Hi,

single datatype definitions only work if you haven’t defined any converters. Let's assume I have a datatype X and want to ship a X -> Y converter (Y -> X is also possible), we will end up with a dependency loop, or? The X repository will depend on the Y repository, but Y is depending on X, because we want to include a Y -> X converter.

Any idea how to solve that?

How to handle versions of datatypes? Extra repositories for stockholm 1.0 and 1.1? If so ... the associated python file (sniffing, splitting ...) should be also versioned, or? What happend if I have two stockholm.py files in my system?

@Peter, can we create a striped-down, python only biopython egg? All parsers should be included, Bio.SeqIO should be sufficient I think.

Ciao,
Bjoern

Am 17.07.2014 19:43, schrieb Greg Von Kuster:
Here's a Trello card for this:

https://trello.com/c/s8tfbW4x

On Jul 17, 2014, at 1:38 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:

Good point Greg.

Let's refine this slightly then, a new special ToolShed repository type for
a *single* datatype definition. That avoids this problem :)

(This does not help with suites of very closely related datatypes -
like different
kinds of BLAST database.)

Peter

On Thu, Jul 17, 2014 at 6:35 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
This would be easy to implement, but could adversely affect reproducibility.
If a repository containing datatypes always had only a single installable
revision (i.e., the chagelog tip), then any datatypes defined in an early
changeset revision that are removed in a later changeset revision would
no longer be available.

Greg

On Jul 17, 2014, at 1:30 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:

On Thu, Jul 17, 2014 at 6:10 PM, Björn Grüning
<bjoern.gruen...@gmail.com> wrote:

... but the problem will stay the same ... one [datatype definition] repository
can have multiple versions ...


I like your idea that like tool dependency definitions, this should be a special
repository type on the ToolShed:

Earlier, Björn Grüning <bjoern.gruen...@gmail.com> wrote:

Imho datatypes should be handled like "Tool dependency definitions".
There should be only one "installable revsion".


This is something Greg will have to comment on - there may be
ramifications I'm not seeing.

Peter

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