chem-spectra-app/pyproject.toml at master · ComPlat/chem-spectra-app · GitHub

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[build-system]
requires = ["setuptools"]
build-backend = "setuptools.build_meta"

[project]
name = "chem-spectra-app"
version = "1.6.0"
requires-python = ">= 3.12"
description = "A backend service to process files obtained from chemical spectroscopy."
license = "MIT"
readme = "README.md"
keywords = ["chemistry", "spectra", "analysis"]
classifiers = [
    "Programming Language :: Python :: 3",
    "Operating System :: POSIX :: Linux"
]
dependencies = [
  "flask==3.*",
  "gunicorn==26.*",
  "matplotlib==3.*",
  "netCDF4==1.*",
  # The 2018 fork we pin below writes `np.dtype('a8')` in fileio/tecmag.py.
  # numpy removed that alias in 2.5, so `import nmrglue` raises TypeError and
  # every test errors at collection. Measured: fails on 2.5.3, imports on
  # 2.4.0. The ceiling is the pin's, not ours -- it lifts when the pin does.
  "numpy>=2.0,<2.5",
  # Imported directly by lib/external/chemotion_converter_lcms.py. It was
  # never declared and arrived only as a pyopenms transitive dependency, so a
  # pyopenms release that drops it would have broken us with an ImportError.
  "pandas>=2.3,<4",
  "pymzml==2.*",
  "requests==2.*",
  "rdkit==2026.*",
  "werkzeug==3.*",
  "scipy==1.*",
  "pyopenms==3.*",
  "nmrglue@git+https://github.com/ComPlat/nmrglue.git@fe75b096f6253084a08a8ce7bf849c7343245c40",
]

# Kept as an extra so `pip install .[dev]` still works for anyone not using uv.
# `just` and CI go through the dependency group below instead.
[project.optional-dependencies]
dev = [
    "coverage",
    "pytest"
]

[dependency-groups]
dev = [
    "coverage[toml]>=7.6",
    "pytest>=8",
    "ruff>=0.14",          # `just lint`; [tool.ruff] below
    "mypy>=1.10",          # `just mypy`; [tool.mypy] below
]

[project.urls]
homepage = "https://chemotion.net/docs/services/chemspectra"
repository = "https://github.com/ComPlat/chem-spectra-app"

[tool.setuptools]
py-modules = []


# Modernization only: pyupgrade (UP) keeps the code on current-Python idioms.
# The target is the floor `requires-python` promises, not the version the image
# runs, so a fix suggested here cannot break the 3.12 leg of the CI matrix.
[tool.ruff]
target-version = "py312"

[tool.ruff.lint]
select = ["UP"]

# A ratchet, in the same spirit as the mypy overrides below: the whole UP set
# is selected, and the rules that already fire are muted so the gate is green
# today and any *new* kind of violation is caught.
#
# These are NOT fixed in this branch on purpose. All 289 are mechanical and
# auto-fixable, but a repo-wide `ruff --fix` would rewrite technique.py,
# base.py and composer/ -- which every open PR (#299-#305) also rewrites. It
# runs once that stack has landed.
#
# The list only ever gets shorter. Counts are from the run that introduced it;
# clear a rule with `just lint-fix`, then delete its line in the same commit.
ignore = [
    "UP032",  # 95x  f-string instead of str.format
    "UP006",  # 69x  builtin generics (List -> list)
    "UP045",  # 61x  X | None instead of Optional[X]
    "UP015",  # 26x  redundant open() mode
    "UP031",  # 14x  f-string instead of percent formatting
    "UP035",  # 9x   deprecated typing imports
]

[tool.mypy]
python_version = "3.12"
ignore_missing_imports = true

# Type checking is a ratchet. The whole tree is checked; the modules listed
# below carry pre-existing errors and are exempted for now.
#
# The list only ever gets shorter: when a change makes a module type-clean,
# delete its entry in the same commit. Never add an entry -- that would mean a
# clean module regressed, which is what this gate exists to prevent.
#
# This buys more than expected for an untyped codebase: 51 of 57 modules are
# already clean, so the gate really does guard most of the tree. The six below
# are the LC/MS and BagIt paths plus two single-error modules that the open PR
# stack rewrites anyway.
[[tool.mypy.overrides]]
ignore_errors = true
# 21 errors across these 6 of 57 modules when the gate was introduced.
# The other 51 are enforced from day one and cannot regress.
module = [
    "chem_spectra.lib.composer.lcms_converter_app",
    "chem_spectra.lib.composer.technique",
    "chem_spectra.lib.converter.bagit.base",
    "chem_spectra.lib.converter.bagit.lcms_builder",
    "chem_spectra.lib.converter.fid.base",
    "chem_spectra.lib.external.chemotion_converter_lcms",
]