On Wed, Jun 24, 2020 at 1:36 AM Thomas Kluyver email@example.com wrote: >
On Tue, 23 Jun 2020, at 23:51, David Mathog wrote:
What I am after is some method of keeping exactly one copy of each package-version in the common area (ie, one might find foo-1.2, foo-1.7, and foo-2.3 there), while also presenting only the one version of each (let's say foo-1.7) to a particular installed program. Conda environments work somewhat like this - all the packages are stored in a central place, and the structure of selected ones is replicated using hardlinks in a site-packages directory belonging to the environment. So if your concern is not to waste disk space by storing copies of the same packages, that might be an option.
I experimented with that one a little. It installs its own copies of python and things like openssl and openblas which are already present from the linux distribution. Similarly, if some python script needs "bwa" it will install its own even though that program is already available. Basically it is yet another "replicate everything we might need whether or not it is already present" type of solution. (The extreme end of that spectrum are systems like docker, which effectively replaces the entire OS.) So there might be only the one version of each python package (not counting duplicates with the OS's python3) but now there are also duplicate copies of system libraries and utilities.
I think I will experiment a little with pipenv and if necessary after each package install use a script to remove the installed libraries and replace them with a hard link to the one in the common area. Maybe it will be possible to put in those links before installing the package of interest (like for scanpy, see first post), which will hopefully keep it from having to rebuild all those packages too.