doctests = True

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

ignore =

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

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

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

D203, # 1 blank line required before class docstring

# deliberately ignore in favour of passing D211: No blank lines

# allowed before class docstring

W503, # line-break before binary operator

# deliberately ignore (in favour of some day enforcing W504?)

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

# Ignores that we have to accept for a while:

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

E123, # closing bracket does not match indentation of opening bracket's line

# TODO? (main/Bio/Tests: 3/91/31 occurrences)

E501, # line too long

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

W504, # line break after binary operator (Bio/Tests/Scripts: 225/119/7) TODO?

B007, # Loop control variable not used within the loop body.

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

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

# Optional ignores for local installations:

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

BLK100, # Black would make changes, only on local installations (so far)

PIE781, # Assigning to temp variable and then returning, not enforcing

per-file-ignores =

Bio/*:E122,E126,F401,F841,D105,B009,B010,B011,C812,C815

Tests/*:F401,F841,D101,D102,D103,B009,B010,B011,C812

# 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/*:E122,E126,F401,F841,D105,B009,B010,B011,C812,C815

/Tests/*:F401,F841,D101,D102,D103,B009,B010,B011,C812

inline-quotes = double