Ideas for Biopython 2
This page is mostly a collection of ideas from discussions on the mailling list regarding a possible version 2 of Biopython.
If I missed something, please accept my apologies and change accordingly.
I am trying to keep a neutral tone, but sometime we might want to include major arguments in favor and against some option
so that readers are made aware of the gist of main arguments
- Depend on matplotlib, numpy and scipy or
- Create a list of acceptable dependencies (e.g. requests or pandas) that developers could use
- There seems to be a consensus that API documentation takes precedence
- numpydoc and Sphinx proposed
- Juptyer notebook vs HTML proposed for tutorials.
- Latex to be discontinued?
Deprecate Python 2?
Which Python 3 version?
- All of them? (no one defended this)
- Most recent version when we start developing Bioython 2 (e.g. now would mean 3.6)
Lower case package and module naming
Lower case for packages and modules seems consensual.
- Name this biopy.? biopython.? biop.*?
- How many modules on the top-level? None or some basic stuff (life exceptions, abstract file management)
- Automatic import of everything, or just partial? or even nothing?
Which sub-packages? Tightly related to the modular approach (see below)
Anyone wants to write a bit here about options?
- Should there be a module system with core modules allowing third parties to to make extensions, a la Biogems
- Bow’s work might be a starting point
Removal of outdated sub-packages
Discuss which packages to remove
Relationship between Biopython 1 and 2
- Is there any code sharing? If so how? Code sharing should jeopardize desired Bioypthon 2 features and architecture
- APIs would probably not be compatible
Is there even time to do this?