Decide on style guides.

[FilipeJesus]

Background

In order to improve legibility and ease of collaboration we should decide on style guides for each of the languages we use inhouse.

Key Changes

Agree on style guide for:

• R
• python
• cwl
• bash

Discussion on this topic should occur below

Tests

• All current tests should pass

[FilipeJesus]

Hi everyone, in this comment we should list the style guides.

• R - tidyverse style guide
• python - black
• cwl - google's style guide
• bash -

[FilipeJesus]

My suggestion for python would be PEP 8

[ajle96]

PEP8 is quite good. I am not sure something similar exists for other languages. Will try to have a look.

https://pypi.org/project/pep8/ this can help to rapidly check and convert the code

[FilipeJesus]

I agree, pylint can also be used to check that our code conforms to pep8.

For R I am a fan of the tidyverse style guide. Its definity not as well known as PEP8 but it is quite complete and they have their own linter (lintr) which is quite useful.

[tonyyzy]

Take a look at Python Black formatter(https://github.com/psf/black), BioPython is gradually adopting Black now. There's no options to set (except line width) so no arguments about any style decisions.

Thanks for pushing this into motion :p

[FilipeJesus]

Very nice, it seems like black is a subset of PEP 8 which is useful as it seems like PEP 8 is already well known in the group. I would be happy with using black but my one caveat is that since black will reformat your code it could lead to us creating code which we find hard reading ourselves since we initially programmed it to look different.

Although i do see the benefit in less time waiste with black reformatting. So, if @ajle96 would also be interested in using black then we shall go with it but if not lets go with PEP8?

[ajle96]

I don't really know anything about black but happy to learn more. If it's the new standard then it makes more sense. Alessandro Pio Greco apg3718@ic.ac.uk MSc Bioinformatics and Theoretical System Biology

…

-------- Original Message -------- Subject: Re: [rawgene/rawg] Decide on style guides. (#3) From: FilipeJesus To: rawgene/rawg CC: "Greco, Alessandro P" ,Mention Very nice, it seems like black is a subset of PEP 8 which is useful as it seems like PEP 8 is already well known in the group. I would be happy with using black but my one caveat is that since black will reformat your code it could lead to us creating code which we find hard reading ourselves since we initially programmed it to look different. Although i do see the benefit in less time waiste with black reformatting. So, if @ajle96<https://github.com/ajle96> would also be interested in using black then we shall go with it but if not lets go with PEP8? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#3?email_source=notifications&email_token=AKVVA5YK3FO5JWUBBOAI62LQTP4N3A5CNFSM4JMZXPE2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOED6DAMI#issuecomment-553398321>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AKVVA57PYNQCXKD2TO7G2W3QTP4N3ANCNFSM4JMZXPEQ>.

[FilipeJesus]

Great, so we will go with black. Any opinions on whether to go with anything other than the tidyverse style guide for R?

[tonyyzy]

Very nice, it seems like black is a subset of PEP 8 which is useful as it seems like PEP 8 is already well known in the group. I would be happy with using black but my one caveat is that since black will reformat your code it could lead to us creating code which we find hard reading ourselves since we initially programmed it to look different.

That was one of the problems raised by BioPython and they have a considerably larger codebase. The solution came up was to migrate to Black incrementally and do a commit for formatting change.

Great, so we will go with black. Any opinions on whether to go with anything other than the tidyverse style guide for R?

Not familiar with R styleguide (don't write much R :p) but happy with what you see fit!