[Biopython-dev] DeprecationWarnings

[Michiel de Hoon]

Hi everybody,

In Python 2.7, DeprecationWarnings are silenced by default; they are shown if Python is started with the -Wd option. Most of our users won't use the -Wd option and therefore won't see any of the DeprecationWarnings. I suggest that we replace all DeprecationWarnings in Biopython with a Biopython-specific warning, perhaps implemented in Bio/__init__.py, to make sure that users actually see these warnings when they occur. At the same time, we can add DeprecationWarnings to all functions marked as obsolete, since most users won't see these DeprecationWarnings anyway (assuming they are using Python 2.7 or later).  This allows us to check if any software depends on obsolete code by using the -Wd option when starting Python.

Any objections?

--Michiel.