pyproject.toml

[project]
name = "nexusLIMS"
version = "2.7.2.dev0"
description = "Electron Microscopy Nexus LIMS project (Datasophos fork)"
authors = [
    {name = "Joshua Taillon", email = "josh@datasophos.co"}
]
maintainers = [
    {name = "Joshua Taillon", email = "josh@datasophos.co"}
]
readme = "README.md"
license = {text = "MIT"}
requires-python = ">=3.11,<3.15"
keywords = ["microscopy", "LIMS", "materials", "electron-microscopy"]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
]

dependencies = [
    "lxml>=6.0,<7.0.0",
    "requests>=2.32.0,<3.0.0",
    "pytz>=2022.7",
    "hyperspy[speed]>=2.1.0,<3.0.0",
    "scikit-learn>=1.2.0,<2.0.0",
    "python-dotenv>=1.0.0,<2.0.0",
    "exspy>=0.3.2",
    "pyxem>=0.21.0",
    "pixstem>=0.4.0",
    "python-benedict>=0.35.0,<1.0.0",
    "pydantic[email]>=2.12.0",
    "pydantic-settings>=2.12.0",
    "email-validator>=2.3.0",
    "click>=8.1.8",
    "rich>=13.0.0",
    "filelock>=3.0.0",
    "tzlocal>=5.3.1",
    "pint>=0.24.0,<1.0.0",
    "rdflib>=7.0.0,<8.0.0",
    "sqlmodel>=0.0.31",
    "alembic>=1.17.2",
    "textual>=8.0.0",
    "squall-sql>=0.1.8",
]

[dependency-groups]
dev = [
    "pytest>=7.2",
    "coverage>=7.0.0",
    "pytest-mpl>=0.16.1",
    "pytest-cov>=4.0.0",
    "sphinx>=9.0.0,<10",
    "pydata-sphinx-theme>=0.16.1",
    "roman-numerals>=4.1.0",
    "ruff>=0.9.0",
    "sphinxcontrib-towncrier>=0.3.2a0",
    "types-lxml>=2025.8.25",
    "responses>=0.25.8",
    "python-semantic-release>=10.5.2",
    "freezegun>=1.5.5",
    "autodoc-pydantic>=2.2.0",
    "sphobjinv>=2.3.1.3",
    "sphinx-autodoc-typehints>=3.5.2",
    "sphinx-autodoc2>=0.5.0",
    "myst-nb>=1.0.0",
    # Integration testing dependencies (optional)
    "pytest-docker>=3.1.1",
    "docker>=7.0.0",
    "pytest-timeout>=2.2.0",
    "sphinxcontrib-mermaid>=1.2.3",
    "sphinx-design>=0.6.1",
    "pre-commit>=4.5.0",
    "imagecodecs>=2025.11.11",
    "sphinx-autobuild>=2025.8.25",
    "sphinx-copybutton>=0.5.2",
    "pytest-asyncio>=1.3.0",
    "textual-dev>=1.8.0",
]

[project.urls]
Homepage = "https://datasophos.github.io/NexusLIMS/stable"
Repository = "https://github.com/datasophos/NexusLIMS.git"
Documentation = "https://datasophos.github.io/NexusLIMS/stable"
"Original-NIST-Repository" = "https://github.com/usnistgov/NexusLIMS.git"

[project.scripts]
nexuslims = "nexusLIMS.cli.main:main"

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

[tool.hatch.build.targets.wheel]
packages = ["nexusLIMS"]

[tool.ruff]

exclude = [
    "nexusLIMS/dev_scripts",
    "tests/dev",
    "tests/integration/docker/elabftw/init_elabftw.py"
]

[tool.ruff.lint]
select = [
    "F", "E", "W", "I", "N", "D", "YTT", "UP", "S", "FBT", "B", "A", "COM", "C4",
    "DTZ", "T10", "EM", "EXE", "ISC", "ICN", "G", "INP", "PIE", "T20", "PYI",
    "PT", "Q", "RSE", "RET", "SLF", "SIM", "TID", "TCH", "ARG", "PTH", "ERA", "PL",
    "TRY", "RUF"
]
ignore = ["N999", "UP006", "UP007", "UP035", "B905", "RUF007", "S603", "COM812"]

[tool.ruff.lint.per-file-ignores]
"tests/**/*.py" = ["S", "PLC0415", "PLR2004", "ARG002", "DTZ001", "DTZ005", "SLF001", "ARG001", "D102", "TRY003", "EM101", "PT017", "N817", "FBT001", "F841"]
"tests/fixtures/**/*.py" = ["F401", "E402"]
"tests/integration/**/*.py" = ["ARG002", "ARG001"]
"migrations/**/*.py" = ["D400"]  # Migration files don't need perfect docstrings
"nexusLIMS/tui/**/*.py" = ["FBT001", "FBT002", "FBT003", "TRY300", "PLR2004"]  # TUI patterns


[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.ruff.format]
# Use Black-compatible formatting
quote-style = "double"
indent-style = "space"
line-ending = "auto"

[tool.towncrier]
directory = "docs/changes"
package = "nexusLIMS"
package_dir = "nexusLIMS"
title_format = "## {version} ({project_date})"
filename = "docs/reference/changelog.md"
issue_format = "[#{issue}](https://github.com/datasophos/NexusLIMS/issues/{issue})"

[[tool.towncrier.type]]
directory = "feature"
name = "New features"
showcontent = true

[[tool.towncrier.type]]
directory = "bugfix"
name = "Bug fixes"
showcontent = true

[[tool.towncrier.type]]
directory = "enhancement"
name = "Enhancements"
showcontent = true

[[tool.towncrier.type]]
directory = "doc"
name = "Documentation improvements"
showcontent = true

[[tool.towncrier.type]]
directory = "misc"
name = "Miscellaneous/Development changes"
showcontent = true

[[tool.towncrier.type]]
directory = "removal"
name = "Deprecations and/or Removals"
showcontent = true

[tool.coverage.run]
relative_files = true
omit = [
    "nexusLIMS/dev_scripts/*",
    "nexusLIMS/tui/demo_helpers.py",
    "tests/dev/*",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "class _CustomEncoder",
    "if TYPE_CHECKING:",
    "@overload",
    "\\.\\.\\.",  # Exclude Protocol abstract methods (ellipsis)
]

[tool.pytest.ini_options]
log_cli = false
log_cli_level = "DEBUG"
# Enable automatic async test detection (for Textual TUI tests)
asyncio_mode = "auto"
# Test discovery paths - unit tests run by default, integration tests require explicit -m integration
testpaths = ["tests/unit"]
norecursedirs = ["tests/unit/files"]
# Python files and test functions/classes pattern
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
# Matplotlib baseline image directory for pytest-mpl
mpl-baseline-path = "tests/unit/files/figs"
# Markers for organizing tests
markers = [
    "unit: Unit tests (isolated, fast)",
    "integration: Integration tests (require Docker services)",
    "slow: Tests that take significant time to run",
    "network: Tests that require network connectivity",
    "database: Tests that interact with database",
    "harvester: Tests for harvester modules (NEMO, SharePoint)",
    "extractor: Tests for metadata extractor modules",
    "record_builder: Tests for record builder functionality",
    "labarchives_live: Live integration tests against a real LabArchives server (requires NX_LABARCHIVES_* env vars)",
]
filterwarnings = [
    "ignore:Using Ntlm\\(\\) is deprecated:DeprecationWarning",
    "ignore:Manually creating the cbt stuct:DeprecationWarning",
    "ignore:Using or importing the ABCs from:DeprecationWarning",
    "ignore:the imp module is deprecated in favour of:DeprecationWarning",
    "ignore:Glyph .* missing from font:UserWarning",
    "ignore:The NumPy module was reloaded:UserWarning",
    "ignore:Corrupt EXIF data.*:UserWarning",
    "ignore:'return' in a 'finally' block:SyntaxWarning:hyperspy\\.roi",
    "ignore:`scipy\\.odr` is deprecated.*:DeprecationWarning:hyperspy\\.model",
    "ignore:codecs\\.open\\(\\) is deprecated.*:DeprecationWarning:rsciio\\.msa\\._api",

]

[tool.pyright]
venvPath = "."
venv = ".venv"
typeCheckingMode = "basic"
reportMissingImports = true
reportMissingTypeStubs = false