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.flake8
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# =================================================
# flake8:
# pycodestyle: E### (error), W### (warning)
# pyflake: F### (error)
# pydocstyle: D1## - Missing Docstrings
# D2## - Whitespace Issues
# D4## - Docstring Content issues
# flake8-bugbear: B###
# flake8-quotes: Q###
# flake8-black : BLK###
# flake8-commas: C#### (in case installed locally)
# flake8-pie : PIE### (in case installed locally)
# flake8-sfs : SFS### (in case installed locally)
# =================================================
[flake8]
doctests = True
# Exclude some file types and folders that shouldn't be checked:
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
E501, # line too long
# Maybe we find a sensible limit, e.g. 88 (black) and enforce it
B007, # Loop control variable not used within the loop body.
# If this is intended, start the name with an underscore
E741, # ambiguous variable name 'l' (lots of these)
# =========================================
# Optional ignores for local installations:
# =========================================
PIE781, # Assigning to temp variable and then returning, not enforcing
SFS101,SFS301, # typical string formatting
# ========================
# Folder specific ignores:
# ========================
per-file-ignores =
Bio/*:F401,F841,D105,B009,B010,B011,C812,C815
Tests/*:F401,F841,D101,D102,D103,W504,B009,B010,B011,C812,BLK100
# 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,D105,B009,B010,B011,C812,C815
/Tests/*:F401,F841,D101,D102,D103,W504,B009,B010,B011,C812,BLK100
#Explanation of the codes being ignored in Bio/ and Tests/:
#
#Bio/*:F401 module imported but unused TODO? (107 occurrences)
# F841 local variable is assigned to but never used TODO? (55 occurrences)
# D105 missing docstring magic method (121 occurrences)
# B009 do not call getattr with a constant attribute value,
# it is not any safer than normal property access
# B010 do not call setattr with a constant attribute value,
# it is not any safer than normal property access
# B011 do not call assert False since python -O removes these calls;
# instead callers should raise AssertionError().
# C812 missing trailing comma
# C815 missing trailing comma in Python 3.5+
#Tests/*:F401 module imported but unused TODO? (88 occurrences)
# F841 local variable is assigned to but never used TODO? (64 occurrences)
# D101 missing docstring in public class (207 occurrences)
# D102 missing docstring in public method (956 occurrences)
# D103 missing docstring in public functions (52 occurrences)
# W504 line break after binary operator (97 occurrences, may be removed by black)
# B009 do not call getattr with a constant attribute value,
# it is not any safer than normal property access
# B010 do not call setattr with a constant attribute value,
# it is not any safer than normal property access
# B011 do not call assert False since python -O removes these calls;
# instead callers should raise AssertionError()
# C812 missing trailing comma
# BLK100 Black would make changes
# =======================
# flake8-quotes settings:
# =======================
inline-quotes = double