add gdb

[alaniwi]

This pull requests adds gdb.

When I tried to resolve the existing environment, I am currently finding that mamba is now installing pip packages instead of a fair number of the conda packages (whether starting from core_packages.yml or initial.yml), which is not a problem that existed before, and which means that the usual check of whether I can reexport and recover the original initial.yml file fails.

Although I don't know why this is happening, what I can see is that if I add the gdb requirement when installing from core_packages.yml, the only difference between the environment this produces and the same thing without the gdb requirement is that the gdb package itself is added; nothing else needs to be installed or updated for dependencies.

For this reason, this pull request contains a hand-edit to the previously exported initial.yml in order to add the gdb package itself at the version that mamba chooses when I do the above. In other words, the new initial.yml is not the output of a conda env export as it usually would be, as this would have a lot of packages changed to pip packages as described above.

The environment successfully adds the gdb executable, and I have checked that it can handle object code from the gcc / gfortran version that is in Jaspy, which is the motivation for adding it.

I also find that the change does not introduce any failures in the quick software tests, other than that gdb introduces a new file libpython.py in the site-packages directory, and test_all_imports finds this and reports that import libpython doesn't work (it contains import gdb and there is no gdb python package). But this might or might not be a valid thing to do anyway, and I haven't had time to work out how you are supposed to use the gdb python extension, so I can't really test that aspect (though there's some docs here). This could be a thing to address later if people want that functionality and something else is required to make it work, but it is not a reason against adding gdb now for sake of C/Fortran code.

[agstephens]

Hi @alaniwi,

I have loads on and I can't prioritise this before Tuesday morning. So I'm going to say that we don't put it in to this version of Jaspy. Please make sure there is an issue so that it gets into the next version. Thanks

[alaniwi]

The pip packages problem is not happening now. We still want to add gdb, but can just do it ordinarily without the hand edit. Closing PR unmerged but keeping #114 open.