modularizing commonly used functions

[JamesRH]

Make lib directory
Four files:

• treefuncs.py : Tree functions
• metadata: e.g. locateDatabase()
• stringfunctions.py (?)
• commondbaccess.py - common functions for getting data from db (e.g. organism name <-> ID), presence\absence slices, ...

Need to rewrite existing imports to use new files and update docs

[mattb112885]

I have started working on this - see the lib/ directory. Treefuncs I've made some pretty good progress on, as well as metadata (but need to update options in some of the functions to use the metadata by default unless someone overrides them for whatever reason). The other ones still need implementing.

[JamesRH]

Do you think it is OK for /scripts to call lib, or only call /src/ (which, in turn call lib). I think direct dependencies are OK but I wanted to check.

James H.

mattb112885 [email protected] wrote:

I have started working on this - see the lib/ directory. Treefuncs I've made some pretty good progress on, as well as metadata (but need to update options in some of the functions to use the metadata by default unless someone overrides them for whatever reason). The other ones still need implementing.

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