipeline."
authors = [
    {name = "Daniel Aharoni", email = "daharoni@mednet.ucla.edu"},
]
dependencies = [
    "numpy>=1.20.2",
    "numpydantic>=1.8",
    # opencv (headless: no GUI libs) backs the brain-motion warp via cv2.warpAffine,
    # ~4x faster than scipy.ndimage.shift for the rigid sub-pixel shift, and is the
    # single shift implementation so a recording is reproducible across environments.
    # It also bundles its own ffmpeg, so it can own video output (dropping the mediapy
    # + system-ffmpeg requirement) -- a tracked follow-up.
    "opencv-python-headless>=4.6",
    "pydantic>=2",
    "scipy>=1.4.1",
    "xarray>=0.17.0",
    # recording.py uses the zarr v2 group API (`create_dataset`), removed in
    # zarr 3. Pinned to v2 to match minian; porting the cache I/O to the zarr 3
    # store/array API is a tracked follow-up.
    "zarr>=2.18,<3",
]

requires-python = ">=3.10"
readme = "README.md"
license = "GPL-3.0-or-later"
license-files = ["LICENSE"]
keywords = [
    "calcium-imaging",
    "miniscope",
    "neuroscience",
    "simulation",
    "synthetic-data",
    "benchmarking",
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Image Processing",
]

[project.scripts]
# Copy the bundled teaching notebooks out to a writable directory.
minisim-notebooks = "minisim.notebooks:main"

[project.urls]
Homepage = "https://github.com/miniscope/minisim"
Documentation = "https://minisim.readthedocs.io/"
Repository = "https://github.com/miniscope/minisim"
Issues = "https://github.com/miniscope/minisim/issues"
Changelog = "https://github.com/miniscope/minisim/blob/main/CHANGELOG.md"

[project.optional-dependencies]
# The teaching notebooks render with matplotlib + ipywidgets under jupyter.
# Kept out of the core so a plain `pip install minisim` (engine only) stays lean.
notebook = [
    "ipympl>=0.10.0",
    "ipywidgets",
    "jupyter",
    "matplotlib",
    "mediapy",
    "tqdm",
]
test = [
    "minisim[notebook]",
    "pytest>=8.4.1",
    "pytest-cov>=7.1.0",
    "ruff>=0.15.14",
]
# The Sphinx documentation site (Read the Docs). Authored in Markdown via MyST;
# the typed Spec/steps render from the live pydantic models via autodoc-pydantic.
docs = [
    "sphinx>=8.1",
    "pydata-sphinx-theme>=0.16",
    "myst-nb>=1.1",
    "autodoc-pydantic>=2.2",
    "sphinx-copybutton>=0.5",
    "sphinx-design>=0.6",
]

[build-system]
requires = ["pdm-backend"]
build-backend = "pdm.backend"

[tool.pdm]
distribution = true

[tool.pdm.version]
# Derive the package version from `v*` git tags via pdm-backend's SCM source.
# Builds between tags get a PEP 440 dev version like `0.1.0.dev41+g<sha>`;
# tagged builds get the clean tag version. No version field to keep in sync.
source = "scm"
tag_filter = "v*"
tag_regex = 'v(?P<version>([1-9][0-9]*!)?(0|[1-9][0-9]*)(\.(0|[1-9][0-9]*))*((a|b|c|rc)(0|[1-9][0-9]*))?(\.post(0|[1-9][0-9]*))?(\.dev(0|[1-9][0-9]*))?$)$'

[tool.pdm.build]
# Keep build artifacts out of the wheel/sdist when the package dir is walked.
# pdm-backend does NOT honor .gitignore, so generated outputs that are gitignored
# but present in a developer's working tree (e.g. a notebook's rendered movies)
# would otherwise be swept into a locally-built wheel. minisim generates every
# movie from code, so videos are outputs and never package inputs: exclude them
# (and notebook checkpoints) outright so a build can never carry large binaries.
excludes = [
    "**/__pycache__",
    "**/*.pyc",
    "**/*.avi",
    "**/*.mp4",
    "**/*.mkv",
    "**/*.mov",
    "**/.ipynb_checkpoints",
]

[tool.pdm.scripts]
lock.composite = [
    'pdm lock --with :all --python=">=3.10,<3.12"',
    'pdm lock --with :all --python=">=3.12,<3.14" --append',
    'pdm lock --with :all --python=">=3.14" --append'
]
test = "pytest"

# Dependency cooldown: exclude packages published in the last 7 days when
# resolving the lockfile, dodging most supply-chain attacks (usually caught
# within ~a week). Reading exclude-newer from this table requires PDM >= 2.26.9;
# older PDMs SILENTLY IGNORE it. CI pins the floor.
[tool.pdm.resolution]
exclude-newer = "7d"

[tool.commitizen]
name = "cz_conventional_commits"
# `version_provider = "scm"` makes commitizen read the current version from the
# latest git tag, so `cz bump` does not write to source files: it just creates
# the next tag and updates the changelog.
version_provider = "scm"
tag_format = "v$version"
changelog_incremental = true

[tool.ruff]
target-version = "py310"
# Teaching notebooks follow notebook conventions (mid-cell imports, explicit
# int() casts for clarity), so they are linted by hand, not by this gate.
extend-exclude = ["*.ipynb"]

[tool.ruff.lint]
# UP (pyupgrade) plus the high-value, low-noise families: pyflakes (F: unused
# imports/vars, undefined names), import sorting (I), bugbear (B), a slice of
# pycodestyle (E4/E7/E9: import/statement/runtime errors, not line length), and
# ruff's own checks (RUF).
select = ["E4", "E7", "E9", "F", "I", "B", "UP", "RUF"]
ignore = [
    # Scientific notation (µ, σ, →, ×, ≈, ⊛) is intentional throughout the
    # docstrings, comments, and Field descriptions; it is not an ambiguous typo.
    "RUF001", "RUF002", "RUF003",
    # Compact `a; b` one-liners are an intentional style choice in a few spots.
    "E702",
    # `int(round(x))` is deliberate: round() on a numpy scalar returns a numpy
    # type, and the int() pins it to a Python int. Not an unnecessary cast.
    "RUF046",
]
fixable = ["ALL"]

[tool.ruff.lint.per-file-ignores]
# numpydantic's `Shape["* unit, * frame"]` DSL is a string ruff parses as a
# Python forward annotation, where the leading `*` is a syntax error. It is valid
# numpydantic, so F722 is a false positive here -- the same root cause that keeps
# recording.py out of the pyright gate (see [tool.pyright].exclude).
"minisim/recording.py" = ["F722"]

[tool.pyright]
include = ["minisim"]
exclude = [
    "**/__pycache__",
    # Tests exercise dynamic xarray/numpy indexing heavily; type-gating them is
    # high-noise, low-value, so they are out of scope.
    "minisim/test",
    # The training-notebook presentation helpers are matplotlib / ipywidgets /
    # mediapy plotting code, not part of minisim's forward-model contract and
    # gated behind the [notebook] extra. Pyright on it is the same high-noise,
    # low-value story as the tests: loose matplotlib stubs (header_visible,
    # add_axes rect, plt.Circle), numpy .shape / Optional narrowing the checker
    # cannot follow through stored lists, and heterogeneous-dict inference. The
    # load-bearing physics lives in the gated library modules these call into.
    "minisim/notebooks",
    # numpydantic's Shape["..."] DSL is not statically parseable, so pyright
    # mis-infers GroundTruth's array fields and the error cascades through the
    # whole module. Excluded *pending* a numpydantic static-typing story (a stub
    # or TYPE_CHECKING-friendly form) -- see the upstream discussion -- not a
    # permanent punt. The rest of the package is gated.
    "minisim/recording.py",
]
venvPath = "."
venv = ".venv"
pythonVersion = "3.10"
typeCheckingMode = "basic"
# pydantic step specs legitimately redeclare the `kind`/`domain` ClassVars the
# StepSpec base declares (the discriminated-union idiom); pyright's
# incompatible-override check is a false positive for that pattern.
reportIncompatibleVariableOverride = false

[tool.pytest.ini_options]
addopts = [
    '-v',
    '--color=yes',
    '--cov=minisim',
]
testpaths = [
  "minisim/test"
]