[Biopython-dev] Deprecations for Biopython 1.61 release; Was: Bio.Motif update

[Peter Cock]

On Fri, Feb 1, 2013 at 3:39 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> --- On Fri, 2/1/13, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> I went over the list in the DEPRECATED file last month, but
>> a second check would be a good idea.
>
> The following were declared obsolete in Biopython 1.60, and can
> in principle be declared deprecated in Biopython 1.61:
>
> ----------
> Bio/Blast/Applications.py:
> BlastallCommandline
> BlastpgpCommandline
> RpsBlastCommandline
>
> Bio/Blast/NCBIStandalone.py overall, and specifically:
> blastall
> blastpgp
> rpsblast
>
> Bio/ParserSupport.py overall
>
> Bio/PDB/AbstractPropertyMap.py:
> The has_key function in class AbstractPropertyMap
>
> Bio/PDB/FragmentMapper.py:
> The has_key function in class FragmentMapper
>
> Bio/UniGene/UniGene.py overall
>
> In BioSQL/BioSeqDatabase.py:
>   class DBServer:
>      remove_database
>   class BioSeqDatabase:
>      get_all_primary_ids
>      get_Seq_by_primary_id
>
> -----------
>
> These functions were deprecated in Biopython 1.59 or earlier, and could be removed for Biopython 1.61:
>
> Bio/Align/__init__.py:
>   class MultipleSeqAlignment:
>      get_column
>      add_sequence
>
> Bio/Align/Generic.py:
>   class Alignment overall
>     get_all_seqs
>     get_seq_by_num
>
> Bio/File.py:
>   class StringHandle
>
> Bio/Graphics/GenomeDiagram/_AbstractDrawer.py:
>   class AbstractDrawer:
>     _set_xcentre, _set_ycentre
>
> Bio/Graphics/GenomeDiagram/_Graph.py:
>   class GraphData:
>     _set_centre
>
> Bio/ParserSupport.py:
>   SGMLStrippingConsumer
>
> Bio/Seq.py:
>   class Seq:
>      .data property
>
> Bio/SeqIO/SffIO.py:
>   _sff_read_roche_index_xml
>
> --------------------
>
> The tostring() method of the class Seq in Bio/Seq.py:
> Can we declare this obsolete?
>
> -Michiel

Bio/SeqIO/SffIO.py function _sff_read_roche_index_xml done:
https://github.com/biopython/biopython/commit/567464d9a5f8b87ec48e95bae127b86463bd4da1

Bio/File.py and Bio/ParserSupport.py bits done:
https://github.com/biopython/biopython/commit/63997ea0afa5f7f6cac5c1b036d56416b04edb2a

GenomeDiagram centre setters done:
https://github.com/biopython/biopython/commit/2424c5ca36cdf4348b54bafdae444a91a6457288

Peter