tox.ini

[gh-actions]
python =
    3.9: py39
    3.10: py310
    # 3.8: py38, rst_linux, rst_mac, readme, linters, coverage-report, qa
    # 3.11: py311, rst_linux, rst_mac, readme, linters, coverage-report, qa
    3.11: py311, rst_linux, rst_mac, readme, coverage-report
    # 3.9: py39
    # 3.10: py310

[tox]
# todo: add back the linters and qa
# envlist = py39, py310, py311, rst_linux, rst_mac, readme, rst, linters, coverage-report, qa
envlist = py39, py310, py311, rst_linux, rst_mac, readme, rst, coverage-report

[testenv]
; conda_deps =
;     rdkit
; conda_channels = rdkit
deps =
    -r{toxinidir}/requirements_dev.txt
commands =
    # coverage run --rcfile=tox.ini -m pytest tests
    python -m pip install --upgrade pip
    # pip install -r requirements.txt
    # pip install .
    python -m pytest -c pyproject.toml --cov-config=.coveragerc --cov-report=xml --color=yes selector

# pytest --cov-config=.coveragerc --cov=selector/test
# can run it if needed
# coverage report -m
# prevent exit when error is encountered
ignore_errors = true

[testenv:readme]
skip_install = true
deps =
    readme_renderer
    twine
    -r{toxinidir}/requirements.txt
commands =
    # https://github.com/pypa/twine/issues/977
    python -m pip install importlib_metadata==7.2.1 build
    python -m build --no-isolation
    twine check dist/*

[testenv:rst_linux]
platform =
    linux
skip_install = true
deps =
    doc8
    rstcheck==3.3.1
commands =
    doc8 --config tox.ini book/content/
# ignore code-block related error because
# the Sphinx support in rstcheck is minimal. This results in false positives
# rstcheck uses Docutils to parse reStructuredText files and extract code blocks
# fixme: check updates on the following website in the future
# coala.gitbooks.io/projects/content/en/projects/rstcheck-with-better-sphinx-suppor.html
    rstcheck --recursive book/content/ --report error \
    --ignore-directives automodule,autoclass,autofunction,bibliography,code-block \
    --ignore-roles cite,mod,class,lineno --ignore-messages code-block

[testenv:rst_mac]
platform =
    darwin
skip_install = true
deps = {[testenv:rst_linux]deps}
commands = {[testenv:rst_linux]commands}

[testenv:linters]
deps =
    flake8
    flake8-docstrings
    flake8-import-order>=0.9
    flake8-colors
    pep8-naming
    pylint==2.13.9
    # black
    bandit
commands =
    flake8 selector/ selector/tests setup.py
    pylint selector --rcfile=tox.ini --disable=similarities
    # black -l 100 --check ./
    # black -l 100 --diff ./
    # Use bandit configuration file
    bandit -r selector -c .bandit.yml

ignore_errors = true

[testenv:coverage-report]
deps = coverage>=4.2
skip_install = true
commands =
# coverage combine --rcfile=tox.ini
    coverage report

[testenv:qa]
deps =
    {[testenv]deps}
    {[testenv:linters]deps}
    {[testenv:coverage-report]deps}
commands =
    {[testenv]commands}
    {[testenv:linters]commands}
# {[testenv:coverage-report]commands}
ignore_errors = true

# pytest configuration
[pytest]
addopts = --cache-clear
          --showlocals
          -v
          -r a
          --cov-report term-missing
          --cov selector
# Do not run tests in the build folder
norecursedirs = build

# flake8 configuration
[flake8]
exclude =
    __init__.py,
    .tox,
    .git,
    __pycache__,
    build,
    dist,
    *.pyc,
    *.egg-info,
    .cache,
    .eggs,
    _version.py,

max-line-length = 100
import-order-style = google
ignore =
# E121 : continuation line under-indented for hanging indent
    E121,
# E123 : closing bracket does not match indentation of opening bracket’s line
    E123,
# E126 : continuation line over-indented for hanging indent
    E126,
# E226 : missing whitespace around arithmetic operator
    E226,
# E241 : multiple spaces after ‘,’
# E242 : tab after ‘,’
    E24,
# E704 : multiple statements on one line (def)
    E704,
# W503 : line break occurred before a binary operator
    W503,
# W504 : Line break occurred after a binary operator
    W504,
# D202: No blank lines allowed after function docstring
    D202,
# E203: Whitespace before ':'
    E203,
# E731: Do not assign a lambda expression, use a def
    E731,
# D401: First line should be in imperative mood: 'Do', not 'Does'
    D401,

per-file-ignores =
# F401: Unused import
# this is used to define the data typing
    selector/utils.py: F401,
# E1101: rdkit.Chem has no attribute xxx
# D403: first word of the first line should be properly capitalized
    selector/feature.py: E1101, D403

# doc8 configuration
[doc8]
# Ignore target directories and autogenerated files
ignore-path = book/content/_build/, build/, selector.egg-info/, selector.egg-info, .*/
# File extensions to use
extensions = .rst, .txt
# Maximal line length should be 100
max-line-length = 100
# Disable some doc8 checks:
# D000: Check RST validity (cannot handle the "linenos" directive)
# D002: Trailing whitespace
# D004: Found literal carriage return
# Both D002 and D004 can be problematic in Windows platform, line ending is `\r\n`,
# but in Linux and MacOS, it's "\n"
# Known issue of doc8, https://bugs.launchpad.net/doc8/+bug/1756704
# ignore = D000,D002,D004
ignore = D000

# pylint configuration
[MASTER]
# This is a known issue of pylint with recognizing numpy members
# https://github.com/PyCQA/pylint/issues/779
# https://stackoverflow.com/questions/20553551/how-do-i-get-pylint-to-recognize-numpy-members
extension-pkg-whitelist=numpy

[FORMAT]
# Maximum number of characters on a single line.
max-line-length=100

[MESSAGES CONTROL]
# disable pylint warnings
disable=
# attribute-defined-outside-init (W0201):
# Attribute %r defined outside __init__ Used when an instance attribute is
# defined outside the __init__ method.
    W0201,
# too-many-instance-attributes (R0902):
# Too many instance attributes (%s/%s) Used when class has too many instance
# attributes, try to reduce this to get a simpler (and so easier to use)
# class.
    R0902,
# too many branches (R0912)
    R0912,
# too-many-arguments (R0913):
# Too many arguments (%s/%s) Used when a function or method takes too many
# arguments.
    R0913,
# Too many local variables (r0914)
    R0914,
# Too many statements (R0915)
    R0915,
# fixme (W0511):
# Used when a warning note as FIXME or XXX is detected.
    W0511,
# bad-continuation (C0330):
# Wrong hanging indentation before block (add 4 spaces).
    C0330,
# wrong-import-order (C0411):
# %s comes before %s Used when PEP8 import order is not respected (standard
# imports first, then third-party libraries, then local imports)
    C0411,
# arguments-differ (W0221):
# Parameters differ from %s %r method Used when a method has a different
# number of arguments than in the implemented interface or in an overridden
# method.
    W0221,
# unecessary "else" after "return" (R1705)
    R1705,
# Value XX is unsubscriptable (E1136). this is a open issue of pylint
# https://github.com/PyCQA/pylint/issues/3139
    E1136,
# Used when a name doesn't doesn't fit the naming convention associated to its type
# (constant, variable, class…).
    C0103,
# Unnecessary pass statement
    W0107,
# Module 'rdkit.Chem' has no 'ForwardSDMolSupplier' member (no-member)
    E1101,
# todo: fix this one later and this is a temporary solution
# E0401: Unable to import xxx (import-error)
    E0401,
# R1721: Unnecessary use of a comprehension
    R1721,
# I1101: Module xxx has no yyy member (no-member)
    I1101,
# R0903: Too few public methods (too-few-public-methods)
    R0903,
# R1702: Too many nested blocks (too-many-nested-blocks)
    R1702,

[SIMILARITIES]
min-similarity-lines=5

# coverage configuration
[run]
branch = True
parallel = True
source = selector

[paths]
source =
    selector
    .tox/*/lib/python*/site-packages/selector
    .tox/pypy*/site-packages/selector