[Biopython-dev] Deprecating Bio.ParserSupport, Bio.Blast.NCBIStandalone

[Michiel de Hoon]

Hi Bow,

Thanks for the explanation.

> Indeed, the doctests functions are two simple small
> functions to make it easier to run doctests. The first
> one looks up the test directory (our Tests directory) and
> the second one simply executes the doctest.

The point of looking up the test directory is to find the example input files, right?
Have a look at Bio/Align/Applications/_Mafft.py.
Its doctest uses the complete path to the example input file:

https://github.com/biopython/biopython/commit/32a6beb1e039fa614398a7dee1c031466e8e42ed#Bio/Align/Applications/_Mafft.py

I like this solution better, since it's more straightforward, it doesn't need a new module, and also allows the user to run the example without having to figure out where the input file is located.

Best,
-Michiel.