[Biopython-dev] Modules to be removed from Biopython

[Michiel de Hoon]

Hi everybody,

In recent releases, we have been using the rule of thumb to remove all modules from a new Biopython release that were deprecated two releases ago.

For the upcoming release, this means that we will remove the modules that were deprecated in Biopython 1.44. In that release, quite a lot of modules were deprecated; these modules will not appear in Biopython 1.46.

Some of the modules to be removed are relatively simple cases, which I think can be removed without causing any real pain to anybody:

Bio.crc (moved to Bio.SeqUtils.CheckSum)
Bio.Fasta.index_file
Bio.Fasta.Dictionary
Bio.GenBank.index_file
Bio.GenBank.Dictionary
Bio.Geo.Iterator (replaced by Bio.Geo.parse)
Bio.KEGG.Compound.Iterator (replaced by Bio.KEGG.Compound.parse)
Bio.KEGG.Enzyme.Iterator (replaced by Bio.KEGG.Enzyme.parse)
Bio.KEGG.Map.Iterator (replaced by Bio.KEGG.Enzyme.parse)
Bio.lcc (moved to Bio.SeqUtils.lcc)
Bio.MarkupEditor
Bio.Medline.NLMMedlineXML
Bio.Medline.nlmmedline_001211_format
Bio.Medline.nlmmedline_010319_format
Bio.Medline.nlmmedline_011101_format
Bio.Medline.nlmmedline_031101_format
Bio.MultiProc
Bio.SeqIO.FASTA.py
Bio.SeqIO.generic.py

But, there is also a set of interconnected modules where it's not 100% clear if they can be removed without causing some surprises:
Bio.builders
Bio.config
Bio.dbdefs
Bio.formatdefs
Bio.dbdefs
Bio.expressions
Bio.FormatIO
Bio.Std
Bio.StdHandler
It is probably OK to remove these, since these were deprecated we did not get a barrage of complaints from our users. Personally, I think it is important to keep the code base clean, so I am in favor of removing these (and see if anybody complains; in that case, we can always put these modules back in and make a new release). But I can live with keeping these modules for another release round. If anybody thinks that that would be better, please let us know.

--Michiel