[Biopython-dev] [Bug 2743] manual installation overwrites previous biopython installations

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Jan 28 11:14:28 UTC 2009


------- Comment #2 from dalloliogm at gmail.com  2009-01-28 06:14 EST -------
(In reply to comment #1)
> (In reply to comment #0)
> > The manual biopython installation (the one made with python setup.py install)
> > installs all the files in a directory like this:
> > - /usr/lib/python2.5/site-packages/Bio
> > 
> > The problem comes when you want to install biopython in a system where there is
> > already an old version installed.
> > In that case, it is not clear what happens to the old installation... are all
> > the old files removed before the new version is installed? Or are the two
> > versions 'mixed'?
> Isn't this what always happens when installing a Python module? If so, then it
> doesn't seem to be a Biopython bug to me.

Well, I don't know if it is the same behaviour for the other python modules,
but it can create dangerous situations, especially if you are 'downgrading' a
biopython installation.
The biopython installer should clarify that, asking the user if he wants to
overwrite the existing installation, change the installation path, or abort.

Anyway. the right way to install biopython should be by using easy_install.
Easy_install downloads the latest code and creates an egg, and then install
everything on a directory like this:
- /usr/lib/python2.5/site-packages/biopython-1.49-py2.5-linux-i686.egg/
automatically changing $PYTHON_PATH.

I suggest to change the biopython's wiki to tell people that they should always
prefer to install biopython with easy_install, which by the way works perfectly
and automatically checks the dependencies.

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