Deprecation policy

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.

We keep a plain text file in the Biopython source code to record these changes, named DEPRECATED.

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,
  • Add “(OBSOLETE)” to the first line of the module docstring,
  • Use the module docstring to explain why the module is obsolete and what should be used instead.
• If there are no apparent users, then actually deprecate it:
  • Note this in the DEPRECATED file,
  • Add “(DEPRECATED)” to the first line of the module docstring
  • Use the module docstring to explain any migration needed, ideally with examples or a reference to the tutorial.
  • Most importantly, add a BiopythonDeprecationWarning to the code (Python’s DeprecationWarning is silent by default):

import warnings
from Bio import BiopythonDeprecationWarning
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 or GitHub.",
              BiopythonDeprecationWarning)

• 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:

http://lists.open-bio.org/pipermail/biopython-dev/2008-November/004920.html