pyproject.toml

[build-system]
requires = ["poetry_core>=1.0.0"]
build-backend = "poetry.core.masonry.api"

[tool.poetry]
name = "networkcommons"
version = "0.4.3"
description = "Integrated framework for network inference and evaluation using prior knowledge and omics data"
license = "gpl-3.0-only"
authors = [
    "Saez Lab <omnipathdb@gmail.com>"
]
packages = [
    { include = "networkcommons" }
]
classifiers = [
    "Development Status :: 2 - Pre-Alpha",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
    "Operating System :: OS Independent",
    "Programming Language :: Python",
    "Natural Language :: English",
    "Topic :: Scientific/Engineering :: Bio-Informatics"
]
keywords = [
    "systems biology", "molecular biology", "signaling network",
    "transcriptomics", "modeling", "mechanistic modeling",
    "network inference", "molecular network", "omics",
    "biomedicine"
]
repository = "https://github.com/saezlab/networkcommons"
homepage = "https://github.com/saezlab/networkcommons"
documentation = "https://networkcommons.readthedocs.io/"
readme = "README.md"

[[tool.poetry.source]]
name = "pypi-public"
url = "https://pypi.org/simple/"

[tool.poetry.dependencies]
python = "^3.9"
toml = "*"
networkx = "*"
pandas = "*"
pypath-common = "^0.2.5"
pydeseq2 = "^0.4.9"
requests = "^2.32.3"
beautifulsoup4 = "^4.12.3"
pypath-omnipath = "^0.16.16"
numpydoc = "^1.7.0"
sphinx-rtd-theme = "^2.0.0"
lazy-import = "^0.2.2"
anndata = "<=0.10.8"
pytest = "^8.2.2"
yfiles-jupyter-graphs = "^1.7.2"
gurobipy = "^11.0.2"
matplotlib = "^3.5.1"
graphviz = "^0.17"
biomart = "^0.9.2"
igraph = {version = "^0.11.6", optional = true}
decoupler = "^1.8.0"
omnipath = "^1.0.8"
pygraphviz = "1.11"
picos = { version = "^2.4.17", optional = true }
cvxpy = "^1.5.1"
corneto = "1.0.0.dev0"
seaborn = "^0.13.2"

[tool.poetry.dev-dependencies]
pytest = ">=6.0"
pytest-timeout = "^2.3.1"
pytest-cov = "^5.0.0"
codecov-cli = "^0.7.2"
tox = ">=3.20.1"
pre-commit = ">=2.17.0"
bump2version = "*"
coverage = ">=6.0"
distlib = "*"
sphinx = "^7.0.0"
sphinx-last-updated-by-git = ">=0.3"
sphinx-autodoc-typehints = ">=1.18.0"
sphinxcontrib-fulltoc = ">=1.2.0"
sphinxcontrib-bibtex = "*"
sphinx-copybutton = "*"
myst-parser = "*"
myst-nb = "*"
jupyterlab = "*"
pydata-sphinx-theme = "*"
sphinx-remove-toctrees = "*"
jupyter-contrib-nbextensions = { git = "https://github.com/deeenes/jupyter_contrib_nbextensions.git", branch = "master" }
nbsphinx = { git = "https://github.com/deeenes/nbsphinx.git", branch = "timings" }

[tool.poetry.extras]
igraph = ["igraph"]
corneto-backends = ["picos"]

[tool.poetry.urls]
"Bug Tracker" = "https://github.com/saezlab/networkcommons/issues"

[tool.black]
line-length = 80
target-version = ['py31*']
include = '\.pyi?$'
exclude = '''
(
  /(
      \.eggs
    | \.git
    | \.hg
    | \.mypy_cache
    | \.tox
    | \.venv
    | _build
    | buck-out
    | build
    | dist
  )/
)
'''

[tool.isort]
from_first = true
line_length = 80
multi_line_output = 3
include_trailing_comma = true
use_parentheses = true
known_num="numpy,pandas"
sections = "FUTURE,STDLIB,THIRDPARTY,NUM,FIRSTPARTY,LOCALFOLDER"
no_lines_before="LOCALFOLDER"
balanced_wrapping = true
force_grid_wrap = 0
length_sort = "1"
indent = "    "
skip = []

[tool.flake8]
extend-select = ["CE101"]
ignore = [
  "D200", "D202", "D401", "D105",
  "W503", "W504",
  "E731", "E131", "E251", "E303"
]
per-file-ignores = [
    "docs/src/conf.py:D100",
    "tests/*:D100,D101,D102",
    "*/__init__.py:F401"
]
max-line-length = 80
count = true
exclude = [
    ".git",
    "__pycache__",
    "build",
    "docs/_build",
    "dist"
]

[tool.yapf]
based_on_style = "facebook"
split_penalty_before_if_expr = 0
split_penalty_import_names = 0
split_penalty_comprehension = 0
split_penalty_for_added_line_split = 0
split_penalty_after_opening_bracket = 0
split_before_first_argument = true
split_before_named_assigns = true
split_complex_comprehension = true

[tool.rstcheck]
report_level = "INFO"
ignore_directives = [
    "automodule",
    "toctree",
]
ignore_roles = ["ref"]
ignore_messages = '(Unknown target name:.*|No (directive|role) entry for "(auto)?(class|method|property|function|func|mod|attr)" in module "docutils\.parsers\.rst\.languages\.en"\.)'

[tool.coverage.paths]
source = [
    "networkcommons",
    "**/site-packages/networkcommons"
]

[tool.coverage.run]
branch = true
parallel = true
source = ["networkcommons"]
omit = [
	"**/test_*.py",
    "**/noi/*",
]

[tool.coverage.report]
show_missing = true
precision = 2
exclude_also = [
    ".*pragma:\\s*no.?cover",
    "if __name__ == .?__main__.?",
    "\\s*raise NotImplementedError",
    "\\s*raise AssertionError",
    "\\s*return NotImplemented",
]

[tool.pytest.ini_options]
testpaths = [
  "tests",
]
xfail_strict = true
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')"
]
addopts = [
    # "-Werror",  # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
    "--import-mode=importlib",  # allow using test files with same name
    "-m not slow",
]
filterwarnings = [
    "ignore: .*fitting did not converge.*:UserWarning",
    "ignore: .*especially asymmetric.*:UserWarning",
    "ignore: .*machine precision times.*:FutureWarning",
    "ignore: .*invalid escape sequence.*:DeprecationWarning",
]