[Biopython-dev] [Bug 2723] Clarify what applies to which version of biopython and other doc cleanup

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sun Jan 4 01:37:26 UTC 2009


------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2009-01-03 20:37 EST -------
(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:

(Someone else had pointed out we were missing a few, which as been fixed, but I
couldn't find the email/bug report while writing this reply).

> 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.

> Bad URL links are in the text:
> 3.3  Database Access (MySQLdb, ...) (optional)
> [cut]
> Additionally, both MySQLdb and psycopg (a PostgreSQL database adaptor) can be
> used for accessing BioSQL databases through Biopython (see ). Again if you
> -----------------------------------------------------------^
> are not going to use BioSQL, there shouldn’t be any need to install these
> modules.
> 3.4  mxTextTools (no longer needed)
> [cut]
> However, we currently recommend you install mxTextTools 2.0, as some of the
> API changes made in 3.0 version were not compatible with Biopython. Goto
> ---------------------------------------------------------------------^^
> to download this.

I'll have to check those... probably something silly in the LaTeX source.

> I haven't found an answer for me yet:
> test_PopGen_FDist ... skipping. Install FDist if you want to use
> Bio.PopGen.FDist.
> ok
> ...
> test_PopGen_SimCoal ... skipping. Install SIMCOAL2 if you want to use
> Bio.PopGen.SimCoal.
> ok
> ...
> test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
> ok
> test_psw ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
> ok

See http://biopython.org/wiki/Download

> Pointer to those packages would have been helpful. From the test suite as well
> as from installation manual.

I'm not keen on making the unit test even more verbose by adding URLs to these
messages.  The information is on the download page, but yes, adding it to the
installation document seems sensible.

> Moreover, what database username/password would
> I have to make to get the BioSQL stuff compiled and tested?  ^H^H^H^H^H^H
> I see, it gets compiled anyway the tests just were not run.

The BioSQL unit test message should say: "Check settings in
Tests/setup_BioSQL.py if you plan to use BioSQL".  i.e. Once you have installed
BioSQL and setup a database, edit the file setup_BioSQL.py to match.  See


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