BSS install about biosimspace HOT 2 CLOSED

Typically these are packages that aren't required for BioSimSpace to work, e.g. conda packages where the maintainer has incorrectly listed the dependencies, or optional dependencies that conda thinks are essential. I could hide these spurious error messages by gobbling the stderr output of conda in the setup script, but chose not to as some time the messages are useful, e.g. when the dependencies genuinely change.

Perhaps I should instead hide the messages, then try importing BioSimSpace (or running a test script) at the very end of the the finally block of the setup script to confirm that everything installed as expected and reporting to the user if the import failed.

Could you try opening an IPython session:

$HOME/sire.app/bin/ipython

Next, try importing BioSimSpace:

import BioSimSpace

If you don't get any errors, then all packages have been installed correctly. If not, then I'll update the setup script with the missing files. (Note that you may see errors because of missing packages that failed to install during the Sire install step, rather than BioSimSpace. This can occur if there is a network issue during the install, or even when the order of the package installation is different. As we've discovered, it can be very hard to maintain a stable conda environment.)

I'll have a better think tomorrow and close this issue when I come up with a more permanent solution.

from biosimspace.

As discussed above, I now capture the stdout/stderr messages from conda and write them to file. At the end of the setup script (in the finally block) I test that the import works and point the user to the files if anything has gone wrong.

The issue will be closed when feature-align is merged into devel.

from biosimspace.