[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 12:46:37 UTC 2009


------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2009-01-28 07:46 EST -------
(In reply to comment #1)
> > 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.

Agreed.  As far as I know, this affects ANY python module installed with
distutils - and indeed this is typical practice for ANY unix tool installed
from source via a make file.  It is essentially NORMAL, although not so nice
for beginners.

Linux distributions will often provide packaged versions of python libraries
(including Biopython) which you can install/update/remove using the system's
package manager (e.g. apt, yum, up2date etc).  The only downside to me is they
won't always have the latest version of each package.

I suppose we could add a hack to setup.py to check if there is already a
Biopython installation present (try doing "import Bio"), and if it is
installed, ask the user if they want to continue.  However, there are
legitimate situations where this just makes things more confusing.  e.g. You
don't have admin rights on a unix machine where your systems administrator has
provided python and an old version of Biopython, so you want to install the
latest version of Biopython under your home directory.

(In reply to comment #2)
> 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.

For now distutils is still the python standard, while easy_install is an
non-standard optional extra.  This in some ways using easy_install is more

Note that easy_install doesn't provide a simple uninstall either:

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