[Biopython-dev] Deprecating Bio.ParserSupport, Bio.Blast.NCBIStandalone

[Wibowo Arindrarto]

Hi everyone,

> --- On Sun, 1/27/13, Wibowo Arindrarto <w.arindrarto at gmail.com> wrote:
>> All of this seems different from Bio.ParserSupport, which
>> attempts to be a one-single solution for writing new parsers
>> (only parsers). Given the wildly incoherent nature of different
>> file output formats, it's not surprising that Bio.ParserSupport's
>> code base has to be quite complicated to accommodate all of them.
>> Naturally it has many related parts and functions, and understanding
>> them all is much harder than to understand the small functions in
>> Bio._utils (in my experience).
>
> It's not just Bio.ParserSupport; previously we also had Bio/listfns.py; Bio/mathfns.py; Bio/stringfns.py; their C versions; and Bio/csupport.c. These all contained small utility functions. But in the end we dropped them.

Hm..in this case (and in light of Eric's points as well), it may be ok
to drop the string formatting functions in Bio._utils. They are used
in Bio.Phylo and Bio.SearchIO for now. In Bio.SearchIO they are used
in multiple submodules, however, so I am still leaning on putting them
at least on Bio.SearchIO's main directory. They were originally in
Bio.SearchIO._utils, after all.

As for the doctest-related functions, do you propose to move them to a
specific doctest-related module as well?

>> Btw, was Bio._utils ever discussed on the mailing list? If yes, I
>> apologize for missing this discussion and raising these issues now.
>
> I think only on the pull request - I'll have a look at the GitHub
> settings as ideally at the minimum new pull requests should
> perhaps be CC'd to the dev list?

Indeed, I did submit a pull request but was not forwarded / discussed
in the mailing list. This is the pull request, for reference:
https://github.com/biopython/biopython/pull/140. For the dev-mailing
list notification, I personally agree, given that the amount of pull
requests received still seems manageable. Is it possible to just
receive the initial email notifying the pull, though?

So far, I've been 'watching' the repository and getting emails from
there ~ perhaps the organization needs to 'watch' the repo to get
notifications as well?

Best,
Bow