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Usually I tend to install things via the package manager, for unixy stuff. However, when I programmed a lot of perl, I would use CPAN, newer versions and all that.
In general, I used to install system stuff via package manager, and language stuff via it’s own package manager ( gem/easy_install|pip/cpan)
Now using python primarily, I am wondering what best practice is?
The system python version and its libraries are often used by software in the distribution. As long as the software you are using are happy with the same versions of python and all the libraries as your distribution is, than using the distribution packages will work just fine.
However, quite often you need development version of packages, or newer version, or older versions. And then it doesn’t work any more.
It is therefore usually recommeded to install your own Python version that you use for development, and create development environments with buildout or virtualenv or both, to isolate the system python and the development environment from each other.