tox.ini

[gh-actions]
python =
    3.9: py39
    3.10: py310
    3.11: py311, rst_linux, readme, rst, linters, coverage-report, qa
    3.12: py312

[tox]
envlist = py39, py310, py311, py312, rst_linux, readme, rst, linters, coverage-report, qa

[testenv]
deps =
    -r{toxinidir}/requirements.txt
    -r{toxinidir}/requirements_dev.txt
    pytest-cov
    coverage>=4.2
commands =
    # coverage run --rcfile=tox.ini -m pytest tests
    python -m pip install --upgrade pip
    pip install .
    python -m pytest --cov-config=.coveragerc --cov=procrustes procrustes
    # pytest --cov-config=.coveragerc --cov=procrustes/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
    build
commands =
    # checks whether distribution’s long description will render correctly on PyPI
    python -m build
    twine check dist/*

[testenv:rst_linux]
platform =
    linux
skip_install = true
deps =
    doc8
    rstcheck>=6.2.4
ignore_outcome = true
commands =
    doc8 --config tox.ini doc/
    # 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
    # https://rstcheck.readthedocs.io/en/latest/usage/cli/
    rstcheck --recursive doc/ --report-level 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 =
    -r{toxinidir}/requirements.txt
    -r{toxinidir}/requirements_dev.txt
    pytest
    flake8>=4.0.1
    flake8-docstrings>=1.6.0
    # flake8 import order checking conflicts with isort
    # because the import order is checked by pylint, we can disable it here
    # flake8-import-order>=0.18.1
    flake8-pyproject
    flake8-colors>=0.1.9
    pep8-naming>=0.12.1
    pylint>=2.13.4
    # black
    bandit>=1.7.4
ignore_errors = true
commands =
    flake8 procrustes/
    python -m pylint procrustes --rcfile=pyproject.toml  --disable=similarities
    # black -l 100 --check ./
    # black -l 100 --diff ./
    # Use bandit configuration file
    bandit -r procrustes -c .bandit.yml


[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
testpaths = procrustes/test
# Enable line length testing with maximum line length of 100
pep8maxlinelength = 100
# 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,

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,

# doc8 configuration
[doc8]
# Ignore target directories and autogenerated files
ignore-path = doc/_build/, build/, procrustes.egg-info/, qc_procrustes.egg-info, .*/, doc/intro_about.rst
# 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
# Maximum number of lines in a module
max-module-lines=2000

[MESSAGES CONTROL]
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,
    # Used when too many positional arguments are given in a function call.
    R0917,

[SIMILARITIES]
min-similarity-lines=5

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

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