Fix flake8 configuration, add reasoning to ignores

* From PyCQA/flake8#1760:
  "surprise surprise! your configuration has been silently wrong for years"

.flake8

@@ -5,17 +5,28 @@ docstring-convention = google
 import-order-style   = google
 application-import-names = eminus
 
-ignore = E741, E743, \  # Ambiguous variable names and function definitions
-         W504, \        # Line break after binary operator
-         D107, \        # Missing docstring in __init__
-         D300, \        # Use double quotes for docstrings
-         D417           # A bug results in false positives
-                        # TODO: Remove if pydocstyle ever gets updated
+ignore =
+    # E741, E743: Ambiguous variable names and function definitions
+    # eminus uses, e.g., l (quantum number) as variables or O (overlap operator) as functions
+    E741, E743,
+    # W504: Line break after binary operator
+    # There will always be a line break around some operators, ignore this over W503
+    W504,
+    # D107: Missing docstring in __init__
+    # Docstrings are present in the class definition instead of the init method
+    D107,
+    # D300: Use double quotes for docstrings
+    # Use triple single quotes for docstrings
+    D300,
+    # D417: A bug results in false positives
+    # TODO: Remove if pydocstyle ever gets updated
+    D417
 
 # D100, D103: Ignore missing docstrings in public modules or functions
 # E501, W505: Ignore line length warnings
-per-file-ignores = examples/*:D100,D103,E501,W505,
-                   tests/*:D103
+per-file-ignores =
+    examples/*:D100,D103,E501,W505,
+    tests/*:D103
 
 # Exclude the generated docs folder
 exclude = public