formatting issues

[fbergmann]

looking at the test results there is a lot of formatting issues, that should be addressed. (can be easily done by running flake8 locally). Here the current results:

7     C901 'EnzymeMLDocument.__getReplicateUnits' is too complex (16)
3     E117 over-indented (comment)
3     E122 continuation line missing indentation or outdented
4     E124 closing bracket does not match visual indentation
19    E127 continuation line over-indented for visual indent
27    E128 continuation line under-indented for visual indent
3     E131 continuation line unaligned for hanging indent
719   E201 whitespace after '['
681   E202 whitespace before ']'
29    E203 whitespace before ','
1     E221 multiple spaces before operator
9     E222 multiple spaces after operator
5     E225 missing whitespace around operator
28    E231 missing whitespace after ','
30    E251 unexpected spaces around keyword / parameter equals
8     E261 at least two spaces before inline comment
4     E262 inline comment should start with '# '
12    E265 block comment should start with '# '
24    E266 too many leading '#' for block comment
5     E272 multiple spaces before keyword
35    E302 expected 2 blank lines, found 1
269   E303 too many blank lines (2)
4     E305 expected 2 blank lines after class or function definition, found 1
1     E401 multiple imports on one line
42    E501 line too long (144 > 127 characters)
1     E502 the backslash is redundant between brackets
79    E701 multiple statements on one line (colon)
21    E703 statement ends with a semicolon
14    E711 comparison to None should be 'if cond is None:'
8     E712 comparison to False should be 'if cond is not False:' or 'if cond:'
1     E722 do not use bare 'except'
9     E731 do not assign a lambda expression, use a def
133   F401 'Tools.scripts.fixcid.rep' imported but unused
2     F402 import 'rep' from line 19 shadowed by loop variable
10    F841 local variable 'inits' is assigned to but never used
217   W291 trailing whitespace
41    W292 no newline at end of file
1496  W293 blank line contains whitespace
4     W391 blank line at end of file
8     W605 invalid escape sequence '\s'
4016

[JR-1991]

Thanks for pointing out! The issues have been removed as far as possible. Some mild issues still remain in comments, but these shouldnt decrease the overall code quality.