[Biopython-dev] 'testseq' update

[Peter Cock]

On Thu, Jun 8, 2017 at 6:31 AM, Adil Iqbal <aiqbal85 at gmail.com> wrote:
> I looked into it and the Scripts, Doc, and Test folders are not included in
> the "lib/site-packages" directory. Which means those folders cannot be
> accessed by importing.

Yes, that is deliberate.

> They also cannot be accessed by a command-line script
> because the path to the Scripts folder would then be variable on a per user
> basis.

Right now the scripts would be where ever the user downloaded
Biopython's source code.

I don't think we (nor any of the downstream packaging like Debian)
explicitly install our scripts on the system $PATH. That should be
possible, although not necessarily desirable for all the files.

> I see two options.
>
> We can scrap the unittest and include testseq in the Scripts folder for
> folks who happen to be perusing the source code.
>
> Or we could keep the unittest and do Andrew's earlier suggestion, which is
> to include it in the SeqUtils submodule, but not import it by default.
>
> I would prefer the latter option, though I understand completely if we
> decide to go with the former. I'm open to suggestions.

Or a third option of my suggestion of putting your code in Scripts/ and
for testing calling it as a script from a dedicated test file in Tests/ as
described earlier?:

http://mailman.open-bio.org/pipermail/biopython-dev/2017-June/021718.html

Regards,

Peter