tox.ini

# Tox (http://tox.testrun.org/) is a tool for running tests
# in multiple virtualenvs. This configuration file will run the
# test suite on all supported python versions. To use it, "pip install tox"
# and then run "tox" from this directory.

[tox]
isolated_build = true
envlist =
    lint
    flake8
    py

[testenv]
commands =
    pip install -e ../pheval
    pip install coverage
    coverage run -p -m pytest --durations=20 {posargs:tests}
    coverage combine
    coverage xml
deps =
    click
    pytest
    coverage

[testenv:lint]
deps =
    black
    isort
skip_install = true
commands =
    black .
    isort .
description = Run linters.

[testenv:flake8]
skip_install = true
deps =
    flake8<5.0.0
    flake8-bandit
    flake8-black
    flake8-bugbear
    flake8-colors
    flake8-isort
    pep8-naming
commands =
    flake8 src/ tests/
description = Run the flake8 tool with several plugins (bandit, docstrings, import order, pep8 naming).

#########################
# Flake8 Configuration  #
# (.flake8)             #
#########################
[flake8]
ignore =
    #E203
    W503
    S607 # Starting a process with a partial executable path
    #C901 # needs code change so ignoring for now.
    #E731 # needs code change so ignoring for now.
    #S101 # asserts are fine
    #S106 # flags false positives with test_table_filler
    #N801 # mixed case is bad but there's a lot of auto-generated code
    #N815 # same ^
    S404 # Consider possible security implications associated with the subprocess module.
    S603 # Check for execution of untrusted input - subprocess call
    #S108 # Probable insecure usage of temp file/directory.
    #S307 # Use of possibly insecure function - consider using safer ast.literal_eval.
    #S603 # subprocess call - check for execution of untrusted input.
    #S607 # Starting a process with a partial executable path ["open" in both cases]
    #S608 # Possible SQL injection vector through string-based query construction.
    #B024 # StreamingWriter is an abstract base class, but it has no abstract methods. 
         # Remember to use @abstractmethod, @abstractclassmethod and/or @abstractproperty decorators.
    #B027 # empty method in an abstract base class, but has no abstract decorator. Consider adding @abstractmethod
    #N803 # math-oriented classes can ignore this (e.g. hypergeometric.py)
    #N806 # math-oriented classes can ignore this (e.g. hypergeometric.py)
    #B019

max-line-length = 120
max-complexity = 13
import-order-style = pycharm
application-import-names =
    pheval_exomiser
    tests
# exclude =
#    datamodels   ## datamodels are auto-generated