pyproject.toml

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

[tool.poetry]
name = "omnipath-metabo"
version = "0.0.1"
description = "Utilities for processing metabolic data."
license = "GNU General Public License Version 3"
authors = [
    "Macabe Daley <omnipath.db@gmail.com>"
]
packages = [
    { include = "omnipath_metabo" }
]
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"
]
repository = "https://github.com/saezlab/omnipath-metabo"
homepage = "https://github.com/saezlab/omnipath-metabo"
documentation = "https://omnipath-metabo.readthedocs.io/"
readme = "README.md"

[tool.poetry.dependencies]
python = "^3.9"
toml = "*"
pypath-omnipath = { git = "https://github.com/saezlab/pypath.git", branch = "master"}
sqlalchemy = "^2.0.35"
psycopg2 = "^2.9.9"
pypath-common = "^0.2.5"

[tool.poetry.dev-dependencies]
pytest = ">=6.0"
tox = ">=3.20.1"
pre-commit = ">=2.17.0"
bump2version = "*"
coverage = ">=6.0"
distlib = "*"
sphinx = ">=5.0.0"
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.urls]
"Bug Tracker" = "https://github.com/saezlab/omnipath-metabo/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.run]
source = ["omnipath_metabo"]
omit = [
	"**/test_*.py",
]

[tool.pytest.ini_options]
testpaths = [
  "tests",
]
xfail_strict = true
addopts = [
    # "-Werror",  # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
    "--import-mode=importlib",  # allow using test files with same name
]
filterwarnings = [
    # "ignore:.*U.*mode is deprecated:DeprecationWarning",
]