pyproject.toml

[build-system]
requires = ["setuptools>=64", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "PycroFlow"
version = "0.1.0"
description = "Microscopy and Fluid automation coordination"
readme = "README.md"
license = { text = "MIT" }
requires-python = ">=3.10"
keywords = ["pycromanager", "microscopy", "fluid-automation", "exchange-paint"]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Operating System :: Microsoft :: Windows :: Windows 10",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
]

# Runtime deps that are needed even for basic library use.
# Heavy hardware-specific deps live in the [hardware] extra so test/dev
# environments don't have to install them.
dependencies = [
    "pyserial>=3.5",
    "loguru",
    "pyyaml>=6.0",
    "pydantic>=2,<3",
]

[project.optional-dependencies]
# Everything required to actually drive the microscope and fluid handler.
# Installed on the lab Windows box.
hardware = [
    "pycromanager==0.29.5",
    "ndtiff==2.2.1",
    "PyHamiltonPSD==1.1.0",
    "ThorlabsPM100>=1.2.2",
    "pyvisa>=1.15",
    "nidaqmx>=1.2",
    "microscope>=0.7",
    "arduino-python3==0.6",
    "msl-equipment @ https://github.com/MSLNZ/msl-equipment/releases/download/v0.2.0/msl_equipment-0.2.0-py3-none-any.whl",
    # TODO: pin to a commit SHA for reproducible builds, e.g.
    #   pycobolt @ git+https://github.com/cobolt-lasers/pycobolt.git@<sha>
    # Floating HEAD means a fresh install can pull breaking upstream changes.
    # Left unpinned here only because the SHA must be resolved against GitHub
    # (no network access during this edit).
    "pycobolt @ git+https://github.com/cobolt-lasers/pycobolt.git",
    # numpy was pinned to ==1.24.4; loosened to the 1.x line so bugfix
    # releases are allowed. Capped below 2.0 because pycromanager 0.29.5 /
    # ndtiff 2.2.1 predate numpy 2's ABI break and are not validated against
    # it. Revisit when bumping pycromanager.
    "numpy>=1.24,<2",
    "pandas>=2.3",
    "openpyxl>=3.1",
    "matplotlib>=3.10",
    "lmfit>=1.3",
    "icecream>=2.1",
    "inputimeout==1.0.4",
]

# Stage 5: Qt GUI frontend that embeds monet's MonetMainWindow as a tab.
# PyQt6 binding, matching monet (also on PyQt6) so its window embeds in-process.
gui = [
    "PyQt6",
]

# Test and dev tooling. Sufficient to run the unit tests under CI without
# any hardware libs (tests/__init__.py + the top-level conftest.py mock
# pycromanager, monet, pycobolt, and nidaqmx). The suite is unittest-style;
# pytest is supported as an alternate runner via conftest.py.
dev = [
    "pytest>=7",
    "pytest-cov>=5",
    "coverage>=7.10",
    "ruff",
    "mypy",
]

[project.scripts]
pycroflow = "PycroFlow.frontend_cli:main"
pycroflow-gui = "PycroFlow.gui.app:main"

[tool.setuptools.packages.find]
include = ["PycroFlow*"]

[tool.setuptools.package-data]
PycroFlow = [
    "TestData/*.yaml",
    "configs/*.yaml",
    "configs/setups/*.yaml",
    "examples/*.yaml",
    "tests/fixtures/configs/*.py",
    "tests/fixtures/snapshots/*.json",
]

[tool.pytest.ini_options]
testpaths = ["PycroFlow/tests"]
addopts = "--cov=PycroFlow"

# Coverage config so `coverage run -m unittest discover` (or `-m pytest`) is
# scoped to the package without any CLI flags. Run:
#   coverage run -m unittest discover && coverage report
#   coverage html        # browsable report in htmlcov/
[tool.coverage.run]
source = ["PycroFlow"]
branch = true
# Don't measure coverage of the test code / hardware emulators themselves.
omit = ["PycroFlow/tests/*"]

[tool.coverage.report]
show_missing = true
skip_covered = true
exclude_also = [
    "if __name__ == .__main__.:",
    "raise NotImplementedError",
    "if TYPE_CHECKING:",
]