[Biopython-dev] [Bug 2723] Minor corrections to the installation document

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sun Jan 4 18:56:22 UTC 2009


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
            Summary|Clarify what applies to     |Minor corrections to the
                   |which version of biopython  |installation document
                   |and other doc cleanup       |

------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2009-01-04 13:56 EST -------
(In reply to comment #1)
> (In reply to comment #0)
> > I went to look around at the docs because the built-in tests of 1.49
> > setup.py spitted some messages about external programs missing. I haven't
> > found any hints on them in
> > http://news.open-bio.org/news/2008/11/biopython-release-149/.
> No, that text and the matching email announcement don't do into details about
> installation - the text was already long enough I felt.  However, the download
> page does list various external programs:
> http://biopython.org/wiki/Download

I've added a section on third party tools to the installation document in CVS.

> > Anyway, looking at 
> > http://biopython.org/DIST/docs/install/Installation.html#htoc17
> > I see: "3.4  mxTextTools (no longer needed)". I would propose:
> > 
> > 3.4  mxTextTools (no longer needed since 1.49)
> > 
> > Similarly:
> > - 3.1  Numerical Python (NumPy) (strongly recommended)
> > + 3.1  Numerical Python (NumPy) (strongly recommended since 1.49)
> That does seem sensible.

On reflection, I don't like the layout with version numbers stuck in the
section names.  The NumPy section is already very clear about the fact that
this applies to 1.49 onwards, and that older versions of Biopython needed
Numeric instead.  I have tried to clarify the mxTextTools section in CVS.

> > Bad URL links are in the text:
> > 
> > 3.3  Database Access (MySQLdb, ...) (optional)
> > ...
> > 3.4  mxTextTools (no longer needed)
> > ...
> I'll have to check those... probably something silly in the LaTeX source.

Fixed in CVS.

I'm leaving this bug open until I've updated the HTML and PDF copies of the
installation document on the website.  I don't have the tools hevea installed
on this machine, so I can't create the HTML version of the installation
document -- just the PDF.  I should be be able to do this next week...

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