[Biopython-dev] PEP8 lower case module names?

Michiel de Hoon mjldehoon at yahoo.com
Thu Sep 6 06:31:57 UTC 2012

> Hack together something that will remove old 'Bio' modules
> on install of the new version.

We could check in setup.py if we can import Bio, and ask the user to remove the old Biopython installation before proceeding. Since we can tell the user exactly which directory to remove, this would be straightforward. I would prefer this to removing the directory automatically.

> I really don't like using "bio" since (due to Python's use
> of folders for package names) you couldn't in general also
> have the old code available under "Bio". i.e. This forces
> a hard switch on our users which is a very bad idea I think.

I don't see why a user would like to have both an old Biopython under Bio and a new Biopython under bio. Unless he wants to run some scripts with the old Biopython and other scripts with the new Biopython, but I don't see the point of that.

> Thus my suggestion of something else like "biopy" [...]
> , or if not already taken "bp".

> However, my vote would be to stick with everything as is.

If the choice is between "bp", "biopy", or "Bio", then I agree with Brad; I prefer keeping a nice but PEP8-noncompliant module name "Bio" rather than switching to a PEP8-compliant but less attractive name like "biopy" or "bp".


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