I am no longer working on this repository and have therefore decided to archive it.

Proof of concept (POC) for a distributed Biopython setup.

POC modules:

• biopy_base: Base Biopython install, contains core sequence objects

• biopy_togows: Pure-python extension

• biopy_nexus: Extension requiring C compilation

• biopy_statistics: Extension depending on numpy

In addition to having separate Python packages (Biopython extensions), the POC also tries to do the following:

• Semantic versioning, with a boolean RELEASE flag (-dev or ``) to denote development versions. Versioning starts at 2.0.0-dev to avoid clashes with current Biopython code

• better PEP8 compliance

• updated namespace for core modules

• (maybe -- other backward incompatible changes?)

This is not for any kind of production use. The codebase are mainly adapted from the official Biopython distribution, except one where it is mentioned explicitly.

1. The one using sys.meta_path (poc_hook)

   All modules inside it are meant to be separate Python packages that lives in its own repository. They are available in pip:

   • biopy_base: pip install poc_hook_Biopython

   • biopy_togows: pip install poc_hook_Biopython-Nexus

   • and so on ..

   (the names were intentionally chosen to be quite ... verbose to avoid clashing with the real production Biopython).