[Biopython-dev] [Bug 2711] GenomeDiagram.py: write() and write_to_string() are inefficient and don't check inputs

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2711





------- Comment #6 from lpritc at scri.sari.ac.uk  2008-12-15 05:11 EST -------
(In reply to comment #2)
> *** Bug 2710 has been marked as a duplicate of this bug. ***
> 

(In reply to comment #0)
> test_GenomeDiagram fails because the renderPM module is not part of standard
> install of reportlab, at least under Linux. 

That's odd - renderPM is in the source for ReportLab 2.2.  Are you using an
up-to-date version?  It seems to install well enough on our 64-bit Linux box
from the ReportLab source.

> I consider that the renderPM module should not be required so
> Graphics/GenomeDiagram/Diagram.py needs to be rewritten to avoid using the
> renderPM module when it is not available. 

renderPM is how raster graphics are drawn, so is, I'm afraid, a necessary part
of GenomeDiagram's functionality.

I prefer your alternative suggestion of making it a 'dynamic' import, but even
then I think that the inconvenience of preparing the diagram, only to find out
at the last possible stage that you can't draw it because you're missing the
library, is worse than getting the error message upfront.  Not that this should
be a problem, since renderPM is part of the main ReportLab source, now.  YMMV
though, and I'm happy for the code to conform to the Biopython house style.

> The installation documentation needs to include something about needing the
> renderPM for JPG, BMP, GIF, PNG, TIFF or TIFF outputs.
> 
> There must be a test for the presence of the renderPM module.

I'm not convinced of the value of this, as renderPM is part of the current
ReportLab source installation.


------- Comment #7 from lpritc at scri.sari.ac.uk  2008-12-15 05:17 EST -------
(In reply to comment #0) (from #2710)
> test_GenomeDiagram fails because the renderPM module is not part of standard
> install of reportlab, at least under Linux. 

renderPM is part of the source install of ReportLab 2.2, and installs correctly
on our 64-bit Linux box.  Are you using an up-to-date version of ReportLab? 
The version that your distro's installer uses may not be the most recent.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.