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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 use the same process to deprecate obsolete modules, methods, functions and classes.

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

This is the current policy for deprecating and removing code from Biopython:

import warnings
from Bio import BiopythonDeprecationWarning

    "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.",
from Bio import BiopythonDeprecationWarning

with warnings.catch_warnings():
    warnings.simplefilter("ignore", BiopythonDeprecationWarning)
    from Bio import SomeModule

See here for the discussion on the mailing list: