As bioinformatics and computational biology are developing quickly, some of previously developed Biopython modules may no longer be relevant in today's world. To keep the code base clean, we aim to deprecate and remove such code from Biopython, while avoiding any nasty surprises for users who may be relying on older code.
This is the current policy for deprecating and removing code from Biopython:
- First, ask on the biopython and biopython-dev mailing lists whether a given piece of code has any users. Please keep in mind that not all users are following the biopython-dev mailing list.
- Consider declaring the module as "obsolete" for a release before deprecation (no code changes, just note this in the DEPRECATED file and the module docstrings).
- If there are no apparent users, you can add a DeprecationWarning to the code.
import warnings warnings.warn("Bio.SomeModule has been deprecated, and we intend to remove it" " in a future release of Biopython. Please use the SomeOtherModule" " instead, as described in the Tutorial. If you would like to" " continue using Bio.SomeModule, please contact the Biopython" " developers via the mailing list.""", DeprecationWarning)
- Also add an entry to the DEPRECATED file, again specifying what module (if any) has replaced the old code.
- In principle, we require that two Biopython releases carrying the deprecation warning are made before the code can be actually removed.
- In addition, at least one year should pass between the first Biopython release carrying the deprecation warning, and the first Biopython release in which the code has been actually removed.
See here for the discussion on the mailing list: