doctests = True

rst-roles =

class,

func,

meth,

mod,

data,

rst-directives =

seealso,

todo,

exclude = .svn,CVS,.bzr,.hg,.git,__pycache__,.tox,.github,build

ignore =

# =============================================================

# Biopython's 'standard' ignores we can agree to always accept:

# =============================================================

W503,

# line-break before binary operator

# deliberately ignore (in favour of enforcing W504)

# ===========================================

# Ignores that we have to accept for a while:

# ===========================================

E203,

# whitespace before ':'

# gives false positives after running black, see

# https://github.com/PyCQA/pycodestyle/issues/373

E122,E131,E124,E126,E127,E128,E201,E241,

# E112 continuation line missing indentation or outdented

# E131 continuation line unaligned for hanging indent

# E124 closing bracket does not match visual indentation

# E126 continuation line over-indented for hanging indent

# E127 continuation line over-indented for visual indent

# E128 continuation line under-indented for visual indent

# E201 whitespace after '['

# E241 multiple spaces after ','

# ignoring as using black for layout (if this is triggered,

# it would be in a snippet explicitly excluded from black)

E501,

# line too long

# Maybe we find a sensible limit, e.g. 88 (black) and enforce it

E704,

# multiple statements on one line (def)

# seeing some false positives with @overload ... for type annotation

B007,

# Loop control variable not used within the loop body.

# If this is intended, start the name with an underscore

B028,

# No explicit stacklevel keyword argument found.

# The warn method from the warnings module uses a stacklevel of 1

# by default... It is therefore recommended to use a stacklevel of

# 2 or greater to provide more information to the user

B902,

# blind except Exception: statement

# =========================================

# Optional ignores for local installations:

# =========================================

PIE781,

# Assigning to temp variable and then returning, not enforcing

SFS101,SFS301,

# typical string formatting

C8,

# everything from flake8-commas - just use black

D,

# using ruff for the historic flake8-pydocstyle codes

per-file-ignores =

Bio/*:F401,F841,B009,B010

Tests/*:F401,F841,W291,B009,B010,B015

# Due to a bug in flake8, we need the following lines for running the

# pre-commit hook. If you made edits above, please change also here!

/Bio/*:F401,F841,B009,B010

/Tests/*:F401,F841,D101,W291,B009,B010,B015

inline-quotes = double