pyproject.toml

[tool.poetry]
authors = [
  "Rob Ewers <r.ewers@imperial.ac.uk>",
  "David Orme <d.orme@imperial.ac.uk>",
  "Jacob Cook <j.cook17@imperial.ac.uk>",
  "Vivienne Groner <v.groner@imperial.ac.uk>",
  "Taran Rallings <t.rallings@imperial.ac.uk>",
  "Olivia Daniel <olivia.daniel08@imperial.ac.uk>",
  "Jaideep Joshi <joshi@iiasa.ac.at>",
  "Anna Rallings <a.rallings@imperial.ac.uk>",
  "Priyanga Amarasekare <pamarasekare@gmail.com>",
  "Diego Alonso Alvarez <d.alonso-alvarez@imperial.ac.uk>",
  "Alex Dewar <a.dewar@imperial.ac.uk>",
]
classifiers = [
  "Development Status :: 2 - Pre-Alpha",
  "Intended Audience :: Science/Research",
  "License :: OSI Approved :: BSD License",
  "Topic :: Scientific/Engineering",
]
description = """An holistic ecosystem simulation model."""
homepage = "https://virtual-ecosystem.readthedocs.io/"
license = "BSD-3-Clause"
name = "virtual_ecosystem"
readme = "README.md"
repository = "https://github.com/ImperialCollegeLondon/virtual_ecosystem"
version = "0.1.1a6"

[tool.poetry.scripts]
ve_run = "virtual_ecosystem.entry_points:ve_run_cli"

[tool.poetry.dependencies]
Shapely = "^2.0"
dask = ">=2023.6,<2025.0"
dpath = "^2.0.6"
jsonschema = "^4.14.0"
netcdf4 = "^1.6.5"
numpy = "^2.0"
pint = "^0.24.1"
python = ">=3.10,<3.13"
scipy = "^1.9.0"
tomli = {version = "^2.0.1", python = "<3.11"}
tomli-w = "^1.0.0"
tqdm = "^4.66.2"
xarray = "^2024.06.0"

[tool.poetry.group.types.dependencies]
types-dataclasses = "^0.6.6"
types-jsonschema = "^4.16.1"
types-tqdm = "^4.66.0.20240106"

[tool.poetry.group.test.dependencies]
hypothesis = "^6.54.2"
pytest = ">=7.1.2,<9.0.0"
pytest-cov = ">=3,<7"
pytest-datadir = "^1.4.1"
pytest-mock = "^3.8.1"

[tool.poetry.group.devenv.dependencies]
ipykernel = "^6.15.0"
ipython = "^8.4.0"
isort = "^5.12.0"
jupyterlab = "^4.2.3"
jupyterlab-myst = "^2.4.2"
jupytext = "^1.16.2"
matplotlib = "^3.5.2"
mdformat = "^0.7.14"
mdformat_frontmatter = ">=0.4.1,<2.1.0"
mdformat_tables = ">=0.4.1,<1.1.0"
mypy = "^1.5.1"
pre-commit = ">=3,<5"

[tool.poetry.group.docs.dependencies]
autodocsumm = "^0.2.8"
myst-nb = "^1.0.0"
pydocstyle = "^6.1.1"
sphinx = "^7.0.0"
sphinx-design = "^0.6.0"
sphinx-external-toc = "^1.0.0"
sphinx-rtd-theme = ">=2,<4"
sphinxcontrib-bibtex = "^2.6.1"
sphinxcontrib-mermaid = ">=0.9.2,<1.1.0"

[build-system]
build-backend = "poetry.core.masonry.api"
requires = ["poetry-core>=1.2.0"]

[tool.pytest.ini_options]
addopts = """	
  -v
  -p no:warnings
  --cov=virtual_ecosystem
  --cov-report=html:htmlcov/coverage
  --doctest-modules --ignore=virtual_ecosystem/__main__.py
  --import-mode importlib
  """
python_files = 'test_*.py'
testpaths = ['tests']

[tool.ruff]
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", # ruff-only checking
  "NPY201", # Numpy 2.0.1
]

# On top of the Google convention, disable:
ignore = [
  "D202", # Blank line after docstring is ok
  "D107", # Location of __init__ docstring in class not __init__"  # "F401", # module imported but unused
]

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

[tool.ruff.lint.per-file-ignores]
"test/test_*.py" = ["D103"]

[tool.mypy]
ignore_missing_imports = true
plugins = "numpy.typing.mypy_plugin"

[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.
cell_metadata_filter = "all,-trusted"