.flake8

# =================================================
# flake8:
#   pycodestyle: E### (error), W### (warning)
#   pyflake:     F### (error)
# pydocstyle: D1## - Missing Docstrings
#             D2## - Whitespace Issues
#             D4## - Docstring Content issues
# flake8-blind-except: B###
# 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)
    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

# ========================
# 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,B015,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/*:F401,F841,D105,B009,B010,B011,C812,C815
    /Tests/*:F401,F841,D101,D102,D103,W504,B009,B010,B011,B015,C812

#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()
#        B015 Pointless comparison. This comparison does nothing ...
#             (Intended to trigger exceptions in our tests)
#        C812 missing trailing comma

# =======================
# flake8-quotes settings:
# =======================
inline-quotes = double