pyproject.toml

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

[project]
name = "dynetan"
authors = [
  { name="Marcelo C. R. Melo", email="melomcr@gmail.com" },
]

dynamic = ["version"]

description = "A Python implementation for Dynamical Network Analysis."
readme = {"file" = "README.md", "content-type" = "text/markdown"}

requires-python = ">=3.9"
dependencies = [
"MDAnalysis",
"NumPy",
"pandas",
"networkx",
"numba",
"h5py",
"python-louvain",
"tqdm",
"colorama",
"nglview"
]

classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
    "Operating System :: OS Independent",
]

[project.urls]
"Homepage" = "https://github.com/melomcr/dynetan"
"Bug Tracker" = "https://github.com/melomcr/dynetan/issues"
"Documentation" = "https://dynamical-network-analysis.readthedocs.io"

[tool.hatch.version]
path = "src/dynetan/version.py"

[tool.hatch.build.targets.sdist]
include = [
  "/src",
  "/tests",
  "/docs",
  "INSTALL.md"
]

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = [
    "--import-mode=importlib",
    "--cov=dynetan",
    "--cov-append",
    "--cov-report=term-missing",
    "--cov-report=xml"
]

# Individual warnings filters are specified as a sequence of fields separated by colons:
# action:message:category:module:line
# https://docs.python.org/3/library/warnings.html#describing-warning-filters
filterwarnings = [
    "error",  #converts all warnings to errors
    "ignore:.*numpy.ndarray size changed.*:RuntimeWarning",
#    "ignore::UserWarning",
    # note the use of single quote below to denote "raw" strings in TOML
    'ignore:.*np.MachAr.* is deprecated:DeprecationWarning',
    'ignore::DeprecationWarning:jupyter*',
    'ignore:.*DCDReader.*independent timesteps.*:DeprecationWarning:MDAnalysis'
]

[tool.mypy]
mypy_path = "src"

# Start off with these
warn_unused_configs = true
warn_redundant_casts = true
warn_unused_ignores = true
no_implicit_optional = true
warn_unreachable = true

# Getting these passing should be easy
strict_equality = true
strict_concatenate = true

# Strongly recommend enabling this one as soon as you can
check_untyped_defs = false

# These shouldn't be too much additional work, but may be tricky to
# get passing if you use a lot of untyped libraries
disallow_subclassing_any = true
#disallow_untyped_decorators = true
#disallow_any_generics = true

# These next few are various gradations of forcing use of type annotations
disallow_untyped_calls = true
disallow_incomplete_defs = true
disallow_untyped_defs = true

# This one isn't too hard to get passing, but return on investment is lower
no_implicit_reexport = true

# This one can be tricky to get passing if you use a lot of untyped libraries
#warn_return_any = true

show_error_codes = true


[[tool.mypy.overrides]]
module = []
ignore_errors = true

[[tool.mypy.overrides]]
module = [
    "MDAnalysis.*",
    "networkx.*",
    "numba",
    "community",
    "tqdm.*",
    "colorama",
    "pandas",
    "h5py"
]
ignore_missing_imports = true