[Biopython-dev] Modules to be removed from Biopython

[Peter]

On Tue, Sep 23, 2008 at 1:55 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> The code in setup.py that causes the DeprecationWarning to appear
> can be fixed relatively easily. Basically, this code was relevant when
> Martel was also being distributed as a separate module. Nowadays,
> Biopython contains the latest version of Martel, so there's no reason
> to check it.

Probably a safe assumption.

> The other function of the code in setup.py was to check if importing
> Martel raises any import errors, in particular for mxTextTools. Then
> we can check by trying to import the dependencies directly, i.e.
> without going through Martel.

As discussed earlier, we've agreed not worry at install time whether
or not mxTextTools is present.

So basically, you recommend we just remove all the Martel special case
code in setup.py, and simply install it automatically like any other
module?  I've made this change locally and it seems to be fine.  If
this is what you had in mind, I can commit this to CVS too.

> After fixing the code in setup.py, we can add a DeprecationWarning to Bio.Martel.

Agreed.

Peter