pyproject.toml

[tool.poetry]
authors = [
  "David Orme <d.orme@imperial.ac.uk>",
  "Alienor Lavergne <alienor.lavergne@springernature.com>",
  "Vivienne Groner <v.groner@imperial.ac.uk>",
  "Marion Weinzierl <mw925@cam.ac.uk>",
  "Tianzhang Cai <tc684@cam.ac.uk>",
  "Surbhi Goel <sg2147@cam.ac.uk>",
  "Alexander Smith <as3402@cam.ac.uk>",
  "James Emberton <je484@cam.ac.uk>",
  "Amy Pike <ap766@cam.ac.uk>",
]
classifiers = [
  "Programming Language :: Python :: 3",
  "License :: OSI Approved :: MIT License",
  "Operating System :: OS Independent",
  "Topic :: Scientific/Engineering",
  "Intended Audience :: Science/Research",
  "Development Status :: 4 - Beta",
]
description = "Python tools for modelling plant productivity and demography."
homepage = "https://pyrealm.readthedocs.io/"
license = "MIT"
name = "pyrealm"
packages = [
  {include = "pyrealm"},
  {include = "pyrealm_build_data", format = "sdist"},
]
readme = "README.md"
repository = "https://github.com/ImperialCollegeLondon/pyrealm"
version = "1.0.0"

[tool.poetry.dependencies]
dacite = "^1.6.0"
numpy = "^2.0.0"
python = ">=3.10"
scipy = "^1.7.3"
tabulate = "^0.8.10"

marshmallow = "^3.22.0"
marshmallow-dataclass = "^8.7.0"
pandas = "^2.2.2"
pandas-stubs = "^2.2.2.240909"
[tool.poetry.group.types.dependencies]
pandas-stubs = "^2.2.0.240218"
types-tabulate = "^0.9.0.0"

[tool.poetry.group.test.dependencies]
graphviz = "*"
pytest = "^7.1.2"
pytest-cov = "^3.0.0"
pytest-mock = "^3.8.1"
pytest-profiling = "^1.7.0"

[tool.poetry.group.dev.dependencies]
ipython = "^8.9.0"
jupyterlab = "^4.2.1"
jupyterlab-myst = "^2.4.2"
jupytext = "^1.16.2"
matplotlib = "^3.5.2"
multiprocess = "^0.70.16"
mypy = "^0.991"
pandas = "^2.2.0"
pre-commit = "^3.2.0"
ruff = "^0.4.1"

[tool.poetry.group.docs.dependencies]
autodocsumm = "^0.2.8"
myst-nb = "^1.0.0"
netcdf4 = "^1.6.3"
pydocstyle = "^6.1.1"
sphinx = "^7.0.0"
sphinx-external-toc = "^1.0.0"
sphinx-rtd-theme = "^2.0.0"
sphinxcontrib-bibtex = "^2.6.1"
xarray = "^2024.6.0"

[build-system]
build-backend = "poetry.core.masonry.api"
requires = ["poetry-core>=1.8.2"]

[tool.mypy]
disallow_incomplete_defs = true
disallow_untyped_calls = true
disallow_untyped_defs = true
exclude = [
  'pyrealm_build_data/splash/splash_py_version/*.py', # Legacy code used for building golden datasets
]
ignore_missing_imports = false
no_implicit_optional = true
plugins = 'numpy.typing.mypy_plugin'
strict_optional = true

[tool.mypy-setup]
ignore_errors = true

[[tool.mypy.overrides]]
disallow_incomplete_defs = false
disallow_untyped_calls = false
disallow_untyped_defs = false
module = "tests.*"

[tool.pytest.ini_options]
addopts = """
  -v 
  -p no:warnings
  -m "not profiling"
  --cov=pyrealm
  --cov-report=html:reports/coverage
  --doctest-modules
  --ignore=pyrealm/__main__.py
  --ignore=tests/pmodel/generate_test_inputs.py
  """
python_files = 'test_*.py'
testpaths = ['tests', 'pyrealm']

[tool.ruff]
exclude = [
  "pyrealm_build_data/splash/splash_py_version/*", # Legacy code used for building golden datasets
]
target-version = "py310"

[tool.ruff.lint]
# Enable all `pydocstyle` rules, limiting to those that adhere to the
# Google convention via `convention = "google"`, below.
select = [
  # "B", # flake8-bugbear
  # "SIM", # flake8-simplify
  "E", # pycodestyle
  "F", # pyflakes
  "D", # pydocstyle
  "I", # isort
  "UP", # pyupgrade
  "RUF", # RUF specific checks
  "NPY201",
]

# On top of the Google convention, disable:
ignore = [
  "D202", # Blank line after docstring is ok
  "D107", # Location of __init__ docstring in class not __init__"
  "D105", # Magic methods do not need docstrings.
]

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

[tool.jupytext]
# Stop jupytext from removing mystnb and other settings in MyST Notebook YAML headers
notebook_metadata_filter = "settings,mystnb,language_info"
# Also stop it from stripping cell metadata, except for specific ones to lose.
cell_metadata_filter = "all,-trusted"