Minor code tidying

[GenevieveBuckley]

Summary:

• [x] Function docstrings elaborated on.
• [x] Function naming: remove implicit 'get_' prefix from function names
• [x] Separated user input argument parsing into its own configure_parser function. Removed nargs kwarg as not needed.
• [x] Add comment indicating that you’re using 1-based indexing (for user input arguments, and for the output pandas data frames). 0-based indexing for the actual programming logic.
• [x] Moved chunk of code out of nested loops in main() and into new function process_image_series()
• [x] Bugfix: tell pims explicitly to always open images with Bioformats (otherwise tiff images won't be returned with image metadata.
• [x] pandas dataframes - replaced all the slow append statements with a much faster method (storing many dataframes in a list, then pd.concat() right at the end)

[pep8speaks]

Hello @GenevieveBuckley! Thanks for updating the PR.

• In the file podocytes/main.py, following are the PEP8 issues :

Line 9:1: E402 module level import not at top of file Line 10:1: E402 module level import not at top of file Line 11:1: E402 module level import not at top of file Line 13:1: E402 module level import not at top of file Line 14:1: E402 module level import not at top of file Line 16:1: E402 module level import not at top of file Line 17:1: E402 module level import not at top of file Line 18:1: E402 module level import not at top of file Line 19:1: E402 module level import not at top of file Line 20:1: E402 module level import not at top of file Line 22:1: E402 module level import not at top of file Line 46:80: E501 line too long (80 > 79 characters) Line 58:13: E128 continuation line under-indented for visual indent Line 60:13: E128 continuation line under-indented for visual indent Line 70:1: E302 expected 2 blank lines, found 0 Line 349:80: E501 line too long (84 > 79 characters) Line 350:80: E501 line too long (84 > 79 characters) Line 454:80: E501 line too long (84 > 79 characters) Line 544:20: E127 continuation line over-indented for visual indent Line 545:20: E127 continuation line over-indented for visual indent Line 551:80: E501 line too long (87 > 79 characters) Line 570:80: E501 line too long (82 > 79 characters)

• In the file podocytes/validate.py, following are the PEP8 issues :

Line 11:1: E402 module level import not at top of file Line 17:1: E402 module level import not at top of file Line 18:1: E402 module level import not at top of file Line 19:1: E402 module level import not at top of file Line 20:1: E402 module level import not at top of file Line 21:1: E402 module level import not at top of file Line 22:1: E402 module level import not at top of file Line 24:1: E402 module level import not at top of file Line 28:1: E302 expected 2 blank lines, found 1 Line 30:80: E501 line too long (136 > 79 characters) Line 31:80: E501 line too long (128 > 79 characters) Line 32:80: E501 line too long (151 > 79 characters) Line 67:31: E711 comparison to None should be 'if cond is None:' Line 83:80: E501 line too long (113 > 79 characters) Line 87:9: E265 block comment should start with '# ' Line 87:80: E501 line too long (86 > 79 characters) Line 100:80: E501 line too long (83 > 79 characters) Line 111:52: E128 continuation line under-indented for visual indent Line 112:52: E128 continuation line under-indented for visual indent Line 113:52: E128 continuation line under-indented for visual indent Line 132:80: E501 line too long (89 > 79 characters) Line 134:80: E501 line too long (95 > 79 characters) Line 140:80: E501 line too long (81 > 79 characters) Line 149:80: E501 line too long (105 > 79 characters) Line 150:80: E501 line too long (110 > 79 characters) Line 152:80: E501 line too long (103 > 79 characters) Line 153:80: E501 line too long (96 > 79 characters) Line 154:80: E501 line too long (88 > 79 characters) Line 155:80: E501 line too long (105 > 79 characters) Line 156:80: E501 line too long (92 > 79 characters) Line 157:80: E501 line too long (110 > 79 characters) Line 158:80: E501 line too long (102 > 79 characters) Line 159:80: E501 line too long (119 > 79 characters) Line 183:80: E501 line too long (85 > 79 characters) Line 187:80: E501 line too long (113 > 79 characters) Line 343:12: E225 missing whitespace around operator

Comment last updated on August 30, 2018 at 00:14 Hours UTC

[GenevieveBuckley]

@jni how do you feel about it now? I'd like to have the PR merged before Friday, so I can increment the release to v0.1.1-alpha. (I have testing scheduled for Friday morning)

[jni]

@GenevieveBuckley imho it's basically ready. There's some very minor comments that can certainly wait for a later PR, but just wanted to get my comments in there. I can merge tomorrow afternoon regardless of whether you get a chance to address these or not.

[jni]

Very nice, clean commits! =)

[jni]

I've changed the merge commit to Major code tidying. =)