[Biopython-dev] Modules to be removed from Biopython

[Michiel de Hoon]

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. The other function of the code in setup.py was to check if importing Martel raises any import errors, in particular for mxTextTools. That we can check by trying to import the dependencies directly, i.e. without going through Martel.
After fixing the code in setup.py, we can add a DeprecationWarning to Bio.Martel.

--Michiel.


--- On Mon, 9/22/08, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: Re: [Biopython-dev] Modules to be removed from Biopython
> To: biopython-dev at biopython.org
> Date: Monday, September 22, 2008, 1:39 PM
> As part of the general Martel/Mindy clean up, I've added
> a deprecation
> warning to Mindy and several other closely related modules,
> but have
> only made a docstring change to Martel.  I'm not sure
> if we should add
> a deprecation warning to Martel directly - it would be
> triggered by
> running the Biopython setup.py file which is nasty. 
> Perhaps for this
> special case, documentation is enough?
> 
> Summary:
> 
> * Martel - labelled as deprecated for 1.49, but no explicit
> warning (see above)
> * Bio.Mindy - deprecated for 1.49
> * Bio.Std - deprecated for 1.49
> * Bio.StdHandler - deprecated for 1.49
> * Bio.builders - deprecated for 1.49
> * Bio.Decode - deprecated for 1.49
> * Bio.Writer (and Bio.writers.*) deprecated in 1.48
> * Bio.expressions - deprecated in 1.44, removed for 1.49
> * Bio.config - effectively deprecated in 1.44, explicitly
> in 1.48,
> removed for 1.49
> * Bio.dbdefs - effectively deprecated in 1.44, explicitly
> in 1.48,
> removed for 1.49
> * Bio.formatdefs - effectively deprecated in 1.44,
> explicitly in 1.48,
> removed for 1.49
> 
> Open questions:
> * Bio.DBXRef - does anyone known what this is for?
> * Bio.SGMLExtractor - deprecated in 1.46, ready for
> removal?
> 
> As a bonus once we've moved from CVS to SVN, we should
> be able to
> remove some of the now empty directories in CVS :)
> 
> Peter
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