/
.flake8
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/
.flake8
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# =================================================
# flake8:
# pycodestyle: E### (error), W### (warning)
# pyflake: F### (error)
# flake8-blind-except: B###
# flake8-bugbear: B###
# flake8-quotes: Q###
# flake8-black : BLK###
# flake8-commas: C8## (in case installed locally)
# flake8-pie : PIE### (in case installed locally)
# flake8-sfs : SFS### (in case installed locally)
# flake8-pydocstyle: D### (in case installed locally)
# =================================================
[flake8]
doctests = True
rst-roles =
class,
func,
meth,
mod,
data,
rst-directives =
seealso,
todo,
# 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
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,
# =========================================
# 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
# ========================
# Folder specific ignores:
# ========================
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
#Explanation of the codes being ignored in Bio/ and Tests/:
#
#Bio/*:F401 module imported but unused TODO? (97 occurrences)
# F841 local variable is assigned to but never used TODO? (58 occurrences)
# B009 do not call getattr with a constant attribute value (5 occurrences),
# it is not any safer than normal property access
# B010 do not call setattr with a constant attribute value (11 occurrences),
# it is not any safer than normal property access
#Tests/*:F401 module imported but unused TODO? (115 occurrences)
# F841 local variable is assigned to but never used TODO? (93 occurrences)
# D101 missing docstring in public class (244 occurrences)
# D102 missing docstring in public method (1368 occurrences)
# D103 missing docstring in public functions (20 occurrences)
# W291 trailing whitespace (due to alignment tests)
# B009 do not call getattr with a constant attribute value (10 occurrences),
# it is not any safer than normal property access
# B010 do not call setattr with a constant attribute value (7 occurrences),
# it is not any safer than normal property access
# B015 Pointless comparison. This comparison does nothing ... (108 occurrences)
# (Intended to trigger exceptions in our tests)
# =======================
# flake8-quotes settings:
# =======================
inline-quotes = double