biopython/.flake8

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