[Biopython-dev] Modules to be removed from Biopython

Peter biopython at maubp.freeserve.co.uk
Fri Jun 27 16:50:17 UTC 2008

On Fri, Jun 27, 2008 at 5:40 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> 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.

I was wondering if there was a stated policy on this.

> 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

Those all look fine to remove.  I agree here.

> 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.

Given some of these are very interconnected, I would be inclined to leave
them in for one more release.  However I'm content to see them go.  If no
one else has any  qualms, then please carry on.


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