[Biopython-dev] uploading coalescent code

Tiago Antão tiagoantao at gmail.com
Tue Nov 13 10:25:32 UTC 2007


I should have done my home work better before asking this in the list, sorry.

According to the manual, there are 2 options:
# 2.6 Installing Package Data
# 2.7 Installing Additional Files

Being strictly correct, we are talking about "additional files", but,
to make things simpler (and avoiding clutering biopython with probably
more top-level directories) I think "package data" is enough.
If nobody sees a problem I will add a data directory inside
Bio/PopGen/SimCoal and upload it to CVS.

But, there is a more serious change: setup.py. For this I suggest:
1. Adding you to the SimCoal feature bug 2375, can I do that?
2. I would put my suggested diff there and you could
evaluate/change/accept/reject it

On Nov 13, 2007 9:52 AM, Michiel De Hoon <mdehoon at c2b2.columbia.edu> wrote:
> Hi Tiago,
> > 3. IMPORTANT: There are some text template files. I suppose that there
> > is no standard way to have datafiles around. I was thinking (actually
> > somebody suggested on this list) in putting it alongside the code.
> > Question: Is there any standard way to know where biopython is installed
> > (so that I can read those datafiles)? We are talking of very small files.
> Have you looked at the manual for distutils? Section 2.6 and 2.7 discuss
> having data files distributed with a Python extension. See
> http://docs.python.org/dist/dist.html
> Given that such an option exists, somebody must already be using it. So I
> think your best option is to google around a bit to find some examples.
> --Michiel


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